diff options
Diffstat (limited to 'academic')
1274 files changed, 30084 insertions, 8004 deletions
diff --git a/academic/3D-ICE/3D-ICE.SlackBuild b/academic/3D-ICE/3D-ICE.SlackBuild new file mode 100644 index 0000000000..05c6d82380 --- /dev/null +++ b/academic/3D-ICE/3D-ICE.SlackBuild @@ -0,0 +1,165 @@ +#!/bin/bash + +# Slackware build script for 3D-ICE + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=3D-ICE +VERSION=${VERSION:-3.1} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +SRCNAM=${PRGNAM,,} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $SRCNAM-$VERSION +tar xvf $CWD/$SRCNAM-$VERSION.tar.gz +cd $SRCNAM-$VERSION + +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +# unpack requirements +tar xvf $CWD/superlu_4.3.tar.gz + +if [ "${SYSTEMC:-no}" == "yes" ]; then + sed -i '/^SYSTEMC_MAIN/ s/$(HOME).*/\/usr/' makefile.def + sed -i '/^SYSTEMC_LIB/ s/-$(SYSTEMC_ARCH)/'${LIBDIRSUFFIX}'/' makefile.def + # it has to use the same standard which was used to compile SystemC + sed -i '/^CXXFLAGS/ s/c++11/c++17/' makefile.def + OPT_BUILD="SYSTEMC_WRAPPER=y" +fi + +# do not test the plugin +sed -i '59s/plugin//' Makefile +sed -i '66s/plugintest//' test/Makefile +sed -i '166,184d' test/Makefile + + +cd SuperLU_4.3 +cp MAKE_INC/make.linux make.inc +sed -i -e '/^SuperLUroot/ s/$(HOME)\/Codes\/SuperLU_4.3/../' make.inc +sed -i -e '/^BLASLIB/ s/-L\/usr\/lib/-L\/usr\/lib\/x86_64-linux-gnu/' make.inc +# doesn't compile with two threads +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +make -j1 +cd .. + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +make $OPT_BUILD +make test +make doc + +# install +install -d $PKG/usr/bin +install -m 0755 bin/3D-ICE-Client $PKG/usr/bin +install -m 0755 bin/3D-ICE-Emulator $PKG/usr/bin +install -m 0755 bin/3D-ICE-Server $PKG/usr/bin + +if [ "${SYSTEMC:-no}" == "yes" ]; then + install -m 0755 bin/3D-ICE-SystemC-Client $PKG/usr/bin +fi + +mkdir -p $PKG/usr/include/3d-ice +cp -av include/* $PKG/usr/include/3d-ice + +mkdir -p $PKG/usr/lib${LIBDIRSUFFIX} +cp -av lib/libthreed-ice-3.1.0.a $PKG/usr/lib${LIBDIRSUFFIX} + +mkdir -p $PKG/usr/libexec/$PRGNAM-$VERSION +cp -av utils/{draw_temp_map.py,draw_temp_map_ani.py} $PKG/usr/libexec/$PRGNAM-$VERSION + +# before copy other document files, let's install the doc folder +# and fix the permissions +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a doc $PKG/usr/doc/$PRGNAM-$VERSION +# fix doc permissions +find -L $PKG/usr/doc/$PRGNAM-$VERSION -type f \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 755 \ + -o -perm 511 \) -exec chmod 644 {} \; + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +find $PKG -depth -type d -empty -delete || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a CHANGELOG COPYING TODO \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/3D-ICE/3D-ICE.info b/academic/3D-ICE/3D-ICE.info new file mode 100644 index 0000000000..f39dc43916 --- /dev/null +++ b/academic/3D-ICE/3D-ICE.info @@ -0,0 +1,10 @@ +PRGNAM="3D-ICE" +VERSION="3.1" +HOMEPAGE="https://www.epfl.ch/labs/esl/research/open-source-software-projects/3d-ice" +DOWNLOAD="https://github.com/esl-epfl/3d-ice/archive/3.1/3d-ice-3.1.tar.gz https://portal.nersc.gov/project/sparse/superlu/superlu_4.3.tar.gz" +MD5SUM="36da449c813c6ec7fcd04fb35f8a1679 b72c6309f25e9660133007b82621ba7c" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="blas" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/3D-ICE/README b/academic/3D-ICE/README new file mode 100644 index 0000000000..414cf1cf4d --- /dev/null +++ b/academic/3D-ICE/README @@ -0,0 +1,10 @@ + 3D-ICE stands for 3D Interlayer Cooling Emulator. It is a +Linux-based Thermal Emulator Library written in C, which can perform +transient thermal analyses of vertically stacked 3D integrated +circuits with inter-tier Microchannel Liquid Cooling. The latest +version, namely 3D-ICE 3.1, supports fully customized non-uniform +thermal modeling and different heat sink models. + + + If you want to enable the SystemC wrapper, set the environment +variable SYSTEMC=yes. diff --git a/academic/3D-ICE/slack-desc b/academic/3D-ICE/slack-desc new file mode 100644 index 0000000000..85ddec2742 --- /dev/null +++ b/academic/3D-ICE/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +3D-ICE: 3D-ICE (Thermal Emulator Library written in C) +3D-ICE: +3D-ICE: +3D-ICE: 3D-ICE stands for 3D Interlayer Cooling Emulator. It is a Linux-based +3D-ICE: Thermal Emulator Library written in C, which can perform transient +3D-ICE: thermal analyses of vertically stacked 3D integrated circuits with +3D-ICE: inter-tier Microchannel Liquid Cooling. The latest version, namely +3D-ICE: 3D-ICE 3.1, supports fully customized non-uniform thermal modeling +3D-ICE: and different heat sink models. +3D-ICE: +3D-ICE: diff --git a/academic/freechartgeany/freechartgeany.SlackBuild b/academic/AlphaPlot/AlphaPlot.SlackBuild index 13ac323d36..5b597e923f 100644 --- a/academic/freechartgeany/freechartgeany.SlackBuild +++ b/academic/AlphaPlot/AlphaPlot.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash -# Slackware build script for freechartgeany - -# Copyright 2012-2016 Larry Hajali <larryhaja[at]gmail[dot]com> +# Slackware build script for AlphaPlot +# +# Copyright 2022, Fellype do Nascimento, Guaratingueta - Brazil # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,26 +22,36 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -PRGNAM=freechartgeany -VERSION=${VERSION:-2.0.3} +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=AlphaPlot +VERSION=${VERSION:-1.02} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -69,30 +79,22 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -qmake QMAKE_CFLAGS+="$SLKCFLAGS" QMAKE_CXXFLAGS+="$SLKCFLAGS" \ - -o Makefile FreeChartGeany.pro - +qmake-qt5 make make install INSTALL_ROOT=$PKG find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true -# Install .desktop item and icons. -sed -i "/^Icon/s|=.*|=${PRGNAM}|" $PKG/usr/share/applications/$PRGNAM.desktop -rm -rf $PKG/usr/share/pixmaps -for i in 16 32 64 128; do - install -D -m 0644 images/icons/logo${i}.png \ - $PKG/usr/share/icons/hicolor/${i}x${i}/apps/$PRGNAM.png -done - mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a COPYING images/icons/Readme.rtf licenses/* $PKG/usr/doc/$PRGNAM-$VERSION +cp -a README.md COPYING Changelog $PKG/usr/doc/$PRGNAM-$VERSION +cp -a $PKG/usr/share/doc/alphaplot/*.* $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +rm -rf $PKG/usr/share/doc mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/AlphaPlot/AlphaPlot.info b/academic/AlphaPlot/AlphaPlot.info new file mode 100644 index 0000000000..8108426b35 --- /dev/null +++ b/academic/AlphaPlot/AlphaPlot.info @@ -0,0 +1,10 @@ +PRGNAM="AlphaPlot" +VERSION="1.02" +HOMEPAGE="https://alphaplot.sourceforge.io/" +DOWNLOAD="https://github.com/narunlifescience/AlphaPlot/archive/1.02/AlphaPlot-1.02.tar.gz" +MD5SUM="c4a0d0b4ff78d4b7a75d13128df534be" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Fellype do Nascimento" +EMAIL="fellype (at) gmail (dot) com" diff --git a/academic/AlphaPlot/README b/academic/AlphaPlot/README new file mode 100644 index 0000000000..c66e461dc1 --- /dev/null +++ b/academic/AlphaPlot/README @@ -0,0 +1,4 @@ +Alpha Plot is a free application for Scientific Data Analysis and +Visualization for Windows, Linux and Mac OS X (probably BSD also). +It can generate different types of publication quality 2D and 3D +plots with extensive visual customization. diff --git a/academic/AlphaPlot/doinst.sh b/academic/AlphaPlot/doinst.sh new file mode 100644 index 0000000000..d4daff51d1 --- /dev/null +++ b/academic/AlphaPlot/doinst.sh @@ -0,0 +1,19 @@ +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 +fi + +if [ -x /usr/bin/update-mime-database ]; then + /usr/bin/update-mime-database usr/share/mime >/dev/null 2>&1 +fi + +if [ -e usr/share/icons/hicolor/icon-theme.cache ]; then + if [ -x /usr/bin/gtk-update-icon-cache ]; then + /usr/bin/gtk-update-icon-cache -f usr/share/icons/hicolor >/dev/null 2>&1 + fi +fi + +if [ -e usr/share/icons/locolor/icon-theme.cache ]; then + if [ -x /usr/bin/gtk-update-icon-cache ]; then + /usr/bin/gtk-update-icon-cache -f usr/share/icons/locolor >/dev/null 2>&1 + fi +fi diff --git a/academic/flashqard/slack-desc b/academic/AlphaPlot/slack-desc index d03f1ed5cc..a03106331a 100644 --- a/academic/flashqard/slack-desc +++ b/academic/AlphaPlot/slack-desc @@ -6,14 +6,14 @@ # customary to leave one space after the ':' except on otherwise blank lines. |-----handy-ruler------------------------------------------------------| -flashqard: flashqard (educational software to improve your learning process) -flashqard: -flashqard: This aim is achieved by using the widely used method, called -flashqard: Leitner System, and the idea of "different card types for -flashqard: different purposes". -flashqard: -flashqard: http://www.flashqard-project.org/ -flashqard: -flashqard: -flashqard: -flashqard: +AlphaPlot: AlphaPlot (data analysis and visualization) +AlphaPlot: +AlphaPlot: Application for statistical analysis and data visualization which can +AlphaPlot: generate different types of publication quality 2D and 3D plots with +AlphaPlot: extensive visual customization. +AlphaPlot: +AlphaPlot: +AlphaPlot: +AlphaPlot: +AlphaPlot: +AlphaPlot: diff --git a/academic/AstroImageJ/AstroImageJ.SlackBuild b/academic/AstroImageJ/AstroImageJ.SlackBuild new file mode 100644 index 0000000000..21d1234e00 --- /dev/null +++ b/academic/AstroImageJ/AstroImageJ.SlackBuild @@ -0,0 +1,113 @@ +#!/bin/bash + +# Slackware build script for astroimagej + +# Copyright 2023 Christopher Duston (christopher.duston@protonmail.com) +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=AstroImageJ +VERSION=${VERSION:-v5.3.2.00} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +#### These lines are to ensure the build can happen on multilib systems. +if [ "$ARCH" = "i586" ] || [ "$ARCH" = "i686" ]; then + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + LIBDIRSUFFIX="64" +else + LIBDIRSUFFIX="" +fi +#### + +set -e + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +rm -rf $PKG +mkdir -p $TMP $PKG +rm -rf $TMP/$PRGNAM-$VERSION +cd $TMP || exit 1 + +tar xvf $CWD/${PRGNAM}-${VERSION}-linux-x86_64Bit.tar.gz || exit 1 + +cd ${PRGNAM} + +chown -R root:root . +chmod -R u+w,go+r-w,a-s . + +# Putting these here so they are correctly removed by removepkg. +mkdir -p $PKG/usr/lib64 $PKG/usr/bin +cp -r $TMP/$PRGNAM $PKG/usr/lib64 +cp $CWD/astroimagej $PKG/usr/bin + +# Documentation +PKGDOC=$PKG/usr/doc/$PRGNAM-$VERSION +mkdir -p $PKGDOC +cp -a LICENSE MANIFEST.MF README.txt $PKG/usr/doc/$PRGNAM-$VERSION +find $PKG/usr/doc/$PRGNAM-$VERSION -type f -exec chmod 644 {} \; +cat $CWD/$PRGNAM.SlackBuild > $PKGDOC/$PRGNAM.SlackBuild + +# Create the ./install directory and copy the slack-desc into it +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +# Strip objects from a bunch of files sbopkglint complains about: +strip $PKG/usr/lib$LIBDIRSUFFIX/$PRGNAM/jre/lib/*.so +strip $PKG/usr/lib$LIBDIRSUFFIX/$PRGNAM/jre/lib/jexec +strip $PKG/usr/lib$LIBDIRSUFFIX/$PRGNAM/jre/lib/server/*.so +strip $PKG/usr/lib$LIBDIRSUFFIX/$PRGNAM/jre/lib/jspawnhelper +strip $PKG/usr/lib$LIBDIRSUFFIX/$PRGNAM/jre/lib/simengine +strip $PKG/usr/lib$LIBDIRSUFFIX/$PRGNAM/jre/lib/criu +strip $PKG/usr/lib$LIBDIRSUFFIX/$PRGNAM/jre/lib/pauseengine +strip $PKG/usr/lib$LIBDIRSUFFIX/$PRGNAM/jre/lib/criuengine +strip $PKG/usr/lib$LIBDIRSUFFIX/$PRGNAM/jre/bin/* +# Make these files executable, for the same reason... +chmod a+x $PKG/usr/lib$LIBDIRSUFFIX/$PRGNAM/jre/lib/*.so +chmod a+x $PKG/usr/lib$LIBDIRSUFFIX/$PRGNAM/jre/lib/jexec +chmod a+x $PKG/usr/lib$LIBDIRSUFFIX/$PRGNAM/jre/lib/server/*.so +chmod a+x $PKG/usr/lib$LIBDIRSUFFIX/$PRGNAM/jre/lib/jspawnhelper +chmod a+x $PKG/usr/lib$LIBDIRSUFFIX/$PRGNAM/jre/lib/simengine +chmod a+x $PKG/usr/lib$LIBDIRSUFFIX/$PRGNAM/jre/lib/criu +chmod a+x $PKG/usr/lib$LIBDIRSUFFIX/$PRGNAM/jre/lib/pauseengine +chmod a+x $PKG/usr/lib$LIBDIRSUFFIX/$PRGNAM/jre/lib/criuengine +chmod a+x $PKG/usr/lib$LIBDIRSUFFIX/$PRGNAM/jre/bin/* +chmod a+x $PKG/usr/bin/astroimagej + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.tgz diff --git a/academic/AstroImageJ/AstroImageJ.info b/academic/AstroImageJ/AstroImageJ.info new file mode 100644 index 0000000000..d8e30979fe --- /dev/null +++ b/academic/AstroImageJ/AstroImageJ.info @@ -0,0 +1,10 @@ +PRGNAM="AstroImageJ" +VERSION="v5.3.2.00" +HOMEPAGE="https://www.astro.louisville.edu/software/astroimagej/" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="https://www.astro.louisville.edu/software/astroimagej/installation_packages/AstroImageJ-v5.3.2.00-linux-x86_64Bit.tar.gz" +MD5SUM_x86_64="0c34050d12a4427ba710c44339af2c61" +REQUIRES="" +MAINTAINER="Christopher L Duston" +EMAIL="christopher.duston@protonmail.com" diff --git a/academic/AstroImageJ/README b/academic/AstroImageJ/README new file mode 100644 index 0000000000..e6d8ec3199 --- /dev/null +++ b/academic/AstroImageJ/README @@ -0,0 +1,32 @@ +ImageJ is a graphical user interface (GUI) driven, public domain, +Java-based, software package for general image processing +traditionally used mainly in life sciences ï¬elds. The image processing +capabilities of ImageJ are useful and extendable to other scientiï¬c +ï¬elds. Here we present AstroImageJ (AIJ), which provides an astronomy +speciï¬c image display environment and tools for astronomy speciï¬c +image calibration and data reduction. Although AIJ maintains the +general purpose image processing capabilities of ImageJ, AIJ is +streamlined for time-series differential photometry, light curve +detrending and ï¬tting, and light curve plotting, especially for +applications requiring ultra-precise light curves (e.g., exoplanet +transits). AIJ reads and +writes standard FITS ï¬les, as well as other common image formats, +provides FITS header viewing and editing, and is World Coordinate +System (WCS) aware, including an automated interface to the +astrometry.net web portal for plate solving images. AIJ provides +research grade image calibration and analysis tools with a GUI driven +approach, and easily installed cross-platform compatibility. It +enables new users, even at the level of undergraduate student, high +school student, or amateur astronomer, to quickly start processing, +modeling, and plotting astronomical image data with one tightly +integrated software package. + +Rather than building from source, this package just copies a binary +into the system. It is recommended that post-installation, the user +changes the permissions of the install directory so that the user can +update the software: + +# chown -R myname.users /usr/lib64/AstroImageJ + +It is further recommend to update to the latest daily build - in +particular, the WCS-finding routine is broken on earlier versions. diff --git a/academic/AstroImageJ/astroimagej b/academic/AstroImageJ/astroimagej new file mode 100644 index 0000000000..1096bd8524 --- /dev/null +++ b/academic/AstroImageJ/astroimagej @@ -0,0 +1,4 @@ +#!/bin/sh +cd /usr/lib64/AstroImageJ/ +./AstroImageJ +exit diff --git a/academic/AstroImageJ/slack-desc b/academic/AstroImageJ/slack-desc new file mode 100644 index 0000000000..dc2aa0aa28 --- /dev/null +++ b/academic/AstroImageJ/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +AstroImageJ: AstroImageJ (Astronomical Image Processing) +AstroImageJ: +AstroImageJ: AstroImageJ is a graphical user interface (GUI) driven, public +AstroImageJ: domain, Java-based, software package for astronomical image +AstroImageJ: processing. +AstroImageJ: +AstroImageJ: It is recommended to change the permissions of the install +AstroImageJ: directory so that the user can update the software: +AstroImageJ: # chown -R myname.users /usr/lib64/AstroImageJ +AstroImageJ: +AstroImageJ: Homepage: https://www.astro.louisville.edu/software/astroimagej/ diff --git a/academic/CAFS_divergence/CAFS_divergence.SlackBuild b/academic/CAFS_divergence/CAFS_divergence.SlackBuild index 28b2385816..0afc945503 100644 --- a/academic/CAFS_divergence/CAFS_divergence.SlackBuild +++ b/academic/CAFS_divergence/CAFS_divergence.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for CAFS_divergence -# Copyright 2017 Petar Petrov slackalaxy@gmail.com +# Copyright 2017-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,33 +22,40 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=CAFS_divergence BINNAM=cafs SYSTOS=linux VERSION=${VERSION:-1.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then - case "$( uname -m )" in - i?86) ARCH=i386 ;; - arm*) ARCH=arm ;; - *) ARCH=$( uname -m ) ;; - esac + ARCH=$( uname -m ) +fi + +# 2023-05-16 DW: 64bit only +if [ "$ARCH" != "x86_64" ]; then + printf "\n$ARCH is not supported... \n" + exit 1 +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 fi -CWD=$(pwd) TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} set -e -if [ "$ARCH" != "i386" ] && [ "$ARCH" != "x86_64" ]; then - printf "\n\n$ARCH is not supported... \n" - exit 1 -fi - rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP @@ -82,4 +89,4 @@ mkdir -p $PKG/install sed "s/@VERSION@/$VERSION/" < $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/CAFS_divergence/README b/academic/CAFS_divergence/README index 9320c24786..61ae3acb06 100644 --- a/academic/CAFS_divergence/README +++ b/academic/CAFS_divergence/README @@ -1,24 +1,25 @@ CAFS: Clustering Analysis of Functional Shifts -CAFS is a simple and fast method for Clustering functionally divergent (FD) -genes by Functional Category. +CAFS is a simple and fast method for Clustering functionally divergent +(FD) genes by Functional Category. -The method implemented in CAFS is one of several sequence-based methods -for identifying the 'interesting' subset of substitutions that might -underpin functional divergence. These methods are based on the idea of that -functionally-important residues are highly conserved, so that evolutionary -rates tend to be low at important sites. Functional divergence can then be -identified by comparing rates (or levels of conservation) between two -clades of proteins at a homologous site. Alternatively, a significant -change in amino acid identity (such as a large, positively-charged residue -in one group of sequences versus a small, neutral residue in the other) -could indicate functional divergence even without a change in rate. +The method implemented in CAFS is one of several sequence-based +methods for identifying the 'interesting' subset of substitutions +that might underpin functional divergence. These methods are based +on the idea of that functionally-important residues are highly +conserved, so that evolutionary rates tend to be low at important +sites. Functional divergence can then be identified by comparing +rates (or levels of conservation) between two clades of proteins at +a homologous site. Alternatively, a significant change in amino acid +identity (such as a large, positively-charged residue in one group of +sequences versus a small, neutral residue in the other) could indicate +functional divergence even without a change in rate. This program analyses alignments and provides the user with the best putative sites under functional divergence. -NOTE: This only repackages the 64bit binary provided from upstream. A 32bit -executable is not available. +NOTE: This only repackages the 64bit binary provided from upstream. A +32bit executable is not available. Citing: Caffrey BE, Williams TA, Jiang X, Toft C, Hokamp K, Fares MA (2011). diff --git a/academic/CAPS_coevolution/CAPS_coevolution.SlackBuild b/academic/CAPS_coevolution/CAPS_coevolution.SlackBuild index 99f177b84b..fe93e4dc6e 100644 --- a/academic/CAPS_coevolution/CAPS_coevolution.SlackBuild +++ b/academic/CAPS_coevolution/CAPS_coevolution.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for CAPS_coevolution -# Copyright 2017 Petar Petrov slackalaxy@gmail.com +# Copyright 2017-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,31 +22,41 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=CAPS_coevolution VERSION=${VERSION:-2.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} +# 2023-05-16 DW: add a real test if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i386 ;; - arm*) ARCH=arm ;; + i?86) ARCH=i586 ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +if [[ $ARCH != i?86 ]] && [ "$ARCH" != "x86_64" ]; then + printf "\n$ARCH is not supported... \n" + exit 1 +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} set -e -if [ "$ARCH" != "i386" ] && [ "$ARCH" != "x86_64" ]; then - printf "\n\n$ARCH is not supported... \n" - exit 1 -fi - # The zipped names of the 32bit and 64bit versions differ too much, so # let's set them here. BINNAM=caps @@ -98,4 +108,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/CAPS_coevolution/README b/academic/CAPS_coevolution/README index b0d477c7a2..47f542a809 100644 --- a/academic/CAPS_coevolution/README +++ b/academic/CAPS_coevolution/README @@ -13,7 +13,10 @@ In addition, a test which assesses whether two proteins are interacting is implemented. NOTE: -The script just repackages the binaries provided from upstream. +The script just repackages the binaries provided from upstream. If you +want to compile the program from source check "vCAPS_coevolution", which +also comes with an unofficial patch that extends the verbosity of the +results. CITING: CAPS: coevolution analysis using protein sequences. Fares MA, McNally D. diff --git a/academic/DRAMPower/DRAMPower.SlackBuild b/academic/DRAMPower/DRAMPower.SlackBuild new file mode 100644 index 0000000000..0d8b89966a --- /dev/null +++ b/academic/DRAMPower/DRAMPower.SlackBuild @@ -0,0 +1,148 @@ +#!/bin/bash + +# Slackware build script for DRAMPower + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=DRAMPower +VERSION=${VERSION:-4.1} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +TRACES_COMMIT=e640d3f7ff3766cdf4a799943f81e6ffe0946fb4 + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +# correct the path for xerces-c library +sed -i '89s#lib#&'${LIBDIRSUFFIX}'#' Makefile + +# disable downloading traces file +sed -i '127,128s/^/#/' Makefile + +# fix for unpacking traces +sed -i '131s/^/#/' Makefile +sed -i '131a\\tmkdir -p traces && unzip -j -d traces traces.zip' Makefile + +# fix example makefile +sed -i 's#DRAMPOWER_PATH ?=.*#DRAMPOWER_PATH ?= /usr/share/'$PRGNAM-$VERSION'#' test/libdrampowertest/Makefile +sed -i 's/MYPATH :=.*/MYPATH := ./' test/libdrampowertest/Makefile +sed -i '72,73s#-iquote ${DRAMPOWER_PATH}/src ##' test/libdrampowertest/Makefile +sed -i '72,73s#-L${DRAMPOWER_PATH}/src/ ##' test/libdrampowertest/Makefile +sed -i '72,73s#$# -I/usr/include/libdrampower#' test/libdrampowertest/Makefile + +sed -i -e 's/test: all/test: $(BINARY) $(BINARY2)/' \ + -e 's/all:/all: $(BINARY) $(BINARY2)\n/' \ + -e '72i $(BINARY):' -e '73i\\n$(BINARY2):' test/libdrampowertest/Makefile +sed -i '34a # Modified for slackbuilds.org at 29 Oct 2022 by William PC - Seattle (USA)' test/libdrampowertest/Makefile + +cp -av $CWD/DRAMPowerTraces-$TRACES_COMMIT.zip traces.zip + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +make + +# installing +install -d $PKG/usr/bin +install -m 755 drampower $PKG/usr/bin +install -d $PKG/usr/include/libdrampower +install -m 644 src/libdrampower/*.h $PKG/usr/include/libdrampower +install -m 644 src/*.h $PKG/usr/include/libdrampower +install -d $PKG/usr/include/libdrampower/xmlparser +install -m 644 src/xmlparser/*.h $PKG/usr/include/libdrampower/xmlparser +install -d $PKG/usr/lib${LIBDIRSUFFIX} +install -m 644 src/{libdrampower.a,libdrampowerxml.a} $PKG/usr/lib${LIBDIRSUFFIX} + +mkdir -p $PKG/usr/share/$PRGNAM-$VERSION +cp -av memspecs traces $PKG/usr/share/$PRGNAM-$VERSION + +mkdir -p $PKG/usr/share/$PRGNAM-$VERSION/examples +cp -av test/libdrampowertest $PKG/usr/share/$PRGNAM-$VERSION/examples + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + ChangeLog README.md \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/DRAMPower/DRAMPower.info b/academic/DRAMPower/DRAMPower.info new file mode 100644 index 0000000000..16fb158264 --- /dev/null +++ b/academic/DRAMPower/DRAMPower.info @@ -0,0 +1,12 @@ +PRGNAM="DRAMPower" +VERSION="4.1" +HOMEPAGE="https://www.uni-kl.de/en/3d-dram/tools/drampower" +DOWNLOAD="https://github.com/tukl-msd/DRAMPower/archive/v4.1/DRAMPower-4.1.tar.gz \ + https://github.com/Sv3n/DRAMPowerTraces/archive/e640d3f7ff3766cdf4a799943f81e6ffe0946fb4/DRAMPowerTraces-e640d3f7ff3766cdf4a799943f81e6ffe0946fb4.zip" +MD5SUM="9f93091c13c01d32f7cc22e609a8f1c3 \ + 8c3bbf7d031f531f5630e0058e22d8e3" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="xerces-c" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/DRAMPower/README b/academic/DRAMPower/README new file mode 100644 index 0000000000..be3cb3f5fa --- /dev/null +++ b/academic/DRAMPower/README @@ -0,0 +1,29 @@ + DRAMPower is an open source tool for fast and accurate DRAM power +and energy estimation for DRAM memories. The latest version of +the tool is v4.0 and features many important improvements, such as +significantly improved analysis speed (at least 10x), enabling +analysis of much larger traces, as well as support for DDR2/DDR3, +LPDDR/LPDDR2, DDR4 and Wide I/O memories. The tool is based on the +DRAM power model developed jointly by the Computer Engineering +Research Group at TU Delft and the Electronic Systems Group at +TU Eindhoven and has been verified by the Microelectronic System +Design Research Group at TU Kaiserslautern with equivalent +circuit-level simulations, which established that the error of +the tool to be < 2% for all memory operations of any granularity +for all memories supported by DRAMPower. DRAMPower is also part +of the computer architecture simulator gem5. + + + Invocation example: + # drampower -m /usr/share/DRAMPower-4.1/memspecs/MICRON_1Gb_DDR3-\ +1066_8bit_G.xml -c /usr/share/DRAMPower-4.1/traces/commands.trace + + Examples of using the library are located at: + # /usr/share/DRAMPower-4.1/examples/libdrampowertest + + You can copy them to a working dir and then run "make test" for +testing, as following: + # cp -av /usr/share/DRAMPower-4.1/examples/libdrampowertest . + # cd libdrampowertest + # make test + diff --git a/academic/DRAMPower/slack-desc b/academic/DRAMPower/slack-desc new file mode 100644 index 0000000000..c7c49f03c4 --- /dev/null +++ b/academic/DRAMPower/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +DRAMPower: DRAMPower (DRAM Power and Energy Estimation for DRAM) +DRAMPower: +DRAMPower: +DRAMPower: DRAMPower is an open source tool for fast and accurate DRAM power +DRAMPower: and energy estimation for DRAM memories. The latest version of +DRAMPower: the tool is v4.0 and features many important improvements, such as +DRAMPower: significantly improved analysis speed (at least 10x), enabling +DRAMPower: analysis of much larger traces, as well as support for DDR2/DDR3, +DRAMPower: LPDDR/LPDDR2, DDR4 and Wide I/O memories. +DRAMPower: +DRAMPower: diff --git a/academic/DRAMSim2/DRAMSim2.SlackBuild b/academic/DRAMSim2/DRAMSim2.SlackBuild new file mode 100644 index 0000000000..e7fa8e329d --- /dev/null +++ b/academic/DRAMSim2/DRAMSim2.SlackBuild @@ -0,0 +1,123 @@ +#!/bin/bash + +# Slackware build script for DRAMSim2 + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=DRAMSim2 +VERSION=${VERSION:-2.2.2} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION + +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +if [ "${DEBUG:-no}" == "yes" ]; then + OPT_BUILD="DEBUG=1" +fi + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +make $OPT_BUILD +make libdramsim.so + +# installing +mkdir -p $PKG/usr/bin +mkdir -p $PKG/usr/lib${LIBDIRSUFFIX} +mkdir -p $PKG/usr/share/$PRGNAM + +cp -a DRAMSim $PKG/usr/bin +cp -a libdramsim.so $PKG/usr/lib${LIBDIRSUFFIX} +cp -a example_app $PKG/usr/share/$PRGNAM +cp -a ini $PKG/usr/share/$PRGNAM +cp -a traces $PKG/usr/share/$PRGNAM +cp -a system.ini.example $PKG/usr/share/$PRGNAM + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a README README.pdf README.tex \ + $PKG/usr/doc/$PRGNAM-$VERSION + +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/DRAMSim2/DRAMSim2.info b/academic/DRAMSim2/DRAMSim2.info new file mode 100644 index 0000000000..7b876bb68c --- /dev/null +++ b/academic/DRAMSim2/DRAMSim2.info @@ -0,0 +1,10 @@ +PRGNAM="DRAMSim2" +VERSION="2.2.2" +HOMEPAGE="https://github.com/umd-memsys/DRAMSim2" +DOWNLOAD="https://github.com/umd-memsys/DRAMSim2/archive/v2.2.2/DRAMSim2-2.2.2.tar.gz" +MD5SUM="c8bf7b58fd67a93f091dcf13bf191602" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="William PC" +EMAIL="w_calandrini@hotmail.com" diff --git a/academic/DRAMSim2/README b/academic/DRAMSim2/README new file mode 100644 index 0000000000..583bc1a5a1 --- /dev/null +++ b/academic/DRAMSim2/README @@ -0,0 +1,7 @@ + DRAMSim2 is a cycle accurate model of a DRAM memory controller, the +DRAM modules which comprise system storage, and the bus by which they +communicate. All major components in a modern memory system are +modeled as their own respective objects within the source, including: +ranks, banks, command queue, the memory controller, etc. + +For setting the DEBUG mode use the enviroment variable DEBUG=1 diff --git a/academic/DRAMSim2/slack-desc b/academic/DRAMSim2/slack-desc new file mode 100644 index 0000000000..311a47785d --- /dev/null +++ b/academic/DRAMSim2/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +DRAMSim2: DRAMSim2 (A cycle accurate DRAM simulator) +DRAMSim2: +DRAMSim2: +DRAMSim2: DRAMSim2 is a cycle accurate model of a DRAM memory controller, the +DRAMSim2: DRAM modules which comprise system storage, and the bus by which they +DRAMSim2: communicate. All major components in a modern memory system are +DRAMSim2: modeled as their own respective objects within the source, including: +DRAMSim2: ranks, banks, command queue, the memory controller, etc. +DRAMSim2: +DRAMSim2: +DRAMSim2: diff --git a/academic/DRAMSys/DRAMSys.SlackBuild b/academic/DRAMSys/DRAMSys.SlackBuild new file mode 100644 index 0000000000..bf56134fd2 --- /dev/null +++ b/academic/DRAMSys/DRAMSys.SlackBuild @@ -0,0 +1,143 @@ +#!/bin/bash + +# Slackware build script for DRAMSys + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=DRAMSys +VERSION=${VERSION:-20220830} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +COMMIT=09f6dcbb91351e6ee7cadfc7bc8b29d97625db8f + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$COMMIT +tar xvf $CWD/$PRGNAM-$COMMIT.tar.gz +cd $PRGNAM-$COMMIT + +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +# unpack requirements +tar xvf $CWD/json-efcc826ecb9b55893397f749e5514316ba8629bb.tar.gz --strip-component 1 -C DRAMSys/library/src/common/third_party/nlohmann +tar xvf $CWD/sqlite-amalgamation-9be05e13408dd8cf8dafe8f11b1700a28194e07e.tar.gz --strip-component 1 -C DRAMSys/library/src/common/third_party/sqlite-amalgamation + +if [ "${POWER:-no}" == "yes" ]; then + # fix for using system installed DRAMPower + sed -i '48,50s/^/#/' DRAMSys/library/CMakeLists.txt + sed -i '247s#PRIVATE.*#PRIVATE /usr/include/libdrampower#' DRAMSys/library/CMakeLists.txt + sed -i '263s/^/#/' DRAMSys/library/CMakeLists.txt + sed -i '266s/DRAMPower/drampower/' DRAMSys/library/CMakeLists.txt + OPT="-DDRAMSYS_WITH_DRAMPOWER:BOOL=ON" +else + OPT="-DDRAMSYS_WITH_DRAMPOWER:BOOL=OFF" +fi + +mkdir -p build +cd build + SYSTEMC_HOME=/usr \ + cmake \ + -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DBUILD_SHARED_LIBS=ON \ + -DCMAKE_CXX_STANDARD=17 \ + $OPT \ + -DCMAKE_BUILD_TYPE=Release ../DRAMSys + make +# make install/strip DESTDIR=$PKG +cd .. + +# installing +install -d $PKG/usr/bin +install -m 0755 build/simulator/DRAMSys $PKG/usr/bin +install -d $PKG/usr/lib${LIBDIRSUFFIX} +install -m 0644 build/library/libDRAMSysLibrary.so $PKG/usr/lib${LIBDIRSUFFIX} + +mkdir -p $PKG/usr/share/DRAMSys/ +cp -av DRAMSys/library/resources/* $PKG/usr/share/$PRGNAM + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +find $PKG -depth -type d -empty -delete || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a LICENSE.txt README.md \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/DRAMSys/DRAMSys.info b/academic/DRAMSys/DRAMSys.info new file mode 100644 index 0000000000..e6cfe22eb2 --- /dev/null +++ b/academic/DRAMSys/DRAMSys.info @@ -0,0 +1,14 @@ +PRGNAM="DRAMSys" +VERSION="20220830" +HOMEPAGE="https://github.com/tukl-msd/DRAMSys" +DOWNLOAD="https://github.com/tukl-msd/DRAMSys/archive/09f6dcbb91351e6ee7cadfc7bc8b29d97625db8f/DRAMSys-09f6dcbb91351e6ee7cadfc7bc8b29d97625db8f.tar.gz \ + https://github.com/nlohmann/json/archive/efcc826ecb9b55893397f749e5514316ba8629bb/json-efcc826ecb9b55893397f749e5514316ba8629bb.tar.gz \ + https://github.com/azadkuh/sqlite-amalgamation/archive/9be05e13408dd8cf8dafe8f11b1700a28194e07e/sqlite-amalgamation-9be05e13408dd8cf8dafe8f11b1700a28194e07e.tar.gz" +MD5SUM="812ef08562d99038669c5eb881e85c63 \ + 14999edd13ec7697cce179e344615c2a \ + d557d04aa385876917d7d63977b94931" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="SystemC" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/DRAMSys/README b/academic/DRAMSys/README new file mode 100644 index 0000000000..c294454387 --- /dev/null +++ b/academic/DRAMSys/README @@ -0,0 +1,13 @@ + DRAMSys4.0 is a flexible DRAM subsystem design space exploration +framework based on SystemC TLM-2.0. It was developed at the +Microelectronic Systems Design Research Group and Fraunhofer IESE. + + + If you want to enable power simulation set the environment variable +POWER=yes, this requires the package DRAMPower. + If you want to run thermal simulations install 3D-ICE with SystemC +wrapper enabled. + +# invocation example +# DRAMSys /usr/share/DRAMSys/simulations/ddr3-example.json \ + /usr/share/DRAMSys diff --git a/academic/QtiPlot/slack-desc b/academic/DRAMSys/slack-desc index c6e9172090..b1fe79727d 100644 --- a/academic/QtiPlot/slack-desc +++ b/academic/DRAMSys/slack-desc @@ -6,14 +6,14 @@ # customary to leave one space after the ':' except on otherwise blank lines. |-----handy-ruler------------------------------------------------------| -QtiPlot: QtiPlot (Data Analysis and Visualisation) -QtiPlot: -QtiPlot: QtiPlot is a program for two- and three-dimensional graphical -QtiPlot: presentation of data sets and for data analysis. Plots can be -QtiPlot: produced from data sets stored in tables or from analytical -QtiPlot: functions. -QtiPlot: -QtiPlot: Home: https://www.qtiplot.com/ -QtiPlot: -QtiPlot: -QtiPlot: +DRAMSys: DRAMSys (DRAM subsystem design space exploration framework) +DRAMSys: +DRAMSys: +DRAMSys: +DRAMSys: DRAMSys4.0 is a flexible DRAM subsystem design space exploration +DRAMSys: framework based on SystemC TLM-2.0. It was developed at the +DRAMSys: Microelectronic Systems Design Research Group and Fraunhofer IESE. +DRAMSys: +DRAMSys: +DRAMSys: +DRAMSys: diff --git a/academic/DRAMsim3/DRAMsim3.SlackBuild b/academic/DRAMsim3/DRAMsim3.SlackBuild new file mode 100644 index 0000000000..25d92d313a --- /dev/null +++ b/academic/DRAMsim3/DRAMsim3.SlackBuild @@ -0,0 +1,127 @@ +#!/bin/bash + +# Slackware build script for DRAMsim3 + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=DRAMsim3 +VERSION=${VERSION:-1.0.0} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION + +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +# NOTE: Not working right now, it requires atlas +# which is unavailable to 15.0 yet. +# enable THERMAL +#if [ "${THERMAL:-no}" == "yes" ];then +# OPTS="-DTHERMAL=ON" +# sed -i 's#../ext/SuperLU_MT_3.1/SRC/##' src/sp_ienv.c +# sed -i 's#../ext/SuperLU_MT_3.1/SRC/##' src/thermal_solver.c +#fi + +mkdir -p build +cd build + cmake \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + $OPTS \ + -DCMAKE_BUILD_TYPE=Release .. + make +# doesn't have install rule +# make install/strip DESTDIR=$PKG +cd .. + +# Manual installation +mkdir -p $PKG/usr/{bin,lib${LIBDIRSUFFIX}} +cp -a build/dramsim3main $PKG/usr/bin +cp -a libdramsim3.so $PKG/usr/lib${LIBDIRSUFFIX} + +# additional stuff +mkdir -p $PKG/usr/share/$PRGNAM-$VERSION +cp -a configs scripts tests $PKG/usr/share/$PRGNAM-$VERSION + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a LICENSE \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/DRAMsim3/DRAMsim3.info b/academic/DRAMsim3/DRAMsim3.info new file mode 100644 index 0000000000..513affc87a --- /dev/null +++ b/academic/DRAMsim3/DRAMsim3.info @@ -0,0 +1,10 @@ +PRGNAM="DRAMsim3" +VERSION="1.0.0" +HOMEPAGE="https://github.com/umd-memsys/DRAMsim3" +DOWNLOAD="https://github.com/umd-memsys/DRAMsim3/archive/1.0.0/DRAMsim3-1.0.0.tar.gz" +MD5SUM="ae5079649cac0987236939b13c28e51e" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="William PC" +EMAIL="w_calandrini@hotmail.com" diff --git a/academic/DRAMsim3/README b/academic/DRAMsim3/README new file mode 100644 index 0000000000..93e5ce9b8d --- /dev/null +++ b/academic/DRAMsim3/README @@ -0,0 +1,7 @@ + DRAMsim3 models the timing paramaters and memory controller behavior +for several DRAM protocols such as DDR3, DDR4, LPDDR3, LPDDR4, GDDR5, +GDDR6, HBM, HMC, STT-MRAM. It is implemented in C++ as an objected +oriented model that includes a parameterized DRAM bank model, DRAM +controllers, command queues and system-level interfaces to interact +with a CPU simulator (GEM5, ZSim) or trace workloads. It is designed +to be accurate, portable and parallel. diff --git a/academic/DRAMsim3/slack-desc b/academic/DRAMsim3/slack-desc new file mode 100644 index 0000000000..1e16441727 --- /dev/null +++ b/academic/DRAMsim3/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +DRAMsim3: DRAMsim3 (DRAM simulator) +DRAMsim3: +DRAMsim3: DRAMsim3 models the timing paramaters and memory controller behavior +DRAMsim3: for several DRAM protocols such as DDR3, DDR4, LPDDR3, LPDDR4, GDDR5, +DRAMsim3: GDDR6, HBM, HMC, STT-MRAM. It is implemented in C++ as an objected +DRAMsim3: oriented model that includes a parameterized DRAM bank model, DRAM +DRAMsim3: controllers, command queues and system-level interfaces to interact +DRAMsim3: with a CPU simulator (GEM5, ZSim) or trace workloads. It is designed +DRAMsim3: to be accurate, portable and parallel. +DRAMsim3: +DRAMsim3: diff --git a/academic/Data2FCS/Data2FCS.SlackBuild b/academic/Data2FCS/Data2FCS.SlackBuild index 161057249d..eb366a5fb8 100644 --- a/academic/Data2FCS/Data2FCS.SlackBuild +++ b/academic/Data2FCS/Data2FCS.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for Data2FCS -# Copyright 2017 Petar Petrov slackalaxy@gmail.com +# Copyright 2017-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,15 +22,25 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=Data2FCS PRGADD=FCS2Data VERSION=${VERSION:-1.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} ARCH=noarch -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -47,7 +57,7 @@ cd $PRGNAM-$VERSION # This is Data2FCS mkdir $PRGNAM cd $PRGNAM -unzip $CWD/${PRGNAM}\ ${VERSION}.zip +unzip $CWD/${PRGNAM}\ ${VERSION}.zip || unzip $CWD/${PRGNAM}%20${VERSION}.zip install -D -m755 $PRGNAM.jar $PKG/usr/bin/$PRGNAM.jar # Rename these, so we include them as documentation @@ -58,7 +68,7 @@ cd .. # This is FCS2Data mkdir $PRGADD cd $PRGADD -unzip $CWD/${PRGADD}\ ${VERSION}.zip +unzip $CWD/${PRGADD}\ ${VERSION}.zip || unzip $CWD/${PRGADD}%20${VERSION}.zip install -D -m755 $PRGADD.jar $PKG/usr/bin/$PRGADD.jar # Rename these, so we include them as documentation, too @@ -84,4 +94,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/Data2FCS/Data2FCS.info b/academic/Data2FCS/Data2FCS.info index 3a6d0bcf0f..f24c6cfcc4 100644 --- a/academic/Data2FCS/Data2FCS.info +++ b/academic/Data2FCS/Data2FCS.info @@ -7,6 +7,6 @@ MD5SUM="59b89861defa64a34ede2ea97e1194b5 \ aa327e522bfc9b18e72f20ae1dbcdace" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="jdk" +REQUIRES="zulu-openjdk11" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/DendroPy/DendroPy.SlackBuild b/academic/DendroPy/DendroPy.SlackBuild index 83d5387ca2..6beba20b5f 100644 --- a/academic/DendroPy/DendroPy.SlackBuild +++ b/academic/DendroPy/DendroPy.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for DendroPy -# Copyright 2019 Petar Petrov slackalaxy@gmail.com +# Copyright 2019-2022 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=DendroPy -VERSION=${VERSION:-4.4.0} +VERSION=${VERSION:-4.5.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -83,4 +93,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/DendroPy/DendroPy.info b/academic/DendroPy/DendroPy.info index 9fd1030ffa..d0ded1b95c 100644 --- a/academic/DendroPy/DendroPy.info +++ b/academic/DendroPy/DendroPy.info @@ -1,8 +1,8 @@ PRGNAM="DendroPy" -VERSION="4.4.0" +VERSION="4.5.1" HOMEPAGE="https://dendropy.org/" -DOWNLOAD="https://github.com/jeetsukumaran/DendroPy/archive/v4.4.0/DendroPy-4.4.0.tar.gz" -MD5SUM="171d9f435bc990778a0460a8224b3d76" +DOWNLOAD="https://github.com/jeetsukumaran/DendroPy/archive/v4.5.1/DendroPy-4.5.1.tar.gz" +MD5SUM="c00c554c26c4a3136c835bb37ecafae7" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/EMBASSY/EMBASSY.SlackBuild b/academic/EMBASSY/EMBASSY.SlackBuild index 81c21fe1b0..337de5f778 100644 --- a/academic/EMBASSY/EMBASSY.SlackBuild +++ b/academic/EMBASSY/EMBASSY.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for EMBASSY -# Copyright 2011-2016 Petar Petrov slackalaxy@gmail.com +# Copyright 2011-2022 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,26 +22,36 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=EMBASSY VERSION=${VERSION:-6.6.0} # Keep this the same version as EMBOSS -BUILD=${BUILD:-1} +BUILD=${BUILD:-4} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -54,6 +64,9 @@ else LIBDIRSUFFIX="" fi +# where to look for libraries +LIBDIRPATH="-Wl,-rpath,/usr/lib${LIBDIRSUFFIX}/EMBOSS" + # EMBASSY components and their versions CBSTOOLS=CBSTOOLS-1.0.0.650 CLUSTALOMEGA=CLUSTALOMEGA-1.1.0 @@ -112,11 +125,13 @@ find -L . \ # Build CBSTOOLS cd $TMP/$PRGNAM-$VERSION/$CBSTOOLS -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ +CFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \ ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ + --libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \ + --bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \ --sysconfdir=/etc \ --localstatedir=/var \ --mandir=/usr/man \ @@ -127,240 +142,272 @@ make install DESTDIR=$PKG # Build CLUSTALOMEGA cd $TMP/$PRGNAM-$VERSION/$CLUSTALOMEGA -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ +CFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \ ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ + --libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \ + --bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \ --sysconfdir=/etc \ --localstatedir=/var \ --mandir=/usr/man \ - --docdir=/usr/doc/$PRGNAM-$VERSION/CLUSTALOMEGA \ + --docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \ --build=$ARCH-slackware-linux make make install DESTDIR=$PKG # Build DOMAINATRIX cd $TMP/$PRGNAM-$VERSION/$DOMAINATRIX -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ +CFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \ ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ + --libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \ + --bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \ --sysconfdir=/etc \ --localstatedir=/var \ --mandir=/usr/man \ - --docdir=/usr/doc/$PRGNAM-$VERSION/DOMAINATRIX \ + --docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \ --build=$ARCH-slackware-linux make make install DESTDIR=$PKG # Build DOMALIGN cd $TMP/$PRGNAM-$VERSION/$DOMALIGN -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ +CFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \ ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ + --libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \ + --bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \ --sysconfdir=/etc \ --localstatedir=/var \ --mandir=/usr/man \ - --docdir=/usr/doc/$PRGNAM-$VERSION/DOMALIGN \ + --docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \ --build=$ARCH-slackware-linux make make install DESTDIR=$PKG # Build DOMSEARCH cd $TMP/$PRGNAM-$VERSION/$DOMSEARCH -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ +CFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \ ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ + --libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \ + --bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \ --sysconfdir=/etc \ --localstatedir=/var \ --mandir=/usr/man \ - --docdir=/usr/doc/$PRGNAM-$VERSION/DOMSEARCH \ + --docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \ --build=$ARCH-slackware-linux make make install DESTDIR=$PKG # Build EMNU cd $TMP/$PRGNAM-$VERSION/$EMNU -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ +CFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \ ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ + --libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \ + --bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \ --sysconfdir=/etc \ --localstatedir=/var \ --mandir=/usr/man \ - --docdir=/usr/doc/$PRGNAM-$VERSION/EMNU \ + --docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \ --build=$ARCH-slackware-linux make make install DESTDIR=$PKG # Build ESIM4 cd $TMP/$PRGNAM-$VERSION/$ESIM4 -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ +CFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \ ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ + --libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \ + --bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \ --sysconfdir=/etc \ --localstatedir=/var \ --mandir=/usr/man \ - --docdir=/usr/doc/$PRGNAM-$VERSION/ESIM4 \ + --docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \ --build=$ARCH-slackware-linux make make install DESTDIR=$PKG # Build HMMER cd $TMP/$PRGNAM-$VERSION/$HMMER -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ +CFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \ ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ + --libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \ + --bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \ --sysconfdir=/etc \ --localstatedir=/var \ --mandir=/usr/man \ - --docdir=/usr/doc/$PRGNAM-$VERSION/HMMER \ + --docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \ --build=$ARCH-slackware-linux make make install DESTDIR=$PKG # Build IPRSCAN cd $TMP/$PRGNAM-$VERSION/$IPRSCAN -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ +CFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \ ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ + --libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \ + --bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \ --sysconfdir=/etc \ --localstatedir=/var \ --mandir=/usr/man \ - --docdir=/usr/doc/$PRGNAM-$VERSION/IPRSCAN \ + --docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \ --build=$ARCH-slackware-linux make make install DESTDIR=$PKG # Build MEME cd $TMP/$PRGNAM-$VERSION/$MEME -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ +CFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \ ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ + --libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \ + --bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \ --sysconfdir=/etc \ --localstatedir=/var \ --mandir=/usr/man \ - --docdir=/usr/doc/$PRGNAM-$VERSION/MEME \ + --docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \ --build=$ARCH-slackware-linux make make install DESTDIR=$PKG # Build MSE cd $TMP/$PRGNAM-$VERSION/$MSE -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ +CFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \ ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ + --libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \ + --bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \ --sysconfdir=/etc \ --localstatedir=/var \ --mandir=/usr/man \ - --docdir=/usr/doc/$PRGNAM-$VERSION/MSE \ + --docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \ --build=$ARCH-slackware-linux make make install DESTDIR=$PKG # Build MYEMBOSS cd $TMP/$PRGNAM-$VERSION/$MYEMBOSS -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ +CFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \ ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ + --libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \ + --bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \ --sysconfdir=/etc \ --localstatedir=/var \ --mandir=/usr/man \ - --docdir=/usr/doc/$PRGNAM-$VERSION/MYEMBOSS \ - --build=$ARCH-slackware-linux + --docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \ + --build=$ARCH-slackware-linuxx make make install DESTDIR=$PKG # Build MYEMBOSSDEMO cd $TMP/$PRGNAM-$VERSION/$MYEMBOSSDEMO -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ +CFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \ ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ + --libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \ + --bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \ --sysconfdir=/etc \ --localstatedir=/var \ --mandir=/usr/man \ - --docdir=/usr/doc/$PRGNAM-$VERSION/MYEMBOSSDEMO \ + --docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \ --build=$ARCH-slackware-linux make make install DESTDIR=$PKG # Build PHYLIPNEW cd $TMP/$PRGNAM-$VERSION/$PHYLIPNEW -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ +CFLAGS="$SLKCFLAGS -fcommon $LIBDIRPATH" \ +CXXFLAGS="$SLKCFLAGS -fcommon $LIBDIRPATH" \ +LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \ ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ + --libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \ + --bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \ --sysconfdir=/etc \ --localstatedir=/var \ --mandir=/usr/man \ - --docdir=/usr/doc/$PRGNAM-$VERSION/PHYLIPNEW \ + --docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \ --build=$ARCH-slackware-linux make make install DESTDIR=$PKG # Build SIGNATURE cd $TMP/$PRGNAM-$VERSION/$SIGNATURE -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ +CFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \ ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ + --libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \ + --bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \ --sysconfdir=/etc \ --localstatedir=/var \ --mandir=/usr/man \ - --docdir=/usr/doc/$PRGNAM-$VERSION/SIGNATURE \ + --docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \ --build=$ARCH-slackware-linux make make install DESTDIR=$PKG # Build STRUCTURE cd $TMP/$PRGNAM-$VERSION/$STRUCTURE -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ +CFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \ ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ + --libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \ + --bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \ --sysconfdir=/etc \ --localstatedir=/var \ --mandir=/usr/man \ - --docdir=/usr/doc/$PRGNAM-$VERSION/STRUCTURE \ + --docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \ --build=$ARCH-slackware-linux make make install DESTDIR=$PKG # Build TOPO cd $TMP/$PRGNAM-$VERSION/$TOPO -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ +CFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \ +LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \ ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ + --libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \ + --bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \ --sysconfdir=/etc \ --localstatedir=/var \ --mandir=/usr/man \ - --docdir=/usr/doc/$PRGNAM-$VERSION/TOPO \ + --docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \ --build=$ARCH-slackware-linux make make install DESTDIR=$PKG @@ -368,19 +415,23 @@ make install DESTDIR=$PKG # Build VIENNA cd $TMP/$PRGNAM-$VERSION/$VIENNA # -std=gnu89 fixes build with gcc-5.2 (inline functions HairpinE and LoopEnergy) -CFLAGS="$SLKCFLAGS -std=gnu89" \ -CXXFLAGS="$SLKCFLAGS -std=gnu89" \ +CFLAGS="$SLKCFLAGS -std=gnu89 $LIBDIRPATH" \ +CXXFLAGS="$SLKCFLAGS -std=gnu89 $LIBDIRPATH" \ +LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \ ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ + --libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \ + --bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \ --sysconfdir=/etc \ --localstatedir=/var \ --mandir=/usr/man \ - --docdir=/usr/doc/$PRGNAM-$VERSION/VIENNA \ + --docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \ --build=$ARCH-slackware-linux make make install DESTDIR=$PKG +mv $PKG/usr/share/PHYLIPNEW $PKG/usr/share/EMBOSS + find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true @@ -388,8 +439,10 @@ mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild cat $CWD/CONTENTS > $PKG/usr/doc/$PRGNAM-$VERSION/CONTENTS +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/EMBOSS/EMBOSS.SlackBuild b/academic/EMBOSS/EMBOSS.SlackBuild index 2d139f3a76..bc69dbfcb6 100644 --- a/academic/EMBOSS/EMBOSS.SlackBuild +++ b/academic/EMBOSS/EMBOSS.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for EMBOSS -# Copyright 2011-2016 Petar Petrov slackalaxy@gmail.com +# Copyright 2011-2022 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,26 +22,33 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=EMBOSS VERSION=${VERSION:-6.6.0} -BUILD=${BUILD:-1} +BUILD=${BUILD:-4} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -76,7 +83,8 @@ CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ + --libdir=/usr/lib${LIBDIRSUFFIX}/$PRGNAM \ + --bindir=/usr/lib${LIBDIRSUFFIX}/$PRGNAM/bin \ --with-x \ --sysconfdir=/etc \ --localstatedir=/var \ @@ -86,6 +94,15 @@ CXXFLAGS="$SLKCFLAGS" \ make make install DESTDIR=$PKG +# Make jEmboss find the binaries +sed -i "s|/usr/bin/|/usr/lib${LIBDIRSUFFIX}/$PRGNAM/bin/|g" $PKG/usr/share/EMBOSS/jemboss/resources/jemboss.properties +sed -i "s|/usr/bin:|/usr/lib${LIBDIRSUFFIX}/$PRGNAM:/usr/bin:|g" $PKG/usr/share/EMBOSS/jemboss/resources/jemboss.properties + +mkdir -p $PKG/usr/bin +cd $PKG/usr/bin +mv $PKG/usr/lib${LIBDIRSUFFIX}/$PRGNAM/bin/runJemboss.sh . +cd - + find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true @@ -96,13 +113,19 @@ cp -a \ cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References +cd $PKG/usr/doc/$PRGNAM-$VERSION +ln -s ../../share/$PRGNAM/doc . +cd - + mkdir -p $PKG/usr/share/{applications,pixmaps} cp $CWD/$PRGNAM.desktop $PKG/usr/share/applications cp $CWD/$PRGNAM.png $PKG/usr/share/pixmaps +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/EMBOSS/EMBOSS.info b/academic/EMBOSS/EMBOSS.info index 6cce29ea76..fa59d8b420 100644 --- a/academic/EMBOSS/EMBOSS.info +++ b/academic/EMBOSS/EMBOSS.info @@ -5,6 +5,6 @@ DOWNLOAD="https://sourceforge.net/projects/sboppetrov/files/EMBOSS/EMBOSS-6.6.0. MD5SUM="cc3fca80cb0618deb10fa0d29fe90e4b" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="jdk" +REQUIRES="zulu-openjdk11" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/FCSalyzer/FCSalyzer.SlackBuild b/academic/FCSalyzer/FCSalyzer.SlackBuild index e39624d4f3..fd95771eb2 100644 --- a/academic/FCSalyzer/FCSalyzer.SlackBuild +++ b/academic/FCSalyzer/FCSalyzer.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for FCSalyzer -# Copyright 2017-2020 Petar Petrov slackalaxy@gmail.com +# Copyright 2017-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,15 +22,25 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=FCSalyzer -VERSION=${VERSION:-0.9.18_alpha} +VERSION=${VERSION:-0.9.22_alpha} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} ARCH=noarch -SRCVER=0.9.18-alpha +SRCVER=0.9.22-alpha + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi -CWD=$(pwd) TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -40,9 +50,10 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf ${PRGNAM}\ ${SRCVER} -unzip $CWD/${PRGNAM}\ ${SRCVER}.zip -cd ${PRGNAM}\ ${SRCVER} +rm -rf $TMP/$PRGNAM-$VERSION +mkdir -p $TMP/$PRGNAM-$VERSION +cd $TMP/$PRGNAM-$VERSION +unzip $CWD/${PRGNAM}\ ${SRCVER}.zip || unzip $CWD/${PRGNAM}%20${SRCVER}.zip chown -R root:root . find -L . \ @@ -51,7 +62,7 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -install -D -m755 ${PRGNAM}.jar $PKG/usr/bin/$PRGNAM.jar +install -D -m755 ${PRGNAM}_alternative.jar $PKG/usr/bin/$PRGNAM.jar mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ @@ -68,4 +79,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/FCSalyzer/FCSalyzer.info b/academic/FCSalyzer/FCSalyzer.info index 9e4a0d1d4e..bd781e3a7d 100644 --- a/academic/FCSalyzer/FCSalyzer.info +++ b/academic/FCSalyzer/FCSalyzer.info @@ -1,10 +1,10 @@ PRGNAM="FCSalyzer" -VERSION="0.9.18_alpha" +VERSION="0.9.22_alpha" HOMEPAGE="https://sourceforge.net/projects/fcsalyzer/" -DOWNLOAD="https://sourceforge.net/projects/fcsalyzer/files/Version%200.9.18-alpha/FCSalyzer%200.9.18-alpha.zip" -MD5SUM="9926d1af7b9865615a525c0e1bf0ada2" +DOWNLOAD="https://sourceforge.net/projects/fcsalyzer/files/Version%200.9.22-alpha/FCSalyzer%200.9.22-alpha.zip" +MD5SUM="5a100f3fb10acfcc3935d847c2a386a1" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="jdk" +REQUIRES="zulu-openjdk11" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/FastTree/FastTree.SlackBuild b/academic/FastTree/FastTree.SlackBuild new file mode 100644 index 0000000000..6c954faf8d --- /dev/null +++ b/academic/FastTree/FastTree.SlackBuild @@ -0,0 +1,85 @@ +#!/bin/bash + +# Slackware build script for FastTree + +# Copyright 2023 Petar Petrov, slackalaxy at gmail dot com +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=FastTree +VERSION=${VERSION:-2.1.11} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" +else + SLKCFLAGS="-O2" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +mkdir -p $PRGNAM-$VERSION +cd $PRGNAM-$VERSION +cp $CWD/$PRGNAM.c . +gcc $SLKCFLAGS -o FastTree FastTree.c -lm +install -D -m755 FastTree $PKG/usr/bin/FastTree + +cd $PKG/usr/bin +ln -s FastTree fasttree + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/FastTree/FastTree.info b/academic/FastTree/FastTree.info new file mode 100644 index 0000000000..006113cf06 --- /dev/null +++ b/academic/FastTree/FastTree.info @@ -0,0 +1,10 @@ +PRGNAM="FastTree" +VERSION="2.1.11" +HOMEPAGE="http://www.microbesonline.org/fasttree/" +DOWNLOAD="http://www.microbesonline.org/fasttree/FastTree.c" +MD5SUM="83bf082910e1d704e1b1b35f5e263ece" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/FastTree/README b/academic/FastTree/README new file mode 100644 index 0000000000..4398c4f343 --- /dev/null +++ b/academic/FastTree/README @@ -0,0 +1,17 @@ +FastTree infers approximately-maximum-likelihood phylogenetic trees from +alignments of nucleotide or protein sequences. FastTree can handle +alignments with up to a million of sequences in a reasonable amount of +time and memory. For large alignments, FastTree is 100-1,000 times +faster than PhyML 3.0 or RAxML 7. FastTree is open-source software. + +FastTree is more accurate than PhyML 3 with default settings, and much +more accurate than the distance-matrix methods that are traditionally +used for large alignments. FastTree uses the Jukes-Cantor or generalized +time-reversible (GTR) models of nucleotide evolution and the JTT +(Jones-Taylor-Thornton 1992), WAG (Whelan & Goldman 2001), or LG (Le and +Gascuel 2008) models of amino acid evolution. To account for the varying +rates of evolution across sites, FastTree uses a single rate for each +site (the "CAT" approximation). To quickly estimate the reliability of +each split in the tree, FastTree computes local support values with the +Shimodaira-Hasegawa test (these are the same as PhyML 3's "SH-like local +supports"). diff --git a/academic/FastTree/References b/academic/FastTree/References new file mode 100644 index 0000000000..01aef49abf --- /dev/null +++ b/academic/FastTree/References @@ -0,0 +1,14 @@ +These papers describe FastTree: the first paper describes FastTree 1.0, +and the second paper describes heuristic minimum-evolution SPR moves, +maximum-likelihood NNIs, and SH-like local supports. We have also +eliminated the O(N2) steps in the neighbor-joining phase, and +implemented maximum-likelihood NNI moves and SH-like supports (see the +ChangeLog). + +Price, M.N., Dehal, P.S., and Arkin, A.P. (2009) FastTree: Computing +Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix. +Molecular Biology and Evolution 26:1641-1650, doi:10.1093/molbev/msp077. + +Price, M.N., Dehal, P.S., and Arkin, A.P. (2010) FastTree 2 -- +Approximately Maximum-Likelihood Trees for Large Alignments. PLoS ONE, +5(3):e9490. doi:10.1371/journal.pone.0009490. diff --git a/academic/FastTree/slack-desc b/academic/FastTree/slack-desc new file mode 100644 index 0000000000..e74540e239 --- /dev/null +++ b/academic/FastTree/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +FastTree: FastTree (Infers approximately-ML phylogenetic trees) +FastTree: +FastTree: FastTree infers approximately-maximum-likelihood phylogenetic trees +FastTree: from alignments of nucleotide or protein sequences. FastTree can +FastTree: handle alignments with up to a million of sequences in a reasonable +FastTree: amount of time and memory. +FastTree: +FastTree: http://www.microbesonline.org/fasttree/ +FastTree: +FastTree: +FastTree: diff --git a/academic/FigTree/FigTree.SlackBuild b/academic/FigTree/FigTree.SlackBuild new file mode 100644 index 0000000000..f70e42ca9a --- /dev/null +++ b/academic/FigTree/FigTree.SlackBuild @@ -0,0 +1,75 @@ +#!/bin/bash + +# Slackware build script for FigTree + +# Copyright 2023 Petar Petrov, slackalaxy@gmail.com +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=FigTree +VERSION=${VERSION:-1.4.4} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +ARCH=noarch + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf ${PRGNAM}_v${VERSION} +tar xvf $CWD/${PRGNAM}_v${VERSION}.tgz +cd ${PRGNAM}_v${VERSION} +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +install -D -m 755 bin/figtree $PKG/usr/bin/figtree +install -D -m 644 lib/figtree.jar $PKG/usr/share/$PRGNAM/figtree.jar +install -D -m 644 images/figtree.png $PKG/usr/share/pixmaps/figtree.png +install -D -m 644 $CWD/FigTree.desktop $PKG/usr/share/applications/FigTree.desktop + +sed -i "s:-Xmx512m:-Xmx1024m:" $PKG/usr/bin/figtree +sed -i "s:lib:/usr/share/$PRGNAM:" $PKG/usr/bin/figtree + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/FigTree/FigTree.desktop b/academic/FigTree/FigTree.desktop new file mode 100644 index 0000000000..1b20f2067f --- /dev/null +++ b/academic/FigTree/FigTree.desktop @@ -0,0 +1,8 @@ +[Desktop Entry] +Name=FigTree +Comment=Phylogenetic Viewer +Exec=figtree +Icon=figtree +StartupNotify=false +Type=Application +Categories=Education diff --git a/academic/FigTree/FigTree.info b/academic/FigTree/FigTree.info new file mode 100644 index 0000000000..eb72999634 --- /dev/null +++ b/academic/FigTree/FigTree.info @@ -0,0 +1,10 @@ +PRGNAM="FigTree" +VERSION="1.4.4" +HOMEPAGE="http://tree.bio.ed.ac.uk/software/figtree/" +DOWNLOAD="https://github.com/rambaut/figtree/releases/download/v1.4.4/FigTree_v1.4.4.tgz" +MD5SUM="7039dbb6109c66512599a1ae7b972be6" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="zulu-openjdk8" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/FigTree/README b/academic/FigTree/README new file mode 100644 index 0000000000..f80a4534f3 --- /dev/null +++ b/academic/FigTree/README @@ -0,0 +1,3 @@ +FigTree is designed as a graphical viewer of phylogenetic trees and as a +program for producing publication-ready figures. It can display +summarized and annotated trees produced by BEAST. diff --git a/academic/FigTree/doinst.sh b/academic/FigTree/doinst.sh new file mode 100644 index 0000000000..5fb28930db --- /dev/null +++ b/academic/FigTree/doinst.sh @@ -0,0 +1,3 @@ +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 +fi diff --git a/academic/FigTree/slack-desc b/academic/FigTree/slack-desc new file mode 100644 index 0000000000..27bc500ce7 --- /dev/null +++ b/academic/FigTree/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +FigTree: FigTree (A graphical viewer of phylogenetic trees) +FigTree: +FigTree: FigTree is designed as a graphical viewer of phylogenetic trees +FigTree: and as a program for producing publication-ready figures. +FigTree: +FigTree: http://tree.bio.ed.ac.uk/software/figtree/ +FigTree: +FigTree: +FigTree: +FigTree: +FigTree: diff --git a/academic/FreeFem/FreeFem.SlackBuild b/academic/FreeFem/FreeFem.SlackBuild index 08df0908f8..982341fdae 100644 --- a/academic/FreeFem/FreeFem.SlackBuild +++ b/academic/FreeFem/FreeFem.SlackBuild @@ -1,9 +1,9 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for FreeFem -# Based on the Slackware 14.2 SlackBuild and on PKGBUILD script for freefem from AUR +# Based on the Slackware 15.0 SlackBuild and on PKGBUILD script for freefem from AUR # -# Copyright 2019-2020, Fellype do Nascimento, Campinas - Brazil +# Copyright 2019-2023, Fellype do Nascimento, Guaratinguetá - Brazil # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,11 +23,14 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=FreeFem -VERSION=${VERSION:-4.5} +VERSION=${VERSION:-4.14} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} -SRCVER=${SRCVER:-4.5} # Variable used in some versions that are numbered as x.y-z +PKGTYPE=${PKGTYPE:-tgz} +SRCVER=${SRCVER:-4.14} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -37,7 +40,11 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -45,12 +52,15 @@ OUTPUT=${OUTPUT:-/tmp} if [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" SPEC="" + LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" SPEC="" + LIBDIRSUFFIX="" elif [ "$ARCH" = "x86_64" ]; then SLKCFLAGS="-O2 -fPIC" SPEC="-spec linux-g++-64" + LIBDIRSUFFIX="64" fi @@ -74,6 +84,7 @@ cp $CWD/tetgen1.5.1-beta1.tar.gz 3rdparty/pkg autoreconf -i ./configure \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ --prefix=/usr \ --sysconfdir=/etc \ --disable-mumps \ @@ -83,23 +94,24 @@ autoreconf -i find . -name Makefile -exec sed -i 's+^gcc+gcc =+' {} \; find . -name Makefile -exec sed -i 's+^dir+dir =+' {} \; +find . -name Makefile -exec sed -i "s:/usr/lib/ff++/:/usr/lib${LIBDIRSUFFIX}/ff++/:" {} \; -## TODO: Enable mumps - FreeFem fails to compile with this option enabled up to now +## TODO: Enable mumps make make install DESTDIR=$PKG -find "$PKG"/usr/lib/ff++/ -name "*.h" -exec chmod o+r {} \; +find "$PKG"/usr/lib${LIBDIRSUFFIX}/ff++/ -name "*.h" -exec chmod o+r {} \; find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a AUTHORS CHANGELOG.md README.md $PKG/usr/doc/$PRGNAM-$VERSION +cp -a AUTHORS CHANGELOG.md LICENSE.md README.md $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/FreeFem/FreeFem.info b/academic/FreeFem/FreeFem.info index c61fc4c006..d936d143c5 100644 --- a/academic/FreeFem/FreeFem.info +++ b/academic/FreeFem/FreeFem.info @@ -1,14 +1,14 @@ PRGNAM="FreeFem" -VERSION="4.5" +VERSION="4.14" HOMEPAGE="https://freefem.org/" -DOWNLOAD="https://github.com/FreeFem/FreeFem-sources/archive/v4.5/FreeFem-sources-4.5.tar.gz \ - http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-5.1.0.tar.gz \ +DOWNLOAD="https://github.com/FreeFem/FreeFem-sources/archive/v4.14/FreeFem-sources-4.14.tar.gz \ + https://master.dl.sourceforge.net/project/openfoam-extend/foam-extend-3.0/ThirdParty/metis-5.1.0.tar.gz \ http://www.tetgen.org/1.5/src/tetgen1.5.1-beta1.tar.gz" -MD5SUM="4df8fe1c1bc2c042df1f74371e846748 \ +MD5SUM="ca73e2353138e6c6cebdd9cc8df60b7f \ 5465e67079419a69e0116de24fce58fe \ 3d55c197bcbfc611b7ced6f343643756" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="arpack-ng hdf5 openmpi suitesparse" +REQUIRES="arpack-ng camd hdf5 suitesparse" MAINTAINER="Fellype do Nascimento" EMAIL="fellype (at) gmail (dot) com" diff --git a/academic/FreeFem/README b/academic/FreeFem/README index 99703a0063..c9a6765f55 100644 --- a/academic/FreeFem/README +++ b/academic/FreeFem/README @@ -1,12 +1,13 @@ FreeFem is a high level multiphysics finite element software -FreeFEM is a popular 2D and 3D partial differential equations (PDE) solver used -by thousands of researchers across the world. It allows you to easily implement -your own physics modules using the provided FreeFEM language. FreeFEM offers a -large list of finite elements, like the Lagrange, Taylor-Hood, etc., usable in -the continuous and discontinuous Galerkin method framework. +FreeFEM is a popular 2D and 3D partial differential equations (PDE) +solver used by thousands of researchers across the world. It allows +you to easily implement your own physics modules using the provided +FreeFEM language. FreeFEM offers a large list of finite elements, +like the Lagrange, Taylor-Hood, etc., usable in the continuous and +discontinuous Galerkin method framework. -FreeFEM has it own internal mesher, called BAMG, and is compatible with the best -open-source mesh and visualization software like Tetgen, Gmsh, Mmg and ParaView. -Written in C++ to optimize for speed, FreeFEM is interfaced with the popular -mumps, PETSc and HPDDM solvers. +FreeFEM has it own internal mesher, called BAMG, and is compatible +with the best open-source mesh and visualization software like Tetgen, +Gmsh, Mmg and ParaView. Written in C++ to optimize for speed, FreeFEM +is interfaced with the popular mumps, PETSc and HPDDM solvers. diff --git a/academic/Gabedit/Gabedit.SlackBuild b/academic/Gabedit/Gabedit.SlackBuild new file mode 100644 index 0000000000..1ee40ab8ca --- /dev/null +++ b/academic/Gabedit/Gabedit.SlackBuild @@ -0,0 +1,123 @@ +#!/bin/bash + +# Slackware build script for Gabedit + +# Copyright 2022 Giancarlo Dessì, Cagliari, IT +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=Gabedit +VERSION=${VERSION:-2.5.1} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} +SRCNAM=GabeditSrc +SRCVER=$( echo ${VERSION} | tr -d . ) + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $SRCNAM$SRCVER +tar xvf $CWD/$SRCNAM$SRCVER.tar.gz +cd $SRCNAM$SRCVER +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +make + +# The source has not an installing process: the build creates only an executable +# binary file in the current directory, so we have todo manually a minimal install +# process + +#Install the executable file +mkdir -p $PKG/usr/bin +cp -av ./gabedit $PKG/usr/bin + +#Create and install desktop entry +mkdir -p $PKG/usr/share/applications +cat <<EOF > $PKG/usr/share/applications/Gabedit.desktop +[Desktop Entry] +Name=Gabedit +Comment=Molecular editor +Exec=gabedit %f +Icon=Gabedit +Terminal=false +Type=Application +Categories=Education;GTK; +StartupNotify=true +MimeType= +EOF + +#Install icons +mkdir -p $PKG/usr/share/pixmaps +cp -a pixmaps/Gabedit.xpm $PKG/usr/share/pixmaps +cp -a icons/Gabedit*.png $PKG/usr/share/pixmaps + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a ChangeLog License $CWD/References $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/Gabedit/Gabedit.info b/academic/Gabedit/Gabedit.info new file mode 100644 index 0000000000..b38c531b20 --- /dev/null +++ b/academic/Gabedit/Gabedit.info @@ -0,0 +1,10 @@ +PRGNAM="Gabedit" +VERSION="2.5.1" +HOMEPAGE="http://gabedit.sourceforge.net/" +DOWNLOAD="https://sourceforge.net/projects/gabedit/files/gabedit/Gabedit251/GabeditSrc251.tar.gz/download" +MD5SUM="8edd3911908ed70c7efbfdd8ec1dea21" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="gtkglext" +MAINTAINER="Giancarlo Dessì" +EMAIL="slack@giand.it" diff --git a/academic/Gabedit/README b/academic/Gabedit/README new file mode 100644 index 0000000000..289199d0b7 --- /dev/null +++ b/academic/Gabedit/README @@ -0,0 +1,8 @@ +Gabedit is a graphical user interface to computational chemistry +packages like deMon2k, Gamess-US, Gaussian, Molcas, Molpro, MPQC, +MOPAC, Orca, PCGamess and Q-Chem. + +It can display a variety of calculation results including support for +most major molecular file formats. The advanced "Molecule Builder" +allows to rapidly sketch in molecules and examine them in 3D. Graphics +can be exported to various formats, including animations. diff --git a/academic/Gabedit/References b/academic/Gabedit/References new file mode 100644 index 0000000000..9114484ed3 --- /dev/null +++ b/academic/Gabedit/References @@ -0,0 +1,7 @@ +Please use the following citations in any report or publication: + +Gabedit: +A graphical user interface for computational chemistry softwares. +Allouche, A.-R., +Journal of Computational Chemistry, 32 (2011) 174–182. +doi: 10.1002/jcc.21600 diff --git a/academic/Gabedit/doinst.sh b/academic/Gabedit/doinst.sh new file mode 100644 index 0000000000..f25bed6fb6 --- /dev/null +++ b/academic/Gabedit/doinst.sh @@ -0,0 +1,19 @@ +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 +fi + +if [ -x /usr/bin/update-mime-database ]; then + /usr/bin/update-mime-database usr/share/mime >/dev/null 2>&1 +fi + +if [ -e usr/share/icons/hicolor/icon-theme.cache ]; then + if [ -x /usr/bin/gtk-update-icon-cache ]; then + /usr/bin/gtk-update-icon-cache -f usr/share/icons/hicolor >/dev/null 2>&1 + fi +fi + +if [ -e usr/share/glib-2.0/schemas ]; then + if [ -x /usr/bin/glib-compile-schemas ]; then + /usr/bin/glib-compile-schemas usr/share/glib-2.0/schemas >/dev/null 2>&1 + fi +fi diff --git a/academic/Gabedit/slack-desc b/academic/Gabedit/slack-desc new file mode 100644 index 0000000000..3c60c50686 --- /dev/null +++ b/academic/Gabedit/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +Gabedit: Gabedit (Graphical User Interface to computational chemistry) +Gabedit: +Gabedit: Gabedit can display a variety of calculation results including +Gabedit: support for most major molecular file formats. +Gabedit: +Gabedit: +Gabedit: +Gabedit: +Gabedit: Home page: http://gabedit.sourceforge.net/ +Gabedit: +Gabedit: diff --git a/academic/Gblocks/Gblocks.SlackBuild b/academic/Gblocks/Gblocks.SlackBuild index 2a71e48b91..aebb925d1f 100644 --- a/academic/Gblocks/Gblocks.SlackBuild +++ b/academic/Gblocks/Gblocks.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for Gblocks -# Copyright 2011-2016 Petar Petrov slackalaxy@gmail.com +# Copyright 2011-2023 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,31 +22,40 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=Gblocks VERSION=${VERSION:-0.91b} -BUILD=${BUILD:-1} +BUILD=${BUILD:-3} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i386 ;; - arm*) ARCH=arm ;; + i?86) ARCH=i586 ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +if [[ $ARCH != i?86 ]] && [ "$ARCH" != "x86_64" ]; then + printf "\n$ARCH is not supported... \n" + exit 1 +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} set -e -if [ "$ARCH" != "i386" ] && [ "$ARCH" != "x86_64" ]; then - printf "\n\n$ARCH is not supported... \n" - exit 1 -fi - # Determine the source arch if [ "$ARCH" = "x86_64" ]; then SRCARCH="64" @@ -65,15 +74,16 @@ tar xvf $CWD/$TARNAME.tar.Z cd ${PRGNAM}_${VERSION} chown -R root:root . find -L . \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; install -D -m755 Gblocks $PKG/usr/bin/$PRGNAM mkdir -p $PKG/usr/share/$PRGNAM -cp -a more_alignments/* $PKG/usr/share/$PRGNAM +cp -a more_alignments nad3.pir paths $PKG/usr/share/$PRGNAM +chmod 0755 $PKG/usr/share/$PRGNAM/more_alignments find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true @@ -87,4 +97,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/Gblocks/Gblocks.info b/academic/Gblocks/Gblocks.info index 0f414d6a29..6e8312a598 100644 --- a/academic/Gblocks/Gblocks.info +++ b/academic/Gblocks/Gblocks.info @@ -3,7 +3,7 @@ VERSION="0.91b" HOMEPAGE="http://molevol.cmima.csic.es/castresana/Gblocks.html" DOWNLOAD="http://ponce.cc/slackware/sources/repo/Gblocks_Linux_0.91b.tar.Z" MD5SUM="8b62e8447eaea37a86c35e1bf5996580" -DOWNLOAD_x86_64="http://molevol.cmima.csic.es/castresana/Gblocks/Gblocks_Linux64_0.91b.tar.Z" +DOWNLOAD_x86_64="https://ponce.cc/slackware/sources/repo/Gblocks_Linux64_0.91b.tar.Z" MD5SUM_x86_64="c2c752ae4cbfda0b8bf09e6662585252" REQUIRES="" MAINTAINER="Petar Petrov" diff --git a/academic/GeoGebra/GeoGebra.SlackBuild b/academic/GeoGebra/GeoGebra.SlackBuild index cf6bdd098f..07bc5d231c 100644 --- a/academic/GeoGebra/GeoGebra.SlackBuild +++ b/academic/GeoGebra/GeoGebra.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for GeoGebra @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=GeoGebra VERSION=${VERSION:-5.0.361.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -92,4 +102,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/GeoGebra/GeoGebra.info b/academic/GeoGebra/GeoGebra.info index 60db5293eb..85644a1b45 100644 --- a/academic/GeoGebra/GeoGebra.info +++ b/academic/GeoGebra/GeoGebra.info @@ -5,6 +5,6 @@ DOWNLOAD="https://sourceforge.net/projects/slackbuildsdirectlinks/files/GeoGebra MD5SUM="55e025c1671d074428a0adb66e1fa3d8" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="openjdk7" +REQUIRES="zulu-openjdk7" MAINTAINER="R. S. Ananda Murthy" EMAIL="rsamurti@gmail.com" diff --git a/academic/Gridcoin-Research/Gridcoin-Research.SlackBuild b/academic/Gridcoin-Research/Gridcoin-Research.SlackBuild index 6010e6a9ab..9a04eb6fc4 100644 --- a/academic/Gridcoin-Research/Gridcoin-Research.SlackBuild +++ b/academic/Gridcoin-Research/Gridcoin-Research.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for Gridcoin-Research -# Copyright 2018-2019 Edward W. Koenig, Vancouver, WA, USA +# Copyright 2018-2021 Edward W. Koenig, Vancouver, WA, USA # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=Gridcoin-Research -VERSION=${VERSION:-4.0.6.0} +VERSION=${VERSION:-5.4.7.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -69,7 +79,7 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -if [ "${QRENC:-no}" = "yes" ]; then +if [ "${QRENC:-yes}" = "yes" ]; then useqr="--with-qrencode" else useqr="--without-qrencode" @@ -92,7 +102,7 @@ CXXFLAGS="$SLKCFLAGS" \ --localstatedir=/var \ --mandir=/usr/man \ --docdir=/usr/doc/$PRGNAM-$VERSION \ - --with-gui=auto \ + --with-gui=yes \ $useqr \ $usepnp \ --build=$ARCH-slackware-linux @@ -119,7 +129,7 @@ cp -a $TMP/$PRGNAM-$VERSION/share/pixmaps/* $PKG/usr/share/pixmaps mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION/doc cp -a \ - COPYING CHANGELOG.md README.md VULNERABILITY_RESPONSE_PROCESS.md \ + COPYING CHANGELOG.md README.md SECURITY.md CONTRIBUTING.md \ $PKG/usr/doc/$PRGNAM-$VERSION cp -a doc/* $PKG/usr/doc/$PRGNAM-$VERSION/doc cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild @@ -132,4 +142,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/Gridcoin-Research/Gridcoin-Research.desktop b/academic/Gridcoin-Research/Gridcoin-Research.desktop deleted file mode 100644 index 5e6896f326..0000000000 --- a/academic/Gridcoin-Research/Gridcoin-Research.desktop +++ /dev/null @@ -1,9 +0,0 @@ -[Desktop Entry] -Type=Application -Name=Gridcoin -Comment=Gridcoin is an open source cryptocurrency (Ticker: GRC) which securely rewards volunteer computing performed on the BOINC platform. -Exec=gridcoinresearch -Icon=grc -Categories=Education;Science; -Terminal=false -Hidden=false diff --git a/academic/Gridcoin-Research/Gridcoin-Research.info b/academic/Gridcoin-Research/Gridcoin-Research.info index 47125005f4..a28295c32f 100644 --- a/academic/Gridcoin-Research/Gridcoin-Research.info +++ b/academic/Gridcoin-Research/Gridcoin-Research.info @@ -1,10 +1,10 @@ PRGNAM="Gridcoin-Research" -VERSION="4.0.6.0" +VERSION="5.4.7.0" HOMEPAGE="https://gridcoin.us/" -DOWNLOAD="https://github.com/gridcoin-community/Gridcoin-Research/archive/4.0.6.0/Gridcoin-Research-4.0.6.0.tar.gz" -MD5SUM="6c924899a3a75f0c072fb3e0a8d64b4f" +DOWNLOAD="https://github.com/gridcoin-community/Gridcoin-Research/archive/5.4.7.0/Gridcoin-Research-5.4.7.0.tar.gz" +MD5SUM="8c42dfd8deaa754d78aa248785e724b0" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" MAINTAINER="Edward W. Koenig" -EMAIL="kingbeowulf@gmail.com" +EMAIL="kingbeowulf@linuxgalaxy.org" diff --git a/academic/Gridcoin-Research/README b/academic/Gridcoin-Research/README index ac7e670e22..2fc9a1a4f5 100644 --- a/academic/Gridcoin-Research/README +++ b/academic/Gridcoin-Research/README @@ -1,16 +1,39 @@ -Gridcoin is an open source cryptocurrency (Ticker: GRC) which securely rewards -volunteer computing performed on the BOINC platform. BOINC is an open source -volunteer computing grid which combines the processing power of individual users -for the purposes of scientific research. - -QT5, qrencode and miniupnpc are optional (available on SBo) to build GUI, QR -and UPnP support. QT5 will be detected automatically, for the others, run -script as - -QRENC=yes ./Gridcoin-Research.SlackBuild -UPNP=yes ./Gridcoin-Research.SlackBuild - -You will need to edit the configuration file gridcoinresearch.conf in -/etc/Gridcoin-Research/ and place it in your home directory ~/.GridcoinResearch/ -to provide the location of your boinc data and any other configurations that you -require. For details, see https://wiki.gridcoin.us/Gridcoinresearch_config_file +Gridcoin is an open source cryptocurrency (Ticker: GRC) which securely +rewards volunteer computing performed on the BOINC platform. BOINC is +an open source volunteer computing grid which combines the processing +power of individual users for the purposes of scientific research. + +qrencode support is detected automatically; override with + QRENC=no ./Gridcoin-Research.SlackBuild + +Miniupnpc (available on SBo) is optional for UPnP support. Run script as + UPNP=yes ./Gridcoin-Research.SlackBuild + +You will need to edit the configuration file gridcoinresearch.conf +in /etc/Gridcoin-Research/ and place it in your home directory +~/.GridcoinResearch/ to provide the location of your boinc data +and any other configurations that you require. For details, see +https://wiki.gridcoin.us/Gridcoinresearch_config_file and in +/usr/share/Gridcoin-Research-$VERSION/doc/ + +Notes: +1. New gridcoinsettings.json file + +This file contains settings changed by the node while running and +settings stored in this file override the read-only settings in the +gridcoinresearch.conf file (see changelog and documentation). + +2. Berkeley DB update + +Previous versions built against Slackware's Berkeley DB version 4.8. +Since [5.4.2.0] 2023-03-26, leisure, "LaVerne", upstream source +includes Berkeley DB version 5.3 in tree and will standardize all +wallet.dat files to the bdb 5.3 format. THIS IS VERY IMPORTANT! +This ugrade will be completely transparent. Please review the +release notes on +https://github.com/gridcoin-community/Gridcoin-Research/releases + +** NOTE: ** +This is a MANDATORY upgrade for versions 5.4.5 and below to fix an +inadvertent fork as a result of an inadvertent protocol change. +If you are already on 5.4.6 this upgrade is "leisure." diff --git a/academic/Gridcoin-Research/gridcoinresearch.conf b/academic/Gridcoin-Research/gridcoinresearch.conf index 7ab2e07a3f..1c66a0b640 100644 --- a/academic/Gridcoin-Research/gridcoinresearch.conf +++ b/academic/Gridcoin-Research/gridcoinresearch.conf @@ -2,44 +2,38 @@ #################### Example gridcoinresearch.conf file ##################### ############################################################################# ## -## For further details on this configuration file please see: -## http://wiki.gridcoin.us/Gridcoinresearch_config_file -## ## Default gridcoinresearch.conf location: ## ## Win: %AppData%\GridcoinResearch\ ## Linux: ~/.GridcoinResearch/ -## MacOS: /Users/USERNAME/Library/Application/Support/GridcoinResearch/ +## macOS: /Users/USERNAME/Library/Application/Support/GridcoinResearch/ ## -## Single # lines are commands, remove the # in Front of the Command to use it +## Single # lines are commands, remove the # in Front of the command to use it ## Double ## lines are comments ## ############################################################################# ####################### Required Settings (All OS's) ######################## ############################################################################# -## Community provided list of addnodes available at -## http://wiki.gridcoin.us/List_of_Addnodes +## Community provided list of addnodes available at https://github.com/gridcoin-community/Gridcoin-Wiki/wiki/List-of-Addnodes #~~~~~Copy & Paste Addnodes here~~~~~ #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -## BOINC account settings, i.e. your BOINC CPID & E-Mail -## Use INVESTOR for Investor or Pool Mining -PrimaryCPID=INVESTOR -email=INVESTOR +## BOINC account E-Mail +## Use blank or INVESTOR for Investor or Pool Mining +## Note the PrimaryCPID field is deprecated and ignored since the 4.0.5.0 +## release. +email= -## Port 32749/TCP required for Inbound Connections +## Port 32749/TCP open or forwarded required for Inbound Connections ## (Not required but highly recommended) -listen=1 +#listen=1 ## Required for Headless set-ups #daemon=1 -## Blocks client from upgrading on its own. -suppressupgrade=true - ############################################################################# ############# RPC Settings for Remote Access and Headless Users ############# ############ Warning: Set a Good Password and Secure Your System ############ @@ -50,25 +44,46 @@ suppressupgrade=true #rpcallowip=<IP Address of Remote System> #rpcport=<Port for RPC Communication> #rpcuser=<A Username for RPC> -#rpcpassword=<A GOOD Password for RPC> +#rpcpassword=<A STRONG Password for RPC> ############################################################################# ######################## Optional BOINC settings ############################ ########### (Required if BOINC installed to non-default location) ########### ############################################################################# +## Windows (Note the double backslashes are necessary) +#boincdatadir=C:\\ProgramData\\BOINC\\ + ## Linux -boincdatadir=$HOME/.boinc_data/ +#boincdatadir=/var/lib/boinc-client/ + +## macOS +#boincdatadir=/Library/Application Support/BOINC Data/ ############################################################################# ######################## Optional Network settings ########################## ############################################################################# -## Maximum number of inbound+outbound connections.Default 125 -maxconnections=125 -## Maximum number of outbound connections.Default 8 -maxoutboundconnections=8 +## Maximum number of inbound+outbound connections. Default 125 +#maxconnections=125 +## Maximum number of outbound connections. Default 8 +#maxoutboundconnections=8 ## Manually Set-up Ports #upnp=false #externalip=<Your IP Address> -#port=32748
\ No newline at end of file + +############################################################################# +############################## Other Entries ################################ +############################################################################# + +## See detailed Other Entries description section below. + +#debug=true +#debug=<category> + +#enablestakesplit=1 +#stakingefficiency=<percentage between 75 and 98, defaults to 90> +#minstakesplitvalue=<value in GRC, minimum and defaults to 800> + +#enablesidestaking=1 +#sidestake=<address>,<allocation percentage> diff --git a/academic/HMMER/HMMER.SlackBuild b/academic/HMMER/HMMER.SlackBuild index 6fc40670d6..923c84093c 100644 --- a/academic/HMMER/HMMER.SlackBuild +++ b/academic/HMMER/HMMER.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for HMMER -# Copyright 2016-2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2016-2023 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=HMMER -VERSION=${VERSION:-3.3} +VERSION=${VERSION:-3.4} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} SRCNAM=hmmer @@ -37,7 +40,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -92,6 +102,8 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr find $PKG/usr/man -type f -exec gzip -9 {} \; for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done +chmod 0644 $PKG/usr/man/man1/* + # Include some tutorial examples mkdir -p $PKG/usr/share/$PRGNAM cp -a testsuite tutorial $PKG/usr/share/$PRGNAM @@ -106,4 +118,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/HMMER/HMMER.info b/academic/HMMER/HMMER.info index f7a4d2d81d..6e938301df 100644 --- a/academic/HMMER/HMMER.info +++ b/academic/HMMER/HMMER.info @@ -1,10 +1,10 @@ PRGNAM="HMMER" -VERSION="3.3" +VERSION="3.4" HOMEPAGE="http://hmmer.org/" -DOWNLOAD="http://eddylab.org/software/hmmer/hmmer-3.3.tar.gz" -MD5SUM="507849e98a5a44b22f2c4a1cf192b36b" +DOWNLOAD="http://eddylab.org/software/hmmer/hmmer-3.4.tar.gz" +MD5SUM="b1ed21ceea33930222c84f8c4d9f4240" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="python3" +REQUIRES="" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/IGV/IGV.SlackBuild b/academic/IGV/IGV.SlackBuild new file mode 100644 index 0000000000..38a9d08e7e --- /dev/null +++ b/academic/IGV/IGV.SlackBuild @@ -0,0 +1,99 @@ +#!/bin/bash + +# Slackware build script for IGV + +# Copyright 2020-2023 Petar Petrov slackalaxy@gmail.com +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=IGV +VERSION=${VERSION:-2.16.2} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +JDK=jdk-11 + +if [ -z "$ARCH" ]; then + ARCH="$( uname -m )" +fi + +if [ "$ARCH" != "x86_64" ]; then + printf "\n\n$ARCH is not supported... \n" >&2 + exit 1 +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf ${PRGNAM}_Linux_${VERSION} +unzip $CWD/${PRGNAM}_Linux_${VERSION}_WithJava.zip +cd ${PRGNAM}_Linux_${VERSION} +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +# Place it in /opt and make a symlink later +mkdir -p $PKG/opt/$PRGNAM +cp -a $JDK lib igv.args igv.sh igv_hidpi.sh $PKG/opt/$PRGNAM +chmod 0755 $PKG/opt/IGV/jdk-11/lib/{jli,server}/*.so +chmod 0755 $PKG/opt/IGV/jdk-11/lib/*.so + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/share/{applications,pixmaps} +cp $CWD/$PRGNAM.png $PKG/usr/share/pixmaps +cp $CWD/$PRGNAM.desktop $PKG/usr/share/applications + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a readme.txt $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References + +mkdir -p $PKG/usr/bin +cd $PKG/usr/bin +ln -s ../../opt/$PRGNAM/igv.sh igv +cd - + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/IGV/IGV.desktop b/academic/IGV/IGV.desktop new file mode 100644 index 0000000000..9dad30517e --- /dev/null +++ b/academic/IGV/IGV.desktop @@ -0,0 +1,8 @@ +[Desktop Entry] +Type=Application +Exec=igv +Terminal=false +Name=IGV +Icon=IGV +Comment=Integrative Genomics Viewer +Categories=Education; diff --git a/academic/IGV/IGV.info b/academic/IGV/IGV.info new file mode 100644 index 0000000000..23341260cc --- /dev/null +++ b/academic/IGV/IGV.info @@ -0,0 +1,10 @@ +PRGNAM="IGV" +VERSION="2.16.2" +HOMEPAGE="http://software.broadinstitute.org/software/igv/home" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="https://data.broadinstitute.org/igv/projects/downloads/2.16/IGV_Linux_2.16.2_WithJava.zip" +MD5SUM_x86_64="19adb2bac44d46373fc021fbad3cce10" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/IGV/IGV.png b/academic/IGV/IGV.png Binary files differnew file mode 100644 index 0000000000..3d618f23a6 --- /dev/null +++ b/academic/IGV/IGV.png diff --git a/academic/IGV/README b/academic/IGV/README new file mode 100644 index 0000000000..16f24fb788 --- /dev/null +++ b/academic/IGV/README @@ -0,0 +1,9 @@ +The Integrative Genomics Viewer (IGV) is a high-performance and easy-to- +use, interactive tool for the visual exploration of genomic data. It +supports flexible integration of all the common types of genomic data +and metadata, investigator-generated or publicly available, loaded from +local or cloud sources. + +Please, check the package's documentation folder for citing information. + +NOTE: this comes with its own JAVA environment. diff --git a/academic/IGV/References b/academic/IGV/References new file mode 100644 index 0000000000..cdbdf3e743 --- /dev/null +++ b/academic/IGV/References @@ -0,0 +1,17 @@ +To cite your use of IGV in your publication, please reference one or more of: + +James T. Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, +Eric S. Lander, Gad Getz, Jill P. Mesirov. Integrative Genomics Viewer. +Nature Biotechnology 29, 24–26 (2011). (Free PMC article here). + +Helga Thorvaldsdóttir, James T. Robinson, Jill P. Mesirov. +Integrative Genomics Viewer (IGV): high-performance genomics data visualization +and exploration. Briefings in Bioinformatics 14, 178-192 (2013). + +James T. Robinson, Helga Thorvaldsdóttir, Aaron M. Wenger, Ahmet Zehir, Jill P. +Mesirov. Variant Review with the Integrative Genomics Viewer (IGV). Cancer +Research 77(21) 31-34 (2017). + +James T. Robinson, Helga Thorvaldsdóttir, Douglass Turner, Jill P. Mesirov. +igv.js: an embeddable JavaScript implementation of the Integrative Genomics +Viewer (IGV). bioRxiv 2020.05.03075499. diff --git a/academic/IGV/doinst.sh b/academic/IGV/doinst.sh new file mode 100644 index 0000000000..5fb28930db --- /dev/null +++ b/academic/IGV/doinst.sh @@ -0,0 +1,3 @@ +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 +fi diff --git a/academic/IGV/slack-desc b/academic/IGV/slack-desc new file mode 100644 index 0000000000..c02edd24c9 --- /dev/null +++ b/academic/IGV/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +IGV: IGV (Integrative Genomics Viewer) +IGV: +IGV: The Integrative Genomics Viewer (IGV) is a high-performance and easy +IGV: to use, interactive tool for the visual exploration of genomic data. +IGV: It supports flexible integration of all the common types of genomic +IGV: data and metadata, investigator-generated or publicly available, +IGV: loaded from local or cloud sources. +IGV: +IGV: http://software.broadinstitute.org/software/igv/home +IGV: +IGV: diff --git a/academic/ITK/ITK.SlackBuild b/academic/ITK/ITK.SlackBuild index afeb3068c8..4ecf6cb456 100644 --- a/academic/ITK/ITK.SlackBuild +++ b/academic/ITK/ITK.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # SlackBuild script for ITK -# Copyright 2018-2019 Benjamin Trigona-Harany <slackbuilds@jaxartes.net> +# Copyright 2018-2021 Benjamin Trigona-Harany <slackbuilds@jaxartes.net> # All rights reserved. # # Redistribution and use in source and binary forms, with or without @@ -24,11 +24,14 @@ # (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=ITK SRCNAM=InsightToolkit VERSION=${VERSION:-4.13.2} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -38,7 +41,11 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -72,54 +79,38 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; +# Do not fail on more recent versions of gcc + sed -i 's,# error "Dunno about this gcc",# define VCL_GCC_80,' \ + "Modules/ThirdParty/VNL/src/vxl/vcl/vcl_compiler.h" + + sed -i "s/lib\b/lib${LIBDIRSUFFIX}/" CMakeLists.txt sed -i "s|/opj_config.h|& \$\{CMAKE_CURRENT_BINARY_DIR\}/openjpeg_mangle.h|" \ Modules/ThirdParty/GDCM/src/gdcm/Utilities/gdcmopenjpeg/src/lib/openjp2/CMakeLists.txt -patch -p1 <<'endpatch' -diff --git a/Modules/ThirdParty/VNL/src/vxl/vcl/vcl_compiler.h b/Modules/ThirdParty/VNL/src/vxl/vcl/vcl_compiler.h -index 4865361421e..220b9cd49a8 100644 ---- a/Modules/ThirdParty/VNL/src/vxl/vcl/vcl_compiler.h -+++ b/Modules/ThirdParty/VNL/src/vxl/vcl/vcl_compiler.h -@@ -97,6 +97,17 @@ - # else - # define VCL_GCC_80 - # endif -+# elif (__GNUC__==9) -+# define VCL_GCC_9 -+# if (__GNUC_MINOR__ > 2 ) -+# define VCL_GCC_93 -+# elif (__GNUC_MINOR__ > 1 ) -+# define VCL_GCC_92 -+# elif (__GNUC_MINOR__ > 0 ) -+# define VCL_GCC_91 -+# else -+# define VCL_GCC_90 -+# endif - # else - # error "Dunno about this gcc" - # endif -endpatch mkdir -p build cd build cmake \ - -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ - -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_C_FLAGS="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS="$SLKCFLAGS -std=c++11" \ -DCMAKE_INSTALL_PREFIX=/usr \ - -DITK_FORBID_DOWNLOADS:BOOL=ON \ - -DITK_WRAP_PYTHON:BOOL=OFF \ - -DBUILD_SHARED_LIBS:BOOL=ON \ - -DBUILD_EXAMPLES:BOOL=OFF \ - -DITK_USE_SYSTEM_LIBRARIES:BOOL=ON \ - -DITK_USE_SYSTEM_DCMTK:BOOL=ON \ - -DITK_USE_SYSTEM_DOUBLECONVERSION:BOOL=ON \ - -DITK_USE_SYSTEM_EXPAT:BOOL=ON \ - -DITK_USE_SYSTEM_FFTW:BOOL=ON \ - -DITK_USE_SYSTEM_HDF5:BOOL=ON \ - -DITK_USE_SYSTEM_JPEG:BOOL=ON \ - -DITK_USE_SYSTEM_PNG:BOOL=ON \ - -DITK_USE_SYSTEM_TIFF:BOOL=ON \ - -DITK_USE_SYSTEM_ZLIB:BOOL=ON \ + -DITK_FORBID_DOWNLOADS=ON \ + -DITK_WRAP_PYTHON=OFF \ + -DBUILD_SHARED_LIBS=ON \ + -DBUILD_EXAMPLES=OFF \ + -DBUILD_TESTING=OFF \ + -DITK_USE_SYSTEM_LIBRARIES=ON \ + -DITK_USE_SYSTEM_DCMTK=ON \ + -DITK_USE_SYSTEM_DOUBLECONVERSION=ON \ + -DITK_USE_SYSTEM_EXPAT=ON \ + -DITK_USE_SYSTEM_FFTW=ON \ + -DITK_USE_SYSTEM_HDF5=ON \ + -DITK_USE_SYSTEM_JPEG=ON \ + -DITK_USE_SYSTEM_PNG=ON \ + -DITK_USE_SYSTEM_TIFF=ON \ + -DITK_USE_SYSTEM_ZLIB=ON \ + -DModule_ITKIOMINC=ON \ + -DModule_ITKIOTransformMINC=ON \ -DCMAKE_BUILD_TYPE=Release .. make install DESTDIR=$PKG cd .. @@ -139,4 +130,4 @@ mkdir $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/ITK/ITK.info b/academic/ITK/ITK.info index d72260cfa6..86da5fa2d4 100644 --- a/academic/ITK/ITK.info +++ b/academic/ITK/ITK.info @@ -5,6 +5,6 @@ DOWNLOAD="https://github.com/InsightSoftwareConsortium/ITK/releases/download/v4. MD5SUM="d140ddabe22428e86bc5053e0d268872" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="double-conversion gtest hdf5" +REQUIRES="double-conversion antlr4 hdf5" MAINTAINER="Benjamin Trigona-Harany" EMAIL="slackbuilds@jaxartes.net" diff --git a/academic/ITK/README b/academic/ITK/README index f152989931..ea82c00fc2 100644 --- a/academic/ITK/README +++ b/academic/ITK/README @@ -1,4 +1,4 @@ ITK is an open-source software toolkit for performing registration and -segmentation. Segmentation is the process of identifying and classifying data -found in a digitally sampled representation. Registration is the task of -aligning or developing correspondences between data. +segmentation. Segmentation is the process of identifying and classifying +data found in a digitally sampled representation. Registration is the +task of aligning or developing correspondences between data. diff --git a/academic/Isabelle/Isabelle b/academic/Isabelle/Isabelle new file mode 100644 index 0000000000..24f157255a --- /dev/null +++ b/academic/Isabelle/Isabelle @@ -0,0 +1,3 @@ +#!/bin/sh + +exec /opt/Isabelle/MY_TEMPLATE $@ diff --git a/academic/Isabelle/Isabelle.SlackBuild b/academic/Isabelle/Isabelle.SlackBuild new file mode 100644 index 0000000000..eb9721e53d --- /dev/null +++ b/academic/Isabelle/Isabelle.SlackBuild @@ -0,0 +1,82 @@ +#!/bin/bash + +# Slackware build script for Isabelle + +# Copyright 2023, Lockywolf +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=Isabelle +VERSION=${VERSION:-2022} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM$VERSION +tar xvf $CWD/$PRGNAM${VERSION}_linux.tar.gz +cd $PRGNAM$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +install -Dm755 $CWD/Isabelle $PKG/usr/bin/Isabelle +install -d -m 755 $PKG/opt/$PRGNAM +cp -r . $PKG/opt/$PRGNAM +sed -i "s/MY_TEMPLATE/$PRGNAM$VERSION/g" $PKG/usr/bin/Isabelle + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ +ANNOUNCE COPYRIGHT doc README ROOTS \ +CONTRIBUTORS Isabelle.options NEWS ROOT \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/Isabelle/Isabelle.info b/academic/Isabelle/Isabelle.info new file mode 100644 index 0000000000..effbc710fb --- /dev/null +++ b/academic/Isabelle/Isabelle.info @@ -0,0 +1,10 @@ +PRGNAM="Isabelle" +VERSION="2022" +HOMEPAGE="https://isabelle.in.tum.de/" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="https://isabelle.in.tum.de/dist/Isabelle2022_linux.tar.gz" +MD5SUM_x86_64="52340538b76b0493beae0a444d623fe6" +REQUIRES="" +MAINTAINER="Lockywolf" +EMAIL="for_sbo.Isabelle_2023-07-17@lockywolf.net" diff --git a/academic/Isabelle/README b/academic/Isabelle/README new file mode 100644 index 0000000000..133899ddbe --- /dev/null +++ b/academic/Isabelle/README @@ -0,0 +1,17 @@ +Isabelle is a generic proof assistant. It allows mathematical formulas +to be expressed in a formal language and provides tools for proving +those formulas in a logical calculus. Isabelle was originally +developed at the University of Cambridge and Technische Universität +München, but now includes numerous contributions from institutions and +individuals worldwide. + +Isabelle is written in polyML, Java, and Scala, but does not require +them to be installed from SBo. + +This build is bundling: jEdit, vscodium, jdk-17, so be careful about +its interference with other packages. + +A lot of proofs certified with Isabelle can be found on +https://www.isa-afp.org/ + +This build repackages the binary build. diff --git a/academic/Isabelle/slack-desc b/academic/Isabelle/slack-desc new file mode 100644 index 0000000000..72e6651a95 --- /dev/null +++ b/academic/Isabelle/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +Isabelle: Isabelle (generic proof assistant) +Isabelle: +Isabelle: Isabelle is a generic proof assistant. It allows mathematical +Isabelle: formulas to be expressed in a formal language and provides tools for +Isabelle: proving those formulas in a logical calculus. Isabelle was +Isabelle: originally developed at the University of Cambridge and Technische +Isabelle: Universitat Munchen, but now includes numerous contributions from +Isabelle: institutions and individuals worldwide. +Isabelle: +Isabelle: +Isabelle: diff --git a/academic/Kst/Kst.SlackBuild b/academic/Kst/Kst.SlackBuild index 527bc6ba1b..44e4fea74b 100644 --- a/academic/Kst/Kst.SlackBuild +++ b/academic/Kst/Kst.SlackBuild @@ -1,13 +1,35 @@ -#!/bin/sh +#!/bin/bash + # Slackware build script for Kst -# Based on Slackware 14.1 SlackBuild and AUR PKGBUILD for Kst -# Written by Fellype do Nascimento <fellype(at)gmail.com> -# last modification of this build script: 2014/12/10 +# Copyright 2014-2023 Fellype do Nascimento, Guaratingueta, Brazil +# SBo team have contributed to the maintenance of this build script :) +# +# Based on Slackware 15.0 SlackBuild and AUR PKGBUILD for Kst +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR ''AS IS'' AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) PRGNAM=Kst -VERSION=${VERSION:-2.0.8} +VERSION=${VERSION:-20221025_5fdd819} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -17,15 +39,22 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686"; SLKLDFLAGS=""; LIBDIRSUFFIX=""; CHOST=i486 +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686"; SLKLDFLAGS=""; LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then - SLKCFLAGS="-O2 -march=i686 -mtune=i686"; SLKLDFLAGS=""; LIBDIRSUFFIX=""; CHOST=i486 + SLKCFLAGS="-O2 -march=i686 -mtune=i686"; SLKLDFLAGS=""; LIBDIRSUFFIX="" elif [ "$ARCH" = "x86_64" ]; then SLKCFLAGS="-O2 -fPIC"; SLKLDFLAGS="-L/usr/lib64"; LIBDIRSUFFIX="64" fi @@ -36,7 +65,7 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $PRGNAM-$VERSION -tar -zxvf $CWD/$PRGNAM-$VERSION.tar.gz +tar -xvf $CWD/$PRGNAM-$VERSION.tar.?z cd $PRGNAM-$VERSION chown -R root:root . find -L . \ @@ -45,19 +74,24 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -# Fix build failure with gsl-2.1 (gsl API change) -patch -p1 < $CWD/Kst_gsl2.patch +# Fix the path for H5Cpp.h +patch -p1 < $CWD/fix_hdf5_path.patch src/datasources/hdf5/hdf5.h + +# Fix an issue with the newer cmake +sed -i "s|else(GCC|elseif(GCC|" CMakeLists.txt || exit 1 sed -i "s/find_package\(PythonLibs REQUIRED\)/SET \(PythonLibs \"\/usr\/lib${LIBDIRSUFFIX}\/libpython2.7.so\"\)/" \ -./cmake/pyKst/CMakeLists.txt -sed -i "s/\${NUMPY_VERSION_PATCH}/0/" ./cmake/modules/FindNumPy.cmake +./cmake/pyKst/CMakeLists.txt || exit 1 +sed -i "s/\${NUMPY_VERSION_PATCH}/0/" ./cmake/modules/FindNumPy.cmake || exit 1 cp -r ./cmake/pyKst/* ./pyKst/ cmake ./ \ --Dkst_release=1 \ --Dkst_version_string=1 \ +-Dkst_release=2 \ +-Dkst_version_string=$VERSION \ -Dkst_svnversion=0 \ -Dkst_python=1 \ --DPYTHON_EXECUTABLE=/usr/bin/python2.7 \ +-Dkst_qt4=OFF \ +-Dkst_qt5=ON \ +-DPYTHON_EXECUTABLE=/usr/bin/python2 \ -Dkst_python_prefix=/usr/lib$LIBDIRSUFFIX/python2.7 \ -Dkst_install_prefix=/usr/ \ -Dkst_install_libdir=/usr/lib$LIBDIRSUFFIX @@ -83,4 +117,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/Kst/Kst.info b/academic/Kst/Kst.info index 8912bc7380..adff979071 100644 --- a/academic/Kst/Kst.info +++ b/academic/Kst/Kst.info @@ -1,10 +1,10 @@ PRGNAM="Kst" -VERSION="2.0.8" -HOMEPAGE="https://kst-plot.kde.org/" -DOWNLOAD="http://netcologne.dl.sourceforge.net/project/kst/Kst%202.0.8/Kst-2.0.8.tar.gz" -MD5SUM="6f52c16edb63e8980520bfdaebed3eae" +VERSION="20221025_5fdd819" +HOMEPAGE="https://apps.kde.org/kst/" +DOWNLOAD="https://sourceforge.net/projects/slackbuildsdirectlinks/files/Kst/Kst-20221025_5fdd819.tar.xz" +MD5SUM="402fac69d4701cd7f223159e70b73439" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="scipy" +REQUIRES="python2-scipy" MAINTAINER="Fellype do Nascimento" -EMAIL="fellype(at)gmail.com" +EMAIL="fellype (at) gmail (dot) com" diff --git a/academic/Kst/Kst_gsl2.patch b/academic/Kst/Kst_gsl2.patch deleted file mode 100644 index 1a7db24321..0000000000 --- a/academic/Kst/Kst_gsl2.patch +++ /dev/null @@ -1,53 +0,0 @@ -diff -u -r Kst-2.0.8/src/plugins/fits/non_linear.h Kst-2.0.8-patched/src/plugins/fits/non_linear.h ---- Kst-2.0.8/src/plugins/fits/non_linear.h 2014-02-13 09:41:44.000000000 +0000 -+++ Kst-2.0.8-patched/src/plugins/fits/non_linear.h 2015-11-18 22:28:40.761417846 +0000 -@@ -18,6 +18,7 @@ - #include <gsl/gsl_blas.h> - #include <gsl/gsl_multifit_nlin.h> - #include <gsl/gsl_statistics.h> -+#include <gsl/gsl_version.h> - #include "common.h" - - struct data { -@@ -177,7 +178,15 @@ - } - iIterations++; - } while( iStatus == GSL_CONTINUE && iIterations < MAX_NUM_ITERATIONS ); -+ -+#if GSL_MAJOR_VERSION >=2 -+ gsl_matrix *J=gsl_matrix_alloc(pSolver->fdf->n, pSolver->fdf->p); -+ gsl_multifit_fdfsolver_jac (pSolver, J); -+ gsl_multifit_covar( J, 0.0, pMatrixCovariance ); -+ gsl_matrix_free(J); -+#else - gsl_multifit_covar( pSolver->J, 0.0, pMatrixCovariance ); -+#endif - - // - // determine the fitted values... -diff -u -r Kst-2.0.8/src/plugins/fits/non_linear_weighted.h Kst-2.0.8-patched/src/plugins/fits/non_linear_weighted.h ---- Kst-2.0.8/src/plugins/fits/non_linear_weighted.h 2014-02-13 09:41:44.000000000 +0000 -+++ Kst-2.0.8-patched/src/plugins/fits/non_linear_weighted.h 2015-11-18 22:28:44.004399807 +0000 -@@ -18,6 +18,7 @@ - #include <gsl/gsl_blas.h> - #include <gsl/gsl_multifit_nlin.h> - #include <gsl/gsl_statistics.h> -+#include <gsl/gsl_version.h> - #include "common.h" - - struct data { -@@ -193,7 +194,14 @@ - } - while( iStatus == GSL_CONTINUE && iIterations < MAX_NUM_ITERATIONS ); - -+#if GSL_MAJOR_VERSION >=2 -+ gsl_matrix *J=gsl_matrix_alloc(pSolver->fdf->n, pSolver->fdf->p); -+ gsl_multifit_fdfsolver_jac (pSolver, J); -+ gsl_multifit_covar( J, 0.0, pMatrixCovariance ); -+ gsl_matrix_free(J); -+#else - gsl_multifit_covar( pSolver->J, 0.0, pMatrixCovariance ); -+#endif - - // - // determine the fitted values... diff --git a/academic/Kst/README b/academic/Kst/README index cfad9f4c4b..314ac53aab 100644 --- a/academic/Kst/README +++ b/academic/Kst/README @@ -8,14 +8,15 @@ Kst is very user-friendly (both the community and the program itself!). Kst contains many powerful built-in features and is expandable with plugins and extensions. -Kst is licensed under the GPL, and is as such freely available for anyone. +Kst is licensed under the GPL, and is as such freely available for +anyone. Note that KDE libraries are an optional dependency (i.e. you can run Kst without KDE, but you get additional features when running on a platform with KDE). Optional dependencies are: -- gsl (a lot of very useful data analysis plugins are based) - RECOMMENDED +- hdf5 (provides support for the HDF5 file formats) - netcdf (which provides support for files in the netCDF format) - muParser (which is used in the general non-linear fitting plugin) - GetData (which provides support for files in the Dirfile format) diff --git a/academic/Kst/fix_hdf5_path.patch b/academic/Kst/fix_hdf5_path.patch new file mode 100644 index 0000000000..bcdc1403ae --- /dev/null +++ b/academic/Kst/fix_hdf5_path.patch @@ -0,0 +1,11 @@ +--- Kst-20220116_2b8e03e/src/datasources/hdf5/hdf5.h 2022-01-15 22:42:17.000000000 -0300 ++++ Kst-20220116_2b8e03e/src/datasources/hdf5/hdf5.h.new 2022-03-01 09:50:10.407808017 -0300 +@@ -18,7 +18,7 @@ + #include <dataplugin.h> + + #include <QFileInfo> +-#include <hdf5/serial/H5Cpp.h> ++#include <H5Cpp.h> + #include <exception> + + #include "debug.h" diff --git a/academic/MetaPhlAn2/MetaPhlAn2.SlackBuild b/academic/MetaPhlAn2/MetaPhlAn2.SlackBuild index 48492049c4..99d17512b7 100644 --- a/academic/MetaPhlAn2/MetaPhlAn2.SlackBuild +++ b/academic/MetaPhlAn2/MetaPhlAn2.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for MetaPhlAn2 -# Copyright 2019-2020 Petar Petrov slackalaxy@gmail.com +# Copyright 2019-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,44 +22,44 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=MetaPhlAn2 -VERSION=${VERSION:-2.9.5.3} +VERSION=${VERSION:-20201202_git4e4416} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} -SRCNAM=metaphlan2 -AUTHOR=biobakery -COMMIT=3a075f914593 +COMMIT=4e4416321c75828ac8ea55d36f5a65ebd39058c5 +ARCH=noarch -if [ -z "$ARCH" ]; then - case "$( uname -m )" in - i?86) ARCH=i586 ;; - arm*) ARCH=arm ;; - *) ARCH=$( uname -m ) ;; - esac +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 fi -CWD=$(pwd) + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -ARCH=noarch - set -e # Construct the source tarball name. if [ -e $CWD/$COMMIT.tar.gz ]; then TARBALL=${COMMIT} else - TARBALL=${AUTHOR}-${SRCNAM}-${COMMIT} + TARBALL=${PRGNAM}-${COMMIT} fi rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf ${AUTHOR}-${SRCNAM}-${COMMIT} +rm -rf ${PRGNAM}-${COMMIT} tar xvf $CWD/$TARBALL.tar.gz -cd ${AUTHOR}-${SRCNAM}-${COMMIT} +cd ${PRGNAM}-${COMMIT} chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -78,9 +78,12 @@ cd $PKG/usr/bin ln -s ../share/$PRGNAM/strainphlan.py cd - +mkdir -p $PKG/usr/share/$PRGNAM +cp -a strainphlan_tutorial $PKG/usr/share/$PRGNAM + mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - README.md changeset.txt license.txt strainphlan_tutorial \ + README.md changeset.txt license.txt \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References @@ -89,4 +92,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/MetaPhlAn2/MetaPhlAn2.info b/academic/MetaPhlAn2/MetaPhlAn2.info index f01033053b..72744ccf5a 100644 --- a/academic/MetaPhlAn2/MetaPhlAn2.info +++ b/academic/MetaPhlAn2/MetaPhlAn2.info @@ -1,10 +1,10 @@ PRGNAM="MetaPhlAn2" -VERSION="2.9.5.3" +VERSION="20201202_git4e4416" HOMEPAGE="http://huttenhower.sph.harvard.edu/metaphlan2" -DOWNLOAD="https://bitbucket.org/biobakery/metaphlan2/get/3a075f914593.tar.gz" -MD5SUM="956f8f6897a40e15cec38eb26cdcf97c" +DOWNLOAD="https://github.com/biobakery/MetaPhlAn2/archive/4e4416/MetaPhlAn2-4e4416321c75828ac8ea55d36f5a65ebd39058c5.tar.gz" +MD5SUM="7f07d766a84b0da247a404c05e6f9eb6" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="pysam biopython msgpack-python pandas scipy DendroPy bowtie2 muscle samtools-legacy bcftools ncbi-blast+ RAxML" +REQUIRES="pysam biopython msgpack-python pandas python2-scipy DendroPy bowtie2 muscle samtools-legacy bcftools ncbi-blast+ RAxML" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/MetaPhlAn2/README b/academic/MetaPhlAn2/README index 15d1bc4265..55665c56e1 100644 --- a/academic/MetaPhlAn2/README +++ b/academic/MetaPhlAn2/README @@ -12,7 +12,7 @@ archaeal and ~500 eukaryotic), allowing: * unambiguous taxonomic assignments; * accurate estimation of organismal relative abundance; -* species-level resolution for bacteria, archaea, eukaryotes and viruses; +* species-level resolution for bacteria, archaea, eukaryotes, viruses; * strain identification and tracking * orders of magnitude speedups compared to existing methods. * metagenomic strain-level population genomics diff --git a/academic/Mnemosyne/Mnemosyne.info b/academic/Mnemosyne/Mnemosyne.info deleted file mode 100644 index 8d6fc3ac9a..0000000000 --- a/academic/Mnemosyne/Mnemosyne.info +++ /dev/null @@ -1,10 +0,0 @@ -PRGNAM="Mnemosyne" -VERSION="2.6.1" -HOMEPAGE="https://mnemosyne-proj.org/" -DOWNLOAD="https://downloads.sourceforge.net/project/mnemosyne-proj/mnemosyne/mnemosyne-2.6.1/Mnemosyne-2.6.1.tar.gz" -MD5SUM="2b2f8fd019370af4d107f696f29ee3a2" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="python3-PyQt5 PyOpenGL CherryPy matplotlib WebOb" -MAINTAINER="R. S. Ananda Murthy" -EMAIL="rsamurti@gmail.com" diff --git a/academic/Mnemosyne/README b/academic/Mnemosyne/README deleted file mode 100644 index 6149871479..0000000000 --- a/academic/Mnemosyne/README +++ /dev/null @@ -1,9 +0,0 @@ -Mnemosyne aims to be a user-friendly flash card program, -with a clean, deceptively simple interface that does not -require you to wrap your head around complicated concepts -before you can start using it. At the same time, under the hood -it is very powerful, and its architecture allows infinite -extensibility and customisibility through plugins and a -scripting API, for the benefit of power users. - -Optional Dependency: texlive (for entering mathematical equations in cards using LaTeX) diff --git a/academic/Mnemosyne/mnemosyne.png b/academic/Mnemosyne/mnemosyne.png Binary files differdeleted file mode 100644 index 6dbd6120b7..0000000000 --- a/academic/Mnemosyne/mnemosyne.png +++ /dev/null diff --git a/academic/NWChem/NWChem.SlackBuild b/academic/NWChem/NWChem.SlackBuild new file mode 100644 index 0000000000..ac62916771 --- /dev/null +++ b/academic/NWChem/NWChem.SlackBuild @@ -0,0 +1,170 @@ +#!/bin/bash + +# Slackware build script for NWChem + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=NWChem +VERSION=${VERSION:-7.0.2} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +SRCNAM="nwchem-$VERSION-release.revision-b9985dfa-srconly.2020-10-12" + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf nwchem-$VERSION +tar xvf $CWD/$SRCNAM.tar.bz2 +cd nwchem-$VERSION + +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +case "$ARCH" in + i?86) NWCHEM_ARCH=LINUX ;; + armv7l) NWCHEM_ARCH=LINUX ;; + aarch64) NWCHEM_ARCH=LINUX64 ;; + *) NWCHEM_ARCH=LINUX64 ;; +esac + +if [ "${BLAS:-no}" == "yes" ]; then + BLASOPT="-lblas" + LAPACK_LIB="/usr/lib${LIBDIRSUFFIX}/liblapack.so" + INTBLAS=n +else + INTBLAS=y +fi + +# whatever set always try to build with MPI, +# actually it checks if the BUILD_MPI is defined or not +# the version 7.0.2 doesn't support buildings without MPI +if [ "${MPI:-no}" == "yes" ]; then + BUILD_MPI="y" +else + BUILD_MPI="n" +fi + +if [ "${PYTHON:-no}" == "yes" ]; then + OPT_MODULE="python" +fi + +# fix for "integer expression expected" +sed -i 's/ $(GNUMAJOR) / "$(GNUMAJOR)" /g' src/config/makefile.h +sed -i 's/ $(GNUMINOR) / "$(GNUMINOR)" /g' src/config/makefile.h +sed -i 's/\(-eq\|-gt\|-ge\) \([0-9]*\)/\1 "\2"/g' src/config/makefile.h + +cd src +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +NWCHEM_TOP=$(pwd)/.. \ +NWCHEM_TARGET=$NWCHEM_ARCH \ +NWCHEM_MODULES="all $OPT_MODULE" \ +USE_MPI=$BUILD_MPI \ +USE_INTERNALBLAS=$INTBLAS \ +BLASOPT=$BLASOPT \ +LAPACK_LIB="$LAPACK_LIB" \ +make +cd .. + +# perform installation +install -d $PKG/usr/bin +install -m 0755 bin/$NWCHEM_ARCH/nwchem $PKG/usr/bin + +mkdir -p $PKG/usr/share/$PKGNAM-$VERSION +cp -ar src/basis/libraries $PKG/usr/share/$PRGNAM-$VERSION +cp -ar src/data $PKG/usr/share/$PRGNAM-$VERSION +cp -ar src/nwpw/libraryps $PKG/usr/share/$PRGNAM-$VERSION + +cat <<EOF >> $PKG/usr/share/$PRGNAM-$VERSION/nwchemrc.default +nwchem_basis_library /usr/share/$PRGNAM-$VERSION/data/libraries/ +nwchem_nwpw_library /usr/share/$PRGNAM-$VERSION/data/libraryps/ +ffield amber +amber_1 /usr/share/$PRGNAM-$VERSION/data/amber_s/ +amber_2 /usr/share/$PRGNAM-$VERSION/data/amber_q/ +amber_3 /usr/share/$PRGNAM-$VERSION/data/amber_x/ +amber_4 /usr/share/$PRGNAM-$VERSION/data/amber_u/ +spce /usr/share/$PRGNAM-$VERSION/data/solvents/spce.rst +charmm_s /usr/share/$PRGNAM-$VERSION/data/charmm_s/ +charmm_x /usr/share/$PRGNAM-$VERSION/data/charmm_x/ +EOF + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +find $PKG -depth -type d -empty -delete || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/NWChem/NWChem.info b/academic/NWChem/NWChem.info new file mode 100644 index 0000000000..4f2effb9d9 --- /dev/null +++ b/academic/NWChem/NWChem.info @@ -0,0 +1,10 @@ +PRGNAM="NWChem" +VERSION="7.0.2" +HOMEPAGE="https://www.nwchem-sw.org" +DOWNLOAD="https://github.com/nwchemgit/nwchem/releases/download/v7.0.2-release/nwchem-7.0.2-release.revision-b9985dfa-srconly.2020-10-12.tar.bz2" +MD5SUM="b39f42eeacd7e984eee8b7ebc3dfe9f8" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="mpich" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/NWChem/README b/academic/NWChem/README new file mode 100644 index 0000000000..59b0933021 --- /dev/null +++ b/academic/NWChem/README @@ -0,0 +1,15 @@ + NWChem aims to provide its users with computational chemistry tools +that are scalable both in their ability to treat large scientific +computational chemistry problems efficiently, and in their use of +available parallel computing resources from high-performance parallel +supercomputers to conventional workstation clusters. + + + The default configuration file is at: + /usr/share/NWChem-VERSION/nwchemrc.default copy it to your working +directory. + + If you want to install the Python module set the environment +variable PYTHON=yes. + By default it uses a internal blas library, if you want to use +another blas library please set BLAS=yes and install blas and lapack. diff --git a/academic/NWChem/slack-desc b/academic/NWChem/slack-desc new file mode 100644 index 0000000000..b1b7a375b8 --- /dev/null +++ b/academic/NWChem/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +NWChem: NWChem (Open Source High-Performance Computational Chemistry) +NWChem: +NWChem: +NWChem: NWChem aims to provide its users with computational chemistry tools +NWChem: that are scalable both in their ability to treat large scientific +NWChem: computational chemistry problems efficiently, and in their use of +NWChem: available parallel computing resources from high-performance parallel +NWChem: supercomputers to conventional workstation clusters. +NWChem: +NWChem: +NWChem: diff --git a/academic/OpenFOAM/OpenFOAM.SlackBuild b/academic/OpenFOAM/OpenFOAM.SlackBuild index 94b7b00d56..3e98f9b8d5 100644 --- a/academic/OpenFOAM/OpenFOAM.SlackBuild +++ b/academic/OpenFOAM/OpenFOAM.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for OpenFOAM -# Copyright 2017, 2018, 2019 Lorenzo Trevisan, Caorle, Venice, Italy +# Copyright 2017, 2018, 2019, 2020, 2021, 2022, 2023, 2024 Lorenzo Trevisan, Caorle, Venice, Italy # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=OpenFOAM -VERSION=${VERSION:-7} +VERSION=${VERSION:-11} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -94,4 +104,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/OpenFOAM/OpenFOAM.info b/academic/OpenFOAM/OpenFOAM.info index 4ca7458532..52786f5932 100644 --- a/academic/OpenFOAM/OpenFOAM.info +++ b/academic/OpenFOAM/OpenFOAM.info @@ -1,10 +1,10 @@ PRGNAM="OpenFOAM" -VERSION="7" +VERSION="11" HOMEPAGE="https://openfoam.org/" -DOWNLOAD="https://github.com/OpenFOAM/OpenFOAM-7/archive/version-7/OpenFOAM-7-version-7.tar.gz \ - https://github.com/OpenFOAM/ThirdParty-7/archive/version-7/ThirdParty-7-version-7.tar.gz" -MD5SUM="638b38ae0e80cbb1201abec3f5c88641 \ - 2a4fe46807730e70ce0b81d4a4dd4fc8" +DOWNLOAD="https://github.com/OpenFOAM/OpenFOAM-11/archive/version-11/OpenFOAM-11-version-11.tar.gz \ + https://github.com/OpenFOAM/ThirdParty-11/archive/version-11/ThirdParty-11-version-11.tar.gz" +MD5SUM="81862ded202dc13eb285d399e2ce1741 \ + fcd80fb7fa8d011d1a055cd30323ae58" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="openmpi CGAL" diff --git a/academic/OpenFOAM/OpenFOAM.sh b/academic/OpenFOAM/OpenFOAM.sh index e6164c0869..02c71aa6ed 100644 --- a/academic/OpenFOAM/OpenFOAM.sh +++ b/academic/OpenFOAM/OpenFOAM.sh @@ -1 +1 @@ -. /opt/OpenFOAM/OpenFOAM-7/etc/bashrc +. /opt/OpenFOAM/OpenFOAM-11/etc/bashrc diff --git a/academic/OpenFOAM/README b/academic/OpenFOAM/README index fd23aef9b7..a72cf10568 100644 --- a/academic/OpenFOAM/README +++ b/academic/OpenFOAM/README @@ -9,4 +9,5 @@ multi-core processors and multi-processor computers. Optional dependency: graphviz (for documentation with graphs) -You can build with multiple jobs by setting the MAKEFLAGS environment variable. +You can build with multiple jobs by setting the MAKEFLAGS environment +variable (e.g. export MAKEFLAGS="-j$(nproc)" at bash prompt). diff --git a/academic/OpenMM/OpenMM.SlackBuild b/academic/OpenMM/OpenMM.SlackBuild new file mode 100644 index 0000000000..2696983b1f --- /dev/null +++ b/academic/OpenMM/OpenMM.SlackBuild @@ -0,0 +1,165 @@ +#!/bin/bash + +# Slackware build script for OpenMM + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=OpenMM +VERSION=${VERSION:-7.7.0} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +SRCNAM=${PRGNAM,,} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $SRCNAM-$VERSION +tar xvf $CWD/$SRCNAM-$VERSION.tar.gz +cd $SRCNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +# fix library installation path +# note: the other solution requires less lines, +# but it was after cmake +sed -i \ + -e 's#/lib RUNTIME_DIRECTORY /lib#/lib'${LIBDIRSUFFIX}' RUNTIME_DIRECTORY /lib'${LIBDIRSUFFIX}'#' \ + -e 's#/lib/plugins RUNTIME_DIRECTORY /lib/plugins#/lib'${LIBDIRSUFFIX}'/plugins RUNTIME_DIRECTORY /lib'${LIBDIRSUFFIX}'/plugins#' \ + platforms/*/*/CMakeLists.txt \ + plugins/*/CMakeLists.txt \ + plugins/*/platforms/*/CMakeLists.txt + +sed -i 's#${CMAKE_INSTALL_PREFIX}/lib#&'${LIBDIRSUFFIX}'#' \ + plugins/*/CMakeLists.txt \ + plugins/*/platforms/*/CMakeLists.txt \ + platforms/*/CMakeLists.txt \ + platforms/*/*/CMakeLists.txt + +# fix installation path for examples and licenses +sed -i 's#\(DESTINATION\) \(examples\)#\1 share/'$PRGNAM'/\2#' \ + examples/CMakeLists.txt +sed -i 's#\(DESTINATION\) \(licenses\)#\1 doc/'$PRGNAM-$VERSION'/\2#' \ + docs-source/CMakeLists.txt + +mkdir -p build +cd build + cmake \ + -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DBUILD_SHARED_LIBS=ON \ + -DPYTHON_EXECUTABLE=/usr/bin/python3 \ + $OPT_BUILD \ + -DCMAKE_BUILD_TYPE=Release .. + + # fix installation path of library "libOpenMM.so" + sed -i 's#${CMAKE_INSTALL_PREFIX}/lib#&'${LIBDIRSUFFIX}'#' \ + cmake_install.cmake + + make + make install/strip DESTDIR=$PKG + + if [ ${PYTHON:-no} == yes ]; then + cd python + # require the CFLAGS for linking with the OpenMM libraries + CFLAGS="-L$PKG/usr/lib${LIBDIRSUFFIX}" \ + OPENMM_INCLUDE_PATH="/usr/include;$PKG/usr/include" \ + OPENMM_LIB_PATH="/usr/lib${LIBDIRSUFFIX};$PKG/usr/lib${LIBDIRSUFFIX}" \ + python3 setup.py install --root=$PKG + # remove temporary folder from python module library path + PYVER=$( python3 -c 'import sys; print("%d.%d" % sys.version_info[:2])' ) + sed -i 's#;'$PKG'/usr/lib'${LIBDIRSUFFIX}'##' $PKG/usr/lib${LIBDIRSUFFIX}/python$PYVER/site-packages/openmm/version.py + cd .. + fi +cd .. + +# update example's makefile +sed -i \ + -e '21s#/usr/local/openmm#/usr#' \ + -e '31s#/lib#&'${LIBDIRSUFFIX}'#' \ + $PKG/usr/share/$PRGNAM/examples/Makefile + +# prune empty dirc "usr/docs" +rm -fr $PKG/usr/docs + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + {CODE_OF_CONDUCT,CONTRIBUTING,SUPPORT}.md \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/OpenMM/OpenMM.info b/academic/OpenMM/OpenMM.info new file mode 100644 index 0000000000..816a633fb0 --- /dev/null +++ b/academic/OpenMM/OpenMM.info @@ -0,0 +1,10 @@ +PRGNAM="OpenMM" +VERSION="7.7.0" +HOMEPAGE="https://openmm.org" +DOWNLOAD="https://github.com/openmm/openmm/archive/7.7.0/openmm-7.7.0.tar.gz" +MD5SUM="659712580bffde569f0c1663f7df7e68" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/OpenMM/README b/academic/OpenMM/README new file mode 100644 index 0000000000..3bd6b80eb9 --- /dev/null +++ b/academic/OpenMM/README @@ -0,0 +1,10 @@ + A high-performance toolkit for molecular simulation. Use it as an +application, a library, or a flexible programming environment. We +include extensive language bindings for Python, C, C++, and even +Fortran. + + If you want to build the Python package set the environment +variable PYTHON=yes (this requires numpy3). + +NOTE: if you want to use the python module with OpenCL you shall, +install a OpenCL runtime, such as pocl, or other vendor specific. diff --git a/academic/pyfits/slack-desc b/academic/OpenMM/slack-desc index 5ff2aaec0b..70197f20a3 100644 --- a/academic/pyfits/slack-desc +++ b/academic/OpenMM/slack-desc @@ -6,14 +6,14 @@ # customary to leave one space after the ':' except on otherwise blank lines. |-----handy-ruler------------------------------------------------------| -pyfits: pyfits (a Python extension for working with FITS files) -pyfits: -pyfits: PyFITS provides an interface to FITS formatted files in the Python -pyfits: scripting language. PyFITS was a development project of the Science -pyfits: Software Branch at the Space Telescope Science Institute. -pyfits: -pyfits: Homepage: https://github.com/spacetelescope/PyFITS -pyfits: -pyfits: -pyfits: -pyfits: +OpenMM: OpenMM (high-performance toolkit for molecular simulation) +OpenMM: +OpenMM: +OpenMM: +OpenMM: A high-performance toolkit for molecular simulation. Use it as an +OpenMM: application, a library, or a flexible programming environment. We +OpenMM: include extensive language bindings for Python, C, C++, and even +OpenMM: Fortran. +OpenMM: +OpenMM: +OpenMM: diff --git a/academic/OpenVSP/OpenVSP.SlackBuild b/academic/OpenVSP/OpenVSP.SlackBuild new file mode 100644 index 0000000000..9cade4a39e --- /dev/null +++ b/academic/OpenVSP/OpenVSP.SlackBuild @@ -0,0 +1,137 @@ +#!/bin/bash + +# Slackware build script for OpenVSP + +# Copyright 2022 Lenard Spencer, Orlando, Florida, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=OpenVSP +VERSION=${VERSION:-3.31.1} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf ${PRGNAM}-${PRGNAM}_$VERSION +tar -xvf $CWD/${PRGNAM}_$VERSION.tar.gz || tar -xvf $CWD/${PRGNAM}-${PRGNAM}_$VERSION.tar.gz +cd $PRGNAM-${PRGNAM}_$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +mkdir -p build buildlibs + +cd buildlibs + cmake \ + -DVSP_USE_SYSTEM_LIBXML2=true \ + -DVSP_USE_SYSTEM_FLTK=true \ + -DVSP_USE_SYSTEM_GLM=false \ + -DVSP_USE_SYSTEM_GLEW=true \ + -DVSP_USE_SYSTEM_CMINPACK=false \ + -DVSP_USE_SYSTEM_LIBIGES=false \ + -DVSP_USE_SYSTEM_EIGEN=true \ + -DVSP_USE_SYSTEM_CODEELI=false \ + -DVSP_USE_SYSTEM_CPPTEST=false \ + -DCMAKE_BUILD_TYPE=Release \ + -Wno-dev \ + ../Libraries + make + +cd ../build + cmake \ + -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DVSP_LIBRARY_PATH=$TMP/${PRGNAM}-${PRGNAM}_$VERSION/buildlibs \ + -DCMAKE_INSTALL_PREFIX=/opt/$PRGNAM \ + -DCMAKE_BUILD_TYPE=Release \ + -Wno-dev .. + make + make install DESTDIR=$PKG +cd .. + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +for i in 16 32 64 128; do + convert vspIcon.png -resize ${i}x${i}! $PRGNAM-${i}.png + install -D -m 0644 $PRGNAM-${i}.png \ + $PKG/usr/share/icons/hicolor/${i}x${i}/apps/$PRGNAM.png +done +install -D -m0644 $CWD/OpenVSP.desktop \ + $PKG/usr/share/applications/OpenVSP.desktop + +# Create symlink to executable: +(mkdir -p $PKG/usr/bin ; cd $PKG/usr/bin ; ln -sf ../../opt/OpenVSP/vsp ) + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + LICENSE README.md \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/OpenVSP/OpenVSP.desktop b/academic/OpenVSP/OpenVSP.desktop new file mode 100644 index 0000000000..b9c345e7fc --- /dev/null +++ b/academic/OpenVSP/OpenVSP.desktop @@ -0,0 +1,9 @@ +[Desktop Entry] +Name=OpenVSP +GenericName=OpenVSP +Comment=3D Aircraft Modeler +Exec=vsp +Icon=OpenVSP +Terminal=false +Type=Application +Categories=Graphics; diff --git a/academic/OpenVSP/OpenVSP.info b/academic/OpenVSP/OpenVSP.info new file mode 100644 index 0000000000..a366bf2c19 --- /dev/null +++ b/academic/OpenVSP/OpenVSP.info @@ -0,0 +1,10 @@ +PRGNAM="OpenVSP" +VERSION="3.31.1" +HOMEPAGE="http://openvsp.org" +DOWNLOAD="https://github.com/OpenVSP/OpenVSP/archive/OpenVSP_3.31.1/OpenVSP-OpenVSP_3.31.1.tar.gz" +MD5SUM="5267cdc9d1c6050fd0b8bc963e179b87" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="fltk" +MAINTAINER="Lenard Spencer" +EMAIL="lenardrspencer@gmail.com" diff --git a/academic/OpenVSP/README b/academic/OpenVSP/README new file mode 100644 index 0000000000..79c0c29acd --- /dev/null +++ b/academic/OpenVSP/README @@ -0,0 +1,13 @@ +OpenVSP is a parametric aircraft geometry tool. OpenVSP allows the +user to create a 3D model of an aircraft defined by common engineering +parameters. This model can be processed into formats suitable for +engineering analysis. + +The predecessors to OpenVSP have been developed by J.R. Gloudemans and +others for NASA since the early 1990's. On January 10 2012, OpenVSP +was released as an open source project under the NASA Open Source +Agreement (NOSA) version 1.3. + +You can download sample aircraft at http://hangar.openvsp.org. + +Requires fltk from Slackware's /extra folder. diff --git a/academic/Mnemosyne/doinst.sh b/academic/OpenVSP/doinst.sh index aea0f894eb..aea0f894eb 100644 --- a/academic/Mnemosyne/doinst.sh +++ b/academic/OpenVSP/doinst.sh diff --git a/academic/OpenVSP/slack-desc b/academic/OpenVSP/slack-desc new file mode 100644 index 0000000000..2aed2df60f --- /dev/null +++ b/academic/OpenVSP/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +OpenVSP: OpenVSP (3D aircraft modeling tool) +OpenVSP: +OpenVSP: OpenVSP is a parametric aircraft geometry tool that allows the user +OpenVSP: to create a 3D model of an aircraft defined by common engineering +OpenVSP: parameters. This model can be processed into formats suitable for +OpenVSP: engineering analysis. OpenVSP was released as an open source project +OpenVSP: under the NASA Open Source Agreement (NOSA) version 1.3. +OpenVSP: +OpenVSP: +OpenVSP: homepage: http://openvsp.org +OpenVSP: diff --git a/academic/PhyML/PhyML.SlackBuild b/academic/PhyML/PhyML.SlackBuild index bddb063c00..351fde6f1f 100644 --- a/academic/PhyML/PhyML.SlackBuild +++ b/academic/PhyML/PhyML.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for PhyML -# Copyright 2011-2020 Petar Petrov slackalaxy@gmail.com +# Copyright 2011-2022 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -24,10 +24,13 @@ # Thanks to Niels Horn for some handy modifications and corrections. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=PhyML -VERSION=${VERSION:-3.3.20190909} +VERSION=${VERSION:-3.3.20220408} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} SRCNAM=$(echo $PRGNAM | tr A-Z a-z) @@ -39,7 +42,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -89,7 +99,9 @@ find -L . \ # Use our CFLAGS sed -i "/^CFLAGS/s/=/+=/" Makefile src/Makefile -CFLAGS="$SLKCFLAGS" CXXFLAGS="$SLKCFLAGS" make +# The -mfma flag is needed for building on 14.2. Help is from here: +# https://github.com/horovod/horovod/issues/1832 +CFLAGS="$SLKCFLAGS -mfma" CXXFLAGS="$SLKCFLAGS -mfma" make make install DESTDIR=$PKG # This is PhyML MPI. If you do not want it, comment the lines below. Then you do @@ -108,48 +120,52 @@ make install DESTDIR=$PKG # Use our CFLAGS sed -i "/^CFLAGS/s/=/+=/" Makefile src/Makefile -CFLAGS="$SLKCFLAGS" CXXFLAGS="$SLKCFLAGS" make +CFLAGS="$SLKCFLAGS -mfma" CXXFLAGS="$SLKCFLAGS -mfma" make make install DESTDIR=$PKG -# This is Phyrex -./autogen.sh -./configure \ - --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ - --sysconfdir=/etc \ - --localstatedir=/var \ - --mandir=/usr/man \ - --enable-phyrex \ - --docdir=/usr/doc/$PRGNAM-$VERSION \ - --build=$ARCH-slackware-linux - -# Use our CFLAGS +# This is Phyrex but it breaks at the moment + ./autogen.sh + ./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --mandir=/usr/man \ + --enable-phyrex \ + --docdir=/usr/doc/$PRGNAM-$VERSION \ + --build=$ARCH-slackware-linux + + # Use our CFLAGS sed -i "/^CFLAGS/s/=/+=/" Makefile src/Makefile -CFLAGS="$SLKCFLAGS" CXXFLAGS="$SLKCFLAGS" make +CFLAGS="$SLKCFLAGS -mfma" CXXFLAGS="$SLKCFLAGS -mfma" make make install DESTDIR=$PKG -# This is PhyTime -./autogen.sh -./configure \ - --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ - --sysconfdir=/etc \ - --localstatedir=/var \ - --mandir=/usr/man \ - --enable-phytime \ - --docdir=/usr/doc/$PRGNAM-$VERSION \ - --build=$ARCH-slackware-linux - -# Use our CFLAGS -sed -i "/^CFLAGS/s/=/+=/" Makefile src/Makefile - -CFLAGS="$SLKCFLAGS" CXXFLAGS="$SLKCFLAGS" make -make install DESTDIR=$PKG +# # This is PhyTime +# ./autogen.sh +# ./configure \ +# --prefix=/usr \ +# --libdir=/usr/lib${LIBDIRSUFFIX} \ +# --sysconfdir=/etc \ +# --localstatedir=/var \ +# --mandir=/usr/man \ +# --enable-phytime \ +# --docdir=/usr/doc/$PRGNAM-$VERSION \ +# --build=$ARCH-slackware-linux +# +# # Use our CFLAGS +# sed -i "/^CFLAGS/s/=/+=/" Makefile src/Makefile +# +# CFLAGS="$SLKCFLAGS -mfma" CXXFLAGS="$SLKCFLAGS -mfma" make +# make install DESTDIR=$PKG find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true +# fix permissions for docs +chmod 0644 doc/*.{pdf,tex,bib} +chmod 0644 doc/fig/*.pdf + # Include some examples mkdir -p $PKG/usr/share/$PRGNAM cp -a examples $PKG/usr/share/$PRGNAM @@ -165,4 +181,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/PhyML/PhyML.info b/academic/PhyML/PhyML.info index f44eaca3de..9b34384c9f 100644 --- a/academic/PhyML/PhyML.info +++ b/academic/PhyML/PhyML.info @@ -1,8 +1,8 @@ PRGNAM="PhyML" -VERSION="3.3.20190909" +VERSION="3.3.20220408" HOMEPAGE="https://github.com/stephaneguindon/phyml/" -DOWNLOAD="https://github.com/stephaneguindon/phyml/archive/v3.3.20190909/phyml-3.3.20190909.tar.gz" -MD5SUM="35698ff61c1db57b238f5b2d2cc784b3" +DOWNLOAD="https://github.com/stephaneguindon/phyml/archive/v3.3.20220408/phyml-3.3.20220408.tar.gz" +MD5SUM="b35e641af77d7f058cf1ddc73be5e0b7" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="openmpi" diff --git a/academic/PyAMG/PyAMG.SlackBuild b/academic/PyAMG/PyAMG.SlackBuild index 6d1b8c0aee..3b16dca8b5 100644 --- a/academic/PyAMG/PyAMG.SlackBuild +++ b/academic/PyAMG/PyAMG.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for PyAMG @@ -22,26 +22,36 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=PyAMG VERSION=${VERSION:-2.1.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -82,4 +92,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/PyAMG/PyAMG.info b/academic/PyAMG/PyAMG.info index 3b3933387b..f2fa54b086 100644 --- a/academic/PyAMG/PyAMG.info +++ b/academic/PyAMG/PyAMG.info @@ -5,6 +5,6 @@ DOWNLOAD="https://github.com/pyamg/pyamg/releases/download/v2.1.0/official_pyamg MD5SUM="b04419a4e751d5333bc97fb1786e9e09" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="nose numpy scipy" +REQUIRES="nose python2-scipy" MAINTAINER="Alexander Bruy" EMAIL="alexander dot bruy at gmail dot com" diff --git a/academic/PyAMG/README b/academic/PyAMG/README index c72262fa35..f5a2ac3fe5 100644 --- a/academic/PyAMG/README +++ b/academic/PyAMG/README @@ -1,9 +1,9 @@ -PyAMG is a library of **Algebraic Multigrid (AMG)** solvers with a convenient -Python interface. +PyAMG is a library of **Algebraic Multigrid (AMG)** solvers with a +convenient Python interface. -AMG is a multilevel technique for solving large-scale linear systems with -optimal or near-optimal efficiency. Unlike geometric multigrid, AMG requires -little or no geometric information about the underlying problem and develops a -sequence of coarser grids directly from the input matrix. This feature is -especially important for problems discretized on unstructured meshes and -irregular grids. +AMG is a multilevel technique for solving large-scale linear systems +with optimal or near-optimal efficiency. Unlike geometric multigrid, +AMG requires little or no geometric information about the underlying +problem and develops a sequence of coarser grids directly from the +input matrix. This feature is especially important for problems +discretized on unstructured meshes and irregular grids. diff --git a/academic/QtiPlot/QtiPlot.SlackBuild b/academic/QtiPlot/QtiPlot.SlackBuild deleted file mode 100644 index db8b2102a3..0000000000 --- a/academic/QtiPlot/QtiPlot.SlackBuild +++ /dev/null @@ -1,219 +0,0 @@ -#!/bin/sh - -# Slackware build script for QtiPlot - -# Copyright 2011-2016 Petar Petrov slackalaxy@gmail.com -# All rights reserved. -# -# Redistribution and use of this script, with or without modification, is -# permitted provided that the following conditions are met: -# -# 1. Redistributions of this script must retain the above copyright -# notice, this list of conditions and the following disclaimer. -# -# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED -# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF -# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO -# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, -# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, -# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; -# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, -# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR -# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF -# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - -PRGNAM=QtiPlot -VERSION=${VERSION:-0.9.8.9} -BUILD=${BUILD:-2} -TAG=${TAG:-_SBo} - -SRCNAM=$(echo $PRGNAM | tr A-Z a-z) - -QTEXENGINE=QTeXEngine-0.3-opensource -UNOFPLUGIN=importOPJ-20111106 - -if [ -z "$ARCH" ]; then - case "$( uname -m )" in - i?86) export ARCH=i486 ;; - arm*) export ARCH=arm ;; - *) export ARCH=$( uname -m ) ;; - esac -fi - -CWD=$(pwd) -TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM -OUTPUT=${OUTPUT:-/tmp} - -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" - LIBDIRSUFFIX="" - QMAKESPEC="linux-g++" -elif [ "$ARCH" = "i686" ]; then - SLKCFLAGS="-O2 -march=i686 -mtune=i686" - LIBDIRSUFFIX="" - QMAKESPEC="linux-g++" -elif [ "$ARCH" = "x86_64" ]; then - SLKCFLAGS="-O2 -fPIC" - LIBDIRSUFFIX="64" - QMAKESPEC="linux-g++-64" -else - SLKCFLAGS="-O2" - LIBDIRSUFFIX="" - QMAKESPEC="linux-g++" -fi - -# Define these here, as numbers change between Slackware releases. The -# folder names are used for some documentation path fixes, needed to -# generate the html manual later on. -DOCBOOK=dsssl-stylesheets-1.79 -CHUNK=xsl-stylesheets-1.78.1 -DOCBOOKX=xml-dtd-4.5 - -set -e - -rm -rf $PKG -mkdir -p $TMP $PKG $OUTPUT -cd $TMP -rm -rf $PRGNAM-$VERSION -mkdir $PRGNAM-$VERSION -cd $PRGNAM-$VERSION -tar xvf $CWD/$SRCNAM-$VERSION.tar.bz2 -unzip $CWD/$QTEXENGINE.zip -tar xvf $CWD/$UNOFPLUGIN.tar.gz -chown -R root:root . -find -L . \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; - -# Copy QTeXEngine and importOPJ to their locations to be built later -cp -a QTeXEngine $SRCNAM-$VERSION/3rdparty -cp -a $UNOFPLUGIN/qtiplot/src/plugins $SRCNAM-$VERSION/qtiplot/src -cp -a $UNOFPLUGIN/qtiplot/importOPJ.pro $SRCNAM-$VERSION/qtiplot -cd $SRCNAM-$VERSION - -# Patches for recent libpng, sip, gsl, etc -# thanks to slack_jack, Raveriux, ponce, Arch and Gentoo -patch -p0 -d 3rdparty/qwtplot3d < $CWD/qwtplot3d-libpng15.patch -patch -p1 < $CWD/sip-4.15.patch -patch -p1 < $CWD/qtiplot-0.9.8.9-private.patch -patch -p1 < $CWD/pyqt-4.11.patch -patch -p1 < $CWD/qtiplot-0.9.8.9_gsl-2.patch - -# Use the custom build.conf -cp $CWD/build.conf.slack build.conf - -# Make qtiplot.pro aware of the unofficial importOPJ plugin. Thanks to -# the author of the plugin, Stephan Zevenhuizen. For more info visit -# this site: http://www.staff.science.uu.nl/~zeven101/qtiplot.html -patch -p1 -i $CWD/importOPJ.patch -sed -i "143 a Q_IMPORT_PLUGIN(FreeSoftwareQtiPlotImportOPJ);" qtiplot/src/core/main.cpp - -# Fix qwtplot3d -sed -i "10 a #include <GL/glu.h>" 3rdparty/qwtplot3d/include/qwt3d_openglhelper.h - -# Make a few path fixes to qtiplot.pro -sed -i "s:/usr/local:/usr/share:" qtiplot/qtiplot.pro -sed -i "s:/share/man:/man:" qtiplot/qtiplot.pro -sed -i "s:/share/doc/qtiplot:/doc/$PRGNAM-$VERSION:" qtiplot/qtiplot.pro - -# Point to the right places of qt-assistant-compat, libreoffice (when -# installed), latex, java, the QtiPlot html manual and fitPlugins -sed -i "s:<QAssistantClient>:<QtAssistant/qassistantclient.h>:" qtiplot/src/core/ApplicationWindow.cpp -sed -i "s:/usr/bin/soffice:/usr/bin/libreoffice:" qtiplot/src/core/ApplicationWindow.cpp -sed -i "s:/usr/bin/latex:/usr/share/texmf/bin/latex:" qtiplot/src/core/ApplicationWindow.cpp -sed -i "s:/usr/bin/java:/usr/lib${LIBDIRSUFFIX}/java/bin/java:" qtiplot/src/core/ApplicationWindow.cpp -sed -i "s:/index.html:/html/index.html:" qtiplot/src/core/ApplicationWindow.cpp -sed -i "s:/local/qtiplot/fitPlugins:/lib${LIBDIRSUFFIX}/qtiplot/plugins:" qtiplot/src/core/ApplicationWindow.cpp - -# Path fixes, needed to generate the html manual -sed -i "s:stylesheet/dsssl/modular:${DOCBOOK}:" manual/qtiplot.dsl -sed -i "s:stylesheet/nwalsh:${CHUNK}:" manual/qtiplot_html.xsl -sed -i "s:schema/dtd/4.4:${DOCBOOKX}:" manual/docbook-en/index.docbook - -# Build QtiPlot's qwt -cd 3rdparty/qwt -qmake -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ -make -j1 - -# Build QtiPlot's qwtplot3d -cd ../qwtplot3d -qmake -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ -make -j1 - -# Build QTeXEngine -cd ../QTeXEngine -qmake -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ -make -j1 - -# Build importOPJ -cd ../../qtiplot -qmake importOPJ.pro -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ -make -j1 - -# Make the html manual. If you want to generate the handbook as a PDF, -# change "web" to "en" below and make sure you have installed dblatex. -cd ../manual -make -j1 web - -# Build QtiPlot -cd ../qtiplot -qmake qtiplot.pro "QMAKESPEC=$QMAKESPEC" -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ -make -j1 "QMAKESPEC=$QMAKESPEC" -make -j1 install INSTALL_ROOT=$PKG - -# Generate translations and copy them to their proper place -lrelease qtiplot.pro -mkdir -p $PKG/usr/share/qtiplot/translations -cp translations/*.qm $PKG/usr/share/qtiplot/translations - -# Copy some python examples -mkdir -p $PKG/usr/share/qtiplot/python-examples -cp examples/python/* $PKG/usr/share/qtiplot/python-examples - -# Build fitPlugins -cd ../fitPlugins -qmake "QMAKESPEC=$QMAKESPEC" -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ -make -j1 "QMAKESPEC=$QMAKESPEC" -make -j1 install INSTALL_ROOT=$PKG -cd .. - -find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ - | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true - -find $PKG/usr/man -type f -exec gzip -9 {} \; -for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done - -# Menu item, icon and mime types. The .xml is from Arch -mkdir -p $PKG/usr/share/{pixmaps,applications,mime/packages} -cp qtiplot_logo.png $PKG/usr/share/pixmaps/qtiplot.png -cp $CWD/qtiplot.desktop $PKG/usr/share/applications -cp $CWD/qtiplot.xml $PKG/usr/share/mime/packages - -mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a \ - README.html gpl_licence.txt qtiplot.css qtiplot_logo.png \ - $PKG/usr/doc/$PRGNAM-$VERSION -cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild -cat $CWD/build.conf.slack > $PKG/usr/doc/$PRGNAM-$VERSION/build.conf.slack - -mkdir -p $PKG/install -cat $CWD/slack-desc > $PKG/install/slack-desc -cat $CWD/doinst.sh > $PKG/install/doinst.sh - -cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} diff --git a/academic/QtiPlot/QtiPlot.info b/academic/QtiPlot/QtiPlot.info deleted file mode 100644 index dcbffe5315..0000000000 --- a/academic/QtiPlot/QtiPlot.info +++ /dev/null @@ -1,14 +0,0 @@ -PRGNAM="QtiPlot" -VERSION="0.9.8.9" -HOMEPAGE="https://www.qtiplot.com/" -DOWNLOAD="http://sourceforge.net/projects/qtiplot.berlios/files/qtiplot-0.9.8.9.tar.bz2 \ - http://sourceforge.net/projects/qtiplot.berlios/files/QTeXEngine-0.3-opensource.zip \ - http://sourceforge.net/projects/sboppetrov/files/QtiPlot/importOPJ-20111106.tar.gz" -MD5SUM="652096a365851da3b5f6fefdcbe2aaec \ - d1b234623770ec6209b14d1b5137f2f1 \ - 6f6925beb9e27f2ea0fbd01f23da548a" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="alglib muParser qt-assistant-compat tamu_anova" -MAINTAINER="Petar Petrov" -EMAIL="slackalaxy@gmail.com" diff --git a/academic/QtiPlot/README b/academic/QtiPlot/README deleted file mode 100644 index 950c7a7f05..0000000000 --- a/academic/QtiPlot/README +++ /dev/null @@ -1,32 +0,0 @@ -QtiPlot is a program for two- and three-dimensional graphical -presentation of data sets and for data analysis. Plots can be produced -from data sets stored in tables or from analytical functions. QtiPlot -offers a complete alternative solution to software like Origin, -SigmaPlot, SPSS, Regressi or Igor Pro. QtiPlot is used for teaching as -well as for complex data analysis and visualisation in companies, high -schools, universities and reseach institutes all over the world. - -Features: - -- Fully Python scriptable -- OpenGL based 3D plotting -- Publication quality plots and easy export to various image formats - (EMF, EPS, PS, PDF, SVG, BMP, JPG, PNG, TIFF, etc ...) -- Easy integration with LaTeX typesetting system -- Powerful and versatile spreadsheets with column-logic calculations - and easy import/export of multiple files -- One-click access to extensive built-in data analysis routines -- Advanced statistical analysis: Student's t-Test, ANOVA, chi-square - test for variance, normality test (Shapiro-Wilk) -- Linear and nonlinear curve fitting with weighting and estimation of - statistical errors of the fit-parameters -- Multi-peak fitting -- Image analysis tools -- Templates support: all settings for plots, tables and matrices can - be saved and restored later on for a fast editing process -- Project files based on folders, a powerful project explorer with - built-in drag and drop and searching facilities - -QtiPlot comes with its own, slightly modified versions of qwt and -qwtplot3d, while the script additionally builds in QTeXEngine and the -unofficial importOPJ plugin. diff --git a/academic/QtiPlot/build.conf.slack b/academic/QtiPlot/build.conf.slack deleted file mode 100644 index 22ac622871..0000000000 --- a/academic/QtiPlot/build.conf.slack +++ /dev/null @@ -1,75 +0,0 @@ -isEmpty( QTI_ROOT ) { - message( "each file including this config needs to set QTI_ROOT to the dir containing this file!" ) -} - -# System specific configuration -SYS_INCLUDEPATH = /usr/include -SYS_LIBS = -L/usr/lib${LIBDIRSUFFIX} -lz -lGLU - -# zlib (http://www.zlib.net/) -#ZLIB_INCLUDEPATH = $$QTI_ROOT/3rdparty/zlib/ -ZLIB_INCLUDEPATH = - - -# muParser (http://muparser.sourceforge.net/) -MUPARSER_INCLUDEPATH = -MUPARSER_LIBS = -lmuparser - -# GNU Sientific Library (http://www.gnu.org/software/gsl/) -GSL_INCLUDEPATH = -GSL_LIBS = -lgsl -lgslcblas - -# QWT - use local copy till upstream catches up -# (http://qwt.sourceforge.net/index.html) -QWT_INCLUDEPATH = $$QTI_ROOT/3rdparty/qwt/src -QWT_LIBS = $$QTI_ROOT/3rdparty/qwt/lib/libqwt.a - -# QwtPlot3D - use local copy till upstream catches up -# (http://qwtplot3d.sourceforge.net/) -QWT3D_INCLUDEPATH = $$QTI_ROOT/3rdparty/qwtplot3d/include -QWT3D_LIBS = $$QTI_ROOT/3rdparty/qwtplot3d/lib/libqwtplot3d.a - -# libpng -LIBPNG_LIBS = -lpng - -# QTeXEngine (http://soft.proindependent.com/qtexengine/) -TEX_ENGINE_INCLUDEPATH = $$QTI_ROOT/3rdparty/QTeXEngine/src -TEX_ENGINE_LIBS = $$QTI_ROOT/3rdparty/QTeXEngine/libQTeXEngine.a - -# ALGLIB (http://www.alglib.net/) -ALGLIB_INCLUDEPATH = /usr/include/libalglib -ALGLIB_LIBS = -lalglib - -# TAMUANOVA (http://www.stat.tamu.edu/~aredd/tamuanova/) -TAMUANOVA_INCLUDEPATH = /usr/include/tamu_anova -TAMUANOVA_LIBS = -ltamuanova - -# the python interpreter to use -PYTHON = python - -# Qt tools - allows to use specific versions -LUPDATE = lupdate -LRELEASE = lrelease - -# Target specific configuration: configure Qtiplot itself -contains( TARGET, qtiplot ) { -# building without muParser doesn't work yet -SCRIPTING_LANGS += muParser -SCRIPTING_LANGS += Python - -# a console displaying output of scripts -DEFINES += SCRIPTING_CONSOLE - -# Uncomment the following line if you want to perform a custom -# installation using the *.path variables defined in ./qtiplot.pro. -CONFIG += CustomInstall - -# Uncomment the following line if you want to build QtiPlot as a browser plugin (not working on Internet Explorer). -#CONFIG += BrowserPlugin - -#CONFIG += release -#CONFIG += debug - -# Uncomment the following line if you want to link statically against Qt. -#CONFIG += StaticBuild -} diff --git a/academic/QtiPlot/importOPJ.patch b/academic/QtiPlot/importOPJ.patch deleted file mode 100644 index 12a0d2073b..0000000000 --- a/academic/QtiPlot/importOPJ.patch +++ /dev/null @@ -1,18 +0,0 @@ -diff -pruN qtiplot-0.9.8.9.orig/qtiplot/qtiplot.pro qtiplot-0.9.8.9/qtiplot/qtiplot.pro ---- qtiplot-0.9.8.9.orig/qtiplot/qtiplot.pro 2011-11-02 18:55:25.000000000 +0200 -+++ qtiplot-0.9.8.9/qtiplot/qtiplot.pro 2012-08-03 01:27:29.649544418 +0300 -@@ -232,3 +232,14 @@ contains(CONFIG, BrowserPlugin){ - RC_FILE = qtiplot.rc - include(../3rdparty/QtSolutions/qtbrowserplugin/src/qtbrowserplugin.pri) - } -+ -+############################################################### -+##################### OriginPlugin ############################ -+############################################################### -+ -+TARGET = qtiplot -+DESTDIR = -+LIBS += ../tmp/qtiplot/libFreeSoftwareQtiPlotImportOPJ.a -+ -+ -+include(src/plugins/OriginPlugin/OriginPlugin.pri) diff --git a/academic/QtiPlot/pyqt-4.11.patch b/academic/QtiPlot/pyqt-4.11.patch deleted file mode 100644 index dc7d56f3e3..0000000000 --- a/academic/QtiPlot/pyqt-4.11.patch +++ /dev/null @@ -1,33 +0,0 @@ - qtiplot/python-sipcmd.py | 21 ++++++++++++++++++--- - 1 file changed, 18 insertions(+), 3 deletions(-) - -diff --git a/qtiplot/python-sipcmd.py b/qtiplot/python-sipcmd.py -index f643194..d8d1ef2 100755 ---- a/qtiplot/python-sipcmd.py -+++ b/qtiplot/python-sipcmd.py -@@ -27,6 +27,21 @@ - # # - ############################################################################ - --from PyQt4 import pyqtconfig --config = pyqtconfig.Configuration() --print " ".join([config.sip_bin, "-I", config.pyqt_sip_dir, config.pyqt_sip_flags]) -+from __future__ import print_function -+ -+import os -+import sipconfig -+import PyQt4.QtCore -+ -+try: -+ # >= 4.10 -+ SIP_FLAGS = PyQt4.QtCore.PYQT_CONFIGURATION['sip_flags'] -+except: -+ import PyQt4.pyqtconfig -+ SIP_FLAGS = PyQt4.pyqtconfig.Configuration().pyqt_sip_flags -+ -+PYQT_SIP_DIR = os.path.join(sipconfig.Configuration().default_sip_dir, 'PyQt4') -+SIP_BIN = sipconfig.Configuration().sip_bin -+SIP_INC_DIR = sipconfig.Configuration().sip_inc_dir -+ -+print(" ".join([SIP_BIN, "-I", PYQT_SIP_DIR, SIP_FLAGS])) - diff --git a/academic/QtiPlot/qtiplot-0.9.8.9-private.patch b/academic/QtiPlot/qtiplot-0.9.8.9-private.patch deleted file mode 100644 index 1dd92fd1a3..0000000000 --- a/academic/QtiPlot/qtiplot-0.9.8.9-private.patch +++ /dev/null @@ -1,16 +0,0 @@ -diff -ruN qtiplot-0.9.8.9.orig/qtiplot/src/plot2D/ImageWidget.h qtiplot-0.9.8.9/qtiplot/src/plot2D/ImageWidget.h ---- qtiplot-0.9.8.9.orig/qtiplot/src/plot2D/ImageWidget.h 2010-10-17 09:04:05.000000000 +0200 -+++ qtiplot-0.9.8.9/qtiplot/src/plot2D/ImageWidget.h 2013-11-01 12:11:36.559973891 +0100 -@@ -67,10 +67,10 @@ - void setWindowName(const QString& name){d_window_name = name;}; - - static QPixmap windowPixmap(ApplicationWindow *mw, const QString& name, const QSize& size); -+ void paintEvent(QPaintEvent *e); - - private: - void draw(QPainter *painter, const QRect& r); -- void paintEvent(QPaintEvent *e); - QPixmap d_pix; - //! The file from which the image was loaded. - QString d_file_name; - diff --git a/academic/QtiPlot/qtiplot-0.9.8.9_gsl-2.patch b/academic/QtiPlot/qtiplot-0.9.8.9_gsl-2.patch deleted file mode 100644 index d6ff7d00b0..0000000000 --- a/academic/QtiPlot/qtiplot-0.9.8.9_gsl-2.patch +++ /dev/null @@ -1,52 +0,0 @@ -diff -u -r qtiplot-0.9.8.9/qtiplot/src/analysis/Fit.cpp qtiplot-0.9.8.9-patched/qtiplot/src/analysis/Fit.cpp ---- qtiplot-0.9.8.9/qtiplot/src/analysis/Fit.cpp 2011-10-17 11:06:00.000000000 +0100 -+++ qtiplot-0.9.8.9-patched/qtiplot/src/analysis/Fit.cpp 2015-11-18 22:26:22.535193469 +0000 -@@ -39,6 +39,7 @@ - #include <gsl/gsl_statistics.h> - #include <gsl/gsl_blas.h> - #include <gsl/gsl_cdf.h> -+#include <gsl/gsl_version.h> - - #include <QApplication> - #include <QMessageBox> -@@ -106,6 +107,10 @@ - gsl_multifit_fdfsolver * Fit::fitGSL(gsl_multifit_function_fdf f, int &iterations, int &status) - { - const gsl_multifit_fdfsolver_type *T; -+#if GSL_MAJOR_VERSION >=2 -+ gsl_matrix *J=0; -+#endif -+ - if (d_solver) - T = gsl_multifit_fdfsolver_lmder; - else -@@ -128,7 +133,14 @@ - } - - if (status){ -+#if GSL_MAJOR_VERSION >=2 -+ J=gsl_matrix_alloc(s->fdf->n, s->fdf->p); -+ gsl_multifit_fdfsolver_jac (s, J); -+ gsl_multifit_covar (J, 0.0, covar); -+ gsl_matrix_free(J); -+#else - gsl_multifit_covar (s->J, 0.0, covar); -+#endif - iterations = 0; - return s; - } -@@ -155,7 +167,14 @@ - status = gsl_multifit_test_delta (s->dx, s->x, d_tolerance, d_tolerance); - } while (inRange && status == GSL_CONTINUE && (int)iter < d_max_iterations); - -+#if GSL_MAJOR_VERSION >=2 -+ J=gsl_matrix_alloc(s->fdf->n, s->fdf->p); -+ gsl_multifit_fdfsolver_jac (s, J); -+ gsl_multifit_covar (J, 0.0, covar); -+ gsl_matrix_free(J); -+#else - gsl_multifit_covar (s->J, 0.0, covar); -+#endif - - iterations = iter; - return s; diff --git a/academic/QtiPlot/qtiplot.desktop b/academic/QtiPlot/qtiplot.desktop deleted file mode 100644 index cf93e4911a..0000000000 --- a/academic/QtiPlot/qtiplot.desktop +++ /dev/null @@ -1,7 +0,0 @@ -[Desktop Entry] -Type=Application -Exec=qtiplot -Terminal=false -Name=QtiPlot -Icon=qtiplot -Categories=Office; diff --git a/academic/QtiPlot/qtiplot.xml b/academic/QtiPlot/qtiplot.xml deleted file mode 100644 index 7ad4c4aa02..0000000000 --- a/academic/QtiPlot/qtiplot.xml +++ /dev/null @@ -1,17 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<mime-info xmlns="http://www.freedesktop.org/standards/shared-mime-info"> - <mime-type type="application/x-qtiplot-project"> - <sub-class-of type="text/plain"/> - <comment>QtiPlot project file</comment> - <glob pattern="*.qti" /> - </mime-type> - <mime-type type="application/x-qtiplot-project-compressed"> - <comment>Compressed QtiPlot project file</comment> - <glob pattern="*.qti.gz" /> - </mime-type> - <mime-type type="application/x-qtiplot-project-backup"> - <sub-class-of type="text/plain"/> - <comment>QtiPlot project file backup</comment> - <glob pattern="*.qti~" /> - </mime-type> -</mime-info> diff --git a/academic/QtiPlot/qwtplot3d-libpng15.patch b/academic/QtiPlot/qwtplot3d-libpng15.patch deleted file mode 100644 index 828f0c6d84..0000000000 --- a/academic/QtiPlot/qwtplot3d-libpng15.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- 3rdparty/gl2ps/gl2ps.c.orig 2012-01-29 18:15:34.000000000 -0500 -+++ 3rdparty/gl2ps/gl2ps.c 2012-01-29 18:16:08.000000000 -0500 -@@ -47,6 +47,7 @@ - #endif - - #if defined(GL2PS_HAVE_LIBPNG) -+#include <zlib.h> - #include <png.h> - #endif - diff --git a/academic/QtiPlot/sip-4.15.patch b/academic/QtiPlot/sip-4.15.patch deleted file mode 100644 index 504223190a..0000000000 --- a/academic/QtiPlot/sip-4.15.patch +++ /dev/null @@ -1,32 +0,0 @@ ---- ./qtiplot/src/analysis/FFT.cpp.orig 2011-07-06 11:51:08.000000000 +0000 -+++ ./qtiplot/src/analysis/FFT.cpp 2013-10-23 23:07:45.674925476 +0000 -@@ -353,7 +353,7 @@ - ml->arrangeLayers(false, false); - } - --bool FFT::setDataFromTable(Table *t, const QString& realColName, const QString& imagColName, int from, int to) -+bool FFT::setDataFromTable(Table *t, const QString& realColName, const QString& imagColName, int from, int to, bool unused) - { - d_init_err = true; - ---- ./qtiplot/src/analysis/FFT.h.orig 2011-07-05 22:05:03.000000000 +0000 -+++ ./qtiplot/src/analysis/FFT.h 2013-10-23 23:11:34.277924367 +0000 -@@ -52,6 +52,8 @@ - Matrix *realOutputMatrix(){return d_re_out_matrix;} - Matrix *imaginaryOutputMatrix(){return d_im_out_matrix;} - -+ bool setDataFromTable(Table *t, const QString& realColName, const QString& imagColName = QString(), int from = 0, int to = -1, bool unused = false); -+ - private: - void init(); - void output(); -@@ -60,8 +62,6 @@ - void fftTable(); - void fftMatrix(); - -- bool setDataFromTable(Table *t, const QString& realColName, const QString& imagColName = QString(), int from = 0, int to = -1); -- - double d_sampling; - //! Flag telling if an inverse FFT must be performed. - bool d_inverse; - diff --git a/academic/R/R.SlackBuild b/academic/R/R.SlackBuild index 6fb687f83a..3ee98369fc 100644 --- a/academic/R/R.SlackBuild +++ b/academic/R/R.SlackBuild @@ -1,10 +1,9 @@ -#!/bin/sh +#!/bin/bash # SlackBuild script for R -# Copyright 2019 Andrew Payne, Boston, MA <phalange@komputermatrix.com> -# Copyright 2014-2017 melikamp, Andrew Rowland. (Contributors are -# listed in order of first participation.) +# Copyright 2019-2022 Andrew Payne <phalange@komputermatrix.com> +# Copyright 2014-2017 melikamp, Andrew Rowland # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -24,10 +23,13 @@ # with this program (most likely, a file named COPYING). If not, see # <http://www.gnu.org/licenses/>. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=R -VERSION=${VERSION:-3.6.2} +VERSION=${VERSION:-4.3.3} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ "${R_SHLIB:-yes}" = "yes" ]; then r_shlib="--enable-R-shlib" @@ -48,7 +50,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -73,7 +82,7 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $PRGNAM-$VERSION -tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +tar xvf $CWD/$PRGNAM-$VERSION.tar.xz cd $PRGNAM-$VERSION chown -R root:root . find -L . \ @@ -106,10 +115,12 @@ find $PKG/usr/man -type f -exec gzip -9 {} \; for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a {COPYING,INSTALL,README,SVN-REVISION,VERSION,VERSION-NICK} \ + $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/R/R.info b/academic/R/R.info index 9ce4d10cd4..45cf892f94 100644 --- a/academic/R/R.info +++ b/academic/R/R.info @@ -1,8 +1,8 @@ PRGNAM="R" -VERSION="3.6.2" -HOMEPAGE="http://www.r-project.org/" -DOWNLOAD="https://cran.r-project.org/src/base/R-3/R-3.6.2.tar.gz" -MD5SUM="90d23d138cee26d275da14b58296e521" +VERSION="4.3.3" +HOMEPAGE="https://www.r-project.org/" +DOWNLOAD="https://cran.r-project.org/src/base/R-4/R-4.3.3.tar.xz" +MD5SUM="5602f5996107c346dba12a16e866d2e2" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/R/README b/academic/R/README index cdd9f7dbd6..0ebd1faa48 100644 --- a/academic/R/README +++ b/academic/R/README @@ -1,20 +1,10 @@ -R is an integrated suite of software facilities for data manipulation, -calculation and graphical display. It includes - -* an effective data handling and storage facility, - -* a suite of operators for calculations on arrays, in particular -matrices, - -* a large, coherent, integrated collection of intermediate tools for -data analysis, - -* graphical facilities for data analysis and display either on-screen -or on hardcopy, and - -* a well-developed, simple and effective programming language which -includes conditionals, loops, user-defined recursive functions and -input and output facilities. +R is a language and environment for statistical computing and +graphics. It is a GNU project which is similar to the S language and +environment which was developed at Bell Laboratories (formerly AT&T, +now Lucent Technologies) by John Chambers and colleagues. R can be +considered as a different implementation of S. There are some +important differences, but much code written for S runs unaltered +under R. Notes: diff --git a/academic/R/slack-desc b/academic/R/slack-desc index f6e2acfb82..bbc419bba3 100644 --- a/academic/R/slack-desc +++ b/academic/R/slack-desc @@ -9,11 +9,11 @@ R: R (language and environment for statistical computing) R: R: R is a language and environment for statistical computing and -R: graphics. It is a GNU project which is similar to the S language -R: and environment which was developed at Bell Laboratories -R: by John Chambers and colleagues. R can be considered as a -R: different implementation of S. There are some important -R: differences, but much code written for S runs unaltered under R. +R: graphics. It is a GNU project which is similar to the S language and +R: environment which was developed at Bell Laboratories (formerly AT&T, +R: now Lucent Technologies) by John Chambers and colleagues. +R: +R: R: R: Homepage: https://www.r-project.org/ R: diff --git a/academic/RAxML/RAxML.SlackBuild b/academic/RAxML/RAxML.SlackBuild index 0c4e98a6ce..a9836a64df 100644 --- a/academic/RAxML/RAxML.SlackBuild +++ b/academic/RAxML/RAxML.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for RAxML -# Copyright 2019 Petar Petrov slackalaxy@gmail.com +# Copyright 2019-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=RAxML VERSION=${VERSION:-8.2.12} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -76,7 +86,7 @@ cp Makefile.gcc Makefile sed -i "/^CFLAGS/s/=/+=/" Makefile sed -i "s|raxmlHPC|raxml|g" Makefile CFLAGS="$SLKCFLAGS" \ -make -f Makefile +make -f Makefile -j1 install -D -m755 raxml $PKG/usr/bin/raxml # Openmpi version @@ -84,7 +94,7 @@ cp Makefile.MPI.gcc Makefile.MPI sed -i "/^CFLAGS/s/=/+=/" Makefile.MPI sed -i "s|raxmlHPC-MPI|raxml-MPI|g" Makefile.MPI CFLAGS="$SLKCFLAGS" \ -make -f Makefile.MPI +make -f Makefile.MPI -j1 install -D -m755 raxml-MPI $PKG/usr/bin/raxml-MPI ########################################################################## @@ -152,4 +162,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/RepeatMasker/README.SLACKWARE b/academic/RepeatMasker/README.SLACKWARE index dd3313fd62..0e92803b9e 100644 --- a/academic/RepeatMasker/README.SLACKWARE +++ b/academic/RepeatMasker/README.SLACKWARE @@ -1,31 +1,22 @@ -After install go fo /opt/RepeatMasker and run the RepeatMasker -Configuration Program: +After install go to /opt/RepeatMasker and run the Configuration Program: # perl ./configure -Paths are as follows: - -**PERL PROGRAM** -/usr/bin/perl - -**REPEATMASKER INSTALLATION DIRECTORY** -/opt/RepeatMasker - -**TRF PROGRAM** -/usr/bin/trf +* The full path including the name for the TRF program. +TRF_PRGM: /usr/bin/trf Add a Search Engine: 1. CrossMatch: you should obtain this yourself, with the proper license, following the instructions here http://www.phrap.org/ 2. RMBlast - NCBI Blast with RepeatMasker extensions: this is available from SBo. -3. WUBlast/ABBlast (required by DupMasker): you should obtain this +3. HMMER3.1 & DFAM: this is available from SBo. +4. ABBlast/WUBlast (required by DupMasker): you should obtain this yourself, with the proper license, following the instructions here https://blast.advbiocomp.com/licensing/ -4. HMMER3.1 & DFAM: this is available from SBo. -**RMBlast (rmblastn) INSTALLATION PATH** +* RMBlast (rmblastn) INSTALLATION PATH /usr/bin -**HMMER INSTALLATION PATH** +* HMMER INSTALLATION PATH /usr/bin diff --git a/academic/RepeatMasker/RepeatMasker.SlackBuild b/academic/RepeatMasker/RepeatMasker.SlackBuild index b94763c2a8..5d15586aeb 100644 --- a/academic/RepeatMasker/RepeatMasker.SlackBuild +++ b/academic/RepeatMasker/RepeatMasker.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for RepeatMasker -# Copyright 2018-2020 Petar Petrov slackalaxy@gmail.com +# Copyright 2018-2023 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,14 +22,24 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=RepeatMasker -VERSION=${VERSION:-4.1.0} +VERSION=${VERSION:-4.1.5} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} ARCH=noarch -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -54,6 +64,8 @@ find -L . \ mkdir -p $PKG/opt/$PRGNAM cp -a * $PKG/opt/$PRGNAM +rm $PKG/opt/$PRGNAM/{bluegrad.jpg,HTMLAnnotHeader.html,INSTALL,LICENSE,README.md,ReleaseNotes} + # Make a symlink mkdir -p $PKG/usr/bin cd $PKG/usr/bin @@ -63,10 +75,9 @@ cd - find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true -# Better just copy these and not move them from their original dir mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - bluegrad.jpg daterepeats.help HTMLAnnotHeader.html INSTALL LICENSE README.md repeatmasker.help ReleaseNotes \ + bluegrad.jpg daterepeats.help HTMLAnnotHeader.html LICENSE README.md repeatmasker.help ReleaseNotes \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild cat $CWD/README.SLACKWARE > $PKG/usr/doc/$PRGNAM-$VERSION/README.SLACKWARE @@ -76,4 +87,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/RepeatMasker/RepeatMasker.info b/academic/RepeatMasker/RepeatMasker.info index 62eacca432..3731dbe0f3 100644 --- a/academic/RepeatMasker/RepeatMasker.info +++ b/academic/RepeatMasker/RepeatMasker.info @@ -1,10 +1,10 @@ PRGNAM="RepeatMasker" -VERSION="4.1.0" +VERSION="4.1.5" HOMEPAGE="http://www.repeatmasker.org/" -DOWNLOAD="http://www.repeatmasker.org/RepeatMasker-4.1.0.tar.gz" -MD5SUM="936894df2b8291f42afce22a5793b4bf" +DOWNLOAD="http://www.repeatmasker.org/RepeatMasker/RepeatMasker-4.1.5.tar.gz" +MD5SUM="cc9c7ea4303ef11c3d2ca56af5207609" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="perl-Text-Soundex trfind HMMER ncbi-rmblastn" +REQUIRES="python3-h5py perl-Text-Soundex trfind HMMER ncbi-rmblastn" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/STAR/README b/academic/STAR/README index 7d410d628f..ae22618ac8 100644 --- a/academic/STAR/README +++ b/academic/STAR/README @@ -2,9 +2,20 @@ STAR aligns short and long RNA-seq reads to a reference genome using uncompressed suffix arrays, resulting in fast, accurate mapping. STAR is capable of unbiased de novo detection of canonical splice junctions, can discover non-canonical splices and chimeric (fusion) -transcripts and can map full-length RNA sequences. Comes with -STARsolo for: mapping, demultiplexing and gene quantification for +transcripts and can map full-length RNA sequences. Comes with +STARsolo for: mapping, demultiplexing and gene quantification for single cell RNA-seq (See STARmanual). +The make command for building the program assumes that the cpu is +supporting AVX extensions, included in intel processors since Sandy +Bridge (2008) and in AMD cpus since Bulldozer (2011). See the +Slackbuild if other processors can be supported. Reference: https://www.ncbi.nlm.nih.gov/pubmed/23104886 + + +LIMITATIONS +This release was tested with the default parameters for human and +mouse genomes. Mammal genomes require at least 16GB of RAM, ideally +32GB. Please contact the author for a list of recommended parameters +for much larger or much smaller genomes. diff --git a/academic/STAR/STAR.SlackBuild b/academic/STAR/STAR.SlackBuild index 0e9417d8bf..bc4913730e 100644 --- a/academic/STAR/STAR.SlackBuild +++ b/academic/STAR/STAR.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for STAR -# Copyright 2018-2019 Rob van Nues +# Copyright 2018-2023 Rob van Nues <sborg63@disroot.org> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,22 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=STAR -VERSION=${VERSION:-2.7.3a} +VERSION=${VERSION:-2.7.11b} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +# This script is set for processors that support "Advanced Vector Extensions", +# (AVX), included since 2008 in Intel processors (Sandy Bridge) and since 2011 +# in AMD cpus (Bulldozer). AVX is an implementation of "Single Instruction +# stream-Multiple Data streams" (SIMD) to process vector type data. +# If no AVX (`cat /proc/cpuinfo | grep 'avx'`) is present, specify the +# available SIMD architecture (https://en.wikichip.org/wiki/x86/extensions), +# e.g. with "Streaming SIMD Extensions" use 'sse', and uncomment the next line. +#SIMD=${SIMD:-sse}; echo "Using ${SIMD} as SIMD" if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +47,11 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -45,7 +61,7 @@ if [ "$ARCH" = "x86_64" ]; then LIBDIRSUFFIX="64" else echo "Sorry, this program does not run/compile on your architecture ($ARCH)" - exit 1 + exit 0 fi set -e @@ -73,16 +89,23 @@ find -L . \ # https://github.com/alexdobin/STAR/issues/447 #so let's forget about this for now +#For processors that do not support AVX extensions, specify the target SIMD architecture +#make STAR CXXFLAGS_SIMD=sse cd source - - make ${PRGNAM} CFLAGS="$SLKCFLAGS" CXXFLAGSextra="$SLKCFLAGS" + if [ ! -z "${SIMD}" ]; then + echo "make with CXXFLAG_SIMD=${SIMD}" + make ${PRGNAM} CFLAGS="$SLKCFLAGS" CXXFLAGSextra="$SLKCFLAGS" CXXFLAGS_SIMD="$SIMD" + else + echo "default make" + make ${PRGNAM} CFLAGS="$SLKCFLAGS" CXXFLAGSextra="$SLKCFLAGS" + fi mkdir -p $PKG/usr/bin install -Dm755 $PRGNAM "$PKG/usr/bin/${PRGNAM}" - make clean - make ${PRGNAM}long CXXFLAGSextra="$CXXFLAGS" - install -Dm755 ${PRGNAM}long "$PKG/usr/bin/${PRGNAM}long" + #make clean + #make ${PRGNAM}long CXXFLAGSextra="$CXXFLAGS" + #install -Dm755 ${PRGNAM}long "$PKG/usr/bin/${PRGNAM}long" cd .. @@ -94,9 +117,10 @@ cp -a \ source/parametersDefault doc/${PRGNAM}manual.pdf CHANGES.md LICENSE README.md RELEASEnotes.md \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +chmod 644 $PKG/usr/doc/$PRGNAM-$VERSION/parametersDefault mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/STAR/STAR.info b/academic/STAR/STAR.info index 2257366358..6c9a4bff5e 100644 --- a/academic/STAR/STAR.info +++ b/academic/STAR/STAR.info @@ -1,10 +1,10 @@ PRGNAM="STAR" -VERSION="2.7.3a" +VERSION="2.7.11b" HOMEPAGE="https://github.com/alexdobin/STAR" DOWNLOAD="UNSUPPORTED" MD5SUM="" -DOWNLOAD_x86_64="https://github.com/alexdobin/STAR/archive/2.7.3a/STAR-2.7.3a.tar.gz" -MD5SUM_x86_64="6642ef8b8404d923fefe7c72348f12f4" +DOWNLOAD_x86_64="https://github.com/alexdobin/STAR/archive/2.7.11b/STAR-2.7.11b.tar.gz" +MD5SUM_x86_64="9e21d9930989b1be3ffc50b818489d55" REQUIRES="" MAINTAINER="Rob van Nues" EMAIL="sborg63@disroot.org" diff --git a/academic/SU2/README b/academic/SU2/README index fd4519ee57..b70ea47277 100644 --- a/academic/SU2/README +++ b/academic/SU2/README @@ -8,12 +8,26 @@ flow, elasticity, electrodynamics, chemically-reacting flows, and many others. Under active development by individuals all around the world on GitHub and is released under an open-source license. -Builds parallel version by default. -For serial version, delete the following configuration lines from -su2.Slackbuild script: +Optional dependencies: mpich or openmpi; OpenBLAS ---enable-mpi ---with-cxx=/usr/bin/mpicxx ---with-cc=/usr/bin/mpicc +Build options can be controlled by passing MESONOPTS to the SlackBuild +script. -and then no need for mpich / openmpi. +Builds parallel version by default if mpich or openmpi installed. If +mpich, use: + +MESONOPTS="-Dcustom-mpi=true -Dextra-deps=mpich" + +For OpenBlas, add "-Denable-openblas=true" + +See the docs for a complete list of options. + +Following installation, add these to your ~/.bashrc: + +export SU2_RUN=/usr/bin +export PATH=$PATH:$SU2_RUN +export PYTHONPATH=$PYTHONPATH:$SU2_RUN + +Warning: This SlackBuild requires network access when it runs, meaning +it downloads files from the Internet with root access. You should +decide for yourself whether or not you think this is a good idea. diff --git a/academic/SU2/SU2.SlackBuild b/academic/SU2/SU2.SlackBuild index a32beff5c2..60fe3cd784 100644 --- a/academic/SU2/SU2.SlackBuild +++ b/academic/SU2/SU2.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for SU2 # -# Copyright 2019 Judah Milgram, Washington DC USA +# Copyright 2019-2023 Judah Milgram, Washington DC USA # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,11 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) PRGNAM=SU2 -VERSION=${VERSION:-6.2.0} +VERSION=${VERSION:-7.5.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -36,7 +38,11 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -70,33 +76,22 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -./bootstrap - -# For serial version, delete --enable-mpi, --with-cxx, and --with-cc +CXXFLAGS="-march=native -funroll-loops -O2" \ + ./meson.py build --prefix=/usr ${MESONOPTS} -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ -./configure \ - --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ - --sysconfdir=/etc \ - --localstatedir=/var \ - --mandir=/usr/man \ - --docdir=/usr/doc/$PRGNAM-$VERSION \ - --build=$ARCH-slackware-linux \ - --enable-mpi \ - --with-cxx=/usr/bin/mpicxx \ - --with-cc=/usr/bin/mpicc +# This fix build on current +sed -i '/#pragma once/a #include <cstdint>' SU2_CFD/include/output/filewriter/CParaviewXMLFileWriter.hpp -make -make install-strip DESTDIR=$PKG +DESTDIR=$PKG ./ninja -C build install -find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ - | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true +find $PKG -print0 | xargs -0 file | \ + grep -e "executable" -e "shared object" | \ + grep ELF | cut -f 1 -d : | \ + xargs strip --strip-unneeded 2> /dev/null || true mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ -COPYING INSTALL README.md \ +AUTHORS.md COPYING LICENSE.md README.md \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild @@ -104,4 +99,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/SU2/SU2.info b/academic/SU2/SU2.info index a7fb802ad1..6350ae105f 100644 --- a/academic/SU2/SU2.info +++ b/academic/SU2/SU2.info @@ -1,10 +1,10 @@ PRGNAM="SU2" -VERSION="6.2.0" +VERSION="7.5.1" HOMEPAGE="https://su2code.github.io/docs/home/" -DOWNLOAD="https://github.com/su2code/SU2/archive/v6.2.0/SU2-6.2.0.tar.gz" -MD5SUM="c74d1dbe52d6239c4f9c75cbd3102a90" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="mpich" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="https://github.com/su2code/SU2/archive/v7.5.1/SU2-7.5.1.tar.gz" +MD5SUM_x86_64="7a9696af3496079dd5df501620e477cb" +REQUIRES="" MAINTAINER="Judah Milgram" -EMAIL="milgram@cgpp.com" +EMAIL="milgram / cgpp / com" diff --git a/academic/SU2/slack-desc b/academic/SU2/slack-desc index 67f9c3b830..cbc26417e8 100644 --- a/academic/SU2/slack-desc +++ b/academic/SU2/slack-desc @@ -16,4 +16,4 @@ SU2: flow, elasticity, electrodynamics, chemically-reacting flows, and many SU2: others. Under active development by individuals all around the world SU2: on GitHub and is released under an open-source license. SU2: -SU2: Home page: https://su2code.github.io/docs/home/ +SU2: Home page: https://su2code.github.io diff --git a/academic/SeqMonk/README b/academic/SeqMonk/README new file mode 100644 index 0000000000..cd6c3a9021 --- /dev/null +++ b/academic/SeqMonk/README @@ -0,0 +1,17 @@ +SeqMonk - A Mapped Sequence Analysis tool +----------------------------------------- + +SeqMonk is a tool for viewing and analysing mapped sequence data. It +was initially written to cope with remapping experiment data from +next generation sequencers, but could be applied to any dataset +consisting of a series of mapped genomic regions. The program allows +you to visualise the positions of your mapped regions against an +annotated genome and to quantify the data in order to make comparisons +between data sets. + +If you have any comments about SeqMonk the authors would like to hear +them. You either enter them in the bug tracking system at: + +https://github.com/s-andrews/seqmonk/issues/ + +NOTE: this comes with its own JAVA environment. diff --git a/academic/SeqMonk/SeqMonk.SlackBuild b/academic/SeqMonk/SeqMonk.SlackBuild new file mode 100644 index 0000000000..b60bcfaf2e --- /dev/null +++ b/academic/SeqMonk/SeqMonk.SlackBuild @@ -0,0 +1,127 @@ +#!/bin/bash + +# Slackware build script for SeqMonk + +# Copyright 2020-2022 Petar Petrov slackalaxy@gmail.com +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=SeqMonk +VERSION=${VERSION:-1.48.1} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +EXENAM=seqmonk +TARNAM=${EXENAM}_v${VERSION}_linux64 + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +if [ "$ARCH" != "x86_64" ]; then + printf "\n\n$ARCH is not supported... \n" + exit 1 +fi + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM +tar xvf $CWD/$TARNAM.tar.gz +cd $PRGNAM +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +# Make sure SeqMonk finds its own java environment +sed -i 's:java -version:$RealBin/jre/bin/java -version:' seqmonk + +# Change icon path and category in the desktop file +sed -i "s:/usr/local/SeqMonk/uk/ac/bbsrc/babraham/SeqMonk/Resources/monk.svg:$EXENAM:" $EXENAM.desktop +sed -i "s:Categories=Application:Categories=Education:" $EXENAM.desktop +sed -i '/Encoding=UTF-8/d' $EXENAM.desktop + +mkdir -p $PKG/opt/$PRGNAM +cp -a \ + com edu Help jre net Scripts Templates uk *.jar seqmonk seqmonk_import \ + $PKG/opt/$PRGNAM + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + LICENSE LICENSE.txt NOTICE_FOR_COMMONS_MATH_CODE.txt README.md README.txt RELEASE_NOTES.txt \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/usr/share/{applications,pixmaps} +cp -a uk/ac/babraham/SeqMonk/Resources/monk_logo.png $PKG/usr/share/pixmaps/$EXENAM.png +cp -a $EXENAM.desktop $PKG/usr/share/applications + +# Leave the program in /opt and create a symlink to it +mkdir -p $PKG/usr/bin +cd $PKG/usr/bin +ln -s ../../opt/$PRGNAM/$EXENAM . +cd - + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/SeqMonk/SeqMonk.info b/academic/SeqMonk/SeqMonk.info new file mode 100644 index 0000000000..96c43dcda5 --- /dev/null +++ b/academic/SeqMonk/SeqMonk.info @@ -0,0 +1,10 @@ +PRGNAM="SeqMonk" +VERSION="1.48.1" +HOMEPAGE="https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/seqmonk_v1.48.1_linux64.tar.gz" +MD5SUM_x86_64="6f2e51bf589682e35fedfcf0fdb2667b" +REQUIRES="R" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/SeqMonk/doinst.sh b/academic/SeqMonk/doinst.sh new file mode 100644 index 0000000000..5fb28930db --- /dev/null +++ b/academic/SeqMonk/doinst.sh @@ -0,0 +1,3 @@ +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 +fi diff --git a/academic/SeqMonk/slack-desc b/academic/SeqMonk/slack-desc new file mode 100644 index 0000000000..632f4c5de1 --- /dev/null +++ b/academic/SeqMonk/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +SeqMonk: SeqMonk (A Mapped Sequence Analysis tool) +SeqMonk: +SeqMonk: SeqMonk is a tool for viewing and analysing mapped sequence data. +SeqMonk: It was initially written to cope with remapping experiment data +SeqMonk: from next generation sequencers, but could be applied to any +SeqMonk: dataset consisting of a series of mapped genomic regions. The +SeqMonk: program allows you to visualise the positions of your mapped +SeqMonk: regions against an annotated genome and to quantify the data in +SeqMonk: order to make comparisons between data sets. +SeqMonk: +SeqMonk: https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/ diff --git a/academic/Shark/Shark.SlackBuild b/academic/Shark/Shark.SlackBuild index e8faee8c7f..4410930928 100644 --- a/academic/Shark/Shark.SlackBuild +++ b/academic/Shark/Shark.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # SlackBuild script for Shark -# Copyright 2018-2019 Benjamin Trigona-Harany <slackbuilds@jaxartes.net> +# Copyright 2018-2021 Benjamin Trigona-Harany <slackbuilds@jaxartes.net> # All rights reserved. # # Redistribution and use in source and binary forms, with or without @@ -24,10 +24,13 @@ # (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=Shark -VERSION=${VERSION:-4.0.0} +VERSION=${VERSION:-4.0.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -37,7 +40,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -99,4 +109,4 @@ mkdir $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/Shark/Shark.info b/academic/Shark/Shark.info index cae38a7659..0f5ef4ed9e 100644 --- a/academic/Shark/Shark.info +++ b/academic/Shark/Shark.info @@ -1,8 +1,8 @@ PRGNAM="Shark" -VERSION="4.0.0" +VERSION="4.0.1" HOMEPAGE="http://image.diku.dk/shark" -DOWNLOAD="https://github.com/Shark-ML/Shark/archive/v4.0.0/Shark-4.0.0.tar.gz" -MD5SUM="a1c240bdbc0e4ad8ed09a855cc8e0444" +DOWNLOAD="https://github.com/Shark-ML/Shark/archive/v4.0.1/Shark-4.0.1.tar.gz" +MD5SUM="8278dd9444e0f48e661344eebc896990" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/SimEng/README b/academic/SimEng/README new file mode 100644 index 0000000000..acc2230a48 --- /dev/null +++ b/academic/SimEng/README @@ -0,0 +1,28 @@ + SimEng is a framework for building modern, cycle-accurate processor +simulators. Its goals are to be: + + - Fast, typically 4-5X faster than gem5 + - Easy to use and modify to model desired microarchitecture + configurations. New cores can be configured in just a few hours + - Scalable, from simple scalar microarchitectures up to the most + sophisticated, superscalar, out-of-order designs + - Capable of supporting a wide range of instruction set + architectures (ISAs), starting with Armv8 but eventually including + RISC-V, x86, POWER, etc. + - Accurate, aiming for simulated cycle times being within 5-10% of + real hardware + - Open source, with a permissive license to enable collaboration + across academia and industry + + SimEng places an emphasis on performance and ease of use, whilst +maintaining a clean, modern, simple and well-documented code base. +For example, the current out-of-order (OoO) model is implemented +in around 10,000 lines of simple C++, with another 9,000 lines or +so implementing the specifics of the Armv8 ISA, and around 13,000 +lines of code in the accompanying test suite. SimEng should be +simple to read and understand, making it ideal to modify to your +requirements and include it in your projects. + + + Invocation example: + # simeng /usr/share/SimEng-0.9.4/configs/a64fx.yaml diff --git a/academic/SimEng/SimEng.SlackBuild b/academic/SimEng/SimEng.SlackBuild new file mode 100644 index 0000000000..fc7a9d8832 --- /dev/null +++ b/academic/SimEng/SimEng.SlackBuild @@ -0,0 +1,142 @@ +#!/bin/bash + +# Slackware build script for SimEng + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=SimEng +VERSION=${VERSION:-0.9.4} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +YAMLCPP_VERSION=yaml-cpp-0.7.0 + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +# fix library installation path +sed -i '55s#DESTINATION lib#&'${LIBDIRSUFFIX}'/'$PRGNAM'#' src/lib/CMakeLists.txt +sed -i '72s#lib#&'${LIBDIRSUFFIX}'/'$PRGNAM'#' CMakeLists.txt + + +mkdir -p build +cd build + +# unpack dependences +mkdir -p _deps/{capstone-lib,yaml-cpp}-src +tar xvf $CWD/capstone-Armv9.2-update.tar.gz -C _deps/capstone-lib-src --strip-components 1 +tar xvf $CWD/yaml-cpp-$YAMLCPP_VERSION.tar.gz -C _deps/yaml-cpp-src --strip-components 1 + + cmake \ + -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DCMAKE_INSTALL_LIBDIR=lib${LIBDIRSUFFIX} \ + -DCMAKE_INSTALL_MANDIR=/usr/man \ + -DCMAKE_INSTALL_DOCDIR=/usr/doc/$PRGNAM-$VERSION \ + -DCMAKE_INSTALL_DATAROOTDIR=/usr \ + -DBUILD_SHARED_LIBS=ON \ + -DFETCHCONTENT_FULLY_DISCONNECTED=ON \ + $OPTS \ + -DCMAKE_BUILD_TYPE=Release .. + make + make install/strip DESTDIR=$PKG +cd .. + +# install libraries used by SimEng +cp -av build/_deps/yaml-cpp-build/libyaml-cpp.so* \ + build/_deps/capstone-lib-build/libcapstone.so* \ + $PKG/usr/lib${LIBDIRSUFFIX}/$PRGNAM + +# install additional files +mkdir -p $PKG/usr/share/$PRGNAM-$VERSION +cp -a configs $PKG/usr/share/$PRGNAM-$VERSION + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + {CONTRIBUTORS,LICENSE,RELEASE-NOTES}.txt docs \ + LICENSE_{CAPSTONE,GTEST,LLVM,YAML-CPP}.txt \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/SimEng/SimEng.info b/academic/SimEng/SimEng.info new file mode 100644 index 0000000000..6b132fdca2 --- /dev/null +++ b/academic/SimEng/SimEng.info @@ -0,0 +1,14 @@ +PRGNAM="SimEng" +VERSION="0.9.4" +HOMEPAGE="https://uob-hpc.github.io/SimEng" +DOWNLOAD="https://github.com/UoB-HPC/SimEng/archive/0.9.4/SimEng-0.9.4.tar.gz \ + https://github.com/UoB-HPC/capstone/archive/Armv9.2-update/capstone-Armv9.2-update.tar.gz \ + https://github.com/jbeder/yaml-cpp/archive/yaml-cpp-0.7.0/yaml-cpp-yaml-cpp-0.7.0.tar.gz" +MD5SUM="2f249f7b38cc716cb13f1a5b41555b92 \ + c837da9aad754299d9ee62007f428e76 \ + 74d646a3cc1b5d519829441db96744f0" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/SimEng/slack-desc b/academic/SimEng/slack-desc new file mode 100644 index 0000000000..0c74a32504 --- /dev/null +++ b/academic/SimEng/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +SimEng: SimEng (framework for cycle-accurate processor simulator) +SimEng: +SimEng: The Simulation Engine (SimEng) is a framework for building modern +SimEng: cycle-accurate processor simulators. It aims to be: +SimEng: - Fast +SimEng: - Easy to use and modify to desired configurations +SimEng: - Scalable, supporting simulation of simple scalar cores, up to +SimEng: superscalar out-of-order designs +SimEng: - Capable of supporting a wide range of ISAs. +SimEng: - Open source, with a permissive license to enable collaboration +SimEng: across academia and industry diff --git a/academic/TreeGraph/TreeGraph.SlackBuild b/academic/TreeGraph/TreeGraph.SlackBuild index 1deeb4c780..f80eaedf9d 100644 --- a/academic/TreeGraph/TreeGraph.SlackBuild +++ b/academic/TreeGraph/TreeGraph.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for TreeGraph -# Copyright 2018-2020 Petar Petrov slackalaxy@gmail.com +# Copyright 2018-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,15 +22,25 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=TreeGraph VERSION=${VERSION:-2.15.0_887_beta} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} ZIPVER=2.15.0-887_beta ARCH=noarch -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -77,4 +87,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/TreeGraph/TreeGraph.info b/academic/TreeGraph/TreeGraph.info index 05ab5af79b..9adcb3a231 100644 --- a/academic/TreeGraph/TreeGraph.info +++ b/academic/TreeGraph/TreeGraph.info @@ -5,6 +5,6 @@ DOWNLOAD="http://treegraph.bioinfweb.info/Download/Complete/TreeGraph_2.15.0-887 MD5SUM="4ca90fbb7cb7aae9a37d99ac742bd22f" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="jdk" +REQUIRES="zulu-openjdk11" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/ViennaRNA/README b/academic/ViennaRNA/README index 6ad531d628..4807f340a8 100644 --- a/academic/ViennaRNA/README +++ b/academic/ViennaRNA/README @@ -3,12 +3,22 @@ A C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures. +A recent addition, RNAxplorer, requires lapacke (which requires +lapack that depends on a version of blas). During configuration the +step for RNAxplorer stalls (on missing lapack) because it does not +find the version of blas that has been used for compiling lapack +(see https://github.com/ViennaRNA/ViennaRNA/issues/206). +An extra variable ($BLAS) in the SlackBuild sets openblas as the +version of blas used for lapack(e). Please, adjust $BLAS to the blas +used on your system. + A tutorial (see /usr/doc/$PRGNAM-$VERSION/RNA-tutorial-$VERSION.pdf) and examples can be found in /usr/share/$PRGNAM/tutorial and /usr/share/$PRGNAM/examples -For those who wish to link the Vienna package to their own C, perl or python programs (see below), -the RNAlib Reference Manual can be assessed at: +For those who wish to link the Vienna package to their own C, perl +or python programs (see below), the RNAlib Reference Manual can be +assessed at: https://www.tbi.univie.ac.at/RNA/ViennaRNA/doc/html/index.html (or unpacked from the src: $PRGNAM-$VERSION/doc/html/) @@ -22,30 +32,17 @@ Amongst other things, the ViennRNA implementations allow you to: - compute various equilibrium probabilities - calculate suboptimal structures in a given energy range - compute local structures in long sequences -- predict consensus secondary structures from a multiple sequence alignment +- predict consensus secondary structures from a multiple sequence + alignment - predict melting curves - search for sequences folding into a given structure -- compare two secondary structures +- compare two secondary structures - predict hybridization structures of two RNA molecules -The package includes `Perl 5` and `Python 3` modules that give -access to almost all functions of the C library from within the respective -scripting languages. For this reason, python3 is a dependency - -The `Python 2` module can be built as well, or instead of the one for `Python 3`; -just edit the SlackBuild or run it by setting build options PYTHON=yes PYTHON3=no. -(e.g. in sbopkg or run it from the commandline -within the directory containing -the SlackBuild script and downloaded source archive- as: -`PYTHON=yes PYTHON3=no ./ViennaRNA.SlackBuild`) - -There is also a set of programs for analyzing sequence and distance -data using split decomposition, statistical geometry, and cluster methods. -They are not maintained any more and not built by default. - -The code very rarely uses static arrays, and all programs should work for -sequences up to a length of 32,700 (if you have huge amounts of memory that -is). +The package includes `Perl` and `Python 3` modules that give access +to almost all functions of the C library from within the respective +scripting languages. -For further info see: +For further/most recent info see: https://www.tbi.univie.ac.at/RNA/documentation.html diff --git a/academic/ViennaRNA/ViennaRNA.SlackBuild b/academic/ViennaRNA/ViennaRNA.SlackBuild index ff63062efc..42ae76bbd7 100644 --- a/academic/ViennaRNA/ViennaRNA.SlackBuild +++ b/academic/ViennaRNA/ViennaRNA.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for ViennaRNA -# Copyright 2018 Rob van Nues +# Copyright 2018-2023 Rob van Nues # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,19 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=ViennaRNA -VERSION=${VERSION:-2.4.14} +VERSION=${VERSION:-2.6.4} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +# RNAxplorer requires lapacke (which requires lapack that requires blas) +# but cannot see what blas is used for compiling lapack +# please adjust $BLAS to the blas installed on your system +BLAS=${BLAS:-openblas} + if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +44,11 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -82,8 +95,7 @@ find -L . \ # - RNAlocmin # - Swig (all scripting interfaces) # - Perl interface -# - Python interface -# - Python 3 interface +# - Python 3 interface (= Python interface) # - Streaming SIMD Extension support # in the case of run time/ make/ or configure problems try turning off: # - Link Time Optimization (LTO) @@ -94,25 +106,24 @@ find -L . \ # for Z-score filtering via statically linked libsvm: # - SVM Z-score filter in RNALfold # - GNU Scientific Library for RNApvmin - -cluster="" ; [ "${CLUSTER:-yes}" != "no" ] && cluster="--with-cluster" -kinwalker="" ; [ "${KINWALKER:-yes}" != "no" ] && kinwalker="--with-kinwalker" +# everything is enabled here +cluster="" ; [ "${CLUSTER:-yes}" != "no" ] && cluster="--with-cluster" +kinwalker="" ; [ "${KINWALKER:-yes}" != "no" ] && kinwalker="--with-kinwalker" # Default enabled features: -forester="" ; [ "${FORESTER:-yes}" != "yes" ] && forester="--without-forester" -kinfold="" ; [ "${KINFOLD:-yes}" != "yes" ] && kinwalk="--without-kinfold" -rnalocmin="" ; [ "${RNALOCMIN:-yes}" != "yes" ] && rnalocmin="--without-rnalocmin" -perl="" ; [ "${PERL:-yes}" != "yes" ] && perl="--without-perl" - -python3="" ; [ "${PYTHON3:-yes}" != "yes" ] && python3="--without-python3" -swig="" ; [ "${SWIG:-yes}" != "yes" ] && swig="--without-swig" -simd="" ; [ "${SIMD:-yes}" != "yes" ] && simd="--disable-simd" -lto="" ; [ "${LTO:-yes}" != "yes" ] && lto="--disable-lto" -openmp="" ; [ "${OPENMP:-yes}" != "yes" ] && openmp="--disable-openmp" -pthreads="" ; [ "${PTHREADS:-yes}" != "yes" ] && pthreads="--disable-pthreads" -svm="" ; [ "${SVM:-yes}" != "yes" ] && svm="--without-svm" -gsl="" ; [ "${GSL:-yes}" != "yes" ] && gsl="--without-gsl" -# Default to python3 (above) only; -python="" ; [ "${PYTHON:-no}" != "yes" ] && python="--without-python" +forester="" ; [ "${FORESTER:-yes}" != "no" ] && forester="--with-forester" +kinfold="" ; [ "${KINFOLD:-yes}" != "no" ] && kinfold="--with-kinfold" +rnalocmin="" ; [ "${RNALOCMIN:-yes}" != "no" ] && rnalocmin="--with-rnalocmin" +perl="" ; [ "${PERL:-yes}" != "no" ] && perl="--with-perl" +# python = python3 +python="" ; [ "${PYTHON:-yes}" != "no" ] && python="--with-python" +swig="" ; [ "${SWIG:-yes}" != "no" ] && swig="--with-swig" +simd="" ; [ "${SIMD:-yes}" != "no" ] && simd="--enable-simd" +lto="" ; [ "${LTO:-yes}" != "no" ] && lto="--enable-lto" +openmp="" ; [ "${OPENMP:-yes}" != "no" ] && openmp="--enable-openmp" +pthreads="" ; [ "${PTHREADS:-yes}" != "no" ] && pthreads="--enable-pthreads" +svm="" ; [ "${SVM:-yes}" != "no" ] && svm="--with-svm" +gsl="" ; [ "${GSL:-yes}" != "no" ] && gsl="--with-gsl" +json="" ; [ "${JSON:-yes}" != "no" ] && json="--with-json" CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ @@ -122,6 +133,9 @@ CXXFLAGS="$SLKCFLAGS" \ --mandir=/usr/man \ --docdir=/usr/doc/$PRGNAM-$VERSION \ --build=$ARCH-slackware-linux \ + --with-blas=$BLAS \ + --with-python2=no \ + --with-doc=no \ $cluster \ $kinwalker \ $forester \ @@ -129,14 +143,15 @@ CXXFLAGS="$SLKCFLAGS" \ $rnalocmin \ $perl \ $python \ - $python3 \ $swig \ $simd \ $lto \ $openmp \ $pthreads \ $svm \ - $gsl || exit 1 + $gsl \ + $json \ + || exit 1 make make install DESTDIR=$PKG @@ -155,11 +170,13 @@ for perlscript in $PKG/usr/share/ViennaRNA/bin/*.pl ; do done rm -r $PKG/usr/share/ViennaRNA/bin -# no need for that file it is outdated anyway +# re-organise info files the Slackware/SBo way +mkdir $PKG/usr/info/ rm $PKG/usr/share/info/dir - -#gzip info file -gzip -9 $PKG/usr/share/info/*.info +#gzip and move info file +gzip -9 $PKG/usr/share/info/*.info* +mv $PKG/usr/share/info/*.info* $PKG/usr/info/ +rmdir $PKG/usr/share/info find $PKG/usr/man -type f -exec gzip -9 {} \; for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done @@ -181,12 +198,16 @@ if [[ -e $PKG/usr/doc/$PRGNAM-$VERSION/RNAlib-$VERSION.pdf ]]; then fi cp -a \ - NEWS README.md AUTHORS COPYING THANKS INSTALL CHANGELOG.md license.txt \ + NEWS README.md AUTHORS COPYING THANKS CHANGELOG.md license.txt \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh +cat $CWD/douninst.sh > $PKG/install/douninst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/ViennaRNA/ViennaRNA.info b/academic/ViennaRNA/ViennaRNA.info index 06e2675530..b871a31ccc 100644 --- a/academic/ViennaRNA/ViennaRNA.info +++ b/academic/ViennaRNA/ViennaRNA.info @@ -1,10 +1,10 @@ PRGNAM="ViennaRNA" -VERSION="2.4.14" +VERSION="2.6.4" HOMEPAGE="https://www.tbi.univie.ac.at/RNA" -DOWNLOAD="https://github.com/ViennaRNA/ViennaRNA/releases/download/v2.4.14/ViennaRNA-2.4.14.tar.gz" -MD5SUM="b9c64be709d3dfef72cc27e615845a04" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="python3 gri" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_6_x/ViennaRNA-2.6.4.tar.gz" +MD5SUM_x86_64="6d8fd8ffe44d70399bff220f709a2b55" +REQUIRES="lapacke" MAINTAINER="Rob van Nues" EMAIL="sborg63@disroot.org" diff --git a/academic/ViennaRNA/doinst.sh b/academic/ViennaRNA/doinst.sh new file mode 100644 index 0000000000..fe39c0a9d2 --- /dev/null +++ b/academic/ViennaRNA/doinst.sh @@ -0,0 +1,4 @@ +if [ -x /usr/bin/install-info ]; then + /usr/bin/install-info --info-dir=usr/info usr/info/RNAlib.info.gz 1> /dev/null 2>&1 +fi + diff --git a/academic/ViennaRNA/douninst.sh b/academic/ViennaRNA/douninst.sh new file mode 100644 index 0000000000..1bef502028 --- /dev/null +++ b/academic/ViennaRNA/douninst.sh @@ -0,0 +1,6 @@ +if [ -x /usr/bin/install-info -a -d usr/info ]; then + ( cd usr/info + rm -f dir + for i in *.info*; do /usr/bin/install-info $i dir 2>/dev/null; done + ) +fi diff --git a/academic/WEVOTE/WEVOTE.SlackBuild b/academic/WEVOTE/WEVOTE.SlackBuild index c9090df979..54b285e704 100644 --- a/academic/WEVOTE/WEVOTE.SlackBuild +++ b/academic/WEVOTE/WEVOTE.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for WEVOTE -# Copyright 2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2018-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,11 +22,14 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=WEVOTE VERSION=${VERSION:-1.8.0} # The version number is found in "install.sh" COMMIT=645523db5aba843b2681e83146783b18e92866b1 BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -36,7 +39,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -102,4 +112,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/WolframEngine/README b/academic/WolframEngine/README new file mode 100644 index 0000000000..d3830009fb --- /dev/null +++ b/academic/WolframEngine/README @@ -0,0 +1,10 @@ +The free Wolfram Engine implements the Wolfram Language with interfaces +suitable for use in software projects. The Wolfram Engine is the heart +of Wolfram products such as Mathematica, Wolfram|One and Wolfram|Alpha. +It is licensed for non-production use. + +The Wolfram Engine and Mathematica are the same core engine, but with a +different interface and different licensing. + +The Wolfram Engine contains a program WolframScript for running the +Wolfram Engine from a command line or script. diff --git a/academic/WolframEngine/WolframEngine.SlackBuild b/academic/WolframEngine/WolframEngine.SlackBuild new file mode 100644 index 0000000000..36198ffaa4 --- /dev/null +++ b/academic/WolframEngine/WolframEngine.SlackBuild @@ -0,0 +1,136 @@ +#!/bin/bash + +# Slackware build script for WolframEngine + +# Copyright 2023-2024, Alexander Verbovetsky, Moscow, Russia +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=WolframEngine +VERSION=${VERSION:-14.0.0} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + ARCH="$( uname -m )" +fi + +if [ "$ARCH" != "x86_64" ]; then + echo "Only x86_64 is supported." + exit 1 +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +mkdir $PRGNAM-$VERSION +cd $PRGNAM-$VERSION + +SCRIPT=$(find -L $CWD -maxdepth 1 -type f -exec grep -al \ +"label=\"Wolfram Engine ${VERSION} for LINUX Installer Archive\"" {} \;) +eval $(grep -a "^filesizes=" -m 1 $SCRIPT) +eval $(grep -a "^MD5=" $SCRIPT) +ssize=$(grep -a offset -m 1 $SCRIPT | sed 's/^.* \([0-9]\+\) .*$/\1/') +((ssize++)) +tail +$ssize $SCRIPT | head -c $filesizes | tee >(tar x) \ + | md5sum | grep $MD5 > /dev/null +MDIR="/opt/$PRGNAM" +mkdir -p $PKG$MDIR +find -L Unix/Files -maxdepth 2 -type f -name "contents.tar.?z" \ + -exec tar xvf '{}' -C $PKG$MDIR \; + +chown -R root:root $PKG$MDIR +find -L $PKG$MDIR \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +mkdir -p $PKG/usr/bin +for i in $(find -L $PKG$MDIR/Executables \ + -maxdepth 1 -type f -printf "%f\n"); do + ln -s $MDIR/Executables/${i} $PKG/usr/bin +done +ln -s $MDIR/SystemFiles/Kernel/Binaries/Linux-x86-64/wolframscript \ + $PKG/usr/bin + +mkdir -p $PKG/usr/share/mime/application +cp -a $PKG$MDIR/SystemFiles/Installation/*.xml \ + $PKG/usr/share/mime/application + +mkdir -p $PKG/usr/share/icons/hicolor/{32x32,64x64,128x128}/{apps,mimetypes} +for i in 32 64 128; do +cp -a $PKG$MDIR/SystemFiles/FrontEnd/SystemResources/X/App-$i.png \ + $PKG/usr/share/icons/hicolor/${i}x${i}/apps/wolfram-wolframlanguage.png +for m in $(basename -a \ + $(ls $PKG$MDIR/SystemFiles/FrontEnd/SystemResources/X/vnd.wolfram.*${i}.png) \ + | cut -d- -f1); do +cp -a $PKG$MDIR/SystemFiles/FrontEnd/SystemResources/X/${m}-${i}.png \ + $PKG/usr/share/icons/hicolor/${i}x${i}/mimetypes/application-${m}.png +done +done + +find -L $PKG/opt/WolframEngine/SystemFiles -type f \ + \( -name "*.so" -o -name '*.so.*' \) -exec chmod 755 {} \; + +mkdir -p $PKG/usr/man/man1 +for i in $(find -L $PKG$MDIR/SystemFiles/SystemDocumentation/Unix \ + -maxdepth 1 -type f -name "*.1" -printf "%f\n"); do +gzip -9 -c $PKG$MDIR/SystemFiles/SystemDocumentation/Unix/${i} \ + > $PKG/usr/man/man1/${i}.gz +done + +INFO=$(find -L Unix/Files -maxdepth 2 -type f -name "info" -exec cat '{}' \+ \ + | sort -u) +CreationID=$(echo "$INFO" | grep "^CreationID" | awk '{print $2}') +VersionNumber=$(echo "$INFO" | grep "^VersionNumber" | awk '{print $2}') +ReleaseNumber=$(echo "$INFO" | grep "^ReleaseNumber" | awk '{print $2}') +MinorReleaseNumber=$(echo "$INFO" | grep "^MinorReleaseNumber" \ + | awk '{print $2}') +FullVersionNumber="${VersionNumber}.${ReleaseNumber}.${MinorReleaseNumber}" + +echo "${CreationID}" > $PKG$MDIR/.CreationID +echo "FullVersionNumber: ${FullVersionNumber}" > $PKG$MDIR/.Revision +echo "CreationID: ${CreationID}" >> $PKG$MDIR/.Revision +echo "${FullVersionNumber}" > $PKG$MDIR/.VersionID + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/WolframEngine/WolframEngine.info b/academic/WolframEngine/WolframEngine.info new file mode 100644 index 0000000000..53c9e9da08 --- /dev/null +++ b/academic/WolframEngine/WolframEngine.info @@ -0,0 +1,10 @@ +PRGNAM="WolframEngine" +VERSION="14.0.0" +HOMEPAGE="https://www.wolfram.com/engine/" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="https://account.wolfram.com/dl/WolframEngine?platform=Linux&version=14.0" +MD5SUM_x86_64="42c9f852a1f6505429e5941e6c699d23" +REQUIRES="" +MAINTAINER="Alexander Verbovetsky" +EMAIL="alik@ejik.org" diff --git a/academic/WolframEngine/doinst.sh b/academic/WolframEngine/doinst.sh new file mode 100644 index 0000000000..1b37a9827f --- /dev/null +++ b/academic/WolframEngine/doinst.sh @@ -0,0 +1,9 @@ +if [ -x /usr/bin/update-mime-database ]; then + /usr/bin/update-mime-database usr/share/mime >/dev/null 2>&1 +fi + +if [ -e usr/share/icons/hicolor/icon-theme.cache ]; then + if [ -x /usr/bin/gtk-update-icon-cache ]; then + /usr/bin/gtk-update-icon-cache -f usr/share/icons/hicolor >/dev/null 2>&1 + fi +fi diff --git a/academic/WolframEngine/slack-desc b/academic/WolframEngine/slack-desc new file mode 100644 index 0000000000..f064200dd5 --- /dev/null +++ b/academic/WolframEngine/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +WolframEngine: WolframEngine (Wolfram Language Engine) +WolframEngine: +WolframEngine: The free Wolfram Engine implements the Wolfram Language with +WolframEngine: interfaces suitable for use in software projects. The Wolfram Engine +WolframEngine: is the heart of Wolfram products such as Mathematica, Wolfram|One +WolframEngine: and Wolfram|Alpha. It is licensed for non-production use. +WolframEngine: +WolframEngine: The Wolfram Engine contains a program WolframScript for running the +WolframEngine: Wolfram Engine from a command line or script. +WolframEngine: +WolframEngine: Homepage: https://www.wolfram.com/engine/ diff --git a/academic/WordNet/README b/academic/WordNet/README index ccebc68f64..836afa9950 100644 --- a/academic/WordNet/README +++ b/academic/WordNet/README @@ -1,8 +1,9 @@ -WordNet(r) is a large lexical database of English, developed under the -direction of George A. Miller. Nouns, verbs, adjectives and adverbs are -grouped into sets of cognitive synonyms (synsets), each expressing a -distinct concept. Synsets are interlinked by means of conceptual-semantic -and lexical relations. The resulting network of meaningfully related words -and concepts can be navigated with the browser. WordNet is also freely -and publicly available for download. WordNet's structure makes it a -useful tool for computational linguistics and natural language processing. +WordNet(r) is a large lexical database of English, developed under +the direction of George A. Miller. Nouns, verbs, adjectives and +adverbs are grouped into sets of cognitive synonyms (synsets), each +expressing a distinct concept. Synsets are interlinked by means of +conceptual-semantic and lexical relations. The resulting network of +meaningfully related words and concepts can be navigated with the +browser. WordNet is also freely and publicly available for download. +WordNet's structure makes it a useful tool for computational +linguistics and natural language processing. diff --git a/academic/WordNet/WordNet.SlackBuild b/academic/WordNet/WordNet.SlackBuild index 80105d9dfc..049ef6008c 100644 --- a/academic/WordNet/WordNet.SlackBuild +++ b/academic/WordNet/WordNet.SlackBuild @@ -1,30 +1,40 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for WordNet # Written by Michael Gabilondo <mgabilo{at}gmail{dot}com> # This work is in the public domain +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=WordNet VERSION=${VERSION:-3.0} BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -88,4 +98,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/Xyce/README b/academic/Xyce/README deleted file mode 100644 index ff16f7e41f..0000000000 --- a/academic/Xyce/README +++ /dev/null @@ -1,42 +0,0 @@ -Xyce is an open source, SPICE-compatible, high-performance analog -circuit simulator, capable of solving extremely large circuit problems -by supporting large-scale parallel computing platforms. It also supports -serial execution on all common desktop platforms, and small-scale parallel -runs on Unix-like systems. In addition to analog electronic simulation, -Xyce has also been used to investigate more general network systems, -such as neural networks and power grids. - -The Xyce Parallel Electronic Simulator is a SPICE-compatible circuit -simulator, developed internally at Sandia National Laboratories and funded -by the National Nuclear Security Administration's Advanced Simulation and -Computing (ASC) Campaign. In continuous development since 1999, Xyce is -designed to run on large-scale parallel computing platforms, though it -also executes efficiently on a variety of architectures, including single -processor workstations. As a mature platform for large-scale parallel -circuit simulation, Xyce supports standard capabilities available from -commercial simulators, in addition to a variety of devices and models -specific to Sandia's needs. - -The package is intalled at: /opt/Xyce -Remember to set the library and path: - -PATH=$PATH:/opt/Xyce/bin - -For 32-bit: -LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/Xyce/lib - -For 64-bit: -LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/Xyce/lib64 - -To run the suite test: -# cd /opt/Xyce/Xyce_Regression-6.3/TestScripts -# ./run_xyce_regression - -For parallel simulation trilinos must be compiled with MPI. - -Additonal requirements: - - MPI (openmpi/mpich) - - parMETIS - -NOTE: Sources are not downloadable via wget. Please download manually -via browser. diff --git a/academic/Xyce/Xyce.SlackBuild b/academic/Xyce/Xyce.SlackBuild deleted file mode 100644 index 1363d6baeb..0000000000 --- a/academic/Xyce/Xyce.SlackBuild +++ /dev/null @@ -1,121 +0,0 @@ -#!/bin/sh - -# Slackware build script for Xyce - -# Copyright 2015 William PC (Slack-it) - Seattle (USA) -# All rights reserved. -# -# Redistribution and use of this script, with or without modification, is -# permitted provided that the following conditions are met: -# -# 1. Redistributions of this script must retain the above copyright -# notice, this list of conditions and the following disclaimer. -# -# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED -# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF -# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO -# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, -# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, -# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; -# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, -# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR -# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF -# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - -PRGNAM=Xyce -VERSION=${VERSION:-6.5} -BUILD=${BUILD:-1} -TAG=${TAG:-_SBo} - -SRCNAM="$PRGNAM" - -if [ -z "$ARCH" ]; then - case "$( uname -m )" in - i?86) ARCH=i486 ;; - arm*) ARCH=arm ;; - *) ARCH=$( uname -m ) ;; - esac -fi - -CWD=$(pwd) -TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM -OUTPUT=${OUTPUT:-/tmp} - -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" - LIBDIRSUFFIX="" -elif [ "$ARCH" = "i686" ]; then - SLKCFLAGS="-O2 -march=i686 -mtune=i686" - LIBDIRSUFFIX="" -elif [ "$ARCH" = "x86_64" ]; then - SLKCFLAGS="-O2 -fPIC" - LIBDIRSUFFIX="64" -else - SLKCFLAGS="-O2" - LIBDIRSUFFIX="" -fi - -set -e - -rm -rf $PKG -mkdir -p $TMP $PKG $OUTPUT -cd $TMP -rm -rf $SRCNAM-$VERSION -tar xvf $CWD/$SRCNAM-$VERSION.tar.gz -tar xvf $CWD/$SRCNAM\_Docs-$VERSION.tar.gz -tar xvf $CWD/$SRCNAM\_Regression-$VERSION.tar.gz -for d in $SRCNAM-$VERSION $SRCNAM\_Docs-$VERSION $SRCNAM\_Regression-$VERSION ; do - chown -R root:root $d - find -L $d \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -done -cd $SRCNAM-$VERSION - -if [ "${NONFREE:-no}" == yes ]; then - COPT_DEPS="-DXyce_NONFREE_MODEL=ON" -else - COPT_DEPS="-DXyce_NONFREE_MODEL=OFF" -fi - -if [ "${PARALLEL:-no}" == yes ]; then - COPT_DEPS="$COPTS_DEPS -DXyce_PARALLEL_MPI=ON \ - -DLIB_MPI=/usr/lib${LIBDIRSUFFIX} -DINC_MPI=/usr/include" -else - COPT_DEPS="$COPTS_DEPS -DXyce_PARALLEL_MPI=OFF" -fi - -mkdir -p build -cd build - cmake \ - -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ - -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS -std=c++11 -DXyce_NOX_SIZETYPE" \ - -DCMAKE_INSTALL_PREFIX=/opt/$PRGNAM \ - $COPT_DEPS \ - -DXyce_ENABLE_SHARED=yes \ - -DCMAKE_BUILD_TYPE=Release .. - make - make install DESTDIR=$PKG -cd .. - -# Install the test suite manually -mv $TMP/$PRGNAM\_Regression-$VERSION \ - $PKG/opt/$PRGNAM - -find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ - | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true - -find $PKG -depth -type d -empty -delete || true - -mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a COPYING $TMP/${PRGNAM}_Docs-$VERSION/*.pdf $PKG/usr/doc/$PRGNAM-$VERSION -cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild - -mkdir -p $PKG/install -cat $CWD/slack-desc > $PKG/install/slack-desc - -cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} diff --git a/academic/Xyce/Xyce.info b/academic/Xyce/Xyce.info deleted file mode 100644 index 79667ceed8..0000000000 --- a/academic/Xyce/Xyce.info +++ /dev/null @@ -1,14 +0,0 @@ -PRGNAM="Xyce" -VERSION="6.5" -HOMEPAGE="https://xyce.sandia.gov/index.html" -DOWNLOAD="https://xyce.sandia.gov/downloads/_assets/documents/Xyce-6.5.tar.gz \ - https://xyce.sandia.gov/downloads/_assets/documents/Xyce_Docs-6.5.tar.gz \ - https://xyce.sandia.gov/downloads/_assets/documents/Xyce_Regression-6.5.tar.gz" -MD5SUM="916c70f4c387b14197d85178c5791ad5 \ - 5bd0f1696e7d6ad9a60cd4868e84fe37 \ - 1346f1fe6b273b8954df43ac0945b329" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="trilinos" -MAINTAINER="William PC" -EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/Xyce/slack-desc b/academic/Xyce/slack-desc deleted file mode 100644 index 56b4252044..0000000000 --- a/academic/Xyce/slack-desc +++ /dev/null @@ -1,19 +0,0 @@ -# HOW TO EDIT THIS FILE: -# The "handy ruler" below makes it easier to edit a package description. -# Line up the first '|' above the ':' following the base package name, and -# the '|' on the right side marks the last column you can put a character in. -# You must make exactly 11 lines for the formatting to be correct. It's also -# customary to leave one space after the ':' except on otherwise blank lines. - - |-----handy-ruler------------------------------------------------------| -Xyce: Xyce (Xyce Parallel Electronic Simulator) -Xyce: -Xyce: The Xyce Parallel Electronic Simulator is a SPICE-compatible circuit -Xyce: simulator, developed internally at Sandia National Laboratories and -Xyce: funded by the National Nuclear Security Administration's Advanced -Xyce: Simulation and Computing (ASC) Campaign. In continuous development -Xyce: since 1999, Xyce is designed to run on large-scale parallel computing -Xyce: platforms, though it also executes efficiently on a variety of xyce: -Xyce: architectures, including single processor workstations. -Xyce: -Xyce: diff --git a/academic/ZeGrapher/ZeGrapher.SlackBuild b/academic/ZeGrapher/ZeGrapher.SlackBuild index 2a79e3142e..05ccd50013 100644 --- a/academic/ZeGrapher/ZeGrapher.SlackBuild +++ b/academic/ZeGrapher/ZeGrapher.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for ZeGrapher @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=ZeGrapher VERSION=${VERSION:-3.0.2} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -88,4 +98,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/ZeGrapher/ZeGrapher.info b/academic/ZeGrapher/ZeGrapher.info index 44efd73a79..9ac639ea98 100644 --- a/academic/ZeGrapher/ZeGrapher.info +++ b/academic/ZeGrapher/ZeGrapher.info @@ -5,6 +5,6 @@ DOWNLOAD="https://github.com/AdelKS/ZeGrapher/archive/v3.0.2/ZeGrapher-3.0.2.tar MD5SUM="a8440300bbf4d178e1469ebce1eb8403" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="qt5-webkit" +REQUIRES="" MAINTAINER="Fernando Lopez Jr." EMAIL="fernando.lopezjr@gmail.com" diff --git a/academic/abella/README b/academic/abella/README deleted file mode 100644 index a6f078794e..0000000000 --- a/academic/abella/README +++ /dev/null @@ -1,30 +0,0 @@ -Abella is an interactive theorem prover based on lambda-tree syntax. - -This means that Abella is well-suited for reasoning about the meta-theory -of programming languages and other logical systems which manipulate -objects with binding. For example, the following applications are included -in the distribution of Abella. - -* Various results on the lambda calculus involving big-step evaluation, small-step evaluation, and typing judgments -* Cut-admissibility for a sequent calculus -* Part 1a and Part 2a of the POPLmark challenge -* Takahashi's proof of the Church-Rosser theorem -* Tait's logical relations argument for weak normalization of the simply-typed lambda calculus -* Girard's proof of strong normalization of the simply-typed lambda calculus -* Some ?-calculus meta-theory -* Relation between ?-reduction and paths in A-calculus - -For Full List: -http://abella-prover.org/examples/index.html - -Abella uses a two-level logic approach to reasoning. Specifications -are made in the logic of second-order hereditary Harrop formulas using -lambda-tree syntax. This logic is executable and is a subset of the -AProlog language (see the Teyjus system for an implementation of this -language). - -The reasoning logic of Abella is the culmination of a series of extensions -to proof theory for the treatment of definitions, lambda-tree syntax, -and generic judgments. The reasoning logic of Abella is able to encode -the semantics of our specification logic as a definition and thereby -reason over specifications in that logic. diff --git a/academic/abella/abella.SlackBuild b/academic/abella/abella.SlackBuild deleted file mode 100644 index ea575be990..0000000000 --- a/academic/abella/abella.SlackBuild +++ /dev/null @@ -1,78 +0,0 @@ -#!/bin/sh -# Slackware build script for abella -# Copyright 2019 Jefferson Rocha <root@slackjeff.com.br> -# All rights reserved. -# -# Redistribution and use of this script, with or without modification, is -# permitted provided that the following conditions are met: -# -# 1. Redistributions of this script must retain the above copyright -# notice, this list of conditions and the following disclaimer. -# -# THIS SOFTWARE IS PROVIDED BY THE AUTHOR ''AS IS'' AND ANY EXPRESS OR IMPLIED -# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF -# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO -# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, -# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, -# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; -# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, -# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR -# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF -# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - -#==========================VARS -PRGNAM=abella -VERSION=${VERSION:-2.0.6} -BUILD=${BUILD:-1} -TAG=${TAG:-_SBo} -ARCH=noarch -CWD=$(pwd) -TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM -OUTPUT=${OUTPUT:-/tmp} - -#Root? -[ "$UID" -ne '0' ] && { echo "Need root."; exit 1 ;} - -#=========================START -set -e - -rm -rf $PKG -mkdir -p $TMP $PKG $OUTPUT -cd $TMP - -rm -rf $PRGNAM-$VERSION -tar xvf $CWD/$PRGNAM-$VERSION.tar.gz -cd $PRGNAM-$VERSION - -# Fix Permissions -chown -R root:root . -find -L . \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; - -# Generate bin -make -strip -s $PRGNAM - -mkdir -p $PKG/usr/bin -cp "$PRGNAM" $PKG/usr/bin - -mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION - -# Send original Docs and archives -for create in "$PRGNAM.SlackBuild" 'LICENSE' 'CHANGES'; do - if [ "$create" = $PRGNAM.SlackBuild ]; then - cp $CWD/$create $PKG/usr/doc/$PRGNAM-$VERSION/ - else - cp $create $PKG/usr/doc/$PRGNAM-$VERSION/ - fi -done - -mkdir -p $PKG/install -cat $CWD/slack-desc > $PKG/install/slack-desc - -cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} diff --git a/academic/abella/abella.info b/academic/abella/abella.info deleted file mode 100644 index 88abb3f04c..0000000000 --- a/academic/abella/abella.info +++ /dev/null @@ -1,10 +0,0 @@ -PRGNAM="abella" -VERSION="2.0.6" -HOMEPAGE="http://abella-prover.org/" -DOWNLOAD="http://abella-prover.org/distributions/abella-2.0.6.tar.gz" -MD5SUM="077cb3fbbdf35159e4b8860faf431c6a" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="ocamlbuild ocaml-findlib" -MAINTAINER="Jefferson Rocha" -EMAIL="root@slackjeff.com.br" diff --git a/academic/abella/slack-desc b/academic/abella/slack-desc deleted file mode 100644 index 15174390e7..0000000000 --- a/academic/abella/slack-desc +++ /dev/null @@ -1,19 +0,0 @@ -# HOW TO EDIT THIS FILE: -# The "handy ruler" below makes it easier to edit a package description. Line -# up the first '|' above the ':' following the base package name, and the '|' on -# the right side marks the last column you can put a character in. You must make -# exactly 11 lines for the formatting to be correct. It's also customary to -# leave one space after the ':'. - - |-----handy-ruler------------------------------------------------------| -abella: abella (interactive theorem prover based on lambda-tree syntax) -abella: -abella: Abella is an interactive theorem prover based on lambda-tree syntax. -abella: This means that Abella is well-suited for reasoning about the meta -abella: theory of programming languages and other logical systems which -abella: manipulate objects with binding. -abella: For example, the following applications are included in the -abella: distribution of Abella. -abella: -abella: http://abella-prover.org/ -abella: diff --git a/academic/abntex/abntex.SlackBuild b/academic/abntex/abntex.SlackBuild index 743140f19a..6728604dc1 100644 --- a/academic/abntex/abntex.SlackBuild +++ b/academic/abntex/abntex.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for abntex @@ -24,31 +24,35 @@ # Slightly modified by Robby Workman <rworkman@slackbuilds.org> +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=abntex -VERSION=${VERSION:-0.9_beta2} +VERSION=${VERSION:-20200715_f0a4d3c} ARCH=noarch BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi -MAJOR=$(echo $VERSION | cut -d _ -f 1) -MINOR=$(echo $VERSION | cut -d _ -f 2) - -CWD=$(pwd) TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -FORCE_LYX=${FORCE_LYX:-NO} -LYX_PATH=${LYX_PATH:-/usr/share/lyx} - set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $PRGNAM-$MAJOR -tar xvf $CWD/$PRGNAM-$MAJOR-$MINOR.tar.gz -cd $PRGNAM-$MAJOR +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.?z +cd $PRGNAM-$VERSION chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \ @@ -56,23 +60,15 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ -exec chmod 644 {} \; -patch < $CWD/Makefile.diff - -find texmf/ lyx/ -type f -exec chmod 644 {} \; - -echo quit | make doc -make install DESTDIR=$PKG - -# Lyx may not have been installed -if [ "$FORCE_LYX" != "NO" ]; then - mkdir -p $PKG/usr/share/lyx - cp -rf lyx/layouts/ $PKG/$LYX_PATH -fi - +find . -name ".gitignore" -exec rm {} \; +make install PREFIX=/usr DESTDIR=$PKG +sh build.sh +cd target +for i in *.zip ; do unzip $i ; done +rm *.zip *.tar.gz mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a \ - LEIAME LEIAME.administracao LEIAME.linux compiled.docs/* lyx/ \ - $PKG/usr/doc/$PRGNAM-$VERSION +find . -name "*.pdf" -exec cp -a {} $PKG/usr/doc/$PRGNAM-$VERSION/ \; +cp ../*.md ../LICENSE $PKG/usr/doc/$PRGNAM-$VERSION find $PKG/usr/doc/$PRGNAM-$VERSION -type f -exec chmod 644 {} \; cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild @@ -81,4 +77,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/abntex/abntex.info b/academic/abntex/abntex.info index 9ced2dab26..a57b0537a5 100644 --- a/academic/abntex/abntex.info +++ b/academic/abntex/abntex.info @@ -1,8 +1,8 @@ PRGNAM="abntex" -VERSION="0.9_beta2" +VERSION="20200715_f0a4d3c" HOMEPAGE="http://www.abntex.net.br/" -DOWNLOAD="http://downloads.sourceforge.net/abntex/abntex-0.9-beta2.tar.gz" -MD5SUM="4c5bc2d5388ddf03df754072116ab1f8" +DOWNLOAD="https://ponce.cc/slackware/sources/repo/abntex-20200715_f0a4d3c.tar.xz" +MD5SUM="f2cc9267ae71b14f9d9780fa824e8878" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/acl2/README b/academic/acl2/README new file mode 100644 index 0000000000..ac87fba1ef --- /dev/null +++ b/academic/acl2/README @@ -0,0 +1,7 @@ +ACL2 is a logic and programming language in which you can model +computer systems, together with a tool to help you prove properties of +those models. "ACL2" denotes "A Computational Logic for Applicative +Common Lisp". ACL2 is part of the Boyer-Moore family of provers, for +which its authors have received the 2005 ACM Software System Award + +There is some support for Emacs >24 in /opt/acl2/books/emacs/ diff --git a/academic/acl2/acl2 b/academic/acl2/acl2 new file mode 100755 index 0000000000..65892c9f9e --- /dev/null +++ b/academic/acl2/acl2 @@ -0,0 +1,4 @@ +#!/bin/sh + +export ACL2_SYSTEM_BOOKS=/opt/acl2/books/ +/opt/acl2/saved_acl2 $@ diff --git a/academic/Mnemosyne/Mnemosyne.SlackBuild b/academic/acl2/acl2.SlackBuild index 6de86d1a48..027caca8ba 100644 --- a/academic/Mnemosyne/Mnemosyne.SlackBuild +++ b/academic/acl2/acl2.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash -# Slackware build script for Mnemosyne +# Slackware build script for acl2 -# Copyright 2014 R. S. Ananda Murthy, Mysore, India +# Copyright 2023, Lockywolf # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -PRGNAM=Mnemosyne -VERSION=${VERSION:-2.6.1} +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=acl2 +VERSION=${VERSION:-8.5} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,11 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -49,6 +56,9 @@ elif [ "$ARCH" = "i686" ]; then elif [ "$ARCH" = "x86_64" ]; then SLKCFLAGS="-O2 -fPIC" LIBDIRSUFFIX="64" +elif [ "$ARCH" = "aarch64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" else SLKCFLAGS="-O2" LIBDIRSUFFIX="" @@ -65,27 +75,24 @@ cd $PRGNAM-$VERSION chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ + -o -perm 511 \) -exec chmod 755 {} + -o \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; - -python3 setup.py build -python3 setup.py install --prefix=/usr --root=$PKG - -# Now I will remove this icon which is not of 48x48 pixels size -rm $PKG/usr/share/icons/mnemosyne.png + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} + -mkdir -p $PKG/usr/share/icons/hicolor/48x48/apps -install -m0644 $CWD/mnemosyne.png $PKG/usr/share/icons/hicolor/48x48/apps/mnemosyne.png -#chmod -x $PKG/usr/share/icons/hicolor/48x48/apps/mnemosyne.png +export SBCL_HOME=/usr/lib${LIBDIRSUFFIX}/sbcl +gmake LISP='sbcl --no-sysinit --no-userinit --disable-debugger' +install -Dm755 $CWD/acl2 $PKG/usr/bin/acl2 +install -d -m755 $PKG/opt/acl2 +cp -r . $PKG/opt/acl2/ mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a README $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + LICENSE doc workshops.html \ + $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc -cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/acl2/acl2.info b/academic/acl2/acl2.info new file mode 100644 index 0000000000..bda4fa3394 --- /dev/null +++ b/academic/acl2/acl2.info @@ -0,0 +1,10 @@ +PRGNAM="acl2" +VERSION="8.5" +HOMEPAGE="https://www.cs.utexas.edu/users/moore/acl2/v8-5/" +DOWNLOAD="https://github.com/acl2-devel/acl2-devel/releases/download/8.5/acl2-8.5.tar.gz" +MD5SUM="ec2c62dbdffdc345252bc5a68ad830fc" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="sbcl" +MAINTAINER="Lockywolf" +EMAIL="for_sbo.acl2_2023-07-16@lockywolf.net" diff --git a/academic/acl2/slack-desc b/academic/acl2/slack-desc new file mode 100644 index 0000000000..1d7f0f6b1b --- /dev/null +++ b/academic/acl2/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +acl2: acl2 (Computational Logic for Applicative Common Lisp) +acl2: +acl2: ACL2 is a logic and programming language in which you can model +acl2: computer systems, together with a tool to help you prove properties +acl2: of those models. "ACL2" denotes "A Computational Logic for +acl2: Applicative Common Lisp". ACL2 is part of the Boyer-Moore family of +acl2: provers, for which its authors have received the 2005 ACM Software +acl2: System Award +acl2: +acl2: +acl2: diff --git a/academic/aenig4/README b/academic/aenig4/README index 3ac2263e9d..ee1505f360 100644 --- a/academic/aenig4/README +++ b/academic/aenig4/README @@ -1,5 +1,5 @@ aenig4 (Enigma M4 Cipher Machine Emulator) -aenig4 emulates the Enigma M4 cipher machine used by the U-boot divsion of -the German Navy during World War II. It can be used as well to emulate the -Enigma I machine (M1, M2, M3). +aenig4 emulates the Enigma M4 cipher machine used by the U-boot +divsion of the German Navy during World War II. It can be used as well +to emulate the Enigma I machine (M1, M2, M3). diff --git a/academic/aenig4/aenig4.SlackBuild b/academic/aenig4/aenig4.SlackBuild index 2a7705b76f..8e66aab54d 100644 --- a/academic/aenig4/aenig4.SlackBuild +++ b/academic/aenig4/aenig4.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for aenig4 @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=aenig4 VERSION=${VERSION:-1.04} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -98,4 +108,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/aeskulap/README b/academic/aeskulap/README new file mode 100644 index 0000000000..5e074de1a0 --- /dev/null +++ b/academic/aeskulap/README @@ -0,0 +1,8 @@ +aeskulap (medical image viewer) + +aeskulap is able to load a series of special images stored in the DICOM +format for review. Additionally Aeskulap is able to query and fetch +DICOM images from archive nodes (also called PACS) over the network. +The goal of this project is to create a full open source replacement +for commercially available DICOM viewers. + diff --git a/academic/aeskulap/aeskulap.SlackBuild b/academic/aeskulap/aeskulap.SlackBuild new file mode 100644 index 0000000000..a9088f66c1 --- /dev/null +++ b/academic/aeskulap/aeskulap.SlackBuild @@ -0,0 +1,122 @@ +#!/bin/bash + +# Slackware build script for aeskulap + +# Copyright 2011 Federico Lupi, flupi@mclink.it, http://www.mclink.it/personal/MG2508 +# Modified by Matt Dinslage (daedra1980@gmail.com) +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR ''AS IS'' AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=aeskulap +VERSION=${VERSION:-0.2.2_e710562d} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \ + -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ + -exec chmod 644 {} \; + +patch -p1 < $CWD/newDicomElement.patch + +# point to the correct lib version depending on the arch +sed -i 's/lib -ldcmjpeg/%{_lib} -ldcmjpeg/' configure.ac +libtoolize --force --copy --install +autoreconf --force --install +intltoolize --force --copy --automake + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --mandir=/usr/man \ + --disable-static \ + --with-gsettings \ + --build=$ARCH-slackware-linux + +make +make install DESTDIR=$PKG + +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG | xargs file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + ABOUT-NLS COPYING NEWS COPYING.DOC COPYING.LIB ChangeLog INSTALL README \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/aeskulap/aeskulap.info b/academic/aeskulap/aeskulap.info new file mode 100644 index 0000000000..4078803b08 --- /dev/null +++ b/academic/aeskulap/aeskulap.info @@ -0,0 +1,10 @@ +PRGNAM="aeskulap" +VERSION="0.2.2_e710562d" +HOMEPAGE="https://gitlab.com/stefanhusmann/aeskulap" +DOWNLOAD="https://www.dropbox.com/s/84xpkwtgj0r2bd8/aeskulap-0.2.2_e710562d.tar.gz" +MD5SUM="6be6239b2bec4744db7e3b203e29d77f" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="dcmtk" +MAINTAINER="M.Dinslage" +EMAIL="daedra1980@gmail.com" diff --git a/academic/aeskulap/doinst.sh b/academic/aeskulap/doinst.sh new file mode 100644 index 0000000000..09b892d002 --- /dev/null +++ b/academic/aeskulap/doinst.sh @@ -0,0 +1,15 @@ +if [ -e usr/share/icons/hicolor/icon-theme.cache ]; then + if [ -x /usr/bin/gtk-update-icon-cache ]; then + /usr/bin/gtk-update-icon-cache -f usr/share/icons/hicolor >/dev/null 2>&1 + fi +fi + +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 +fi + +if [ -e usr/share/glib-2.0/schemas ]; then + if [ -x /usr/bin/glib-compile-schemas ]; then + /usr/bin/glib-compile-schemas usr/share/glib-2.0/schemas >/dev/null 2>&1 + fi +fi diff --git a/academic/aeskulap/newDicomElement.patch b/academic/aeskulap/newDicomElement.patch new file mode 100644 index 0000000000..4ffc76015b --- /dev/null +++ b/academic/aeskulap/newDicomElement.patch @@ -0,0 +1,269 @@ +Author: Gert Wollny <gewo@debian.org> +Description: correct code for newDicomElement now being a member of DcmItem +Bug: https://bugs.debian.org/865591 + +--- a/imagepool/netloader.cpp ++++ b/imagepool/netloader.cpp +@@ -102,29 +102,29 @@ bool NetLoader::run() { + DcmDataset query; + DcmElement* e = NULL; + +- e = newDicomElement(DCM_QueryRetrieveLevel); ++ e = DcmItem::newDicomElement(DCM_QueryRetrieveLevel); + e->putString("STUDY"); + query.insert(e); + +- e = newDicomElement(DCM_PatientName); ++ e = DcmItem::newDicomElement(DCM_PatientName); + query.insert(e); + +- e = newDicomElement(DCM_PatientID); ++ e = DcmItem::newDicomElement(DCM_PatientID); + query.insert(e); + +- e = newDicomElement(DCM_StudyDate); ++ e = DcmItem::newDicomElement(DCM_StudyDate); + query.insert(e); + +- e = newDicomElement(DCM_StudyTime); ++ e = DcmItem::newDicomElement(DCM_StudyTime); + query.insert(e); + +- e = newDicomElement(DCM_AccessionNumber); ++ e = DcmItem::newDicomElement(DCM_AccessionNumber); + query.insert(e); + +- e = newDicomElement(DCM_StudyID); ++ e = DcmItem::newDicomElement(DCM_StudyID); + query.insert(e); + +- e = newDicomElement(DCM_StudyInstanceUID); ++ e = DcmItem::newDicomElement(DCM_StudyInstanceUID); + e->putString(studyinstanceuid.c_str()); + query.insert(e); + +@@ -150,22 +150,22 @@ bool NetLoader::run() { + DcmDataset query; + DcmElement* e = NULL; + +- e = newDicomElement(DCM_QueryRetrieveLevel); ++ e = DcmItem::newDicomElement(DCM_QueryRetrieveLevel); + e->putString("SERIES"); + query.insert(e); + +- e = newDicomElement(DCM_StudyInstanceUID); ++ e = DcmItem::newDicomElement(DCM_StudyInstanceUID); + e->putString(studyinstanceuid.c_str()); + query.insert(e); + +- e = newDicomElement(DCM_SeriesInstanceUID); ++ e = DcmItem::newDicomElement(DCM_SeriesInstanceUID); + e->putString(i->c_str()); + query.insert(e); + +- e = newDicomElement(DCM_Modality); ++ e = DcmItem::newDicomElement(DCM_Modality); + query.insert(e); + +- e = newDicomElement(DCM_SeriesNumber); ++ e = DcmItem::newDicomElement(DCM_SeriesNumber); + query.insert(e); + + std::cout << "C-Move request:" << std::endl; +--- a/imagepool/netquery.cpp ++++ b/imagepool/netquery.cpp +@@ -196,64 +196,64 @@ void query_from_net( + DcmDataset query; + DcmElement* e = NULL; + +- e = newDicomElement(DCM_QueryRetrieveLevel); ++ e = DcmItem::newDicomElement(DCM_QueryRetrieveLevel); + e->putString("STUDY"); + query.insert(e); + +- e = newDicomElement(DCM_SpecificCharacterSet); ++ e = DcmItem::newDicomElement(DCM_SpecificCharacterSet); + e->putString(dicom_enc.c_str()); + query.insert(e); + +- e = newDicomElement(DCM_PatientName); ++ e = DcmItem::newDicomElement(DCM_PatientName); + e->putString(patientsname.c_str()); + query.insert(e); + +- e = newDicomElement(DCM_PatientID); ++ e = DcmItem::newDicomElement(DCM_PatientID); + e->putString(convert_string_to(patientid.c_str(), system_enc).c_str()); + query.insert(e); + +- e = newDicomElement(DCM_SOPClassesInStudy); ++ e = DcmItem::newDicomElement(DCM_SOPClassesInStudy); + query.insert(e); + +- e = newDicomElement(DCM_ModalitiesInStudy); ++ e = DcmItem::newDicomElement(DCM_ModalitiesInStudy); + e->putString(modality.c_str()); + query.insert(e); + +- e = newDicomElement(DCM_PatientBirthDate); ++ e = DcmItem::newDicomElement(DCM_PatientBirthDate); + query.insert(e); + +- e = newDicomElement(DCM_PatientSex); ++ e = DcmItem::newDicomElement(DCM_PatientSex); + query.insert(e); + +- e = newDicomElement(DCM_StudyDate); ++ e = DcmItem::newDicomElement(DCM_StudyDate); + e->putString(date.c_str()); + query.insert(e); + +- e = newDicomElement(DCM_StudyTime); ++ e = DcmItem::newDicomElement(DCM_StudyTime); + query.insert(e); + +- e = newDicomElement(DCM_NumberOfStudyRelatedSeries); ++ e = DcmItem::newDicomElement(DCM_NumberOfStudyRelatedSeries); + query.insert(e); + +- e = newDicomElement(DCM_NumberOfStudyRelatedInstances); ++ e = DcmItem::newDicomElement(DCM_NumberOfStudyRelatedInstances); + query.insert(e); + +- e = newDicomElement(DCM_AccessionNumber); ++ e = DcmItem::newDicomElement(DCM_AccessionNumber); + e->putString(accessionnumber.c_str()); + query.insert(e); + +- e = newDicomElement(DCM_StudyID); ++ e = DcmItem::newDicomElement(DCM_StudyID); + query.insert(e); + +- e = newDicomElement(DCM_StudyInstanceUID); ++ e = DcmItem::newDicomElement(DCM_StudyInstanceUID); + query.insert(e); + +- e = newDicomElement(DCM_StudyDescription); ++ e = DcmItem::newDicomElement(DCM_StudyDescription); + e->putString(description.c_str()); + query.insert(e); + + // StationName not allowed in StudyRoot +- /*e = newDicomElement(DCM_StationName); ++ /*e = DcmItem::newDicomElement(DCM_StationName); + e->putString(station.c_str()); + query.insert(e);*/ + +@@ -284,36 +284,36 @@ void query_series_from_net(const std::st + DcmDataset query; + DcmElement* e = NULL; + +- e = newDicomElement(DCM_QueryRetrieveLevel); ++ e = DcmItem::newDicomElement(DCM_QueryRetrieveLevel); + e->putString("SERIES"); + query.insert(e); + +- e = newDicomElement(DCM_SpecificCharacterSet); ++ e = DcmItem::newDicomElement(DCM_SpecificCharacterSet); + query.insert(e); + +- e = newDicomElement(DCM_StudyInstanceUID); ++ e = DcmItem::newDicomElement(DCM_StudyInstanceUID); + e->putString(studyinstanceuid.c_str()); + query.insert(e); + +- e = newDicomElement(DCM_SeriesInstanceUID); ++ e = DcmItem::newDicomElement(DCM_SeriesInstanceUID); + query.insert(e); + +- e = newDicomElement(DCM_SeriesNumber); ++ e = DcmItem::newDicomElement(DCM_SeriesNumber); + query.insert(e); + +- e = newDicomElement(DCM_Modality); ++ e = DcmItem::newDicomElement(DCM_Modality); + query.insert(e); + +- e = newDicomElement(DCM_SeriesDescription); ++ e = DcmItem::newDicomElement(DCM_SeriesDescription); + query.insert(e); + +- e = newDicomElement(DCM_SeriesTime); ++ e = DcmItem::newDicomElement(DCM_SeriesTime); + query.insert(e); + +- e = newDicomElement(DCM_StationName); ++ e = DcmItem::newDicomElement(DCM_StationName); + query.insert(e); + +- e = newDicomElement(DCM_NumberOfSeriesRelatedInstances); ++ e = DcmItem::newDicomElement(DCM_NumberOfSeriesRelatedInstances); + query.insert(e); + + +@@ -357,22 +357,22 @@ int query_series_instances(const std::st + DcmDataset query; + DcmElement* e = NULL; + +- e = newDicomElement(DCM_QueryRetrieveLevel); ++ e = DcmItem::newDicomElement(DCM_QueryRetrieveLevel); + e->putString("IMAGE"); + query.insert(e); + +- e = newDicomElement(DCM_StudyInstanceUID); ++ e = DcmItem::newDicomElement(DCM_StudyInstanceUID); + e->putString(studyinstanceuid.c_str()); + query.insert(e); + +- e = newDicomElement(DCM_SeriesInstanceUID); ++ e = DcmItem::newDicomElement(DCM_SeriesInstanceUID); + e->putString(seriesinstanceuid.c_str()); + query.insert(e); + +- e = newDicomElement(DCM_SOPInstanceUID); ++ e = DcmItem::newDicomElement(DCM_SOPInstanceUID); + query.insert(e); + +- e = newDicomElement(DCM_InstanceNumber); ++ e = DcmItem::newDicomElement(DCM_InstanceNumber); + query.insert(e); + + std::cout << "NEW QUERY:" << std::endl; +@@ -394,21 +394,21 @@ int query_study_series(const std::string + DcmDataset query; + DcmElement* e = NULL; + +- e = newDicomElement(DCM_QueryRetrieveLevel); ++ e = DcmItem::newDicomElement(DCM_QueryRetrieveLevel); + e->putString("SERIES"); + query.insert(e); + +- e = newDicomElement(DCM_StudyInstanceUID); ++ e = DcmItem::newDicomElement(DCM_StudyInstanceUID); + e->putString(studyinstanceuid.c_str()); + query.insert(e); + +- e = newDicomElement(DCM_SeriesInstanceUID); ++ e = DcmItem::newDicomElement(DCM_SeriesInstanceUID); + query.insert(e); + +- e = newDicomElement(DCM_SeriesNumber); ++ e = DcmItem::newDicomElement(DCM_SeriesNumber); + query.insert(e); + +- e = newDicomElement(DCM_Modality); ++ e = DcmItem::newDicomElement(DCM_Modality); + query.insert(e); + + std::cout << "NEW QUERY:" << std::endl; +--- a/imagepool/poolassociation.h ++++ b/imagepool/poolassociation.h +@@ -101,7 +101,7 @@ public: + return false; + } + +- DcmElement *elem = newDicomElement(tag); ++ DcmElement *elem = DcmItem::newDicomElement(tag); + if (elem == NULL) { + printf("cannot create element for tag: (%04x,%04x)", g, e); + return false; diff --git a/academic/aeskulap/slack-desc b/academic/aeskulap/slack-desc new file mode 100644 index 0000000000..5a3a8776e8 --- /dev/null +++ b/academic/aeskulap/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +aeskulap: aeskulap (medical image viewer) +aeskulap: +aeskulap: It is able to load a series of special images stored in the DICOM +aeskulap: format for review. Additionally Aeskulap is able to query and fetch +aeskulap: DICOM images from archive nodes (also called PACS) over the network. +aeskulap: The goal of this project is to create a full open source replacement +aeskulap: for commercially available DICOM viewers. +aeskulap: +aeskulap: http://aeskulap.nongnu.org/ +aeskulap: +aeskulap: diff --git a/academic/aline/README b/academic/aline/README index 41b2e6e5ee..deba4d32ce 100644 --- a/academic/aline/README +++ b/academic/aline/README @@ -18,3 +18,4 @@ for more information and installation instructions if you want it. CITING Bond, C.S. and Schuttelkopf, A.W. (2009), Acta cryst. D65, 510-512 +https://crystal.scb.uwa.edu.au/charlie/software/aline/actad_65_510.pdf diff --git a/academic/aline/aline.SlackBuild b/academic/aline/aline.SlackBuild index 161ed68f3f..4a7ee98a35 100644 --- a/academic/aline/aline.SlackBuild +++ b/academic/aline/aline.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for aline -# Copyright 2013-2016 Petar Petrov slackalaxy@gmail.com +# Copyright 2013-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,15 +22,25 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=aline VERSION=${VERSION:-1.0.025} BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} SRCVER=011208 ARCH=noarch -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -86,4 +96,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/aline/aline.info b/academic/aline/aline.info index 63f7ee3446..177b2fff14 100644 --- a/academic/aline/aline.info +++ b/academic/aline/aline.info @@ -1,7 +1,7 @@ PRGNAM="aline" VERSION="1.0.025" HOMEPAGE="http://crystal.scb.uwa.edu.au/charlie/software/aline/" -DOWNLOAD="http://crystal.scb.uwa.edu.au/charlie/software/aline/aline_011208.tar.gz" +DOWNLOAD="https://slackware.uk/sbosrcarch/by-name/academic/aline/aline_011208.tar.gz" MD5SUM="6e462b37bb016de731a3352cc9503cd9" DOWNLOAD_x86_64="" MD5SUM_x86_64="" diff --git a/academic/aliview/aliview.SlackBuild b/academic/aliview/aliview.SlackBuild index 89b70e0ceb..22c0580eac 100644 --- a/academic/aliview/aliview.SlackBuild +++ b/academic/aliview/aliview.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for aliview -# Copyright 2018-2019 Petar Petrov slackalaxy@gmail.com +# Copyright 2018-2022 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,18 +22,28 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=aliview -VERSION=${VERSION:-1.26} +VERSION=${VERSION:-1.28} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +ARCH=noarch + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi -CWD=$(pwd) TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -ARCH=noarch - set -e rm -rf $PKG @@ -74,4 +84,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/aliview/aliview.info b/academic/aliview/aliview.info index 6f392759ae..41abed4471 100644 --- a/academic/aliview/aliview.info +++ b/academic/aliview/aliview.info @@ -1,10 +1,10 @@ PRGNAM="aliview" -VERSION="1.26" +VERSION="1.28" HOMEPAGE="http://www.ormbunkar.se/aliview/" -DOWNLOAD="http://www.ormbunkar.se/aliview/downloads/linux/linux-versions-all/linux-version-1.26/aliview.tgz" -MD5SUM="9aac430a5f9e1cc465815cea0bf69af8" +DOWNLOAD="http://www.ormbunkar.se/aliview/downloads/linux/linux-versions-all/linux-version-1.28/aliview.tgz" +MD5SUM="1eac87a0f88f3815707df27d3a9970dc" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="jdk" +REQUIRES="zulu-openjdk11" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/amd/README b/academic/amd/README index 07e4dcafc0..b2ae697056 100644 --- a/academic/amd/README +++ b/academic/amd/README @@ -1,6 +1,7 @@ -AMD is a set of routines for ordering a sparse matrix prior to Cholesky -factorization (or for LU factorization with diagonal pivoting). There are -versions in both C and Fortran. Note that this software has nothing to do -with AMD the company. This package runs on any platform. +AMD is a set of routines for ordering a sparse matrix prior to +Cholesky factorization (or for LU factorization with diagonal +pivoting). There are versions in both C and Fortran. Note that this +software has nothing to do with AMD the company. This package runs on +any platform. This package is part of SuiteSparse. diff --git a/academic/amd/amd.SlackBuild b/academic/amd/amd.SlackBuild index 796d4d8885..4cca1d563e 100644 --- a/academic/amd/amd.SlackBuild +++ b/academic/amd/amd.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for AMD -# Copyright 2013-2020 Kyle Guinn <elyk03@gmail.com> +# Copyright 2013-2021 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,13 +22,16 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=amd SRCNAM=SuiteSparse SUBDIR=AMD VERSION=${VERSION:-2.4.6} -SRCVER=${SRCVER:-5.6.0} -BUILD=${BUILD:-6} +SRCVER=${SRCVER:-5.8.1} +BUILD=${BUILD:-7} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$(uname -m)" in @@ -38,15 +41,22 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM-$VERSION +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="README.txt Doc/ChangeLog Doc/License.txt Doc/lesser.txt" -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" @@ -109,4 +119,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/amd/amd.info b/academic/amd/amd.info index 5a6b836b8c..da6c16b92b 100644 --- a/academic/amd/amd.info +++ b/academic/amd/amd.info @@ -1,8 +1,8 @@ PRGNAM="amd" VERSION="2.4.6" HOMEPAGE="http://faculty.cse.tamu.edu/davis/suitesparse.html" -DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.6.0/SuiteSparse-5.6.0.tar.gz" -MD5SUM="af8b97cbded4cd5c6672e878bc0c37c2" +DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.8.1/SuiteSparse-5.8.1.tar.gz" +MD5SUM="c414679bbc9432a3def01b31ad921140" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="suitesparseconfig" diff --git a/academic/amplicon/README b/academic/amplicon/README index 395b56f031..de8c35014b 100644 --- a/academic/amplicon/README +++ b/academic/amplicon/README @@ -1,3 +1,15 @@ +Oligonucleotide (primer) design for polymerase chain reaction (PCR) +experiments is an important stage in successfully obtaining desired PCR +products (amplicons). PCR primer design may be assisted by software that +helps the user assess features of the oligonucleotides that determine +how they may interact with each other and with target and non-target DNA +sequences in a solution. The design of PCR primers where multiple target +sequences may be present in a solution is a difficult problem. This +situation has not been extensively investigated and is difficult to +address with software solutions, especially given a surprising lack of +knowledge relating to Tm calculation of mismatched oligonucleotide and +target sequences. + Amplicon is a tool for designing PCR primers where groups of related DNA sequences can be assessed in aligned form. Other useful features that are not common in other PCR primer design software are handling @@ -5,6 +17,13 @@ of gapped sequences and degenerate sites in aligned DNA. Amplicon can import aligned DNA sequences produced by Clustal, or aligned sequences in MEGA or Fasta format. +Amplicon can import aligned DNA sequences produced by ClustalW or +ClustalX (Thompson et al., 1997); or aligned sequences in MEGA (Kumar et +al., 1997) or Fasta format. Primer analyses can be saved to text files +for editing in any text editor or word processor. Alignments that have +been altered in Amplicon can be saved in Fasta, MEGA, .aln, PAUP +(Swofford, 2003) or Phylip (Felsenstein, 1993) formats. + For details and citation: Jarman SN (2004) Amplicon: software for designing PCR primers on aligned DNA sequences. Bioinformatics 20: 1644-1645. diff --git a/academic/amplicon/amplicon.SlackBuild b/academic/amplicon/amplicon.SlackBuild index 0ab897e091..451c9779ec 100644 --- a/academic/amplicon/amplicon.SlackBuild +++ b/academic/amplicon/amplicon.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for amplicon -# Copyright 2011-2016 Petar Petrov slackalaxy@gmail.com +# Copyright 2011-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,14 +22,24 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=amplicon VERSION=${VERSION:-b09.1} BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} ARCH=noarch -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -64,4 +74,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/amplifx/amplifx.SlackBuild b/academic/amplifx/amplifx.SlackBuild index 5fa2210e3a..72ed55d7e4 100644 --- a/academic/amplifx/amplifx.SlackBuild +++ b/academic/amplifx/amplifx.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for amplifx -# Copyright 2015-2016 Petar Petrov slackalaxy@gmail.com +# Copyright 2015-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,15 +22,36 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=amplifx SRCNAM=AmplifX_Lin_Latest VERSION=${VERSION:-1.7.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +# 2023-05-16 DW: do a proper test for ARCH +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [[ $ARCH != i?86 ]]; then + printf "\n$ARCH is not supported... \n" >/dev/stderr + exit 1 +fi -ARCH=i386 +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi -CWD=$(pwd) TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -72,4 +93,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/amplifx/amplifx.info b/academic/amplifx/amplifx.info index 1ec2301b5b..22c69f2e7b 100644 --- a/academic/amplifx/amplifx.info +++ b/academic/amplifx/amplifx.info @@ -1,7 +1,7 @@ PRGNAM="amplifx" VERSION="1.7.0" -HOMEPAGE="http://crn2m.univ-mrs.fr/AmplifX" -DOWNLOAD="http://crn2m.univ-mrs.fr/IMG/zip/AmplifX_Lin_Latest.zip" +HOMEPAGE="https://inp.univ-amu.fr/en/amplifx-manage-test-and-design-your-primers-for-pcr" +DOWNLOAD="https://slackware.uk/~urchlay/src/AmplifX_Lin_Latest.zip" MD5SUM="ff84d1c4a800dcb651beaa877ff7b1ca" DOWNLOAD_x86_64="UNSUPPORTED" MD5SUM_x86_64="" diff --git a/academic/amplifx/slack-desc b/academic/amplifx/slack-desc index 2de0b1133a..670bbfccee 100644 --- a/academic/amplifx/slack-desc +++ b/academic/amplifx/slack-desc @@ -14,6 +14,6 @@ amplifx: which can be use to amplify a fragment into a target sequence, amplifx: for example, and particularly, to design strategies to screen amplifx: recombinant clones by PCR. amplifx: -amplifx: Home: http://crn2m.univ-mrs.fr/AmplifX -amplifx: References: /usr/doc/amplifx-1.7.0/References +amplifx: +amplifx: amplifx: diff --git a/academic/antiprism/README b/academic/antiprism/README index e81e3a4e32..6d7cca97a3 100644 --- a/academic/antiprism/README +++ b/academic/antiprism/README @@ -1,2 +1,2 @@ -Antiprism is a set of programs for generating, manipulating, transforming -and visualising polyhedra. +Antiprism is a set of programs for generating, manipulating, +transforming and visualising polyhedra. diff --git a/academic/antiprism/antiprism.SlackBuild b/academic/antiprism/antiprism.SlackBuild index 271184a166..a294efedfd 100644 --- a/academic/antiprism/antiprism.SlackBuild +++ b/academic/antiprism/antiprism.SlackBuild @@ -1,29 +1,39 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for antiprism # Written by (Jorge Barros de Abreu) (ficmatin10 at gmail dot com) +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=antiprism VERSION=${VERSION:-0.23} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -55,7 +65,7 @@ find -L . \ sed "/^docdir/s|= .*|= @docdir@|" -i Makefile.in CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS -fpermissive" \ ./configure \ --prefix=/usr \ --libdir=/usr/lib$LIBDIRSUFFIX \ @@ -73,8 +83,10 @@ for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; r mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/archaeopteryx/archaeopteryx.SlackBuild b/academic/archaeopteryx/archaeopteryx.SlackBuild index c72ba3b9e7..61b5da5a14 100644 --- a/academic/archaeopteryx/archaeopteryx.SlackBuild +++ b/academic/archaeopteryx/archaeopteryx.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for archaeopteryx -# Copyright 2014-2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2014-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,16 +22,26 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=archaeopteryx VERSION=${VERSION:-0.9928b} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} SRCNAM=forester SRCVER=1050 ARCH=noarch -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -61,4 +71,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/archaeopteryx/archaeopteryx.info b/academic/archaeopteryx/archaeopteryx.info index 7bccba509a..94a8958bb5 100644 --- a/academic/archaeopteryx/archaeopteryx.info +++ b/academic/archaeopteryx/archaeopteryx.info @@ -5,6 +5,6 @@ DOWNLOAD="http://www.phyloxml.org/download/forester/forester_1050.jar" MD5SUM="023de2f0a48cbd236c5054fe839b1d72" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="jdk" +REQUIRES="zulu-openjdk11" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/archaeopteryx/archaeopteryx.png b/academic/archaeopteryx/archaeopteryx.png Binary files differindex 5663c1b87e..edb7bb66bc 100644 --- a/academic/archaeopteryx/archaeopteryx.png +++ b/academic/archaeopteryx/archaeopteryx.png diff --git a/academic/aris/README b/academic/aris/README index 65cf47df47..13f3372b78 100644 --- a/academic/aris/README +++ b/academic/aris/README @@ -1,6 +1,6 @@ -GNU Aris is a sequential proof program, designed to assist anyone interested -in solving logical proofs. Aris supports both propositional and predicate -logic, as well as Boolean algebra and arithmetical logic in the form of -abstract sequences. It uses a predefined set of both inference and equivalence -rules, however gives the user options to use older proofs as lemmas, including -Isabelle's Isar proofs. +GNU Aris is a sequential proof program, designed to assist anyone +interested in solving logical proofs. Aris supports both propositional +and predicate logic, as well as Boolean algebra and arithmetical logic +in the form of abstract sequences. It uses a predefined set of both +inference and equivalence rules, however gives the user options to use +older proofs as lemmas, including Isabelle's Isar proofs. diff --git a/academic/aris/aris.SlackBuild b/academic/aris/aris.SlackBuild index a377d31a7f..6230b1e7d5 100644 --- a/academic/aris/aris.SlackBuild +++ b/academic/aris/aris.SlackBuild @@ -1,39 +1,62 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for GNU aris -# Written by Juan M. Lasca <juanmlasca@gmail.com> +# Copyright 2013-2020 Juan M. Lasca <juanmlasca@gmail.com> +# Copyright 2020-2022 Philip Lacroix <slackph at posteo dot de> +# Copyright 2022 Juan M. Lasca <juanmlasca@gmail.com> +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) PRGNAM=aris -VERSION=${VERSION:-2.1.1} -BUILD=${BUILD:-1} +VERSION=${VERSION:-2.2} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" - LIBDIRSUFFIX="" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" - LIBDIRSUFFIX="" elif [ "$ARCH" = "x86_64" ]; then SLKCFLAGS="-O2 -fPIC" - LIBDIRSUFFIX="64" else SLKCFLAGS="-O2" - LIBDIRSUFFIX="" fi set -e @@ -46,26 +69,19 @@ tar xvf $CWD/$PRGNAM-$VERSION.tar.bz2 cd $PRGNAM-$VERSION chown -R root:root . find -L . \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; - + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ - --sysconfdir=/etc \ - --localstatedir=/var \ - --docdir=/usr/doc/$PRGNAM-$VERSION \ - --htmldir=/usr/doc/$PRGNAM-$VERSION/html \ --build=$ARCH-slackware-linux -# this will allow aris to find its documentation -# in a better place. -patch -p1 < $CWD/html_doc.patch +# Fix path for local manual and multiple symbol definitions +cat $CWD/docs_and_build.patch | patch -p1 || exit make make install DESTDIR=$PKG @@ -73,19 +89,16 @@ make install DESTDIR=$PKG find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true -# "make install" won't locate the aris.info file in DESTDIR. -# Workaround: -mkdir -p $PKG/usr/info +mkdir -p $PKG/usr/info $PKG/usr/doc/$PRGNAM-$VERSION cp -a doc/$PRGNAM.info $PKG/usr/info/ gzip -9 $PKG/usr/info/$PRGNAM.info - -mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a README $PKG/usr/doc/$PRGNAM-$VERSION -cp -ar doc/$PRGNAM/ $PKG/usr/doc/$PRGNAM-$VERSION/html +cp -a README AUTHORS ChangeLog NEWS THANKS TODO $PKG/usr/doc/$PRGNAM-$VERSION/ +cp -ar doc/$PRGNAM/ $PKG/usr/doc/$PRGNAM-$VERSION/html/ +cp -ar doc/proofs $PKG/usr/doc/$PRGNAM-$VERSION/ cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/aris/aris.info b/academic/aris/aris.info index 8362eaa9bb..f22ad0f438 100644 --- a/academic/aris/aris.info +++ b/academic/aris/aris.info @@ -1,10 +1,10 @@ PRGNAM="aris" -VERSION="2.1.1" -HOMEPAGE="http://www.gnu.org/software/aris/" -DOWNLOAD="http://ftp.gnu.org/gnu/aris/aris-2.1.1.tar.bz2" -MD5SUM="ef1b8f3be8edac44305e36493068f745" +VERSION="2.2" +HOMEPAGE="https://www.gnu.org/software/aris/" +DOWNLOAD="https://ftp.gnu.org/gnu/aris/aris-2.2.tar.bz2" +MD5SUM="523e2c40f17e6e857b533c22a26ff4e1" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" -MAINTAINER="Philip Lacroix" -EMAIL="slackph at posteo dot de" +MAINTAINER="Juan M. Lasca" +EMAIL="juanmlasca@gmail.com" diff --git a/academic/aris/docs_and_build.patch b/academic/aris/docs_and_build.patch new file mode 100644 index 0000000000..e1335922c7 --- /dev/null +++ b/academic/aris/docs_and_build.patch @@ -0,0 +1,66 @@ +# * Change documentation location +# * Instead of allowing multiple definitions (allocations in header files), +# declare global variables in headers, and allocate them in their +# corresponding .c files, with a reasonable initial value. + +diff -u3 aris-2.2/src/app.c aris-2.2-patched/src/app.c +--- aris-2.2/src/app.c 2014-02-28 10:17:24.000000000 -0300 ++++ aris-2.2-patched/src/app.c 2022-08-11 15:28:59.318566050 -0300 +@@ -46,6 +46,9 @@ + #include "elm-conn.xpm" + #include "nil-conn.xpm" + ++ ++aris_app * the_app = 0; ++ + // Macro to get the length of a file. + + #ifndef WIN32 +diff -u3 aris-2.2/src/app.h aris-2.2-patched/src/app.h +--- aris-2.2/src/app.h 2014-02-27 22:32:07.000000000 -0300 ++++ aris-2.2-patched/src/app.h 2022-08-11 13:01:06.315136621 -0300 +@@ -106,6 +106,6 @@ + + int app_set_color (aris_app * app, int index, int red, int green, int blue); + /* The main application */ +-aris_app * the_app; ++extern aris_app * the_app; + + #endif /* ARIS_APP_H */ +diff -u3 aris-2.2/src/aris.c aris-2.2-patched/src/aris.c +--- aris-2.2/src/aris.c 2014-02-28 10:29:10.000000000 -0300 ++++ aris-2.2-patched/src/aris.c 2022-08-11 15:38:22.990593330 -0300 +@@ -844,8 +844,7 @@ + + if (the_app->working_dir) + { +- parent = g_file_get_parent (parent); +- sprintf (the_app->help_file, "file://%s/doc/aris/index.html", g_file_get_path (parent)); ++ sprintf (the_app->help_file, "file:///usr/doc/aris-" PACKAGE_VERSION "/html/index.html"); + } + + int ret; +diff -u3 aris-2.2/src/process.c aris-2.2-patched/src/process.c +--- aris-2.2/src/process.c 2014-03-06 17:53:32.000000000 -0300 ++++ aris-2.2-patched/src/process.c 2022-08-11 15:27:56.582563013 -0300 +@@ -26,6 +26,8 @@ + #include <ctype.h> + #include <math.h> + ++struct connectives_list main_conns = { 0 }; ++ + /* Eliminates a negation from a string. + * input: + * not_str - the string from which to eliminate the negation. +diff -u3 aris-2.2/src/process.h aris-2.2-patched/src/process.h +--- aris-2.2/src/process.h 2014-03-02 16:30:39.000000000 -0300 ++++ aris-2.2-patched/src/process.h 2022-08-11 13:04:45.004147205 -0300 +@@ -170,7 +170,7 @@ + + // The main connectives. + +-struct connectives_list main_conns; ++extern struct connectives_list main_conns; + + // Definitions. + diff --git a/academic/aris/html_doc.patch b/academic/aris/html_doc.patch deleted file mode 100644 index 1b359b73d6..0000000000 --- a/academic/aris/html_doc.patch +++ /dev/null @@ -1,19 +0,0 @@ ---- aris-2.0/configure 2012-09-25 05:06:22.000000000 -0300 -+++ aris-2.0b/configure 2013-03-23 18:34:59.483719378 -0300 -@@ -4610,3 +4610,1 @@ --cat >>confdefs.h <<_ACEOF --#define HELP_FILE "file://`pwd`/doc/aris/index.html" --_ACEOF -+echo "#define HELP_FILE \"file://"$htmldir"/index.html\"" >>confdefs.h ---- aris-2.0/src/aris.c 2012-09-25 05:06:22.000000000 -0300 -+++ aris-2.0b/src/aris.c 2013-03-23 18:45:25.290749474 -0300 -@@ -1064,0 +1065,6 @@ -+#ifdef HELP_FILE /* Which should be defined in config.h */ -+ -+ strcpy (the_app->help_file, HELP_FILE); -+ -+#else -+ -@@ -1076,0 +1083,2 @@ -+ -+#endif /* HELP FILE */ diff --git a/academic/aris/slack-desc b/academic/aris/slack-desc index 218444d055..c061cf1dc4 100644 --- a/academic/aris/slack-desc +++ b/academic/aris/slack-desc @@ -15,5 +15,5 @@ aris: in the form of abstract sequences. It uses a predefined set of both aris: inference and equivalence rules, however gives the user options to use aris: older proofs as lemmas, including Isabelle's Isar proofs. aris: -aris: Home page: http://www.gnu.org/software/aris/ +aris: Home page: https://www.gnu.org/software/aris/ aris: diff --git a/academic/arka/arka.SlackBuild b/academic/arka/arka.SlackBuild index eea4b48a41..75f7d2cd93 100644 --- a/academic/arka/arka.SlackBuild +++ b/academic/arka/arka.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for arka -# Copyright 2011-2016 Petar Petrov slackalaxy@gmail.com +# Copyright 2011-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,26 +22,36 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=arka VERSION=${VERSION:-0.11} -BUILD=${BUILD:-1} +BUILD=${BUILD:-3} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -62,14 +72,16 @@ cd $TMP rm -rf $PRGNAM-$VERSION tar xvf $CWD/$PRGNAM-$VERSION.tgz cd $PRGNAM-$VERSION + # Remove the pre-existing binary, just in case rm arka + chown -R root:root . find -L . \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; # A few path fixes to the Makefile, although it will work anyways. sed "s:/usr/X11R6/bin:/usr/bin:" -i Makefile @@ -81,8 +93,8 @@ sed "s:/usr/X11R6/include/X11/pixmaps:/usr/share/pixmaps:" -i Makefile sed -i "/^CFLAGS/s/=/+=/" src/Makefile # Fix for gcc-5.2.0 linker errors: add -fgnu89-inline -CFLAGS="$SLKCFLAGS -fgnu89-inline" \ -CXXFLAGS="$SLKCFLAGS -fgnu89-inline" \ +CFLAGS="$SLKCFLAGS -fgnu89-inline -fcommon" \ +CXXFLAGS="$SLKCFLAGS -fgnu89-inline -fcommon" \ make # The Makefile does not support "make DESTDIR install". So... @@ -109,4 +121,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/armadillo/README b/academic/armadillo/README index 17bef8f786..9327750b8d 100644 --- a/academic/armadillo/README +++ b/academic/armadillo/README @@ -2,9 +2,10 @@ Armadillo is a high quality C++ linear algebra library useful for development of algorithms in machine learning, pattern recognition, signal processing, bioinformatics, statistics, etc. -Armadillo makes extensive use of template meta-programming, recursive templates -and template based function overloading. As such, C++ compilers which do not -fully implement the C++ standard may not work correctly. +Armadillo makes extensive use of template meta-programming, recursive +templates and template based function overloading. As such, C++ +compilers which do not fully implement the C++ standard may not work +correctly. The functionality of Armadillo is partly dependent on other libraries: LAPACK, BLAS and ARPACK. The LAPACK and BLAS libraries are used for diff --git a/academic/armadillo/armadillo.SlackBuild b/academic/armadillo/armadillo.SlackBuild index 2035220bdb..dbe7598f03 100644 --- a/academic/armadillo/armadillo.SlackBuild +++ b/academic/armadillo/armadillo.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for Armadillo @@ -22,10 +22,17 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +# 20220402 bkw: Modified by SlackBuilds.org, BUILD=2: +# - fix download URL. +# - add SlackBuild to doc dir. + +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=armadillo VERSION=${VERSION:-8.100.0} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} DOCS="README.txt examples/ index.html LICENSE.txt docs.html rcpp_armadillo_csda_2014.pdf" @@ -37,7 +44,11 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -67,9 +78,9 @@ cd $PRGNAM-$VERSION chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ + -o -perm 511 \) -exec chmod 755 {} \+ -o \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \+ mkdir -p build cd build @@ -78,17 +89,15 @@ cd build -DCMAKE_INSTALL_PREFIX=/usr \ -DCMAKE_BUILD_TYPE=Release .. make - make install DESTDIR=$PKG + make install/strip DESTDIR=$PKG cd .. -find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ - | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true - mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a $DOCS $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/armadillo/armadillo.info b/academic/armadillo/armadillo.info index 9d8c336afc..5a883d954f 100644 --- a/academic/armadillo/armadillo.info +++ b/academic/armadillo/armadillo.info @@ -1,7 +1,7 @@ PRGNAM="armadillo" VERSION="8.100.0" HOMEPAGE="http://arma.sourceforge.net/" -DOWNLOAD="http://sourceforge.net/projects/arma/files/armadillo-8.100.0.tar.xz" +DOWNLOAD="https://slackware.uk/~urchlay/src/armadillo-8.100.0.tar.xz" MD5SUM="5f4aa46d15d9d364874fa4bde1a7add0" DOWNLOAD_x86_64="" MD5SUM_x86_64="" diff --git a/academic/arpack-ng/README b/academic/arpack-ng/README index e24427e956..596f89a447 100644 --- a/academic/arpack-ng/README +++ b/academic/arpack-ng/README @@ -4,15 +4,18 @@ large scale eigenvalue problems. This is a fork of ARPACK that is actively maintained. As such, this package will conflict with the ARPACK package. Do not install both. -This requires a BLAS/LAPACK implementation. Choose one of these package sets: +This requires a BLAS/LAPACK implementation. Choose one of these +package sets: * OpenBLAS (includes both a BLAS and a LAPACK implementation) * atlas (includes both a BLAS and a LAPACK implementation) * blas, lapack (the Netlib reference implementations) -If more than one set is installed (assuming there are no packaging conflicts) -then the auto-detection will use the first implementation from this list that -it finds. If in doubt, choose the Netlib reference implementations; other -packages that require a BLAS or LAPACK implementation may not build if they -are not configured to detect/use alternate implementations. +If more than one set is installed (assuming there are no packaging +conflicts) then the auto-detection will use the first implementation +from this list that it finds. If in doubt, choose the Netlib +reference implementations; other packages that require a BLAS or +LAPACK implementation may not build if they are not configured to +detect/use alternate implementations. -If the `make check` command fails, try switching to the Netlib reference -implementations, or comment out that command at your own risk. +If the `make check` command fails, try switching to the Netlib +reference implementations, or comment out that command at your own +risk. diff --git a/academic/arpack-ng/arpack-ng.SlackBuild b/academic/arpack-ng/arpack-ng.SlackBuild index b5639de58b..7893fe9968 100644 --- a/academic/arpack-ng/arpack-ng.SlackBuild +++ b/academic/arpack-ng/arpack-ng.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for arpack-ng -# Copyright 2014-2019 Kyle Guinn <elyk03@gmail.com> +# Copyright 2014-2024 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=arpack-ng -VERSION=${VERSION:-3.7.0} +VERSION=${VERSION:-3.9.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$(uname -m)" in @@ -35,17 +38,18 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -DOCS="CHANGES COPYING PARPACK_CHANGES README.md TODO" +DOCS="CHANGES COPYING README.md TODO" -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" - LIBDIRSUFFIX="" -elif [ "$ARCH" = "i586" ]; then +if [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then @@ -70,19 +74,18 @@ cd $PRGNAM-$VERSION chown -R root:root . chmod -R u+w,go-w,a+rX-st . +patch -p1 < $CWD/patches/pkgconfig.diff patch -p1 < $CWD/patches/atlas-lib-rename.diff ./bootstrap ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ + --libdir=\${exec_prefix}/lib${LIBDIRSUFFIX} \ --sysconfdir=/etc \ --localstatedir=/var \ - --mandir=/usr/man \ - --infodir=/usr/info \ - --docdir=/usr/doc/$PRGNAM-$VERSION \ - --enable-shared \ - --disable-static \ + --mandir=\${prefix}/man \ + --infodir=\${prefix}/info \ + --docdir=\${prefix}/doc/$PRGNAM-$VERSION \ --disable-dependency-tracking \ --enable-icb \ --build=$ARCH-slackware-linux \ @@ -105,4 +108,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/arpack-ng/arpack-ng.info b/academic/arpack-ng/arpack-ng.info index 9af4707aa5..6f6426c4bf 100644 --- a/academic/arpack-ng/arpack-ng.info +++ b/academic/arpack-ng/arpack-ng.info @@ -1,10 +1,10 @@ PRGNAM="arpack-ng" -VERSION="3.7.0" +VERSION="3.9.1" HOMEPAGE="https://github.com/opencollab/arpack-ng" -DOWNLOAD="https://github.com/opencollab/arpack-ng/archive/3.7.0/arpack-ng-3.7.0.tar.gz" -MD5SUM="6fc6c6bf78dbd4f144595ef0675c8430" +DOWNLOAD="https://github.com/opencollab/arpack-ng/archive/3.9.1/arpack-ng-3.9.1.tar.gz" +MD5SUM="8f66485ae9d7e676b42aeead2bf5757e" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="blas lapack" +REQUIRES="lapack" MAINTAINER="Kyle Guinn" EMAIL="elyk03@gmail.com" diff --git a/academic/arpack-ng/patches/pkgconfig.diff b/academic/arpack-ng/patches/pkgconfig.diff new file mode 100644 index 0000000000..73a00eb23d --- /dev/null +++ b/academic/arpack-ng/patches/pkgconfig.diff @@ -0,0 +1,142 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -807,7 +807,7 @@ + set(prefix ${CMAKE_INSTALL_PREFIX}) + set(exec_prefix \${prefix}) + set(libdir ${CMAKE_INSTALL_FULL_LIBDIR}) +-set(includedir ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_INCLUDEDIR}) ++set(includedir ${CMAKE_INSTALL_FULL_INCLUDEDIR}) + set(PACKAGE_NAME ${PROJECT_NAME}) + set(PACKAGE_VERSION ${arpack_ng_VERSION}) + set(PACKAGE_URL "https://github.com/opencollab/arpack-ng/") +@@ -830,15 +830,15 @@ + endforeach() + string(REPLACE ";" " " PARPACK_PC_LIBS_PRIVATE "${PARPACK_PC_LIBS_PRIVATE}") + +-configure_file(pkg-config/arpack.pc.in "${PROJECT_BINARY_DIR}/arpack${LIBSUFFIX}${ITF64SUFFIX}.pc" @ONLY) +-configure_file(pkg-config/parpack.pc.in "${PROJECT_BINARY_DIR}/parpack${LIBSUFFIX}${ITF64SUFFIX}.pc" @ONLY) ++configure_file(SRC/arpack.pc.in "${PROJECT_BINARY_DIR}/SRC/arpack${LIBSUFFIX}${ITF64SUFFIX}.pc" @ONLY) ++configure_file(PARPACK/SRC/MPI/parpack.pc.in "${PROJECT_BINARY_DIR}/PARPACK/SRC/MPI/parpack${LIBSUFFIX}${ITF64SUFFIX}.pc" @ONLY) + + install(TARGETS arpack + EXPORT arpackngTargets + ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} + LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} + RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}) +-install(FILES "${PROJECT_BINARY_DIR}/arpack${LIBSUFFIX}${ITF64SUFFIX}.pc" ++install(FILES "${PROJECT_BINARY_DIR}/SRC/arpack${LIBSUFFIX}${ITF64SUFFIX}.pc" + DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig) + + if (MPI) +@@ -847,7 +847,7 @@ + ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} + LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} + RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}) +- install(FILES "${PROJECT_BINARY_DIR}/parpack${LIBSUFFIX}${ITF64SUFFIX}.pc" ++ install(FILES "${PROJECT_BINARY_DIR}/PARPACK/SRC/MPI/parpack${LIBSUFFIX}${ITF64SUFFIX}.pc" + DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig) + endif () + +diff --git a/Makefile.am b/Makefile.am +--- a/Makefile.am ++++ b/Makefile.am +@@ -26,8 +26,3 @@ + + EXTRA_DIST = README.md PARPACK_CHANGES CHANGES DOCUMENTS VISUAL_STUDIO \ + detect_arpack_bug.m4 CMakeLists.txt +- +-pkgconfig_DATA = arpack@LIBSUFFIX@@ITF64SUFFIX@.pc parpack@LIBSUFFIX@@ITF64SUFFIX@.pc +- +-# Due to the LIBSUFFIX/ITF64SUFFIX, configure doesn't automatically clean this file: +-DISTCLEANFILES = arpack@LIBSUFFIX@@ITF64SUFFIX@.pc parpack@LIBSUFFIX@@ITF64SUFFIX@.pc +diff --git a/PARPACK/SRC/MPI/Makefile.am b/PARPACK/SRC/MPI/Makefile.am +--- a/PARPACK/SRC/MPI/Makefile.am ++++ b/PARPACK/SRC/MPI/Makefile.am +@@ -46,3 +46,8 @@ + libparpack@LIBSUFFIX@@ITF64SUFFIX@_la_LIBADD += $(top_builddir)/ICB/libdbgicb.la $(top_builddir)/ICB/libstaicb.la + libparpack@LIBSUFFIX@@ITF64SUFFIX@_la_CPPFLAGS = $(AM_CPPFLAGS) -I$(top_builddir) + endif ++ ++pkgconfig_DATA = parpack@LIBSUFFIX@@ITF64SUFFIX@.pc ++ ++# Due to the LIBSUFFIX/ITF64SUFFIX, configure doesn't automatically clean this file: ++DISTCLEANFILES = parpack@LIBSUFFIX@@ITF64SUFFIX@.pc +diff --git a/pkg-config/parpack.pc.in b/PARPACK/SRC/MPI/parpack.pc.in +rename from pkg-config/parpack.pc.in +rename to PARPACK/SRC/MPI/parpack.pc.in +--- a/pkg-config/parpack.pc.in ++++ b/PARPACK/SRC/MPI/parpack.pc.in +@@ -1,7 +1,7 @@ + prefix=@prefix@ + exec_prefix=@exec_prefix@ + libdir=@libdir@ +-includedir=@includedir@/arpack@ITF64SUFFIX@ ++includedir=@includedir@ + + Name: @PACKAGE_NAME@ + Description: Collection of Fortran77 subroutines designed to solve large scale eigenvalue problems +@@ -10,4 +10,4 @@ + Requires.private: arpack@LIBSUFFIX@@ITF64SUFFIX@ + Libs: -L${libdir} -lparpack@LIBSUFFIX@@ITF64SUFFIX@ + Libs.private: @PARPACK_PC_LIBS_PRIVATE@ +-Cflags: -I${includedir} ++Cflags: -I${includedir}/arpack@ITF64SUFFIX@ +diff --git a/SRC/Makefile.am b/SRC/Makefile.am +--- a/SRC/Makefile.am ++++ b/SRC/Makefile.am +@@ -33,3 +33,8 @@ + libarpack@LIBSUFFIX@@ITF64SUFFIX@_la_LIBADD += $(top_builddir)/ICB/libdbgicb.la $(top_builddir)/ICB/libstaicb.la + libarpack@LIBSUFFIX@@ITF64SUFFIX@_la_CPPFLAGS = $(AM_CPPFLAGS) -I$(top_builddir) + endif ++ ++pkgconfig_DATA = arpack@LIBSUFFIX@@ITF64SUFFIX@.pc ++ ++# Due to the LIBSUFFIX/ITF64SUFFIX, configure doesn't automatically clean this file: ++DISTCLEANFILES = arpack@LIBSUFFIX@@ITF64SUFFIX@.pc +diff --git a/pkg-config/arpack.pc.in b/SRC/arpack.pc.in +rename from pkg-config/arpack.pc.in +rename to SRC/arpack.pc.in +--- a/pkg-config/arpack.pc.in ++++ b/SRC/arpack.pc.in +@@ -1,7 +1,7 @@ + prefix=@prefix@ + exec_prefix=@exec_prefix@ + libdir=@libdir@ +-includedir=@includedir@/arpack@ITF64SUFFIX@ ++includedir=@includedir@ + + Name: @PACKAGE_NAME@ + Description: Collection of Fortran77 subroutines designed to solve large scale eigenvalue problems +@@ -9,4 +9,4 @@ + URL: @PACKAGE_URL@ + Libs: -L${libdir} -larpack@LIBSUFFIX@@ITF64SUFFIX@ + Libs.private: @ARPACK_PC_LIBS_PRIVATE@ +-Cflags: -I${includedir} ++Cflags: -I${includedir}/arpack@ITF64SUFFIX@ +diff --git a/configure.ac b/configure.ac +--- a/configure.ac ++++ b/configure.ac +@@ -347,14 +347,12 @@ + AC_SUBST([PARPACK_PC_LIBS_PRIVATE], ["$LAPACK_LIBS $BLAS_LIBS $MPI_Fortran_LIBS"]) + + AC_CONFIG_FILES([ +- arpack$LIBSUFFIX$ITF64SUFFIX.pc:pkg-config/arpack.pc.in +- parpack$LIBSUFFIX$ITF64SUFFIX.pc:pkg-config/parpack.pc.in ++ SRC/arpack$LIBSUFFIX$ITF64SUFFIX.pc:SRC/arpack.pc.in ++ PARPACK/SRC/MPI/parpack$LIBSUFFIX$ITF64SUFFIX.pc:PARPACK/SRC/MPI/parpack.pc.in + ], [], [LIBSUFFIX="$LIBSUFFIX"; ITF64SUFFIX="$ITF64SUFFIX"]) + + dnl We do NOT want arpackng*.cmake files to be created: @MPI@ can not be replaced. +-AC_CONFIG_FILES([ +- tstAutotoolsInstall.sh:pkg-config/tstAutotoolsInstall.sh.in +-], [], [abs_top_builddir="$abs_top_builddir"]) ++AC_CONFIG_FILES([tstAutotoolsInstall.sh], [chmod +x tstAutotoolsInstall.sh], [abs_top_builddir="$abs_top_builddir"]) + + AC_CONFIG_FILES([ + arpackdef.h +diff --git a/pkg-config/tstAutotoolsInstall.sh.in b/tstAutotoolsInstall.sh.in +old mode 100755 +new mode 100644 +rename from pkg-config/tstAutotoolsInstall.sh.in +rename to tstAutotoolsInstall.sh.in diff --git a/academic/arpack/arpack.SlackBuild b/academic/arpack/arpack.SlackBuild index d2d2e937c4..cc21abf76f 100644 --- a/academic/arpack/arpack.SlackBuild +++ b/academic/arpack/arpack.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for arpack @@ -23,26 +23,36 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=arpack VERSION=${VERSION:-2.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -78,6 +88,9 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ -exec chmod 644 {} \; +# Disable parallel building otherwise build fails +MAKEFLAGS=-j1 + mkdir static shared cd shared for dir in ../SRC ../UTIL; do @@ -115,4 +128,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/artha/README b/academic/artha/README index dc6d794f61..5e08f3e1fd 100644 --- a/academic/artha/README +++ b/academic/artha/README @@ -4,7 +4,7 @@ off-line and is based on WordNet. The main focus of Artha is high usability, with much simplicity. It has distinct features like: -* hotkey press - word look-up (select text and press a hotkey for look-up) +* hotkey press - word lookup (select text and press a hotkey for lookup) * regex-based search (find words using wild-cards like *, ?, etc.) * passive desktop notifications (of word definitions for uninterrupted workflow) diff --git a/academic/artha/artha.SlackBuild b/academic/artha/artha.SlackBuild index 53eb0478d2..50e50e93e2 100644 --- a/academic/artha/artha.SlackBuild +++ b/academic/artha/artha.SlackBuild @@ -1,29 +1,39 @@ -#!/bin/sh +#!/bin/bash # # Slackware build script for artha # # Written by Mikhail Zotov <mikhail dot ru at gmail dot com> +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=artha -VERSION=${VERSION:-1.0.3} +VERSION=${VERSION:-1.0.5} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -83,4 +93,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/artha/artha.info b/academic/artha/artha.info index 1512888a8b..40037f5817 100644 --- a/academic/artha/artha.info +++ b/academic/artha/artha.info @@ -1,8 +1,8 @@ PRGNAM="artha" -VERSION="1.0.3" +VERSION="1.0.5" HOMEPAGE="http://artha.sourceforge.net/" -DOWNLOAD="http://ponce.cc/slackware/sources/repo/artha-1.0.3.tar.bz2" -MD5SUM="9bc69f5666a1f494e21a0a0add9ebb16" +DOWNLOAD="https://downloads.sourceforge.net/artha/artha-1.0.5.tar.bz2" +MD5SUM="a916a7a943ac676a60f03cc839b04f37" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="WordNet" diff --git a/academic/avl/avl.SlackBuild b/academic/avl/avl.SlackBuild index 424ffaa5d1..ab88aed70d 100644 --- a/academic/avl/avl.SlackBuild +++ b/academic/avl/avl.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for avl @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=avl VERSION=${VERSION:-3.36} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -101,4 +111,4 @@ cp -a runs $PKG/usr/share/$PRGNAM cp -a movie $PKG/usr/share/$PRGNAM cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/avogadro/README b/academic/avogadro/README deleted file mode 100644 index 531f972b75..0000000000 --- a/academic/avogadro/README +++ /dev/null @@ -1,5 +0,0 @@ -Avogadro is a molecular graphics and modelling system targeted at molecules -and biomolecules. It can visualize properties like molecular orbitals or -electrostatic potentials and features an intuitive molecular builder. - -Optionally numpy can be installed for python support. diff --git a/academic/avogadro/avogadro-1.1.1-python_openbabel.patch b/academic/avogadro/avogadro-1.1.1-python_openbabel.patch deleted file mode 100644 index c819b08502..0000000000 --- a/academic/avogadro/avogadro-1.1.1-python_openbabel.patch +++ /dev/null @@ -1,14 +0,0 @@ -diff -up avogadro-1.1.1/libavogadro/src/python/CMakeLists.txt.openbabel avogadro-1.1.1/libavogadro/src/python/CMakeLists.txt ---- avogadro-1.1.1/libavogadro/src/python/CMakeLists.txt.openbabel 2013-12-06 09:50:04.000000000 -0600 -+++ avogadro-1.1.1/libavogadro/src/python/CMakeLists.txt 2016-01-25 13:50:10.469758655 -0600 -@@ -20,8 +20,8 @@ if (WIN32) - set_target_properties(python-module PROPERTIES SUFFIX ".pyd") - target_link_libraries(python-module avogadro ${PYTHON_LIBRARIES}) - else() -- target_link_libraries(python-module stdc++ avogadro -- ${QT_LIBRARIES} ${PYTHON_LIBRARIES} ${Boost_LIBRARIES}) -+ target_link_libraries(python-module stdc++ avogadro -+ ${QT_LIBRARIES} ${PYTHON_LIBRARIES} ${OPENBABEL2_LIBRARIES} ${Boost_LIBRARIES}) - endif() - - # Let's try to use this instead: diff --git a/academic/avogadro/avogadro-1.2.0-libmsym.patch b/academic/avogadro/avogadro-1.2.0-libmsym.patch deleted file mode 100644 index 818b2e434b..0000000000 --- a/academic/avogadro/avogadro-1.2.0-libmsym.patch +++ /dev/null @@ -1,29 +0,0 @@ -diff -Naur avogadro-1.2.0.orig/libavogadro/src/extensions/symmetry/libmsym/CMakeLists.txt avogadro-1.2.0/libavogadro/src/extensions/symmetry/libmsym/CMakeLists.txt ---- avogadro-1.2.0.orig/libavogadro/src/extensions/symmetry/libmsym/CMakeLists.txt 2016-06-08 14:19:45.000000000 +0000 -+++ avogadro-1.2.0/libavogadro/src/extensions/symmetry/libmsym/CMakeLists.txt 2016-08-01 04:18:55.910888721 +0000 -@@ -7,13 +7,13 @@ - set(LIBMSYM_PATCH_VERSION 0) - set(LIBMSYM_VERSION ${LIBMSYM_MAJOR_VERSION}.${LIBMSYM_MINOR_VERSION}.${LIBMSYM_PATCH_VERSION}) - --set(INSTALL_LIB_DIR lib CACHE PATH "Installation directory for msym library") -+set(INSTALL_LIB_DIR lib${LIB_SUFFIX} CACHE PATH "Installation directory for msym library") - set(INSTALL_INCLUDE_DIR include CACHE PATH "Installation directory for header files") - - if(WIN32 AND NOT CYGWIN) - set(DEF_INSTALL_CMAKE_DIR CMake) - else() -- set(DEF_INSTALL_CMAKE_DIR lib/cmake/libmsym) -+ set(DEF_INSTALL_CMAKE_DIR lib${LIB_SUFFIX}/cmake/libmsym) - endif() - set(INSTALL_CMAKE_DIR ${DEF_INSTALL_CMAKE_DIR} CACHE PATH "Installation directory for CMake files") - -@@ -29,6 +29,9 @@ - file (GLOB source src/*.c) - add_library (msym ${source}) - if (BUILD_SHARED_LIBS) -+ if(CMAKE_SYSTEM_NAME MATCHES Linux) -+ target_link_libraries(msym m) -+ endif() - set_target_properties (msym PROPERTIES - POSITION_INDEPENDENT_CODE "TRUE") - endif () diff --git a/academic/avogadro/avogadro.info b/academic/avogadro/avogadro.info deleted file mode 100644 index 68813ecc75..0000000000 --- a/academic/avogadro/avogadro.info +++ /dev/null @@ -1,10 +0,0 @@ -PRGNAM="avogadro" -VERSION="1.2.0" -HOMEPAGE="http://avogadro.cc/" -DOWNLOAD="http://ponce.cc/slackware/sources/repo/avogadro-1.2.0.tar.gz" -MD5SUM="3206068fc27bd3b717c568ee72f1e5ec" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="openbabel" -MAINTAINER="Larry Hajali" -EMAIL="larryhaja[at]gmail[dot]com" diff --git a/academic/avogadroapp/README b/academic/avogadroapp/README new file mode 100644 index 0000000000..692ec7f1c2 --- /dev/null +++ b/academic/avogadroapp/README @@ -0,0 +1,23 @@ +Avogadro Application is the graphic user interface of Avogadro 2. + +Avogadro is an advanced molecular editor designed for cross-platform +use in computational chemistry, molecular modeling, bioinformatics, +materials science, and related areas. It offers flexible rendering and +a powerful plugin architecture. + +Managed by OpenChemistry, Avogadro 2 it is based on QT5 libraries and +it is a rewrite of the old Avogadro 1.x. + +By default the script builds avogadroapp with shared libraries. If you +want to enable the building with static libraries, pass the variable +SHARED=no to the script: + + SHARED=no ./avogadroapp.SlackBuild (hdf5 required) + +Warning: the computational settings made through the Input Generator +require the MoleQueue server running to submit jobs to local +applications or remote HPC clusters. + +Since Avogadro 2 version 1.98.0, the build requires cmake at version +3.24 or greater. This version is the latest compatible with Slackware +15.0 that has cmake remained at the version 3.21. diff --git a/academic/avogadro/avogadro.SlackBuild b/academic/avogadroapp/avogadroapp.SlackBuild index 481347fe3c..e8b6905bd1 100644 --- a/academic/avogadro/avogadro.SlackBuild +++ b/academic/avogadroapp/avogadroapp.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash -# Slackware build script for Avogadro +# Slackware build script for avogadroapp -# Copyright 2010-2016 Larry Hajali <larryhaja[at]gmail[dot]com> +# Copyright 2020-2022 Giancarlo Dessì, Cagliari, IT # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,26 +22,35 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -PRGNAM=avogadro -VERSION=${VERSION:-1.2.0} +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=avogadroapp +VERSION=${VERSION:-1.97.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +SHAREDLIBS="" ; [ "${SHARED:-yes}" = "yes" ] && SHAREDLIBS="-DBUILD_SHARED_LIBS=ON" + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -59,8 +68,15 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $PRGNAM-$VERSION +rm -rf $PRGNAM-$VERSION avogadro-i18n* tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +# Following archive must be unpacked in /tmp since the build process +# searches it as parallel directory and tries to connect to github if +# not found +tar xvf $CWD/avogadro-i18n-$VERSION.tar.gz +mv avogadro-i18n-$VERSION avogadro-i18n + +# Now we can change directory to $PRGNAM-$VERSION cd $PRGNAM-$VERSION chown -R root:root . find -L . \ @@ -69,50 +85,34 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -# Fix manpage directory. -sed -i 's|share/man|man|' doc/CMakeLists.txt -# Fix install directory and linking for libmsym library. -patch -p1 < $CWD/avogadro-1.2.0-libmsym.patch - -# fix build (with recent swig/linker/python?) -# http://pkgs.fedoraproject.org/cgit/rpms/avogadro.git/tree/avogadro-1.1.1-python_openbabel.patch -patch -p1 < $CWD/avogadro-1.1.1-python_openbabel.patch - mkdir -p build cd build cmake \ - -DCMAKE_INSTALL_PREFIX=/usr \ -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ - -DLIB_SUFFIX=${LIBDIRSUFFIX} \ - -DENABLE_RPATH=OFF \ - -DCMAKE_SKIP_RPATH=YES \ - -DENABLE_GLSL:BOOL=ON \ - -DENABLE_UPDATE_CHECKER=OFF \ - -DENABLE_VERSIONED_PLUGIN_DIR:BOOL=OFF \ - -DBUILD_SHARED_LIBS:BOOL=ON \ - -DQT_MKSPECS_RELATIVE=lib${LIBDIRSUFFIX}/qt/mkspecs \ - -DCMAKE_BUILD_TYPE=Release .. - - make VERBOSE=1 + -DCMAKE_INSTALL_PREFIX=/usr \ + -DCMAKE_BUILD_TYPE=Release \ + $SHAREDLIBS \ + .. + make make install DESTDIR=$PKG -cd - +cd .. + +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true -find $PKG/usr/man -type f -exec gzip -9 {} \; - mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a \ - AUTHORS COPYING INSTALL README \ - libavogadro/src/extensions/gl2ps/{COPYING*,*.txt,*.pdf} \ - $PKG/usr/doc/$PRGNAM-$VERSION +cp -a *.md LICENSE $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +# Remove doc files installed by make install in /usr/share/doc/AvogadroApp that is redundant +rm -rf $PKG/usr/share/doc + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/avogadroapp/avogadroapp.info b/academic/avogadroapp/avogadroapp.info new file mode 100644 index 0000000000..e98567822d --- /dev/null +++ b/academic/avogadroapp/avogadroapp.info @@ -0,0 +1,12 @@ +PRGNAM="avogadroapp" +VERSION="1.97.0" +HOMEPAGE="https://github.com/OpenChemistry/avogadroapp" +DOWNLOAD="https://github.com/OpenChemistry/avogadroapp/archive/1.97.0/avogadroapp-1.97.0.tar.gz \ + https://github.com/OpenChemistry/avogadro-i18n/archive/1.97.0/avogadro-i18n-1.97.0.tar.gz" +MD5SUM="748afd9c2af5d7e193fbbb7c939223a3 \ + 58b31e2047e4467befb2e63eff59672b" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="avogadrolibs" +MAINTAINER="Giancarlo Dessì" +EMAIL="slack@giand.it" diff --git a/academic/drawtiming/doinst.sh b/academic/avogadroapp/doinst.sh index 65c7e2eeb9..65c7e2eeb9 100644 --- a/academic/drawtiming/doinst.sh +++ b/academic/avogadroapp/doinst.sh diff --git a/academic/avogadroapp/slack-desc b/academic/avogadroapp/slack-desc new file mode 100644 index 0000000000..030caebdb3 --- /dev/null +++ b/academic/avogadroapp/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +avogadroapp: avogadroapp (graphic user interface of Avogadro 2) +avogadroapp: +avogadroapp: Avogadro Application is the graphic interface of Avogadro 2, an +avogadroapp: advanced molecular editor designed for cross-platform use in +avogadroapp: computational chemistry, molecular modeling, bioinformatics, +avogadroapp: materials science, and related areas. It offers flexible rendering +avogadroapp: and a powerful application on one plugin architecture. +avogadroapp: +avogadroapp: Homepage: https://github.com/OpenChemistry/avogadroapp +avogadroapp: +avogadroapp: diff --git a/academic/avogadrolibs/README b/academic/avogadrolibs/README new file mode 100644 index 0000000000..4990e7bf74 --- /dev/null +++ b/academic/avogadrolibs/README @@ -0,0 +1,37 @@ +Avogadro Libraries is a subproject of Avogadro 2 as implementation of +Avogadro 1.x mantained by OpenChemistry. It provides 3D rendering, +visualization, analysis and data processing useful in computational +chemistry, molecular modeling, bioinformatics, materials science, and +related areas. +Avogadro Libraries is a dependency required by the graphic interface +user Avogadro Application (avogadroapp). + +This slackbuild requires as needed some dependencies (autodetected) +that improve Avogadro Libraries. You can enable or disable them by +passing variables to the script +(e.g. VAR=yes|no ./avogadrolibs.SlackBuild): + +LIBMSYM=yes|no (default: yes, libmsym required) +SPGLIB=yes|no (default: yes, spglib required) +MMTF=yes|no (default: yes, mmtf-cpp required) +HDF5=yes|no (default: no, hdf5 required) +VTK=yes|no (default: no, VTK required) + +The extension Avogadro Generators (disabled by default) installs +Python input generators that can be run by the Avogadro 2 application +(avogadroapp) to generate input for various codes (Dalton, Q-Chem, +Orca, NWChem, ecc.): these scripts will be installed in a location +where the Avogadro 2 application can find them if the Plugin +Downloader is executed from the graphic interface user. +To enable the extension the dependency pybind11 is required and you +have to pass the variable PYTHON=yes to the slackbuild script: + +PYTHON=yes ./avogadrolibs.SlackBuild + +WARNING: the build enabling the support of VTK libraries works only +with VTK < 9.0 or VTK >= 9.2.6. The build against VTK 9.0.x fails. +Other versions of VTK 9.x earlier than 9.2.6 are not tested. + +Since Avogadro 2 version 1.98.0, the build requires cmake at version +3.24 or greater. This version is the latest compatible with Slackware +15.0 that has cmake remained at the version 3.21. diff --git a/academic/avogadrolibs/avogadrolibs.SlackBuild b/academic/avogadrolibs/avogadrolibs.SlackBuild new file mode 100644 index 0000000000..825baf7b68 --- /dev/null +++ b/academic/avogadrolibs/avogadrolibs.SlackBuild @@ -0,0 +1,157 @@ +#!/bin/bash + +# Slackware build script for avogadrolibs + +# Copyright 2020-2022 Giancarlo Dessì, Cagliari, IT +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=avogadrolibs +VERSION=${VERSION:-1.97.0} +BUILD=${BUILD:-3} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} +MVERSION=${MVERSION:-1.0.0} +CVERSION=${CVERSION:-1.0.1} +AVERSION=${AVERSION:-1.97.0} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +#These are features which are disabled by default +USEHDF5="" ; [ "${HDF5:-no}" = "yes" ] && USEHDF5="-DUSE_HDF5=ON" +USEPYTHON="" ; [ "${PYTHON:-no}" = "yes" ] && USEPYTHON="-DUSE_PYTHON=ON" +USEVTK="" ; [ "${VTK:-no}" = "yes" ] && USEVTK="-DUSE_VTK=ON" + +#These are features which are enabled by default +USELIBMSYM="" ; [ "${LIBMSYM:-yes}" = "no" ] && USELIBMSYM="-DUSE_LIBMSYM=OFF" +USESPGLIB="-DSPGLIB_INCLUDE_DIR=/usr/include/spglib" ; [ "${SPGLIB:-yes}" = "no" ] && \ + USESPGLIB="-DUSE_SPGLIB=OFF" +USEMMTF="" ; [ "${MMTF:-yes}" = "no" ] && USEMMTF="-DUSE_MMTF=OFF" + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} +GENXRDPATH=$TMP/$PRGNAM-$VERSION/build/avogadro/qtplugins/plotxrd/bin + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION molecules crystals avogadrogenerators +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +# Following archives must be unpacked in /tmp since the build process +# searches them as parallel directories and tries to connect to github +# if not found +tar xvf $CWD/molecules-$MVERSION.tar.gz +tar xvf $CWD/crystals-$CVERSION.tar.gz +mv molecules-$MVERSION molecules +mv crystals-$CVERSION crystals +if [ "${PYTHON}" = "yes" ]; then + tar xvf $CWD/avogenerators-$AVERSION.tar.gz + mv avogenerators-$AVERSION avogadrogenerators +fi + +# Now we can change directory to $PRGNAM-$VERSION +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +# fix issues that generate cmake warnings +patch -p1 < $CWD/fix_cmake-find-package.diff +# fix build error cause ambiguous definition in source code +# (thanks to StefanBruens from OpenChemistry in GitHub) +patch -p1 < $CWD/fix_mmtfformat_cpp.diff + +mkdir -p build +# Following steps prevent the download of the executable genXrdPattern +# needed by the build process and include it in the source tree +mkdir -p $GENXRDPATH +cp $CWD/linux64-genXrdPattern $GENXRDPATH +mv $GENXRDPATH/linux64-genXrdPattern $GENXRDPATH/genXrdPattern +chmod 755 $GENXRDPATH/genXrdPattern + +cd build + cmake \ + -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DCMAKE_BUILD_TYPE=Release \ + -DCMAKE_POLICY_DEFAULT_CMP0072=NEW \ + -DENABLE_TESTING=OFF \ + -DENABLE_TRANSLATIONS=ON \ + $USEHDF5 \ + $USEPYTHON \ + $USELIBMSYM \ + $USESPGLIB \ + $USEMMTF \ + $USEVTK \ + .. + make + make install DESTDIR=$PKG +cd .. + +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a *.md LICENSE CITATION.cff $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +# Remove doc files installed by make install in /usr/share/doc/AvogadroLibs that are redundant +rm -rf $PKG/usr/share/doc + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/avogadrolibs/avogadrolibs.info b/academic/avogadrolibs/avogadrolibs.info new file mode 100644 index 0000000000..50472adccb --- /dev/null +++ b/academic/avogadrolibs/avogadrolibs.info @@ -0,0 +1,18 @@ +PRGNAM="avogadrolibs" +VERSION="1.97.0" +HOMEPAGE="https://github.com/OpenChemistry/avogadrolibs" +DOWNLOAD="https://github.com/OpenChemistry/avogadrolibs/archive/1.97.0/avogadrolibs-1.97.0.tar.gz \ + https://github.com/OpenChemistry/molecules/archive/1.0.0/molecules-1.0.0.tar.gz \ + https://github.com/OpenChemistry/crystals/archive/1.0.1/crystals-1.0.1.tar.gz \ + https://github.com/OpenChemistry/avogenerators/archive/1.97.0/avogenerators-1.97.0.tar.gz \ + https://github.com/psavery/genXrdPattern/releases/download/1.0-static/linux64-genXrdPattern" +MD5SUM="a7cc488fb0ab65516117304df62fb2e9 \ + bad118f80a942fe0f082b2a9075ae3b9 \ + b05b526928b89fd27a5784b24c419613 \ + d115ab0f5f4dbf10d2ba2d1191c80a59 \ + e1b3c1d6b951ed83a037567490d75f1d" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="molequeue mmtf-cpp libmsym spglib" +MAINTAINER="Giancarlo Dessì" +EMAIL="slack@giand.it" diff --git a/academic/avogadrolibs/fix_cmake-find-package.diff b/academic/avogadrolibs/fix_cmake-find-package.diff new file mode 100644 index 0000000000..542919c2cc --- /dev/null +++ b/academic/avogadrolibs/fix_cmake-find-package.diff @@ -0,0 +1,42 @@ +--- avogadrolibs-1.95.1/cmake/FindSpglib.cmake 2022-17-04 15:40:00.000000000 +0200 ++++ avogadrolibs-1.95.1-fixed/cmake/FindSpglib.cmake 2022-17-04 15:40:01.000000000 +0200 +@@ -12,7 +12,7 @@ + set(SPGLIB_INCLUDE_DIRS "${SPGLIB_INCLUDE_DIR}") + + include(FindPackageHandleStandardArgs) +-find_package_handle_standard_args(SPGLIB DEFAULT_MSG SPGLIB_INCLUDE_DIR ++find_package_handle_standard_args(Spglib DEFAULT_MSG SPGLIB_INCLUDE_DIR + SPGLIB_LIBRARY) + + mark_as_advanced(SPGLIB_INCLUDE_DIR SPGLIB_LIBRARY) +--- avogadrolibs-1.95.1/cmake/FindLibArchive.cmake 2022-17-04 15:50:00.000000000 +0200 ++++ avogadrolibs-1.95.1-fixed/cmake/FindLibArchive.cmake 2022-17-04 15:50:01.000000000 +0200 +@@ -14,7 +14,7 @@ + set(LIBARCHIVE_LIBRARIES "${LIBARCHIVE_LIBRARY}") + + include(FindPackageHandleStandardArgs) +-find_package_handle_standard_args(LIBARCHIVE DEFAULT_MSG LIBARCHIVE_INCLUDE_DIR ++find_package_handle_standard_args(LibArchive DEFAULT_MSG LIBARCHIVE_INCLUDE_DIR + LIBARCHIVE_LIBRARY) + + mark_as_advanced(LIBARCHIVE_INCLUDE_DIR LIBARCHIVE_LIBRARY) +--- avogadrolibs-1.95.1/python/CMakeLists.txt 2022-17-04 16:00:00.000000000 +0200 ++++ avogadrolibs-1.95.1-fixed/python/CMakeLists.txt 2022-17-04 16:00:01.000000000 +0200 +@@ -1,7 +1,7 @@ + find_package(PythonInterp 3 REQUIRED) + find_package(PythonLibs 3 REQUIRED) + set(PYBIND11_PYTHON_VERSION "3" CACHE STRING "") +-set(PYBIND11_CPP_STANDARD "-std=c++11" CACHE STRING "") ++set(CMAKE_CXX_STANDARD 14 CACHE STRING "") + find_package(pybind11 REQUIRED) + + find_package(Eigen3 REQUIRED) +--- avogadrolibs-1.95.1/avogadro/qtplugins/quantuminput/CMakeLists.txt 2022-18-04 19:00:00.000000000 +0200 ++++ avogadrolibs-1.95.1-fixed/avogadro/qtplugins/quantuminput/CMakeLists.txt 2022-18-04 19:00:01.000000000 +0200 +@@ -41,3 +41,5 @@ + else() ++ if(USE_PYTHON) +- message("Avogadro Generators not found at ${_prefix}!") ++ message("Avogadro Generators not found at ${_prefix}!") ++ endif() + endif() diff --git a/academic/avogadrolibs/fix_mmtfformat_cpp.diff b/academic/avogadrolibs/fix_mmtfformat_cpp.diff new file mode 100644 index 0000000000..03b3994b29 --- /dev/null +++ b/academic/avogadrolibs/fix_mmtfformat_cpp.diff @@ -0,0 +1,31 @@ +Ref: https://github.com/OpenChemistry/avogadrolibs/commit/0db79eb15b2f1dda1dd07a807b98086698cfee7a +Thanks to StefanBruens from OpenChemistry project + +--- avogadrolibs-1.97.0/avogadro/io/mmtfformat.cpp 2023-20-03 18:50:00.000000000 +0200 ++++ avogadrolibs-1.97.0-fixed/avogadro/io/mmtfformat.cpp 2023-20-03 18:50:01.000000000 +0200 +@@ -33,21 +33,25 @@ + + MMTFFormat::~MMTFFormat() = default; + ++namespace { + // from latest MMTF code, under the MIT license + // https://github.com/rcsb/mmtf-cpp/blob/master/include/mmtf/structure_data.hpp ++#if MMTF_SPEC_VERSION_MAJOR <= 1 && MMTF_SPEC_VERSION_MINOR < 1 + bool is_polymer(const unsigned int chain_index, + const std::vector<mmtf::Entity>& entity_list) + { + for (const auto & i : entity_list) { + if (std::find(i.chainIndexList.begin(), + i.chainIndexList.end(), + chain_index) != i.chainIndexList.end()) { + return (i.type == "polymer" || + i.type == "POLYMER"); + } + } + return false; + } ++#endif ++} // namespace + + bool MMTFFormat::read(std::istream& file, Molecule& molecule) + { diff --git a/academic/avogadrolibs/slack-desc b/academic/avogadrolibs/slack-desc new file mode 100644 index 0000000000..a04b7ca223 --- /dev/null +++ b/academic/avogadrolibs/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +avogadrolibs: avogadrolibs (Libraries for Avogadro 2) +avogadrolibs: +avogadrolibs: Avogadro libraries provide 3D rendering, visualization, analysis and +avogadrolibs: data processing useful in computational chemistry, molecular +avogadrolibs: modeling, bioinformatics, materials science, and related areas. +avogadrolibs: Avogadro 2 is being developed as part of the Open Chemistry project +avogadrolibs: at Kitware, along with companion tools and libraries to support. +avogadrolibs: +avogadrolibs: Homepage: https://github.com/OpenChemistry/avogadrolibs +avogadrolibs: +avogadrolibs: diff --git a/academic/bcftools/README b/academic/bcftools/README index aef002668d..51b0b0b55b 100644 --- a/academic/bcftools/README +++ b/academic/bcftools/README @@ -4,6 +4,6 @@ vcfisec, etc.) and the samtools BCF calling from bcftools subdirectory of the previous samtools. BCFtools are meant as a faster replacement for most of the perl VCFtools commands. -Prior to the introduction of HTSlib, SAMtools and BCFtools were distributed -in a single samtools-0.1.x package. This old version remains available from -SBo as samtools-legacy. +Prior to the introduction of HTSlib, SAMtools and BCFtools were +distributed in a single samtools-0.1.x package. This old version remains +available from SBo as samtools-legacy. diff --git a/academic/bcftools/bcftools.SlackBuild b/academic/bcftools/bcftools.SlackBuild index 526b44d687..b7a8433557 100644 --- a/academic/bcftools/bcftools.SlackBuild +++ b/academic/bcftools/bcftools.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash -# Slackware build script for samtools +# Slackware build script for bcftools -# Copyright 2017-2020 Rob van Nues # All rights reserved. +# Copyright 2017-2023 Rob van Nues # All rights reserved. # # Redistribution and use of this script, with or without modification, is # permitted provided that the following conditions are met: @@ -21,11 +21,14 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) -PRGNAM=bcftools -VERSION=${VERSION:-1.10.2} +PRGNAM=bcftools +VERSION=${VERSION:-1.19} +HTSLIBV=${HTSLIBV:-1.19} BUILD=${BUILD:-1} -TAG=${TAG:-_SBo} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,13 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -69,7 +78,7 @@ find -L . \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; # Force linking to installed htslib -rm -r htslib-$VERSION +rm -r htslib-$HTSLIBV CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ @@ -99,7 +108,7 @@ for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; r mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - AUTHORS README LICENSE INSTALL NEWS \ + AUTHORS README LICENSE NEWS \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild @@ -107,4 +116,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/bcftools/bcftools.info b/academic/bcftools/bcftools.info index b8201d734d..1998ed001c 100644 --- a/academic/bcftools/bcftools.info +++ b/academic/bcftools/bcftools.info @@ -1,8 +1,8 @@ PRGNAM="bcftools" -VERSION="1.10.2" +VERSION="1.19" HOMEPAGE="http://www.htslib.org" -DOWNLOAD="https://github.com/samtools/bcftools/releases/download/1.10.2/bcftools-1.10.2.tar.bz2" -MD5SUM="081ebb6138f5fdf394cb6a074effadb3" +DOWNLOAD="https://github.com/samtools/bcftools/releases/download/1.19/bcftools-1.19.tar.bz2" +MD5SUM="9b4e8be279024d19f36bbaad1d2bdb41" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="htslib" diff --git a/academic/bcftools/slack-desc b/academic/bcftools/slack-desc index 2f85ffb7dd..f4c0b9871b 100644 --- a/academic/bcftools/slack-desc +++ b/academic/bcftools/slack-desc @@ -10,9 +10,9 @@ bcftools: bcftools (BCF calling tools) bcftools: bcftools: bcftools contains all the "vcf..." commands which previously lived in bcftools: the htslib repository (such as vcfcheck, vcfmerge, vcfisec, etc.) and -bcftools: the samtools BCF calling from bcftools subdirectory of the previous +bcftools: the samtools BCF calling from bcftools subdirectory of the 'legacy' bcftools: samtools. BCFtools are meant as a faster replacement for most of the -bcftools: perl VCFtools commands. Bcftools comes with its own hstlib sources. +bcftools: perl VCFtools commands. bcftools: bcftools: Homepage: http://www.htslib.org bcftools: diff --git a/academic/bedGraphToBigWig/bedGraphToBigWig.SlackBuild b/academic/bedGraphToBigWig/bedGraphToBigWig.SlackBuild index b270b511bc..0c04857e46 100644 --- a/academic/bedGraphToBigWig/bedGraphToBigWig.SlackBuild +++ b/academic/bedGraphToBigWig/bedGraphToBigWig.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for bedGraphToBigWig -# Copyright 2016 Petar Petrov slackalaxy@gmail.com +# Copyright 2016-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,20 +22,30 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +# 20220404 bkw: Modified by SlackBuilds.org, BUILD=2: +# - strip binary. + +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=bedGraphToBigWig VERSION=${VERSION:-4} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -54,7 +64,7 @@ rm -rf $PRGNAM-$VERSION tar xvf $CWD/$PRGNAM-$VERSION.tar.gz cd $PRGNAM-$VERSION -install -D -m755 $PRGNAM $PKG/usr/bin/$PRGNAM +install -s -D -m755 $PRGNAM $PKG/usr/bin/$PRGNAM mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild @@ -63,4 +73,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/bedtools/bedtools.SlackBuild b/academic/bedtools/bedtools.SlackBuild index ee87fbbbe4..19307cc286 100644 --- a/academic/bedtools/bedtools.SlackBuild +++ b/academic/bedtools/bedtools.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for bedtools -# Copyright 2014-2019 Petar Petrov slackalaxy@gmail.com +# Copyright 2014-2023 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,11 +22,14 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=bedtools DIRNAM=bedtools2 -VERSION=${VERSION:-2.28.0} +VERSION=${VERSION:-2.31.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -36,7 +39,11 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -70,11 +77,7 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -# Use our CFLAGS -sed -i "/CXXFLAGS/s/=/+=/" Makefile - -CXXFLAGS="$SLKCFLAGS -std=c++11" \ -make +CXXFLAGS="$SLKCFLAGS" make # Install the binary and scripts cd bin @@ -91,11 +94,11 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a LICENSE README.md RELEASE_HISTORY $PKG/usr/doc/$PRGNAM-$VERSION +cp -a LICENSE README.md $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/bedtools/bedtools.info b/academic/bedtools/bedtools.info index 8ebd0862f4..ceec5617fd 100644 --- a/academic/bedtools/bedtools.info +++ b/academic/bedtools/bedtools.info @@ -1,8 +1,8 @@ PRGNAM="bedtools" -VERSION="2.28.0" +VERSION="2.31.1" HOMEPAGE="http://bedtools.readthedocs.org/" -DOWNLOAD="https://github.com/arq5x/bedtools2/releases/download/v2.28.0/bedtools-2.28.0.tar.gz" -MD5SUM="611d55ab9f03a7ee0fa6639af7299acf" +DOWNLOAD="https://github.com/arq5x/bedtools2/releases/download/v2.31.1/bedtools-2.31.1.tar.gz" +MD5SUM="d1eb463c07c0753a4ee3af614b2ae387" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/biblesync/README b/academic/biblesync/README index 6a70d6d96d..d2d91161ca 100644 --- a/academic/biblesync/README +++ b/academic/biblesync/README @@ -9,7 +9,7 @@ Bible program induces the audience's programs to follow along. Some History. Up until and including xiphos 4.0.0 biblesync was included as part of -the xiphos source code. It has been removed from the source in xiphos 4.0.1 -and set to be a general library for any bible software that wants to use -shared navigation. +the xiphos source code. It has been removed from the source in xiphos +4.0.1 and set to be a general library for any bible software that +wants to use shared navigation. biblesync is a requirement for xiphos 4.0.1 or higher. diff --git a/academic/biblesync/biblesync.SlackBuild b/academic/biblesync/biblesync.SlackBuild index dfdd60598a..f3820b5f67 100644 --- a/academic/biblesync/biblesync.SlackBuild +++ b/academic/biblesync/biblesync.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for biblesync -# Copyright (c) 2015/2018 Tim Dickson <dickson.tim@googlemail.com> +# Copyright (c) 2015/2020 Tim Dickson <dickson.tim@googlemail.com> # # Redistribution and use in source and binary forms, with or without # modification, are permitted provided that the following conditions are @@ -30,10 +30,13 @@ # (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=biblesync -VERSION=${VERSION:-2.0.1} +VERSION=${VERSION:-2.1.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -43,7 +46,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -91,23 +101,18 @@ make install DESTDIR=$PKG find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true -# Compress man page -mkdir -p $PKG/usr/man/man7 -mv $PKG/usr/share/man/man7/$PRGNAM.7 $PKG/usr/man/man7/$PRGNAM.7 +mv $PKG/usr/share/man $PKG/usr/ gzip $PKG/usr/man/man7/$PRGNAM.7 #remove old man path rm -r $PKG/usr/share -#copy over docs etc. mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a $DOCS $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc -cat $CWD/doinst.sh > $PKG/install/doinst.sh -#now to make the package cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/biblesync/biblesync.info b/academic/biblesync/biblesync.info index 00a1bb56d4..560d81ec74 100644 --- a/academic/biblesync/biblesync.info +++ b/academic/biblesync/biblesync.info @@ -1,8 +1,8 @@ PRGNAM="biblesync" -VERSION="2.0.1" +VERSION="2.1.0" HOMEPAGE="https://github.com/karlkleinpaste/biblesync" -DOWNLOAD="https://github.com/karlkleinpaste/biblesync/releases/download/2.0.1/biblesync-2.0.1.tar.gz" -MD5SUM="b9db8aae61bb0f9a4545c0782968466e" +DOWNLOAD="https://github.com/karlkleinpaste/biblesync/releases/download/2.1.0/biblesync-2.1.0.tar.gz" +MD5SUM="51b0deef468812a1f5b3c87ae5d14fb9" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/biblesync/doinst.sh b/academic/biblesync/doinst.sh deleted file mode 100644 index 682c942551..0000000000 --- a/academic/biblesync/doinst.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/sh -#we installed a library so run ldconfig -/sbin/ldconfig diff --git a/academic/bibletime/README b/academic/bibletime/README index b6137880cc..3a862cfa06 100644 --- a/academic/bibletime/README +++ b/academic/bibletime/README @@ -1,6 +1,9 @@ -BibleTime is a Bible study application for Linux. It is based on the K Desktop -Environment and uses the Sword programming library to work with Bible texts, -commentaries, dictionaries, and books provided by the Crosswire Bible Society. +BibleTime is a Bible study application for Linux. It is based on the K +Desktop Environment and uses the Sword programming library to work with +Bible texts, commentaries, dictionaries, and books provided by the +Crosswire Bible Society. -This version requires sword version 1.8.1 or higher, and qt5.9 or higher. -Homepage: http://bibletime.info/ +You will need bible text as well as the dependencies listed. +sword-data-KJV available on slackbuilds.org provides a basic +King James Version with strongs. bibletime includes bookshelf manager +which allows you to download other versions over the internet. diff --git a/academic/bibletime/bibletime.SlackBuild b/academic/bibletime/bibletime.SlackBuild index 9af701fef1..a25bde4b12 100644 --- a/academic/bibletime/bibletime.SlackBuild +++ b/academic/bibletime/bibletime.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # A slackbuild script to build the BibleTime Sword frontend @@ -26,12 +26,18 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. # Modified by Robert Delahunt [twinreverb[at]puresimplicity.net -# Modified 2018/9 by Tim Dickson (dickson.tim@googlemail.com) +# Modified 2018/19/20 by Tim Dickson (dickson.tim@googlemail.com) +# Modified 20200918 by B. Watson <urchlay@slackware.uk> +# Modified 20220412 by Tim Dickson (dickson.tim@googlemail.com) +# updated for v3.0.3 and fix doc location by Tim Dickson (dickson.tim@googlemail.com) + +cd $(dirname $0) ; CWD=$(pwd) PRGNAM=bibletime -VERSION=${VERSION:-3.0_beta2} +VERSION=${VERSION:-3.0.3} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -41,7 +47,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -68,20 +81,8 @@ cd $TMP rm -rf $PRGNAM-$VERSION tar -xJvf $CWD/$PRGNAM-$VERSION.tar.xz cd $PRGNAM-$VERSION -chown -R root:root . -find -L . \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; - -mkdir build -#patch CMakeLists.txt so it works with verson of cmake on slack14.2 -#these patches can be removed once cmake gets to 3.10 or higher -sed -i "s/VERSION 3.10/VERSION 3.5/g" CMakeLists.txt -sed -i "s/^CHECK_IPO_SUPPORTED(RESULT HAVE_IPO)/SET(HAVE_IPO FALSE)/g" CMakeLists.txt -sed -i "s/^INCLUDE(CheckIPO/#INCLUDE(CheckIPO/g" CMakeLists.txt -sed -i "/TARGET_COMPILE_FEATURES/s/.*/SET(CMAKE_CXX_STANDARD 11)/" CMakeLists.txt + +mkdir -p build cd build cmake \ -Wno-dev \ @@ -90,7 +91,8 @@ cd build -DCMAKE_SKIP_RPATH:BOOL=ON \ -DCMAKE_C_FLAGS="$SLKCFLAGS" \ -DCMAKE_CXX_FLAGS="$SLKCFLAGS" \ - -DLIB_SUFFIX=$LIBDIRSUFFIX .. + -DBT_DOCDIR="doc/$PRGNAM-$VERSION" \ + -DLIB_SUFFIX=$LIBDIRSUFFIX .. make make install DESTDIR=$PKG cd .. @@ -110,4 +112,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/bibletime/bibletime.info b/academic/bibletime/bibletime.info index 06b7202b16..dc3f8b1300 100644 --- a/academic/bibletime/bibletime.info +++ b/academic/bibletime/bibletime.info @@ -1,10 +1,10 @@ PRGNAM="bibletime" -VERSION="3.0_beta2" +VERSION="3.0.3" HOMEPAGE="http://www.bibletime.info/" -DOWNLOAD="https://github.com/bibletime/bibletime/releases/download/v3.0_beta2/bibletime-3.0_beta2.tar.xz" -MD5SUM="1874d442546791b5611343fbcf2aed73" +DOWNLOAD="https://github.com/bibletime/bibletime/releases/download/v3.0.3/bibletime-3.0.3.tar.xz" +MD5SUM="07c4f717f15be1418c0e3f434ee2983c" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="sword qt5" +REQUIRES="sword po4a fop" MAINTAINER="Tim Dickson" EMAIL="dickson.tim@googlemail.com" diff --git a/academic/bibus/README b/academic/bibus/README index 80e25c8602..4286359d52 100644 --- a/academic/bibus/README +++ b/academic/bibus/README @@ -1,4 +1,5 @@ -Bibus is a bibliographic and reference management software. As with other -such tools, Bibus allows one to search, edit, and sort bibliographic records. -In addition, Bibus contains features that makes it unique among open source -and even commercial bibliographic databases. +Bibus is bibliographic and reference management software. +As with other such tools, Bibus allows one to search, edit, and sort +bibliographic records. In addition, Bibus contains features that +makes it unique among open source and even commercial bibliographic +databases. diff --git a/academic/bibus/bibus.SlackBuild b/academic/bibus/bibus.SlackBuild index f00affaf8a..8ce9825499 100644 --- a/academic/bibus/bibus.SlackBuild +++ b/academic/bibus/bibus.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for bibus @@ -27,13 +27,23 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=bibus VERSION=${VERSION:-1.5.2} ARCH=noarch BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi -CWD=$(pwd) TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -82,4 +92,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/biopython/biopython.SlackBuild b/academic/biopython/biopython.SlackBuild index 22bd291d1f..d21249dac8 100644 --- a/academic/biopython/biopython.SlackBuild +++ b/academic/biopython/biopython.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for biopython -# Copyright 2019 Petar Petrov slackalaxy@gmail.com +# Copyright 2019-2023 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=biopython -VERSION=${VERSION:-1.74} +VERSION=${VERSION:-1.81} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -69,7 +79,7 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -python setup.py install --root=$PKG +python3 setup.py install --root=$PKG find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true @@ -83,4 +93,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/biopython/biopython.info b/academic/biopython/biopython.info index 9906f1df81..db278d6620 100644 --- a/academic/biopython/biopython.info +++ b/academic/biopython/biopython.info @@ -1,10 +1,10 @@ PRGNAM="biopython" -VERSION="1.74" +VERSION="1.81" HOMEPAGE="https://biopython.org/" -DOWNLOAD="http://biopython.org/DIST/biopython-1.74.tar.gz" -MD5SUM="cead2bfe9e7be45267eba00635f68d5c" +DOWNLOAD="http://biopython.org/DIST/biopython-1.81.tar.gz" +MD5SUM="06cabd14f55d624db366ff75efb60ed2" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="numpy" +REQUIRES="python2-numpy" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/boinc/README b/academic/boinc/README index 5c3f695a28..f63d0e2e4c 100644 --- a/academic/boinc/README +++ b/academic/boinc/README @@ -1,37 +1,32 @@ The Berkeley Open Infrastructure for Network Computing (BOINC) -BOINC is an open source middleware system for volunteer and grid computing. -It was originally developed to support the SETI@home project before it became -useful as a platform for other distributed applications in areas as diverse as -mathematics, medicine, molecular biology, climatology, and astrophysics. The -intent of BOINC is to make it possible for researchers to tap into the -enormous processing power of personal computers around the world. - -Use the idle time on your computer (Windows, Mac, or Linux) to cure diseases, -study global warming, discover pulsars, and do many other types of scientific -research. It's safe, secure, and easy. - +BOINC is an open source middleware system for volunteer and grid +computing. It was originally developed to support the SETI@home +project before it became useful as a platform for other distributed +applications in areas as diverse as mathematics, medicine, molecular +biology, climatology, and astrophysics. The intent of BOINC is to make +it possible for researchers to tap into the enormous processing power +of personal computers around the world. + +Use the idle time on your computer (Windows, Mac, or Linux) to cure +diseases, study global warming, discover pulsars, and do many other +types of scientific research. It's safe, secure, and easy. Building -(1) BOINC needs a static library for wxGTK3, compile with - - STATIC=yes ./wxGTK3.SlackBuild - -(2) Edit DATADIR in the script or run +(1) Edit DATADIR in the script or run DATADIR="/home/<user>/.boinc_data" ./boinc.SlackBuild -to set the data directory in your user's home and build the package. +to set the data directory in your user's home, or prefered data path, +and build the package. The default data path is /var/lib/boinc_data. -(3) If you do not wish to build the boincmgr GUI, +(2) If you do not wish to build the boincmgr GUI, BOINCMGR=no ./boinc.SlackBuild -then you do not need to install the dependencies (webp, webkit, wxGTK3). - - -After installation +then you do not need to install the dependencies (wxWidgets). See +README.Slackware for details on headless configuration. After installation you need to join a BOINC project: http://boinc.berkeley.edu/projects.php diff --git a/academic/boinc/README.Slackware b/academic/boinc/README.Slackware new file mode 100644 index 0000000000..c0f1ceb4e3 --- /dev/null +++ b/academic/boinc/README.Slackware @@ -0,0 +1,34 @@ +For headless operation, a start up script is included. The script will +execute as root with the data directory as '/var/lib/boinc_data'. +Modify as needed: + +BOINC_DIR=/var/lib/boinc_data # directory of boinc data files +BOINC_USER=root # user that will run boinc process +BOINC_OPTIONS="--dir $BOINC_DIR --redirectio" + +Refer to the boinc manpage for parameters you can add to +BOINC_OPTIONS. + +To run boinc on boot, add the following code to /etc/rc.d/rc.local: + +if [ -x /etc/rc.d/rc.boinc ]; then + /etc/rc.d/rc.boinc start +fi + +and to /etc/rc.d/rc.local_shutdown + +if [ -x /etc/rc.d/rc.boinc ]; then + /etc/rc.d/rc.boinc stop +fi + +Note 1: +The default configuration enables boinc control on the running +host via boinccmg or boincmgr on the same running host. To truly run +headless, you will need to configure boinc to allow RPC access from +another host. + +Note 2: +If you use the default data path of /var/lib/boinc_data as a non-root +user, before first use, you will need to create that path and set the +appropriate user permissions. + diff --git a/academic/boinc/boinc.SlackBuild b/academic/boinc/boinc.SlackBuild index 7e94c5251c..8f8330ac87 100644 --- a/academic/boinc/boinc.SlackBuild +++ b/academic/boinc/boinc.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for boinc -# Copyright 2013-2018 Edward Koenig, Vancouver, WA, USA <kingbeowulf@gmail.com> +# Copyright 2013-2022 Edward Koenig, Vancouver, WA, USA # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,13 +22,19 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. # -# TODO: add rc.boinc. +# 08DEC2022: +# Version update +# switched to wxWidgets-3.2 +# Bypass wxconfig symlink for compatibility. + +cd $(dirname $0) ; CWD=$(pwd) PRGNAM=boinc -VERSION=${VERSION:-7.16.4} -BRANCH=${BRANCH:-7.16} +VERSION=${VERSION:-7.24.1} +BRANCH=${BRANCH:-7.24} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -38,7 +44,11 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -60,7 +70,7 @@ fi set -e # Your default working directory location. Pass with DATADIR=<dir> Boinc.SlackBuild -DATADIR=${DATADIR:-'~/.boinc_data'} +DATADIR=${DATADIR:-'/var/lib/boinc_data'} BOINCMGR=${BOINCMGR:-yes} if [ "$BOINCMGR" = "yes" ]; then @@ -97,6 +107,7 @@ CXXFLAGS="$SLKCFLAGS" \ --disable-shared \ $do_mgr \ --with-x \ + --with-wx-config=/usr/lib$LIBDIRSUFFIX/wx/config/gtk3-unicode-3.2 \ --build=$ARCH-slackware-linux make @@ -111,18 +122,28 @@ for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; r cat $CWD/boincgui.sh > $PKG/usr/bin/boincgui.sh sed -i "s|WORKDIR|$DATADIR|g" $PKG/usr/bin/boincgui.sh chmod +x $PKG/usr/bin/boincgui.sh +mkdir -p $PKG/etc/rc.d +cat $CWD/rc.boinc.txt > $PKG/etc/rc.d/rc.boinc.new mkdir -p $PKG/usr/share/{applications,pixmaps} cp $CWD/boinc.desktop $PKG/usr/share/applications cp $CWD/boinc.png $PKG/usr/share/pixmaps mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a COPYING COPYING.LESSER COPYRIGHT INSTALL todo notes $PKG/usr/doc/$PRGNAM-$VERSION +cp -a COPYING COPYING.LESSER COPYRIGHT INSTALL notes $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +rm -f $PKG/usr/lib*/*.la + +# remove unneeded init script, systemd service +rm -rf $PKG/etc/default +rm -rf $PKG/etc/init.d +rm -rf $PKG/usr/lib +rm -f $PKG/usr/bin/boinc_client + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/boinc/boinc.info b/academic/boinc/boinc.info index 8a3e9be145..4d1bb74cdd 100644 --- a/academic/boinc/boinc.info +++ b/academic/boinc/boinc.info @@ -1,10 +1,10 @@ PRGNAM="boinc" -VERSION="7.16.4" +VERSION="7.24.1" HOMEPAGE="https://boinc.berkeley.edu/" -DOWNLOAD="https://github.com/BOINC/boinc/archive/client_release/7.16/7.16.4/boinc-client_release-7.16-7.16.4.tar.gz" -MD5SUM="33aa0de75425d7c0b8acca0301df18b1" +DOWNLOAD="https://github.com/BOINC/boinc/archive/client_release/7.24/7.24.1/boinc-client_release-7.24-7.24.1.tar.gz" +MD5SUM="1844352e5b2ef9c9cf2325e1f991a5cc" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="libwebp wxGTK3" +REQUIRES="wxWidgets" MAINTAINER="Edward W. Koenig" -EMAIL="kingbeowulf@gmail.com" +EMAIL="kingbeowulf@linuxgalaxy.org" diff --git a/academic/boinc/boincgui.sh b/academic/boinc/boincgui.sh index 435bb29e63..5251e68d78 100644 --- a/academic/boinc/boincgui.sh +++ b/academic/boinc/boincgui.sh @@ -1,6 +1,6 @@ #!/bin/bash # -# Copyright 2013-2014 Edward Koenig, Vancouver, WA, USA <kingbeowulf@gmail.com> +# Copyright 2013-2014 Edward W. Koenig, Vancouver, WA, USA # All rights reserved. # # Redistribution and use of this script, with or without modification, is diff --git a/academic/boinc/doinst.sh b/academic/boinc/doinst.sh index 5fb28930db..9634ecf6f7 100644 --- a/academic/boinc/doinst.sh +++ b/academic/boinc/doinst.sh @@ -1,3 +1,29 @@ +config() { + NEW="$1" + OLD="$(dirname $NEW)/$(basename $NEW .new)" + # If there's no config file by that name, mv it over: + if [ ! -r $OLD ]; then + mv $NEW $OLD + elif [ "$(cat $OLD | md5sum)" = "$(cat $NEW | md5sum)" ]; then + # toss the redundant copy + rm $NEW + fi + # Otherwise, we leave the .new copy for the admin to consider... +} + +preserve_perms() { + NEW="$1" + OLD="$(dirname $NEW)/$(basename $NEW .new)" + if [ -e $OLD ]; then + cp -a $OLD ${NEW}.incoming + cat $NEW > ${NEW}.incoming + mv ${NEW}.incoming $NEW + fi + config $NEW +} + +preserve_perms etc/rc.d/rc.boinc.new + if [ -x /usr/bin/update-desktop-database ]; then /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 fi diff --git a/academic/boinc/rc.boinc.txt b/academic/boinc/rc.boinc.txt new file mode 100644 index 0000000000..e84583ed0b --- /dev/null +++ b/academic/boinc/rc.boinc.txt @@ -0,0 +1,105 @@ +#!/bin/bash + +# rc.boinc - BOINC startup/control script for Slackware Linux +# +# Copyright 2022 Edward Koenig, Vancouver, WA, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR ''AS IS'' AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +BOINC_DIR=//var/lib/boinc_data # directory of boinc files +BOINC_BIN=/usr/bin/boinc # name of the boinc binary +BOINC_USER=root # user that will run boinc process +BOINC_OPTIONS="--dir $BOINC_DIR --redirectio" +# "--dir $BOINC_DIR --daemon" will send logs syslog instead of +# stdoutdae.txt and stderrdae.txt + +boinc_status() { + if ( ps -ef | grep "$BOINC_BIN$" > /dev/null 2>&1 ); then + return 0 + else + return 3 +fi +} + +boinc_start() { + boinc_status + if [ $? = 0 ]; then + echo "BOINC is already running" + exit 1 + fi + + if [ ! -d $BOINC_DIR ]; then + echo "ERROR: $BOINC_DIR does not exist" + exit 1 + elif [ ! -x $BOINC_BIN ]; then + echo "ERROR: $BOINC_BIN does not exist or not executable" + exit 1 + fi + + echo "Starting BOINC client" + su - $BOINC_USER -c "cd $BOINC_DIR; exec $BOINC_BIN $BOINC_OPTIONS" & + +} + +boinc_stop() { + echo "Stopping BOINC client" + killall $BOINC_BIN +} + +boinc_restart() { + echo "Restarting BOINC client" + + boinc_status + if [ $? = 0 ]; then + boinc_stop + sleep 3 + boinc_start + else + boinc_start +fi +} + + +case "$1" in + start) + boinc_start + exit 0 + ;; + stop) + boinc_stop + exit 0 + ;; + restart) + boinc_restart + exit 0 + ;; + status) + boinc_status + if [ $? = 0 ]; then + echo "BOINC is running" + else + echo "BOINC is not running" + fi + ;; + *) + echo "Usage: $0 start|stop|restart|status" + exit 1 + ;; + +esac diff --git a/academic/bowtie/bowtie.SlackBuild b/academic/bowtie/bowtie.SlackBuild index 0f5beae851..ad3c81770e 100644 --- a/academic/bowtie/bowtie.SlackBuild +++ b/academic/bowtie/bowtie.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for bowtie -# Copyright 2013-2016 Petar Petrov slackalaxy@gmail.com +# Copyright 2013-2022 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,36 +22,40 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=bowtie -VERSION=${VERSION:-1.0.0} -BUILD=${BUILD:-1} +VERSION=${VERSION:-1.3.1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" - LIBDIRSUFFIX="" -elif [ "$ARCH" = "i686" ]; then - SLKCFLAGS="-O2 -march=i686 -mtune=i686" - LIBDIRSUFFIX="" -elif [ "$ARCH" = "x86_64" ]; then +if [ "$ARCH" = "x86_64" ]; then SLKCFLAGS="-O2 -fPIC" LIBDIRSUFFIX="64" else - SLKCFLAGS="-O2" - LIBDIRSUFFIX="" + printf "\n$ARCH is unsupported by bowtie\n" + exit 1 fi set -e @@ -59,8 +63,8 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $PRGNAM-$VERSION -tar xvf $CWD/${PRGNAM}_${VERSION}.orig.tar.gz +rm -rf $PRGNAM-$VERSION-src +tar xvf $CWD/${PRGNAM}-${VERSION}.tar.gz cd $PRGNAM-$VERSION chown -R root:root . find -L . \ @@ -69,19 +73,14 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -# Thanks to Debian for the set of patches! -patch -p1 -i $CWD/patches/disable_bits_flag.patch -patch -p1 -i $CWD/patches/no_hash_style_both_for_mips.patch -patch -p1 -i $CWD/patches/seqan-fix-setBegin-call.patch -patch -p1 -i $CWD/patches/use-dpkg-buildflags.patch - -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ +sed -i "s|-O3|$SLKCFLAGS -O3|" Makefile make install -D -m755 $PRGNAM $PKG/usr/bin/$PRGNAM -install -D -m755 $PRGNAM-build $PKG/usr/bin/$PRGNAM-build -install -D -m755 $PRGNAM-inspect $PKG/usr/bin/$PRGNAM-inspect +executables=$( ls bowtie-* ) +for b in ${executables[@]}; do + install -D -m755 $b $PKG/usr/bin/$b +done # Copy genomic data, scripts and more mkdir -p $PKG/usr/share/$PRGNAM @@ -107,4 +106,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/bowtie/bowtie.info b/academic/bowtie/bowtie.info index 49d8c838cb..4713d9bae4 100644 --- a/academic/bowtie/bowtie.info +++ b/academic/bowtie/bowtie.info @@ -1,10 +1,10 @@ PRGNAM="bowtie" -VERSION="1.0.0" -HOMEPAGE="http://bowtie-bio.sourceforge.net/" -DOWNLOAD="https://sourceforge.net/projects/sboppetrov/files/bowtie/bowtie_1.0.0.orig.tar.gz" -MD5SUM="75d402c856b64958ec4bc0f67d011eb9" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" +VERSION="1.3.1" +HOMEPAGE="http://bowtie-bio.sourceforge.net/index.shtml" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="https://github.com/BenLangmead/bowtie/archive/v1.3.1/bowtie-1.3.1.tar.gz" +MD5SUM_x86_64="06b0377e967501ce73bca087e6c5fcb0" REQUIRES="" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/bowtie2-legacy/bowtie2-legacy.SlackBuild b/academic/bowtie2-legacy/bowtie2-legacy.SlackBuild index 882dd6040e..262e05cab7 100644 --- a/academic/bowtie2-legacy/bowtie2-legacy.SlackBuild +++ b/academic/bowtie2-legacy/bowtie2-legacy.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for bowtie2-legacy @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=bowtie2-legacy VERSION=${VERSION:-2.1.0} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} SRCNAM=bowtie2 @@ -37,7 +40,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -71,6 +81,7 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; +sed -i "s,flag > 0,flag != 0," aligner_result.cpp # Use our FLAGS sed -i "/RELEASE_FLAGS/s/=/+=/" Makefile @@ -107,4 +118,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/bowtie2/bowtie2.SlackBuild b/academic/bowtie2/bowtie2.SlackBuild index 370b409bc0..37f440626e 100644 --- a/academic/bowtie2/bowtie2.SlackBuild +++ b/academic/bowtie2/bowtie2.SlackBuild @@ -1,9 +1,9 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for bowtie2 # Copyright 2013-2016 Petar Petrov slackalaxy@gmail.com -# Copyright 2018-2020 Rob van Nues sborg63@disroot.org +# Copyright 2018-2024 Rob van Nues sborg63@disroot.org # # All rights reserved. # @@ -24,10 +24,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=bowtie2 -VERSION=${VERSION:-2.4.1} +VERSION=${VERSION:-2.5.3} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -37,23 +40,21 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i586" ]; then - SLKCFLAGS="-O2 -march=i586 -mtune=i686" - LIBDIRSUFFIX="" -elif [ "$ARCH" = "i686" ]; then - SLKCFLAGS="-O2 -march=i686 -mtune=i686" - LIBDIRSUFFIX="" -elif [ "$ARCH" = "x86_64" ]; then +if [ "$ARCH" = "x86_64" ]; then SLKCFLAGS="-O2 -fPIC" LIBDIRSUFFIX="64" else - SLKCFLAGS="-O2" - LIBDIRSUFFIX="" + printf "\n$ARCH is unsupported by $PRGNAM\n" + exit 1 fi set -e @@ -72,8 +73,6 @@ find -L . \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; #Use our FLAGS -#sed -i "/RELEASE_FLAGS/s/=/+=/" Makefile - RELEASE_FLAGS+="$SLKCFLAGS" \ make @@ -102,7 +101,7 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - AUTHORS LICENSE MANUAL NEWS TUTORIAL VERSION doc \ + AUTHORS LICENSE MANUAL NEWS TUTORIAL BOWTIE2_VERSION doc \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild @@ -110,4 +109,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/bowtie2/bowtie2.info b/academic/bowtie2/bowtie2.info index 8c3fb45d87..6942bdcfcd 100644 --- a/academic/bowtie2/bowtie2.info +++ b/academic/bowtie2/bowtie2.info @@ -1,10 +1,10 @@ PRGNAM="bowtie2" -VERSION="2.4.1" +VERSION="2.5.3" HOMEPAGE="https://github.com/BenLangmead/bowtie2/releases" -DOWNLOAD="https://github.com/BenLangmead/bowtie2/archive/v2.4.1/bowtie2-2.4.1.tar.gz" -MD5SUM="5938482fab363c6356f9662cce38f99c" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="tbb python3" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="https://github.com/BenLangmead/bowtie2/archive/v2.5.3/bowtie2-2.5.3.tar.gz" +MD5SUM_x86_64="c9bb6edaf47c4487efd4b2a055912182" +REQUIRES="tbb" MAINTAINER="Rob van Nues" EMAIL="sborg63@disroot.org" diff --git a/academic/bpp-core/bpp-core.SlackBuild b/academic/bpp-core/bpp-core.SlackBuild index ab7439f63a..ea5ae35b52 100644 --- a/academic/bpp-core/bpp-core.SlackBuild +++ b/academic/bpp-core/bpp-core.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for bpp-core -# Copyright 2017-2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2017-2022 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=bpp-core VERSION=${VERSION:-2.4.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,11 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -69,6 +76,9 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; +# thanks Debian +patch -p1 -i $CWD/gcc11.patch + sed -i "s|cmake-package-location lib/cmake|cmake-package-location lib${LIBDIRSUFFIX}/cmake|" CMakeLists.txt mkdir -p build @@ -86,11 +96,11 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a AUTHORS.txt ChangeLog COPYING.txt INSTALL.txt $PKG/usr/doc/$PRGNAM-$VERSION +cp -a AUTHORS.txt ChangeLog COPYING.txt $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/bpp-core/gcc11.patch b/academic/bpp-core/gcc11.patch new file mode 100644 index 0000000000..d4db303a25 --- /dev/null +++ b/academic/bpp-core/gcc11.patch @@ -0,0 +1,13 @@ +Description: Including limits lib to fix gcc-11 FTBFS +Author: Nilesh Patra <nilesh@debian.org> +Last-Update: 2021-04-15 +--- a/src/Bpp/Graph/GlobalGraph.cpp ++++ b/src/Bpp/Graph/GlobalGraph.cpp +@@ -42,6 +42,7 @@ + #include <sstream> + #include <string> + #include <vector> ++#include <limits> + + #include "../Exceptions.h" + #include "../Text/TextTools.h" diff --git a/academic/bpp-phyl-omics/bpp-phyl-omics.SlackBuild b/academic/bpp-phyl-omics/bpp-phyl-omics.SlackBuild index 52411415e4..31a4b60cc8 100644 --- a/academic/bpp-phyl-omics/bpp-phyl-omics.SlackBuild +++ b/academic/bpp-phyl-omics/bpp-phyl-omics.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for bpp-phyl-omics -# Copyright 2017-2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2017-2022 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=bpp-phyl-omics VERSION=${VERSION:-2.4.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,11 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -86,11 +93,11 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a AUTHORS.txt ChangeLog COPYING.txt INSTALL.txt $PKG/usr/doc/$PRGNAM-$VERSION +cp -a AUTHORS.txt ChangeLog COPYING.txt $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/bpp-phyl/bpp-phyl.SlackBuild b/academic/bpp-phyl/bpp-phyl.SlackBuild index 4666e9c966..d1de4c4a79 100644 --- a/academic/bpp-phyl/bpp-phyl.SlackBuild +++ b/academic/bpp-phyl/bpp-phyl.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for bpp-phyl -# Copyright 2017-2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2017-2022 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=bpp-phyl VERSION=${VERSION:-2.4.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,11 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -86,11 +93,11 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a AUTHORS.txt ChangeLog COPYING.txt INSTALL.txt $PKG/usr/doc/$PRGNAM-$VERSION +cp -a AUTHORS.txt ChangeLog COPYING.txt $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/bpp-popgen/bpp-popgen.SlackBuild b/academic/bpp-popgen/bpp-popgen.SlackBuild index b82387f45c..11e65b03be 100644 --- a/academic/bpp-popgen/bpp-popgen.SlackBuild +++ b/academic/bpp-popgen/bpp-popgen.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for bpp-popgen -# Copyright 2017-2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2017-2022 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=bpp-popgen VERSION=${VERSION:-2.4.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,11 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -86,11 +93,11 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a AUTHORS.txt ChangeLog COPYING.txt INSTALL.txt $PKG/usr/doc/$PRGNAM-$VERSION +cp -a AUTHORS.txt ChangeLog COPYING.txt $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/bpp-seq-omics/bpp-seq-omics.SlackBuild b/academic/bpp-seq-omics/bpp-seq-omics.SlackBuild index 254bdc60da..c81730ea5a 100644 --- a/academic/bpp-seq-omics/bpp-seq-omics.SlackBuild +++ b/academic/bpp-seq-omics/bpp-seq-omics.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for bpp-seq-omics -# Copyright 2017-2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2017-2022 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=bpp-seq-omics VERSION=${VERSION:-2.4.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,11 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -86,11 +93,11 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a AUTHORS.txt ChangeLog COPYING.txt INSTALL.txt $PKG/usr/doc/$PRGNAM-$VERSION +cp -a AUTHORS.txt ChangeLog COPYING.txt $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/bpp-seq/bpp-seq.SlackBuild b/academic/bpp-seq/bpp-seq.SlackBuild index 0239590a07..298386625e 100644 --- a/academic/bpp-seq/bpp-seq.SlackBuild +++ b/academic/bpp-seq/bpp-seq.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for bpp-seq -# Copyright 2017-2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2017-2022 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=bpp-seq VERSION=${VERSION:-2.4.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,12 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -86,11 +94,11 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a AUTHORS.txt ChangeLog COPYING.txt INSTALL.txt $PKG/usr/doc/$PRGNAM-$VERSION +cp -a AUTHORS.txt ChangeLog COPYING.txt $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/bpp1.9-numcalc/README b/academic/bpp1.9-numcalc/README new file mode 100644 index 0000000000..a514a0450e --- /dev/null +++ b/academic/bpp1.9-numcalc/README @@ -0,0 +1,10 @@ +Bio++ is a set of C++ libraries for Bioinformatics, including sequence +analysis, phylogenetics, molecular evolution and population genetics. +Bio++ is Object Oriented and is designed to be both easy to use and +computer efficient. Bio++ intends to help programmers to write +computer expensive programs, by providing them a set of re-usable +tools. + +This contains the Bio++ 1.9 (April 2010) NumCalc Library. It can be +installed along the current Bio++ suite libraries, however they better +not be present at compile time. diff --git a/academic/bpp1.9-numcalc/bpp1.9-numcalc.SlackBuild b/academic/bpp1.9-numcalc/bpp1.9-numcalc.SlackBuild new file mode 100644 index 0000000000..ea548edbdf --- /dev/null +++ b/academic/bpp1.9-numcalc/bpp1.9-numcalc.SlackBuild @@ -0,0 +1,116 @@ +#!/bin/bash + +# Slackware build script for bpp1.9-utils + +# Copyright 2020-2022 Petar Petrov slackalaxy@gmail.com +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=bpp1.9-numcalc +SRCNAM=bpp-numcalc +VERSION=${VERSION:-1.8.0} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +LIBDIRPATH="-Wl,-rpath,/usr/lib${LIBDIRSUFFIX}/Bpp1.9" + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $SRCNAM-$VERSION +tar xvf $CWD/$SRCNAM-$VERSION.tar.gz +cd $SRCNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +# Use custom install place, so libs can coexist with latest bpp +export PATH="/usr/lib${LIBDIRSUFFIX}/Bpp1.9/:$PATH" +sed -i "s:/lib/:/lib${LIBDIRSUFFIX}/Bpp1.9/:g" NumCalc.spec + +source /etc/profile.d/gcc5.sh + +mkdir -p build +cd build + cmake \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS $LIBDIRPATH" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DCMAKE_BUILD_TYPE=Release .. + +sed -i "s:/lib/:/lib${LIBDIRSUFFIX}/Bpp1.9/:g" NumCalc/cmake_install.cmake +sed -i "s:/lib\b:/lib${LIBDIRSUFFIX}/Bpp1.9:g" NumCalc/cmake_install.cmake + + make + make DESTDIR=$PKG install +cd .. + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +chmod 0644 AUTHORS ChangeLog COPYING +cp -a \ + AUTHORS ChangeLog COPYING \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/bpp1.9-numcalc/bpp1.9-numcalc.info b/academic/bpp1.9-numcalc/bpp1.9-numcalc.info new file mode 100644 index 0000000000..026698cbb2 --- /dev/null +++ b/academic/bpp1.9-numcalc/bpp1.9-numcalc.info @@ -0,0 +1,10 @@ +PRGNAM="bpp1.9-numcalc" +VERSION="1.8.0" +HOMEPAGE="http://biopp.univ-montp2.fr/" +DOWNLOAD="https://raw.githubusercontent.com/slackalaxy/sources/main/bpp-numcalc-1.8.0.tar.gz" +MD5SUM="0d6d51aaefcb4f89816704feae010bc9" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="bpp1.9-utils" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/freechartgeany/slack-desc b/academic/bpp1.9-numcalc/slack-desc index e59bc3b7d8..0b1db4fe56 100644 --- a/academic/freechartgeany/slack-desc +++ b/academic/bpp1.9-numcalc/slack-desc @@ -6,14 +6,14 @@ # customary to leave one space after the ':' except on otherwise blank lines. |-----handy-ruler------------------------------------------------------| -freechartgeany: freechartgeany (market analysis tool) -freechartgeany: -freechartgeany: Free Chart Geany is a multi platform software solution for market -freechartgeany: technical analysis and charting. -freechartgeany: -freechartgeany: Homepage: http://freechartgeany.sourceforge.net/ -freechartgeany: -freechartgeany: -freechartgeany: -freechartgeany: -freechartgeany: +bpp1.9-numcalc: bpp1.9-numcalc (Bio++ 1.9 NumCalc Library) +bpp1.9-numcalc: +bpp1.9-numcalc: Contains the Bio++ 1.9 NumCalc Library. +bpp1.9-numcalc: +bpp1.9-numcalc: +bpp1.9-numcalc: +bpp1.9-numcalc: +bpp1.9-numcalc: +bpp1.9-numcalc: +bpp1.9-numcalc: +bpp1.9-numcalc: diff --git a/academic/bpp1.9-phyl/README b/academic/bpp1.9-phyl/README new file mode 100644 index 0000000000..292485c428 --- /dev/null +++ b/academic/bpp1.9-phyl/README @@ -0,0 +1,10 @@ +Bio++ is a set of C++ libraries for Bioinformatics, including sequence +analysis, phylogenetics, molecular evolution and population genetics. +Bio++ is Object Oriented and is designed to be both easy to use and +computer efficient. Bio++ intends to help programmers to write +computer expensive programs, by providing them a set of re-usable +tools. + +This contains the Bio++ 1.9 (April 2010) Phyl Library. It can be +installed along the current Bio++ suite libraries, however they better +not be present at compile time. diff --git a/academic/bpp1.9-phyl/bpp1.9-phyl.SlackBuild b/academic/bpp1.9-phyl/bpp1.9-phyl.SlackBuild new file mode 100644 index 0000000000..fa951d6f2e --- /dev/null +++ b/academic/bpp1.9-phyl/bpp1.9-phyl.SlackBuild @@ -0,0 +1,119 @@ +#!/bin/bash + +# Slackware build script for bpp1.9-phyl + +# Copyright 2020-2022 Petar Petrov slackalaxy@gmail.com +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=bpp1.9-phyl +SRCNAM=bpp-phyl +VERSION=${VERSION:-1.9.0} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +LIBDIRPATH="-Wl,-rpath,/usr/lib${LIBDIRSUFFIX}/Bpp1.9" + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $SRCNAM-$VERSION +tar xvf $CWD/$SRCNAM-$VERSION.tar.gz +cd $SRCNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +# CAPS wants TreeTemplateTools to be modified a bit... +patch -p1 -i $CWD/caps_TreeTemplateTools.patch + +# Use custom install place, so libs can coexist with latest bpp +export PATH="/usr/lib${LIBDIRSUFFIX}/Bpp1.9/:$PATH" +sed -i "s:/lib/:/lib${LIBDIRSUFFIX}/Bpp1.9/:g" Phyl.spec + +source /etc/profile.d/gcc5.sh + +mkdir -p build +cd build + cmake \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS $LIBDIRPATH" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DCMAKE_BUILD_TYPE=Release .. + + sed -i "s:/lib/:/lib${LIBDIRSUFFIX}/Bpp1.9/:g" Phyl/cmake_install.cmake + sed -i "s:/lib\b:/lib${LIBDIRSUFFIX}/Bpp1.9:g" Phyl/cmake_install.cmake + + make + make DESTDIR=$PKG install +cd .. + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +chmod 0644 AUTHORS ChangeLog COPYING +cp -a \ + AUTHORS ChangeLog COPYING \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/bpp1.9-phyl/bpp1.9-phyl.info b/academic/bpp1.9-phyl/bpp1.9-phyl.info new file mode 100644 index 0000000000..ae873c0a59 --- /dev/null +++ b/academic/bpp1.9-phyl/bpp1.9-phyl.info @@ -0,0 +1,10 @@ +PRGNAM="bpp1.9-phyl" +VERSION="1.9.0" +HOMEPAGE="http://biopp.univ-montp2.fr/" +DOWNLOAD="https://raw.githubusercontent.com/slackalaxy/sources/main/bpp-phyl-1.9.0.tar.gz" +MD5SUM="1b100b688faca52419e9f782798b8add" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="bpp1.9-seq" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/bpp1.9-phyl/caps_TreeTemplateTools.patch b/academic/bpp1.9-phyl/caps_TreeTemplateTools.patch new file mode 100644 index 0000000000..b4f79029de --- /dev/null +++ b/academic/bpp1.9-phyl/caps_TreeTemplateTools.patch @@ -0,0 +1,39 @@ +diff -pruN orig/Phyl/TreeTemplateTools.h new/Phyl/TreeTemplateTools.h +--- orig/Phyl/TreeTemplateTools.h 2010-04-01 16:37:04.000000000 +0300 ++++ new/Phyl/TreeTemplateTools.h 2017-02-03 14:33:11.000000000 +0200 +@@ -191,7 +191,7 @@ class TreeTemplateTools + static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception) + { + N* leaf = tree.getNode(leafName); +- if (!leaf->hasfather()) ++ if (!leaf->hasFather()) + throw Exception("TreeTemplateTools::dropLeaf(). Leaf is the only node in the tree, can't remove it."); + N* parent = leaf->getFather(); + if (parent->getNumberOfSons() > 2) +@@ -203,7 +203,7 @@ class TreeTemplateTools + else if (parent->getNumberOfSons() == 2) + { + //We have to delete the parent node as well: +- N* brother = parent->getson(0); ++ N* brother = parent->getSon(0); + if (brother == leaf) brother = parent->getSon(1); + if (!parent->hasFather()) + { +@@ -212,7 +212,7 @@ class TreeTemplateTools + { + brother->setDistanceToFather(brother->getDistanceToFather() + leaf->getDistanceToFather()); + } +- tree->setRootNode(brother); ++ tree.setRootNode(brother); + delete parent; + delete leaf; + } +@@ -223,7 +223,7 @@ class TreeTemplateTools + { + brother->setDistanceToFather(brother->getDistanceToFather() + parent->getDistanceToFather()); + } +- unsigned int pos = gParent->getsonPosition(parent); ++ unsigned int pos = gParent->getSonPosition(parent); + gParent->setSon(pos, brother); + delete parent; + delete leaf; diff --git a/academic/wxmacmolplt/slack-desc b/academic/bpp1.9-phyl/slack-desc index 096a520d43..05245c02f1 100644 --- a/academic/wxmacmolplt/slack-desc +++ b/academic/bpp1.9-phyl/slack-desc @@ -6,14 +6,14 @@ # customary to leave one space after the ':' except on otherwise blank lines. |-----handy-ruler------------------------------------------------------| -wxmacmolplt: wxmacmolplt (The MacMolPlt molecular visualization program) -wxmacmolplt: -wxmacmolplt: MacMolPlt is designed to display the input and output of -wxmacmolplt: the GAMESS quantum chemistry package. It produces animations -wxmacmolplt: and/or publication quality output from a variety of input file -wxmacmolplt: formats. -wxmacmolplt: -wxmacmolplt: -wxmacmolplt: -wxmacmolplt: -wxmacmolplt: +bpp1.9-phyl: bpp1.9-phyl (Bio++ 1.9 Phyl Library) +bpp1.9-phyl: +bpp1.9-phyl: Contains the Bio++ 1.9 Phyl Library. +bpp1.9-phyl: +bpp1.9-phyl: +bpp1.9-phyl: +bpp1.9-phyl: +bpp1.9-phyl: +bpp1.9-phyl: +bpp1.9-phyl: +bpp1.9-phyl: diff --git a/academic/bpp1.9-seq/README b/academic/bpp1.9-seq/README new file mode 100644 index 0000000000..eaeb91d929 --- /dev/null +++ b/academic/bpp1.9-seq/README @@ -0,0 +1,10 @@ +Bio++ is a set of C++ libraries for Bioinformatics, including sequence +analysis, phylogenetics, molecular evolution and population genetics. +Bio++ is Object Oriented and is designed to be both easy to use and +computer efficient. Bio++ intends to help programmers to write +computer expensive programs, by providing them a set of re-usable +tools. + +This contains the Bio++ 1.9 (April 2010) Seq Library. It can be +installed along the current Bio++ suite libraries, however they better +not be present at compile time. diff --git a/academic/bpp1.9-seq/bpp1.9-seq.SlackBuild b/academic/bpp1.9-seq/bpp1.9-seq.SlackBuild new file mode 100644 index 0000000000..fcea3aef1d --- /dev/null +++ b/academic/bpp1.9-seq/bpp1.9-seq.SlackBuild @@ -0,0 +1,116 @@ +#!/bin/bash + +# Slackware build script for bpp1.9-seq + +# Copyright 2020-2022 Petar Petrov slackalaxy@gmail.com +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=bpp1.9-seq +SRCNAM=bpp-seq +VERSION=${VERSION:-1.7.0} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +LIBDIRPATH="-Wl,-rpath,/usr/lib${LIBDIRSUFFIX}/Bpp1.9" + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $SRCNAM-$VERSION +tar xvf $CWD/$SRCNAM-$VERSION.tar.gz +cd $SRCNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +# Use custom install place, so libs can coexist with latest bpp +export PATH="/usr/lib${LIBDIRSUFFIX}/Bpp1.9/:$PATH" +sed -i "s:/lib/:/lib${LIBDIRSUFFIX}/Bpp1.9/:g" Seq.spec + +source /etc/profile.d/gcc5.sh + +mkdir -p build +cd build + cmake \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS $LIBDIRPATH" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DCMAKE_BUILD_TYPE=Release .. + + sed -i "s:/lib/:/lib${LIBDIRSUFFIX}/Bpp1.9/:g" Seq/cmake_install.cmake + sed -i "s:/lib\b:/lib${LIBDIRSUFFIX}/Bpp1.9:g" Seq/cmake_install.cmake + + make + make DESTDIR=$PKG install +cd .. + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +chmod 0644 AUTHORS ChangeLog COPYING +cp -a \ + AUTHORS ChangeLog COPYING \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/bpp1.9-seq/bpp1.9-seq.info b/academic/bpp1.9-seq/bpp1.9-seq.info new file mode 100644 index 0000000000..0d6d9f38df --- /dev/null +++ b/academic/bpp1.9-seq/bpp1.9-seq.info @@ -0,0 +1,10 @@ +PRGNAM="bpp1.9-seq" +VERSION="1.7.0" +HOMEPAGE="http://biopp.univ-montp2.fr/" +DOWNLOAD="https://raw.githubusercontent.com/slackalaxy/sources/main/bpp-seq-1.7.0.tar.gz" +MD5SUM="4256293637ac4131c0d030f5265b8b8b" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="bpp1.9-numcalc" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/bpp1.9-seq/slack-desc b/academic/bpp1.9-seq/slack-desc new file mode 100644 index 0000000000..bd154ce1f1 --- /dev/null +++ b/academic/bpp1.9-seq/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +bpp1.9-seq: bpp1.9-seq (Bio++ 1.9 Seq Library) +bpp1.9-seq: +bpp1.9-seq: Contains the Bio++ 1.9 Seq Library. +bpp1.9-seq: +bpp1.9-seq: +bpp1.9-seq: +bpp1.9-seq: +bpp1.9-seq: +bpp1.9-seq: +bpp1.9-seq: +bpp1.9-seq: diff --git a/academic/bpp1.9-utils/README b/academic/bpp1.9-utils/README new file mode 100644 index 0000000000..5ee42d9632 --- /dev/null +++ b/academic/bpp1.9-utils/README @@ -0,0 +1,10 @@ +Bio++ is a set of C++ libraries for Bioinformatics, including sequence +analysis, phylogenetics, molecular evolution and population genetics. +Bio++ is Object Oriented and is designed to be both easy to use and +computer efficient. Bio++ intends to help programmers to write +computer expensive programs, by providing them a set of re-usable +tools. + +This contains the Bio++ 1.9 (April 2010) Utils Library. It can be +installed along the current Bio++ suite libraries, however they better +not be present at compile time. diff --git a/academic/bpp1.9-utils/bpp1.9-utils.SlackBuild b/academic/bpp1.9-utils/bpp1.9-utils.SlackBuild new file mode 100644 index 0000000000..6840376b84 --- /dev/null +++ b/academic/bpp1.9-utils/bpp1.9-utils.SlackBuild @@ -0,0 +1,120 @@ +#!/bin/bash + +# Slackware build script for bpp1.9-utils + +# Copyright 2020-2022 Petar Petrov slackalaxy@gmail.com +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=bpp1.9-utils +SRCNAM=bpp-utils +VERSION=${VERSION:-1.5.0} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +# This is needed for vCAPS to find its libraries at runtime. Thanks Urchlay! +LIBDIRPATH="-Wl,-rpath,/usr/lib${LIBDIRSUFFIX}/Bpp1.9" + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $SRCNAM-$VERSION +tar xvf $CWD/$SRCNAM-$VERSION.tar.gz +cd $SRCNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +# This is needed on newer systems (-current) +#sed -i "s:file;:file.good();:g" Utils/FileTools.cpp + +# Use custom install place, so libs can coexist with latest Bio++ +sed -i "s:/lib/:/lib${LIBDIRSUFFIX}/Bpp1.9/:g" Utils.spec + +source /etc/profile.d/gcc5.sh + +mkdir -p build +cd build + cmake \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS $LIBDIRPATH" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DCMAKE_BUILD_TYPE=Release .. + +# More about word boundary and sed: +# https://linuxize.com/post/how-to-use-sed-to-find-and-replace-string-in-files/ +sed -i "s:/lib/:/lib${LIBDIRSUFFIX}/Bpp1.9/:g" Utils/cmake_install.cmake +sed -i "s:/lib\b:/lib${LIBDIRSUFFIX}/Bpp1.9:g" Utils/cmake_install.cmake + + make + make DESTDIR=$PKG install +cd .. + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + AUTHORS ChangeLog COPYING \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/bpp1.9-utils/bpp1.9-utils.info b/academic/bpp1.9-utils/bpp1.9-utils.info new file mode 100644 index 0000000000..8ee8062200 --- /dev/null +++ b/academic/bpp1.9-utils/bpp1.9-utils.info @@ -0,0 +1,10 @@ +PRGNAM="bpp1.9-utils" +VERSION="1.5.0" +HOMEPAGE="http://biopp.univ-montp2.fr/" +DOWNLOAD="https://raw.githubusercontent.com/slackalaxy/sources/main/bpp-utils-1.5.0.tar.gz" +MD5SUM="4625b7f2146caa1815ed7dc433d5eb78" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="gcc5" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.copm" diff --git a/academic/bpp1.9-utils/slack-desc b/academic/bpp1.9-utils/slack-desc new file mode 100644 index 0000000000..be9d333c61 --- /dev/null +++ b/academic/bpp1.9-utils/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +bpp1.9-utils: bpp1.9-utils (Bio++ 1.9 Utils Library) +bpp1.9-utils: +bpp1.9-utils: Contains the Bio++ 1.9 Utils Library. +bpp1.9-utils: +bpp1.9-utils: +bpp1.9-utils: +bpp1.9-utils: +bpp1.9-utils: +bpp1.9-utils: +bpp1.9-utils: +bpp1.9-utils: diff --git a/academic/bppsuite/bppsuite.SlackBuild b/academic/bppsuite/bppsuite.SlackBuild index fba8911812..4e4bc8c2d2 100644 --- a/academic/bppsuite/bppsuite.SlackBuild +++ b/academic/bppsuite/bppsuite.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for bppsuite -# Copyright 2017-2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2017-2022 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=bppsuite VERSION=${VERSION:-2.4.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,11 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -96,11 +103,11 @@ rm -f $PKG/usr/info/dir gzip -9 $PKG/usr/info/*.info* mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a AUTHORS.txt ChangeLog COPYING.txt INSTALL.txt README.md $PKG/usr/doc/$PRGNAM-$VERSION +cp -a AUTHORS.txt ChangeLog COPYING.txt README.md $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/bppsuite/bppsuite.info b/academic/bppsuite/bppsuite.info index 97626a2bff..ccd92962fe 100644 --- a/academic/bppsuite/bppsuite.info +++ b/academic/bppsuite/bppsuite.info @@ -5,6 +5,6 @@ DOWNLOAD="https://github.com/BioPP/bppsuite/archive/v2.4.1/bppsuite-2.4.1.tar.gz MD5SUM="d254ffd9e121b408aed36f49e62920d1" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="bpp-seq-omics bpp-phyl-omics bpp-popgen" +REQUIRES="bpp-phyl-omics bpp-popgen" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/btf/README b/academic/btf/README index 3666aedf6b..625663f5fe 100644 --- a/academic/btf/README +++ b/academic/btf/README @@ -1,5 +1,5 @@ -BTF permutes an unsymmetric matrix (square or rectangular) into its block -upper triangular form (more precisely, it computes a Dulmage-Mendelsohn -decomposition). +BTF permutes an unsymmetric matrix (square or rectangular) into +its block upper triangular form (more precisely, it computes a +Dulmage-Mendelsohn decomposition). This package is part of SuiteSparse. diff --git a/academic/btf/btf.SlackBuild b/academic/btf/btf.SlackBuild index 39ef98cc23..453b49631f 100644 --- a/academic/btf/btf.SlackBuild +++ b/academic/btf/btf.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for BTF -# Copyright 2013-2020 Kyle Guinn <elyk03@gmail.com> +# Copyright 2013-2021 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,13 +22,16 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=btf SRCNAM=SuiteSparse SUBDIR=BTF VERSION=${VERSION:-1.2.6} -SRCVER=${SRCVER:-5.6.0} -BUILD=${BUILD:-6} +SRCVER=${SRCVER:-5.8.1} +BUILD=${BUILD:-7} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$(uname -m)" in @@ -38,15 +41,22 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM-$VERSION +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="README.txt Doc/ChangeLog Doc/License.txt Doc/lesser.txt" -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" @@ -105,4 +115,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/btf/btf.info b/academic/btf/btf.info index 0b80a8d5cc..df3056d279 100644 --- a/academic/btf/btf.info +++ b/academic/btf/btf.info @@ -1,8 +1,8 @@ PRGNAM="btf" VERSION="1.2.6" HOMEPAGE="http://faculty.cse.tamu.edu/davis/suitesparse.html" -DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.6.0/SuiteSparse-5.6.0.tar.gz" -MD5SUM="af8b97cbded4cd5c6672e878bc0c37c2" +DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.8.1/SuiteSparse-5.8.1.tar.gz" +MD5SUM="c414679bbc9432a3def01b31ad921140" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="suitesparseconfig" diff --git a/academic/bwa/bwa.SlackBuild b/academic/bwa/bwa.SlackBuild index 7b5fc48a08..0f38e66b24 100644 --- a/academic/bwa/bwa.SlackBuild +++ b/academic/bwa/bwa.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for bwa -# Copyright 2013-2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2013-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=bwa VERSION=${VERSION:-0.7.17} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -73,7 +83,7 @@ find -L . \ sed -i "/^C.*.*FLAGS/s/=/+=/" Makefile # Thanks to Willy for the -msse2 fix! -CFLAGS="$SLKCFLAGS -msse2" \ +CFLAGS="$SLKCFLAGS -msse2 -fcommon" \ CXXFLAGS="$SLKCFLAGS" \ make @@ -98,4 +108,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/cadabra2/README b/academic/cadabra2/README index 5e8287722a..e26c444234 100644 --- a/academic/cadabra2/README +++ b/academic/cadabra2/README @@ -1,11 +1,12 @@ Cadabra is a symbolic computer algebra system (CAS) designed specifically for the solution of problems encountered in field theory. It has extensive functionality for tensor computer algebra, tensor -polynomial simplification including multi-term symmetries, fermions and -anti-commuting variables, Clifford algebras and Fierz transformations, -component computations, implicit coordinate dependence, multiple index -types and many more. The input format is a subset of TeX. Both a -command-line and a graphical interface are available. +polynomial simplification including multi-term symmetries, fermions +and anti-commuting variables, Clifford algebras and Fierz +transformations, component computations, implicit coordinate +dependence, multiple index types and many more. The input format is a +subset of TeX. Both a command-line and a graphical interface are +available. * Designed for field-theory problems, with handling of anti-commuting and non-commuting objects without special notations for their @@ -21,12 +22,14 @@ command-line and a graphical interface are available. * Allows for both abstract and component computations. -* A standalone graphical notebook interface which can also be used as a - front-end for SymPy. +* A standalone graphical notebook interface which can also be used as + a front-end for SymPy. * Input and output using a subset of LaTeX notation. * Programmable using Python. -Mathematica (not on SBo) is an optional dependency, it will be -autodetected at build time. +If this SlackBuild is running on a system which has WolframEngine +(available on SBo) or Mathematica (not on SBo) installed, its support +in Cadabra can be enabled by setting the environment variable MMA=ON +(default: MMA=OFF). diff --git a/academic/cadabra2/cadabra2.SlackBuild b/academic/cadabra2/cadabra2.SlackBuild index 53b6152b13..0172ff5550 100644 --- a/academic/cadabra2/cadabra2.SlackBuild +++ b/academic/cadabra2/cadabra2.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for cadabra2 -# Copyright 2017-2019, Alexander Verbovetsky, Moscow, Russia +# Copyright 2017-2024, Alexander Verbovetsky, Moscow, Russia # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,14 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=cadabra2 -VERSION=${VERSION:-2.2.8} +VERSION=${VERSION:-2.4.5.7} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} +MMA=${MMA:-OFF} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +39,11 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -70,24 +78,15 @@ find -L . \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; sed --in-place \ - -e "s/\(DESTINATION lib\)/\1${LIBDIRSUFFIX}/" \ - client_server/CMakeLists.txt - -sed --in-place \ - -e "s/\(CMAKE_INSTALL_PREFIX}\/lib\)/\1${LIBDIRSUFFIX}/" \ - CMakeLists.txt + -e "s|/lib/python|/lib${LIBDIRSUFFIX}/python|" \ + CMakeLists.txt core/cadabra2-cli.cc client_server/Server.cc sed --in-place \ -e '/^execute_process(COMMAND texhash)$/d' \ frontend/latex/install.cmake -sed --in-place \ - -e '/^install(CODE\s\+"execute_process(COMMAND \(touch\|gtk-update-icon-cache.*\|chmod go+r\) ${ICON_PREFIX}\/share\/icons\/hicolor\(\|\/icon-theme\.cache\))")$/d' \ - frontend/gtkmm/CMakeLists.txt - find ./ -type f -name '*.py' -exec \ - sed -i -e 's|#!/usr/bin/python\>|#!/usr/bin/python3|' \ - -e 's|#!/usr/bin/env python\>|#!/usr/bin/env python3|' {} \; + sed -i -e 's|#!/usr/bin/env python\>|#!/usr/bin/env python3|' {} \; mkdir -p build cd build @@ -95,6 +94,8 @@ cd build -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ -DCMAKE_INSTALL_PREFIX=/usr \ + -DSQLITE3_INCLUDE_DIR=/usr/include \ + -DENABLE_MATHEMATICA=${MMA^^} \ -DCMAKE_BUILD_TYPE=Release .. make make install DESTDIR=$PKG @@ -108,7 +109,8 @@ find $PKG/usr/man -type f -exec gzip -9 {} \; for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a doc examples README.rst $PKG/usr/doc/$PRGNAM-$VERSION +cp -a contrib doc examples paper CONTRIBUTING.md JUPYTER.rst README.rst \ + $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install @@ -116,4 +118,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/cadabra2/cadabra2.info b/academic/cadabra2/cadabra2.info index eba8bf8144..2bd6e73540 100644 --- a/academic/cadabra2/cadabra2.info +++ b/academic/cadabra2/cadabra2.info @@ -1,8 +1,8 @@ PRGNAM="cadabra2" -VERSION="2.2.8" +VERSION="2.4.5.7" HOMEPAGE="https://cadabra.science" -DOWNLOAD="https://downloads.sourceforge.net/slackbuildsdirectlinks/cadabra2/cadabra2-2.2.8.tar.gz" -MD5SUM="a4c91eca89e75a079038e9dae3c5d00e" +DOWNLOAD="https://github.com/kpeeters/cadabra2/archive/2.4.5.7/cadabra2-2.4.5.7.tar.gz" +MD5SUM="0114198388cc3d11e7318a1319b46aae" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="python3-matplotlib python3-gmpy2 python3-sympy" diff --git a/academic/calc/calc.SlackBuild b/academic/calc/calc.SlackBuild index 043faff559..8b51ed982c 100644 --- a/academic/calc/calc.SlackBuild +++ b/academic/calc/calc.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for calc # Copyright 2017 Dhaby Xiloj <slack.dhabyx@gmail.com> @@ -23,10 +23,13 @@ # Modified by Robby Workman <rworkman@slackbuilds.org> +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=calc -VERSION=${VERSION:-2.12.7.2} +VERSION=${VERSION:-2.14.1.5} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -36,7 +39,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -105,4 +115,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/calc/calc.info b/academic/calc/calc.info index a14bf23ea6..9ba6856746 100644 --- a/academic/calc/calc.info +++ b/academic/calc/calc.info @@ -1,10 +1,10 @@ PRGNAM="calc" -VERSION="2.12.7.2" +VERSION="2.14.1.5" HOMEPAGE="http://www.isthe.com/chongo/tech/comp/calc/" -DOWNLOAD="http://www.isthe.com/chongo/src/calc/calc-2.12.7.2.tar.bz2" -MD5SUM="86ba447318108da52e4d9ab93e00aca9" +DOWNLOAD="http://www.isthe.com/chongo/src/calc/calc-2.14.1.5.tar.bz2" +MD5SUM="57607be276a3998fa76376e41dc49a03" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" -MAINTAINER="Dave Woodfall" +MAINTAINER="D Woodfall" EMAIL="dave@slackbuilds.org" diff --git a/academic/calcoo/README b/academic/calcoo/README index 5c4e7ef8c3..d9891857aa 100644 --- a/academic/calcoo/README +++ b/academic/calcoo/README @@ -1,4 +1,5 @@ -Calcoo is an RPN and scientific calculator that uses the GTK library. It -features both RPN and algebraic modes, bitmapped button labels and display -glyths, undo/redo options, copy/paste interaction with the X clipboard, two -memory registers with displays, and displays for Y, Z, and T registers. +Calcoo is an RPN and scientific calculator that uses the GTK library. +It features both RPN and algebraic modes, bitmapped button labels and +display glyths, undo/redo options, copy/paste interaction with the X +clipboard, two memory registers with displays, and displays for Y, Z, +and T registers. diff --git a/academic/calcoo/calcoo.SlackBuild b/academic/calcoo/calcoo.SlackBuild index 29a8d1a067..9083c396ba 100644 --- a/academic/calcoo/calcoo.SlackBuild +++ b/academic/calcoo/calcoo.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for calcoo -# Copyright 2006-2013 Robby Workman, Northport, Alabama, USA +# Copyright 2006-2013,2021 Robby Workman, Tuscaloosa, Alabama, USA # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,14 +22,24 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=calcoo VERSION=${VERSION:-2.1.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} ARCH=noarch -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -54,4 +64,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/calcoo/calcoo.info b/academic/calcoo/calcoo.info index e05dcb7ba6..cb01da56f7 100644 --- a/academic/calcoo/calcoo.info +++ b/academic/calcoo/calcoo.info @@ -5,6 +5,6 @@ DOWNLOAD="http://downloads.sourceforge.net/project/calcoo/calcoo/2.1.0/calcoo.ja MD5SUM="78880e375fb50cb6b945e43713c11065" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="jdk" +REQUIRES="zulu-openjdk8" MAINTAINER="Robby Workman" EMAIL="rworkman@slackbuilds.org" diff --git a/academic/camd/camd.SlackBuild b/academic/camd/camd.SlackBuild index 15bf62a012..2823459a12 100644 --- a/academic/camd/camd.SlackBuild +++ b/academic/camd/camd.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for CAMD -# Copyright 2013-2020 Kyle Guinn <elyk03@gmail.com> +# Copyright 2013-2021 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,13 +22,16 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=camd SRCNAM=SuiteSparse SUBDIR=CAMD VERSION=${VERSION:-2.4.6} -SRCVER=${SRCVER:-5.6.0} -BUILD=${BUILD:-6} +SRCVER=${SRCVER:-5.8.1} +BUILD=${BUILD:-7} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$(uname -m)" in @@ -38,15 +41,22 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM-$VERSION +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="README.txt Doc/ChangeLog Doc/License.txt Doc/lesser.txt" -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" @@ -108,4 +118,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/camd/camd.info b/academic/camd/camd.info index fc2cbaa211..a02b5c633d 100644 --- a/academic/camd/camd.info +++ b/academic/camd/camd.info @@ -1,8 +1,8 @@ PRGNAM="camd" VERSION="2.4.6" HOMEPAGE="http://faculty.cse.tamu.edu/davis/suitesparse.html" -DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.6.0/SuiteSparse-5.6.0.tar.gz" -MD5SUM="af8b97cbded4cd5c6672e878bc0c37c2" +DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.8.1/SuiteSparse-5.8.1.tar.gz" +MD5SUM="c414679bbc9432a3def01b31ad921140" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="suitesparseconfig" diff --git a/academic/cap3/README b/academic/cap3/README index 62792bb4c7..a4023eccfa 100644 --- a/academic/cap3/README +++ b/academic/cap3/README @@ -1,14 +1,21 @@ CAP3: A DNA sequence assembly program. CAP3 if the third generation of the CAP sequence assembly program. The -program has a capability to clip 5' and 3' low-quality regions of reads. -It uses base quality values in computation of overlaps between reads, -construction of multiple sequence alignments of reads, and generation -of consensus sequences. The program also uses forward-reverse constraints -to correct assembly errors and link contigs. +program has a capability to clip 5' and 3' low-quality regions +of reads. It uses base quality values in computation of overlaps +between reads, construction of multiple sequence alignments of +reads, and generation of consensus sequences. The program also uses +forward-reverse constraints to correct assembly errors and link +contigs. This just repackages the binaries provided from upstream. If you use CAP3 in any published work, please cite: Huang, X. and Madan, A. (1999) CAP3: A DNA sequence assembly program. Genome Res., 9, 868-877. + +*NOTE* +The downloads are available here: +https://faculty.sites.iastate.edu/xqhuang/cap3-assembly-program + +Sources are also hosted by the maintainer to ease automatic download. diff --git a/academic/cap3/cap3.SlackBuild b/academic/cap3/cap3.SlackBuild index 12ee761b1e..65359adf4b 100644 --- a/academic/cap3/cap3.SlackBuild +++ b/academic/cap3/cap3.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for cap3 -# Copyright 2013-2016 Petar Petrov slackalaxy@gmail.com +# Copyright 2013-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,37 +22,43 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +# 20220405 bkw: Modified by SlackBuilds.org, BUILD=3: fix doc permissions. + +# 20220318 bkw: Modified by SlackBuilds.org: fix 32-bit build when ARCH +# set to i586 or i686 in environment. + +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=cap3 VERSION=${VERSION:-20091029} # Use the last modification date as version -BUILD=${BUILD:-1} +BUILD=${BUILD:-3} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i386 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} set -e -if [ "$ARCH" != "i386" ] && [ "$ARCH" != "x86_64" ]; then - printf "\n\n$ARCH is not supported... \n" - exit 1 -fi - -# Determine the tarball arch -if [ "$ARCH" = "x86_64" ]; then - SRCARCH=".opteron64" -else - SRCARCH="" -fi +case "$ARCH" in + x86_64) SRCARCH=".x86_64" ;; + i?86) SRCARCH="" ;; + *) echo "Unsupported ARCH '$ARCH'"; exit 1 ;; +esac # Construct tarball name TARNAME=${PRGNAM}.linux${SRCARCH} @@ -67,18 +73,15 @@ cd $DIRNAM chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ + -exec chmod 755 {} \+ -o \ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; - -install -D -m755 $PRGNAM $PKG/usr/bin/$PRGNAM -install -D -m755 formcon $PKG/usr/bin/formcon + -exec chmod 644 {} \+ -find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ - | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true +install -s -D -m755 $PRGNAM $PKG/usr/bin/$PRGNAM +install -s -D -m755 formcon $PKG/usr/bin/formcon mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a \ +install -m0644 \ aceform doc README \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild @@ -89,4 +92,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/cap3/cap3.info b/academic/cap3/cap3.info index d72fab6233..e4293f8054 100644 --- a/academic/cap3/cap3.info +++ b/academic/cap3/cap3.info @@ -1,10 +1,10 @@ PRGNAM="cap3" VERSION="20091029" HOMEPAGE="http://seq.cs.iastate.edu/" -DOWNLOAD="http://seq.cs.iastate.edu/CAP3/cap3.linux.tar" +DOWNLOAD="https://raw.githubusercontent.com/slackalaxy/sources/main/cap3.linux.tar" MD5SUM="55f57f61e588d4de06c0506cf2696c29" -DOWNLOAD_x86_64="http://seq.cs.iastate.edu/CAP3/cap3.linux.opteron64.tar" -MD5SUM_x86_64="2d924766f6e8b5cf03bd2db81016d821" +DOWNLOAD_x86_64="https://raw.githubusercontent.com/slackalaxy/sources/main/cap3.linux.x86_64.tar" +MD5SUM_x86_64="5393d937978ecc5f18fcb741140e1f02" REQUIRES="" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/cblas/README b/academic/cblas/README index 37cd0e0795..96f920457b 100644 --- a/academic/cblas/README +++ b/academic/cblas/README @@ -1,9 +1,10 @@ -CBLAS is a collection of wrappers that provide a C interface to the FORTRAN -BLAS library. The interface can be consulted by opening /usr/include/cblas.h +CBLAS is a collection of wrappers that provide a C interface to the +FORTRAN BLAS library. The interface can be consulted by opening +/usr/include/cblas.h -This package is intended for use with the Netlib reference BLAS. It should -also work with other BLAS implementations that do not already provide a CBLAS -implementation. +This package is intended for use with the Netlib reference BLAS. +It should also work with other BLAS implementations that do not +already provide a CBLAS implementation. To build a static library in addition to the shared library, pass STATIC=yes to the script. diff --git a/academic/cblas/cblas.SlackBuild b/academic/cblas/cblas.SlackBuild index a7cadea464..7334c23998 100644 --- a/academic/cblas/cblas.SlackBuild +++ b/academic/cblas/cblas.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for CBLAS -# Copyright 2016-2020 Kyle Guinn <elyk03@gmail.com> +# Copyright 2016-2024 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,11 +22,14 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=cblas SRCNAM=lapack -VERSION=${VERSION:-3.9.0} +VERSION=${VERSION:-3.12.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$(uname -m)" in @@ -36,15 +39,19 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM-$VERSION +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="LICENSE CBLAS/README" -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" elif [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" elif [ "$ARCH" = "i686" ]; then @@ -118,4 +125,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/cblas/cblas.info b/academic/cblas/cblas.info index 6c54824791..ff8d8b3070 100644 --- a/academic/cblas/cblas.info +++ b/academic/cblas/cblas.info @@ -1,8 +1,8 @@ PRGNAM="cblas" -VERSION="3.9.0" -HOMEPAGE="http://www.netlib.org/blas/" -DOWNLOAD="https://github.com/Reference-LAPACK/lapack/archive/v3.9.0/lapack-3.9.0.tar.gz" -MD5SUM="0b251e2a8d5f949f99b50dd5e2200ee2" +VERSION="3.12.0" +HOMEPAGE="https://www.netlib.org/blas/" +DOWNLOAD="https://github.com/Reference-LAPACK/lapack/archive/v3.12.0/lapack-3.12.0.tar.gz" +MD5SUM="c1b38bef123584d86a1bd8000784a7b2" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="blas" diff --git a/academic/cblas/patches/cmake-piecewise.diff b/academic/cblas/patches/cmake-piecewise.diff index b1bdfaec1e..37cde2acaa 100644 --- a/academic/cblas/patches/cmake-piecewise.diff +++ b/academic/cblas/patches/cmake-piecewise.diff @@ -2,69 +2,37 @@ diff --git a/CBLAS/CMakeLists.txt b/CBLAS/CMakeLists.txt --- a/CBLAS/CMakeLists.txt +++ b/CBLAS/CMakeLists.txt @@ -1,8 +1,6 @@ - message(STATUS "CBLAS enable") + message(STATUS "CBLAS enabled") enable_language(C) --set(LAPACK_INSTALL_EXPORT_NAME cblas-targets) +-set(LAPACK_INSTALL_EXPORT_NAME ${CBLASLIB}-targets) - # Create a header file cblas.h for the routines called in my C programs - include(FortranCInterface) - ## Ensure that the fortran compiler and c compiler specified are compatible -@@ -41,54 +39,8 @@ - add_subdirectory(examples) - endif() - --if(NOT BLAS_FOUND) -- set(ALL_TARGETS ${ALL_TARGETS} blas) --endif() -- --# Export cblas targets from the --# install tree, if any. --set(_cblas_config_install_guard_target "") --if(ALL_TARGETS) -- install(EXPORT cblas-targets -- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/cblas-${LAPACK_VERSION} -- COMPONENT Development -- ) -- # Choose one of the cblas targets to use as a guard for -- # cblas-config.cmake to load targets from the install tree. -- list(GET ALL_TARGETS 0 _cblas_config_install_guard_target) --endif() -- --# Export cblas targets from the build tree, if any. --set(_cblas_config_build_guard_target "") --if(ALL_TARGETS) -- export(TARGETS ${ALL_TARGETS} FILE cblas-targets.cmake) -- -- # Choose one of the cblas targets to use as a guard -- # for cblas-config.cmake to load targets from the build tree. -- list(GET ALL_TARGETS 0 _cblas_config_build_guard_target) --endif() + include(CheckLanguage) + check_language(Fortran) +@@ -54,22 +52,3 @@ + DESTINATION ${PKG_CONFIG_DIR} + COMPONENT Development + ) - -configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cmake/cblas-config-version.cmake.in -- ${LAPACK_BINARY_DIR}/cblas-config-version.cmake @ONLY) +- ${LAPACK_BINARY_DIR}/${CBLASLIB}-config-version.cmake @ONLY) -configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cmake/cblas-config-build.cmake.in -- ${LAPACK_BINARY_DIR}/cblas-config.cmake @ONLY) -- -- - configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cblas.pc.in ${CMAKE_CURRENT_BINARY_DIR}/cblas.pc @ONLY) - install(FILES - ${CMAKE_CURRENT_BINARY_DIR}/cblas.pc - DESTINATION ${PKG_CONFIG_DIR} - ) +- ${LAPACK_BINARY_DIR}/${CBLASLIB}-config.cmake @ONLY) - -configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cmake/cblas-config-install.cmake.in -- ${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/cblas-config.cmake @ONLY) +- ${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/${CBLASLIB}-config.cmake @ONLY) -install(FILES -- ${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/cblas-config.cmake -- ${LAPACK_BINARY_DIR}/cblas-config-version.cmake -- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/cblas-${LAPACK_VERSION} +- ${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/${CBLASLIB}-config.cmake +- ${LAPACK_BINARY_DIR}/${CBLASLIB}-config-version.cmake +- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/${CBLASLIB}-${LAPACK_VERSION} +- COMPONENT Development - ) - --#install(EXPORT cblas-targets --# DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/cblas-${LAPACK_VERSION} --# COMPONENT Development --# ) +-install(EXPORT ${CBLASLIB}-targets +- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/${CBLASLIB}-${LAPACK_VERSION} +- COMPONENT Development +- ) diff --git a/CBLAS/cmake/cblas-config-build.cmake.in b/CBLAS/cmake/cblas-config-build.cmake.in deleted file mode 100644 --- a/CBLAS/cmake/cblas-config-build.cmake.in @@ -76,41 +44,37 @@ deleted file mode 100644 - -# Load lapack targets from the build tree, including lapacke targets. -if(NOT TARGET lapacke) -- include("@LAPACK_BINARY_DIR@/lapack-targets.cmake") +- include("@LAPACK_BINARY_DIR@/@LAPACKLIB@-targets.cmake") -endif() - -# Report cblas header search locations from build tree. -set(CBLAS_INCLUDE_DIRS "@LAPACK_BINARY_DIR@/include") - -# Report cblas libraries. --set(CBLAS_LIBRARIES cblas) +-set(CBLAS_LIBRARIES @CBLASLIB@) diff --git a/CBLAS/cmake/cblas-config-install.cmake.in b/CBLAS/cmake/cblas-config-install.cmake.in deleted file mode 100644 --- a/CBLAS/cmake/cblas-config-install.cmake.in +++ /dev/null -@@ -1,23 +0,0 @@ +@@ -1,19 +0,0 @@ -# Compute locations from <prefix>/@{LIBRARY_DIR@/cmake/lapacke-<v>/<self>.cmake -get_filename_component(_CBLAS_SELF_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH) --get_filename_component(_CBLAS_PREFIX "${_CBLAS_SELF_DIR}" PATH) --get_filename_component(_CBLAS_PREFIX "${_CBLAS_PREFIX}" PATH) --get_filename_component(_CBLAS_PREFIX "${_CBLAS_PREFIX}" PATH) - -# Load the LAPACK package with which we were built. --set(LAPACK_DIR "${_CBLAS_PREFIX}/@CMAKE_INSTALL_LIBDIR@/cmake/lapack-@LAPACK_VERSION@") +-set(LAPACK_DIR "@CMAKE_INSTALL_FULL_LIBDIR@/cmake/@LAPACKLIB@-@LAPACK_VERSION@") -find_package(LAPACK NO_MODULE) - -# Load lapacke targets from the install tree. --if(NOT TARGET cblas) -- include(${_CBLAS_SELF_DIR}/cblas-targets.cmake) +-if(NOT TARGET @CBLASLIB@) +- include(${_CBLAS_SELF_DIR}/@CBLASLIB@-targets.cmake) -endif() - -# Report lapacke header search locations. --set(CBLAS_INCLUDE_DIRS ${_CBLAS_PREFIX}/include) +-set(CBLAS_INCLUDE_DIRS @CMAKE_INSTALL_FULL_INCLUDEDIR@) - -# Report lapacke libraries. --set(CBLAS_LIBRARIES cblas) +-set(CBLAS_LIBRARIES @CBLASLIB@) - --unset(_CBLAS_PREFIX) -unset(_CBLAS_SELF_DIR) diff --git a/CBLAS/cmake/cblas-config-version.cmake.in b/CBLAS/cmake/cblas-config-version.cmake.in deleted file mode 100644 @@ -128,16 +92,16 @@ deleted file mode 100644 diff --git a/CBLAS/src/CMakeLists.txt b/CBLAS/src/CMakeLists.txt --- a/CBLAS/src/CMakeLists.txt +++ b/CBLAS/src/CMakeLists.txt -@@ -120,9 +120,5 @@ - VERSION ${LAPACK_VERSION} - SOVERSION ${LAPACK_MAJOR_VERSION} - ) --target_include_directories(cblas PUBLIC -- $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/../include> +@@ -172,9 +172,5 @@ + if(HAS_ATTRIBUTE_WEAK_SUPPORT) + target_compile_definitions(${CBLASLIB} PRIVATE HAS_ATTRIBUTE_WEAK_SUPPORT) + endif() +-target_include_directories(${CBLASLIB} PUBLIC +- $<BUILD_INTERFACE:${LAPACK_BINARY_DIR}/include> - $<INSTALL_INTERFACE:include> -) - target_link_libraries(cblas PRIVATE ${BLAS_LIBRARIES}) - lapack_install_library(cblas) + target_link_libraries(${CBLASLIB} PUBLIC ${BLAS_LIBRARIES}) + lapack_install_library(${CBLASLIB}) diff --git a/CMAKE/lapack-config-build.cmake.in b/CMAKE/lapack-config-build.cmake.in deleted file mode 100644 --- a/CMAKE/lapack-config-build.cmake.in @@ -146,7 +110,7 @@ deleted file mode 100644 -# Load lapack targets from the build tree if necessary. -set(_LAPACK_TARGET "@_lapack_config_build_guard_target@") -if(_LAPACK_TARGET AND NOT TARGET "${_LAPACK_TARGET}") -- include("@LAPACK_BINARY_DIR@/lapack-targets.cmake") +- include("@LAPACK_BINARY_DIR@/@LAPACKLIB@-targets.cmake") -endif() -unset(_LAPACK_TARGET) - @@ -168,7 +132,7 @@ deleted file mode 100644 -# Load lapack targets from the install tree if necessary. -set(_LAPACK_TARGET "@_lapack_config_install_guard_target@") -if(_LAPACK_TARGET AND NOT TARGET "${_LAPACK_TARGET}") -- include("${_LAPACK_SELF_DIR}/lapack-targets.cmake") +- include("${_LAPACK_SELF_DIR}/@LAPACKLIB@-targets.cmake") -endif() -unset(_LAPACK_TARGET) - @@ -184,11 +148,11 @@ deleted file mode 100644 diff --git a/CMakeLists.txt b/CMakeLists.txt --- a/CMakeLists.txt +++ b/CMakeLists.txt -@@ -112,11 +112,8 @@ - +@@ -155,11 +155,8 @@ + endif() # -------------------------------------------------- --set(LAPACK_INSTALL_EXPORT_NAME lapack-targets) +-set(LAPACK_INSTALL_EXPORT_NAME ${LAPACKLIB}-targets) - macro(lapack_install_library lib) install(TARGETS ${lib} @@ -196,30 +160,8 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} COMPONENT Development LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} COMPONENT RuntimeLibraries RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} COMPONENT RuntimeLibraries -@@ -155,21 +152,6 @@ - include(CheckLAPACKCompilerFlags) - CheckLAPACKCompilerFlags() +@@ -218,8 +215,9 @@ --# -------------------------------------------------- --# Check second function -- --include(CheckTimeFunction) --set(TIME_FUNC NONE ${TIME_FUNC}) --CHECK_TIME_FUNCTION(NONE TIME_FUNC) --CHECK_TIME_FUNCTION(INT_CPU_TIME TIME_FUNC) --CHECK_TIME_FUNCTION(EXT_ETIME TIME_FUNC) --CHECK_TIME_FUNCTION(EXT_ETIME_ TIME_FUNC) --CHECK_TIME_FUNCTION(INT_ETIME TIME_FUNC) --message(STATUS "--> Will use second_${TIME_FUNC}.f and dsecnd_${TIME_FUNC}.f as timing function.") -- --set(SECOND_SRC ${LAPACK_SOURCE_DIR}/INSTALL/second_${TIME_FUNC}.f) --set(DSECOND_SRC ${LAPACK_SOURCE_DIR}/INSTALL/dsecnd_${TIME_FUNC}.f) -- - # deprecated LAPACK and LAPACKE routines - option(BUILD_DEPRECATED "Build deprecated routines" OFF) - message(STATUS "Build deprecated routines: ${BUILD_DEPRECATED}") -@@ -193,8 +175,9 @@ - endif() # -------------------------------------------------- -# Subdirectories that need to be processed @@ -229,7 +171,7 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt # Check the usage of the user provided BLAS libraries if(BLAS_LIBRARIES) -@@ -205,113 +188,108 @@ +@@ -230,59 +228,41 @@ if(BLAS_FOUND) message(STATUS "--> BLAS supplied by user is WORKING, will use ${BLAS_LIBRARIES}.") else() @@ -250,7 +192,7 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt - message(STATUS "Using supplied NETLIB BLAS implementation") - add_subdirectory(BLAS) +elseif(BUILD_BLAS) - set(BLAS_LIBRARIES blas) + set(BLAS_LIBRARIES ${BLASLIB}) -else() - set(CMAKE_EXE_LINKER_FLAGS - "${CMAKE_EXE_LINKER_FLAGS} ${BLAS_LINKER_FLAGS}" @@ -300,21 +242,28 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt # Check the usage of the user provided or automatically found LAPACK libraries if(LAPACK_LIBRARIES) - include(CheckFortranFunctionExists) - set(CMAKE_REQUIRED_LIBRARIES ${LAPACK_LIBRARIES}) - # Check if new routine of 3.4.0 is in LAPACK_LIBRARIES -- CHECK_FORTRAN_FUNCTION_EXISTS("dgeqrt" LATESTLAPACK_FOUND) -+ CHECK_FORTRAN_FUNCTION_EXISTS("dgeqrt" LAPACK_FOUND) - unset(CMAKE_REQUIRED_LIBRARIES) -- if(LATESTLAPACK_FOUND) -+ if(LAPACK_FOUND) - message(STATUS "--> LAPACK supplied by user is WORKING, will use ${LAPACK_LIBRARIES}.") +@@ -293,27 +273,28 @@ + include(CheckFortranFunctionExists) + set(CMAKE_REQUIRED_LIBRARIES ${LAPACK_LIBRARIES}) + # Check if new routine of 3.4.0 is in LAPACK_LIBRARIES +- CHECK_FORTRAN_FUNCTION_EXISTS("dgeqrt" LATESTLAPACK_FOUND) ++ CHECK_FORTRAN_FUNCTION_EXISTS("dgeqrt" LAPACK_FOUND) + unset(CMAKE_REQUIRED_LIBRARIES) +- if(LATESTLAPACK_FOUND) ++ if(LAPACK_FOUND) + message(STATUS "--> LAPACK supplied by user is WORKING, will use ${LAPACK_LIBRARIES}.") + else() +- message(ERROR "--> LAPACK supplied by user is not WORKING or is older than LAPACK 3.4.0, CANNOT USE ${LAPACK_LIBRARIES}.") +- message(ERROR "--> Will use REFERENCE LAPACK (by default)") +- message(ERROR "--> Or Correct your LAPACK_LIBRARIES entry ") +- message(ERROR "--> Or Consider checking USE_OPTIMIZED_LAPACK") ++ message(SEND_ERROR "--> LAPACK supplied by user is NOT WORKING or is older than LAPACK 3.4.0, cannot use ${LAPACK_LIBRARIES}.") + endif() else() -- message(ERROR "--> LAPACK supplied by user is not WORKING or is older than LAPACK 3.4.0, CANNOT USE ${LAPACK_LIBRARIES}.") -- message(ERROR "--> Will use REFERENCE LAPACK (by default)") -- message(ERROR "--> Or Correct your LAPACK_LIBRARIES entry ") -- message(ERROR "--> Or Consider checking USE_OPTIMIZED_LAPACK") -+ message(SEND_ERROR "--> LAPACK supplied by user is NOT WORKING or is older than LAPACK 3.4.0, cannot use ${LAPACK_LIBRARIES}.") + message(STATUS "--> LAPACK supplied by user is ${LAPACK_LIBRARIES}.") + message(STATUS "--> CMake couldn't find a Fortran compiler, so it cannot check if the provided LAPACK library works.") +- set(LATESTLAPACK_FOUND TRUE) ++ set(LAPACK_FOUND TRUE) endif() -endif() @@ -326,24 +275,16 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt + find_package(LAPACK) + +elseif(BUILD_LAPACK) - set(LAPACK_LIBRARIES lapack) + set(LAPACK_LIBRARIES ${LAPACKLIB}) + set(LAPACK_FOUND TRUE) + + set(NEED_BLAS TRUE) -+ -+ # Check second function -+ include(CheckTimeFunction) -+ set(TIME_FUNC NONE ${TIME_FUNC}) -+ CHECK_TIME_FUNCTION(NONE TIME_FUNC) -+ CHECK_TIME_FUNCTION(INT_CPU_TIME TIME_FUNC) -+ CHECK_TIME_FUNCTION(EXT_ETIME TIME_FUNC) -+ CHECK_TIME_FUNCTION(EXT_ETIME_ TIME_FUNC) -+ CHECK_TIME_FUNCTION(INT_ETIME TIME_FUNC) -+ message(STATUS "--> Will use second_${TIME_FUNC}.f and dsecnd_${TIME_FUNC}.f as timing function.") -+ -+ set(SECOND_SRC ${LAPACK_SOURCE_DIR}/INSTALL/second_${TIME_FUNC}.f) -+ set(DSECOND_SRC ${LAPACK_SOURCE_DIR}/INSTALL/dsecnd_${TIME_FUNC}.f) -+ + + enable_language(Fortran) + +@@ -336,67 +317,38 @@ + set(DSECOND_SRC ${LAPACK_SOURCE_DIR}/INSTALL/dsecnd_${TIME_FUNC}.f) + add_subdirectory(SRC) -else() - set(CMAKE_EXE_LINKER_FLAGS @@ -363,9 +304,9 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt + add_subdirectory(TESTING) + endif() + -+ configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapack.pc.in ${CMAKE_CURRENT_BINARY_DIR}/lapack.pc @ONLY) ++ configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapack.pc.in ${CMAKE_CURRENT_BINARY_DIR}/${LAPACKLIB}.pc @ONLY) + install(FILES -+ ${CMAKE_CURRENT_BINARY_DIR}/lapack.pc ++ ${CMAKE_CURRENT_BINARY_DIR}/${LAPACKLIB}.pc + DESTINATION ${PKG_CONFIG_DIR} + COMPONENT Development + ) @@ -381,11 +322,37 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt option(LAPACKE_WITH_TMG "Build LAPACKE with tmglib routines" OFF) if(LAPACKE_WITH_TMG) - set(LAPACKE ON) +-endif() +- +-# TMGLIB +-# Cache export target +-set(LAPACK_INSTALL_EXPORT_NAME_CACHE ${LAPACK_INSTALL_EXPORT_NAME}) +-if(BUILD_TESTING OR LAPACKE_WITH_TMG) +- enable_language(Fortran) +- if(LATESTLAPACK_FOUND AND LAPACKE_WITH_TMG) +- set(CMAKE_REQUIRED_LIBRARIES ${LAPACK_LIBRARIES}) +- # Check if dlatms (part of tmg) is found +- include(CheckFortranFunctionExists) +- CHECK_FORTRAN_FUNCTION_EXISTS("dlatms" LAPACK_WITH_TMGLIB_FOUND) +- unset(CMAKE_REQUIRED_LIBRARIES) +- if(NOT LAPACK_WITH_TMGLIB_FOUND) +- # Build and install TMG as part of LAPACKE targets (as opposed to LAPACK +- # targets) +- set(LAPACK_INSTALL_EXPORT_NAME ${LAPACKELIB}-targets) +- endif() +- endif() +- add_subdirectory(TESTING/MATGEN) + set(BUILD_LAPACKE ON) endif() - if(BUILD_TESTING OR LAPACKE_WITH_TMG) #already included, avoid double inclusion - add_subdirectory(TESTING/MATGEN) - endif() +-# Reset export target +-set(LAPACK_INSTALL_EXPORT_NAME ${LAPACK_INSTALL_EXPORT_NAME_CACHE}) +-unset(LAPACK_INSTALL_EXPORT_NAME_CACHE) +- + +-#------------------------------------- +-# LAPACKE + # Include lapack.h and lapacke_mangling.h even if LAPACKE is not built + add_subdirectory(LAPACKE/include) -if(LAPACKE) +if(BUILD_LAPACKE) @@ -393,8 +360,12 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt add_subdirectory(LAPACKE) endif() -@@ -338,109 +316,12 @@ - _display_cpp_implementation_msg("LAPACK") +- + #------------------------------------- + # BLAS++ / LAPACK++ + option(BLAS++ "Build BLAS++" OFF) +@@ -446,111 +398,16 @@ + ExternalProject_Add_StepDependencies(lapackpp build blaspp ${BLAS_LIBRARIES} ${LAPACK_LIBRARIES}) endif() -# -------------------------------------------------- @@ -411,7 +382,7 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt -set(CPACK_PACKAGE_INSTALL_DIRECTORY "LAPACK") -if(WIN32 AND NOT UNIX) - # There is a bug in NSI that does not handle full unix paths properly. Make -- # sure there is at least one set of four (4) backlasshes. +- # sure there is at least one set of four (4) backslashes. - set(CPACK_NSIS_HELP_LINK "http:\\\\\\\\http://icl.cs.utk.edu/lapack-forum") - set(CPACK_NSIS_URL_INFO_ABOUT "http:\\\\\\\\www.netlib.org/lapack") - set(CPACK_NSIS_CONTACT "lapack@eecs.utk.edu") @@ -430,23 +401,19 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt -# -------------------------------------------------- - -if(NOT BLAS_FOUND) -- set(ALL_TARGETS ${ALL_TARGETS} blas) +- set(ALL_TARGETS ${ALL_TARGETS} ${BLASLIB}) -endif() - -if(NOT LATESTLAPACK_FOUND) -- set(ALL_TARGETS ${ALL_TARGETS} lapack) --endif() -- --if(BUILD_TESTING OR LAPACKE_WITH_TMG) -- set(ALL_TARGETS ${ALL_TARGETS} tmglib) +- set(ALL_TARGETS ${ALL_TARGETS} ${LAPACKLIB}) -endif() - -# Export lapack targets, not including lapacke, from the -# install tree, if any. -set(_lapack_config_install_guard_target "") -if(ALL_TARGETS) -- install(EXPORT lapack-targets -- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/lapack-${LAPACK_VERSION} +- install(EXPORT ${LAPACKLIB}-targets +- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/${LAPACKLIB}-${LAPACK_VERSION} - COMPONENT Development - ) - @@ -457,12 +424,16 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt - -# Include cblas in targets exported from the build tree. -if(CBLAS) -- set(ALL_TARGETS ${ALL_TARGETS} cblas) +- set(ALL_TARGETS ${ALL_TARGETS} ${CBLASLIB}) -endif() - -# Include lapacke in targets exported from the build tree. -if(LAPACKE) -- set(ALL_TARGETS ${ALL_TARGETS} lapacke) +- set(ALL_TARGETS ${ALL_TARGETS} ${LAPACKELIB}) +-endif() +- +-if(NOT LAPACK_WITH_TMGLIB_FOUND AND LAPACKE_WITH_TMG) +- set(ALL_TARGETS ${ALL_TARGETS} ${TMGLIB}) +# Neither user specified or optimized BLAS libraries can be used +if(NEED_BLAS AND NOT BLAS_FOUND) + message(FATAL_ERROR "--> No BLAS library found. Specify BLAS_LIBRARIES or enable USE_OPTIMIZED_BLAS or BUILD_BLAS.") @@ -471,7 +442,7 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt -# Export lapack and lapacke targets from the build tree, if any. -set(_lapack_config_build_guard_target "") -if(ALL_TARGETS) -- export(TARGETS ${ALL_TARGETS} FILE lapack-targets.cmake) +- export(TARGETS ${ALL_TARGETS} FILE ${LAPACKLIB}-targets.cmake) - - # Choose one of the lapack or lapacke targets to use as a guard - # for lapack-config.cmake to load targets from the build tree. @@ -480,84 +451,85 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt +if(NEED_LAPACK AND NOT LAPACK_FOUND) + message(FATAL_ERROR "--> No LAPACK library found. Specify LAPACK_LIBRARIES or enable USE_OPTIMIZED_LAPACK or BUILD_LAPACK.") endif() -- + -configure_file(${LAPACK_SOURCE_DIR}/CMAKE/lapack-config-build.cmake.in -- ${LAPACK_BINARY_DIR}/lapack-config.cmake @ONLY) +- ${LAPACK_BINARY_DIR}/${LAPACKLIB}-config.cmake @ONLY) - - --configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapack.pc.in ${CMAKE_CURRENT_BINARY_DIR}/lapack.pc @ONLY) +-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapack.pc.in ${CMAKE_CURRENT_BINARY_DIR}/${LAPACKLIB}.pc @ONLY) - install(FILES -- ${CMAKE_CURRENT_BINARY_DIR}/lapack.pc +- ${CMAKE_CURRENT_BINARY_DIR}/${LAPACKLIB}.pc - DESTINATION ${PKG_CONFIG_DIR} - COMPONENT Development - ) - -configure_file(${LAPACK_SOURCE_DIR}/CMAKE/lapack-config-install.cmake.in -- ${LAPACK_BINARY_DIR}/CMakeFiles/lapack-config.cmake @ONLY) +- ${LAPACK_BINARY_DIR}/CMakeFiles/${LAPACKLIB}-config.cmake @ONLY) - -include(CMakePackageConfigHelpers) -write_basic_package_version_file( -- ${LAPACK_BINARY_DIR}/lapack-config-version.cmake +- ${LAPACK_BINARY_DIR}/${LAPACKLIB}-config-version.cmake - VERSION ${LAPACK_VERSION} - COMPATIBILITY SameMajorVersion - ) - -install(FILES -- ${LAPACK_BINARY_DIR}/CMakeFiles/lapack-config.cmake -- ${LAPACK_BINARY_DIR}/lapack-config-version.cmake -- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/lapack-${LAPACK_VERSION} +- ${LAPACK_BINARY_DIR}/CMakeFiles/${LAPACKLIB}-config.cmake +- ${LAPACK_BINARY_DIR}/${LAPACKLIB}-config-version.cmake +- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/${LAPACKLIB}-${LAPACK_VERSION} - COMPONENT Development - ) -- -\ No newline at end of file + if (LAPACK++) + install( + DIRECTORY "${LAPACK_BINARY_DIR}/lib/" diff --git a/LAPACKE/CMakeLists.txt b/LAPACKE/CMakeLists.txt --- a/LAPACKE/CMakeLists.txt +++ b/LAPACKE/CMakeLists.txt @@ -1,8 +1,6 @@ - message(STATUS "LAPACKE enable") + message(STATUS "LAPACKE enabled") enable_language(C) --set(LAPACK_INSTALL_EXPORT_NAME lapacke-targets) +-set(LAPACK_INSTALL_EXPORT_NAME ${LAPACKELIB}-targets) - - # Create a header file lapacke_mangling.h for the routines called in my C programs - include(FortranCInterface) - ## Ensure that the fortran compiler and c compiler specified are compatible -@@ -79,14 +77,6 @@ + include_directories(include ${LAPACK_BINARY_DIR}/include) + add_subdirectory(src) + add_subdirectory(utils) +@@ -74,14 +72,6 @@ VERSION ${LAPACK_VERSION} SOVERSION ${LAPACK_MAJOR_VERSION} ) --target_include_directories(lapacke PUBLIC -- $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include> +-target_include_directories(${LAPACKELIB} PUBLIC +- $<BUILD_INTERFACE:${LAPACK_BINARY_DIR}/include> - $<INSTALL_INTERFACE:include> -) -if(WIN32 AND NOT UNIX) -- target_compile_definitions(lapacke PUBLIC HAVE_LAPACK_CONFIG_H LAPACK_COMPLEX_STRUCTURE) +- target_compile_definitions(${LAPACKELIB} PUBLIC HAVE_LAPACK_CONFIG_H LAPACK_COMPLEX_STRUCTURE) - message(STATUS "Windows BUILD") -endif() if(LAPACKE_WITH_TMG) - target_link_libraries(lapacke PRIVATE tmglib) -@@ -111,22 +101,3 @@ + target_link_libraries(${LAPACKELIB} PRIVATE ${TMGLIB}) +@@ -106,22 +96,3 @@ DESTINATION ${PKG_CONFIG_DIR} COMPONENT Development ) - -configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cmake/lapacke-config-version.cmake.in -- ${LAPACK_BINARY_DIR}/lapacke-config-version.cmake @ONLY) +- ${LAPACK_BINARY_DIR}/${LAPACKELIB}-config-version.cmake @ONLY) -configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cmake/lapacke-config-build.cmake.in -- ${LAPACK_BINARY_DIR}/lapacke-config.cmake @ONLY) +- ${LAPACK_BINARY_DIR}/${LAPACKELIB}-config.cmake @ONLY) - -configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cmake/lapacke-config-install.cmake.in -- ${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/lapacke-config.cmake @ONLY) +- ${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/${LAPACKELIB}-config.cmake @ONLY) -install(FILES -- ${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/lapacke-config.cmake -- ${LAPACK_BINARY_DIR}/lapacke-config-version.cmake -- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/lapacke-${LAPACK_VERSION} +- ${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/${LAPACKELIB}-config.cmake +- ${LAPACK_BINARY_DIR}/${LAPACKELIB}-config-version.cmake +- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/${LAPACKELIB}-${LAPACK_VERSION} - COMPONENT Development - ) - --install(EXPORT lapacke-targets -- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/lapacke-${LAPACK_VERSION} +-install(EXPORT ${LAPACKELIB}-targets +- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/${LAPACKELIB}-${LAPACK_VERSION} - COMPONENT Development - ) diff --git a/LAPACKE/cmake/lapacke-config-build.cmake.in b/LAPACKE/cmake/lapacke-config-build.cmake.in @@ -570,8 +542,8 @@ deleted file mode 100644 -find_package(LAPACK NO_MODULE) - -# Load lapack targets from the build tree, including lapacke targets. --if(NOT TARGET lapacke) -- include("@LAPACK_BINARY_DIR@/lapack-targets.cmake") +-if(NOT TARGET @LAPACKELIB@) +- include("@LAPACK_BINARY_DIR@/@LAPACKLIB@-targets.cmake") -endif() - -# Hint for project building against lapack @@ -581,37 +553,33 @@ deleted file mode 100644 -set(LAPACKE_INCLUDE_DIRS "@LAPACK_BINARY_DIR@/include") - -# Report lapacke libraries. --set(LAPACKE_LIBRARIES lapacke ${LAPACK_LIBRARIES}) +-set(LAPACKE_LIBRARIES @LAPACKELIB@ ${LAPACK_LIBRARIES}) diff --git a/LAPACKE/cmake/lapacke-config-install.cmake.in b/LAPACKE/cmake/lapacke-config-install.cmake.in deleted file mode 100644 --- a/LAPACKE/cmake/lapacke-config-install.cmake.in +++ /dev/null -@@ -1,26 +0,0 @@ +@@ -1,22 +0,0 @@ -# Compute locations from <prefix>/@{LIBRARY_DIR@/cmake/lapacke-<v>/<self>.cmake -get_filename_component(_LAPACKE_SELF_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH) --get_filename_component(_LAPACKE_PREFIX "${_LAPACKE_SELF_DIR}" PATH) --get_filename_component(_LAPACKE_PREFIX "${_LAPACKE_PREFIX}" PATH) --get_filename_component(_LAPACKE_PREFIX "${_LAPACKE_PREFIX}" PATH) - -# Load the LAPACK package with which we were built. --set(LAPACK_DIR "${_LAPACKE_PREFIX}/@CMAKE_INSTALL_LIBDIR@/cmake/lapack-@LAPACK_VERSION@") +-set(LAPACK_DIR "@CMAKE_INSTALL_FULL_LIBDIR@/cmake/@LAPACKLIB@-@LAPACK_VERSION@") -find_package(LAPACK NO_MODULE) - -# Load lapacke targets from the install tree. --if(NOT TARGET lapacke) -- include(${_LAPACKE_SELF_DIR}/lapacke-targets.cmake) +-if(NOT TARGET @LAPACKELIB@) +- include(${_LAPACKE_SELF_DIR}/@LAPACKELIB@-targets.cmake) -endif() - -# Hint for project building against lapack -set(LAPACKE_Fortran_COMPILER_ID ${LAPACK_Fortran_COMPILER_ID}) - -# Report lapacke header search locations. --set(LAPACKE_INCLUDE_DIRS ${_LAPACKE_PREFIX}/include) +-set(LAPACKE_INCLUDE_DIRS @CMAKE_INSTALL_FULL_INCLUDEDIR@) - -# Report lapacke libraries. --set(LAPACKE_LIBRARIES lapacke ${LAPACK_LIBRARIES}) +-set(LAPACKE_LIBRARIES @LAPACKELIB@ ${LAPACK_LIBRARIES}) - --unset(_LAPACKE_PREFIX) -unset(_LAPACKE_SELF_DIR) diff --git a/LAPACKE/cmake/lapacke-config-version.cmake.in b/LAPACKE/cmake/lapacke-config-version.cmake.in deleted file mode 100644 @@ -626,3 +594,20 @@ deleted file mode 100644 - endif() -endif() - +diff --git a/LAPACKE/include/CMakeLists.txt b/LAPACKE/include/CMakeLists.txt +--- a/LAPACKE/include/CMakeLists.txt ++++ b/LAPACKE/include/CMakeLists.txt +@@ -1,5 +1,5 @@ + set(LAPACKE_INCLUDE lapack.h) +-IF(LAPACKE) ++IF(BUILD_LAPACKE) + list(APPEND LAPACKE_INCLUDE lapacke.h lapacke_config.h lapacke_utils.h) + endif() + +@@ -23,4 +23,4 @@ + message(WARNING "Reverting to pre-defined include/lapacke_mangling.h") + configure_file(lapacke_mangling_with_flags.h.in + ${LAPACK_BINARY_DIR}/include/lapacke_mangling.h) +-endif() +\ No newline at end of file ++endif() diff --git a/academic/ccolamd/ccolamd.SlackBuild b/academic/ccolamd/ccolamd.SlackBuild index cec5eb80f1..504b1668e9 100644 --- a/academic/ccolamd/ccolamd.SlackBuild +++ b/academic/ccolamd/ccolamd.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for CCOLAMD -# Copyright 2013-2020 Kyle Guinn <elyk03@gmail.com> +# Copyright 2013-2021 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,13 +22,16 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=ccolamd SRCNAM=SuiteSparse SUBDIR=CCOLAMD VERSION=${VERSION:-2.9.6} -SRCVER=${SRCVER:-5.6.0} -BUILD=${BUILD:-6} +SRCVER=${SRCVER:-5.8.1} +BUILD=${BUILD:-7} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$(uname -m)" in @@ -38,15 +41,22 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM-$VERSION +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="README.txt Doc/ChangeLog Doc/License.txt Doc/lesser.txt" -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" @@ -105,4 +115,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/ccolamd/ccolamd.info b/academic/ccolamd/ccolamd.info index e32e2118a3..a7d008e0e5 100644 --- a/academic/ccolamd/ccolamd.info +++ b/academic/ccolamd/ccolamd.info @@ -1,8 +1,8 @@ PRGNAM="ccolamd" VERSION="2.9.6" HOMEPAGE="http://faculty.cse.tamu.edu/davis/suitesparse.html" -DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.6.0/SuiteSparse-5.6.0.tar.gz" -MD5SUM="af8b97cbded4cd5c6672e878bc0c37c2" +DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.8.1/SuiteSparse-5.8.1.tar.gz" +MD5SUM="c414679bbc9432a3def01b31ad921140" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="suitesparseconfig" diff --git a/academic/cdo/README b/academic/cdo/README new file mode 100644 index 0000000000..a7fcde9c55 --- /dev/null +++ b/academic/cdo/README @@ -0,0 +1,16 @@ +CDO (Climate Data Operators) + +CDO is a collection of command line Operators to manipulate and analyse +Climate and NWP model Data. + +Supported data formats are GRIB 1/2, netCDF 3/4, SERVICE, EXTRA and +IEG. There are more than 600 operators available. + +REQUIRES: proj udunits netcdf eccodes + +By default, the script does not build nor run the tests. You can use the +option TESTBUILD=YES to build and run the tests before the make install +part. Note that the hdf5 slackbuild builds the library in a +non-thread-safe manner so one of the test will fail with a note in the +test log about requiring the use of the -L flag to compensate, but the +tests themself to not use that flag so fails. diff --git a/academic/cdo/cdo.SlackBuild b/academic/cdo/cdo.SlackBuild new file mode 100644 index 0000000000..bc0583a4da --- /dev/null +++ b/academic/cdo/cdo.SlackBuild @@ -0,0 +1,120 @@ +#!/bin/bash + +# Slackware build script for cdo + +# Copyright 2020-2024 Gregory J. L. Tourte <artourter@gmail.com> +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=cdo +VERSION=${VERSION:-2.4.0} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +TESTBUILD=${TESTBUILD:-NO} + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + -perm /111 -a \! -perm 755 -a -exec chmod 755 {} + -o \ + \! -perm /111 -a \! -perm 644 -a -exec chmod 644 {} + + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --docdir=/usr/doc/$PRGNAM-$VERSION \ + --disable-static \ + --with-eccodes=yes \ + --with-szlib=yes \ + --with-netcdf=yes \ + --with-hdf5=yes \ + --with-threads=yes \ + --with-udunits2 \ + --with-fftw3 \ + --with-proj \ + --with-curl \ + --with-libxml2 \ + --enable-silent-rules \ + --build=$ARCH-slackware-linux + +make +[[ $TESTBUILD == "YES" ]] && make check +make install DESTDIR=$PKG + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + AUTHORS ChangeLog LICENSE NEWS OPERATORS README \ + doc/*.pdf \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/cdo/cdo.info b/academic/cdo/cdo.info new file mode 100644 index 0000000000..f3ca4cd66b --- /dev/null +++ b/academic/cdo/cdo.info @@ -0,0 +1,10 @@ +PRGNAM="cdo" +VERSION="2.4.0" +HOMEPAGE="https://code.mpimet.mpg.de/projects/cdo" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="https://code.mpimet.mpg.de/attachments/download/29313/cdo-2.4.0.tar.gz" +MD5SUM_x86_64="797d3c2257f73937dc95b280dd21fd8b" +REQUIRES="proj udunits netcdf eccodes" +MAINTAINER="ArTourter" +EMAIL="artourter@gmail.com" diff --git a/academic/coq/slack-desc b/academic/cdo/slack-desc index a5c16bf092..49f7b868c9 100644 --- a/academic/coq/slack-desc +++ b/academic/cdo/slack-desc @@ -6,14 +6,14 @@ # customary to leave one space after the ':' except on otherwise blank lines. |-----handy-ruler------------------------------------------------------| -coq: coq (The Coq Proof Assistant) -coq: -coq: coq is a formal proof management system. It provides a formal language -coq: to write mathematical definitions, executable algorithms and theorems -coq: together with an environment for semi-interactive development of -coq: machine-checked proofs. -coq: -coq: Homepage: https://coq.inria.fr/ -coq: -coq: -coq: +cdo: cdo (Climate Data Operators) +cdo: +cdo: CDO is a collection of command line Operators to manipulate and +cdo: analyse Climate and NWP model Data. +cdo: +cdo: Supported data formats are GRIB 1/2, netCDF 3/4, SERVICE, EXTRA and +cdo: IEG. There are more than 600 operators available. +cdo: +cdo: +cdo: +cdo: diff --git a/academic/celestia/README b/academic/celestia/README index 84faa8608e..1e99d61175 100644 --- a/academic/celestia/README +++ b/academic/celestia/README @@ -1,9 +1,11 @@ -A real-time space simulation that lets you experience our universe -in three dimensions. +A real-time space simulation that lets you experience our universe in +three dimensions. -There are four frontend possibilities to choose. The Glut one works out -of the box, the GTK one needs gtkglext, and the Gnome one is untested. -The KDE frontend requires kde3 and will not work with the kde3 compat -packages, so it's essentially nonfunctional. +There are four frontend possibilities to choose. The Glut one works +out of the box, the GTK one needs gtkglext, and the Gnome one is +untested. The KDE frontend hasn't been updated since kde3 times, so +it's practically non-functional. -This requires lua, and gtkglext is optional but recommended. +Since the GTK frontend is the default, gtkglext is a required +dependency. Further, lua53 is listed as required dependency, but lua +or lua52 will work as well. diff --git a/academic/celestia/celestia-1.6.1-gcc47.patch b/academic/celestia/celestia-1.6.1-gcc47.patch deleted file mode 100644 index 385f39a205..0000000000 --- a/academic/celestia/celestia-1.6.1-gcc47.patch +++ /dev/null @@ -1,22 +0,0 @@ -diff -up celestia-1.6.1/src/celengine/frametree.h.gcc47 celestia-1.6.1/src/celengine/frametree.h ---- celestia-1.6.1/src/celengine/frametree.h.gcc47 2012-03-22 12:56:56.096087430 -0400 -+++ celestia-1.6.1/src/celengine/frametree.h 2012-03-22 12:57:04.333022427 -0400 -@@ -13,6 +13,7 @@ - #ifndef _CELENGINE_FRAMETREE_H_ - #define _CELENGINE_FRAMETREE_H_ - -+#include <unistd.h> - #include <vector> - - class Star; -diff -up celestia-1.6.1/src/celengine/planetgrid.cpp.gcc47 celestia-1.6.1/src/celengine/planetgrid.cpp ---- celestia-1.6.1/src/celengine/planetgrid.cpp.gcc47 2012-03-22 12:53:01.496950513 -0400 -+++ celestia-1.6.1/src/celengine/planetgrid.cpp 2012-03-22 12:53:08.812891865 -0400 -@@ -12,6 +12,7 @@ - - #include <cstdio> - #include <cmath> -+#include <celmath/mathlib.h> - #include <celmath/intersect.h> - #include "planetgrid.h" - #include "body.h" diff --git a/academic/celestia/celestia-1.6.1-libpng15.patch b/academic/celestia/celestia-1.6.1-libpng15.patch deleted file mode 100644 index 5dffbab246..0000000000 --- a/academic/celestia/celestia-1.6.1-libpng15.patch +++ /dev/null @@ -1,14 +0,0 @@ -imagecapture.cpp:184:40: error: ‘Z_BEST_COMPRESSION’ was not declared in this scope - ---- src/celestia/imagecapture.cpp -+++ src/celestia/imagecapture.cpp -@@ -31,6 +31,9 @@ - #include "png.h" - #endif - -+// Z_BEST_COMPRESSION -+#include <zlib.h> -+ - // Define png_jmpbuf() in case we are using a pre-1.0.6 version of libpng - #ifndef png_jmpbuf - #define png_jmpbuf(png_ptr) png_ptr->jmpbuf diff --git a/academic/celestia/celestia-1.6.1-libpng16.patch b/academic/celestia/celestia-1.6.1-libpng16.patch deleted file mode 100644 index 78911cb557..0000000000 --- a/academic/celestia/celestia-1.6.1-libpng16.patch +++ /dev/null @@ -1,25 +0,0 @@ -image.cpp:530:61: error: ‘memcpy’ was not declared in this scope - -https://bugs.gentoo.org/show_bug.cgi?id=464764 - -Patch written by Lars Wendler <polynomial-c@gentoo.org> ---- a/celestia/src/celengine/image.cpp -+++ b/celestia/src/celengine/image.cpp -@@ -42,6 +42,7 @@ extern "C" { - #include "jpeglib.h" - #else - #include <cstdio> -+#include <string.h> - #include <jpeglib.h> - #endif - } ---- a/celestia/src/celengine/texture.cpp -+++ b/celestia/src/celengine/texture.cpp -@@ -28,6 +28,7 @@ - #include <cstdlib> - #include <cstdio> - #include <cassert> -+#include <string.h> - - #ifndef _WIN32 - #ifndef TARGET_OS_MAC diff --git a/academic/celestia/celestia.SlackBuild b/academic/celestia/celestia.SlackBuild index 16f553a970..8697c7ce48 100644 --- a/academic/celestia/celestia.SlackBuild +++ b/academic/celestia/celestia.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for celestia -# Copyright 2008-2011 Heinz Wiesinger <pprkut@liwjatan.at> +# Copyright 2008-2021 Heinz Wiesinger, Amsterdam, The Netherlands # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -11,21 +11,25 @@ # 1. Redistributions of this script must retain the above copyright # notice, this list of conditions and the following disclaimer. # -# THIS SOFTWARE IS PROVIDED BY THE AUTHOR ''AS IS'' AND ANY EXPRESS OR IMPLIED -# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF -# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO -# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, -# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, -# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; -# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, -# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR -# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF -# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) PRGNAM=celestia -VERSION=${VERSION:-1.6.1} -BUILD=${BUILD:-2} +SRCNAM=Celestia +VERSION=${VERSION:-1.6.2.2} +BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +39,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -56,9 +67,9 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $PRGNAM-$VERSION -tar xvf $CWD/$PRGNAM-$VERSION.tar.gz -cd $PRGNAM-$VERSION +rm -rf $SRCNAM-$VERSION +tar xvf $CWD/$SRCNAM-$VERSION.tar.gz +cd $SRCNAM-$VERSION chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \ @@ -72,12 +83,7 @@ find -L . \ # Note that the kde frontend will only build with kde3 FRONTEND=${FRONTEND:-gtk} -# Fix incompatibility with gcc 4.7 -patch -p1 -i $CWD/celestia-1.6.1-gcc47.patch - -# Fix libpng incompatibilities (thanks to Arch Linux) -patch -p0 -i $CWD/celestia-1.6.1-libpng15.patch -patch -p2 -i $CWD/celestia-1.6.1-libpng16.patch +autoreconf -vif CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ @@ -93,6 +99,10 @@ CXXFLAGS="$SLKCFLAGS" \ make make install-strip DESTDIR=$PKG +# Fix name of executable in desktop file +sed -i "s|celestia-gtk|celestia|" \ + $PKG/usr/share/applications/celestia.desktop + mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a ABOUT-NLS AUTHORS ChangeLog COPYING INSTALL NEWS README TRANSLATORS \ $PKG/usr/doc/$PRGNAM-$VERSION @@ -103,4 +113,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/celestia/celestia.info b/academic/celestia/celestia.info index b1dcef0319..b8c4371e03 100644 --- a/academic/celestia/celestia.info +++ b/academic/celestia/celestia.info @@ -1,10 +1,10 @@ PRGNAM="celestia" -VERSION="1.6.1" -HOMEPAGE="http://www.shatters.net/celestia/" -DOWNLOAD="http://downloads.sourceforge.net/celestia/celestia-1.6.1.tar.gz" -MD5SUM="02208982a431b984502fac909bf380f4" +VERSION="1.6.2.2" +HOMEPAGE="https://celestia.space/" +DOWNLOAD="https://github.com/CelestiaProject/Celestia/archive/1.6.2.2/Celestia-1.6.2.2.tar.gz" +MD5SUM="0f4871b44f05e0eb9e3714bb13fed2b7" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="gtkglext lua" +REQUIRES="gtkglext lua53" MAINTAINER="Heinz Wiesinger" -EMAIL="pprkut@liwjatan.at" +EMAIL="pprkut@slackbuilds.org" diff --git a/academic/celestia/slack-desc b/academic/celestia/slack-desc index a0b2b9d767..60881f44da 100644 --- a/academic/celestia/slack-desc +++ b/academic/celestia/slack-desc @@ -11,7 +11,7 @@ celestia: celestia: A real-time space simulation that lets you experience our universe celestia: in three dimensions. celestia: -celestia: Homepage: http://www.shatters.net/celestia/ +celestia: Homepage: https://celestia.space/ celestia: celestia: celestia: diff --git a/academic/chartgeany/README b/academic/chartgeany/README new file mode 100644 index 0000000000..7bcb44052d --- /dev/null +++ b/academic/chartgeany/README @@ -0,0 +1,6 @@ +Chart Geany is a cross platform software solution for market technical +analysis and charting. + +To build the qt5 GUI pass the script the parameter QT5GUI=yes, like + + QT5GUI=yes ./chartgeany.SlackBuild diff --git a/academic/chartgeany/chartgeany.SlackBuild b/academic/chartgeany/chartgeany.SlackBuild new file mode 100644 index 0000000000..d84cc81720 --- /dev/null +++ b/academic/chartgeany/chartgeany.SlackBuild @@ -0,0 +1,116 @@ +#!/bin/bash + +# Slackware build script for chartgeany + +# Copyright 2020 Larry Hajali <larryhaja[at]gmail[dot]com> +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=chartgeany +VERSION=${VERSION:-6.1.5} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +# Fix file locaations. +sed -i '/^target.path/s|= /opt/$$PKG_NAME|= /usr/bin|' \ + ChartGeany/ChartGeany.pro cgtool/cgtool.pro +sed -i '/^images.path/s|= /opt/$$PKG_NAME|= /usr/share/pixmaps|' \ + ChartGeany/ChartGeany.pro +sed -i "s|/opt/$PRGNAM/||" ChartGeany/chartgeany.desktop + +if [ "${QT5GUI:-no}" == "yes" ]; then + qmake-qt5 PREFIX="/usr" QMAKE_CFLAGS+="$SLKCFLAGS" QMAKE_CXXFLAGS+="$SLKCFLAGS" \ + -o Makefile $PRGNAM.pro +else + qmake PREFIX="/usr" QMAKE_CFLAGS+="$SLKCFLAGS" QMAKE_CXXFLAGS+="$SLKCFLAGS" \ + -o Makefile $PRGNAM.pro +fi + +make +make install INSTALL_ROOT=$PKG + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +chmod 0644 $PKG/usr/share/applications/$PRGNAM.desktop + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + COPYING Changelog \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/chartgeany/chartgeany.info b/academic/chartgeany/chartgeany.info new file mode 100644 index 0000000000..83d6be57c8 --- /dev/null +++ b/academic/chartgeany/chartgeany.info @@ -0,0 +1,10 @@ +PRGNAM="chartgeany" +VERSION="6.1.5" +HOMEPAGE="https://sourceforge.net/projects/chart-geany/" +DOWNLOAD="https://downloads.sourceforge.net/chart-geany/chartgeany-6.1.5.tar.gz" +MD5SUM="c2f0acdc7025de66ff6cbcba65212751" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="libxls" +MAINTAINER="Larry Hajali" +EMAIL="larryhaja[at]gmail[dot]com" diff --git a/academic/chartgeany/doinst.sh b/academic/chartgeany/doinst.sh new file mode 100644 index 0000000000..5fb28930db --- /dev/null +++ b/academic/chartgeany/doinst.sh @@ -0,0 +1,3 @@ +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 +fi diff --git a/academic/chartgeany/slack-desc b/academic/chartgeany/slack-desc new file mode 100644 index 0000000000..cb4c4a3b5c --- /dev/null +++ b/academic/chartgeany/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +chartgeany: chartgeany (market analysis tool) +chartgeany: +chartgeany: Chart Geany is a cross platform software solution for market technical +chartgeany: analysis and charting. +chartgeany: +chartgeany: Homepage: https://sourceforge.net/projects/chart-geany/ +chartgeany: +chartgeany: +chartgeany: +chartgeany: +chartgeany: diff --git a/academic/chemtool/chemtool.SlackBuild b/academic/chemtool/chemtool.SlackBuild index 52acf74472..975235e59a 100644 --- a/academic/chemtool/chemtool.SlackBuild +++ b/academic/chemtool/chemtool.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for chemtool -# Copyright 2006,2008-2013 Robby Workman, Northport, Alabama, USA +# Copyright 2006-2013,2021 Robby Workman, Tuscaloosa, Alabama, USA # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,26 +22,36 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=chemtool VERSION=${VERSION:-1.6.14} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -69,6 +79,10 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; +# Thanks, Debian +# https://salsa.debian.org/debichem-team/chemtool/-/blob/7d0413fe4f5bce35fe9c16fd196758319df05442/debian/patches/957084_gcc10.patch +patch -p1 < $CWD/gcc10.patch + CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ @@ -101,4 +115,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -p -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -p -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/chemtool/gcc10.patch b/academic/chemtool/gcc10.patch new file mode 100644 index 0000000000..d782f8e4a6 --- /dev/null +++ b/academic/chemtool/gcc10.patch @@ -0,0 +1,37 @@ +--- a/ct1.h ++++ b/ct1.h +@@ -273,12 +273,12 @@ + extern float importfactor; + extern int importoffset; + +-char **intype; +-char **inmode; +-int babelin; +-char **outtype; +-char **outmode; +-int babelout; ++extern char **intype; ++extern char **inmode; ++extern int babelin; ++extern char **outtype; ++extern char **outmode; ++extern int babelout; + extern char *babel; + extern GdkGC *mygc[8],*background_gc,*hlgc; + extern int curpen; +--- a/inout.c ++++ b/inout.c +@@ -30,6 +30,13 @@ + extern GdkFont *font[7],*smallfont[7],*symbfont[7],*boldfont[7],*slfont[7]; + #endif + ++char **intype; ++char **inmode; ++int babelin; ++char **outtype; ++char **outmode; ++int babelout; ++ + static char babeloutp[4]; + + int diff --git a/academic/cholmod/README b/academic/cholmod/README index 46350dc390..f91a13d263 100644 --- a/academic/cholmod/README +++ b/academic/cholmod/README @@ -1,16 +1,18 @@ -CHOLMOD is a set of ANSI C routines for sparse Cholesky factorization and -update/downdate. +CHOLMOD is a set of ANSI C routines for sparse Cholesky factorization +and update/downdate. This package is part of SuiteSparse. -This requires a BLAS/LAPACK implementation. Choose one of these package sets: +This requires a BLAS/LAPACK implementation. Choose one of these +package sets: * OpenBLAS (includes both a BLAS and a LAPACK implementation) * atlas (includes both a BLAS and a LAPACK implementation) * blas, lapack (the Netlib reference implementations) -If more than one set is installed (assuming there are no packaging conflicts) -then the auto-detection will use the first implementation from this list that -it finds. If in doubt, choose the Netlib reference implementations; other -packages that require a BLAS or LAPACK implementation may not build if they -are not configured to detect/use alternate implementations. +If more than one set is installed (assuming there are no packaging +conflicts) then the auto-detection will use the first implementation +from this list that it finds. If in doubt, choose the Netlib +reference implementations; other packages that require a BLAS or +LAPACK implementation may not build if they are not configured to +detect/use alternate implementations. metis is an optional dependency and will be used if found. diff --git a/academic/cholmod/cholmod.SlackBuild b/academic/cholmod/cholmod.SlackBuild index aae466f098..4daabb7bf7 100644 --- a/academic/cholmod/cholmod.SlackBuild +++ b/academic/cholmod/cholmod.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for CHOLMOD -# Copyright 2013-2020 Kyle Guinn <elyk03@gmail.com> +# Copyright 2013-2021 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,13 +22,16 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=cholmod SRCNAM=SuiteSparse SUBDIR=CHOLMOD -VERSION=${VERSION:-3.0.13} -SRCVER=${SRCVER:-5.6.0} -BUILD=${BUILD:-2} +VERSION=${VERSION:-3.0.14} +SRCVER=${SRCVER:-5.8.1} +BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$(uname -m)" in @@ -38,15 +41,22 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM-$VERSION +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="README.txt Doc/ChangeLog Doc/License.txt Core/lesser.txt Modify/gpl.txt" -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" @@ -110,4 +120,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/cholmod/cholmod.info b/academic/cholmod/cholmod.info index 9b41a522e8..468deec03d 100644 --- a/academic/cholmod/cholmod.info +++ b/academic/cholmod/cholmod.info @@ -1,10 +1,10 @@ PRGNAM="cholmod" -VERSION="3.0.13" +VERSION="3.0.14" HOMEPAGE="http://faculty.cse.tamu.edu/davis/suitesparse.html" -DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.6.0/SuiteSparse-5.6.0.tar.gz" -MD5SUM="af8b97cbded4cd5c6672e878bc0c37c2" +DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.8.1/SuiteSparse-5.8.1.tar.gz" +MD5SUM="c414679bbc9432a3def01b31ad921140" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="blas lapack suitesparseconfig amd camd colamd ccolamd" +REQUIRES="lapack amd camd colamd ccolamd" MAINTAINER="Kyle Guinn" EMAIL="elyk03@gmail.com" diff --git a/academic/cholmod/patches/autoconfiscate.diff b/academic/cholmod/patches/autoconfiscate.diff index 6cdb2b7b6a..36736536c4 100644 --- a/academic/cholmod/patches/autoconfiscate.diff +++ b/academic/cholmod/patches/autoconfiscate.diff @@ -1469,7 +1469,7 @@ new file mode 100644 +# Process this file with autoconf to produce a configure script. + +AC_PREREQ([2.69]) -+AC_INIT([CHOLMOD],[3.0.13],[https://github.com/DrTimothyAldenDavis/SuiteSparse],[cholmod],[http://www.suitesparse.com/]) ++AC_INIT([CHOLMOD],[3.0.14],[https://github.com/DrTimothyAldenDavis/SuiteSparse],[cholmod],[http://www.suitesparse.com/]) +AC_CONFIG_SRCDIR([Core/cholmod_common.c]) +AC_CONFIG_AUX_DIR([build-aux]) +AC_CONFIG_MACRO_DIR([m4]) @@ -1690,7 +1690,7 @@ diff --git a/m4/ax_blas.m4 b/m4/ax_blas.m4 new file mode 100644 --- /dev/null +++ b/m4/ax_blas.m4 -@@ -0,0 +1,238 @@ +@@ -0,0 +1,241 @@ +# =========================================================================== +# https://www.gnu.org/software/autoconf-archive/ax_blas.html +# =========================================================================== @@ -1729,6 +1729,7 @@ new file mode 100644 +# LICENSE +# +# Copyright (c) 2008 Steven G. Johnson <stevenj@alum.mit.edu> ++# Copyright (c) 2019 Geoffrey M. Oxberry <goxberry@gmail.com> +# +# This program is free software: you can redistribute it and/or modify it +# under the terms of the GNU General Public License as published by the @@ -1756,7 +1757,7 @@ new file mode 100644 +# modified version of the Autoconf Macro, you may extend this special +# exception to the GPL to apply to your modified version as well. + -+#serial 16 ++#serial 17 + +AU_ALIAS([ACX_BLAS], [AX_BLAS]) +AC_DEFUN([AX_BLAS], [ @@ -1770,7 +1771,9 @@ new file mode 100644 +case $with_blas in + yes | "") ;; + no) ax_blas_ok=disable ;; -+ -* | */* | *.a | *.so | *.so.* | *.o) BLAS_LIBS="$with_blas" ;; ++ -* | */* | *.a | *.so | *.so.* | *.dylib | *.dylib.* | *.o) ++ BLAS_LIBS="$with_blas" ++ ;; + *) BLAS_LIBS="-l$with_blas" ;; +esac + @@ -2209,7 +2212,7 @@ diff --git a/m4/ax_lapack.m4 b/m4/ax_lapack.m4 new file mode 100644 --- /dev/null +++ b/m4/ax_lapack.m4 -@@ -0,0 +1,131 @@ +@@ -0,0 +1,134 @@ +# =========================================================================== +# https://www.gnu.org/software/autoconf-archive/ax_lapack.html +# =========================================================================== @@ -2249,6 +2252,7 @@ new file mode 100644 +# LICENSE +# +# Copyright (c) 2009 Steven G. Johnson <stevenj@alum.mit.edu> ++# Copyright (c) 2019 Geoffrey M. Oxberry <goxberry@gmail.com> +# +# This program is free software: you can redistribute it and/or modify it +# under the terms of the GNU General Public License as published by the @@ -2276,7 +2280,7 @@ new file mode 100644 +# modified version of the Autoconf Macro, you may extend this special +# exception to the GPL to apply to your modified version as well. + -+#serial 9 ++#serial 10 + +AU_ALIAS([ACX_LAPACK], [AX_LAPACK]) +AC_DEFUN([AX_LAPACK], [ @@ -2288,7 +2292,9 @@ new file mode 100644 +case $with_lapack in + yes | "") ;; + no) ax_lapack_ok=disable ;; -+ -* | */* | *.a | *.so | *.so.* | *.o) LAPACK_LIBS="$with_lapack" ;; ++ -* | */* | *.a | *.so | *.so.* | *.dylib | *.dylib.* | *.o) ++ LAPACK_LIBS="$with_lapack" ++ ;; + *) LAPACK_LIBS="-l$with_lapack" ;; +esac + diff --git a/academic/cistrome-CEAS/cistrome-CEAS.SlackBuild b/academic/cistrome-CEAS/cistrome-CEAS.SlackBuild index 3e0270e266..5c87590162 100644 --- a/academic/cistrome-CEAS/cistrome-CEAS.SlackBuild +++ b/academic/cistrome-CEAS/cistrome-CEAS.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for cistrome-CEAS -# Copyright 2013-2020 Petar Petrov slackalaxy@gmail.com +# Copyright 2013-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=cistrome-CEAS VERSION=${VERSION:-1.0.2} BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} SRCNAM=CEAS-Package @@ -37,7 +40,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -91,4 +101,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/cistrome-MACS/cistrome-MACS.SlackBuild b/academic/cistrome-MACS/cistrome-MACS.SlackBuild index ad93aefcdf..98f279db3c 100644 --- a/academic/cistrome-MACS/cistrome-MACS.SlackBuild +++ b/academic/cistrome-MACS/cistrome-MACS.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for cistrome-MACS -# Copyright 2013-2020 Petar Petrov slackalaxy@gmail.com +# Copyright 2013-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=cistrome-MACS VERSION=${VERSION:-1.4.2} BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} SRCNAM=MACS SRCVER=1.4.2-1 @@ -38,7 +41,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -57,13 +67,20 @@ else LIBDIRSUFFIX="" fi +# 20220222 bkw: depending on what client was used to download the file, +# it may have CGI parameters in the filename. +TARBALL=$CWD/${SRCNAM}-$SRCVER.tar.gz +if [ ! -e $TARBALL ]; then + TARBALL="$( /bin/ls $TARBALL\?* | head -1 )" +fi + set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $SRCNAM-$VERSION -tar xvf $CWD/$SRCNAM-$SRCVER.tar.gz +tar xvf $TARBALL cd $SRCNAM-$VERSION chown -R root:root . find -L . \ @@ -92,4 +109,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/cistrome-MACS/cistrome-MACS.info b/academic/cistrome-MACS/cistrome-MACS.info index 02eb7b8547..7ca43c2935 100644 --- a/academic/cistrome-MACS/cistrome-MACS.info +++ b/academic/cistrome-MACS/cistrome-MACS.info @@ -1,7 +1,7 @@ PRGNAM="cistrome-MACS" VERSION="1.4.2" HOMEPAGE="https://github.com/taoliu/MACS/" -DOWNLOAD="https://github.com/downloads/taoliu/MACS/MACS-1.4.2-1.tar.gz" +DOWNLOAD="https://slackware.uk/sbosrcarch/by-name/academic/cistrome-MACS/MACS-1.4.2-1.tar.gz" MD5SUM="950dab09fe1335c8bbb34a896c21e3e2" DOWNLOAD_x86_64="" MD5SUM_x86_64="" diff --git a/academic/cistrome-conductGO/cistrome-conductGO.SlackBuild b/academic/cistrome-conductGO/cistrome-conductGO.SlackBuild index 28dc36ec8f..0a4913c9df 100644 --- a/academic/cistrome-conductGO/cistrome-conductGO.SlackBuild +++ b/academic/cistrome-conductGO/cistrome-conductGO.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for cistrome-conductGO -# Copyright 2016 Petar Petrov slackalaxy@gmail.com +# Copyright 2016-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=cistrome-conductGO VERSION=${VERSION:-1.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -74,4 +84,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/cistrome-extra/cistrome-extra.SlackBuild b/academic/cistrome-extra/cistrome-extra.SlackBuild index c4c2bef3db..9bb3b21eb0 100644 --- a/academic/cistrome-extra/cistrome-extra.SlackBuild +++ b/academic/cistrome-extra/cistrome-extra.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for cistrome-extra -# Copyright 2016 Petar Petrov slackalaxy@gmail.com +# Copyright 2016-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=cistrome-extra VERSION=${VERSION:-git_20170829_6334683} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} SRCNAM=cistrome-cistrome-applications-harvard SRCVER=63346832a22a @@ -38,7 +41,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -98,4 +108,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/cistrome-extra/cistrome-extra.info b/academic/cistrome-extra/cistrome-extra.info index e3fa027874..db04a687ac 100644 --- a/academic/cistrome-extra/cistrome-extra.info +++ b/academic/cistrome-extra/cistrome-extra.info @@ -1,7 +1,7 @@ PRGNAM="cistrome-extra" VERSION="git_20170829_6334683" HOMEPAGE="http://cistrome.org/" -DOWNLOAD="https://bitbucket.org/cistrome/cistrome-applications-harvard/get/63346832a22a.zip" +DOWNLOAD="http://slackware.uk/sbosrcarch/by-name/academic/cistrome-extra/63346832a22a.zip" MD5SUM="0441f0c1bb3ffa156dfe9ed0fccd5dc8" DOWNLOAD_x86_64="" MD5SUM_x86_64="" diff --git a/academic/cistrome-mdseqpos/cistrome-mdseqpos.SlackBuild b/academic/cistrome-mdseqpos/cistrome-mdseqpos.SlackBuild index 95867993fa..2fbd96ec14 100644 --- a/academic/cistrome-mdseqpos/cistrome-mdseqpos.SlackBuild +++ b/academic/cistrome-mdseqpos/cistrome-mdseqpos.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for cistrome-mdseqpos -# Copyright 2016-2017 Petar Petrov slackalaxy@gmail.com +# Copyright 2016-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=cistrome-mdseqpos VERSION=${VERSION:-git_20170829_6334683} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} SRCNAM=cistrome-cistrome-applications-harvard SRCVER=63346832a22a @@ -38,7 +41,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -98,4 +108,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/cistrome-mdseqpos/cistrome-mdseqpos.info b/academic/cistrome-mdseqpos/cistrome-mdseqpos.info index 37ca6fdfdb..b1e6afd6e2 100644 --- a/academic/cistrome-mdseqpos/cistrome-mdseqpos.info +++ b/academic/cistrome-mdseqpos/cistrome-mdseqpos.info @@ -5,6 +5,6 @@ DOWNLOAD="https://bitbucket.org/cistrome/cistrome-applications-harvard/get/63346 MD5SUM="0441f0c1bb3ffa156dfe9ed0fccd5dc8" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="numpy python-django R Jinja2" +REQUIRES="python2-numpy python2-django R" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/clark-ugene/clark-ugene.SlackBuild b/academic/clark-ugene/clark-ugene.SlackBuild index 6fd7166595..9289eaf23b 100644 --- a/academic/clark-ugene/clark-ugene.SlackBuild +++ b/academic/clark-ugene/clark-ugene.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for clark-ugene -# Copyright 2018-2019 Petar Petrov slackalaxy@gmail.com +# Copyright 2018-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,11 +22,14 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=clark-ugene VERSION=${VERSION:-git_6917bf9} COMMIT=${COMMIT:-6917bf93df9a8c2b80155db367f6672c1b143d9b} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} SRCNAM=clark @@ -38,7 +41,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -101,4 +111,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/cld2/README b/academic/cld2/README index 164357bf4f..d7d86bd3d4 100644 --- a/academic/cld2/README +++ b/academic/cld2/README @@ -1,9 +1,11 @@ -The Compact Language Detection library can detect the language of UTF8-encoded -text. CLD2 supports over 160 languages and can parse both plain text and HTML. +The Compact Language Detection library can detect the language of +UTF8-encoded text. CLD2 supports over 160 languages and can parse both +plain text and HTML. -The Slackware script builds two shared libraries, libcld2 and libcld2_full. The -libcld2 library can recognise the core 83 languages while the libcld2_full -library has support for the entire set of 160+ language tables. +The Slackware script builds two shared libraries, libcld2 and +libcld2_full. The libcld2 library can recognise the core 83 languages +while the libcld2_full library has support for the entire set of 160+ +language tables. -The script also builds a commandline tool, cld2, which is compiled against the -libcld2_full library. +The script also builds a commandline tool, cld2, which is compiled +against the libcld2_full library. diff --git a/academic/cld2/cld2.SlackBuild b/academic/cld2/cld2.SlackBuild index ba04d548fd..ed17cd8de9 100644 --- a/academic/cld2/cld2.SlackBuild +++ b/academic/cld2/cld2.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # SlackBuild script for cld2 @@ -24,11 +24,14 @@ # (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=cld2 VERSION=${VERSION:-20150820} SRCREV=b56fa78a2fe44ac2851bae5bf4f4693a0644da7b BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -38,7 +41,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -128,4 +138,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/clustalo/clustalo.SlackBuild b/academic/clustalo/clustalo.SlackBuild index bd06c3e763..828c94a785 100644 --- a/academic/clustalo/clustalo.SlackBuild +++ b/academic/clustalo/clustalo.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for clustalo -# Copyright 2011-2017 Petar Petrov slackalaxy@gmail.com +# Copyright 2011-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=clustalo VERSION=${VERSION:-1.2.4} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} SRCNAM=clustal-omega @@ -37,7 +40,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -97,8 +107,10 @@ cp -a \ cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/clustalw/clustalw.SlackBuild b/academic/clustalw/clustalw.SlackBuild index 17f5f46bab..83931e066d 100644 --- a/academic/clustalw/clustalw.SlackBuild +++ b/academic/clustalw/clustalw.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for clustalw -# Copyright 2011-2016 Petar Petrov slackalaxy@gmail.com +# Copyright 2011-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,26 +22,36 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=clustalw VERSION=${VERSION:-2.1} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -64,10 +74,10 @@ tar xvf $CWD/$PRGNAM-$VERSION.tar.gz cd $PRGNAM-$VERSION chown -R root:root . find -L . \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ @@ -105,4 +115,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/clustalx/QT.patch b/academic/clustalx/QT.patch new file mode 100644 index 0000000000..72907ea824 --- /dev/null +++ b/academic/clustalx/QT.patch @@ -0,0 +1,200 @@ +diff -urN clustalx-2.1/AlignOutputFileNames.cpp clustalx-2.1-bak/AlignOutputFileNames.cpp +--- clustalx-2.1/AlignOutputFileNames.cpp 2010-11-17 11:12:30.000000000 +0100 ++++ clustalx-2.1-bak/AlignOutputFileNames.cpp 2015-09-18 18:59:38.582405761 +0200 +@@ -13,6 +13,7 @@ + * 18-06-07,Nigel Brown(EMBL): Made the 'ok' button in each dialogue be the + * default instead of a Browse button. + */ ++#include <QtGui> + #include <QPushButton> + #include <QGroupBox> + #include <QCheckBox> +@@ -20,8 +21,8 @@ + #include <QGridLayout> + #include <QSizePolicy> + #include <QComboBox> +-#include <QtGui> + #include <QLabel> ++#include <QLineEdit> + #include <iostream> + #include "AlignOutputFileNames.h" + #include "clustalW/general/userparams.h" +diff -urN clustalx-2.1/AlignmentViewerWidget.cpp clustalx-2.1-bak/AlignmentViewerWidget.cpp +--- clustalx-2.1/AlignmentViewerWidget.cpp 2010-11-17 11:12:30.000000000 +0100 ++++ clustalx-2.1-bak/AlignmentViewerWidget.cpp 2015-09-18 18:50:09.762563103 +0200 +@@ -69,6 +69,11 @@ + #include "PSPrinter.h" + #include "FileDialog.h" + #include <QFontMetrics> ++#include <QVBoxLayout> ++#include <QScrollBar> ++#include <QScrollArea> ++#include <QMessageBox> ++#include <QGroupBox> + + AlignmentViewerWidget::AlignmentViewerWidget(QWidget *parent) + : QWidget(parent), +diff -urN clustalx-2.1/AlignmentWidget.cpp clustalx-2.1-bak/AlignmentWidget.cpp +--- clustalx-2.1/AlignmentWidget.cpp 2010-11-17 11:12:30.000000000 +0100 ++++ clustalx-2.1-bak/AlignmentWidget.cpp 2015-09-18 18:58:36.656119118 +0200 +@@ -46,6 +46,7 @@ + ****************************************************************************/ + + #include <QtGui> ++#include <QScrollArea> + #include "AlignmentWidget.h" + #include "clustalW/general/userparams.h" + #include "ClustalQtParams.h" +diff -urN clustalx-2.1/BootstrapTreeDialog.cpp clustalx-2.1-bak/BootstrapTreeDialog.cpp +--- clustalx-2.1/BootstrapTreeDialog.cpp 2010-11-17 11:12:30.000000000 +0100 ++++ clustalx-2.1-bak/BootstrapTreeDialog.cpp 2015-09-18 19:00:09.782214298 +0200 +@@ -5,6 +5,7 @@ + * 12-4-07, Mark Larkin, Removed destructor. No need to delete QObjects. Also removed + * setAllPtrsToNull function. + */ ++#include <QtGui> + #include <QPushButton> + #include <QGroupBox> + #include <QCheckBox> +@@ -12,8 +13,8 @@ + #include <QGridLayout> + #include <QSizePolicy> + #include <QComboBox> +-#include <QtGui> + #include <QLabel> ++#include <QLineEdit> + #include <iostream> + #include "BootstrapTreeDialog.h" + #include "clustalW/general/userparams.h" +diff -urN clustalx-2.1/ColorFileXmlParser.cpp clustalx-2.1-bak/ColorFileXmlParser.cpp +--- clustalx-2.1/ColorFileXmlParser.cpp 2010-11-17 11:12:30.000000000 +0100 ++++ clustalx-2.1-bak/ColorFileXmlParser.cpp 2015-09-18 19:00:42.695345653 +0200 +@@ -1,4 +1,5 @@ + #include <QtGui> ++#include <QMessageBox> + + #include "ColorFileXmlParser.h" + #include "ClustalQtParams.h" +@@ -202,4 +203,4 @@ + rule = rule.nextSiblingElement("resrule"); + } + return numOfRules; +-} +\ No newline at end of file ++} +diff -urN clustalx-2.1/HelpDisplayWidget.cpp clustalx-2.1-bak/HelpDisplayWidget.cpp +--- clustalx-2.1/HelpDisplayWidget.cpp 2010-11-17 11:12:30.000000000 +0100 ++++ clustalx-2.1-bak/HelpDisplayWidget.cpp 2015-09-18 19:34:51.692771579 +0200 +@@ -16,6 +16,8 @@ + #include <QTextEdit> + #include <iostream> + #include <fstream> ++#include <QPushButton> ++#include <QVBoxLayout> + #include <QtGui> + #include "Resources.h" + +diff -urN clustalx-2.1/PSPrinter.cpp clustalx-2.1-bak/PSPrinter.cpp +--- clustalx-2.1/PSPrinter.cpp 2010-11-17 11:12:30.000000000 +0100 ++++ clustalx-2.1-bak/PSPrinter.cpp 2015-09-18 19:20:36.528019466 +0200 +@@ -17,6 +17,7 @@ + #include <iomanip> + #include <sstream> + #include <QtGui> ++#include <QMessageBox> + #include "PSPrinter.h" + #include "ColorFileXmlParser.h" + #include "clustalW/general/userparams.h" +diff -urN clustalx-2.1/ProteinGapParameters.cpp clustalx-2.1-bak/ProteinGapParameters.cpp +--- clustalx-2.1/ProteinGapParameters.cpp 2010-11-17 11:12:30.000000000 +0100 ++++ clustalx-2.1-bak/ProteinGapParameters.cpp 2015-09-18 19:20:07.311532091 +0200 +@@ -9,6 +9,7 @@ + #include <QLabel> + #include <QString> + #include <QMessageBox> ++#include <QLineEdit> + #include "ProteinGapParameters.h" + #include "clustalW/general/userparams.h" + +diff -urN clustalx-2.1/SaveSeqFile.cpp clustalx-2.1-bak/SaveSeqFile.cpp +--- clustalx-2.1/SaveSeqFile.cpp 2010-11-17 11:12:30.000000000 +0100 ++++ clustalx-2.1-bak/SaveSeqFile.cpp 2015-09-18 19:21:28.231035513 +0200 +@@ -20,6 +20,8 @@ + #include <QComboBox> + #include <QtGui> + #include <QLabel> ++#include <QMessageBox> ++#include <QLineEdit> + #include "SaveSeqFile.h" + #include "clustalW/general/userparams.h" + #include "clustalW/general/utils.h" +diff -urN clustalx-2.1/SeqNameWidget.cpp clustalx-2.1-bak/SeqNameWidget.cpp +--- clustalx-2.1/SeqNameWidget.cpp 2010-11-17 11:12:30.000000000 +0100 ++++ clustalx-2.1-bak/SeqNameWidget.cpp 2015-09-18 19:22:48.903873782 +0200 +@@ -56,6 +56,7 @@ + ****************************************************************************/ + + #include <QtGui> ++#include <QScrollArea> + #include "SeqNameWidget.h" + #include "KeyController.h" //- nige + #include "clustalW/alignment/Alignment.h" +diff -urN clustalx-2.1/TreeOutputFileNames.cpp clustalx-2.1-bak/TreeOutputFileNames.cpp +--- clustalx-2.1/TreeOutputFileNames.cpp 2010-11-17 11:12:30.000000000 +0100 ++++ clustalx-2.1-bak/TreeOutputFileNames.cpp 2015-09-18 19:23:37.006911921 +0200 +@@ -13,6 +13,7 @@ + #include <QComboBox> + #include <QtGui> + #include <QLabel> ++#include <QLineEdit> + #include <iostream> + #include "TreeOutputFileNames.h" + #include "clustalW/general/userparams.h" +diff -urN clustalx-2.1/WritePostscriptFile.cpp clustalx-2.1-bak/WritePostscriptFile.cpp +--- clustalx-2.1/WritePostscriptFile.cpp 2010-11-17 11:12:30.000000000 +0100 ++++ clustalx-2.1-bak/WritePostscriptFile.cpp 2015-09-18 19:24:30.429917414 +0200 +@@ -20,6 +20,8 @@ + #include <QComboBox> + #include <QtGui> + #include <QLabel> ++#include <QLineEdit> ++#include <QMessageBox> + #include <iostream> + #include "WritePostscriptFile.h" + #include "clustalW/general/userparams.h" +Binary files clustalx-2.1/clustalx and clustalx-2.1-bak/clustalx differ +diff -urN clustalx-2.1/clustalx.pro clustalx-2.1-bak/clustalx.pro +--- clustalx-2.1/clustalx.pro 2010-11-17 11:12:30.000000000 +0100 ++++ clustalx-2.1-bak/clustalx.pro 2015-09-18 19:14:42.666857671 +0200 +@@ -4,8 +4,11 @@ + + TEMPLATE = app + TARGET = clustalx +-CONFIG += release static ++CONFIG += release + QT += xml ++QT += widgets ++DEFINES += QT_DISABLE_DEPRECATED_BEFORE=0x000000 ++ + VERSION = 2.1 + win32 { + DEFINES += OS_WINDOWS +diff -urN clustalx-2.1/mainwindow.cpp clustalx-2.1-bak/mainwindow.cpp +--- clustalx-2.1/mainwindow.cpp 2010-11-17 11:12:30.000000000 +0100 ++++ clustalx-2.1-bak/mainwindow.cpp 2015-09-18 19:19:03.545256739 +0200 +@@ -94,6 +94,15 @@ + #include <cstdlib> + #include <QCheckBox> + #include <QStringList> ++#include <QMenu> ++#include <QMenuBar> ++#include <QAction> ++#include <QMessageBox> ++#include <QApplication> ++#include <QScrollBar> ++#include <QHBoxLayout> ++#include <QGroupBox> ++#include <QVBoxLayout> + #include "SecStructOptions.h" + #include "mainwindow.h" + #include "WritePostscriptFile.h" diff --git a/academic/clustalx/clustalx.SlackBuild b/academic/clustalx/clustalx.SlackBuild index 0e0932e730..756d1eaff4 100644 --- a/academic/clustalx/clustalx.SlackBuild +++ b/academic/clustalx/clustalx.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for clustalx -# Copyright 2011-2016 Petar Petrov slackalaxy@gmail.com +# Copyright 2011-2022 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,26 +25,36 @@ # With help from http://aur.archlinux.org/packages.php?ID=25080 # PKGBUILD submitter is mickelliot and maintainer is machoo02 +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=clustalx VERSION=${VERSION:-2.1} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) export ARCH=i486 ;; + i?86) export ARCH=i586 ;; arm*) export ARCH=arm ;; *) export ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -66,8 +76,9 @@ rm -rf $PRGNAM-$VERSION tar xvf $CWD/$PRGNAM-$VERSION.tar.gz cd $PRGNAM-$VERSION -# The patch is from Archlinux AUR, as mentioned above. +# The patches are from Archlinux AUR, as mentioned above. patch -p1 < $CWD/fix-static.patch +patch -p1 < $CWD/QT.patch chown -R root:root . find -L . \ @@ -78,7 +89,7 @@ find -L . \ sed -i 's/static//g' clustalx.pro -qmake +qmake-qt5 #Use our CFLAGS/CXXFLAGS sed -i "/^C.*.*FLAGS/s/=/+=/" Makefile @@ -113,4 +124,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/colamd/colamd.SlackBuild b/academic/colamd/colamd.SlackBuild index ab7e39cb5a..3f9a632954 100644 --- a/academic/colamd/colamd.SlackBuild +++ b/academic/colamd/colamd.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for COLAMD -# Copyright 2013-2020 Kyle Guinn <elyk03@gmail.com> +# Copyright 2013-2021 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,13 +22,16 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=colamd SRCNAM=SuiteSparse SUBDIR=COLAMD VERSION=${VERSION:-2.9.6} -SRCVER=${SRCVER:-5.6.0} -BUILD=${BUILD:-6} +SRCVER=${SRCVER:-5.8.1} +BUILD=${BUILD:-7} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$(uname -m)" in @@ -38,15 +41,22 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM-$VERSION +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="README.txt Doc/ChangeLog Doc/License.txt Doc/lesser.txt" -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" @@ -105,4 +115,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/colamd/colamd.info b/academic/colamd/colamd.info index f558ba3958..132c96f5d0 100644 --- a/academic/colamd/colamd.info +++ b/academic/colamd/colamd.info @@ -1,8 +1,8 @@ PRGNAM="colamd" VERSION="2.9.6" HOMEPAGE="http://faculty.cse.tamu.edu/davis/suitesparse.html" -DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.6.0/SuiteSparse-5.6.0.tar.gz" -MD5SUM="af8b97cbded4cd5c6672e878bc0c37c2" +DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.8.1/SuiteSparse-5.8.1.tar.gz" +MD5SUM="c414679bbc9432a3def01b31ad921140" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="suitesparseconfig" diff --git a/academic/colin/README b/academic/colin/README new file mode 100644 index 0000000000..7b913061cc --- /dev/null +++ b/academic/colin/README @@ -0,0 +1,5 @@ +colin (a structural analysis application) + +Colin is a structural analysis application with a lightweight +interface. This software for civil engineering students provides an +easier way to learn civil engineering. diff --git a/academic/colin/colin.SlackBuild b/academic/colin/colin.SlackBuild new file mode 100644 index 0000000000..4b3e3b0b5e --- /dev/null +++ b/academic/colin/colin.SlackBuild @@ -0,0 +1,104 @@ +#!/bin/bash + +# SlackBuild build script for colin + +# Copyright (c) 2000-2020 Prof. Horstmann <wmh (at) eipg.fr> +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=colin +VERSION=${VERSION:-1.8.2} +BUILD=${BUILD:-2} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.?z* +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +. /etc/profile.d/qt4.sh +qmake +make + +# make install DESTDIR not implemented so go manual ! +install -Dm 0644 xdg/colin.desktop $PKG/usr/share/applications/colin.desktop +install -Dm 0644 xdg/colin.xpm $PKG/usr/share/colin/pixmaps/colin.xpm +install -Dm 0644 xdg/colin.png $PKG/usr/share/colin/pixmaps/colin.png +cp -a icons $PKG/usr/share/colin/ +install -Dm 0755 colin $PKG/usr/bin/colin + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a doc/* $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/colin/colin.info b/academic/colin/colin.info new file mode 100644 index 0000000000..5a19ff7802 --- /dev/null +++ b/academic/colin/colin.info @@ -0,0 +1,10 @@ +PRGNAM="colin" +VERSION="1.8.2" +HOMEPAGE="https://sourceforge.net/projects/colin2" +DOWNLOAD="https://sourceforge.net/projects/colin2/files/colin-1.8.2.tar.xz" +MD5SUM="e7260f262dbc563b40b6de529d6aa519" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="qt4" +MAINTAINER="Prof. HORSTMANN" +EMAIL="wmh@eipg.fr" diff --git a/academic/colin/slack-desc b/academic/colin/slack-desc new file mode 100644 index 0000000000..73ce0befc5 --- /dev/null +++ b/academic/colin/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +colin: colin (a structural analysis application) +colin: +colin: Colin is a structural analysis application with a lightweight +colin: interface. This structural analysis software for civil engineering +colin: students, provide an easier way to learn civil engineering. +colin: +colin: Some tutorials (in German) can be found on youtube.com: +colin: http://www.youtube.com/user/ognop42 +colin: +colin: By Prof. Horstmann www.eipg.fr <wmh (at) eipg.fr> +colin: diff --git a/academic/convertall/README b/academic/convertall/README index f0cf40819c..9739c0472c 100644 --- a/academic/convertall/README +++ b/academic/convertall/README @@ -1,7 +1,6 @@ ConvertAll (unit conversion) -With ConvertAll, you can convert units as necessary, or combine any units any -way you want. If you want to convert from inches per decade, that's fine. Or -from meter-pounds. Or from cubic nautical miles. The units don't have to make -sense to anyone else. - +With ConvertAll, you can convert units as necessary, or combine any +units any way you want. If you want to convert from inches per decade, +that's fine. Or from meter-pounds. Or from cubic nautical miles. The +units don't have to make sense to anyone else. diff --git a/academic/convertall/convertall.SlackBuild b/academic/convertall/convertall.SlackBuild index 796ea42d07..c7cb4bf170 100644 --- a/academic/convertall/convertall.SlackBuild +++ b/academic/convertall/convertall.SlackBuild @@ -1,11 +1,13 @@ -#!/bin/sh +#!/bin/bash # # Slackware build script for convertall # -# Copyright 2012 John Berger <irgunii ampersand gmail . com>, TN, USA +# Copyright 2012-2021 John Berger <irgunii ampersand gmail . com>, TN, USA # I couldn't have made this script work without the help of -# Willy Sudiarto Raharjo <willysr@slackware-id.org>, so -# all thanks go to him. +# Willy Sudiarto Raharjo <willysr@slackware-id.org>, so big thanks to him. +# Also a big thank you to Kevin McCormick for helping with a python 3 +# problem I'd missed. +# # # All rights reserved. # @@ -26,27 +28,37 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +# 20220405 bkw: Modified by SlackBuilds.org, BUILD=2: +# - remove /usr/share/doc and useless INSTALL instructions. + +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=convertall SRCNAM=ConvertAll -VERSION=${VERSION:-0.5.2} -BUILD=${BUILD:-1} +VERSION=${VERSION:-0.8.0} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -70,18 +82,20 @@ cd $SRCNAM chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ + -exec chmod 755 {} \+ -o \ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; + -exec chmod 644 {} \+ # Change installation directory to /usr and use LIBDIRSUFFIX sed -i -e "s/usr\/local/usr/" -e "s/'lib'/'lib$LIBDIRSUFFIX'/" install.py -python install.py -b $PKG +python3 install.py -b $PKG find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true +rm -rf doc/INSTALL $PKG/usr/share/doc + mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ doc/* \ @@ -93,4 +107,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/convertall/convertall.info b/academic/convertall/convertall.info index 38fc747b7f..9c62719446 100644 --- a/academic/convertall/convertall.info +++ b/academic/convertall/convertall.info @@ -1,8 +1,8 @@ PRGNAM="convertall" -VERSION="0.5.2" -HOMEPAGE="http://www.convertall.bellz.org/index.html" -DOWNLOAD="http://downloads.sourceforge.net/convertall/convertall-0.5.2.tar.gz" -MD5SUM="9378cb3ab40cf944570d53bcc5718ee8" +VERSION="0.8.0" +HOMEPAGE="https://www.convertall.bellz.org/index.html" +DOWNLOAD="https://github.com/doug-101/ConvertAll/releases/download/v0.8.0/convertall-0.8.0.tar.gz" +MD5SUM="6e2513d056bc10e2f037591bc08a8e21" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/convertall/doinst.sh b/academic/convertall/doinst.sh index 4f83cde390..7443749d1c 100644 --- a/academic/convertall/doinst.sh +++ b/academic/convertall/doinst.sh @@ -9,6 +9,6 @@ fi if [ -e usr/share/icons/hicolor/icon-theme.cache ]; then if [ -x /usr/bin/gtk-update-icon-cache ]; then - /usr/bin/gtk-update-icon-cache -f usr/share/icons/hicolor >/dev/null 2>&1 + /usr/bin/gtk-update-icon-cache usr/share/icons/hicolor >/dev/null 2>&1 fi fi diff --git a/academic/convertall/slack-desc b/academic/convertall/slack-desc index 7f4ae4d1c2..59999208c7 100644 --- a/academic/convertall/slack-desc +++ b/academic/convertall/slack-desc @@ -1,9 +1,9 @@ # HOW TO EDIT THIS FILE: -# The "handy ruler" below makes it easier to edit a package description. -# Line up the first '|' above the ':' following the base package name, and -# the '|' on the right side marks the last column you can put a character in. -# You must make exactly 11 lines for the formatting to be correct. It's also -# customary to leave one space after the ':' except on otherwise blank lines. +# The "handy ruler" below makes it easier to edit a package description. Line +# up the first '|' above the ':' following the base package name, and the '|' +# on the right side marks the last column you can put a character in. You must +# make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':'. |-----handy-ruler------------------------------------------------------| convertall: convertall (unit conversion) @@ -14,6 +14,6 @@ convertall: decade, that's fine. Or from meter-pounds. Or from cubic convertall: nautical miles. The units don't have to make sense to convertall: anyone but you. convertall: -convertall: Project website: http://www.convertall.bellz.org +convertall: Project website: https://www.convertall.bellz.org convertall: convertall: diff --git a/academic/copasi/README b/academic/copasi/README index 4da8b74120..1ebe37a34d 100644 --- a/academic/copasi/README +++ b/academic/copasi/README @@ -1,17 +1,17 @@ -COPASI is a package for modeling and simulation of biochemical networks, -popular in the field of systems biology. +COPASI is a package for modeling and simulation of chemical reaction +networks and other dynamical systems. -COPASI is a stand-alone program that simulates models of biochemical -networks using ODE solvers or Gillespie's stochastic simulation -algorithm. COPASI is compatible with models in SBML format. It also -performs several analyses, such as steady state, stability, parameter -sensitivity, elementary modes, Lyapunov exponents, optimization, and -parameter estimation. Data can be visualized in plots, histograms and -animations of network diagrams. COPASI's GUI is based on QT, but a -command line version is also included that allows for processing -computations in batch mode. +COPASI is a stand-alone program that simulates models of chemical +reaction networks using ODE/SDE solvers or Gillespie's stochastic +simulation algorithm. COPASI is compatible with models in SBML format. +It also performs several analyses, such as steady state, stability, +parameter sensitivity, elementary modes, Lyapunov exponents, +optimization, and parameter estimation. Data can be visualized in +plots, histograms and animations of network diagrams. COPASI's GUI is +based on QT, but a command line version is also included that allows +for processing computations in batch mode. COPASI is a collaboration between research groups at the Biocomplexity -Institute at Virginia Tech, University of Heidelberg, University of -Connecticut, and previously the University of Manchester and the -EML-Research. +Institute and Initiative at University of Virginia, University of +Heidelberg, University of Connecticut, and previously the University +of Manchester, Virginia Tech, and the EML-Research. diff --git a/academic/copasi/copasi.SlackBuild b/academic/copasi/copasi.SlackBuild index d446a59979..0a6da4fcfd 100644 --- a/academic/copasi/copasi.SlackBuild +++ b/academic/copasi/copasi.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for copasi @@ -22,31 +22,43 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=copasi -VERSION=${VERSION:-4.27.217} +VERSION=${VERSION:-4.42.284} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + ARCH="$(uname -m)" +fi -case "$(uname -m)" in - i?86) ARCH=i586 ;; - arm*) ARCH=arm ;; - *) ARCH=$(uname -m) ;; +case "$ARCH" in + i?86) + BINNAME="Linux-32bit" + ;; + x86_64) + BINNAME="Linux-64bit" + ;; + *) + echo "$ARCH is not supported by the $PRGNAM build script..." + exit 1 + ;; esac -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i586" ]; then - BINNAME="Linux-32bit" -elif [ "$ARCH" = "x86_64" ]; then - BINNAME="Linux-64bit" -else - echo "$ARCH is not supported by the $PRGNAM build script..." - exit 1 -fi - # This is a repackage of a binary distribution # CFLAGS are not required @@ -56,7 +68,7 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf COPASI-$VERSION-$BINNAME $PRGNAM-$VERSION -tar xvf $CWD/COPASI-$VERSION-$BINNAME.tar.gz +sh $CWD/COPASI-$VERSION-$BINNAME.sh -e . mv COPASI-$VERSION-$BINNAME $PRGNAM-$VERSION cd $PRGNAM-$VERSION chown -R root:root . @@ -80,4 +92,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/copasi/copasi.desktop b/academic/copasi/copasi.desktop index 80dcef7083..6690ec34a4 100644 --- a/academic/copasi/copasi.desktop +++ b/academic/copasi/copasi.desktop @@ -1,5 +1,5 @@ [Desktop Entry] -Exec=sh -c "COPASIDIR=/usr /usr/bin/CopasiUI" +Exec=/usr/bin/CopasiUI %u Icon=/usr/share/pixmaps/copasi.xpm Type=Application Name=COPASI diff --git a/academic/copasi/copasi.info b/academic/copasi/copasi.info index 6e5b69b94a..75e1b966a6 100644 --- a/academic/copasi/copasi.info +++ b/academic/copasi/copasi.info @@ -1,10 +1,10 @@ PRGNAM="copasi" -VERSION="4.27.217" -HOMEPAGE="http://www.copasi.org" -DOWNLOAD="https://github.com/copasi/COPASI/releases/download/Build-217/COPASI-4.27.217-Linux-32bit.tar.gz" -MD5SUM="a218e91000bba6ca3071feddd95fd0d2" -DOWNLOAD_x86_64="https://github.com/copasi/COPASI/releases/download/Build-217/COPASI-4.27.217-Linux-64bit.tar.gz" -MD5SUM_x86_64="f9fd439a6b6a9f60bb2b54c666235aec" +VERSION="4.42.284" +HOMEPAGE="https://copasi.org" +DOWNLOAD="https://github.com/copasi/COPASI/releases/download/Build-284/COPASI-4.42.284-Linux-32bit.sh" +MD5SUM="66ae94a23f8d7745835e3639f1c567f6" +DOWNLOAD_x86_64="https://github.com/copasi/COPASI/releases/download/Build-284/COPASI-4.42.284-Linux-64bit.sh" +MD5SUM_x86_64="87f09230f64ea4c69a6695963e4f2594" REQUIRES="" MAINTAINER="Pedro Mendes" EMAIL="pedro@gepasi.org" diff --git a/academic/copasi/slack-desc b/academic/copasi/slack-desc index 713b2c5d95..46fa181d4b 100644 --- a/academic/copasi/slack-desc +++ b/academic/copasi/slack-desc @@ -9,11 +9,11 @@ copasi: copasi (tool for modeling and simulation of biochemical networks) copasi: copasi: COPASI is a stand-alone program that simulates models of biochemical -copasi: networks using ODE solvers or Gillespie's stochastic simulation +copasi: networks using ODE/SDE solvers or Gillespie's stochastic simulation copasi: algorithm. COPASI is compatible with models in SBML format. It also copasi: performs several analyses: stability, parameter sensitivity, copasi: elementary modes, Lyapunov exponents, optimization, and parameter copasi: estimation. Data can be visualized in plots, histograms and animations copasi: of network diagrams. Both GUI and a command line version are included. copasi: -copasi: Homepage: http://www.copasi.org/ +copasi: Homepage: https://copasi.org/ diff --git a/academic/coq/README b/academic/coq/README deleted file mode 100644 index e21de9a5fa..0000000000 --- a/academic/coq/README +++ /dev/null @@ -1,7 +0,0 @@ -coq is a formal proof management system. It provides a formal language -to write mathematical definitions, executable algorithms and theorems -together with an environment for semi-interactive development of -machine-checked proofs. - -To build CoqIDE, add COQIDE=yes, e.g.: COQIDE=yes ./coq.SlackBuild. -You will need the lablgtk package built with gtksourceview support. diff --git a/academic/coq/coq.info b/academic/coq/coq.info deleted file mode 100644 index 93554ae125..0000000000 --- a/academic/coq/coq.info +++ /dev/null @@ -1,10 +0,0 @@ -PRGNAM="coq" -VERSION="8.9.0" -HOMEPAGE="http://coq.inria.fr/" -DOWNLOAD="https://github.com/coq/coq/archive/V8.9.0/coq-8.9.0.tar.gz" -MD5SUM="490c89609c1271fe7f20e6ea1bd107b5" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="camlp5 ocaml-findlib" -MAINTAINER="Nick Smallbone" -EMAIL="nick@smallbone.se" diff --git a/academic/coq/gpl.txt.gz b/academic/coq/gpl.txt.gz Binary files differdeleted file mode 100644 index 0ef740a4c7..0000000000 --- a/academic/coq/gpl.txt.gz +++ /dev/null diff --git a/academic/cryptominisat/cryptominisat.SlackBuild b/academic/cryptominisat/cryptominisat.SlackBuild index 8a59f1367e..74cbbb84e1 100644 --- a/academic/cryptominisat/cryptominisat.SlackBuild +++ b/academic/cryptominisat/cryptominisat.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for cryptominisat -# Copyright 2019 Alan Aversa USA +# Copyright 2024 Caterino Tommaso, T.O.P. USA # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=cryptominisat -VERSION=${VERSION:-5.6.8} +VERSION=${VERSION:-5.11.21} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -36,7 +39,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -79,12 +89,17 @@ cd build -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ -DCMAKE_INSTALL_PREFIX=/usr \ -DCMAKE_INSTALL_LIBDIR=lib${LIBDIRSUFFIX} \ - -DUSE_GAUSS=ON \ + -DIPASIR=ON \ + -DSTATICCOMPILE=ON \ -DCMAKE_BUILD_TYPE=Release .. make make install DESTDIR=$PKG cd .. +# include source code: +mkdir -p $PKG/usr/src +cp -a src $PKG/usr/src/$PRGNAM + find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true @@ -101,4 +116,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/cryptominisat/cryptominisat.info b/academic/cryptominisat/cryptominisat.info index 4ceb3bef16..cb39e89a62 100644 --- a/academic/cryptominisat/cryptominisat.info +++ b/academic/cryptominisat/cryptominisat.info @@ -1,10 +1,10 @@ PRGNAM="cryptominisat" -VERSION="5.6.8" +VERSION="5.11.21" HOMEPAGE="https://www.msoos.org/cryptominisat5/" -DOWNLOAD="https://github.com/msoos/cryptominisat/archive/5.6.8/cryptominisat-5.6.8.tar.gz" -MD5SUM="ca1bf853e568c19968daa5464ab86843" +DOWNLOAD="https://github.com/msoos/cryptominisat/archive/5.11.21/cryptominisat-5.11.21.tar.gz" +MD5SUM="7f2fbe1975c9045d351a7921f4028b38" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" -MAINTAINER="Alan Aversa" -EMAIL="aveNOrsa@email.ariSPAMzona.edu" +MAINTAINER="Caterino Tommaso, T.O.P." +EMAIL="alaNOn_aversa@lavabSPAMit.com (remove NO and SPAM)" diff --git a/academic/csparse/README b/academic/csparse/README index 7119c1bf65..2726898d3c 100644 --- a/academic/csparse/README +++ b/academic/csparse/README @@ -1,5 +1,5 @@ -CSparse is a small yet feature-rich sparse matrix package. Its purpose is -to demonstrate a wide range of sparse matrix algorithms in as concise a -code as possible. +CSparse is a small yet feature-rich sparse matrix package. Its +purpose is to demonstrate a wide range of sparse matrix algorithms in +as concise a code as possible. This package is part of SuiteSparse. diff --git a/academic/csparse/csparse.SlackBuild b/academic/csparse/csparse.SlackBuild index 3f008bbe0b..9725887ad3 100644 --- a/academic/csparse/csparse.SlackBuild +++ b/academic/csparse/csparse.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for CSparse -# Copyright 2013-2020 Kyle Guinn <elyk03@gmail.com> +# Copyright 2013-2021 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,13 +22,16 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=csparse SRCNAM=SuiteSparse SUBDIR=CSparse VERSION=${VERSION:-3.2.0} -SRCVER=${SRCVER:-5.6.0} -BUILD=${BUILD:-4} +SRCVER=${SRCVER:-5.8.1} +BUILD=${BUILD:-5} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$(uname -m)" in @@ -38,15 +41,22 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM-$VERSION +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="README.txt Doc/ChangeLog Doc/License.txt Doc/lesser.txt" -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" @@ -105,4 +115,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/csparse/csparse.info b/academic/csparse/csparse.info index 4435e41189..861a2ed4c5 100644 --- a/academic/csparse/csparse.info +++ b/academic/csparse/csparse.info @@ -1,8 +1,8 @@ PRGNAM="csparse" VERSION="3.2.0" HOMEPAGE="http://faculty.cse.tamu.edu/davis/suitesparse.html" -DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.6.0/SuiteSparse-5.6.0.tar.gz" -MD5SUM="af8b97cbded4cd5c6672e878bc0c37c2" +DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.8.1/SuiteSparse-5.8.1.tar.gz" +MD5SUM="c414679bbc9432a3def01b31ad921140" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/cufflinks/README b/academic/cufflinks/README index 7afb95ee6e..5c851b1d27 100644 --- a/academic/cufflinks/README +++ b/academic/cufflinks/README @@ -11,6 +11,8 @@ Berkeley, Steven Salzberg's computational genomics group at the Institute of Genetic Medicine at Johns Hopkins University, and Barbara Wold's lab at Caltech. +NOTE: This just repackages the binaries provided from upstream. + Reference: Ali Mortazavi, Brian A Williams, Kenneth McCue, Lorian Schaeffer and Barbara Wold, "Mapping and quantifying mammalian transcriptomes by diff --git a/academic/cufflinks/cufflinks.SlackBuild b/academic/cufflinks/cufflinks.SlackBuild index 33a09282e1..dc1fd7f6de 100644 --- a/academic/cufflinks/cufflinks.SlackBuild +++ b/academic/cufflinks/cufflinks.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for cufflinks -# Copyright 2013-2019 Petar Petrov slackalaxy@gmail.com +# Copyright 2013-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,50 +22,47 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -# With help from Archlinux AUR and Gentoo: -# https://aur.archlinux.org/packages/cufflinks/ -# http://euscan.iksaif.net/package/sci-biology/cufflinks/ +# For Slackware 15.0 I switched to just repackaging the upstream binaries. +# When I find a patch that fixes the build against boost and a bunch of other +# fixes, I will revert back to source build. Let's have ot like this for now. + +cd $(dirname $0) ; CWD=$(pwd) PRGNAM=cufflinks VERSION=${VERSION:-2.2.1} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then - case "$( uname -m )" in - i?86) ARCH=i586 ;; - arm*) ARCH=arm ;; - *) ARCH=$( uname -m ) ;; - esac + ARCH="$( uname -m )" +fi + +if [ "$ARCH" != "x86_64" ]; then + printf "\n\n$ARCH is not supported... \n" >&2 + exit 1 +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 fi -CWD=$(pwd) TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i586" ]; then - SLKCFLAGS="-O2 -march=i586 -mtune=i686" - LIBDIRSUFFIX="" -elif [ "$ARCH" = "i686" ]; then - SLKCFLAGS="-O2 -march=i686 -mtune=i686" - LIBDIRSUFFIX="" -elif [ "$ARCH" = "x86_64" ]; then - SLKCFLAGS="-O2 -fPIC" - LIBDIRSUFFIX="64" -else - SLKCFLAGS="-O2" - LIBDIRSUFFIX="" -fi - set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $PRGNAM-$VERSION -tar xvf $CWD/$PRGNAM-$VERSION.tar.gz -cd $PRGNAM-$VERSION +rm -rf $PRGNAM-${VERSION}.Linux_${ARCH} +tar xvf $CWD/$PRGNAM-${VERSION}.Linux_${ARCH}.tar.gz +cd $PRGNAM-${VERSION}.Linux_${ARCH} chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -73,22 +70,17 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -export EIGEN_CPPFLAGS="-I/usr/include/eigen3" - -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ -./configure \ - --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ - --sysconfdir=/etc \ - --disable-optim \ - --with-boost-libdir=/usr/lib${LIBDIRSUFFIX} \ - --localstatedir=/var \ - --mandir=/usr/man \ - --build=$ARCH-slackware-linux +# Just in case... +sed -i "s:python:python2:" cuffmerge -make -make install DESTDIR=$PKG +install -D -m755 cuffcompare $PKG/usr/bin/cuffcompare +install -D -m755 cuffdiff $PKG/usr/bin/cuffdiff +install -D -m755 cufflinks $PKG/usr/bin/cufflinks +install -D -m755 cuffmerge $PKG/usr/bin/cuffmerge +install -D -m755 cuffnorm $PKG/usr/bin/cuffnorm +install -D -m755 cuffquant $PKG/usr/bin/cuffquant +install -D -m755 gffread $PKG/usr/bin/gffread +install -D -m755 gtf_to_sam $PKG/usr/bin/gtf_to_sam find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true @@ -104,4 +96,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/cufflinks/cufflinks.info b/academic/cufflinks/cufflinks.info index 6f858f0065..b35162c3e6 100644 --- a/academic/cufflinks/cufflinks.info +++ b/academic/cufflinks/cufflinks.info @@ -1,10 +1,10 @@ PRGNAM="cufflinks" VERSION="2.2.1" HOMEPAGE="http://cufflinks.cbcb.umd.edu/" -DOWNLOAD="http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.tar.gz" -MD5SUM="9a5ba7a7710cd864932cf205c17851f0" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.Linux_x86_64.tar.gz" +MD5SUM_x86_64="7e693d182dcfda8aeef8523219ea9ea7" REQUIRES="samtools-legacy" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/cutadapt/cutadapt.SlackBuild b/academic/cutadapt/cutadapt.SlackBuild index 38a1c0f535..eb103094cd 100644 --- a/academic/cutadapt/cutadapt.SlackBuild +++ b/academic/cutadapt/cutadapt.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for cutadapt -# Copyright 2015-2017 Petar Petrov slackalaxy@gmail.com +# Copyright 2015-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=cutadapt VERSION=${VERSION:-1.14} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -82,4 +92,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/cvc4/README b/academic/cvc4/README index 830c7394fb..ed00fa62b8 100644 --- a/academic/cvc4/README +++ b/academic/cvc4/README @@ -4,4 +4,8 @@ either prove the formula or find a counterexample. CVC4 supports arithmetic, reasoning about arrays, and several other built-in theories. Input problems are written in SMT-LIB format. -This package includes the cvc4 program as well as libraries. +This package includes the cvc4 program, libraries, and Python 2 +bindings. + +Note that this SlackBuild builds CVC4 with readline support, which means +the resulting executable is licensed under the GPLv3. diff --git a/academic/cvc4/cvc4.SlackBuild b/academic/cvc4/cvc4.SlackBuild index ce4b43bebf..0d2d843636 100644 --- a/academic/cvc4/cvc4.SlackBuild +++ b/academic/cvc4/cvc4.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for cvc4 -# Copyright 2019 Nick Smallbone, Gothenburg, Sweden +# Copyright 2019-2020 Nick Smallbone, Gothenburg, Sweden # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,17 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +# TO DO: +# Add new Python bindings (requires a newer version of Cython?) +# Add Java bindings (requires a newer version of CMake?) + +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=cvc4 -VERSION=${VERSION:-1.7} +VERSION=${VERSION:-1.8} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} SRCNAM=CVC4 if [ -z "$ARCH" ]; then @@ -36,7 +43,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -70,22 +84,29 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -sed -i "s/DESTINATION lib/DESTINATION lib${LIBDIRSUFFIX}/" src/CMakeLists.txt src/parser/CMakeLists.txt -chmod +x $CWD/run-antlr +sed -i "s/LIBRARY_INSTALL_DIR lib/&${LIBDIRSUFFIX}/" CMakeLists.txt +install -m 755 $CWD/run-antlr . +cp $CWD/antlr-3.4-complete.jar . cmake \ -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ -DCMAKE_INSTALL_PREFIX=/usr \ -DCMAKE_BUILD_TYPE=Production \ - -DENABLE_OPTIMIZED=ON \ -DANTLR_INCLUDE_DIR=/usr/include/antlr3 \ - -DANTLR_BINARY="$CWD/run-antlr" \ + -DANTLR_BINARY="$TMP/$SRCNAM-$VERSION/run-antlr" \ + -DUSE_READLINE=OFF \ + -DBUILD_BINDINGS_PYTHON=OFF \ + -DBUILD_SWIG_BINDINGS_PYTHON=ON \ + -DBUILD_SWIG_BINDINGS_JAVA=OFF \ . make -make doc -make install/strip DESTDIR=$PKG +make install DESTDIR=$PKG + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + mv $PKG/usr/share/man $PKG/usr/man find $PKG/usr/man -type f -exec gzip -9 {} \; @@ -101,4 +122,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/cvc4/cvc4.info b/academic/cvc4/cvc4.info index 9058f04efd..379b15bffa 100644 --- a/academic/cvc4/cvc4.info +++ b/academic/cvc4/cvc4.info @@ -1,12 +1,12 @@ PRGNAM="cvc4" -VERSION="1.7" +VERSION="1.8" HOMEPAGE="https://cvc4.cs.stanford.edu/" -DOWNLOAD="https://github.com/CVC4/CVC4/archive/1.7/CVC4-1.7.tar.gz \ +DOWNLOAD="https://ponce.cc/slackware/sources/repo/CVC4-1.8.tar.gz \ https://www.antlr3.org/download/antlr-3.4-complete.jar" -MD5SUM="eadb05f5092c4310f3bbe52745f9b7b9 \ +MD5SUM="9f7657e21fec3c4042225b0b8f513c34 \ 1b91dea1c7d480b3223f7c8a9aa0e172" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="jdk libantlr3c" +REQUIRES="zulu-openjdk8 libantlr3c python2-toml" MAINTAINER="Nick Smallbone" EMAIL="nick@smallbone.se" diff --git a/academic/cxsparse/cxsparse.SlackBuild b/academic/cxsparse/cxsparse.SlackBuild index 4695454e67..4d8c288e24 100644 --- a/academic/cxsparse/cxsparse.SlackBuild +++ b/academic/cxsparse/cxsparse.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for CXSparse -# Copyright 2013-2020 Kyle Guinn <elyk03@gmail.com> +# Copyright 2013-2021 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,13 +22,16 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=cxsparse SRCNAM=SuiteSparse SUBDIR=CXSparse VERSION=${VERSION:-3.2.0} -SRCVER=${SRCVER:-5.6.0} -BUILD=${BUILD:-4} +SRCVER=${SRCVER:-5.8.1} +BUILD=${BUILD:-5} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$(uname -m)" in @@ -38,15 +41,22 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM-$VERSION +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="README.txt Doc/ChangeLog Doc/License.txt Doc/lesser.txt" -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" @@ -105,4 +115,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/cxsparse/cxsparse.info b/academic/cxsparse/cxsparse.info index eb05c702a6..06c815be7c 100644 --- a/academic/cxsparse/cxsparse.info +++ b/academic/cxsparse/cxsparse.info @@ -1,8 +1,8 @@ PRGNAM="cxsparse" VERSION="3.2.0" HOMEPAGE="http://faculty.cse.tamu.edu/davis/suitesparse.html" -DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.6.0/SuiteSparse-5.6.0.tar.gz" -MD5SUM="af8b97cbded4cd5c6672e878bc0c37c2" +DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.8.1/SuiteSparse-5.8.1.tar.gz" +MD5SUM="c414679bbc9432a3def01b31ad921140" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="suitesparseconfig" diff --git a/academic/dakota/README b/academic/dakota/README index 01d05fcdec..7a5783c44c 100644 --- a/academic/dakota/README +++ b/academic/dakota/README @@ -1,12 +1,16 @@ The Dakota toolkit provides a flexible, extensible interface between analysis codes and iteration methods. Dakota contains algorithms for optimization with gradient and nongradient-based methods; uncertainty -quantification with sampling, reliability, stochastic expansion, and -epistemic methods; parameter estimation with nonlinear least squares -methods; and sensitivity/variance analysis with design of experiments -and parameter study capabilities. These capabilities may be used on -their own or as components within advanced strategies such as -surrogate-based optimization, mixed integer nonlinear programming, or -optimization under uncertainty. +quantification with sampling, reliability, stochastic expansion, +and epistemic methods; parameter estimation with nonlinear least +squares methods; and sensitivity/variance analysis with design of +experiments and parameter study capabilities. These capabilities may +be used on their own or as components within advanced strategies such +as surrogate-based optimization, mixed integer nonlinear programming, +or optimization under uncertainty. -Optional dependency: openmpi +Optional dependency: openmpi (for distributed memory parallel +capabilities) + +You can build with multiple jobs by setting the MAKEFLAGS environment +variable (e.g. export MAKEFLAGS="-j$(nproc)" at bash prompt). diff --git a/academic/dakota/dakota.SlackBuild b/academic/dakota/dakota.SlackBuild index cc8e00e755..2e907ef4f2 100644 --- a/academic/dakota/dakota.SlackBuild +++ b/academic/dakota/dakota.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for Dakota -# Copyright 2017 Lorenzo Trevisan, Caorle, Venice, Italy +# Copyright 2017, 2018, 2019, 2020, 2021, 2022, 2023, 2024 Lorenzo Trevisan, Caorle, Venice, Italy # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=dakota -VERSION=${VERSION:-6.8} +VERSION=${VERSION:-6.19.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -59,9 +69,9 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $PRGNAM-$VERSION-release-public.src-UI -tar xvf $CWD/$PRGNAM-$VERSION-release-public.src-UI.tar.gz -cd $PRGNAM-$VERSION-release-public.src-UI +rm -rf $PRGNAM-$VERSION-public-src-cli +tar xvf $CWD/$PRGNAM-$VERSION-public-src-cli.tar.gz + chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -69,6 +79,10 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; +cd $PRGNAM-$VERSION-public-src-cli + +sed -i -e '11 a #include <math.h>' ./src/unit/dakota_tolerance_intervals/test_tolerance_intervals.cpp + mkdir -p build cd build cmake \ @@ -87,7 +101,11 @@ install -D -m755 $CWD/$PRGNAM.sh $PKG/etc/profile.d/$PRGNAM.sh.new install -D -m755 $CWD/$PRGNAM.csh $PKG/etc/profile.d/$PRGNAM.csh.new mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a COPYRIGHT LICENSE INSTALL README $PKG/usr/doc/$PRGNAM-$VERSION +cp -a COPYRIGHT LICENSE README $PKG/usr/doc/$PRGNAM-$VERSION +tar xvf $CWD/html-dev-${VERSION}.tar.gz -C $PKG/usr/doc/$PRGNAM-$VERSION +tar xvf $CWD/user-html-${VERSION}.tar.gz -C $PKG/usr/doc/$PRGNAM-$VERSION +chown -R root:root $PKG/usr/doc/$PRGNAM-$VERSION +chmod 755 $(find $PKG/usr/doc/$PRGNAM-$VERSION -type d) cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install @@ -95,4 +113,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/dakota/dakota.info b/academic/dakota/dakota.info index f20e72ed14..9e43bb02f6 100644 --- a/academic/dakota/dakota.info +++ b/academic/dakota/dakota.info @@ -1,10 +1,14 @@ PRGNAM="dakota" -VERSION="6.8" +VERSION="6.19.0" HOMEPAGE="https://dakota.sandia.gov/" -DOWNLOAD="https://dakota.sandia.gov/sites/default/files/distributions/public/dakota-6.8-release-public.src-UI.tar.gz" -MD5SUM="85375e8c4df406fe017beda63ab28215" +DOWNLOAD="https://github.com/snl-dakota/dakota/releases/download/v6.19.0/dakota-6.19.0-public-src-cli.tar.gz \ + https://snl-dakota.github.io/docs/6.19.0/downloads/user-html-6.19.0.tar.gz \ + https://snl-dakota.github.io/docs/6.19.0/downloads/html-dev-6.19.0.tar.gz" +MD5SUM="78210b4aa56dc15b5e05054b83f265f0 \ + da5c00e92c271a451295e2ac26ee02f5 \ + 10fbfb5a564e79c3ffcbb8ee246c0973" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="blas lapack" +REQUIRES="lapack" MAINTAINER="Lorenzo Trevisan" EMAIL="lorenzo.trevisan@gmail.com" diff --git a/academic/datamash/README b/academic/datamash/README new file mode 100644 index 0000000000..01d8fd598d --- /dev/null +++ b/academic/datamash/README @@ -0,0 +1,6 @@ +GNU Datamash is a command-line program which performs basic numeric, +textual and statistical operations on input textual data files. + +It is designed to be portable and reliable, and aid researchers +to easily automate analysis pipelines, without writing code or even +short scripts. diff --git a/academic/drawtiming/drawtiming.SlackBuild b/academic/datamash/datamash.SlackBuild index 8fde14c99a..65806834f5 100644 --- a/academic/drawtiming/drawtiming.SlackBuild +++ b/academic/datamash/datamash.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash -# Slackware build script for drawtiming +# Slackware build script for datamash -# Copyright 2014 R. S. Ananda Murthy, Mysore, India +# Copyright 2020-2022 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,27 +22,36 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -PRGNAM=drawtiming -VERSION=${VERSION:-0.7.1} +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=datamash +VERSION=${VERSION:-1.8} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) -STARTDIR=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -66,14 +75,9 @@ cd $PRGNAM-$VERSION chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; - -patch -p1 < $STARTDIR/InitializeMagick.diff -patch -p1 < $STARTDIR/manpage-fix.diff -patch -p1 < $STARTDIR/missing-includes.diff -patch -p1 < $STARTDIR/switch_LDFLAGS_LDADD.diff + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ @@ -82,10 +86,14 @@ CXXFLAGS="$SLKCFLAGS" \ --libdir=/usr/lib${LIBDIRSUFFIX} \ --sysconfdir=/etc \ --localstatedir=/var \ + --infodir=/usr/info \ --mandir=/usr/man \ + --docdir=/usr/doc/$PRGNAM-$VERSION \ --build=$ARCH-slackware-linux + make -make DESTDIR=$PKG install +make check +make install DESTDIR=$PKG find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true @@ -93,16 +101,17 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr find $PKG/usr/man -type f -exec gzip -9 {} \; for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done -mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION/samples -cp -r $TMP/$PRGNAM-$VERSION/samples/* $PKG/usr/doc/$PRGNAM-$VERSION/samples -rm $PKG/usr/doc/$PRGNAM-$VERSION/samples/runsamples.sh -rm $PKG/usr/doc/$PRGNAM-$VERSION/samples/Makefile* -cp -a COPYING INSTALL NEWS README AUTHORS THANKS $PKG/usr/doc/$PRGNAM-$VERSION +rm -f $PKG/usr/info/dir +gzip -9 $PKG/usr/info/*.info* + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + ABOUT-NLS AUTHORS ChangeLog COPYING INSTALL NEWS README THANKS \ + $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install -cat $CWD/doinst.sh > $PKG/install/doinst.sh cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/datamash/datamash.info b/academic/datamash/datamash.info new file mode 100644 index 0000000000..bc70b16d84 --- /dev/null +++ b/academic/datamash/datamash.info @@ -0,0 +1,10 @@ +PRGNAM="datamash" +VERSION="1.8" +HOMEPAGE="https://www.gnu.org/software/datamash/" +DOWNLOAD="https://ftp.gnu.org/gnu/datamash/datamash-1.8.tar.gz" +MD5SUM="b5f2dcfcefb2d41f88c54619b08727e3" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/avogadro/slack-desc b/academic/datamash/slack-desc index 50fba281d9..86ef966a72 100644 --- a/academic/avogadro/slack-desc +++ b/academic/datamash/slack-desc @@ -6,14 +6,14 @@ # customary to leave one space after the ':' except on otherwise blank lines. |-----handy-ruler------------------------------------------------------| -avogadro: avogadro (An advanced molecular editor based on Qt 4.) -avogadro: -avogadro: Avogadro is a molecular graphics and modelling system targetted at -avogadro: molecules and biomolecules. It can visualize properties like -avogadro: molecular orbitals or electrostatic potentials and features an -avogadro: intuitive molecular builder. -avogadro: -avogadro: Homepage: http://avogadro.cc/ -avogadro: -avogadro: -avogadro: +datamash: datamash (Basic numeric, textual and statistical operations) +datamash: +datamash: GNU Datamash is a command-line program which performs basic +datamash: numeric, textual and statistical operations on input textual +datamash: data files. +datamash: +datamash: https://www.gnu.org/software/datamash/ +datamash: +datamash: +datamash: +datamash: diff --git a/academic/diamond/diamond.SlackBuild b/academic/diamond/diamond.SlackBuild index 06d783043f..0c85f52415 100644 --- a/academic/diamond/diamond.SlackBuild +++ b/academic/diamond/diamond.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for diamond -# Copyright 2018-2020 Petar Petrov slackalaxy@gmail.com +# Copyright 2018-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=diamond -VERSION=${VERSION:-0.9.29} +VERSION=${VERSION:-0.9.36} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -85,7 +95,7 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - ${PRGNAM}_manual.pdf LICENSE README.md src/ChangeLog \ + LICENSE README.md src/ChangeLog \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References @@ -94,4 +104,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/diamond/diamond.info b/academic/diamond/diamond.info index e94f42b60b..e1160377d7 100644 --- a/academic/diamond/diamond.info +++ b/academic/diamond/diamond.info @@ -1,10 +1,10 @@ PRGNAM="diamond" -VERSION="0.9.29" +VERSION="0.9.36" HOMEPAGE="https://github.com/bbuchfink/diamond" -DOWNLOAD="UNSUPPORTED" -MD5SUM="" -DOWNLOAD_x86_64="https://github.com/bbuchfink/diamond/archive/v0.9.29/diamond-0.9.29.tar.gz" -MD5SUM_x86_64="c9a1cb0f2128e621695f7ee0a05c2af8" +DOWNLOAD="https://github.com/bbuchfink/diamond/archive/v0.9.36/diamond-0.9.36.tar.gz" +MD5SUM="ce6f019e2e5dbc22e1210ba408ccefb4" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" REQUIRES="" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/dimod/README b/academic/dimod/README new file mode 100644 index 0000000000..23a53588f8 --- /dev/null +++ b/academic/dimod/README @@ -0,0 +1,12 @@ + dimod is a shared API for samplers. It provides: + + - classes for quadratic models---such as the binary quadratic model + (BQM) class that contains Ising and QUBO models used by samplers + such as the D-Wave system---and higher-order (non-quadratic) + models. + - reference examples of samplers and composed samplers. + - abstract base classes for constructing new samplers and composed + samplers. + + + If you want to run the tests set the environment variable TESTS=yes. diff --git a/academic/dimod/dimod.SlackBuild b/academic/dimod/dimod.SlackBuild new file mode 100644 index 0000000000..095c740e7e --- /dev/null +++ b/academic/dimod/dimod.SlackBuild @@ -0,0 +1,119 @@ +#!/bin/bash + +# Slackware build script for dimod + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM="dimod" +VERSION=${VERSION:-0.12.0} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +python3 setup.py install --root=$PKG + +if [ "${TESTS:-no}" == "yes" ]; then + IGNORE_TESTS="test_(bqm|cyutilities|discrete_quadratic_model|lp|quadratic_model|serialization_fileview|variables).py" + PYVER=$( python3 -c 'import sys; print( "%d.%d" % sys.version_info[:2] )' ) + cd tests + for file in $(ls test_*.py | grep -v -E $IGNORE_TESTS); do + echo -n "$file " + PYTHONPATH=../build/lib.linux-$(uname -m)-$PYVER python3 $file + if [ "$?" -eq "0" ]; then + echo "OK" + else + echo "\n$file - fail" + fi + done + cd .. +fi + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + LICENSE README.rst docs \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/dimod/dimod.info b/academic/dimod/dimod.info new file mode 100644 index 0000000000..83925dbffe --- /dev/null +++ b/academic/dimod/dimod.info @@ -0,0 +1,10 @@ +PRGNAM="dimod" +VERSION="0.12.0" +HOMEPAGE="https://github.com/dwavesystems" +DOWNLOAD="https://github.com/dwavesystems/dimod/archive/0.12.0/dimod-0.12.0.tar.gz" +MD5SUM="20dfa5a1cb6f06b3f928c0538f8a021c" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="python3-numpy" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/dimod/slack-desc b/academic/dimod/slack-desc new file mode 100644 index 0000000000..fb746b8f61 --- /dev/null +++ b/academic/dimod/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +dimod: dimod (A shared API for samplers) +dimod: +dimod: dimod is a shared API for samplers. It provides: +dimod: +dimod: - classes for quadratic models---such as the binary quadratic +dimod: model (BQM) class that contains Ising and QUBO models used by +dimod: samplers such as the D-Wave system---and higher-order +dimod: (non-quadratic) models. +dimod: - reference examples of samplers and composed samplers. +dimod: - abstract base classes for constructing new samplers and composed +dimod: samplers. diff --git a/academic/drawtiming/InitializeMagick.diff b/academic/drawtiming/InitializeMagick.diff deleted file mode 100644 index d610544a76..0000000000 --- a/academic/drawtiming/InitializeMagick.diff +++ /dev/null @@ -1,30 +0,0 @@ -Description: Properly initialize GraphicsMagick - Quoting from GraphicsMagick's NEWS file " - 1.3.8 (January 21, 2010) - ======================== - [...] - Behavior Changes: - InitializeMagick() MUST be invoked prior to using any Magick API function. - Failure to do so will likely lead to an immediate application crash. This is - due to initialization and runtime changes intended to improve thread safety - and efficiency. Previously it was only strongly recommended to invoke - InitializeMagick(). - " -Author: Galland (https://launchpad.net/~victor-lopez) -Bug-Ubuntu: https://bugs.launchpad.net/bugs/636021 -Bug-Debian: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=599915 -Bug: http://sourceforge.net/tracker/index.php?func=detail&aid=3136111&group_id=118983&atid=682742 -Forwarded: yes - ---- a/src/main.cc -+++ b/src/main.cc -@@ -97,6 +97,9 @@ - double scale = 1; - int flags = 0; - -+#ifndef LITE -+ InitializeMagick(NULL); -+#endif /* ! LITE */ - int k, c; - while ((c = getopt_long (argc, argv, "ac:f:hl:o:p:vVw:x:", opts, &k)) != -1) - switch (c) { diff --git a/academic/drawtiming/README b/academic/drawtiming/README deleted file mode 100644 index 32f4e261c2..0000000000 --- a/academic/drawtiming/README +++ /dev/null @@ -1,6 +0,0 @@ -DrawTiming provides a command line tool for documenting hardware and -software designs through timing diagrams. It reads signal descriptions -from a text file with an intuitive syntax, and outputs a timing diagram -to an image file. Notation typical of timing diagrams found in the -Electrical Engineering discipline is used, including arrows -indicating causal relationships between signal transitions. diff --git a/academic/drawtiming/drawtiming.info b/academic/drawtiming/drawtiming.info deleted file mode 100644 index 3e15375061..0000000000 --- a/academic/drawtiming/drawtiming.info +++ /dev/null @@ -1,10 +0,0 @@ -PRGNAM="drawtiming" -VERSION="0.7.1" -HOMEPAGE="http://drawtiming.sourceforge.net/" -DOWNLOAD="http://downloads.sourceforge.net/project/drawtiming/drawtiming/0.7.1/drawtiming-0.7.1.tar.gz" -MD5SUM="bc25f43f5301ee6cfb65ed8e151a2e1d" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="" -MAINTAINER="R. S. Ananda Murthy" -EMAIL="rsamurti@gmail.com" diff --git a/academic/drawtiming/manpage-fix.diff b/academic/drawtiming/manpage-fix.diff deleted file mode 100644 index 2aa56c124d..0000000000 --- a/academic/drawtiming/manpage-fix.diff +++ /dev/null @@ -1,62 +0,0 @@ -Description: Fix typos and hyphenation -Author: Ø£Øمد المØمودي (Ahmed El-Mahmoudy) <aelmahmoudy@sabily.org> -Forwarded: yes ---- a/doc/drawtiming.1 -+++ b/doc/drawtiming.1 -@@ -56,7 +56,7 @@ - .It Fl -pagesize Ar WidthxHeight - Scale the diagram to fit given image size. - .It Fl -aspect --Maintain fixed aspect ratio if --pagesize given. -+Maintain fixed aspect ratio if \-\-pagesize given. - .It Fl -cell-height Ar H - Height of the each signal in pixels. Default is 32. - .It Fl -cell-width Ar W -@@ -101,23 +101,23 @@ - changing its value. - .El - .Pp --Statements are seperated by the following symbols: -+Statements are separated by the following symbols: - .Bl -tag -width "-tD>" - .It , --The comma seperator is used to seperate statements without -+The comma separator is used to separate statements without - affecting the dependency list or clock (ie: the next statement will - add to the dependency list). - .It ; --The semicolon seperator resets the list of dependencies without -+The semicolon separator resets the list of dependencies without - incrementing the clock - .It . --The period seperator resets the list of dependencies and -+The period separator resets the list of dependencies and - increments the clock. - .It => --The "causes" seperator renders dependency arrows based on the -+The "causes" separator renders dependency arrows based on the - current list of dependencies and then resets the dependency list. - .It -tD> --The "delay" seperator renders a delay arrow from the last dependency -+The "delay" separator renders a delay arrow from the last dependency - with the annotation - .Em tD . - .El -@@ -173,7 +173,7 @@ - value if their initial value is not given. - .Pp - Independent signal transitions which occur simultaneously are normally --seperated by commas. Since signals aren't normally expected to change -+separated by commas. Since signals aren't normally expected to change - simultaneously, the initial state is a good example of this: - .Pp - .Dl POWER=0, FIRE=0, ARMED=0, LED=OFF, COUNT=N. -@@ -194,7 +194,7 @@ - .Pp - .Dl POWER=1 => LED=GREEN. - .Pp --For signal state changes with multiple dependencies, seperate the -+For signal state changes with multiple dependencies, separate the - dependencies with commas: - .Pp - .Dl FIRE, ARMED => LED=RED. diff --git a/academic/drawtiming/missing-includes.diff b/academic/drawtiming/missing-includes.diff deleted file mode 100644 index 7dbad2192e..0000000000 --- a/academic/drawtiming/missing-includes.diff +++ /dev/null @@ -1,13 +0,0 @@ -Description: Add missing string.h include. -Author: Wesley J. Landaker <wjl@icecavern.net> -Forwarded: yes ---- a/src/timing.cc -+++ b/src/timing.cc -@@ -23,6 +23,7 @@ - #include "timing.h" - #include <map> - #include <fstream> -+#include <string.h> - using namespace std; - using namespace timing; - using namespace Magick; diff --git a/academic/drawtiming/slack-desc b/academic/drawtiming/slack-desc deleted file mode 100644 index a406fa95ca..0000000000 --- a/academic/drawtiming/slack-desc +++ /dev/null @@ -1,19 +0,0 @@ -# HOW TO EDIT THIS FILE: -# The "handy ruler" below makes it easier to edit a package description. -# Line up the first '|' above the ':' following the base package name, and -# the '|' on the right side marks the last column you can put a character in. -# You must make exactly 11 lines for the formatting to be correct. It's also -# customary to leave one space after the ':' except on otherwise blank lines. - - |-----handy-ruler------------------------------------------------------| -drawtiming: drawtiming (tool for drawing timing diagrams) -drawtiming: -drawtiming: DrawTiming provides a command line tool for documenting hardware and -drawtiming: software designs through timing diagrams. It reads signal -drawtiming: descriptions from a text file with an intuitive syntax, -drawtiming: and outputs a timing diagram to an image file. Notation typical -drawtiming: of timing diagrams found in the Electrical Engineering discipline -drawtiming: is used, including arrows indicating causal relationships between -drawtiming: signal transitions. -drawtiming: -drawtiming: diff --git a/academic/drawtiming/switch_LDFLAGS_LDADD.diff b/academic/drawtiming/switch_LDFLAGS_LDADD.diff deleted file mode 100644 index 8ae536630d..0000000000 --- a/academic/drawtiming/switch_LDFLAGS_LDADD.diff +++ /dev/null @@ -1,36 +0,0 @@ -Description: Switch LDADD with LDFLAGS - This change is to move the objects before the libs. to fix an FTBFS when - --as-needed is passed to gcc. -Author: Ø£Øمد المØمودي (Ahmed El-Mahmoudy) <aelmahmoudy@sabily.org> -Forwarded: yes ---- drawtiming-0.7.1.orig/src/Makefile.am -+++ drawtiming-0.7.1/src/Makefile.am -@@ -3,7 +3,7 @@ - - bin_PROGRAMS = drawtiming - drawtiming_SOURCES = main.cc globals.h parser.yy scanner.ll timing.cc timing.h --drawtiming_LDFLAGS = @MAGICK_LIBS@ -+drawtiming_LDADD = @MAGICK_LIBS@ - - EXTRA_DIST = parser.h - BUILT_SOURCES = parser.h ---- drawtiming-0.7.1.orig/src/Makefile.in -+++ drawtiming-0.7.1/src/Makefile.in -@@ -51,7 +51,7 @@ - am_drawtiming_OBJECTS = main.$(OBJEXT) parser.$(OBJEXT) \ - scanner.$(OBJEXT) timing.$(OBJEXT) - drawtiming_OBJECTS = $(am_drawtiming_OBJECTS) --drawtiming_LDADD = $(LDADD) -+drawtiming_LDADD = @MAGICK_LIBS@ $(LDADD) - DEFAULT_INCLUDES = -I. -I$(srcdir) -I$(top_builddir) - depcomp = $(SHELL) $(top_srcdir)/depcomp - am__depfiles_maybe = depfiles -@@ -159,7 +159,7 @@ - AM_CXXFLAGS = @MAGICK_CFLAGS@ -DYYDEBUG=1 - AM_YFLAGS = -d - drawtiming_SOURCES = main.cc globals.h parser.yy scanner.ll timing.cc timing.h --drawtiming_LDFLAGS = @MAGICK_LIBS@ -+drawtiming_LDFLAGS = @LDFLAGS@ - EXTRA_DIST = parser.h - BUILT_SOURCES = parser.h - all: $(BUILT_SOURCES) diff --git a/academic/ds9/README b/academic/ds9/README index 5bffb53e7f..3569e0678c 100644 --- a/academic/ds9/README +++ b/academic/ds9/README @@ -1,7 +1,13 @@ -SAOImage DS9 is an application for astronomical imaging and data -visualization. It supports the FITS format and binary tables. As well -as standard imaging manipulation tools, it includes many advanced -features such as multiple frame buffers, 2D, 3D, RGB frame buffers, -region and colormap manipulation, mosaic images and geometric markers. -DS9 supports a variety of coordinate systems and it has a user -configurable interface. +SAOImageDS9 is an astronomical imaging and data visualization +application. DS9 supports FITS images and binary tables, multiple +frame buffers, region manipulation, and many scale algorithms and +colormaps. All versions and platforms support a consistent set of GUI +and functional capabilities. DS9 supports advanced features such as +2-D, 3-D and RGB frame buffers, mosaic images, tiling, blinking, +geometric markers, colormap manipulation, scaling, arbitrary zoom, +cropping, rotation, pan, and a variety of coordinate systems. +Furthermore, the application is stand-alone and requires no +installation or support files. The GUI for DS9 is user configurable. +GUI elements such as the coordinate display, panner, magnifier, +horizontal and vertical graphs, button bar, and color bar can be +configured via menus or the command line. diff --git a/academic/ds9/ds9-icon.png b/academic/ds9/ds9-icon.png Binary files differdeleted file mode 100644 index 09254821f3..0000000000 --- a/academic/ds9/ds9-icon.png +++ /dev/null diff --git a/academic/ds9/ds9.SlackBuild b/academic/ds9/ds9.SlackBuild index f6767b091d..096402f85e 100644 --- a/academic/ds9/ds9.SlackBuild +++ b/academic/ds9/ds9.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash -# Slackware build script for SAOImage DS9 +# Slackware build script for ds9 (SAOImageDS9) -# Copyright 2020 Nitish Ragoomundun, Mauritius +# Copyright 2022 Nitish Ragoomundun, Mauritius # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=ds9 -VERSION=${VERSION:-8.1} +VERSION=${VERSION:-8.4.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -72,15 +82,18 @@ find -L . \ CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ -./unix/configure \ +unix/configure \ --prefix=/usr \ --bindir=/usr/bin \ --sysconfdir=/etc \ --localstatedir=/var \ --docdir=/usr/doc/$PRGNAM-$VERSION \ - --with-arch=${ARCH}-slackware-linux + --x-includes=/usr/include \ + --x-libraries=/usr/lib$LIBDIRSUFFIX \ + --with-x \ + --with-arch=$ARCH-slackware-linux -make -j1 +make # Install the ds9 executable mkdir -p $PKG/usr/{bin,doc/$PRGNAM-$VERSION} @@ -89,8 +102,8 @@ install -D -m755 bin/ds9 $PKG/usr/bin/ # Install icon mkdir -p $PKG/usr/share/applications mkdir -p $PKG/usr/share/pixmaps +install -m 644 ds9/doc/sun.png $PKG/usr/share/pixmaps/ds9-icon.png install -m 644 $CWD/ds9.desktop $PKG/usr/share/applications -install -m 644 $CWD/ds9-icon.png $PKG/usr/share/pixmaps # Copy documentation cp -a BUILD.txt LICENSE README.md ds9/doc/* $PKG/usr/doc/$PRGNAM-$VERSION @@ -102,4 +115,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/ds9/ds9.desktop b/academic/ds9/ds9.desktop index 318d5d41c2..d942e73988 100644 --- a/academic/ds9/ds9.desktop +++ b/academic/ds9/ds9.desktop @@ -1,9 +1,10 @@ [Desktop Entry] -Name=DS9 -GenericName=SAOImage DS9 -Comment=SAOImage DS9 Astronomical Software Exec=ds9 Icon=ds9-icon -Terminal=false Type=Application Categories=Education;Science;Astronomy; +Name=ds9 +GenericName=SAOImageDS9 +Comment=Astronomical Software and FITS viewing program +MimeType=image/fits; +Terminal=false diff --git a/academic/ds9/ds9.info b/academic/ds9/ds9.info index 17023a3adf..59d26462bc 100644 --- a/academic/ds9/ds9.info +++ b/academic/ds9/ds9.info @@ -1,8 +1,8 @@ PRGNAM="ds9" -VERSION="8.1" -HOMEPAGE="http://ds9.si.edu/site/Home.html" -DOWNLOAD="http://ds9.si.edu/archive/source/ds9.8.1.tar.gz" -MD5SUM="3dd24162553617565182d1016d24a6de" +VERSION="8.4.1" +HOMEPAGE="https://sites.google.com/cfa.harvard.edu/saoimageds9/home" +DOWNLOAD="https://ds9.si.edu/archive/source/ds9.8.4.1.tar.gz" +MD5SUM="b227d7ce367d3d7901d88cd5fccd23f7" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/ds9/slack-desc b/academic/ds9/slack-desc index b07917b061..713bb9386a 100644 --- a/academic/ds9/slack-desc +++ b/academic/ds9/slack-desc @@ -8,12 +8,12 @@ |-----handy-ruler------------------------------------------------------| ds9: ds9 (Astronomical tool) ds9: -ds9: DS9 is an astronomical imaging and visualization tool. It supports -ds9: the FITS format and binary tables. It includes many imaging features -ds9: such as tiling, cropping, as well as advanced features such as -ds9: multiple 2D, 3D, RGB frame buffers, colormap manipulation and mosaic -ds9: images. DS9 also supports a variety of coordinate systems and has a -ds9: user configurable interface. -ds9: -ds9: Homepage: http://ds9.si.edu/site/Home.html +ds9: SAOImageDS9 is an astronomical imaging and data visualization tool. +ds9: It supports FITS images and binary tables. It also includes many +ds9: advanced imaging features such as 2-D, 3-D and RGB frame buffers, +ds9: mosaic images, tiling, blinking, geometric markers, colormap +ds9: manipulation, scaling, arbitrary zoom, cropping, rotation, pan, and a +ds9: variety of coordinate systems. DS9 also has user configurable GUI +ds9: elements. +ds9: Homepage: https://sites.google.com/cfa.harvard.edu/saoimageds9/home ds9: diff --git a/academic/dwave-cloud-client/README b/academic/dwave-cloud-client/README new file mode 100644 index 0000000000..d37eefb206 --- /dev/null +++ b/academic/dwave-cloud-client/README @@ -0,0 +1,8 @@ + A minimal implementation of the REST interface used to communicate +with D-Wave Solver API (SAPI) servers. + + SAPI is an application layer built to provide resource discovery, +permissions, and scheduling for quantum annealing resources at +D-Wave Systems. This package provides a minimal Python interface to +that layer without compromising the quality of interactions and +workflow. diff --git a/academic/dwave-cloud-client/dwave-cloud-client.SlackBuild b/academic/dwave-cloud-client/dwave-cloud-client.SlackBuild new file mode 100644 index 0000000000..61e4e1cf71 --- /dev/null +++ b/academic/dwave-cloud-client/dwave-cloud-client.SlackBuild @@ -0,0 +1,103 @@ +#!/bin/bash + +# Slackware build script for dwave-cloud-client + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM="dwave-cloud-client" +VERSION=${VERSION:-0.10.3} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +python3 setup.py install --root=$PKG + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + LICENSE README.rst docs \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/dwave-cloud-client/dwave-cloud-client.info b/academic/dwave-cloud-client/dwave-cloud-client.info new file mode 100644 index 0000000000..170b17eb99 --- /dev/null +++ b/academic/dwave-cloud-client/dwave-cloud-client.info @@ -0,0 +1,10 @@ +PRGNAM="dwave-cloud-client" +VERSION="0.10.3" +HOMEPAGE="https://github.com/dwavesystems/dwave-cloud-client" +DOWNLOAD="https://github.com/dwavesystems/dwave-cloud-client/archive/0.10.3/dwave-cloud-client-0.10.3.tar.gz" +MD5SUM="00a192d9aa86c07ed7b5a42a2011d78f" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/dwave-cloud-client/slack-desc b/academic/dwave-cloud-client/slack-desc new file mode 100644 index 0000000000..b3a744ce10 --- /dev/null +++ b/academic/dwave-cloud-client/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +dwave-cloud-client: dwave-cloud-client (REST interface for communicating to D-Wave API) +dwave-cloud-client: +dwave-cloud-client: +dwave-cloud-client: +dwave-cloud-client: A minimal implementation of the REST interface used to communicate +dwave-cloud-client: with D-Wave Solver API (SAPI) servers. +dwave-cloud-client: +dwave-cloud-client: +dwave-cloud-client: +dwave-cloud-client: +dwave-cloud-client: diff --git a/academic/dwave-greedy/README b/academic/dwave-greedy/README new file mode 100644 index 0000000000..3e3fb8d475 --- /dev/null +++ b/academic/dwave-greedy/README @@ -0,0 +1,13 @@ + An implementation of a steepest descent solver for binary quadratic +models. + + Steepest descent is the discrete analogue of gradient descent, but +the best move is computed using a local minimization rather rather +than computing a gradient. At each step, we determine the dimension +along which to descend based on the highest energy drop caused by a +variable flip. + + + Optional building mode set with environment variables: + - TESTS=yes (performs tests, requires dimod) + diff --git a/academic/dwave-greedy/dwave-greedy.SlackBuild b/academic/dwave-greedy/dwave-greedy.SlackBuild new file mode 100644 index 0000000000..62db8ce464 --- /dev/null +++ b/academic/dwave-greedy/dwave-greedy.SlackBuild @@ -0,0 +1,120 @@ +#!/bin/bash + +# Slackware build script for dwave-greedy + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM="dwave-greedy" +VERSION=${VERSION:-0.2.5} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +python3 setup.py install --root=$PKG + +make -C tests +if [ "${TESTS:-no}" == "yes" ]; then + IGNORE_TESTS="test_(composite|sampler).py" + PYVER=$( python3 -c 'import sys; print( "%d.%d" % sys.version_info[:2] )' ) + cd tests + for file in $(ls test_*.py | grep -v -E $IGNORE_TESTS); do + echo -n "$file " + PYTHONPATH=../build/lib.linux-$(uname -m)-$PYVER python3 $file + if [ "$?" -eq "0" ]; then + echo "OK" + else + echo "\n$file - fail" + fi + done + cd .. +fi + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + LICENSE README.rst docs \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/dwave-greedy/dwave-greedy.info b/academic/dwave-greedy/dwave-greedy.info new file mode 100644 index 0000000000..a3c9b5ee9e --- /dev/null +++ b/academic/dwave-greedy/dwave-greedy.info @@ -0,0 +1,10 @@ +PRGNAM="dwave-greedy" +VERSION="0.2.5" +HOMEPAGE="https://github.com/dwavesystems/dwave-greedy" +DOWNLOAD="https://github.com/dwavesystems/dwave-greedy/archive/0.2.5/dwave-greedy-0.2.5.tar.gz" +MD5SUM="8805c6bfa59c9b33d1e00e713e62fb98" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="python3-numpy" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/dwave-greedy/slack-desc b/academic/dwave-greedy/slack-desc new file mode 100644 index 0000000000..15d483f32f --- /dev/null +++ b/academic/dwave-greedy/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +dwave-greedy: dwave-greedy (Implementation of a steepest descent solver for (BQM)) +dwave-greedy: +dwave-greedy: An implementation of a steepest descent solver for binary +dwave-greedy: quadratic models. +dwave-greedy: Steepest descent is the discrete analogue of gradient descent, +dwave-greedy: but the best move is computed using a local minimization rather +dwave-greedy: rather than computing a gradient. At each step, we determine the +dwave-greedy: dimension along which to descend based on the highest energy drop +dwave-greedy: caused by a variable flip. +dwave-greedy: +dwave-greedy: diff --git a/academic/dwave-hybrid/README b/academic/dwave-hybrid/README new file mode 100644 index 0000000000..d1b5b77883 --- /dev/null +++ b/academic/dwave-hybrid/README @@ -0,0 +1,15 @@ + A general, minimal Python framework for building hybrid asynchronous +decomposition samplers for quadratic unconstrained binary optimization +(QUBO) problems. + + dwave-hybrid facilitates three aspects of solution development: + + - Hybrid approaches to combining quantum and classical compute + resources + - Evaluating a portfolio of algorithmic components and + problem-decomposition trategies + - Experimenting with workflow structures and parameters to obtain + the best application results + + The framework enables rapid development and insight into expected +performance of productized versions of its experimental prototypes. diff --git a/academic/dwave-hybrid/dwave-hybrid.SlackBuild b/academic/dwave-hybrid/dwave-hybrid.SlackBuild new file mode 100644 index 0000000000..48f688e505 --- /dev/null +++ b/academic/dwave-hybrid/dwave-hybrid.SlackBuild @@ -0,0 +1,112 @@ +#!/bin/bash + +# Slackware build script for dwave-hybrid + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM="dwave-hybrid" +VERSION=${VERSION:-0.6.9} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +python3 setup.py install --root=$PKG + +# install libexec +mkdir -p $PKG/usr/libexec/$PRGNAM +cp -av scripts/* $PKG/usr/libexec/$PRGNAM + +# install examples and problems +mkdir -p $PKG/usr/share/$PRGNAM-$VERSION +cp -av examples $PKG/usr/share/$PRGNAM-$VERSION +cp -av problems $PKG/usr/share/$PRGNAM-$VERSION + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + LICENSE README.rst docs \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/dwave-hybrid/dwave-hybrid.info b/academic/dwave-hybrid/dwave-hybrid.info new file mode 100644 index 0000000000..c45b1d0cf0 --- /dev/null +++ b/academic/dwave-hybrid/dwave-hybrid.info @@ -0,0 +1,10 @@ +PRGNAM="dwave-hybrid" +VERSION="0.6.9" +HOMEPAGE="https://github.com/dwavesystems/dwave-hybrid" +DOWNLOAD="https://github.com/dwavesystems/dwave-hybrid/archive/0.6.9/dwave-hybrid-0.6.9.tar.gz" +MD5SUM="406d8439c122b7e6f1dd6b3427f5c954" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/dwave-hybrid/slack-desc b/academic/dwave-hybrid/slack-desc new file mode 100644 index 0000000000..025491ccfe --- /dev/null +++ b/academic/dwave-hybrid/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +dwave-hybrid: dwave-hybrid (Hybrid Async Decomposition Sampler prototype framework) +dwave-hybrid: +dwave-hybrid: +dwave-hybrid: +dwave-hybrid: A general, minimal Python framework for building hybrid +dwave-hybrid: asynchronous decomposition samplers for quadratic unconstrained +dwave-hybrid: binary optimization (QUBO) problems. +dwave-hybrid: +dwave-hybrid: +dwave-hybrid: +dwave-hybrid: diff --git a/academic/dwave-inspector/README b/academic/dwave-inspector/README new file mode 100644 index 0000000000..ed70d96276 --- /dev/null +++ b/academic/dwave-inspector/README @@ -0,0 +1,2 @@ + A tool for visualizing problems submitted to, and answers received +from, a D-Wave structured solver such as an Advantage quantum computer. diff --git a/academic/dwave-inspector/dwave-inspector.SlackBuild b/academic/dwave-inspector/dwave-inspector.SlackBuild new file mode 100644 index 0000000000..0aac87aea0 --- /dev/null +++ b/academic/dwave-inspector/dwave-inspector.SlackBuild @@ -0,0 +1,107 @@ +#!/bin/bash + +# Slackware build script for dwave-inspector + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM="dwave-inspector" +VERSION=${VERSION:-0.3.0} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +python3 setup.py install --root=$PKG + +# install examples +mkdir -p $PKG/usr/share/$PRGNAM-$VERSION +cp -av examples $PKG/usr/share/$PRGNAM-$VERSION + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + LICENSE README.rst docs \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/dwave-inspector/dwave-inspector.info b/academic/dwave-inspector/dwave-inspector.info new file mode 100644 index 0000000000..a501f460c4 --- /dev/null +++ b/academic/dwave-inspector/dwave-inspector.info @@ -0,0 +1,10 @@ +PRGNAM="dwave-inspector" +VERSION="0.3.0" +HOMEPAGE="https://github.com/dwavesystems/dwave-inspector" +DOWNLOAD="https://github.com/dwavesystems/dwave-inspector/archive/0.3.0/dwave-inspector-0.3.0.tar.gz" +MD5SUM="db97afcfbf90e989859737954f2786cc" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/dwave-inspector/slack-desc b/academic/dwave-inspector/slack-desc new file mode 100644 index 0000000000..17dfab47eb --- /dev/null +++ b/academic/dwave-inspector/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +dwave-inspector: dwave-inspector (Tool for visualizing D-Wave structured solver) +dwave-inspector: +dwave-inspector: +dwave-inspector: +dwave-inspector: A tool for visualizing problems submitted to, and answers +dwave-inspector: received from, a D-Wave structured solver such as an Advantage +dwave-inspector: quantum computer. +dwave-inspector: +dwave-inspector: +dwave-inspector: +dwave-inspector: diff --git a/academic/dwave-neal/README b/academic/dwave-neal/README new file mode 100644 index 0000000000..45dd6fdd1d --- /dev/null +++ b/academic/dwave-neal/README @@ -0,0 +1,11 @@ + An implementation of a simulated annealing sampler. + + A simulated annealing sampler can be used for approximate Boltzmann +sampling or heuristic optimization. This implementation approaches +the equilibrium distribution by performing updates at a sequence of +increasing beta values, beta_schedule, terminating at the target +beta. Each spin is updated once in a fixed order per point in the +beta_schedule according to a Metropolis- Hastings update. When beta +is large the target distribution concentrates, at equilibrium, +over ground states of the model. Samples are guaranteed to match +the equilibrium for long 'smooth' beta schedules. diff --git a/academic/dwave-neal/dwave-neal.SlackBuild b/academic/dwave-neal/dwave-neal.SlackBuild new file mode 100644 index 0000000000..a6f1fe8909 --- /dev/null +++ b/academic/dwave-neal/dwave-neal.SlackBuild @@ -0,0 +1,116 @@ +#!/bin/bash + +# Slackware build script for dwave-neal + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM="dwave-neal" +VERSION=${VERSION:-0.5.9} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +python3 setup.py install --root=$PKG + +PYVER=$( python3 -c 'import sys; print( "%d.%d" % sys.version_info[:2] )' ) +cd tests + for file in $(ls test_*.py); do + echo -n "$file " + PYTHONPATH=../build/lib.linux-$(uname -m)-$PYVER python3 $file + if [ "$?" -eq "0" ]; then + echo "OK" + else + echo "\n$file - fail" + fi + done +cd .. + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + LICENSE README.rst docs \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/dwave-neal/dwave-neal.info b/academic/dwave-neal/dwave-neal.info new file mode 100644 index 0000000000..3f928a533d --- /dev/null +++ b/academic/dwave-neal/dwave-neal.info @@ -0,0 +1,10 @@ +PRGNAM="dwave-neal" +VERSION="0.5.9" +HOMEPAGE="https://github.com/dwavesystems/dwave-neal" +DOWNLOAD="https://github.com/dwavesystems/dwave-neal/archive/0.5.9/dwave-neal-0.5.9.tar.gz" +MD5SUM="f01bae63001966835a0677e8b9b07ea8" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="dimod" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/dwave-neal/slack-desc b/academic/dwave-neal/slack-desc new file mode 100644 index 0000000000..da4cd80d24 --- /dev/null +++ b/academic/dwave-neal/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +dwave-neal: dwave-neal (An implementation of a simulated annealing sampler) +dwave-neal: +dwave-neal: An implementation of a simulated annealing sampler. +dwave-neal: +dwave-neal: A simulated annealing sampler can be used for approximate Boltzmann +dwave-neal: sampling or heuristic optimization. This implementation approaches +dwave-neal: the equilibrium distribution by performing updates at a sequence of +dwave-neal: increasing beta values, beta_schedule, terminating at the target +dwave-neal: beta. +dwave-neal: +dwave-neal: diff --git a/academic/dwave-networkx/README b/academic/dwave-networkx/README new file mode 100644 index 0000000000..9c0129351a --- /dev/null +++ b/academic/dwave-networkx/README @@ -0,0 +1,10 @@ + D-Wave NetworkX is an extension of NetworkX---a Python language +package for exploration and analysis of networks and network +algorithms---for users of D-Wave Systems. It provides tools for +working with Chimera graphs and implementations of graph-theory +algorithms on the D-Wave system and other binary quadratic model +samplers. + + + If you want to run the tests set the environment variable TESTS=yes, +this requires networkx, dimod and numpy3. diff --git a/academic/dwave-networkx/dwave-networkx.SlackBuild b/academic/dwave-networkx/dwave-networkx.SlackBuild new file mode 100644 index 0000000000..3c1570af2e --- /dev/null +++ b/academic/dwave-networkx/dwave-networkx.SlackBuild @@ -0,0 +1,119 @@ +#!/bin/bash + +# Slackware build script for dwave-networkx + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM="dwave-networkx" +VERSION=${VERSION:-0.8.12} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +python3 setup.py install --root=$PKG + +if [ "${TESTS:-no}" == "yes" ]; then + IGNORE_TESTS="test_(matching).py" + PYVER=$( python3 -c 'import sys; print( "%d.%d" % sys.version_info[:2] )' ) + cd tests + for file in $(ls test_*.py | grep -v -E $IGNORE_TESTS); do + echo -n "$file " + PYTHONPATH=../build/lib python3 $file + if [ "$?" -eq "0" ]; then + echo "OK" + else + echo "\n$file - fail" + fi + done + cd .. +fi + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + LICENSE.txt README.rst docs \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/dwave-networkx/dwave-networkx.info b/academic/dwave-networkx/dwave-networkx.info new file mode 100644 index 0000000000..25a6ac6260 --- /dev/null +++ b/academic/dwave-networkx/dwave-networkx.info @@ -0,0 +1,10 @@ +PRGNAM="dwave-networkx" +VERSION="0.8.12" +HOMEPAGE="https://www.dwavesys.com" +DOWNLOAD="https://github.com/dwavesystems/dwave-networkx/archive/0.8.12/dwave-networkx-0.8.12.tar.gz" +MD5SUM="5bd9d71bc6ebd723d1b741debc4abcef" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/dwave-networkx/slack-desc b/academic/dwave-networkx/slack-desc new file mode 100644 index 0000000000..db55ee6e77 --- /dev/null +++ b/academic/dwave-networkx/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +dwave-networkx: dwave-networkx (Network exploration and analysis for D-Wave Systems) +dwave-networkx: +dwave-networkx: +dwave-networkx: D-Wave NetworkX is an extension of NetworkX---a Python language +dwave-networkx: package for exploration and analysis of networks and network +dwave-networkx: algorithms---for users of D-Wave Systems. It provides tools for +dwave-networkx: working with Chimera graphs and implementations of graph-theory +dwave-networkx: algorithms on the D-Wave system and other binary quadratic model +dwave-networkx: samplers. +dwave-networkx: +dwave-networkx: diff --git a/academic/dwave-ocean-sdk/README b/academic/dwave-ocean-sdk/README new file mode 100644 index 0000000000..fc830b8659 --- /dev/null +++ b/academic/dwave-ocean-sdk/README @@ -0,0 +1,23 @@ + Ocean is D-Wave's suite of tools for solving hard problems with +quantum computers. + + After installing you can run "dwave setup" to configure your +system. If you don't have yet you shall get an API token after +registering at dwavesystem's webpage. + + +NOTE: slackbuilds.org, doesn't request to include packages that isn't +necessary to build the package nonetheless there is a few packages +required for running the dwave ocean sdk: + - python3-dateutil + - python3-plucky + - python-diskcache + - click + - homebase + - python3-pydantic + - PySocks + - rectangle-packer + +Other packages for development + - scipy3 + - fasteners diff --git a/academic/dwave-ocean-sdk/dwave-ocean-sdk.SlackBuild b/academic/dwave-ocean-sdk/dwave-ocean-sdk.SlackBuild new file mode 100644 index 0000000000..cfad5737ba --- /dev/null +++ b/academic/dwave-ocean-sdk/dwave-ocean-sdk.SlackBuild @@ -0,0 +1,134 @@ +#!/bin/bash + +# Slackware build script for dwave-ocean-sdk + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=dwave-ocean-sdk +VERSION=${VERSION:-6.0.0} +BUILD=${BUILD:-2} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION + +# unpack components +for source_file in $(ls $CWD/{dimod,dwave-{cloud-client,greedy,hybrid,inspector,neal,networkx,preprocessing,system,tabu},dwavebinarycsp,minorminer,penaltymodel,dwavebinarycsp}-*.tar.gz); do + dir_name=$(basename $source_file | sed 's/-[0-9].*//') + tar xvf $source_file -C $dir_name --strip-component 1 +done + +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +PYVER=$( python3 -c 'import sys; print( "%d.%d" % sys.version_info[:2] )' ) + +for source_file in $(ls $CWD/{dimod,dwave-{cloud-client,greedy,hybrid,inspector,neal,networkx,preprocessing,system,tabu},dwavebinarycsp,minorminer,penaltymodel,dwavebinarycsp}-*.tar.gz); do + dir_name=$(basename $source_file | sed 's/-[0-9].*//') + echo "Installing: $dir_name" + cd $dir_name + + # set path to installed package modules + PYTHONPATH=$PKG/usr/lib${LIBDIRSUFFIX}/python$PYVER/site-packages \ + python3 setup.py install --root=$PKG + + # install documentation + mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION/$dir_name + cp -avL docs $PKG/usr/doc/$PRGNAM-$VERSION/$dir_name + + # install examples if exists + if [ -d examples ]; then + mkdir -p $PKG/usr/share/$PRGNAM-$VERSION/$dir_name + cp -av examples $PKG/usr/share/$PRGNAM-$VERSION/$dir_name + fi + cd .. +done + +# install dwave-ocean-sdk +python3 setup.py install --root=$PKG + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + CONTRIBUTING.rst LICENSE README.rst \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/dwave-ocean-sdk/dwave-ocean-sdk.info b/academic/dwave-ocean-sdk/dwave-ocean-sdk.info new file mode 100644 index 0000000000..0a3328a777 --- /dev/null +++ b/academic/dwave-ocean-sdk/dwave-ocean-sdk.info @@ -0,0 +1,10 @@ +PRGNAM="dwave-ocean-sdk" +VERSION="6.0.0" +HOMEPAGE="https://www.dwavesys.com/solutions-and-products/ocean" +DOWNLOAD="https://github.com/dwavesystems/dwave-ocean-sdk/archive/6.0.0/dwave-ocean-sdk-6.0.0.tar.gz https://github.com/dwavesystems/dimod/archive/0.12.0/dimod-0.12.0.tar.gz https://github.com/dwavesystems/dwave-cloud-client/archive/0.10.3/dwave-cloud-client-0.10.3.tar.gz https://github.com/dwavesystems/dwave-greedy/archive/0.2.5/dwave-greedy-0.2.5.tar.gz https://github.com/dwavesystems/dwave-hybrid/archive/0.6.9/dwave-hybrid-0.6.9.tar.gz https://github.com/dwavesystems/dwave-inspector/archive/0.3.0/dwave-inspector-0.3.0.tar.gz https://github.com/dwavesystems/dwave-neal/archive/0.5.9/dwave-neal-0.5.9.tar.gz https://github.com/dwavesystems/dwave-networkx/archive/0.8.12/dwave-networkx-0.8.12.tar.gz https://github.com/dwavesystems/dwave-preprocessing/archive/0.5.0/dwave-preprocessing-0.5.0.tar.gz https://github.com/dwavesystems/dwave-system/archive/1.16.0/dwave-system-1.16.0.tar.gz https://github.com/dwavesystems/dwave-tabu/archive/0.4.5/dwave-tabu-0.4.5.tar.gz https://github.com/dwavesystems/dwavebinarycsp/archive/0.2.0/dwavebinarycsp-0.2.0.tar.gz https://github.com/dwavesystems/minorminer/archive/0.2.9/minorminer-0.2.9.tar.gz https://github.com/dwavesystems/penaltymodel/archive/1.0.2/penaltymodel-1.0.2.tar.gz" +MD5SUM="23c03fae1a25ca9246b46fdf01e36a88 20dfa5a1cb6f06b3f928c0538f8a021c 00a192d9aa86c07ed7b5a42a2011d78f 8805c6bfa59c9b33d1e00e713e62fb98 406d8439c122b7e6f1dd6b3427f5c954 db97afcfbf90e989859737954f2786cc f01bae63001966835a0677e8b9b07ea8 5bd9d71bc6ebd723d1b741debc4abcef 68de0e23a6c8023f30f056e5aae2cbfb 450b6fbdf0829ec7e2dddec4e9d0b23b 861fe9eb8b0771b97c6240e228ac5e50 59fe60257afe4725a50dc7cf4fb7b972 de59a2d16a94ee5853938cbf19d61a6f 26c6d33ac5a17620c4d6de76985cc552" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="python3-numpy" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/dwave-ocean-sdk/slack-desc b/academic/dwave-ocean-sdk/slack-desc new file mode 100644 index 0000000000..8aad645d3e --- /dev/null +++ b/academic/dwave-ocean-sdk/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +dwave-ocean-sdk: dwave-ocean-sdk (D-Wave Ocean SDK) +dwave-ocean-sdk: +dwave-ocean-sdk: +dwave-ocean-sdk: +dwave-ocean-sdk: Ocean is D-Wave's suite of tools for solving hard problems with +dwave-ocean-sdk: quantum computers. +dwave-ocean-sdk: +dwave-ocean-sdk: +dwave-ocean-sdk: +dwave-ocean-sdk: +dwave-ocean-sdk: diff --git a/academic/dwave-preprocessing/README b/academic/dwave-preprocessing/README new file mode 100644 index 0000000000..b0f9a0feab --- /dev/null +++ b/academic/dwave-preprocessing/README @@ -0,0 +1,2 @@ + dwave-preprocessing is a package of common preprocessing tools that +can aid in solving binary quadratic models (BQM). diff --git a/academic/dwave-preprocessing/dwave-preprocessing.SlackBuild b/academic/dwave-preprocessing/dwave-preprocessing.SlackBuild new file mode 100644 index 0000000000..4314c1f173 --- /dev/null +++ b/academic/dwave-preprocessing/dwave-preprocessing.SlackBuild @@ -0,0 +1,117 @@ +#!/bin/bash + +# Slackware build script for dwave-preprocessing + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM="dwave-preprocessing" +VERSION=${VERSION:-0.5.0} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +python3 setup.py install --root=$PKG + +# run tests +PYVER=$( python3 -c 'import sys; print( "%d.%d" % sys.version_info[:2] )' ) +cd tests + for file in $(ls test_*.py); do + echo -n "$file " + PYTHONPATH=../build/lib.linux-$(uname -m)-$PYVER python3 $file + if [ "$?" -eq "0" ]; then + echo "OK" + else + echo "\n$file - fail" + fi + done +cd .. + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + LICENSE README.rst docs \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/dwave-preprocessing/dwave-preprocessing.info b/academic/dwave-preprocessing/dwave-preprocessing.info new file mode 100644 index 0000000000..6b4a6f3e81 --- /dev/null +++ b/academic/dwave-preprocessing/dwave-preprocessing.info @@ -0,0 +1,10 @@ +PRGNAM="dwave-preprocessing" +VERSION="0.5.0" +HOMEPAGE="https://www.dwavesys.com" +DOWNLOAD="https://github.com/dwavesystems/dwave-preprocessing/archive/0.5.0/dwave-preprocessing-0.5.0.tar.gz" +MD5SUM="68de0e23a6c8023f30f056e5aae2cbfb" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="dimod" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/dwave-preprocessing/slack-desc b/academic/dwave-preprocessing/slack-desc new file mode 100644 index 0000000000..fbf08c0c18 --- /dev/null +++ b/academic/dwave-preprocessing/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +dwave-preprocessing: dwave-preprocessing (preprocessing tools for binary quadratic models) +dwave-preprocessing: +dwave-preprocessing: +dwave-preprocessing: dwave-preprocessing is a package of common preprocessing tools +dwave-preprocessing: that can aid in solving binary quadratic models (BQM). +dwave-preprocessing: +dwave-preprocessing: +dwave-preprocessing: +dwave-preprocessing: +dwave-preprocessing: +dwave-preprocessing: diff --git a/academic/dwave-system/README b/academic/dwave-system/README new file mode 100644 index 0000000000..4ff6726c99 --- /dev/null +++ b/academic/dwave-system/README @@ -0,0 +1,9 @@ + dwave-system is a basic API for easily incorporating the D-Wave +system as a sampler in the D-Wave Ocean software stack, directly +or through Leap's cloud-based hybrid solvers. It includes +DWaveSampler, a dimod sampler that accepts and passes system +parameters such as system identification and authentication down +the stack, LeapHybridSampler, for Leap's hybrid solvers, and other. +It also includes several useful composites---layers of pre- and +post-processing---that can be used with DWaveSampler to handle +minor-embedding, optimize chain strength, etc. diff --git a/academic/dwave-system/dwave-system.SlackBuild b/academic/dwave-system/dwave-system.SlackBuild new file mode 100644 index 0000000000..c2f1f2e2c0 --- /dev/null +++ b/academic/dwave-system/dwave-system.SlackBuild @@ -0,0 +1,103 @@ +#!/bin/bash + +# Slackware build script for dwave-system + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM="dwave-system" +VERSION=${VERSION:-1.16.0} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +python3 setup.py install --root=$PKG + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + LICENSE README.rst docs \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/dwave-system/dwave-system.info b/academic/dwave-system/dwave-system.info new file mode 100644 index 0000000000..260dccfdf2 --- /dev/null +++ b/academic/dwave-system/dwave-system.info @@ -0,0 +1,10 @@ +PRGNAM="dwave-system" +VERSION="1.16.0" +HOMEPAGE="https://www.dwavesys.com" +DOWNLOAD="https://github.com/dwavesystems/dwave-system/archive/1.16.0/dwave-system-1.16.0.tar.gz" +MD5SUM="450b6fbdf0829ec7e2dddec4e9d0b23b" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/dwave-system/slack-desc b/academic/dwave-system/slack-desc new file mode 100644 index 0000000000..60573eac9d --- /dev/null +++ b/academic/dwave-system/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +dwave-system: dwave-system (basic API for D-Wave system) +dwave-system: +dwave-system: dwave-system is a basic API for easily incorporating the D-Wave +dwave-system: system as a sampler in the D-Wave Ocean software stack, directly or +dwave-system: through Leap's cloud-based hybrid solvers. It includes DWaveSampler, +dwave-system: a dimod sampler that accepts and passes system parameters such as +dwave-system: system identification and authentication down the stack, +dwave-system: LeapHybridSampler, for Leap's hybrid solvers, and other. It also +dwave-system: includes several useful composites---layers of pre- and +dwave-system: post-processing---that can be used with DWaveSampler to handle +dwave-system: minor-embedding, optimize chain strength, etc. diff --git a/academic/dwave-tabu/README b/academic/dwave-tabu/README new file mode 100644 index 0000000000..0a82867af8 --- /dev/null +++ b/academic/dwave-tabu/README @@ -0,0 +1,7 @@ + A C/C++ implementation of the MST2 multistart tabu search algorithm +for quadratic unconstrained binary optimization (QUBO) problems with +a dimod sampler Python interface. + + + For running tests set the environment variable TESTS=yes, this +requires dimod. diff --git a/academic/dwave-tabu/dwave-tabu.SlackBuild b/academic/dwave-tabu/dwave-tabu.SlackBuild new file mode 100644 index 0000000000..fe9ce1a14b --- /dev/null +++ b/academic/dwave-tabu/dwave-tabu.SlackBuild @@ -0,0 +1,118 @@ +#!/bin/bash + +# Slackware build script for dwave-tabu + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM="dwave-tabu" +VERSION=${VERSION:-0.4.5} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +python3 setup.py install --root=$PKG + +if [ "${TESTS:-no}" == "yes" ]; then + PYVER=$( python3 -c 'import sys; print( "%d.%d" % sys.version_info[:2] )' ) + cd tests + for file in $(ls test_*.py); do + echo -n "$file " + PYTHONPATH=../build/lib.linux-$(uname -m)-$PYVER python3 $file + if [ "$?" -eq "0" ]; then + echo "OK" + else + echo "\n$file - fail" + fi + done + cd .. +fi + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + LICENSE README.rst docs \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/dwave-tabu/dwave-tabu.info b/academic/dwave-tabu/dwave-tabu.info new file mode 100644 index 0000000000..ffc2d1fb68 --- /dev/null +++ b/academic/dwave-tabu/dwave-tabu.info @@ -0,0 +1,10 @@ +PRGNAM="dwave-tabu" +VERSION="0.4.5" +HOMEPAGE="https://github.com/dwavesystems/dwave-tabu" +DOWNLOAD="https://github.com/dwavesystems/dwave-tabu/archive/0.4.5/dwave-tabu-0.4.5.tar.gz" +MD5SUM="861fe9eb8b0771b97c6240e228ac5e50" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="python3-numpy" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/dwave-tabu/slack-desc b/academic/dwave-tabu/slack-desc new file mode 100644 index 0000000000..cfea47c422 --- /dev/null +++ b/academic/dwave-tabu/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +dwave-tabu: dwave-tabu (C/C++ implementation of MST2 for QUBO) +dwave-tabu: +dwave-tabu: +dwave-tabu: +dwave-tabu: A C/C++ implementation of the MST2 multistart tabu search algorithm +dwave-tabu: for quadratic unconstrained binary optimization (QUBO) problems with +dwave-tabu: a dimod sampler Python interface. +dwave-tabu: +dwave-tabu: +dwave-tabu: +dwave-tabu: diff --git a/academic/dwavebinarycsp/README b/academic/dwavebinarycsp/README new file mode 100644 index 0000000000..9f177497e7 --- /dev/null +++ b/academic/dwavebinarycsp/README @@ -0,0 +1,7 @@ + Library to construct a binary quadratic model from a constraint +satisfaction problem with small constraints over binary variables. + + + If you want to run the tests set the environment variable TESTS=yes +this requires: blas, lapack, dimod, homebase, networkx, numpy3, +penaltymodel and scipy3. diff --git a/academic/dwavebinarycsp/dwavebinarycsp.SlackBuild b/academic/dwavebinarycsp/dwavebinarycsp.SlackBuild new file mode 100644 index 0000000000..d5951f4fbc --- /dev/null +++ b/academic/dwavebinarycsp/dwavebinarycsp.SlackBuild @@ -0,0 +1,118 @@ +#!/bin/bash + +# Slackware build script for dwavebinarycsp + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM="dwavebinarycsp" +VERSION=${VERSION:-0.2.0} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +python3 setup.py install --root=$PKG + +if [ "${TESTS:-no}" == "yes" ]; then + PYVER=$( python3 -c 'import sys; print( "%d.%d" % sys.version_info[:2] )' ) + cd tests + for file in $(ls test_*.py); do + echo -n "$file " + PYTHONPATH=../build/lib python3 $file + if [ "$?" -eq "0" ]; then + echo "OK" + else + echo "\n$file - fail" + fi + done + cd .. +fi + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + LICENSE README.rst docs \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/dwavebinarycsp/dwavebinarycsp.info b/academic/dwavebinarycsp/dwavebinarycsp.info new file mode 100644 index 0000000000..084a44c3e7 --- /dev/null +++ b/academic/dwavebinarycsp/dwavebinarycsp.info @@ -0,0 +1,10 @@ +PRGNAM="dwavebinarycsp" +VERSION="0.2.0" +HOMEPAGE="https://github.com/dwavesystems" +DOWNLOAD="https://github.com/dwavesystems/dwavebinarycsp/archive/0.2.0/dwavebinarycsp-0.2.0.tar.gz" +MD5SUM="59fe60257afe4725a50dc7cf4fb7b972" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/dwavebinarycsp/slack-desc b/academic/dwavebinarycsp/slack-desc new file mode 100644 index 0000000000..d288947374 --- /dev/null +++ b/academic/dwavebinarycsp/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +dwavebinarycsp: dwavebinarycsp (Library for contructing binary quadratic models) +dwavebinarycsp: +dwavebinarycsp: +dwavebinarycsp: +dwavebinarycsp: Library to construct a binary quadratic model from a constraint +dwavebinarycsp: satisfaction problem with small constraints over binary variables. +dwavebinarycsp: +dwavebinarycsp: +dwavebinarycsp: +dwavebinarycsp: +dwavebinarycsp: diff --git a/academic/easy_spice/easy_spice.SlackBuild b/academic/easy_spice/easy_spice.SlackBuild index fed5192d96..3dc14450cc 100644 --- a/academic/easy_spice/easy_spice.SlackBuild +++ b/academic/easy_spice/easy_spice.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for easy_spice @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=easy_spice VERSION=${VERSION:-0.6.8} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -118,4 +128,4 @@ cat $CWD/doinst.sh > $PKG/install/doinst.sh cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/ed-v6/README b/academic/ed-v6/README index 373767752c..f116d5fc40 100644 --- a/academic/ed-v6/README +++ b/academic/ed-v6/README @@ -71,7 +71,7 @@ info page. This is the closest I can find to the original man page: -https://www.freebsd.org/cgi/man.cgi?query=ed&apropos=0&sektion=0&manpath=Unix%20Seventh%20Edition&arch=default&format=html +https://freebsd.org/cgi/man.cgi?query=ed&manpath=Unix+Seventh+Edition Among other things, there is no -p option, single , or ; will throw errors, no G//, and r does not support shell diff --git a/academic/ed-v6/ed-v6.SlackBuild b/academic/ed-v6/ed-v6.SlackBuild index e2da7582a0..ab0b073b0e 100644 --- a/academic/ed-v6/ed-v6.SlackBuild +++ b/academic/ed-v6/ed-v6.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for ed-v6 # Copyright 2019 Dave Woodfall <dave@slackbuilds.org> @@ -21,11 +21,14 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=ed-v6 VERSION=${VERSION:-c72c0e} SRCVERSION=${SRCVERSION:-c72c0e9445af26bd9fde2d39da5628e6dabf36dd} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -60,7 +70,7 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $PRGNAM-$SRCVERSION -tar xvf $CWD/$SRCVERSION.tar.gz +tar xvf $CWD/$PRGNAM-$SRCVERSION.tar.gz cd $PRGNAM-$SRCVERSION chown -R root:root . find -L . \ @@ -87,4 +97,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/ed-v6/ed-v6.info b/academic/ed-v6/ed-v6.info index 35e5735a5a..c7d239ec09 100644 --- a/academic/ed-v6/ed-v6.info +++ b/academic/ed-v6/ed-v6.info @@ -1,10 +1,10 @@ PRGNAM="ed-v6" VERSION="c72c0e" HOMEPAGE="https://github.com/geocar/ed-v6" -DOWNLOAD="https://github.com/geocar/ed-v6/archive/c72c0e9/c72c0e9445af26bd9fde2d39da5628e6dabf36dd.tar.gz" +DOWNLOAD="https://github.com/geocar/ed-v6/archive/c72c0e9/ed-v6-c72c0e9445af26bd9fde2d39da5628e6dabf36dd.tar.gz" MD5SUM="797a81796fdaf0b35bbce721d08d7bd7" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" -MAINTAINER="Dave Woodfall" +MAINTAINER="D Woodfall" EMAIL="dave@slackbuilds.org" diff --git a/academic/edsim51di/edsim51di.SlackBuild b/academic/edsim51di/edsim51di.SlackBuild index 4f85b23a99..22dc9adb1e 100644 --- a/academic/edsim51di/edsim51di.SlackBuild +++ b/academic/edsim51di/edsim51di.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for EdSim51Di @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=edsim51di VERSION=${VERSION:-2.1.20} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,8 +38,15 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) STARTDIR=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -108,4 +118,4 @@ EOF chmod +x $PKG/usr/bin/edsim51di cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/edsim51di/edsim51di.info b/academic/edsim51di/edsim51di.info index ff9f94cec3..03325ce1ce 100644 --- a/academic/edsim51di/edsim51di.info +++ b/academic/edsim51di/edsim51di.info @@ -1,10 +1,10 @@ PRGNAM="edsim51di" VERSION="2.1.20" -HOMEPAGE="http://www.edsim51.com/" -DOWNLOAD="http://www.edsim51.com/8051simulator/edsim51di.zip" -MD5SUM="b97b326e8d74a2f5ade7f30e617d8ce8" +HOMEPAGE="https://www.edsim51.com/" +DOWNLOAD="https://www.edsim51.com/8051simulator/edsim51di.zip" +MD5SUM="b72c84a29560237e310b3eacfd61e9b7" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="openjdk7" +REQUIRES="zulu-openjdk11" MAINTAINER="R. S. Ananda Murthy" EMAIL="rsamurti@gmail.com" diff --git a/academic/elk/README b/academic/elk/README new file mode 100644 index 0000000000..2acde1734e --- /dev/null +++ b/academic/elk/README @@ -0,0 +1,20 @@ +An all-electron full-potential linearised augmented-plane wave +(LAPW) code with many advanced features. Written originally at +Karl-Franzens-Universitat Graz as a milestone of the EXCITING EU +Research and Training Network, the code is designed to be as simple +as possible so that new developments in the field of density +functional theory (DFT) can be added quickly and reliably. The code +is freely available under the GNU General Public License. + + + The code is made to use OpenMP and only build with -fopenmp flag, +although the default building doesn't use additional optimization +flags to OpenMP. + However there is some building options available, that can be set +using the environment variables as following: + If you want to enable more optimizations to OpenMP set OMP_OPT=yes + You can also enable MPI, set MPI=yes and install openmpi or mpich. + It's also possible to use OMP_OPT=yes and MPI=yes together. + + Optional dependence: libxc + To use libxc set LIBXC=yes, this requires libxc diff --git a/academic/elk/elk.SlackBuild b/academic/elk/elk.SlackBuild new file mode 100644 index 0000000000..fdcc077a89 --- /dev/null +++ b/academic/elk/elk.SlackBuild @@ -0,0 +1,154 @@ +#!/bin/bash + +# Slackware build script for elk + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=elk +VERSION=${VERSION:-8.5.10} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tgz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +# set default compiler flags to all modes +# NOTE: doesn't compile without openmp +FORTRAN_COMPILER="gfortran" +BUILD_FLAGS="-Wall -std=legacy -fopenmp" + +if [ "${OMP_OPT:-no}" == "yes" ]; then + BUILD_FLAGS="$BUILD_FLAGS -ffast-math -funroll-loops -fopenmp" +fi + +if [ "${MPI:-no}" == "yes" ]; then + FORTRAN_COMPILER="mpif90" +fi + +# configure building +echo > make.inc +echo "MAKE = make" >> make.inc +echo "F90 = $FORTRAN_COMPILER" >> make.inc +echo "F90_OPTS = -O2 $BUILD_FLAGS" >> make.inc +echo "F77 = $FORTRAN_COMPILER" >> make.inc +echo "F77_OPTS = -O2 $BUILD_FLAGS" >> make.inc +echo "AR = ar" >> make.inc +echo "LIB_LPK = lapack.a blas.a" >> make.inc +echo "LIB_FFT = fftlib.a" >> make.inc +cat make.def >> make.inc + +if [ "${LIBXC:-no}" == "yes" ]; then + sed -i '47aLIB_libxc = /usr/lib'${LIBDIRSUFFIX}'/libxc.so' make.inc + sed -i 's/^#SRC_libxc/SRC_libxc/' make.inc +fi + +# fix eos and spacegroup makefile "cannot open module file modmain.mod" +sed -i '20s/$(OBJ)/$(SRC)/' src/eos/Makefile +sed -i '20a\\t$(F90) $(F90_OPTS) -c $(SRC)' src/eos/Makefile +sed -i '28s/$(OBJ)/$(SRC)/' src/spacegroup/Makefile +sed -i '28a\\t$(F90) $(F90_OPTS) -c $(SRC)' src/spacegroup/Makefile + +make all + +# not rule to install, so perform it manually +install -d $PKG/usr/bin +install -m 755 src/elk $PKG/usr/bin + +install -d $PKG/usr/libexec/$PRGNAM +install -m 755 src/{grepelk,protex,rmspaces,vimelk} $PKG/usr/libexec/$PRGNAM +install -m 755 src/eos/eos $PKG/usr/libexec/$PRGNAM +install -m 755 src/spacegroup/spacegroup $PKG/usr/libexec/$PRGNAM + +# install examples and some tools +mkdir -p $PKG/usr/share/$PRGNAM-$VERSION +cp -a examples species utilities $PKG/usr/share/$PRGNAM-$VERSION + +# update examples to search expecies at system installation path +for file in $(grep -lr "" $PKG/usr/share/$PRGNAM-$VERSION/examples); do + sed -i 's#\(../../..\)\(/species\)#/usr/share/'$PRGNAM-$VERSION'\2#' $file +done + + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + COPYING docs \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/elk/elk.info b/academic/elk/elk.info new file mode 100644 index 0000000000..5e2bbbb368 --- /dev/null +++ b/academic/elk/elk.info @@ -0,0 +1,10 @@ +PRGNAM="elk" +VERSION="8.5.10" +HOMEPAGE="https://elk.sourceforge.io" +DOWNLOAD="https://sourceforge.net/projects/elk/files/elk-8.5.10.tgz" +MD5SUM="31666536723d352b07c9df3af4b9ac12" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/elk/slack-desc b/academic/elk/slack-desc new file mode 100644 index 0000000000..341d56c177 --- /dev/null +++ b/academic/elk/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +elk: elk (linearized augmented-plane-wave (LAPW) software) +elk: +elk: An all-electron full-potential linearised augmented-plane wave +elk: (LAPW) code with many advanced features. Written originally at +elk: Karl-Franzens-Universitat Graz as a milestone of the EXCITING EU +elk: Research and Training Network, the code is designed to be as simple +elk: as possible so that new developments in the field of density +elk: functional theory (DFT) can be added quickly and reliably. The code +elk: is freely available under the GNU General Public License. +elk: +elk: diff --git a/academic/engauge/README b/academic/engauge/README index 8e946775e7..a1c9e75bbf 100644 --- a/academic/engauge/README +++ b/academic/engauge/README @@ -1,7 +1,8 @@ -Engauge digitizing software converts an image file showing a graph or map, -into numbers. The image file can come from a scanner, digital camera or -screenshot. The numbers can be read on the screen, and written or copied -to a spreadsheet. Engauge Digitizer compensates for rotation, scaling -and skew (also known as shearing) in graphs. Engauge recognizes BMP, CUR, -DDS, GIF, ICNS, ICO, JP2, JPG, MNG, PBM, PDF, PGM, PNG, PPM, SVG, SVGZ, -TGA, TIFF, WBMP, WEBP, XBM and XPM image files. +Engauge digitizing software converts an image file showing a graph or +map, into numbers. The image file can come from a scanner, digital +camera or screenshot. The numbers can be read on the screen, and +written or copied to a spreadsheet. Engauge Digitizer compensates for +rotation, scaling and skew (also known as shearing) in graphs. Engauge +recognizes BMP, CUR, DDS, GIF, ICNS, ICO, JP2, JPG, MNG, PBM, PDF, +PGM, PNG, PPM, SVG, SVGZ, TGA, TIFF, WBMP, WEBP, XBM and XPM image +files. diff --git a/academic/engauge/engauge.SlackBuild b/academic/engauge/engauge.SlackBuild index 59cf65ae74..2840fef1ae 100644 --- a/academic/engauge/engauge.SlackBuild +++ b/academic/engauge/engauge.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for engauge # written by <pedro@gepasi.org> @@ -21,10 +21,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=engauge -VERSION=${VERSION:-10.10} +VERSION=${VERSION:-12.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -34,7 +37,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -71,7 +81,7 @@ find -L . \ POPPLER_INCLUDE=/usr/include/poppler/qt5 \ POPPLER_LIB=/usr/lib${LIBDIRSUFFIX} \ -OPENJPEG_INCLUDE=/usr/include/openjpeg-2.3 \ +OPENJPEG_INCLUDE=/usr/include/openjpeg-2.4 \ OPENJPEG_LIB=/usr/lib${LIBDIRSUFFIX} \ qmake-qt5 \ QMAKE_CFLAGS+="$SLKCFLAGS" \ @@ -114,4 +124,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/engauge/engauge.info b/academic/engauge/engauge.info index ec1d664a96..baec06a791 100644 --- a/academic/engauge/engauge.info +++ b/academic/engauge/engauge.info @@ -1,10 +1,10 @@ PRGNAM="engauge" -VERSION="10.10" +VERSION="12.1" HOMEPAGE="http://markummitchell.github.io/engauge-digitizer/" -DOWNLOAD="https://github.com/markummitchell/engauge-digitizer/archive/v10.10/engauge-digitizer-10.10.tar.gz" -MD5SUM="fe00faf453ff25f355fc46f81280d69a" +DOWNLOAD="https://github.com/markummitchell/engauge-digitizer/archive/v12.1/engauge-digitizer-12.1.tar.gz" +MD5SUM="842ec1769723018845b0a1acb3f1484c" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="log4cpp poppler-qt5" +REQUIRES="log4cpp" MAINTAINER="Pedro Mendes" EMAIL="pedro@gepasi.org" diff --git a/academic/ent/ent.SlackBuild b/academic/ent/ent.SlackBuild index df134133cf..90786516a8 100644 --- a/academic/ent/ent.SlackBuild +++ b/academic/ent/ent.SlackBuild @@ -1,15 +1,18 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for ent -# Written by B. Watson (yalhcru@gmail.com) +# Written by B. Watson (urchlay@slackware.uk) # Licensed under the WTFPL. See http://www.wtfpl.net/txt/copying/ for details. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=ent VERSION=${VERSION:-20080128} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} ARCHIVE=random.zip @@ -21,23 +24,23 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} if [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" - LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" - LIBDIRSUFFIX="" elif [ "$ARCH" = "x86_64" ]; then SLKCFLAGS="-O2 -fPIC" - LIBDIRSUFFIX="64" else SLKCFLAGS="-O2" - LIBDIRSUFFIX="" fi set -e @@ -50,11 +53,8 @@ mkdir -p $PRGNAM cd $PRGNAM unzip $CWD/$ARCHIVE chown -R root:root . -find -L . \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; +find -L . -perm /111 -a \! -perm 755 -a -exec chmod 755 {} \+ -o \ + \! -perm /111 -a \! -perm 644 -a -exec chmod 644 {} \+ make CC=gcc CFLAGS="$SLKCFLAGS" strip $PRGNAM @@ -74,4 +74,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/ent/ent.info b/academic/ent/ent.info index 6e12c713a0..fc59242126 100644 --- a/academic/ent/ent.info +++ b/academic/ent/ent.info @@ -1,10 +1,10 @@ PRGNAM="ent" VERSION="20080128" -HOMEPAGE="http://www.fourmilab.ch/random/" -DOWNLOAD="http://www.fourmilab.ch/random/random.zip" +HOMEPAGE="https://www.fourmilab.ch/random/" +DOWNLOAD="https://www.fourmilab.ch/random/random.zip" MD5SUM="8104a83af1ea5b280da96c92da18eae4" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" MAINTAINER="B. Watson" -EMAIL="yalhcru@gmail.com" +EMAIL="urchlay@slackware.uk" diff --git a/academic/ephem/README b/academic/ephem/README new file mode 100644 index 0000000000..3a9ea4f24c --- /dev/null +++ b/academic/ephem/README @@ -0,0 +1,7 @@ +Ephem is a program that displays ephemerides for all the planets plus +any two additional objects. The additional objects may be fixed or +specified via heliocentric elliptical, hyperbolic or parabolic orbital +elements to accommodate solar system objects such as asteroids or +comets. + +The user manual can be found at /usr/share/doc/ephem-4.32/Man.txt. diff --git a/academic/ephem/ephem.SlackBuild b/academic/ephem/ephem.SlackBuild new file mode 100644 index 0000000000..207f8a9ec3 --- /dev/null +++ b/academic/ephem/ephem.SlackBuild @@ -0,0 +1,103 @@ +#!/bin/bash + +# Slackware build script for ephem + +# Copyright 2023 Dario Nicodemi Italy +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=ephem +VERSION=${VERSION:-4.32} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +elif [ "$ARCH" = "aarch64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +make CFLAGS="$SLKCFLAGS -DANSI_COLORS -DGLOBE_PHOON -fcommon" +mkdir -p $PKG/usr/bin +cp $PRGNAM $PKG/usr/bin + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + Man.txt \ + README \ + ephem.cfg \ + ephem.db \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/ephem/ephem.info b/academic/ephem/ephem.info new file mode 100644 index 0000000000..88a3337d51 --- /dev/null +++ b/academic/ephem/ephem.info @@ -0,0 +1,10 @@ +PRGNAM="ephem" +VERSION="4.32" +HOMEPAGE="http://www.clearskyinstitute.com/ephem/" +DOWNLOAD="http://www.clearskyinstitute.com/ephem/ephem-4.32.tar.gz" +MD5SUM="953e5f97c610140b29d729c44aecd6b8" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Dario Nicodemi" +EMAIL="dario.sbo@gmail.com" diff --git a/academic/ephem/slack-desc b/academic/ephem/slack-desc new file mode 100644 index 0000000000..48c0038ad2 --- /dev/null +++ b/academic/ephem/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +ephem: ephem (ephemeris program for 24x80 character display) +ephem: +ephem: Ephem is a program that displays ephemerides for all the planets plus +ephem: any two additional objects. The additional objects may be fixed or +ephem: specified via heliocentric elliptical, hyperbolic or parabolic +ephem: orbital elements accommodate solar system objects such as asteroids +ephem: or comets. +ephem: +ephem: +ephem: +ephem: diff --git a/academic/eprover/eprover.SlackBuild b/academic/eprover/eprover.SlackBuild index af3094b78b..f70a215559 100644 --- a/academic/eprover/eprover.SlackBuild +++ b/academic/eprover/eprover.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for eprover -# Copyright 2019 Nick Smallbone, Gothenburg, Sweden +# Copyright 2019-2020 Nick Smallbone, Gothenburg, Sweden # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=eprover -VERSION=${VERSION:-2.4} +VERSION=${VERSION:-2.5} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -90,7 +100,7 @@ for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; r mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - README.md COPYING DOC/CONTRIBUTORS DOC/eprover.pdf DOC/NEWS \ + README COPYING DOC/CONTRIBUTORS DOC/eprover.pdf DOC/NEWS \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild @@ -98,4 +108,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/eprover/eprover.info b/academic/eprover/eprover.info index 542d9c982e..9371d82d3e 100644 --- a/academic/eprover/eprover.info +++ b/academic/eprover/eprover.info @@ -1,8 +1,8 @@ PRGNAM="eprover" -VERSION="2.4" +VERSION="2.5" HOMEPAGE="http://www.eprover.org" -DOWNLOAD="http://wwwlehre.dhbw-stuttgart.de/~sschulz/WORK/E_DOWNLOAD/V_2.4/E.tgz" -MD5SUM="a303126a27deaedb0ce1bb884ab9ab97" +DOWNLOAD="http://wwwlehre.dhbw-stuttgart.de/~sschulz/WORK/E_DOWNLOAD/V_2.5/E.tgz" +MD5SUM="f73852315dde1071acfa552b9532c7ab" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/equalx/equalx.SlackBuild b/academic/equalx/equalx.SlackBuild index 900e97e5e6..21a6bc3c6b 100644 --- a/academic/equalx/equalx.SlackBuild +++ b/academic/equalx/equalx.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for equalx @@ -23,7 +23,9 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -# Now maintained by B. Watson <yalhcru@gmail.com> +# Now maintained by B. Watson <urchlay@slackware.uk> + +# 20210802 bkw: BUILD=3, update for qt5 on -current. # 20200101 bkw: # - take over maintenance @@ -34,10 +36,13 @@ # - use a .desktop file that validates # - minor cleanups/etc in script, slack-desc, README +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=equalx VERSION=${VERSION:-0.7.1} -BUILD=${BUILD:-2} +BUILD=${BUILD:-3} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -47,7 +52,11 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -78,13 +87,18 @@ chown -R root:root . find -L . -perm /111 -a \! -perm 755 -a -exec chmod 755 {} \+ -o \ \! -perm /111 -a \! -perm 644 -a -exec chmod 644 {} \+ +# Note: patches are gzipped because they have a mix of \n and \r\n +# line endings. git can have issues with that. + # Make sure the application can find the external binaries it runs, # without defaulting to silly things like .exe files. The patch actually # makes it look for pdflatex in both places it might be found (/usr/bin # for texlive, /usr/share/texmf/bin for tetex). zcat $CWD/externpaths.diff.gz | patch -p1 -CFLAGS="$SLKCFLAGS" CXXFLAGS="$SLKCFLAGS" qmake +zcat $CWD/qt5fix.diff.gz | patch -p1 + +CFLAGS="$SLKCFLAGS" CXXFLAGS="$SLKCFLAGS" qmake-qt5 sed -i "s,-O2,$SLKCFLAGS," Makefile make @@ -111,5 +125,5 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/equalx/equalx.info b/academic/equalx/equalx.info index c99a016018..5b43393881 100644 --- a/academic/equalx/equalx.info +++ b/academic/equalx/equalx.info @@ -7,4 +7,4 @@ DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="exempi" MAINTAINER="B. Watson" -EMAIL="yalhcru@gmail.com" +EMAIL="urchlay@slackware.uk" diff --git a/academic/equalx/qt5fix.diff.gz b/academic/equalx/qt5fix.diff.gz Binary files differnew file mode 100644 index 0000000000..cae6023bfd --- /dev/null +++ b/academic/equalx/qt5fix.diff.gz diff --git a/academic/ess/README b/academic/ess/README index 75a031fca0..79cd22990b 100644 --- a/academic/ess/README +++ b/academic/ess/README @@ -1,4 +1,4 @@ -Emacs Speaks Statistics is an add-on package for emacs-based text editors -such as GNU Emacs and XEmacs. It is designed to support editing of scripts -and interaction with various statistical analysis programs such S-Plus, R, -SAS, Stata, and others. +Emacs Speaks Statistics is an add-on package for emacs-based text +editors such as GNU Emacs and XEmacs. It is designed to support +editing of scripts and interaction with various statistical analysis +programs such S-Plus, R, SAS, Stata, and others. diff --git a/academic/ess/ess.SlackBuild b/academic/ess/ess.SlackBuild index 30cf886824..55192e86a6 100644 --- a/academic/ess/ess.SlackBuild +++ b/academic/ess/ess.SlackBuild @@ -1,18 +1,28 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for ESS (Emacs Speaks Statistics) # Written by Joel J. Adamson <adamsonj@email.unc.edu> # Maintained by Nicky Chorley <nick.chorley@gmail.com> +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=ess VERSION=${VERSION:-17.11} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} ARCH=noarch -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -48,4 +58,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/evopedia_qt/evopedia_qt.SlackBuild b/academic/evopedia_qt/evopedia_qt.SlackBuild index 783878ba4a..b146f57090 100644 --- a/academic/evopedia_qt/evopedia_qt.SlackBuild +++ b/academic/evopedia_qt/evopedia_qt.SlackBuild @@ -1,23 +1,33 @@ -#!/bin/sh +#!/bin/bash # # Slackware build script for evopedia # # Written by Dan-Simon Myrland <dansimon@radiotube.org> +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=evopedia_qt VERSION=${VERSION:-0.4.4} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -37,6 +47,7 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; +. /etc/profile.d/qt4.sh # uncomment NO_GUI option for a gui less installation qmake PREFIX=$PKG/usr #DEFINES+=NO_GUI make @@ -52,4 +63,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/evopedia_qt/evopedia_qt.info b/academic/evopedia_qt/evopedia_qt.info index a918ec4dd3..8f212fa1c6 100644 --- a/academic/evopedia_qt/evopedia_qt.info +++ b/academic/evopedia_qt/evopedia_qt.info @@ -5,6 +5,6 @@ DOWNLOAD="https://github.com/evopedia/evopedia_qt/archive/v0.4.4/evopedia_qt-0.4 MD5SUM="3418c22e5d69baa06fe0de7de7c57110" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="" +REQUIRES="qt4" MAINTAINER="Dan-Simon Myrland" EMAIL="dansimon@radiotube.org" diff --git a/academic/exonerate/exonerate.SlackBuild b/academic/exonerate/exonerate.SlackBuild index 6fef2cf6de..03c9ba763d 100644 --- a/academic/exonerate/exonerate.SlackBuild +++ b/academic/exonerate/exonerate.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for exonerate -# Copyright 2017 Petar petrov slackalaxy@gmail.com +# Copyright 2017-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=exonerate VERSION=${VERSION:-2.4.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -80,7 +90,7 @@ CXXFLAGS="$SLKCFLAGS" \ --docdir=/usr/doc/$PRGNAM-$VERSION \ --build=$ARCH-slackware-linux -make +make -j1 make install DESTDIR=$PKG find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ @@ -97,4 +107,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/extrema/extrema.SlackBuild b/academic/extrema/extrema.SlackBuild index d13f7d00a4..66760b5c5d 100644 --- a/academic/extrema/extrema.SlackBuild +++ b/academic/extrema/extrema.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for extrema @@ -25,10 +25,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=extrema VERSION=${VERSION:-4.4.5} -BUILD=${BUILD:-2} +BUILD=${BUILD:-3} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -38,7 +41,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -110,9 +120,11 @@ cp -a doc/* AUTHORS COPYING ChangeLog INSTALL NEWS README THANKS \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/fann/README b/academic/fann/README index 8fd6161fd4..936d077cc7 100644 --- a/academic/fann/README +++ b/academic/fann/README @@ -1,7 +1,8 @@ -Fast Artificial Neural Network Library is a free open source neural network -library, which implements multilayer artificial neural networks in C with -support for both fully connected and sparsely connected networks. -Cross-platform execution in both fixed and floating point are supported. It -includes a framework for easy handling of training data sets. It is easy to -use, versatile, well documented, and fast. Bindings to more than 15 programming -languages are available. +Fast Artificial Neural Network Library is a free open source neural +network library, which implements multilayer artificial neural +networks in C with support for both fully connected and sparsely +connected networks. Cross-platform execution in both fixed and +floating point are supported. It includes a framework for easy +handling of training data sets. It is easy to use, versatile, well +documented, and fast. Bindings to more than 15 programming languages +are available. diff --git a/academic/fann/fann.SlackBuild b/academic/fann/fann.SlackBuild index cd11930822..d57e66a8e0 100644 --- a/academic/fann/fann.SlackBuild +++ b/academic/fann/fann.SlackBuild @@ -1,31 +1,41 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for fann # Written by Andrew Conway (ajc AT countingthoughts DOT com) +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=fann VERSION=${VERSION:-2.2.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} SRCNAME=FANN-$VERSION-Source if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -84,4 +94,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/fastqc/doinst.sh b/academic/fastqc/doinst.sh index d9483a16ab..5fb28930db 100644 --- a/academic/fastqc/doinst.sh +++ b/academic/fastqc/doinst.sh @@ -1,8 +1,3 @@ if [ -x /usr/bin/update-desktop-database ]; then /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 fi - -( cd usr/bin ; rm -rf fastqc ) -( cd usr/bin ; ln -sf ../share/java/fastqc/fastqc fastqc ) -( cd usr/doc/fastqc-0.11.8 ; rm -rf Help ) -( cd usr/doc/fastqc-0.11.8 ; ln -sf ../../share/java/fastqc/Help Help ) diff --git a/academic/fastqc/fastqc.SlackBuild b/academic/fastqc/fastqc.SlackBuild index d0add9f9cd..c8127dac3f 100644 --- a/academic/fastqc/fastqc.SlackBuild +++ b/academic/fastqc/fastqc.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for fastqc -# Copyright 2015-2018 Petar Petrov slackalaxy@gmail.com; 2018-2020 Rob van Nues sborg63.org +# Copyright 2015-2018 Petar Petrov slackalaxy@gmail.com; 2018-2023 Rob van Nues sborg63.org # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,22 +22,32 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=fastqc SRCNAM=FastQC -VERSION=${VERSION:-0.11.9} -SRCVER=${SRCVER:-v0.11.9} +VERSION=${VERSION:-0.12.1} +SRCVER=${SRCVER:-v0.12.1} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} ARCH=noarch # Jar files names and versions JBZIP=jbzip2-0.9.jar -SAM=sam-1.103.jar +HTS=htsjdk.jar CISD=cisd-jhdf5.jar -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -57,8 +67,11 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; +# remove .svn folders causing java errors e.g. when using help +find -d -name .svn -exec rm -r '{}' ';' + install -D -m755 $PRGNAM $PKG/usr/share/java/$PRGNAM/$PRGNAM -cp -a Configuration net org Templates Help uk $JBZIP $SAM $CISD $PKG/usr/share/java/$PRGNAM +cp -a Configuration net org Templates Help uk $JBZIP $HTS $CISD $PKG/usr/share/java/$PRGNAM mkdir -p $PKG/usr/bin cd $PKG/usr/bin @@ -85,4 +98,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/fastqc/fastqc.info b/academic/fastqc/fastqc.info index a84ec6f99d..e043400da1 100644 --- a/academic/fastqc/fastqc.info +++ b/academic/fastqc/fastqc.info @@ -1,10 +1,10 @@ PRGNAM="fastqc" -VERSION="0.11.9" -HOMEPAGE="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/" -DOWNLOAD="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.9.zip" -MD5SUM="ee7901b681bb2762d75d5a56c7ec6958" +VERSION="0.12.1" +HOMEPAGE="https://www.bioinformatics.babraham.ac.uk/projects/fastqc/" +DOWNLOAD="https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.12.1.zip" +MD5SUM="a628c84cf19235d47fd979d4bb786a60" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="jdk" +REQUIRES="zulu-openjdk11" MAINTAINER="Rob van Nues" EMAIL="sborg63@disroot.org" diff --git a/academic/fet/README b/academic/fet/README index 3021e9183e..d32c44ad69 100644 --- a/academic/fet/README +++ b/academic/fet/README @@ -3,4 +3,5 @@ FET (A free software for automatic generation of timetable) This is a free software for automatically scheduling the timetable of a school, high-school or university. It uses a fast and efficient timetabling algorithm. -It is licensed under GNU GPL. +It is licensed under GNU Affero General Public License +version 3 or later. diff --git a/academic/fet/fet.SlackBuild b/academic/fet/fet.SlackBuild index c7faf86780..6962abec49 100644 --- a/academic/fet/fet.SlackBuild +++ b/academic/fet/fet.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for fet @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=fet -VERSION=${VERSION:-5.44.0} +VERSION=${VERSION:-6.19.3} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -101,4 +111,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/fet/fet.info b/academic/fet/fet.info index f4b827febb..2093219a59 100644 --- a/academic/fet/fet.info +++ b/academic/fet/fet.info @@ -1,10 +1,10 @@ PRGNAM="fet" -VERSION="5.44.0" +VERSION="6.19.3" HOMEPAGE="https://www.lalescu.ro/liviu/fet/" -DOWNLOAD="https://www.lalescu.ro/liviu/fet/download/fet-5.44.0.tar.bz2" -MD5SUM="d511f430034cac86be9d7e8c9bc8202d" +DOWNLOAD="https://www.lalescu.ro/liviu/fet/download/fet-6.19.3.tar.bz2" +MD5SUM="5af48c9d1fdf303d7f2ed8ec306a257d" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="qt5" +REQUIRES="" MAINTAINER="R.S.Ananda Murthy" EMAIL="rsamurti@gmail.com" diff --git a/academic/fet/slack-desc b/academic/fet/slack-desc index 9a8953386d..7d6260d777 100644 --- a/academic/fet/slack-desc +++ b/academic/fet/slack-desc @@ -13,7 +13,7 @@ fet: the timetable of a school, high-school or university. fet: It uses a fast and efficient timetabling algorithm. fet: It is licensed under GNU GPL. fet: -fet: +fet: https://www.lalescu.ro/liviu/fet/ fet: fet: fet: diff --git a/academic/fiji/ImageJ2.desktop b/academic/fiji/ImageJ2.desktop index 6ea0bc5041..404207c1ec 100644 --- a/academic/fiji/ImageJ2.desktop +++ b/academic/fiji/ImageJ2.desktop @@ -2,7 +2,7 @@ Name=Fiji (ImageJ 2) Comment=Fiji is just ImageJ Type=Application -Categories=Graphics; +Categories=Graphics;Education; Exec=fiji Terminal=false Icon=fiji diff --git a/academic/fiji/README b/academic/fiji/README index 873045e097..1b51100f6a 100644 --- a/academic/fiji/README +++ b/academic/fiji/README @@ -32,6 +32,8 @@ Fiji is Just ImageJ, with extras. It is a distribution of ImageJ with many plugins useful for scientific image analysis in fields such as life sciences. It is actively maintained, with updates released often. +NOTE: This comes with its own Java environment. + Citing Schindelin, J.; Arganda-Carreras, I. & Frise, E. et al. (2012) "Fiji: an open-source platform for biological-image analysis" diff --git a/academic/fiji/fiji.SlackBuild b/academic/fiji/fiji.SlackBuild index bad800afcd..137669d5c6 100644 --- a/academic/fiji/fiji.SlackBuild +++ b/academic/fiji/fiji.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for fiji -# Copyright 2018-2020 Petar Petrov slackalaxy@gmail.com +# Copyright 2018-2023 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,41 +22,47 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=fiji -VERSION=${VERSION:-20191216_2110} +VERSION=${VERSION:-20230801_1717} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} DIRNAM=Fiji.app if [ -z "$ARCH" ]; then - case "$( uname -m )" in - i?86) ARCH=i386 ;; - arm*) ARCH=arm ;; - *) ARCH=$( uname -m ) ;; - esac + ARCH=$( uname -m ) +fi + +# Stop if arch is not supported +# 2023-05-16 DW: better if it's before PRINT_PACKAGE_NAME +if [ "$ARCH" != "x86_64" ]; then + printf "\n$ARCH is not supported... \n" + exit 1 +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 fi -CWD=$(pwd) TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -UPDATER=imagej-updater-0.10.3.jar - set -e -# Stop if arch is not supported -if [ "$ARCH" != "i386" ] && [ "$ARCH" != "x86_64" ]; then - printf "\n\n$ARCH is not supported... \n" - exit 1 -fi - rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $DIRNAM -tar xvf $CWD/${PRGNAM}-nojre.tar.gz +#tar xvf $CWD/${PRGNAM}-linux64.tar.gz +unzip $CWD/${PRGNAM}-linux64.zip cd $DIRNAM chown -R root:root . find -L . \ @@ -66,11 +72,7 @@ find -L . \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; # Rename the binary we need -if [ "$ARCH" = "x86_64" ]; then - mv ImageJ-linux64 $PRGNAM -else - mv ImageJ-linux32 $PRGNAM -fi +mv ImageJ-linux64 $PRGNAM # We will put here two tools, so they are not run at startup. mkdir -p unused @@ -85,21 +87,25 @@ mv ../plugins/Scripts/Plugins/AutoRun/Check_Required_Update_Sites.js . # is your system, so if you want this functionality, then comment out # the line below. You can always "enable" it, by placing it in the jars # folder. -mv ../jars/$UPDATER . +mv ../jars/imagej-updater-* . cd .. # Update plugins, so that the latest are included in the package. This # will download stuff during the package creation, something that is -# against the policy of SlackBuilds.org. However, it is your system, +# against the policy of SlackBuilds.org. However, it is _your_ system, # so if you _really_ want this, uncomment the line below. # ./$PRGNAM --update list-local-only # Copy the folders, db.xml and the renamed binary to /opt mkdir -p $PKG/opt/$PRGNAM cp -a \ + Contents \ images \ jars \ + java \ + lib \ + licenses \ luts \ macros \ plugins \ @@ -119,7 +125,7 @@ $PKG/opt/$PRGNAM cp $CWD/ImageJ2.desktop $PKG/opt/$PRGNAM # Install the simple wrapper -install -D -m755 $CWD/$PRGNAM $PKG/usr/bin/$PRGNAM +install -D -m 755 $CWD/$PRGNAM $PKG/usr/bin/$PRGNAM find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true @@ -138,4 +144,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/fiji/fiji.info b/academic/fiji/fiji.info index bab997b64e..ac7d400024 100644 --- a/academic/fiji/fiji.info +++ b/academic/fiji/fiji.info @@ -1,10 +1,10 @@ PRGNAM="fiji" -VERSION="20191216_2110" +VERSION="20230801_1717" HOMEPAGE="https://fiji.sc/" -DOWNLOAD="https://downloads.imagej.net/fiji/archive/20191216-2110/fiji-nojre.tar.gz" -MD5SUM="692b2b0920d5d86bf5dfb6661444f19d" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="jdk" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="https://downloads.imagej.net/fiji/archive/20230801-1717/fiji-linux64.zip" +MD5SUM_x86_64="9965c8c1c101866c66019a0a511da143" +REQUIRES="" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/finchtv/finchtv.SlackBuild b/academic/finchtv/finchtv.SlackBuild index e94229af50..0a8f1321a9 100644 --- a/academic/finchtv/finchtv.SlackBuild +++ b/academic/finchtv/finchtv.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for finchtv -# Copyright 2015-2017 Petar Petrov slackalaxy@gmail.com +# Copyright 2015-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,15 +22,37 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=finchtv VERSION=${VERSION:-1.3.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} SRCVER=1_3_1 -ARCH=i386 # This will work on a stock Slackware64 as well. -CWD=$(pwd) +# 2023-05-16 DW: check for ARCH and kick wronguns +if [ -z "$ARCH" ]; then + case "$ARCH" in + i?86) ARCH=i586 ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if ! [ "$ARCH" = "x86_64" ] && ! [[ $ARCH =~ i?86 ]]; then + printf "\n$ARCH is not supported... \n" >/dev/stderr + exit 1 +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -50,7 +72,7 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -install -D -m755 $PRGNAM $PKG/usr/bin/$PRGNAM +install -D -m 755 $PRGNAM $PKG/usr/bin/$PRGNAM find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true @@ -74,4 +96,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/finchtv/finchtv.info b/academic/finchtv/finchtv.info index d2a1ab4fb0..35feb66ca6 100644 --- a/academic/finchtv/finchtv.info +++ b/academic/finchtv/finchtv.info @@ -1,6 +1,6 @@ PRGNAM="finchtv" VERSION="1.3.1" -HOMEPAGE="http://jblseqdat.bioc.cam.ac.uk/gnmweb/download/soft/FinchTV_1.4/doc/" +HOMEPAGE="https://digitalworldbiology.com/FinchTV" DOWNLOAD="https://sourceforge.net/projects/sboppetrov/files/finchtv/finchtv_1_3_1.tar.gz" MD5SUM="bafea0b08c5348cbe745d1a4857948a4" DOWNLOAD_x86_64="" diff --git a/academic/fityk/README b/academic/fityk/README index c3e6500623..0217e00966 100644 --- a/academic/fityk/README +++ b/academic/fityk/README @@ -1,6 +1,7 @@ Fityk (program for data processing and nonlinear curve fitting) -Fityk [fi:tik] is a program for data processing and nonlinear curve fitting. +Fityk [fi:tik] is a program for data processing and nonlinear curve +fitting. Primarily used: @@ -15,4 +16,5 @@ but it is suitable for fitting any curve to 2D (x,y) data. Fityk is distributed under an open source licence (GPLv2+). -Optional dependency: gnuplot (can be used with the CLI) +Optional dependency: Sphinx. If installed, it will be used to generate +HTML documentation, which will be installed in /usr/share/fityk/html. diff --git a/academic/fityk/fityk.SlackBuild b/academic/fityk/fityk.SlackBuild index c09ec3cc59..adc1ee2c44 100644 --- a/academic/fityk/fityk.SlackBuild +++ b/academic/fityk/fityk.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for fityk -# Based on Slackware 14.2 SlackBuild +# Based on Slackware 15.0 SlackBuild # -# Copyright 2017, Fellype do Nascimento, Campinas - Brazil +# Copyright 2017-2023, Fellype do Nascimento, Guaratinguetá - Brazil # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,11 +22,16 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +# The SlackBuilds.org team contributed with improvements and maintenance of +# this script + +cd $(dirname $0) ; CWD=$(pwd) PRGNAM=fityk -VERSION=${VERSION:-1.3.1} +VERSION=${VERSION:-1.3.2} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -36,7 +41,11 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -61,38 +70,40 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $PRGNAM-$VERSION -tar xvf $CWD/$PRGNAM-$VERSION.tar.bz2 +tar xvf $CWD/$PRGNAM-$VERSION.tar.?z* cd $PRGNAM-$VERSION chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ + -o -perm 511 \) -exec chmod 755 {} \+ -o \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \+ +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS -std=c++14" \ ./configure \ --prefix=/usr \ --bindir=/usr/bin \ --libdir=/usr/lib${LIBDIRSUFFIX} \ --mandir=/usr/man \ --enable-python \ + --with-wx-config=/usr/lib$LIBDIRSUFFIX/wx/config/gtk3-unicode-3.0 \ --build=$ARCH-slackware-linux make -make DESTDIR=$PKG install - -find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ - | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true +make DESTDIR=$PKG install-strip mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a COPYING INSTALL NEWS README.md TODO $PKG/usr/doc/$PRGNAM-$VERSION +cp -a COPYING NEWS README.md TODO $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild gzip -9 $PKG/usr/man/man1/fityk.1 +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/fityk/fityk.info b/academic/fityk/fityk.info index 76de4f6ab5..c9bdbeba0a 100644 --- a/academic/fityk/fityk.info +++ b/academic/fityk/fityk.info @@ -1,10 +1,10 @@ PRGNAM="fityk" -VERSION="1.3.1" +VERSION="1.3.2" HOMEPAGE="http://fityk.nieto.pl/" -DOWNLOAD="https://github.com/wojdyr/fityk/releases/download/v1.3.1/fityk-1.3.1.tar.bz2" -MD5SUM="41c9a2589e2eac4317a480b364ff493a" +DOWNLOAD="https://github.com/wojdyr/fityk/releases/download/v1.3.2/fityk-1.3.2.tar.bz2" +MD5SUM="b5c24bc3cafd0e30f32f6daf56375fac" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="lua xylib" MAINTAINER="Fellype do Nascimento" -EMAIL="fellype(at)gmail.com" +EMAIL="fellype (at) gmail (dot) com" diff --git a/academic/flann/README b/academic/flann/README index c47071aeab..23c6f4c075 100644 --- a/academic/flann/README +++ b/academic/flann/README @@ -1,7 +1,8 @@ -FLANN is a library for performing fast approximate nearest neighbor searches -in high dimensional spaces. It contains a collection of algorithms we found -to work best for nearest neighbor search and a system for automatically -choosing the best algorithm and optimum parameters depending on the dataset. +FLANN is a library for performing fast approximate nearest neighbor +searches in high dimensional spaces. It contains a collection of +algorithms we found to work best for nearest neighbor search and +a system for automatically choosing the best algorithm and optimum +parameters depending on the dataset. -FLANN is written in C++ and contains bindings for the following languages: -C, MATLAB and Python. +FLANN is written in C++ and contains bindings for the following +languages: C, MATLAB and Python. diff --git a/academic/flann/flann.SlackBuild b/academic/flann/flann.SlackBuild index 12233f7101..eadcc1568c 100644 --- a/academic/flann/flann.SlackBuild +++ b/academic/flann/flann.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for flann @@ -25,10 +25,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=flann VERSION=${VERSION:-1.9.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -38,7 +41,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -72,6 +82,12 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; +sed -i "s|setup\.py install|setup.py install --root=$PKG --optimize=1|" src/python/CMakeLists.txt + +touch src/cpp/empty.cpp +sed -i -e 's/flann_cpp SHARED \"\"/flann_cpp SHARED \"empty\.cpp\"/g' src/cpp/CMakeLists.txt +sed -i -e 's/flann SHARED \"\"/flann SHARED \"empty\.cpp\"/g' src/cpp/CMakeLists.txt + mkdir -p build cd build cmake \ @@ -79,19 +95,27 @@ cd build -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ -DCMAKE_INSTALL_PREFIX=/usr \ -DLIB_SUFFIX=${LIBDIRSUFFIX} \ + -DBUILD_MATLAB_BINDINGS=OFF \ + -DBUILD_PYTHON_BINDINGS=ON \ + -DPYTHON_EXECUTABLE=/usr/bin/python3 \ + -DBUILD_TESTS=OFF \ + -DBUILD_EXAMPLES=OFF \ -DCMAKE_BUILD_TYPE=Release .. make make install DESTDIR=$PKG cd .. +rm -fR $PKG/usr/share/$PRGNAM find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true +rm -fR $PKG/usr/share/doc mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp COPYING ChangeLog README.md $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/flashqard/README b/academic/flashqard/README deleted file mode 100644 index 0e0fa5eaaf..0000000000 --- a/academic/flashqard/README +++ /dev/null @@ -1,8 +0,0 @@ -FlashQard is an educational software to improve your learning process. -It is designed to help you learn not only a new language but anything -that can be learned! This aim is achieved by using the widely used -method called the Leitner System and the idea of "different card types -for different purposes". Leitner System (proposed by Sebastian Leitner -in the 1970s) is one the most efficient methods for learning, which -allows you to focus on the most difficult flashcards and not waste your -time on what you have already learned. diff --git a/academic/flashqard/flashqard-0.15.0_qt-4.8.7.patch b/academic/flashqard/flashqard-0.15.0_qt-4.8.7.patch deleted file mode 100644 index 57bce20dce..0000000000 --- a/academic/flashqard/flashqard-0.15.0_qt-4.8.7.patch +++ /dev/null @@ -1,22 +0,0 @@ -diff -u -r flashqard-0.15.0/src/PrettyButton.cpp flashqard-0.15.0-patched/src/PrettyButton.cpp ---- flashqard-0.15.0/src/PrettyButton.cpp 2009-09-08 22:56:54.000000000 +0100 -+++ flashqard-0.15.0-patched/src/PrettyButton.cpp 2015-07-28 11:49:56.506872447 +0100 -@@ -25,6 +25,7 @@ - #include "PrettyButton.h" - #include "TextEditor.h" - #include "MimeData.h" -+#include <QApplication> - #include <QPainter> - #include <QTimerEvent> - #include <QDropEvent> -diff -u -r flashqard-0.15.0/src/Utilities.cpp flashqard-0.15.0-patched/src/Utilities.cpp ---- flashqard-0.15.0/src/Utilities.cpp 2009-09-08 22:56:54.000000000 +0100 -+++ flashqard-0.15.0-patched/src/Utilities.cpp 2015-07-28 11:45:33.484870666 +0100 -@@ -22,6 +22,7 @@ - // | Author: Shahab Shirazi <shahab@flashqard-project.org> | - // +-------------------------------------------------------------------------+ - -+#include <QDir> - #include <QRegExp> - #include <QToolBar> - #include <QMessageBox> diff --git a/academic/flashqard/flashqard.SlackBuild b/academic/flashqard/flashqard.SlackBuild deleted file mode 100644 index f749eb317b..0000000000 --- a/academic/flashqard/flashqard.SlackBuild +++ /dev/null @@ -1,83 +0,0 @@ -#!/bin/sh - -# Slackware build script for flashqard -# written by Mehdi Esmaeelpour ariarat@gmail.com www.slack-world.com - -PRGNAM=flashqard -VERSION=${VERSION:-0.15.0} -BUILD=${BUILD:-1} -TAG=${TAG:-_SBo} - -if [ -z "$ARCH" ]; then - case "$( uname -m )" in - i?86) ARCH=i486 ;; - arm*) ARCH=arm ;; - *) ARCH=$( uname -m ) ;; - esac -fi - -CWD=$(pwd) -TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM -OUTPUT=${OUTPUT:-/tmp} - -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" - LIBDIRSUFFIX="" -elif [ "$ARCH" = "i686" ]; then - SLKCFLAGS="-O2 -march=i686 -mtune=i686" - LIBDIRSUFFIX="" -elif [ "$ARCH" = "x86_64" ]; then - SLKCFLAGS="-O2 -fPIC" - LIBDIRSUFFIX="64" -else - SLKCFLAGS="-O2" - LIBDIRSUFFIX="" -fi - -set -e - -rm -rf $PKG -mkdir -p $TMP $PKG $OUTPUT -cd $TMP -rm -rf $PRGNAM-$VERSION -tar xvf $CWD/$PRGNAM-$VERSION.tar.gz -cd $PRGNAM-$VERSION -chown -R root:root . -find -L . \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; - -# Patch for missing includes with qt-4.8.7 -patch -p1 < $CWD/flashqard-0.15.0_qt-4.8.7.patch - -mkdir -p build -cd build - cmake \ - -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ - -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ - -DCMAKE_INSTALL_PREFIX=/usr \ - -DLIB_SUFFIX=${LIBDIRSUFFIX} \ - -DMAN_INSTALL_DIR=/usr/man \ - -DCMAKE_BUILD_TYPE=Release .. - make - make install DESTDIR=$PKG -cd .. - -find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ - | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true - -mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a \ - COPYING ChangeLog README AUTHORS INSTALL \ - $PKG/usr/doc/$PRGNAM-$VERSION -cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild - -mkdir -p $PKG/install -cat $CWD/slack-desc > $PKG/install/slack-desc -cat $CWD/doinst.sh > $PKG/install/doinst.sh - -cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} diff --git a/academic/flashqard/flashqard.info b/academic/flashqard/flashqard.info deleted file mode 100644 index 85b44828be..0000000000 --- a/academic/flashqard/flashqard.info +++ /dev/null @@ -1,10 +0,0 @@ -PRGNAM="flashqard" -VERSION="0.15.0" -HOMEPAGE="http://www.flashqard-project.org/" -DOWNLOAD="http://downloads.sourceforge.net/flashqard/flashqard-0.15.0.tar.gz" -MD5SUM="aa2c58d3b18f0ce8d2a31ece9d299647" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="" -MAINTAINER="ariarat" -EMAIL="ariarat@gmail.com" diff --git a/academic/flexbar/Migrate_from_tbb_to_onetbb_seqan_flexbar_pull_41.patch b/academic/flexbar/Migrate_from_tbb_to_onetbb_seqan_flexbar_pull_41.patch new file mode 100644 index 0000000000..12068e9337 --- /dev/null +++ b/academic/flexbar/Migrate_from_tbb_to_onetbb_seqan_flexbar_pull_41.patch @@ -0,0 +1,710 @@ +From 195a1ab2c2715b07df5acff58dc2a0396d9cd52d Mon Sep 17 00:00:00 2001 +From: Liam Keegan <liam@keegan.ch> +Date: Thu, 9 Feb 2023 16:27:37 +0100 +Subject: [PATCH 1/4] Migrate from tbb to onetbb + +- add `FlexbarAtomic` + - a simple wrapper around `std::atomic` which adds a copy constructor + - to replace `tbb::atomic` member variables in classes with default copy constructors +- replace removed `tbb::atomic` + - with `FlexbarAtomic` if copy constructor was assumed + - with `std::atomic` otherwise +- filters (PairedAlign, PairedInput, PairedOutput) + - no longer inherit from tbb::filter + - take and return pointers to actual type instead of void* + - operator() is now const +- pipeline + - use parallel_pipeline and make_filter +- use global_control to set max threads +- use `oneapi::tbb` namespace +- add find_package for TBB to CMakeLists.txt +--- + src/CMakeLists.txt | 9 ++------- + src/Flexbar.h | 27 +++++++++++++++------------ + src/FlexbarTypes.h | 16 +++++++++++++++- + src/LoadAdapters.h | 4 ++-- + src/LoadFasta.h | 6 +++--- + src/Options.h | 2 +- + src/PairedAlign.h | 23 ++++++++++------------- + src/PairedInput.h | 10 ++++------ + src/PairedOutput.h | 29 ++++++++++++----------------- + src/SeqAlign.h | 12 ++++++------ + src/SeqAlignPair.h | 6 +++--- + src/SeqInput.h | 2 +- + src/SeqOutput.h | 6 +++--- + src/SeqOutputFiles.h | 2 +- + 14 files changed, 78 insertions(+), 76 deletions(-) + +diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt +index a5643ca..ca4e5db 100644 +--- a/src/CMakeLists.txt ++++ b/src/CMakeLists.txt +@@ -32,9 +32,9 @@ else() + endif() + + add_executable( flexbar Flexbar.cpp ) +-target_link_libraries( flexbar tbb -lpthread ) +- + ++find_package(TBB CONFIG REQUIRED) ++target_link_libraries(flexbar TBB::tbb) + find_package( ZLIB ) + if( ZLIB_FOUND ) + include_directories( ${ZLIB_INCLUDE_DIRS} ) +@@ -53,9 +53,4 @@ else() + message( STATUS "Build will not support bzip2." ) + endif() + +-# find_package( TBB REQUIRED ) +-# if( NOT TBB_FOUND ) +-# message( FATAL_ERROR "TBB library not found." ) +-# endif() +- + set( SEQAN_CTD_EXECUTABLES ${SEQAN_CTD_EXECUTABLES} flexbar CACHE INTERNAL "" ) +diff --git a/src/Flexbar.h b/src/Flexbar.h +index 67c07d7..d1a8f31 100644 +--- a/src/Flexbar.h ++++ b/src/Flexbar.h +@@ -12,10 +12,9 @@ + #include <iostream> + #include <vector> + +-#include <tbb/pipeline.h> +-#include <tbb/task_scheduler_init.h> +-#include <tbb/concurrent_vector.h> +-#include <tbb/mutex.h> ++#include <oneapi/tbb/parallel_pipeline.h> ++#include <oneapi/tbb/global_control.h> ++#include <oneapi/tbb/concurrent_vector.h> + + #include <seqan/basic.h> + #include <seqan/sequence.h> +@@ -240,14 +239,18 @@ void startProcessing(Options &o){ + PairedAlign<TSeqStr, TString> alignFilter(o); + PairedOutput<TSeqStr, TString> outputFilter(o); + +- tbb::task_scheduler_init init_serial(o.nThreads); +- tbb::pipeline pipe; +- +- pipe.add_filter(inputFilter); +- pipe.add_filter(alignFilter); +- pipe.add_filter(outputFilter); +- pipe.run(o.nThreads); +- ++ oneapi::tbb::global_control control( ++ oneapi::tbb::global_control::max_allowed_parallelism, o.nThreads); ++ oneapi::tbb::parallel_pipeline(o.nThreads, ++ oneapi::tbb::make_filter<void, TPairedReadBundle *>( ++ oneapi::tbb::filter_mode::serial_in_order, inputFilter) ++ & ++ oneapi::tbb::make_filter<TPairedReadBundle *, TPairedReadBundle *>( ++ oneapi::tbb::filter_mode::parallel, alignFilter) ++ & ++ oneapi::tbb::make_filter<TPairedReadBundle *, void>( ++ oneapi::tbb::filter_mode::serial_in_order, outputFilter) ++ ); + if(o.logAlign == TAB) *out << "\n"; + *out << "done.\n" << endl; + +diff --git a/src/FlexbarTypes.h b/src/FlexbarTypes.h +index 8abdf66..f1bce0f 100644 +--- a/src/FlexbarTypes.h ++++ b/src/FlexbarTypes.h +@@ -3,6 +3,20 @@ + #ifndef FLEXBAR_FLEXBARTYPES_H + #define FLEXBAR_FLEXBARTYPES_H + ++#include <atomic> ++ ++// A simple wrapper around std::atomic<T> with a copy-constructor ++// This is a drop-in replacement for the previously used tbb::atomic (which is copyable), ++// to avoid having to add copy-constructors to classes that used it ++template<typename T> ++struct FlexbarAtomic : public std::atomic<T> { ++ FlexbarAtomic() = default; ++ explicit constexpr FlexbarAtomic(T t) : std::atomic<T>(t) {} ++ constexpr FlexbarAtomic(const FlexbarAtomic<T>& other) : ++ FlexbarAtomic(other.load(std::memory_order_acquire)) ++ {} ++}; ++ + + template <typename TSeqStr, typename TString> + class SeqRead { +@@ -126,7 +140,7 @@ namespace flexbar{ + FSeqStr seq; + bool rcAdapter; + +- tbb::atomic<unsigned long> rmOverlap, rmFull; ++ FlexbarAtomic<unsigned long> rmOverlap, rmFull; + + TBar() : + rmOverlap(0), +diff --git a/src/LoadAdapters.h b/src/LoadAdapters.h +index 046e799..6168775 100644 +--- a/src/LoadAdapters.h ++++ b/src/LoadAdapters.h +@@ -10,7 +10,7 @@ class LoadAdapters { + private: + + std::ostream *out; +- tbb::concurrent_vector<flexbar::TBar> adapters; ++ oneapi::tbb::concurrent_vector<flexbar::TBar> adapters; + + flexbar::Adapters a; + +@@ -134,7 +134,7 @@ class LoadAdapters { + }; + + +- tbb::concurrent_vector<flexbar::TBar> getAdapters(){ ++ oneapi::tbb::concurrent_vector<flexbar::TBar> getAdapters(){ + return adapters; + } + +diff --git a/src/LoadFasta.h b/src/LoadFasta.h +index 3e69594..ccd0550 100644 +--- a/src/LoadFasta.h ++++ b/src/LoadFasta.h +@@ -10,7 +10,7 @@ class LoadFasta { + private: + + std::ostream *out; +- tbb::concurrent_vector<flexbar::TBar> bars; ++ oneapi::tbb::concurrent_vector<flexbar::TBar> bars; + + const bool m_isAdapter; + const flexbar::RevCompMode m_rcMode; +@@ -94,12 +94,12 @@ class LoadFasta { + }; + + +- tbb::concurrent_vector<flexbar::TBar> getBars(){ ++ oneapi::tbb::concurrent_vector<flexbar::TBar> getBars(){ + return bars; + } + + +- void setBars(tbb::concurrent_vector<flexbar::TBar> &newBars){ ++ void setBars(oneapi::tbb::concurrent_vector<flexbar::TBar> &newBars){ + bars = newBars; + } + +diff --git a/src/Options.h b/src/Options.h +index 6299c50..21d7710 100644 +--- a/src/Options.h ++++ b/src/Options.h +@@ -46,7 +46,7 @@ struct Options{ + flexbar::AdapterPreset aPreset; + flexbar::AdapterTrimmed aTrimmed; + +- tbb::concurrent_vector<flexbar::TBar> barcodes, adapters, barcodes2, adapters2; ++ oneapi::tbb::concurrent_vector<flexbar::TBar> barcodes, adapters, barcodes2, adapters2; + + std::ostream *out; + std::fstream fstrmOut; +diff --git a/src/PairedAlign.h b/src/PairedAlign.h +index d6f9956..59c4473 100644 +--- a/src/PairedAlign.h ++++ b/src/PairedAlign.h +@@ -9,7 +9,7 @@ + + + template <typename TSeqStr, typename TString> +-class PairedAlign : public tbb::filter { ++class PairedAlign { + + private: + +@@ -31,9 +31,9 @@ class PairedAlign : public tbb::filter { + const flexbar::TrimEnd m_aTrimEnd, m_arcTrimEnd, m_bTrimEnd; + const flexbar::PairOverlap m_poMode; + +- tbb::atomic<unsigned long> m_unassigned; +- tbb::concurrent_vector<flexbar::TBar> *m_adapters, *m_adapters2; +- tbb::concurrent_vector<flexbar::TBar> *m_barcodes, *m_barcodes2; ++ mutable FlexbarAtomic<unsigned long> m_unassigned; ++ oneapi::tbb::concurrent_vector<flexbar::TBar> *m_adapters, *m_adapters2; ++ oneapi::tbb::concurrent_vector<flexbar::TBar> *m_barcodes, *m_barcodes2; + + typedef SeqAlign<TSeqStr, TString, SeqAlignAlgo<TSeqStr> > TSeqAlign; + TSeqAlign *m_a1, *m_b1, *m_a2, *m_b2; +@@ -47,7 +47,6 @@ class PairedAlign : public tbb::filter { + + PairedAlign(Options &o) : + +- filter(parallel), + m_format(o.format), + m_log(o.logAlign), + m_runType(o.runType), +@@ -102,7 +101,7 @@ class PairedAlign : public tbb::filter { + }; + + +- void alignPairedReadToBarcodes(flexbar::TPairedRead* pRead, flexbar::TAlignBundle &alBundle, std::vector<flexbar::ComputeCycle> &cycle, std::vector<unsigned int> &idxAl, const flexbar::AlignmentMode &alMode){ ++ void alignPairedReadToBarcodes(flexbar::TPairedRead* pRead, flexbar::TAlignBundle &alBundle, std::vector<flexbar::ComputeCycle> &cycle, std::vector<unsigned int> &idxAl, const flexbar::AlignmentMode &alMode) const { + + using namespace flexbar; + +@@ -122,7 +121,7 @@ class PairedAlign : public tbb::filter { + } + + +- void alignPairedReadToAdapters(flexbar::TPairedRead* pRead, flexbar::TAlignBundle &alBundle, std::vector<flexbar::ComputeCycle> &cycle, std::vector<unsigned int> &idxAl, const flexbar::AlignmentMode &alMode, const flexbar::TrimEnd trimEnd){ ++ void alignPairedReadToAdapters(flexbar::TPairedRead* pRead, flexbar::TAlignBundle &alBundle, std::vector<flexbar::ComputeCycle> &cycle, std::vector<unsigned int> &idxAl, const flexbar::AlignmentMode &alMode, const flexbar::TrimEnd trimEnd) const { + + using namespace flexbar; + +@@ -173,7 +172,7 @@ class PairedAlign : public tbb::filter { + } + + +- void trimLeftHPS(flexbar::TSeqRead* seqRead){ ++ void trimLeftHPS(flexbar::TSeqRead* seqRead) const{ + + using namespace std; + using namespace flexbar; +@@ -223,7 +222,7 @@ class PairedAlign : public tbb::filter { + } + + +- void trimRightHPS(flexbar::TSeqRead* seqRead){ ++ void trimRightHPS(flexbar::TSeqRead* seqRead) const{ + + using namespace std; + using namespace flexbar; +@@ -275,13 +274,11 @@ class PairedAlign : public tbb::filter { + + + // tbb filter operator +- void* operator()(void* item){ ++ flexbar::TPairedReadBundle* operator()(flexbar::TPairedReadBundle* prBundle) const{ + + using namespace flexbar; + +- if(item != NULL){ +- +- TPairedReadBundle *prBundle = static_cast<TPairedReadBundle* >(item); ++ if(prBundle != NULL){ + + if(m_umiTags){ + for(unsigned int i = 0; i < prBundle->size(); ++i){ +diff --git a/src/PairedInput.h b/src/PairedInput.h +index 94a54e5..f7a6c9e 100644 +--- a/src/PairedInput.h ++++ b/src/PairedInput.h +@@ -7,7 +7,7 @@ + + + template <typename TSeqStr, typename TString> +-class PairedInput : public tbb::filter { ++class PairedInput { + + private: + +@@ -15,14 +15,13 @@ class PairedInput : public tbb::filter { + const bool m_isPaired, m_useBarRead, m_useNumberTag, m_interleaved; + const unsigned int m_bundleSize; + +- tbb::atomic<unsigned long> m_uncalled, m_uncalledPairs, m_tagCounter, m_nBundles; ++ mutable FlexbarAtomic<unsigned long> m_uncalled, m_uncalledPairs, m_tagCounter, m_nBundles; + SeqInput<TSeqStr, TString> *m_f1, *m_f2, *m_b; + + public: + + PairedInput(const Options &o) : + +- filter(serial_in_order), + m_format(o.format), + m_useNumberTag(o.useNumberTag), + m_interleaved(o.interleavedInput), +@@ -55,7 +54,7 @@ class PairedInput : public tbb::filter { + } + + +- void* loadPairedReadBundle(){ ++ void* loadPairedReadBundle() const{ + + using namespace std; + using namespace flexbar; +@@ -207,8 +206,7 @@ class PairedInput : public tbb::filter { + + + // tbb filter operator +- void* operator()(void*){ +- ++ flexbar::TPairedReadBundle* operator()(oneapi::tbb::flow_control& fc) const { + using namespace flexbar; + + TPairedReadBundle *prBundle = NULL; +diff --git a/src/PairedOutput.h b/src/PairedOutput.h +index 6c3fad7..c0d3626 100644 +--- a/src/PairedOutput.h ++++ b/src/PairedOutput.h +@@ -9,7 +9,7 @@ + + + template <typename TSeqStr, typename TString> +-class PairedOutput : public tbb::filter { ++class PairedOutput { + + private: + +@@ -18,8 +18,8 @@ class PairedOutput : public tbb::filter { + const bool m_isPaired, m_writeUnassigned, m_writeSingleReads, m_writeSingleReadsP; + const bool m_twoBarcodes, m_qtrimPostRm; + +- tbb::atomic<unsigned long> m_nSingleReads, m_nLowPhred; +- ++ mutable FlexbarAtomic<unsigned long> m_nSingleReads, m_nLowPhred; ++ + const std::string m_target; + + const flexbar::FileFormat m_format; +@@ -34,14 +34,13 @@ class PairedOutput : public tbb::filter { + TOutFiles *m_outMap; + std::ostream *out; + +- tbb::concurrent_vector<flexbar::TBar> *m_adapters, *m_barcodes; +- tbb::concurrent_vector<flexbar::TBar> *m_adapters2, *m_barcodes2; ++ oneapi::tbb::concurrent_vector<flexbar::TBar> *m_adapters, *m_barcodes; ++ oneapi::tbb::concurrent_vector<flexbar::TBar> *m_adapters2, *m_barcodes2; + + public: + + PairedOutput(Options &o) : + +- filter(serial_in_order), + m_target(o.targetName), + m_format(o.format), + m_runType(o.runType), +@@ -57,6 +56,8 @@ class PairedOutput : public tbb::filter { + m_writeSingleReads(o.writeSingleReads), + m_writeSingleReadsP(o.writeSingleReadsP), + m_twoBarcodes(o.barDetect == flexbar::WITHIN_READ_REMOVAL2 || o.barDetect == flexbar::WITHIN_READ2), ++ m_nSingleReads(0), ++ m_nLowPhred(0), + out(o.out){ + + using namespace std; +@@ -68,9 +69,7 @@ class PairedOutput : public tbb::filter { + m_adapters2 = &o.adapters2; + + m_mapsize = 0; +- m_nSingleReads = 0; +- m_nLowPhred = 0; +- ++ + switch(m_runType){ + + case PAIRED_BARCODED:{ +@@ -237,7 +236,7 @@ class PairedOutput : public tbb::filter { + }; + + +- void writePairedRead(flexbar::TPairedRead* pRead){ ++ void writePairedRead(flexbar::TPairedRead* pRead) const{ + + using namespace flexbar; + +@@ -346,13 +345,11 @@ class PairedOutput : public tbb::filter { + + + // tbb filter operator +- void* operator()(void* item){ ++ void operator()(flexbar::TPairedReadBundle* prBundle) const{ + + using namespace flexbar; + +- if(item != NULL){ +- +- TPairedReadBundle *prBundle = static_cast< TPairedReadBundle* >(item); ++ if(prBundle != NULL){ + + for(unsigned int i = 0; i < prBundle->size(); ++i){ + +@@ -361,8 +358,6 @@ class PairedOutput : public tbb::filter { + } + delete prBundle; + } +- +- return NULL; + } + + +@@ -457,7 +452,7 @@ class PairedOutput : public tbb::filter { + + using namespace std; + +- tbb::concurrent_vector<flexbar::TBar> *adapters; ++ oneapi::tbb::concurrent_vector<flexbar::TBar> *adapters; + const unsigned int maxSpaceLen = 20; + + int startLen = 8; +diff --git a/src/SeqAlign.h b/src/SeqAlign.h +index 221a901..b10aafa 100644 +--- a/src/SeqAlign.h ++++ b/src/SeqAlign.h +@@ -3,7 +3,7 @@ + #ifndef FLEXBAR_SEQALIGN_H + #define FLEXBAR_SEQALIGN_H + +-tbb::mutex ouputMutex; ++std::mutex ouputMutex; + + template <typename TSeqStr, typename TString, class TAlgorithm> + class SeqAlign { +@@ -21,16 +21,16 @@ class SeqAlign { + const float m_errorRate; + const unsigned int m_bundleSize; + +- tbb::atomic<unsigned long> m_nPreShortReads, m_modified; +- tbb::concurrent_vector<flexbar::TBar> *m_queries; +- tbb::concurrent_vector<unsigned long> m_rmOverlaps; ++ std::atomic<unsigned long> m_nPreShortReads, m_modified; ++ oneapi::tbb::concurrent_vector<flexbar::TBar> *m_queries; ++ oneapi::tbb::concurrent_vector<unsigned long> m_rmOverlaps; + + std::ostream *m_out; + TAlgorithm m_algo; + + public: + +- SeqAlign(tbb::concurrent_vector<flexbar::TBar> *queries, const Options &o, int minOverlap, float errorRate, const int tailLength, const int match, const int mismatch, const int gapCost, const bool isBarcoding): ++ SeqAlign(oneapi::tbb::concurrent_vector<flexbar::TBar> *queries, const Options &o, int minOverlap, float errorRate, const int tailLength, const int match, const int mismatch, const int gapCost, const bool isBarcoding): + + m_minOverlap(minOverlap), + m_errorRate(errorRate), +@@ -51,7 +51,7 @@ class SeqAlign { + m_algo(TAlgorithm(o, match, mismatch, gapCost, ! isBarcoding)){ + + m_queries = queries; +- m_rmOverlaps = tbb::concurrent_vector<unsigned long>(flexbar::MAX_READLENGTH + 1, 0); ++ m_rmOverlaps = oneapi::tbb::concurrent_vector<unsigned long>(flexbar::MAX_READLENGTH + 1, 0); + }; + + +diff --git a/src/SeqAlignPair.h b/src/SeqAlignPair.h +index d5d1079..2479242 100644 +--- a/src/SeqAlignPair.h ++++ b/src/SeqAlignPair.h +@@ -20,8 +20,8 @@ class SeqAlignPair { + const float m_errorRate; + const unsigned int m_bundleSize; + +- tbb::atomic<unsigned long> m_nPreShortReads, m_overlaps, m_modified; +- tbb::concurrent_vector<unsigned long> m_overlapLengths; ++ std::atomic<unsigned long> m_nPreShortReads, m_overlaps, m_modified; ++ oneapi::tbb::concurrent_vector<unsigned long> m_overlapLengths; + + std::ostream *m_out; + TAlgorithm m_algo; +@@ -45,7 +45,7 @@ class SeqAlignPair { + m_modified(0), + m_algo(TAlgorithm(o, match, mismatch, gapCost, true)){ + +- m_overlapLengths = tbb::concurrent_vector<unsigned long>(flexbar::MAX_READLENGTH + 1, 0); ++ m_overlapLengths = oneapi::tbb::concurrent_vector<unsigned long>(flexbar::MAX_READLENGTH + 1, 0); + }; + + +diff --git a/src/SeqInput.h b/src/SeqInput.h +index 4dcbe74..7a8f8d0 100644 +--- a/src/SeqInput.h ++++ b/src/SeqInput.h +@@ -18,7 +18,7 @@ class SeqInput { + + const bool m_preProcess, m_useStdin, m_qtrimPostRm, m_iupacInput; + const int m_maxUncalled, m_preTrimBegin, m_preTrimEnd, m_qtrimThresh, m_qtrimWinSize; +- tbb::atomic<unsigned long> m_nrReads, m_nrChars, m_nLowPhred; ++ std::atomic<unsigned long> m_nrReads, m_nrChars, m_nLowPhred; + + public: + +diff --git a/src/SeqOutput.h b/src/SeqOutput.h +index 9a63e6a..64cab91 100644 +--- a/src/SeqOutput.h ++++ b/src/SeqOutput.h +@@ -18,8 +18,8 @@ class SeqOutput { + const bool m_switch2Fasta, m_writeLenDist, m_useStdout; + const unsigned int m_minLength, m_cutLen_read; + +- tbb::atomic<unsigned long> m_countGood, m_countGoodChars; +- tbb::concurrent_vector<unsigned long> m_lengthDist; ++ std::atomic<unsigned long> m_countGood, m_countGoodChars; ++ oneapi::tbb::concurrent_vector<unsigned long> m_lengthDist; + + public: + +@@ -48,7 +48,7 @@ class SeqOutput { + } + m_filePath += o.outCompression; + +- m_lengthDist = tbb::concurrent_vector<unsigned long>(MAX_READLENGTH + 1, 0); ++ m_lengthDist = oneapi::tbb::concurrent_vector<unsigned long>(MAX_READLENGTH + 1, 0); + + if(m_useStdout){ + +diff --git a/src/SeqOutputFiles.h b/src/SeqOutputFiles.h +index fe6b50e..8ece58c 100644 +--- a/src/SeqOutputFiles.h ++++ b/src/SeqOutputFiles.h +@@ -14,7 +14,7 @@ class SeqOutputFiles { + typedef SeqOutput<TSeqStr, TString> TSeqOutput; + + TSeqOutput *f1, *f2, *single1, *single2; +- tbb::atomic<unsigned long> m_nShort_1, m_nShort_2; ++ std::atomic<unsigned long> m_nShort_1, m_nShort_2; + + SeqOutputFiles() : + f1(0), + +From 1c872fa10d474f090633fc95d409aa60607a3f96 Mon Sep 17 00:00:00 2001 +From: Liam Keegan <liam@keegan.ch> +Date: Fri, 10 Feb 2023 09:55:58 +0100 +Subject: [PATCH 2/4] Fix parallel_pipeline issues + +- pass a lambda with a reference to the filter instead of directly passing the filter to parallel_pipeline + - passed filters may be copied and/or deleted by tbb + - flexbar continues to use the filter objects after the pipeline is finished +- call fc.stop() in PairedInput when there is no more input + - required control flow for first filter in parallel_pipeline that was previously missing +--- + src/Flexbar.h | 9 ++++++--- + src/PairedInput.h | 9 +++++++-- + 2 files changed, 13 insertions(+), 5 deletions(-) + +diff --git a/src/Flexbar.h b/src/Flexbar.h +index d1a8f31..46261cf 100644 +--- a/src/Flexbar.h ++++ b/src/Flexbar.h +@@ -243,13 +243,16 @@ void startProcessing(Options &o){ + oneapi::tbb::global_control::max_allowed_parallelism, o.nThreads); + oneapi::tbb::parallel_pipeline(o.nThreads, + oneapi::tbb::make_filter<void, TPairedReadBundle *>( +- oneapi::tbb::filter_mode::serial_in_order, inputFilter) ++ oneapi::tbb::filter_mode::serial_in_order, ++ [&inputFilter](auto &fc) { return inputFilter(fc); }) + & + oneapi::tbb::make_filter<TPairedReadBundle *, TPairedReadBundle *>( +- oneapi::tbb::filter_mode::parallel, alignFilter) ++ oneapi::tbb::filter_mode::parallel, ++ [&alignFilter](TPairedReadBundle *tprb) { return alignFilter(tprb); }) + & + oneapi::tbb::make_filter<TPairedReadBundle *, void>( +- oneapi::tbb::filter_mode::serial_in_order, outputFilter) ++ oneapi::tbb::filter_mode::serial_in_order, ++ [&outputFilter](TPairedReadBundle *tprb) { return outputFilter(tprb); }) + ); + if(o.logAlign == TAB) *out << "\n"; + *out << "done.\n" << endl; +diff --git a/src/PairedInput.h b/src/PairedInput.h +index f7a6c9e..4fc4441 100644 +--- a/src/PairedInput.h ++++ b/src/PairedInput.h +@@ -221,9 +221,14 @@ class PairedInput { + + prBundle = static_cast< TPairedReadBundle* >(loadPairedReadBundle()); + +- if(prBundle == NULL) return prBundle; ++ if(prBundle == NULL){ ++ fc.stop(); ++ return prBundle; ++ } + } +- } ++ } else { ++ fc.stop(); ++ } + + return prBundle; + } + +From 19722f2743c96235ff57948eda82f963cf734131 Mon Sep 17 00:00:00 2001 +From: Liam Keegan <liam@keegan.ch> +Date: Fri, 10 Feb 2023 10:21:22 +0100 +Subject: [PATCH 3/4] revert accidental removal of pthread linking in + src/CMakeLists.txt + +--- + src/CMakeLists.txt | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt +index ca4e5db..fb42cc4 100644 +--- a/src/CMakeLists.txt ++++ b/src/CMakeLists.txt +@@ -32,6 +32,7 @@ else() + endif() + + add_executable( flexbar Flexbar.cpp ) ++target_link_libraries( flexbar -lpthread ) + + find_package(TBB CONFIG REQUIRED) + target_link_libraries(flexbar TBB::tbb) + +From a9b0eb87a391aeaf760f8116dca777749c8b4f96 Mon Sep 17 00:00:00 2001 +From: Liam Keegan <liam@keegan.ch> +Date: Fri, 10 Feb 2023 10:52:35 +0100 +Subject: [PATCH 4/4] use `std::atomic` instead of `FlexbarAtomic` in filters + as they are no longer require copy constructors + +--- + src/FlexbarTypes.h | 2 +- + src/PairedAlign.h | 2 +- + src/PairedInput.h | 2 +- + src/PairedOutput.h | 2 +- + 4 files changed, 4 insertions(+), 4 deletions(-) + +diff --git a/src/FlexbarTypes.h b/src/FlexbarTypes.h +index f1bce0f..3cf241e 100644 +--- a/src/FlexbarTypes.h ++++ b/src/FlexbarTypes.h +@@ -139,7 +139,7 @@ namespace flexbar{ + FString id; + FSeqStr seq; + bool rcAdapter; +- ++ + FlexbarAtomic<unsigned long> rmOverlap, rmFull; + + TBar() : +diff --git a/src/PairedAlign.h b/src/PairedAlign.h +index 59c4473..d3b50ae 100644 +--- a/src/PairedAlign.h ++++ b/src/PairedAlign.h +@@ -31,7 +31,7 @@ class PairedAlign { + const flexbar::TrimEnd m_aTrimEnd, m_arcTrimEnd, m_bTrimEnd; + const flexbar::PairOverlap m_poMode; + +- mutable FlexbarAtomic<unsigned long> m_unassigned; ++ mutable std::atomic<unsigned long> m_unassigned; + oneapi::tbb::concurrent_vector<flexbar::TBar> *m_adapters, *m_adapters2; + oneapi::tbb::concurrent_vector<flexbar::TBar> *m_barcodes, *m_barcodes2; + +diff --git a/src/PairedInput.h b/src/PairedInput.h +index 4fc4441..230474b 100644 +--- a/src/PairedInput.h ++++ b/src/PairedInput.h +@@ -15,7 +15,7 @@ class PairedInput { + const bool m_isPaired, m_useBarRead, m_useNumberTag, m_interleaved; + const unsigned int m_bundleSize; + +- mutable FlexbarAtomic<unsigned long> m_uncalled, m_uncalledPairs, m_tagCounter, m_nBundles; ++ mutable std::atomic<unsigned long> m_uncalled, m_uncalledPairs, m_tagCounter, m_nBundles; + SeqInput<TSeqStr, TString> *m_f1, *m_f2, *m_b; + + public: +diff --git a/src/PairedOutput.h b/src/PairedOutput.h +index c0d3626..fae5d3f 100644 +--- a/src/PairedOutput.h ++++ b/src/PairedOutput.h +@@ -18,7 +18,7 @@ class PairedOutput { + const bool m_isPaired, m_writeUnassigned, m_writeSingleReads, m_writeSingleReadsP; + const bool m_twoBarcodes, m_qtrimPostRm; + +- mutable FlexbarAtomic<unsigned long> m_nSingleReads, m_nLowPhred; ++ mutable std::atomic<unsigned long> m_nSingleReads, m_nLowPhred; + + const std::string m_target; + diff --git a/academic/flexbar/flexbar.SlackBuild b/academic/flexbar/flexbar.SlackBuild index f4c28a8ef6..803163e046 100644 --- a/academic/flexbar/flexbar.SlackBuild +++ b/academic/flexbar/flexbar.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for flexbar -# Copyright 2017-18 Rob van Nues +# Copyright 2017-2023 Rob van Nues # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=flexbar VERSION=${VERSION:-3.5.0} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} LIBNAM=seqan-library LIBVER=${LIBVER:-2.4.0} @@ -38,7 +41,11 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -73,6 +80,9 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; +patch -p 1 < $CWD/seqan_flexbar_pull_20.patch +patch -p 1 < $CWD/Migrate_from_tbb_to_onetbb_seqan_flexbar_pull_41.patch + mkdir -p build cd build cmake \ @@ -98,4 +108,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/flexbar/flexbar.info b/academic/flexbar/flexbar.info index 23efa136d8..6ac4dd0920 100644 --- a/academic/flexbar/flexbar.info +++ b/academic/flexbar/flexbar.info @@ -1,12 +1,12 @@ PRGNAM="flexbar" VERSION="3.5.0" HOMEPAGE="https://github.com/seqan/flexbar" -DOWNLOAD="https://github.com/seqan/flexbar/archive/v3.5.0/flexbar-3.5.0.tar.gz \ +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="https://github.com/seqan/flexbar/archive/v3.5.0/flexbar-3.5.0.tar.gz \ https://github.com/seqan/seqan/releases/download/seqan-v2.4.0/seqan-library-2.4.0.tar.xz" -MD5SUM="0e07bf4afebfd731c4718b401383224a \ +MD5SUM_x86_64="0e07bf4afebfd731c4718b401383224a \ eeadf5544555c1e196537a888d02d09f" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" REQUIRES="tbb" MAINTAINER="Rob van Nues" EMAIL="sborg63@disroot.org" diff --git a/academic/flexbar/seqan_flexbar_pull_20.patch b/academic/flexbar/seqan_flexbar_pull_20.patch new file mode 100644 index 0000000000..96db258a6b --- /dev/null +++ b/academic/flexbar/seqan_flexbar_pull_20.patch @@ -0,0 +1,44 @@ +From 707f9381be5d42c6acd122a3c268deb66600cf9a Mon Sep 17 00:00:00 2001 +From: svnbgnk <swb@live.de> +Date: Thu, 25 Jul 2019 16:35:47 +0200 +Subject: [PATCH] added mutex lock to log output + +--- + src/Flexbar.h | 1 + + src/SeqAlign.h | 3 +++ + 2 files changed, 4 insertions(+) + +diff --git a/src/Flexbar.h b/src/Flexbar.h +index 2f82f18..67c07d7 100644 +--- a/src/Flexbar.h ++++ b/src/Flexbar.h +@@ -15,6 +15,7 @@ + #include <tbb/pipeline.h> + #include <tbb/task_scheduler_init.h> + #include <tbb/concurrent_vector.h> ++#include <tbb/mutex.h> + + #include <seqan/basic.h> + #include <seqan/sequence.h> +diff --git a/src/SeqAlign.h b/src/SeqAlign.h +index 979d05f..221a901 100644 +--- a/src/SeqAlign.h ++++ b/src/SeqAlign.h +@@ -3,6 +3,7 @@ + #ifndef FLEXBAR_SEQALIGN_H + #define FLEXBAR_SEQALIGN_H + ++tbb::mutex ouputMutex; + + template <typename TSeqStr, typename TString, class TAlgorithm> + class SeqAlign { +@@ -305,7 +306,9 @@ class SeqAlign { + << "read seq " << seqRead.seq << "\n\n" << endl; + } + ++ ouputMutex.lock(); + *m_out << s.str(); ++ ouputMutex.unlock(); + + return ++qIndex; + } diff --git a/academic/free42/README b/academic/free42/README index 3c30f40e9f..dea3c02b7c 100644 --- a/academic/free42/README +++ b/academic/free42/README @@ -1,6 +1,7 @@ -Free42 is a re-implementation of the HP-42S calculator and the HP-82240 printer. -It is a complete rewrite, not using any HP code, and it does not require an -HP-42S ROM image. Free42 is an Open Source project. The executables and source -code are released under the terms of the GNU General Public License, version 2. -All third-party code used in Free42 is either in the public domain, or licensed -under terms compatible with GPLv2, or used with the authors' permission. +Free42 is a re-implementation of the HP-42S calculator and the +HP-82240 printer. It is a complete rewrite, not using any HP code, +and it does not require an HP-42S ROM image. Free42 is an Open Source +project. The executables and source code are released under the terms +of the GNU General Public License, version 2. All third-party code +used in Free42 is either in the public domain, or licensed under terms +compatible with GPLv2, or used with the authors' permission. diff --git a/academic/free42/free42.SlackBuild b/academic/free42/free42.SlackBuild index 86af1ffdb0..537de2fc00 100644 --- a/academic/free42/free42.SlackBuild +++ b/academic/free42/free42.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for free42 @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=free42 VERSION=${VERSION:-2.0.4} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -97,4 +107,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/freechartgeany/README b/academic/freechartgeany/README deleted file mode 100644 index 82ef887a59..0000000000 --- a/academic/freechartgeany/README +++ /dev/null @@ -1,15 +0,0 @@ -Free Chart Geany is a multi platform software solution for market technical -analysis and charting. - -Key features of Free Chart Geany: - -* Support for major technical analysis indicators like: Simple Moving Average, -Exponential Moving Average, MACD, Relative Strength Index, Bollinger Bands and -Parabolic SAR. -* Support for various Comma Separated Values (CSV) formats like Metastock 7, -Metastock 8, AMI Broker, Yahoo Finance, Google Finance and Standard CSV. -* Support for various drawing and text objects like Labels, Trailing Text, -Horizontal Lines, Vertical Lines, Trend Lines and Fibonacci Retracements. -* Easy download of quotes from Yahoo Finance or Google Finance. -* Free Chart Geany is a tab based application. You can manage the opened charts -the same way you manage the open pages of your web browser. diff --git a/academic/freechartgeany/freechartgeany.info b/academic/freechartgeany/freechartgeany.info deleted file mode 100644 index 265aec66fc..0000000000 --- a/academic/freechartgeany/freechartgeany.info +++ /dev/null @@ -1,10 +0,0 @@ -PRGNAM="freechartgeany" -VERSION="2.0.3" -HOMEPAGE="http://freechartgeany.sourceforge.net/" -DOWNLOAD="http://downloads.sourceforge.net/freechartgeany/freechartgeany-2.0.3.tar.gz" -MD5SUM="20a084279ea44f99ffb5b18cebbcc217" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="" -MAINTAINER="Larry Hajali" -EMAIL="larryhaja[at]gmail[dot]com" diff --git a/academic/g3data/g3data.SlackBuild b/academic/g3data/g3data.SlackBuild index 7e6b547441..c877a3fe84 100644 --- a/academic/g3data/g3data.SlackBuild +++ b/academic/g3data/g3data.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # # Slackware build script for g3data # @@ -23,10 +23,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=g3data VERSION=${VERSION:-1.5.4} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -36,7 +39,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -61,7 +71,12 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $PRGNAM-$VERSION -tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +# respecting content-disposition may include cgi params in the filename +TARBALL=$CWD/$PRGNAM-$VERSION.tar.gz +if [ ! -e $TARBALL ]; then + TARBALL="$(/bin/ls $TARBALL\?* | head -1)" +fi +tar xvf $TARBALL cd $PRGNAM-$VERSION chown -R root:root . find -L . \ @@ -99,4 +114,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/g3data/g3data.info b/academic/g3data/g3data.info index c85e2d1a5a..e19e7437af 100644 --- a/academic/g3data/g3data.info +++ b/academic/g3data/g3data.info @@ -1,7 +1,7 @@ PRGNAM="g3data" VERSION="1.5.4" HOMEPAGE="https://github.com/pn2200/g3data" -DOWNLOAD="https://github.com/downloads/pn2200/g3data/g3data-1.5.4.tar.gz" +DOWNLOAD="https://slackware.uk/sbosrcarch/by-name/academic/g3data/g3data-1.5.4.tar.gz" MD5SUM="acb41e54ee5fbf167413218f209c4e3f" DOWNLOAD_x86_64="" MD5SUM_x86_64="" diff --git a/academic/gaiasky/README b/academic/gaiasky/README new file mode 100644 index 0000000000..ba6a28970a --- /dev/null +++ b/academic/gaiasky/README @@ -0,0 +1,37 @@ +Gaia Sky is a real-time, 3D, astronomy visualisation software free +and open source that provides a number of features that allows people +to observe and study the space in Virtual Reality. This slackbuild +install the prebuilt package released for Ubuntu. + +Gaia Sky is developed in the framework of ESA's Gaia mission to chart +about 1 billion stars of our Galaxy in the Gaia group of the +Astronomisches Rechen-Institut (ZAH, Universität Heidelberg). + +Hardware requirements: CPU 4 core or higher, GPU with 1 GB RAM with +support for OpenGL (at least 3.2) and GLSL 3.3, memory with 2-6 GB RAM +depending on catalog, and at least 1 GB of free disk space depending +on datasets. + +*** WARNING *** +1. Datasets +Gaia Sky requires pre-packed datasets (Gaia eDR3, NBG, SDSS, OCDR2, +ecc.) provided by the project, but can be used with other datasets in +VOTable, FITS, CSV and other formats (STIL). +When Gaia Sky starts for the first time, the application searches the +default dataset in ~/.local/share/gaiasky/data. If any dataset is not +found, Gaia Sky launches the Download Manager, a graphic interface +that allows to users to download the default dataset required. The +repository provides also other optional datasets which improve the +features of Gaia Sky (some datasets have very large size). For further +information, please read the README.SBo file. + +2. How to start Gaia Sky +A Desktop entry which launches the GUI is provided with the +installation (in Education > Science), but Gaia Sky can be started by +command-line if you want apply some flags. About this mode please read +the README.SBo file. + +3. Virtual Reality +The VR rendering is still in alpha mode: it is uncomplete and may +cause issues depending on the configuration. + diff --git a/academic/gaiasky/README.SBo b/academic/gaiasky/README.SBo new file mode 100644 index 0000000000..ce5288a0de --- /dev/null +++ b/academic/gaiasky/README.SBo @@ -0,0 +1,43 @@ +Further information + +1. About datasets +The Graphic Interface of the Download Manager starts if no datasets +are found in ~/.local/gaiasky/data, otherwise Gaia Sky won't start. + +The datasets available for download are the following: + +Data Packs: +- Basic data pack (REQUIRED): size 88,5 MB. It is the default-data + with 2,573 objects (Solar System objects as planets, satellites, + asteroids, eccetera, Milk Way, Constellations, orbits, ecc.) + +Texture Packs: +- High resolution textures: size 258 MB. + +Gaia stars catalogs: +- Gaia DR3 default: size 1 GB +- Gaia DR3 small: size 560 MB +- Gaia DR3 medium: size 3,3 GB +- Gaia DR3 large: size 8 GB +- Gaia DR3 very large: size 30 GB +- Gaia DR3 extra large: size 45 GB +- Gaia DR3 bright: 566 MB + +These datasets may be downloaded also manually through a web browser: +the Download Manager window provides a link (Manual Download) which +opens the default web browser at the address of the repository. + +Users can install also own or third part datasets. About this please +refer to the documentation on line. + +2. Start with a command-line from a console +This is needed if you want to apply some flags. This is needed if you +want to launch Gaia Sky in Virtual Reality mode: you have to open a +terminal and digit the command + + $ gaiasky -vr (or --openvr) + +Other available flags may be listed with the command + + $ gaiasky -h + diff --git a/academic/QtiPlot/doinst.sh b/academic/gaiasky/doinst.sh index 9a8ded3c60..91a7c14948 100644 --- a/academic/QtiPlot/doinst.sh +++ b/academic/gaiasky/doinst.sh @@ -2,6 +2,6 @@ if [ -x /usr/bin/update-desktop-database ]; then /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 fi -if [ -x /usr/bin/update-mime-database ]; then - /usr/bin/update-mime-database usr/share/mime >/dev/null 2>&1 +if [ -x /sbin/setcap ]; then + /sbin/setcap cap_ipc_lock,cap_sys_nice=ep /usr/lib64/zulu-openjdk17/bin/java fi diff --git a/academic/gaiasky/gaiasky.SlackBuild b/academic/gaiasky/gaiasky.SlackBuild new file mode 100644 index 0000000000..a736f4b832 --- /dev/null +++ b/academic/gaiasky/gaiasky.SlackBuild @@ -0,0 +1,135 @@ +#!/bin/bash + +# Slackware build script for gaiasky + +# Copyright 2023-2024 Giancarlo Dessì, Cagliari, IT +# Based on Booktab.SlackBuild written by Matteo Bernardini +# at https://ponce.cc/slackware/testing/Booktab/ +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=gaiasky +VERSION=${VERSION:-"3.6.0"} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +SRCVERSION=$( echo ${VERSION//./_} ) + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "x86_64" ]; then + SRCARCH="x86-64" + PKGARCH="$ARCH" +elif [ "$ARCH" = "arm" ]; then + printf "\n$ARCH is unsupported for gaiasky...\n\n" + exit 1 +else + SRCARCH="x86" + PKGARCH="i586" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +rm -rf $TMP/$PRGNAM-$VERSION +mkdir $TMP/$PRGNAM-$VERSION + +#Extract the application from the Ubuntu package +ar xv $CWD/${PRGNAM}_linux_$SRCVERSION.deb data.tar.gz +tar xvf data.tar.gz -C $TMP/$PRGNAM-$VERSION +rm -f data.tar.gz + +cd $TMP/$PRGNAM-$VERSION + +# patch the application entry: as is provided it won't work +# in Slackware/KDE +patch -p0 << 'EOF' +--- opt/gaiasky/gaiasky.desktop 2023-04-05 16:00:00.000000000 +0200 ++++ opt/gaiasky/gaiasky.desktop 2023-04-05 16:00:01.000000000 +0200 +@@ -3,6 +3,8 @@ + Name=Gaia Sky + Comment=3D universe simulator for desktop and VR with support for more than a billion objects +-Exec=gaiasky ++Exec=/opt/gaiasky/gaiasky ++GenericName=Desktop 3D universe viewer + Icon=/opt/gaiasky/gs_icon.svg + Terminal=false +-Categories=Science; ++Categories=Education;Science;Astronomy; ++StartupNotify=true + +EOF + +chown -R root:root . + +# The application will be installed in /opt but some files will be moved or +# linked in /usr according to the standard of Slackware installations +mkdir -p usr/share/applications +mkdir -p usr/doc/$PRGNAM-$VERSION +mkdir -p usr/bin + +# link the executable in /usr/bin +cd usr/bin +ln -s ../../opt/gaiasky/gaiasky gaiasky +cd ../../ + +# link the application desktop entry +cp -a opt/gaiasky/gaiasky.desktop usr/share/applications/gaiasky.desktop + +# move the entire tree in package-gaiasky +cp -a * $PKG/ + +# strip ELF objects +find $PKG/opt/gaiasky -type f -print0 | \ + xargs -0 file -m /etc/file/magic/elf | \ + grep 'ELF.*dynamic.*not stripped' | \ + cut -d: -f1 | xargs strip + +chmod 755 $PKG/opt/gaiasky/jre/lib/*.so +chmod 755 $PKG/opt/gaiasky/jre/lib/server/*.so + +# move some documentation files in /usr/doc/gaiasky-x.y.z +mv opt/gaiasky/*.md opt/gaiasky/releasenotes.txt $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/gaiasky/gaiasky.info b/academic/gaiasky/gaiasky.info new file mode 100644 index 0000000000..ecb5220e4e --- /dev/null +++ b/academic/gaiasky/gaiasky.info @@ -0,0 +1,10 @@ +PRGNAM="gaiasky" +VERSION="3.6.0" +HOMEPAGE="https://zah.uni-heidelberg.de/gaia/outreach/gaiasky" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="https://gaia.ari.uni-heidelberg.de/gaiasky/releases/3.6.0.afdd9547d/gaiasky_linux_3_6_0.deb" +MD5SUM_x86_64="f681a23056f157d1a7dc4257318dd16c" +REQUIRES="zulu-openjdk17" +MAINTAINER="Giancarlo Dessi" +EMAIL="slack@giand.it" diff --git a/academic/gaiasky/slack-desc b/academic/gaiasky/slack-desc new file mode 100644 index 0000000000..cc7ca93657 --- /dev/null +++ b/academic/gaiasky/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +gaiasky: gaiasky (3D universe simulator for desktop and VR) +gaiasky: +gaiasky: Gaia Sky is a real-time, 3D, astronomy visualisation software +gaiasky: developed in the framework of ESA's Gaia mission to chart about +gaiasky: 1 billion stars of our Galaxy in the Gaia group of the +gaiasky: Astronomisches Rechen-Institut (ZAH, Universitat Heidelberg). +gaiasky: +gaiasky: +gaiasky: https://zah.uni-heidelberg.de/gaia/outreach/gaiasky +gaiasky: +gaiasky: diff --git a/academic/galculator/galculator.SlackBuild b/academic/galculator/galculator.SlackBuild index 186bf89553..6edd8131a3 100644 --- a/academic/galculator/galculator.SlackBuild +++ b/academic/galculator/galculator.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for galculator @@ -23,10 +23,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=galculator VERSION=${VERSION:-2.1.4} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -36,7 +39,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -70,7 +80,7 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -CFLAGS="$SLKCFLAGS" \ +CFLAGS="$SLKCFLAGS -fcommon" \ CXXFLAGS="$SLKCFLAGS" \ ./autogen.sh \ --prefix=/usr \ @@ -96,4 +106,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/gaw3/gaw3.SlackBuild b/academic/gaw3/gaw3.SlackBuild index 88a77eaf61..3227c027ea 100644 --- a/academic/gaw3/gaw3.SlackBuild +++ b/academic/gaw3/gaw3.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for Gaw3 @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=gaw3 -VERSION=${VERSION:-20170716} +VERSION=${VERSION:-20220315} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -99,4 +109,4 @@ rm $PKG/usr/share/applications/gaw.desktop rm -r $PKG/usr/share/pixmaps cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/gaw3/gaw3.info b/academic/gaw3/gaw3.info index b829c40a98..fdcb7422af 100644 --- a/academic/gaw3/gaw3.info +++ b/academic/gaw3/gaw3.info @@ -1,8 +1,8 @@ PRGNAM="gaw3" -VERSION="20170716" +VERSION="20220315" HOMEPAGE="http://www.rvq.fr/linux/gaw.php" -DOWNLOAD="http://download.tuxfamily.org/gaw/download/gaw3-20170716.tar.gz" -MD5SUM="e9870cf8859cd4d99461e2351c34a2ff" +DOWNLOAD="http://download.tuxfamily.org/gaw/download/gaw3-20220315.tar.gz" +MD5SUM="725382012612626a79149685364d5886" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/gchemutils/README b/academic/gchemutils/README index 9b7f1eeb7f..f8efabc980 100644 --- a/academic/gchemutils/README +++ b/academic/gchemutils/README @@ -9,14 +9,10 @@ Six programs are available: 5) A Spectrum viewer (GSpectrum) 6) A periodic table of the elements application (GChemTable) -Three plugins for external programs are included: -1) A GOffice plugin allows embedding GChemPaint supported files in - programs supporting the GOffice component framework -2) A Gnumeric plugin provides a molar mass function for the spreadsheet -3) A Mozilla plugin allows embedding 2D, 3D and crystal structures as - well as spectra in web pages +A GOffice plugin is included, which allows embedding GChemPaint +supported files in programs supporting the GOffice component +framework. -An optional build-time dependency is gnumeric for building its plugin. - -NOTES: The Mozilla plugin might not be very stable, so if you want -to prevent it from building, pass MOZILLA=NO to the script. +Note: previously, there were also plugins for Mozilla and Gnumeric. +These have been removed because they no longer build with modern +versions of Mozilla and Gnumeric. diff --git a/academic/gchemutils/gchemutils.SlackBuild b/academic/gchemutils/gchemutils.SlackBuild index 99eb6046b1..c06dfb9ab6 100644 --- a/academic/gchemutils/gchemutils.SlackBuild +++ b/academic/gchemutils/gchemutils.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for gchemutils -# Copyright 2011-2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2011-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,13 +22,22 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +# 20220308 bkw: Modified by SlackBuilds.org, BUILD=3: +# - disable the mozilla plugin, since it doesn't build. +# - disable the gnumeric plugin, since it doesn't build either. +# - update the README to explain the above. +# - do not install useless INSTALL in doc dir. + +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=gchemutils VERSION=${VERSION:-0.14.17} -BUILD=${BUILD:-1} +BUILD=${BUILD:-3} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} SRCNAM=gnome-chemistry-utils -MOZILLA=${MOZILLA:-YES} # Build the Mozilla plugin +MOZILLA=${MOZILLA:-NO} # Don't build the Mozilla plugin (it doesn't build) if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -38,7 +47,11 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -69,16 +82,22 @@ cd $SRCNAM-$VERSION chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ + -o -perm 511 \) -exec chmod 755 {} \+ -o \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \+ # Disable Mozilla plugin building if anything other than YES # was given as an argument to MOZILLA= at runtime -[ ! "$MOZILLA" = "YES" ] && mozplug="disable" || mozplug="enable" +#[ ! "$MOZILLA" = "YES" ] && mozplug="disable" || mozplug="enable" + +# 20220308 bkw: force-disable, it no longer builds. +mozplug=disable + +# 20220308 bkw: dike out the gnumeric support, since it's broken. +sed -i.bak '/\(ver\|libspreadsheet\)/s,1\.12,999.99,g' configure CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS -std=c++14" \ ./configure \ --prefix=/usr \ --libdir=/usr/lib${LIBDIRSUFFIX} \ @@ -93,23 +112,20 @@ CXXFLAGS="$SLKCFLAGS" \ --build=$ARCH-slackware-linux make -make install DESTDIR=$PKG - -find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ - | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true - -find $PKG/usr/man -type f -exec gzip -9 {} \; -for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done +make install-strip DESTDIR=$PKG +gzip -9 $PKG/usr/man/man*/* mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - AUTHORS ChangeLog COPYING* INSTALL NEWS README TODO \ + AUTHORS ChangeLog COPYING* NEWS README TODO \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/gcompris-qt/README b/academic/gcompris-qt/README new file mode 100644 index 0000000000..72416bbd9c --- /dev/null +++ b/academic/gcompris-qt/README @@ -0,0 +1,18 @@ +GCompris is a high quality educational software suite, including +a large number of activities for children aged 2 to 10. Some of the +activities are game oriented, but nonetheless still educational. + +Currently GCompris offers more than 100 activities, and more are +being developed. + +This is Qt5-based version of gcompris. + +NOTE: +This software runs better on a platform that has OpenGL 2 support. +If you do not have OpenGL 2 support, you have 2 options: +- Add the following parameter "--software-renderer" at the end of + the last line of the script in /opt/gcompris-qt/bin/gcompris-qt.sh + This will affect all users, system-wide. +- Replace "renderer=auto" into "renderer=software" in your local config, + located in ~/.config/gcompris-qt/gcompris-qt.conf + This will affect current user only. diff --git a/academic/gcompris-qt/doinst.sh b/academic/gcompris-qt/doinst.sh new file mode 100644 index 0000000000..3e5691a052 --- /dev/null +++ b/academic/gcompris-qt/doinst.sh @@ -0,0 +1,9 @@ +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 +fi + +if [ -e usr/share/icons/hicolor/icon-theme.cache ]; then + if [ -x /usr/bin/gtk-update-icon-cache ]; then + /usr/bin/gtk-update-icon-cache usr/share/icons/hicolor >/dev/null 2>&1 + fi +fi diff --git a/academic/gcompris-qt/gcompris-qt b/academic/gcompris-qt/gcompris-qt new file mode 100644 index 0000000000..f77dbd5de6 --- /dev/null +++ b/academic/gcompris-qt/gcompris-qt @@ -0,0 +1,4 @@ +#!/bin/sh + +cd /opt/gcompris-qt/bin +./gcompris-qt.sh diff --git a/academic/gcompris/gcompris.SlackBuild b/academic/gcompris-qt/gcompris-qt.SlackBuild index 0d240c7b0c..01ad6255dc 100644 --- a/academic/gcompris/gcompris.SlackBuild +++ b/academic/gcompris-qt/gcompris-qt.SlackBuild @@ -1,9 +1,8 @@ -#!/bin/sh +#!/bin/bash -# Slackware build script for gcompris +# Slackware build script for gcompris-qt -# Copyright (c) 2009, Paul Liconti -# Copyright 2013-2017 Willy Sudiarto Raharjo <willysr@slackbuilds.org> +# Copyright 2020-2024 Willy Sudiarto Raharjo <willysr@slackbuilds.org> # All rights reserved. # # Redistribution and use in source and binary forms, with or without modification, @@ -27,73 +26,74 @@ # NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS # SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -PRGNAM=gcompris -VERSION=${VERSION:-17.05} +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=gcompris-qt +VERSION=${VERSION:-4.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then - case "$( uname -m )" in - i?86) ARCH=i586 ;; - arm*) ARCH=arm ;; - *) ARCH=$( uname -m ) ;; - esac + ARCH="$( uname -m )" +fi + +case "$ARCH" in + i?86) + ARCH=i586 + SRCARCH=32 + ;; + x86_64) + ARCH=x86_64 + SRCARCH=64 + ;; + *) + echo "Unsupported architecture" + exit 1 + ;; +esac + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 fi -CWD=$(pwd) TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i586" ]; then - SLKCFLAGS="-O2 -march=i586 -mtune=i686" - LIBDIRSUFFIX="" -elif [ "$ARCH" = "i686" ]; then - SLKCFLAGS="-O2 -march=i686 -mtune=i686" - LIBDIRSUFFIX="" -elif [ "$ARCH" = "x86_64" ]; then - SLKCFLAGS="-O2 -fPIC" - LIBDIRSUFFIX="64" -else - SLKCFLAGS="-O2" - LIBDIRSUFFIX="" -fi - set -e rm -rf $PKG -mkdir -p $TMP $PKG $OUTPUT -cd $TMP -rm -rf $PRGNAM-$VERSION -tar xvf $CWD/$PRGNAM-$VERSION.tar.bz2 -cd $PRGNAM-$VERSION -chown -R root:root . -find -L . \ +mkdir -p $PKG/opt/gcompris-qt $OUTPUT +cd $PKG/opt/gcompris-qt + +sh $CWD/$PRGNAM-$VERSION-Linux${SRCARCH}.sh \ + --prefix=$PKG/opt/gcompris-qt \ + --exclude-subdir \ + --skip-license + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +find -L $PKG \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ -./configure \ - --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ - --sysconfdir=/etc \ - --localstatedir=/var \ - --mandir=/usr/man \ - --infodir=/usr/info \ - --docdir=/usr/doc/$PRGNAM-$VERSION \ - --build=$ARCH-slackware-linux - -make -make install DESTDIR=$PKG +install -D -m644 $CWD/gcompris-qt.desktop \ + $PKG/usr/share/applications/gcompris-qt.desktop -find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ - | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true +install -D -m644 $CWD/gcompris-qt.png \ + $PKG/usr/share/icons/hicolor/256x256/apps/gcompris-qt.png + +install -D -m755 $CWD/gcompris-qt $PKG/usr/bin/gcompris-qt + +# move this here to catch anything that may not have proper ownership +chown -R root:root $PKG mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a AUTHORS ChangeLog COPYING INSTALL NEWS README TODO $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install @@ -101,4 +101,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/gcompris-qt/gcompris-qt.desktop b/academic/gcompris-qt/gcompris-qt.desktop new file mode 100644 index 0000000000..6940f39c97 --- /dev/null +++ b/academic/gcompris-qt/gcompris-qt.desktop @@ -0,0 +1,88 @@ +[Desktop Entry] +Name=GCompris +Name[ca]=GCompris +Name[cs]=GCompris +Name[el]=GCompris +Name[en_GB]=GCompris +Name[es]=GCompris +Name[et]=GCompris +Name[eu]=GCompris +Name[fr]=GCompris +Name[gl]=GCompris +Name[it]=GCompris +Name[ml]=ജികോംപàµà´°à´¿ +Name[nl]=GCompris +Name[nn]=GCompris +Name[pl]=GCompris +Name[pt]=GCompris +Name[pt_BR]=GCompris +Name[ro]=GCompris +Name[sk]=GCompris +Name[sv]=GCompris +Name[uk]=GCompris +Name[x-test]=xxGComprisxx +Name[zh_TW]=GCompris +GenericName=Educational Game +GenericName[ca]=Joc educatiu +GenericName[cs]=Výuková hra +GenericName[el]=Εκπαιδευτικό παιχνίδι +GenericName[en_GB]=Educational Game +GenericName[es]=Juego educativo +GenericName[et]=Hariv mäng +GenericName[eu]=Hezkuntza-jokoa +GenericName[fr]=Jeu éducatif +GenericName[gl]=Xogo educativo +GenericName[it]=Gioco didattico +GenericName[ml]=വിദàµà´¯à´¾à´àµà´¯à´¾à´¸à´ªà´°à´®à´¾à´¯ കളി +GenericName[nl]=Educatief spel +GenericName[nn]=Leik-og-lær-spel +GenericName[pl]=Gra edukacyjna +GenericName[pt]=Jogo Educativo +GenericName[pt_BR]=Jogo educacional +GenericName[ro]=Joc educaÈ›ional +GenericName[sk]=Výuková hra +GenericName[sv]=Pedagogiskt spel +GenericName[uk]=ОÑÐ²Ñ–Ñ‚Ð½Ñ Ð³Ñ€Ð° +GenericName[x-test]=xxEducational Gamexx +GenericName[zh_CN]=æ•™è‚²æ¸¸æˆ +GenericName[zh_TW]=教育éŠæˆ² +Comment=Multi-Activity Educational game for children 2 to 10 +Comment[br]=C'hoari kelennadel gant oberezhioù a bep seurt evit ar vugale etre 2 ha 10 vloaz +Comment[ca]=Joc educatiu amb múltiples activitats per a infants de 2 a 10 anys +Comment[ca@valencia]=Joc educatiu amb múltiples activitats per a infants de 2 a 10 anys +Comment[de]=Lernspiel mit vielen Aktivitäten für Kinder von 2 bis 10 Jahren +Comment[el]=Εκπαιδευτικό παιχνίδι πολλαπλών δÏαστηÏιοτήτων για ηλικίες 2 Îως 10 ετών +Comment[en_GB]=Multi-Activity Educational game for children 2 to 10 +Comment[es]=Juego educativo multiactividad para niños de 2 a 10 años +Comment[et]=Rohkete tegevustega hariv mäng lastele vanuses 2-10 +Comment[eu]=Jarduera anitzeko Hezkuntza-jokoa 2 eta 10 urte arteko haurrentzat +Comment[fi]=Useampitoimintoinen opettavainen peli 2–10-vuotiaille lapsille +Comment[fr]=Jeu éducatif multi-activités pour les enfants de 2 à 10 ans +Comment[gl]=Xogo educativo con varias actividades para nenos entre 2 e 10 anos +Comment[hi]=२ से १० वरà¥à¤· के बचà¥à¤šà¥‹à¤‚ के लिठविà¤à¤¿à¤¨à¥à¤¨ कà¥à¤°à¤¿à¤¯à¤¾à¤à¤‚ वाला शेकà¥à¤·à¤£à¤¿à¤• खेल +Comment[id]=GCompris adalah kumpulan permainan kegiatan pendidikan untuk anak umur 2 sampai 10 tahun +Comment[it]=Gioco didattico multi-attività per bambini da 2 a 10 anni +Comment[ko]=2-10세 어린ì´ë¥¼ 위한 다양한 활ë™ì´ 있는 êµìœ¡ìš© 게임 +Comment[ml]=2 à´®àµà´¤àµ½ 10 വയസàµà´¸àµà´µà´°àµ†à´¯àµà´³àµà´³ à´•àµà´Ÿàµà´Ÿà´¿à´•àµ¾à´•àµà´•àµ വിവിധ à´ªàµà´°à´µàµ¼à´¤àµà´¤à´¨à´™àµà´™à´³à´¿à´²àµ‚ടെ പഠികàµà´•à´¾à´¨à´¾à´¯àµà´³àµà´³ കളി. +Comment[nl]=Educatief spel met meerdere activiteiten voor kinderen van 2 tot 10 +Comment[nn]=Leik-og-lærspel med mange aktivitetar – for barn frÃ¥ 2 til 10 Ã¥r +Comment[pl]=Gra edukacyjna z wieloma aktywnoÅ›ciami dla dzieci w wieku od 2 do 10 lat +Comment[pt]=Jogo educativo multi-actividades para crianças dos 2 aos 10 anos +Comment[pt_BR]=Jogo educacional com várias atividades para crianças de 2 a 10 anos +Comment[ro]=Joc educaÈ›ional cu activități multiple pentru copii între 2 È™i 10 ani +Comment[ru]=Обучающие игры Ð´Ð»Ñ Ð´ÐµÑ‚ÐµÐ¹ от 2 до 10 лет +Comment[sk]=Viac-aktivitová výuková hra pre deti od 2 do 10 rokov +Comment[sl]=Izobraževalna igra z veÄ dejavnostmi za otroke med drugim in desetim letom starosti +Comment[sv]=Pedagogiskt multiaktivitetsspel för barn frÃ¥n 2 till 10 Ã¥r +Comment[tr]=2-10 yaÅŸ arası çocuklar için Çoklu EtkileÅŸimli EÄŸitici oyun +Comment[uk]=Ðабір оÑвітніх ігор Ð´Ð»Ñ Ð´Ñ–Ñ‚ÐµÐ¹ від 2 до 10 років +Comment[x-test]=xxMulti-Activity Educational game for children 2 to 10xx +Comment[zh_CN]=为 2 到 10 å²å„¿ç«¥å‡†å¤‡çš„å¤šåŠŸèƒ½æ•™è‚²æ¸¸æˆ +Comment[zh_TW]=為 2-10 æ²å©åè¨è¨ˆçš„教育éŠæˆ² +Exec=gcompris-qt +Icon=gcompris-qt +Terminal=false +Type=Application +Categories=Education;Game;KidsGame; +StartupNotify=true +X-DocPath=gcompris/index.html diff --git a/academic/gcompris-qt/gcompris-qt.info b/academic/gcompris-qt/gcompris-qt.info new file mode 100644 index 0000000000..835328b6ce --- /dev/null +++ b/academic/gcompris-qt/gcompris-qt.info @@ -0,0 +1,10 @@ +PRGNAM="gcompris-qt" +VERSION="4.0" +HOMEPAGE="https://gcompris.net/" +DOWNLOAD="https://gcompris.net/download/qt/linux/gcompris-qt-4.0-Linux32.sh" +MD5SUM="c28334c56e8c7f74888a2b641cbcca6f" +DOWNLOAD_x86_64="https://gcompris.net/download/qt/linux/gcompris-qt-4.0-Linux64.sh" +MD5SUM_x86_64="3f0714ef303ea3bc3799b614bcbd5857" +REQUIRES="" +MAINTAINER="Willy Sudiarto Raharjo" +EMAIL="willysr@slackbuilds.org" diff --git a/academic/gcompris-qt/gcompris-qt.png b/academic/gcompris-qt/gcompris-qt.png Binary files differnew file mode 100644 index 0000000000..40cec079f4 --- /dev/null +++ b/academic/gcompris-qt/gcompris-qt.png diff --git a/academic/gcompris-qt/slack-desc b/academic/gcompris-qt/slack-desc new file mode 100644 index 0000000000..995c085f2f --- /dev/null +++ b/academic/gcompris-qt/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +gcompris-qt: gcompris-qt (an educational software suite) +gcompris-qt: +gcompris-qt: GCompris is a high quality educational software suite, including +gcompris-qt: a large number of activities for children aged 2 to 10. Some of the +gcompris-qt: activities are game orientated, but nonetheless still educational. +gcompris-qt: +gcompris-qt: Currently GCompris offers more than 100 activities, and more are +gcompris-qt: being developed. +gcompris-qt: +gcompris-qt: Homepage: http://gcompris.net/ +gcompris-qt: diff --git a/academic/gcompris/README b/academic/gcompris/README deleted file mode 100644 index ec155c2ea3..0000000000 --- a/academic/gcompris/README +++ /dev/null @@ -1,5 +0,0 @@ -GCompris is an educational software suite comprising of numerous activities -for children aged 2 to 10. Some of the activities are game oriented, but -nonetheless still educational. Currently GCompris offers in excess of 140 -activities and more are being developed. GCompris currently is translated -in more than 40 languages. diff --git a/academic/gcompris/doinst.sh b/academic/gcompris/doinst.sh deleted file mode 100644 index 3857649f50..0000000000 --- a/academic/gcompris/doinst.sh +++ /dev/null @@ -1,3 +0,0 @@ -if [ -x /usr/bin/update-desktop-database ]; then - /usr/bin/update-desktop-database -q usr/share/applications &> /dev/null -fi diff --git a/academic/gcompris/gcompris.info b/academic/gcompris/gcompris.info deleted file mode 100644 index 61262a62e5..0000000000 --- a/academic/gcompris/gcompris.info +++ /dev/null @@ -1,10 +0,0 @@ -PRGNAM="gcompris" -VERSION="17.05" -HOMEPAGE="http://gcompris.net/" -DOWNLOAD="http://gcompris.net/download/gtk/src/gcompris-17.05.tar.bz2" -MD5SUM="6c0733db29ca3d6b4100cdccc7a7a720" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="" -MAINTAINER="Willy Sudiarto Raharjo" -EMAIL="willysr@slackbuilds.org" diff --git a/academic/gcompris/slack-desc b/academic/gcompris/slack-desc deleted file mode 100644 index fa37de57dc..0000000000 --- a/academic/gcompris/slack-desc +++ /dev/null @@ -1,19 +0,0 @@ -# HOW TO EDIT THIS FILE: -# The "handy ruler" below makes it easier to edit a package description. -# Line up the first '|' above the ':' following the base package name, and -# the '|' on the right side marks the last column you can put a character in. -# You must make exactly 11 lines for the formatting to be correct. It's also -# customary to leave one space after the ':' except on otherwise blank lines. - - |-----handy-ruler------------------------------------------------------| -gcompris: gcompris (an educational software suite for children ages 2 to 10) -gcompris: -gcompris: GCompris is an educational software suite comprising of numerous -gcompris: activities for children aged 2 to 10. Some of the activities are game -gcompris: orientated, but nonetheless still educational. Currently GCompris -gcompris: offers in excess of 140 activities and more are being developed. -gcompris: GCompris currently is translated in more than 40 languages. -gcompris: -gcompris: Homepage: http://gcompris.net/ -gcompris: -gcompris: diff --git a/academic/gdstk/README b/academic/gdstk/README new file mode 100644 index 0000000000..2d5a39f1c5 --- /dev/null +++ b/academic/gdstk/README @@ -0,0 +1,12 @@ +gdstk (C++ library for manipulation of GDSII and OASIS files. ) + +Gdstk (GDSII Tool Kit) is a C++ library for creation and +manipulation of GDSII and OASIS files. It is also available as a +Python module meant to be a successor to Gdspy. Key features for the +creation of complex CAD layouts are included: Boolean operations on +polygons (AND, OR, NOT, XOR) based on clipping algorithm, Polygon +offset (inward and outward rescaling of polygons), Efficient +point-in-polygon solutions for large array sets. +Typical applications of Gdstk are in the fields of electronic chip +design, planar lightwave circuit design, and mechanical engineering. + diff --git a/academic/gdstk/gdstk.SlackBuild b/academic/gdstk/gdstk.SlackBuild new file mode 100644 index 0000000000..7a14390770 --- /dev/null +++ b/academic/gdstk/gdstk.SlackBuild @@ -0,0 +1,119 @@ +#!/bin/bash + +# Slackware build script for gdstk + +# Copyright 2023, Lockywolf +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=gdstk +VERSION=${VERSION:-0.9.46} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +elif [ "$ARCH" = "aarch64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} + -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} + + +#sed -i 's/qh_nextfacet2d/qh_nextfacet/g' src/utils.cpp + +sed -i 's|add_library(gdstk|add_library(gdstk SHARED|g' src/CMakeLists.txt + +mkdir -p build +cd build + cmake \ + -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DLIB_SUFFIX=${LIBDIRSUFFIX} \ + -DMAN_INSTALL_DIR=/usr/man \ + -DCMAKE_CXX_COMPILER_LAUNCHER=ccache \ + -DCMAKE_C_COMPILER_LAUNCHER=ccache \ + -DCMAKE_BUILD_TYPE=Release .. + make + make install/strip DESTDIR=$PKG +cd .. + +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + README.md \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/gdstk/gdstk.info b/academic/gdstk/gdstk.info new file mode 100644 index 0000000000..4634504c1c --- /dev/null +++ b/academic/gdstk/gdstk.info @@ -0,0 +1,10 @@ +PRGNAM="gdstk" +VERSION="0.9.46" +HOMEPAGE="https://heitzmann.github.io/gdstk/" +DOWNLOAD="https://github.com/heitzmann/gdstk/archive/v0.9.46/gdstk-0.9.46.tar.gz" +MD5SUM="618e717dde0a136612254d3f0022d510" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="qhull" +MAINTAINER="Lockywolf" +EMAIL="for_sbo.gdstk_2023-11-19@lockywolf.net" diff --git a/academic/gdstk/slack-desc b/academic/gdstk/slack-desc new file mode 100644 index 0000000000..fe5d87eea6 --- /dev/null +++ b/academic/gdstk/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +gdstk: gdstk (C++ library for manipulation of GDSII and OASIS files. ) +gdstk: +gdstk: Gdstk (GDSII Tool Kit) is a C++ library for creation and +gdstk: manipulation of GDSII and OASIS files. It is also available as a +gdstk: Python module meant to be a successor to Gdspy. Key features for the +gdstk: creation of complex CAD layouts are included: Boolean operations on +gdstk: polygons (AND, OR, NOT, XOR) based on clipping algorithm, Polygon +gdstk: offset (inward and outward rescaling of polygons), Efficient +gdstk: point-in-polygon solutions for large array sets. +gdstk: Typical applications of Gdstk are in the fields of electronic chip +gdstk: design, planar lightwave circuit design, and mechanical engineering. diff --git a/academic/geda-gaf/README b/academic/geda-gaf/README index 58eabd38cd..d5484fbf37 100644 --- a/academic/geda-gaf/README +++ b/academic/geda-gaf/README @@ -1,8 +1,8 @@ -The gEDA project has produced and continues working on a full GPL'd suite -and toolkit of Electronic Design Automation tools. These tools are used for -electrical circuit design, schematic capture, simulation, prototyping, and -production. Currently, the gEDA project offers a mature suite of free -software applications for electronics design, including schematic capture, -attribute management, bill of materials (BOM) generation, netlisting into -over 20 netlist formats, analog and digital simulation, and printed circuit -board (PCB) layout. +The gEDA project has produced and continues working on a full GPL'd +suite and toolkit of Electronic Design Automation tools. These tools +are used for electrical circuit design, schematic capture, simulation, +prototyping, and production. Currently, the gEDA project offers a +mature suite of free software applications for electronics design, +including schematic capture, attribute management, bill of materials +(BOM) generation, netlisting into over 20 netlist formats, analog and +digital simulation, and printed circuit board (PCB) layout. diff --git a/academic/geda-gaf/geda-gaf.SlackBuild b/academic/geda-gaf/geda-gaf.SlackBuild index 790eb328a6..0feae7e775 100644 --- a/academic/geda-gaf/geda-gaf.SlackBuild +++ b/academic/geda-gaf/geda-gaf.SlackBuild @@ -1,32 +1,42 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for gEDA / gaf # Written by Stephen Van Berg stephen_van_berg@earlicker.com # Updated by Kyle Guinn <elyk03@gmail.com> +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=geda-gaf -VERSION=${VERSION:-1.8.2} -BUILD=${BUILD:-1} +VERSION=${VERSION:-1.10.2} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="ABOUT-NLS AUTHORS COPYING* ChangeLog HACKING INSTALL NEWS README" -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -80,9 +90,11 @@ mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a $DOCS $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/geda-gaf/geda-gaf.info b/academic/geda-gaf/geda-gaf.info index 3664fa7fb5..7cb0caa577 100644 --- a/academic/geda-gaf/geda-gaf.info +++ b/academic/geda-gaf/geda-gaf.info @@ -1,10 +1,10 @@ PRGNAM="geda-gaf" -VERSION="1.8.2" +VERSION="1.10.2" HOMEPAGE="http://www.geda-project.org/" -DOWNLOAD="http://ftp.geda-project.org/geda-gaf/stable/v1.8/1.8.2/geda-gaf-1.8.2.tar.gz" -MD5SUM="fa8a807615decf47027e22a217dd0ded" +DOWNLOAD="http://ftp.geda-project.org/geda-gaf/stable/v1.10/1.10.2/geda-gaf-1.10.2.tar.gz" +MD5SUM="39377764735bd4ce5360371614541a25" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="" +REQUIRES="guile2.2" MAINTAINER="Stephen Van Berg" EMAIL="stephen_van_berg@earlicker.com" diff --git a/academic/gelemental/gelemental.SlackBuild b/academic/gelemental/gelemental.SlackBuild index e4b332e18a..7541dfe91b 100644 --- a/academic/gelemental/gelemental.SlackBuild +++ b/academic/gelemental/gelemental.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for gelemental -# Copyright 2011-2019 Petar Petrov slackalaxy@gmail.com +# Copyright 2011-2023 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=gelemental -VERSION=${VERSION:-2.0.0} +VERSION=${VERSION:-2.0.2} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -90,15 +100,20 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr find $PKG/usr/man -type f -exec gzip -9 {} \; for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done +# Only one category... +sed -i "s:GTK;Education;Science;Chemistry;:Education:" $PKG/usr/share/applications/$PRGNAM.desktop + mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - AUTHORS ChangeLog COPYING COPYING.DATA INSTALL README NEWS NEWS-GPeriodic TODO TRANSLATORS \ + AUTHORS ChangeLog COPYING COPYING.DATA README NEWS NEWS-GPeriodic TODO TRANSLATORS \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/gelemental/gelemental.info b/academic/gelemental/gelemental.info index 17d587816a..5b79c725b8 100644 --- a/academic/gelemental/gelemental.info +++ b/academic/gelemental/gelemental.info @@ -1,8 +1,8 @@ PRGNAM="gelemental" -VERSION="2.0.0" -HOMEPAGE="http://freecode.com/projects/gelemental" -DOWNLOAD="https://github.com/ginggs/gelemental/archive/v2.0.0/gelemental-2.0.0.tar.gz" -MD5SUM="8d38d7599b0f2fc96e2bd622cd762b9a" +VERSION="2.0.2" +HOMEPAGE="https://github.com/ginggs/gelemental/" +DOWNLOAD="https://github.com/ginggs/gelemental/archive/v2.0.2/gelemental-2.0.2.tar.gz" +MD5SUM="cbbc25d9648c76d8f17a96db3fa30314" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/gem5/README b/academic/gem5/README new file mode 100644 index 0000000000..c3de9f48c4 --- /dev/null +++ b/academic/gem5/README @@ -0,0 +1,20 @@ + The gem5 simulator is a modular platform for computer-system +architecture research, encompassing system-level architecture as +well as processor microarchitecture. gem5 is a community led project + with an open governance model. + + gem5 was originally conceived for computer architecture research +in academia, but it has grown to be used in computer system design +by academia, industry for research, and in teaching. + +By default it's build the X86 simulator, you can set to other +architectures with a environment variable as following: + - MIPS=yes + - POWER=yes + - RISCV=yes + - SPARC=yes + +Optional: + - protobuf-c (for tracing support) + - hdf5 + diff --git a/academic/gem5/gem5.SlackBuild b/academic/gem5/gem5.SlackBuild new file mode 100644 index 0000000000..81ce3cbb77 --- /dev/null +++ b/academic/gem5/gem5.SlackBuild @@ -0,0 +1,160 @@ +#!/bin/bash + +# Slackware build script for gem5 + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=gem5 +VERSION=${VERSION:-20.1.0.5} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION + +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +if [ "${ARM:-no}" == "yes" ]; then + GEM5_ISA="ARM" + SCONS_OPTS="USE_SYSTEMC=no" +fi + +if [ "${MIPS:-no}" == "yes" ]; then + GEM5_ISA="$GEM5_ISA MIPS" +fi + +if [ "${POWER:-no}" == "yes" ]; then + GEM5_ISA="$GEM5_ISA POWER" +fi + +if [ "${RISCV:-no}" == "yes" ]; then + GEM5_ISA="$GEM5_ISA RISCV" +fi + +if [ "${RISCV:-no}" == "yes" ]; then + GEM5_ISA="$GEM5_ISA SPARC" +fi + +if [ ! "${X86:-yes}" == "no" ]; then + GEM5_ISA="$GEM5_ISA X86" +elif [ -z $GEM5_ISA ]; then + echo "At least one ISA must be enabled" + echo "The following ISA are available" + echo "X86 ARM MIPS POWER RISCV SPARC" +fi + +if [ "${DEBUG:-no}" == "yes" ]; then + VARIANT=debug +elif [ "${OPT:-no}" == "yes" ]; then + VARIANT=opt +else + VARIANT=fast +fi + +for gem5_isa in $GEM5_ISA; do + CCFLAGS_EXTRA="$SLKCFLAGS" \ + scons $SCONS_OPTS build/$gem5_isa/gem5.$VARIANT +done + +INSTALL_DIR=$PKG/opt/gem5-$VERSION + +# install binary +mkdir -p $INSTALL_DIR/bin +for gem5_isa in $GEM5_ISA; do + cp -a build/$gem5_isa/gem5.$VARIANT \ + $INSTALL_DIR/bin/gem5-$gem5_isa\.$VARIANT +done + +# install auxiliar files/tools +cp -a configs $INSTALL_DIR +cp -a system $INSTALL_DIR +cp -a tests $INSTALL_DIR +cp -a util $INSTALL_DIR + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +find $PKG -depth -type d -empty -delete || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a CODE-OF-CONDUCT.md CONTRIBUTING.md COPYING LICENSE \ + MAINTAINERS RELEASE-NOTES.md $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/gem5/gem5.info b/academic/gem5/gem5.info new file mode 100644 index 0000000000..6855672c44 --- /dev/null +++ b/academic/gem5/gem5.info @@ -0,0 +1,10 @@ +PRGNAM="gem5" +VERSION="20.1.0.5" +HOMEPAGE="https://www.gem5.org" +DOWNLOAD="https://github.com/gem5/gem5/archive/v20.1.0.5/gem5-20.1.0.5.tar.gz" +MD5SUM="323f9a6eab649fbf7e12746695c0aeed" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/gem5/slack-desc b/academic/gem5/slack-desc new file mode 100644 index 0000000000..2654f3f312 --- /dev/null +++ b/academic/gem5/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +gem5: gem5 (gem5 is an open-source system-level and processor simulator) +gem5: +gem5: The gem5 simulator is a modular platform for computer-system +gem5: architecture research, encompassing system-level architecture as +gem5: well as processor microarchitecture. gem5 is a community led project +gem5: with an open governance model. +gem5: gem5 was originally conceived for computer architecture research +gem5: in academia, but it has grown to be used in computer system design +gem5: by academia, industry for research, and in teaching. +gem5: +gem5: diff --git a/academic/geneconv/README b/academic/geneconv/README index 885f156f08..b759ef4c55 100644 --- a/academic/geneconv/README +++ b/academic/geneconv/README @@ -25,3 +25,8 @@ geneconv myfile.nex -nolog CITING: For references and citation information, check the documentation folder of the package. + +NOTE! +The program GENECONV is free for academic use, but commercial rights are +reserved. The program may be freely distributed for academic use, as +long as it is not altered or renamed. diff --git a/academic/geneconv/geneconv.SlackBuild b/academic/geneconv/geneconv.SlackBuild index 6deb7a5204..e3d01aa1bb 100644 --- a/academic/geneconv/geneconv.SlackBuild +++ b/academic/geneconv/geneconv.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for geneconv -# Copyright 2014-2016 Petar Petrov slackalaxy@gmail.com +# Copyright 2014-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,29 +22,39 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=geneconv VERSION=${VERSION:-1.81a} -BUILD=${BUILD:-2} +BUILD=${BUILD:-3} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} SRCNAM=unix.source DOCNAM=unix.examples if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" elif [ "$ARCH" = "x86_64" ]; then @@ -93,4 +103,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/genius/README b/academic/genius/README index d4a270574c..844fbd0219 100644 --- a/academic/genius/README +++ b/academic/genius/README @@ -5,7 +5,3 @@ in some aspects to BC, Matlab, Maple or Mathematica. It is useful both as a simple calculator and as a research or educational tool. The syntax is very intuitive and is designed to mimic how mathematics is usually written. - -If you would like the GUI interface as well, it requires -libgnomeui and gtksourceview. If you have these dependencies, -pass the variable of GNOME=YES (or anything that isn't NO ;) diff --git a/academic/genius/genius.SlackBuild b/academic/genius/genius.SlackBuild index b1a8669355..6170b1f2c0 100644 --- a/academic/genius/genius.SlackBuild +++ b/academic/genius/genius.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for genius # Copyright 2009,2010,2018 Vincent Batts, vbatts@hashbangbash.com, http://hashbangbash.com/ @@ -22,32 +22,36 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. # +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=genius -VERSION=${VERSION:-1.0.23} +VERSION=${VERSION:-1.0.27} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -GNOME=${GNOME:-NO} -GNOME_FLAGS="--disable-gtksourceview --disable-gnome" -if [ "$GNOME" != "NO" ] ; then - GNOME_FLAGS="" -fi - -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -75,8 +79,10 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -CFLAGS="$SLKCFLAGS -std=gnu89" \ -CXXFLAGS="$SLKCFLAGS -std=gnu89" \ +autoreconf -vif + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ ./configure \ --prefix=/usr \ --libdir=/usr/lib${LIBDIRSUFFIX} \ @@ -84,9 +90,7 @@ CXXFLAGS="$SLKCFLAGS -std=gnu89" \ --localstatedir=/var \ --mandir=/usr/man \ --docdir=/usr/doc/$PRGNAM-$VERSION \ - --disable-scrollkeeper \ --disable-update-mimedb \ - $GNOME_FLAGS \ --build=$ARCH-slackware-linux make @@ -105,4 +109,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/genius/genius.info b/academic/genius/genius.info index b072a17292..f4eaec93fb 100644 --- a/academic/genius/genius.info +++ b/academic/genius/genius.info @@ -1,10 +1,10 @@ PRGNAM="genius" -VERSION="1.0.23" +VERSION="1.0.27" HOMEPAGE="http://www.5z.com/jirka/genius.html" -DOWNLOAD="http://ftp.5z.com/pub/genius/genius-1.0.23.tar.xz" -MD5SUM="3e94a5898e59c069c564f00136c2450d" +DOWNLOAD="https://download.gnome.org/sources/genius/1.0/genius-1.0.27.tar.xz" +MD5SUM="d510beed59c2b9ad52a56153e5825fb8" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="rarian" +REQUIRES="gtksourceview4" MAINTAINER="Vincent Batts" EMAIL="vbatts@hashbangbash.com" diff --git a/academic/genometools/genometools.SlackBuild b/academic/genometools/genometools.SlackBuild index f4af4db0f9..47f6ca9adf 100644 --- a/academic/genometools/genometools.SlackBuild +++ b/academic/genometools/genometools.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for genometools -# Copyright 2014-2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2014-2022 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=genometools -VERSION=${VERSION:-1.5.10} +VERSION=${VERSION:-1.6.2} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -66,17 +76,26 @@ rm -rf $PRGNAM-$VERSION tar xvf $CWD/$PRGNAM-$VERSION.tar.gz cd $PRGNAM-$VERSION chown -R root:root . + +# This is a looping symlink that the 'find' step below complains about. +# The only thing that is used from this location is 'sam.h', so let's +# just make a proper folder and copy it there. +rm src/external/samtools-0.1.18/samtools +mkdir -p src/external/samtools-0.1.18/samtools +cp src/external/samtools-0.1.18/sam.h src/external/samtools-0.1.18/samtools + find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ -o -perm 511 \) -exec chmod 755 {} \; -o \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -# Fix library path +# Fix library and man pages path sed -i "s:lib/libgenometools:lib${LIBDIRSUFFIX}/libgenometools:g" Makefile sed -i "s:\$(prefix)/lib:\$(prefix)/lib${LIBDIRSUFFIX}:g" Makefile +sed -i "s:/share/man/:/man/:g" Makefile -CFLAGS="$SLKCFLAGS" \ +CFLAGS="$SLKCFLAGS -Wno-error=format-truncation=" \ CXXFLAGS="$SLKCFLAGS" \ make $BUILDARCH \ prefix=/usr @@ -90,10 +109,6 @@ cd gtpython python setup.py install --root=$PKG cd .. -# We don't need this -rm -rf $PKG/usr/bin/genometools-config -rm -rf $PKG/usr/lib${LIBDIRSUFFIX}/libgenometools.a - find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true @@ -108,4 +123,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/genometools/genometools.info b/academic/genometools/genometools.info index 5026cd2a29..cac6f3b826 100644 --- a/academic/genometools/genometools.info +++ b/academic/genometools/genometools.info @@ -1,8 +1,8 @@ PRGNAM="genometools" -VERSION="1.5.10" +VERSION="1.6.2" HOMEPAGE="http://genometools.org/" -DOWNLOAD="http://genometools.org/pub/genometools-1.5.10.tar.gz" -MD5SUM="2c654825746692b968e1c58873b6a3d2" +DOWNLOAD="http://genometools.org/pub/genometools-1.6.2.tar.gz" +MD5SUM="431e34d5490148dbcbc95e3de7ac4b78" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/genpak/genpak.SlackBuild b/academic/genpak/genpak.SlackBuild index 9cf201f994..0a6ecb902c 100644 --- a/academic/genpak/genpak.SlackBuild +++ b/academic/genpak/genpak.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for genpak -# Copyright 2011-2016 Petar Petrov slackalaxy@gmail.com +# Copyright 2011-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,26 +22,37 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +# 20220408 bkw: Modified by SlackBuilds.org, BUILD=7: +# - get rid of /usr/doc/gp symlink. +# - remove useless INSTALL.TXT from doc dir. + +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=genpak VERSION=${VERSION:-0.26} -BUILD=${BUILD:-4} +BUILD=${BUILD:-7} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -64,16 +75,16 @@ tar xvf $CWD/gp-$VERSION.tgz cd gp-$VERSION chown -R root:root . find -L . \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \+ -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \+ # arch-independent data files belong in /usr/share: sed -i "s,usr/lib/,usr/share/,g" src/* man1/* html/* *.TXT make \ - CFLAGS="$SLKCFLAGS" \ + CFLAGS="$SLKCFLAGS -fcommon" \ TREE=/usr \ BINDIR=/usr/bin \ DATADIR=/usr/share \ @@ -92,14 +103,13 @@ make install docs \ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true -find $PKG/usr/man -type f -exec gzip -9 {} \; -for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done +gzip -9 $PKG/usr/man/man*/* -( cd $PKG/usr/doc ; mv gp $PRGNAM-$VERSION ; ln -s $PRGNAM-$VERSION gp ) +( cd $PKG/usr/doc ; rm gp/INSTALL.TXT ; mv gp $PRGNAM-$VERSION ) cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/geomview/README b/academic/geomview/README index 07f1a998fa..2a98653434 100644 --- a/academic/geomview/README +++ b/academic/geomview/README @@ -1,9 +1,9 @@ Geomview is an interactive 3D viewing program for Unix. -Geomview lets you view and manipulate three-dimensional objects: you -use the mouse to rotate, translate, zoom in and out, and so on. +Geomview lets you view and manipulate three-dimensional objects: +you use the mouse to rotate, translate, zoom in and out, and so on. Geomview can be used as a standalone viewer for static objects (it supports a variety of file formats) or as a display engine for other programs which produce dynamically changing geometry. -This slackBuild uses the configure option --with-opengl. +This SlackBuild uses the configure option --with-opengl. diff --git a/academic/geomview/geomview.SlackBuild b/academic/geomview/geomview.SlackBuild index 23786322ec..546d3fb357 100644 --- a/academic/geomview/geomview.SlackBuild +++ b/academic/geomview/geomview.SlackBuild @@ -1,30 +1,57 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for geomview -# Written by (Jorge Barros de Abreu) -# (http://sites.google.com/site/ficmatinf) +# Copyright 2013 Jorge Barros de Abreu +# 2013-2022 Maintained by the SBo team +# 2023 Updated to 1.9.5 by Philip Lacroix <slackph at posteo dot de> +# +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) PRGNAM=geomview -VERSION=${VERSION:-1.9.4} +VERSION=${VERSION:-1.9.5} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -52,10 +79,6 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ -exec chmod 644 {} \; -# -#geomview compilation -# - CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ @@ -86,15 +109,27 @@ for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; r gzip -c -9 $PRGNAM-2 > $PRGNAM.info-2.gz rm -fr dir figs $PRGNAM-* $PRGNAM ) -mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +# Install documentation. +PRGDOC=$PKG/usr/doc/$PRGNAM-$VERSION +mkdir -p $PRGDOC cp -a \ doc/figs doc/*.txt doc/*.c doc/*.tcl doc/README* doc/*.gvplot doc/oogltour* \ - $PKG/usr/doc/$PRGNAM-$VERSION -rm -f $PKG/usr/doc/$PRGNAM-$VERSION/*.pdf # We already have the html ones -cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + $PRGDOC +# +# Move plain text files (no troff) to /usr/doc. +( cd $PKG/usr/man/man3 + zcat lisp.3gv.gz > $PRGDOC/lisp.txt + rm -rf lisp.3gv.gz ) +( cd $PKG/usr/man/man5 + zcat geomview.5gv.gz > $PRGDOC/geomview.txt + zcat oogl.5gv.gz > $PRGDOC/oogl.txt + rm -rf geomview.5gv.gz oogl.5gv.gz ) +cat $CWD/$PRGNAM.SlackBuild > $PRGDOC/$PRGNAM.SlackBuild + +rm -f $PKG/usr/lib*/*.la mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/geomview/geomview.info b/academic/geomview/geomview.info index 012d830954..c8601b3d2c 100644 --- a/academic/geomview/geomview.info +++ b/academic/geomview/geomview.info @@ -1,8 +1,8 @@ PRGNAM="geomview" -VERSION="1.9.4" +VERSION="1.9.5" HOMEPAGE="http://www.geomview.org" -DOWNLOAD="http://downloads.sourceforge.net/geomview/geomview-1.9.4.tar.gz" -MD5SUM="29c7e6d678af7b9968980f92954419bb" +DOWNLOAD="https://downloads.sourceforge.net/geomview/geomview-1.9.5.tar.gz" +MD5SUM="98ada147dfcbabca7c48137590e74a85" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/geomview/slack-desc b/academic/geomview/slack-desc index d3d3e38801..58bedec367 100644 --- a/academic/geomview/slack-desc +++ b/academic/geomview/slack-desc @@ -8,12 +8,12 @@ |-----handy-ruler------------------------------------------------------| geomview: geomview (3D geometrical package) geomview: -geomview: Geomview is an interactive 3D viewing program for Unix. -geomview: Geomview lets you view and manipulate three-dimensional objects: you -geomview: use the mouse to rotate, translate, zoom in and out, and so on. -geomview: Geomview can be used as a standalone viewer for static objects (it -geomview: supports a variety of file formats) or as a display engine for other -geomview: programs which produce dynamically changing geometry. +geomview: Geomview is an interactive 3D viewing program for Unix. It lets you +geomview: view and manipulate three-dimensional objects: you use the mouse to +geomview: rotate, translate, zoom in and out, etc. Geomview can be used as a +geomview: standalone viewer for static objects (it supports a variety of file +geomview: formats) or as a display engine for other programs which produce +geomview: dynamically changing geometry. geomview: -geomview: homepage: http://www.geomview.org +geomview: Homepage: http://www.geomview.org geomview: diff --git a/academic/gephi/README b/academic/gephi/README new file mode 100644 index 0000000000..1f997e187b --- /dev/null +++ b/academic/gephi/README @@ -0,0 +1,42 @@ +The Open Graph Viz Platform + +Gephi is the leading visualization and exploration software for all +kinds of graphs and networks. Gephi is open-source and free. + +Exploratory Data Analysis: intuition-oriented analysis by networks +manipulations in real time. + +Link Analysis: revealing the underlying structures of associations +between objects. + +Social Network Analysis: easy creation of social data connectors to +map community organizations and small-world networks. + +Biological Network analysis: representing patterns of biological data. + +Poster creation: scientific work promotion with hi-quality printable +maps. + +METRICS READY + +Centrality: used in sociology to indicate how well a node is +connected. Available: degree (power-law), betweenness, closeness. + +And more: density, path length, diameter, HITS, modularity, clustering +coefficient. + +TECHNOLOGY + +Ergonomic interface: no programming skills needed + +High-performance: built-in rendering engine. + +Native file formats: GDF (GUESS), GraphML (NodeXL), GML, NET (Pajek), +GEXF and more. + +Customizable by plugins: layouts, metrics, data sources, manipulation +tools, rendering presets and more. + +NOTE: Gephi's support for importing even non-trivial Graphviz dot is +totally broken, so do not rely on it. For dot, the graphviz package +is providing the gvedit tool. diff --git a/academic/freechartgeany/doinst.sh b/academic/gephi/doinst.sh index 65c7e2eeb9..65c7e2eeb9 100644 --- a/academic/freechartgeany/doinst.sh +++ b/academic/gephi/doinst.sh diff --git a/academic/gephi/gephi.SlackBuild b/academic/gephi/gephi.SlackBuild new file mode 100644 index 0000000000..d9d650d503 --- /dev/null +++ b/academic/gephi/gephi.SlackBuild @@ -0,0 +1,88 @@ +#!/bin/bash + +# Slackware build script for gephi + +# Copyright 2023, Lockywolf +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=gephi +VERSION=${VERSION:-0.10.1} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION-linux-x64.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} + -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} + + +install -d -m 755 $PKG/usr/bin +install -d -m 755 $PKG/opt/$PRGNAM +cp -r . $PKG/opt/$PRGNAM +echo "#!/bin/bash +exec /opt/$PRGNAM/bin/gephi $@" > $PKG/usr/bin/$PRGNAM +chmod +x $PKG/usr/bin/$PRGNAM + +install -d -m0755 $PKG/usr/share/applications/ +install -m0644 $PKG/opt/$PRGNAM/flathub/org.gephi.Gephi.desktop $PKG/usr/share/applications/ +install -d -m0755 $PKG/usr/share/icons/hicolor/512x512/apps/ +install -m0644 $PKG/opt/$PRGNAM/flathub/gephi.png $PKG/usr/share/icons/hicolor/512x512/apps/ + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION + +cat $CWD/gephi-tutorial-quick_start.pdf > $PKG/usr/doc/$PRGNAM-$VERSION/gephi-tutorial-quick_start.pdf + +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/gephi/gephi.info b/academic/gephi/gephi.info new file mode 100644 index 0000000000..1d7443d07d --- /dev/null +++ b/academic/gephi/gephi.info @@ -0,0 +1,12 @@ +PRGNAM="gephi" +VERSION="0.10.1" +HOMEPAGE="https://gephi.org/" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="https://github.com/gephi/gephi/releases/download/v0.10.1/gephi-0.10.1-linux-x64.tar.gz\ + https://gephi.org/tutorials/gephi-tutorial-quick_start.pdf" +MD5SUM_x86_64="b387916d8addb79935cff824b9973307\ + a5e956a201ac957a4acd09a3cdc06506" +REQUIRES="" +MAINTAINER="Lockywolf" +EMAIL="for_sbo.gephi_2023-07-18@lockywolf.net" diff --git a/academic/gephi/slack-desc b/academic/gephi/slack-desc new file mode 100644 index 0000000000..881315966d --- /dev/null +++ b/academic/gephi/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +gephi: gephi (The Open Graph Viz Platform) +gephi: +gephi: Gephi is the leading visualization and exploration software for all +gephi: kinds of graphs and networks. +gephi: +gephi: +gephi: +gephi: +gephi: +gephi: +gephi: diff --git a/academic/gerbv/README b/academic/gerbv/README index df4a71fc61..9cd537e588 100644 --- a/academic/gerbv/README +++ b/academic/gerbv/README @@ -2,9 +2,9 @@ Gerbv is one of the utilities affiliated with the gEDA project, an umbrella organization dedicated to producing free software tools for electronic design. -Gerbv is a viewer for Gerber RS-274X files, Excellon drill files, and -CSV pick-and-place files. It is a native Linux application, and it runs -on many common unix platforms. Gerbv is free / open-source software. The -core functionality of gerbv is located in a separate library (libgerbv), -allowing developers to include Gerber parsing/editing/exporting/rendering -into other programs. +Gerbv is a viewer for Gerber RS-274X files, Excellon drill files, +and CSV pick-and-place files. It is a native Linux application, and +it runs on many common unix platforms. Gerbv is free / open-source +software. The core functionality of gerbv is located in a separate +library (libgerbv), allowing developers to include Gerber parsing, +editing, exporting, rendering into other programs. diff --git a/academic/gerbv/doinst.sh b/academic/gerbv/doinst.sh index 4a25de5e6f..e924bab47c 100644 --- a/academic/gerbv/doinst.sh +++ b/academic/gerbv/doinst.sh @@ -8,3 +8,9 @@ if [ -e usr/share/icons/hicolor/icon-theme.cache ]; then fi fi +if [ -e usr/share/glib-2.0/schemas ]; then + if [ -x /usr/bin/glib-compile-schemas ]; then + /usr/bin/glib-compile-schemas usr/share/glib-2.0/schemas >/dev/null 2>&1 + fi +fi + diff --git a/academic/gerbv/gerbv.SlackBuild b/academic/gerbv/gerbv.SlackBuild index 9b2e8a2576..0b4d1094a2 100644 --- a/academic/gerbv/gerbv.SlackBuild +++ b/academic/gerbv/gerbv.SlackBuild @@ -1,29 +1,57 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for gerbv -# Written by Felix Pfeifer (pfeifer [dot] felix [at] googlemail [dot] com) +# Copyright 2024 Juan M. Lasca juanmlasca@gmail.com +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +# Originally written by Felix Pfeifer (pfeifer.felix@googlemail.com) +# Thanks to Andrzej Telszewski for his suggestions + +cd $(dirname $0) ; CWD=$(pwd) PRGNAM=gerbv -VERSION=${VERSION:-2.6.0} -BUILD=${BUILD:-1} +VERSION=${VERSION:-2.10.0} +BUILD=${BUILD:-3} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -51,7 +79,9 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ -exec chmod 644 {} \; -CFLAGS="$SLKCFLAGS" \ +autoreconf -fi + +CFLAGS="$SLKCFLAGS -w -Wl,--allow-multiple-definition" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ --prefix=/usr \ @@ -61,21 +91,33 @@ CXXFLAGS="$SLKCFLAGS" \ --mandir=/usr/man \ --docdir=/usr/doc/$PRGNAM-$VERSION \ --disable-update-desktop-database \ + --disable-static \ --build=$ARCH-slackware-linux make make install DESTDIR=$PKG +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + find $PKG | xargs file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true find $PKG/usr/man -type f -exec gzip -9 {} \; for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done +# fix .desktop file: +sed -i '/^Encoding/d; s/^Categories.*/Categories=Science;Electronics;/' \ + $PKG/usr/share/applications/gerbv.desktop; + +gzip -9 ChangeLog COPYING + +rm -f */*.in */*.am + mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - [ABCHINRT]*\ - $PKG/usr/doc/$PRGNAM-$VERSION + AUTHORS BUGS CONTRIBUTORS ChangeLog.gz COPYING.gz \ + HACKING NEWS README doc/ example/ \ + $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install @@ -83,5 +125,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} - +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/gerbv/gerbv.info b/academic/gerbv/gerbv.info index 8e8e99d40d..2791874287 100644 --- a/academic/gerbv/gerbv.info +++ b/academic/gerbv/gerbv.info @@ -1,10 +1,10 @@ PRGNAM="gerbv" -VERSION="2.6.0" -HOMEPAGE="http://gerbv.gpleda.org/" -DOWNLOAD="http://downloads.sourceforge.net/gerbv/gerbv-2.6.0.tar.gz" -MD5SUM="44a37dd202bc60fab54cbc298a477572" +VERSION="2.10.0" +HOMEPAGE="https://gerbv.github.io/" +DOWNLOAD="https://github.com/gerbv/gerbv/archive/v2.10.0/gerbv-2.10.0.tar.gz" +MD5SUM="69c122c7fcba29ed9abae733419a913c" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" -MAINTAINER="Felix Pfeifer" -EMAIL="pfeifer[dot]felix[at]googlemail[dot]com" +MAINTAINER="Juan M. Lasca" +EMAIL="juanmlasca@gmail.com" diff --git a/academic/getdp/Kernel_Operation__Broadcast.patch b/academic/getdp/Kernel_Operation__Broadcast.patch deleted file mode 100644 index 621e3e25aa..0000000000 --- a/academic/getdp/Kernel_Operation__Broadcast.patch +++ /dev/null @@ -1,11 +0,0 @@ -#diff a/Kernel/Operation_Broadcast.cpp b/Kernel/Operation_Broadcast.cpp -#--- a/Kernel/Operation_Broadcast.cpp -#+++ b/Kernel/Operation_Broadcast.cpp -@@ -5,6 +5,7 @@ - - #include <vector> - #include <string> -+#include <cstring> // for strncpy() - #include <sstream> - #include <stdio.h> - #include <stdlib.h> diff --git a/academic/getdp/README b/academic/getdp/README index dd3d1673d9..4e131496bc 100644 --- a/academic/getdp/README +++ b/academic/getdp/README @@ -1,3 +1,18 @@ GetDP (A General Environment for the Treatment of Discrete Problems) -GetDP is a free finite element solver using mixed elements to discretize de Rham-type complexes in one, two and three dimensions. The main feature of GetDP is the closeness between the input data defining discrete problems (written by the user in ASCII data files) and the symbolic mathematical expressions of these problems. +GetDP is a free finite element solver using mixed elements +to discretize de Rham-type complexes in one, two and three +dimensions. The main feature of GetDP is the closeness between +the input data defining discrete problems (written by the user in +ASCII data files) and the symbolic mathematical expressions of these +problems. + +Optional dependency: gmsh + +Note: +If you want to build Getdp with Gmsh support it is necessary to +install the Gmsh package first, but compiled with both static and +dynamic libraries. If you use the build script for Gmsh available at +SBo you just need to pass: +BUILDSTATICLIB=yes +prior to run gmsh.SlackBuild diff --git a/academic/getdp/getdp.SlackBuild b/academic/getdp/getdp.SlackBuild index 240d073028..751b64a88c 100644 --- a/academic/getdp/getdp.SlackBuild +++ b/academic/getdp/getdp.SlackBuild @@ -1,7 +1,7 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for getdp -# Copyright 2020 Fellype do Nascimento, Campinas, Brazil +# Copyright 2020-2022 Fellype do Nascimento, Guaratingueta, Brazil # # Redistribution and use of this script, with or without modification, is # permitted provided that the following conditions are met: @@ -20,10 +20,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=getdp -VERSION=${VERSION:-3.3.0} +VERSION=${VERSION:-3.5.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -33,7 +36,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -67,9 +77,6 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -# Patch that allow compilation without a fail (credits to: DragonFlyBSD/DPorts) -patch -p1 < $CWD/Kernel_Operation__Broadcast.patch Kernel/Operation_Broadcast.cpp - mkdir build cd build cmake -DCMAKE_INSTALL_PREFIX:PATH=/usr \ @@ -77,13 +84,14 @@ cmake -DCMAKE_INSTALL_PREFIX:PATH=/usr \ -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ -DENABLE_BUILD_SHARED=ON \ + -DENABLE_GMSH=ON \ -DENABLE_PETSC=OFF \ -DENABLE_SLEPC=OFF \ .. -# only demos/ and templates/ folders will be leaved in the /usr/share/getdp dir +# only demos/ and templates/ folders will be left in the /usr/share/getdp dir make -make install DESTDIR=$PKG +make -j1 install DESTDIR=$PKG cd - find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ @@ -106,4 +114,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/getdp/getdp.info b/academic/getdp/getdp.info index 8b5b964589..bfacafe5f2 100644 --- a/academic/getdp/getdp.info +++ b/academic/getdp/getdp.info @@ -1,10 +1,10 @@ PRGNAM="getdp" -VERSION="3.3.0" +VERSION="3.5.0" HOMEPAGE="http://getdp.info/" -DOWNLOAD="http://getdp.info/src/getdp-3.3.0-source.tgz" -MD5SUM="0f3e4388bcecd454ff1a19fcfa5979ef" +DOWNLOAD="http://getdp.info/src/getdp-3.5.0-source.tgz" +MD5SUM="157d6604cc6a26ead0b0b4121216074a" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="arpack-ng OpenBLAS" +REQUIRES="arpack-ng OpenBLAS %README%" MAINTAINER="Fellype do Nascimento" EMAIL="fellype (at) gmail (dot) com" diff --git a/academic/getdp/slack-desc b/academic/getdp/slack-desc index 7e8b01e9fd..bed2d36f97 100644 --- a/academic/getdp/slack-desc +++ b/academic/getdp/slack-desc @@ -5,15 +5,15 @@ # exactly 11 lines for the formatting to be correct. It's also customary to # leave one space after the ':'. - |-----handy-ruler---------------------------------------------------------| + |-----handy-ruler------------------------------------------------------| getdp: getdp (Finite Element Solver) getdp: -getdp: GetDP a free finite element solver using mixed elements to discretize de -getdp: Rham-type complexes in one, two and three dimensions. The main feature of -getdp: GetDP is the closeness between the input data defining discrete problems -getdp: (written by the user in ASCII data files) and the symbolic mathematical -getdp: expressions of these problems. -getdp: -getdp: GetDP is distributed under the terms of the GNU General Public License. -getdp: +getdp: GetDP a free finite element solver using mixed elements +getdp: to discretize de Rham-type complexes in one, two and three +getdp: dimensions. The main feature of GetDP is the closeness between +getdp: the input data defining discrete problems (written by the user +getdp: in ASCII data files) and the symbolic mathematical expressions +getdp: of these problems. getdp: +getdp: GetDP is distributed under the terms of the GNU General Public +getdp: License. diff --git a/academic/getfem/README b/academic/getfem/README new file mode 100644 index 0000000000..41f7a614a6 --- /dev/null +++ b/academic/getfem/README @@ -0,0 +1,22 @@ +GetFEM is an open source library based on collaborative development. +It aims to offer the most flexible framework for solving potentially +coupled systems of linear and nonlinear partial differential equations +with the finite element method. GetFEM is interfaced with some script +languages (Python, Octave, Scilab and Matlab) so that almost all of +the functionalities can be used just writing scripts. + +If you have matlab installed in your machine, you can also add support +to it by adding '--enable-matlab' to ./configure command + +Take a look at http://getfem.org/install/install_linux.html if you +build GetFEM with support to octave, scilab or matlab in order to make +those tools work properly. + +Optional dependencies are (if you add '--enable-FEATURE', e.g.: +--enable-octave, to ./configure command: + +- octave +- scilab +- qhull +- mumps +- metis diff --git a/academic/getfem/getfem.SlackBuild b/academic/getfem/getfem.SlackBuild new file mode 100644 index 0000000000..d4567aa2e7 --- /dev/null +++ b/academic/getfem/getfem.SlackBuild @@ -0,0 +1,114 @@ +#!/bin/bash + +# Slackware build script for GetFEM +# +# Copyright 2022, Fellype do Nascimento, Guaratingueta - Brazil +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=getfem +VERSION=${VERSION:-5.4.2} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +./configure \ + --prefix=/usr \ + --sysconfdir=/etc \ + --docdir=/usr/share/doc \ + --with-pic \ + --enable-python \ + --enable-shared \ + --enable-static=no \ + --mandir=/usr/man \ + --libdir=/usr/lib$LIBDIRSUFFIX + +make +make install DESTDIR=$PKG + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a AUTHORS ChangeLog COPYING README $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +# move getfem_toolbox dir to /usr/share/getfem +mkdir -p $PKG/usr/share/$PRGNAM +mv $PKG/usr/getfem_toolbox $PKG/usr/share/$PRGNAM/ + +# remove .la files +rm -f $PKG/usr/lib*/*.la + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/getfem/getfem.info b/academic/getfem/getfem.info new file mode 100644 index 0000000000..9a61fe097c --- /dev/null +++ b/academic/getfem/getfem.info @@ -0,0 +1,10 @@ +PRGNAM="getfem" +VERSION="5.4.2" +HOMEPAGE="https://getfem.org/" +DOWNLOAD="http://download-mirror.savannah.gnu.org/releases/getfem/stable/getfem-5.4.2.tar.gz" +MD5SUM="90ba2a270ec8c559796f2a7c90a79d32" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="python3-scipy" +MAINTAINER="Fellype do Nascimento" +EMAIL="fellype (at) gmail (dot) com" diff --git a/academic/getfem/slack-desc b/academic/getfem/slack-desc new file mode 100644 index 0000000000..275f3df7bf --- /dev/null +++ b/academic/getfem/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +getfem: getfem (finite element modeling software) +getfem: +getfem: GetFEM is an open source library based on collaborative development. +getfem: +getfem: It aims to offer the most flexible framework for solving potentially +getfem: coupled systems of linear and nonlinear partial differential +getfem: equations with the finite element method. +getfem: +getfem: For more information visit: http://getfem.org/ +getfem: +getfem: diff --git a/academic/ggobi/README b/academic/ggobi/README index 2a325c43df..1bb21d26b4 100644 --- a/academic/ggobi/README +++ b/academic/ggobi/README @@ -1,7 +1,8 @@ -GGobi is an interactive, direct manipulation tool for visualizing high -dimensional data across linked plots. It provides highly dynamic and -interactive graphics such as tours, as well as familiar graphics such -as the scatterplot, barchart and parallel coordinates plots. Plots are -interactive and linked with brushing and identification. The GUI is built -using Gtk+. It reads data in regular ASCII format and more richly using -an XML format. Plugins for other formats are also available. +GGobi is an interactive, direct manipulation tool for visualizing +high dimensional data across linked plots. It provides highly dynamic +and interactive graphics such as tours, as well as familiar graphics +such as the scatterplot, barchart and parallel coordinates plots. +Plots are interactive and linked with brushing and identification. The +GUI is built using Gtk+. It reads data in regular ASCII format and +more richly using an XML format. Plugins for other formats are also +available. diff --git a/academic/ggobi/ggobi.SlackBuild b/academic/ggobi/ggobi.SlackBuild index 849bbb432f..61f6523a37 100644 --- a/academic/ggobi/ggobi.SlackBuild +++ b/academic/ggobi/ggobi.SlackBuild @@ -1,13 +1,19 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for ggobi # Written by Pedro Mendes pedro@gepasi.org # hereby put in the public domain +# 20220308 bkw: Modified by SlackBuilds.org: fix build on 15.0, +# by upgrading to v2.1.11. + +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=ggobi -VERSION=${VERSION:-2.1.8} +VERSION=${VERSION:-2.1.11} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -17,7 +23,11 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -47,9 +57,9 @@ cd $PRGNAM-$VERSION chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ + -o -perm 511 \) -exec chmod 755 {} \+ -o \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \+ CXXFLAGS="$SLKCFLAGS" \ CFLAGS="$SLKCFLAGS" \ @@ -64,9 +74,6 @@ CFLAGS="$SLKCFLAGS" \ --with-all-plugins \ --build=$ARCH-slackware-linux -# fix problem with graphviz plugin -patch -p1 < $CWD/ggobi-2.1.8-graphviz.patch - make make install-strip DESTDIR=$PKG make ggobirc @@ -76,13 +83,18 @@ cp ggobirc $PKG/etc/xdg/ggobi/ggobirc rm -f $PKG/usr/info/dir -mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a AUTHORS COPYING CPLicense.txt ChangeLog INSTALL NEWS README \ - $PKG/usr/doc/$PRGNAM-$VERSION -cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +# 20220308 bkw: PDF docs go in the regular doc dir, we don't use /usr/share/doc +PKGDOC=$PKG/usr/doc/$PRGNAM-$VERSION +mkdir -p $PKGDOC +mv $PKG/usr/share/doc/$PRGNAM/* $PKGDOC +rm -rf $PKG/usr/share/doc +cp -a AUTHORS COPYING CPLicense.txt ChangeLog NEWS README $PKGDOC +cat $CWD/$PRGNAM.SlackBuild > $PKGDOC/$PRGNAM.SlackBuild + +rm -f $PKG/usr/lib*/*.la mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/ggobi/ggobi.info b/academic/ggobi/ggobi.info index 770af33fa2..b69169c2f4 100644 --- a/academic/ggobi/ggobi.info +++ b/academic/ggobi/ggobi.info @@ -1,8 +1,8 @@ PRGNAM="ggobi" -VERSION="2.1.8" +VERSION="2.1.11" HOMEPAGE="http://www.ggobi.org/" -DOWNLOAD="http://www.ggobi.org/downloads/ggobi-2.1.8.tar.bz2" -MD5SUM="0b07adffcf4379e819b1a26e4cd60d7b" +DOWNLOAD="http://ggobi.org/downloads/ggobi-2.1.11.tar.bz2" +MD5SUM="6e95e987f3a7b3f3d7ac4f4d0cd693e9" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/ghemical/fix_clang_ftbfs.patch b/academic/ghemical/fix_clang_ftbfs.patch new file mode 100644 index 0000000000..af3fd4f099 --- /dev/null +++ b/academic/ghemical/fix_clang_ftbfs.patch @@ -0,0 +1,37 @@ +Description: Fix FTBFS with clang instead of gcc +Bug-Debian: https://bugs.debian.org/756440 +Author: Alexander <sanek23994@gmail.com> +Last-Update: 2014-07-30 +--- a/src/project.h ++++ b/src/project.h +@@ -122,6 +122,14 @@ + graphical user interface. + */ + ++class project; ++ ++bool ReadGPR_OLD(project &, istream &, bool, bool = false); ///< this is for the very old version. ++bool ReadGPR_v100(project &, istream &, bool, bool = false); ///< this is for the version 1.00. ++bool ReadGPR_v110(project &, istream &, bool, bool = false); ///< this is for the version 1.10. ++/// This is an input function for the v1.11 ghemical file format. ++bool ReadGPR(project &, istream &, bool, bool = false); ++ + class project : + public custom_transformer_client, + public model +@@ -207,11 +215,11 @@ + + // methods for file I/O : ReadGPR and WriteGPR are friend functions so that it would be easier to "borrow" them elsewhere... + // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +- friend bool ReadGPR_OLD(project &, istream &, bool, bool = false); ///< this is for the very old version. +- friend bool ReadGPR_v100(project &, istream &, bool, bool = false); ///< this is for the version 1.00. +- friend bool ReadGPR_v110(project &, istream &, bool, bool = false); ///< this is for the version 1.10. ++ friend bool ReadGPR_OLD(project &, istream &, bool, bool); ///< this is for the very old version. ++ friend bool ReadGPR_v100(project &, istream &, bool, bool); ///< this is for the version 1.00. ++ friend bool ReadGPR_v110(project &, istream &, bool, bool); ///< this is for the version 1.10. + /// This is an input function for the v1.11 ghemical file format. +- friend bool ReadGPR(project &, istream &, bool, bool = false); ++ friend bool ReadGPR(project &, istream &, bool, bool); + + friend void WriteGPR_v100(project &, ostream &); ///< this is for the version 1.00. + /// This is an output function for the v1.11 ghemical file format. diff --git a/academic/ghemical/ghemical.SlackBuild b/academic/ghemical/ghemical.SlackBuild index f1afe7370b..18c464ad65 100644 --- a/academic/ghemical/ghemical.SlackBuild +++ b/academic/ghemical/ghemical.SlackBuild @@ -1,13 +1,16 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for ghemical # Written by Daniil Bratashov (dn2010@gmail.com) +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=ghemical VERSION=${VERSION:-3.0.0} BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -17,7 +20,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -51,6 +61,9 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ -exec chmod 644 {} \; +# Thanks Debian! +patch -p1 < $CWD/fix_clang_ftbfs.patch + CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}" \ @@ -89,4 +102,4 @@ mkdir -p $PKG/usr/share/icons/hicolor/48x48/apps cp $CWD/ghemical.png $PKG/usr/share/icons/hicolor/48x48/apps cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/glpk/glpk.SlackBuild b/academic/glpk/glpk.SlackBuild index 140eae9aa1..8c63ea3f9e 100644 --- a/academic/glpk/glpk.SlackBuild +++ b/academic/glpk/glpk.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for glpk # Ryan P.C. McQuen | Everett, WA | ryanpcmcquen@member.fsf.org @@ -24,10 +24,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=glpk VERSION=${VERSION:-4.61} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -37,7 +40,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -86,6 +96,9 @@ LDFLAGS="$SLKCFLAGS" \ make make install DESTDIR=$PKG +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a AUTHORS COPYING ChangeLog INSTALL NEWS README THANKS doc examples \ $PKG/usr/doc/$PRGNAM-$VERSION @@ -96,8 +109,10 @@ cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/glvis/README b/academic/glvis/README new file mode 100644 index 0000000000..acb344d7cb --- /dev/null +++ b/academic/glvis/README @@ -0,0 +1,2 @@ + GLVis is a lightweight tool for accurate and flexible finite element +visualization. diff --git a/academic/glvis/doinst.sh b/academic/glvis/doinst.sh new file mode 100644 index 0000000000..5fb28930db --- /dev/null +++ b/academic/glvis/doinst.sh @@ -0,0 +1,3 @@ +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 +fi diff --git a/academic/glvis/glvis.SlackBuild b/academic/glvis/glvis.SlackBuild new file mode 100644 index 0000000000..62309cb23d --- /dev/null +++ b/academic/glvis/glvis.SlackBuild @@ -0,0 +1,128 @@ +#!/bin/bash + +# Slackware build script for GLVIs + +# Copyright 2022 William PC, Seattle (USA) +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=glvis +VERSION=${VERSION:-4.2} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +# create a shared library +sed -i '270s/$/ -fPIC/' makefile +sed -i '278s/.a/.so/' makefile +sed -i '304i\\nlib/libglvis.so: $(OBJECT_FILES)\ +\t$(CCC) -shared -o $@ $^ $(GLVIS_FLAGS) $(LIBS)' makefile + +# fix install permissions +sed -i 's/-m 750/-m 755/' makefile + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +make CONFIG_MK=/usr/share/mfem-4.5/config.mk +make install \ + CONFIG_MK=/usr/share/mfem-4.5/config.mk \ + PREFIX=$PKG/usr/bin + +# install lib +install -d $PKG/usr/lib${LIBDIRSUFFIX} +install -m 755 lib/libglvis.so $PKG/usr/lib${LIBDIRSUFFIX} + +# install other files +install -d $PKG/usr/share/$PRGNAM +install -m 644 share/logo.ico $PKG/usr/share/$PRGNAM +install -d $PKG/usr/share/applications +install -m 644 $CWD/glvis.desktop $PKG/usr/share/applications + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + CHANGELOG CONTRIBUTING.md LICENSE NOTICE README.md \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/glvis/glvis.desktop b/academic/glvis/glvis.desktop new file mode 100644 index 0000000000..0b65734a7e --- /dev/null +++ b/academic/glvis/glvis.desktop @@ -0,0 +1,10 @@ +[Desktop Entry] +Name=GLVIs +Comment=Lightweight OpenGL finite element visualization +TryExec=/usr/bin/glvis +Exec=/usr/bin/glvis +Icon=/usr/share/glvis/logo.ico +Terminal=true +Type=Application +Categories=Education;Science;Math; +StartupNotify=false diff --git a/academic/glvis/glvis.info b/academic/glvis/glvis.info new file mode 100644 index 0000000000..0022d2c170 --- /dev/null +++ b/academic/glvis/glvis.info @@ -0,0 +1,10 @@ +PRGNAM="glvis" +VERSION="4.2" +HOMEPAGE="https://glvis.org" +DOWNLOAD="https://github.com/GLVis/glvis/archive/v4.2/glvis-4.2.tar.gz" +MD5SUM="a228c65c285e7a66e38b1ec2f2812842" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="glm mfem" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/glvis/slack-desc b/academic/glvis/slack-desc new file mode 100644 index 0000000000..3336f83588 --- /dev/null +++ b/academic/glvis/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +glvis: glvis (lightweight finite element visualization tool) +glvis: +glvis: +glvis: +glvis: GLVis is a lightweight tool for accurate and flexible finite +glvis: element visualization. +glvis: +glvis: +glvis: +glvis: +glvis: diff --git a/academic/gmsh/README b/academic/gmsh/README index 4414b6009d..cbc93a7222 100644 --- a/academic/gmsh/README +++ b/academic/gmsh/README @@ -1,7 +1,30 @@ -Gmsh (A three-dimensional finite element mesh generator with built-in pre- and post-processing facilities) +Gmsh (A three-dimensional finite element mesh generator with built-in +pre- and post-processing facilities) -Gmsh is an open source 3D finite element mesh generator with a built-in CAD engine and post-processor. Its design goal is to provide a fast, light and user-friendly meshing tool with parametric input and advanced visualization capabilities. Gmsh is built around four modules: geometry, mesh, solver and post-processing. The specification of any input to these modules is done either interactively using the graphical user interface, in ASCII text files using Gmsh's own scripting language (.geo files), or using the C++, C, Python or Julia Application Programming Interface (API). +Gmsh is an open source 3D finite element mesh generator with a +built-in CAD engine and post-processor. Its design goal is to provide +a fast, light and user-friendly meshing tool with parametric input +and advanced visualization capabilities. Gmsh is built around four +modules: geometry, mesh, solver and post-processing. The specification +of any input to these modules is done either interactively using +the graphical user interface, in ASCII text files using Gmsh's own +scripting language (.geo files), or using the C++, C, Python or Julia +Application Programming Interface (API). -See this general presentation for a high-level overview of Gmsh and recent developments, the screencasts for a quick tour of Gmsh's graphical user interface, and the reference manual for a more thorough overview of Gmsh's capabilities, some frequently asked questions and the documentation of the C++, C, Python and Julia API. +See this general presentation for a high-level overview of Gmsh +and recent developments, the screencasts for a quick tour of Gmsh's +graphical user interface, and the reference manual for a more thorough +overview of Gmsh's capabilities, some frequently asked questions and +the documentation of the C++, C, Python and Julia API. -The source code repository contains many examples written using both the built-in script language (see e.g. the tutorials and demos) and the API. +The source code repository contains many examples written using both +the built-in script language (see e.g. the tutorials and demos) and +the API. + +Note: +If you want to build Getdp with Gmsh support is necessary to compile +also a static gmsh library (libgmsh.a). This can be done by passing +BUILDSTATICLIB=yes +prior to run gmsh.SlackBuild +In that case, you will also need to recompile Getdp when Gmsh is +updated. diff --git a/academic/gmsh/doinst.sh b/academic/gmsh/doinst.sh new file mode 100644 index 0000000000..8a5ffa8af5 --- /dev/null +++ b/academic/gmsh/doinst.sh @@ -0,0 +1,20 @@ + +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 +fi + +if [ -x /usr/bin/update-mime-database ]; then + /usr/bin/update-mime-database usr/share/mime >/dev/null 2>&1 +fi + +if [ -e usr/share/icons/hicolor/icon-theme.cache ]; then + if [ -x /usr/bin/gtk-update-icon-cache ]; then + /usr/bin/gtk-update-icon-cache -f usr/share/icons/hicolor >/dev/null 2>&1 + fi +fi + +if [ -e usr/share/glib-2.0/schemas ]; then + if [ -x /usr/bin/glib-compile-schemas ]; then + /usr/bin/glib-compile-schemas usr/share/glib-2.0/schemas >/dev/null 2>&1 + fi +fi diff --git a/academic/gmsh/gmsh.SlackBuild b/academic/gmsh/gmsh.SlackBuild index 3632982bf4..e318452d91 100644 --- a/academic/gmsh/gmsh.SlackBuild +++ b/academic/gmsh/gmsh.SlackBuild @@ -1,7 +1,7 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for gmsh -# Copyright 2020 Fellype do Nascimento, Campinas, Brazil +# Copyright 2020-2024 Fellype do Nascimento, Guaratingueta, Brazil # # Based on SlackBuild by Loris Vincenzi and PKGBUILD for gmsh at AUR # @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=gmsh -VERSION=${VERSION:-4.5.4} +VERSION=${VERSION:-4.12.2} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -69,17 +79,53 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; +# In order build getdp with gmsh support it is needed to build +# a small static Gmsh library first +# do it using BUILDSTATICLIB=yes ./gmsh.SlackBuild +# default is BUILDSTATICLIB=no +if [ "${BUILDSTATICLIB:-no}" = "yes" ]; then + echo " " + echo "** building a static library for gmsh **" + echo " " + mkdir lib + cd lib + cmake -DDEFAULT=0 \ + -DENABLE_PARSER=1 \ + -DENABLE_POST=1 \ + -DENABLE_ANN=1 \ + -DENABLE_BLAS_LAPACK=1 \ + -DENABLE_BUILD_LIB=1 \ + -DENABLE_PRIVATE_API=1 \ + -DENABLE_MED=OFF \ + -DENABLE_CGNS=OFF \ + -DCMAKE_INSTALL_PREFIX:PATH=/usr \ + -DCMAKE_INSTALL_DOCDIR:PATH=/usr/share/gmsh \ + .. + make lib + make install/fast DESTDIR=$PKG/ + cd .. + echo " " + echo "** finished building the static library **" + echo " " +fi + mkdir build cd build cmake -DCMAKE_INSTALL_PREFIX:PATH=/usr \ -DCMAKE_INSTALL_DOCDIR:PATH=/usr/share/gmsh \ -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ - -DENABLE_BUILD_SHARED=ON \ + -DENABLE_BLAS_LAPACK=1 \ + -DENABLE_BUILD_SHARED=1 \ + -DENABLE_PRIVATE_API=1 \ -DENABLE_PETSC=OFF \ -DENABLE_SLEPC=OFF \ + -DENABLE_MED=OFF \ + -DENABLE_CGNS=OFF \ .. -# only demos/ and tutorial/ folders will be leaved in the /usr/share/gmsh dir +# only demos/ and tutorial/ folders will be left in the /usr/share/gmsh dir +# TODO: Solve runtime issues with HDF5 - this is the reason for disabling +# MED and CGNS in gmsh 4.12.x make make install DESTDIR=$PKG @@ -90,7 +136,6 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr install -d "$PKG/usr/share/pixmaps/$PRGNAM" install -m644 utils/icons/*.png "$PKG/usr/share/pixmaps/$PRGNAM" -install -D -m644 utils/icons/solid_32x32.png "$PKG/usr/share/icons/$PRGNAM.png" install -D -m644 utils/icons/$PRGNAM.svg "$PKG/usr/share/icons/hicolor/scalable/apps/$PRGNAM.svg" desktop-file-install --dir="$PKG/usr/share/applications" "$CWD/$PRGNAM.desktop" @@ -106,10 +151,13 @@ mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a CHANGELOG.txt CREDITS.txt LICENSE.txt README.txt $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild rm $PKG/usr/share/gmsh/*.txt -rm -Rf $PKG/tmp + +# Remove onelab.py launcher from /usr/bin, since we are not using it here +rm $PKG/usr/bin/onelab.py mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/gmsh/gmsh.desktop b/academic/gmsh/gmsh.desktop index ad08eb309c..16f09b07af 100644 --- a/academic/gmsh/gmsh.desktop +++ b/academic/gmsh/gmsh.desktop @@ -4,7 +4,6 @@ Name=Gmsh Comment=Automatic 3D finite element mesh generator Icon=gmsh Exec=gmsh -Encoding=UTF-8 Terminal=false Type=Application -Categories=Education;Science;Math; +Categories=Science; diff --git a/academic/gmsh/gmsh.info b/academic/gmsh/gmsh.info index f628e2a4c5..f56d44b835 100644 --- a/academic/gmsh/gmsh.info +++ b/academic/gmsh/gmsh.info @@ -1,10 +1,10 @@ PRGNAM="gmsh" -VERSION="4.5.4" -HOMEPAGE="http://gmsh.info/" -DOWNLOAD="http://gmsh.info/src/gmsh-4.5.4-source.tgz" -MD5SUM="dc225d64508468107eda763915d9c959" +VERSION="4.12.2" +HOMEPAGE="https://gmsh.info/" +DOWNLOAD="https://gmsh.info/src/gmsh-4.12.2-source.tgz" +MD5SUM="2c99a1b94d1a4c597b8febb6e9b02f5b" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="fltk lapack med OpenCASCADE" +REQUIRES="fltk lapack OpenCASCADE" MAINTAINER="Fellype do Nascimento" EMAIL="fellype (at) gmail (dot) com" diff --git a/academic/gmsh/slack-desc b/academic/gmsh/slack-desc index f88f19320c..3fe2e76a5d 100644 --- a/academic/gmsh/slack-desc +++ b/academic/gmsh/slack-desc @@ -5,15 +5,15 @@ # exactly 11 lines for the formatting to be correct. It's also customary to # leave one space after the ':'. - |-----handy-ruler---------------------------------------------------------| + |-----handy-ruler------------------------------------------------------| gmsh: gmsh (finite element mesh generator) gmsh: gmsh: Gmsh is an automatic three-dimensional finite element mesh generator gmsh: with built-in pre- and post-processing facilities. -gmsh: -gmsh: Gmsh is copyright (C) 1997-2019 C. Geuzaine and J.-F. Remacle, and is -gmsh: distributed under the terms of the GNU General Public License, Version 2 -gmsh: or later, with an exception to allow for easier linking with external -gmsh: libraries. +gmsh: +gmsh: Gmsh is copyright (C) 1997- C. Geuzaine and J.-F. Remacle, +gmsh: and is distributed under the terms of the GNU General Public +gmsh: License, Version 2 or later, with an exception to allow for +gmsh: easier linking with external libraries. gmsh: gmsh: diff --git a/academic/gnucap/README b/academic/gnucap/README index a13ef46e8f..c03f05979f 100644 --- a/academic/gnucap/README +++ b/academic/gnucap/README @@ -1,5 +1,5 @@ -Gnucap is a modern "post-spice" analog and mixed signal circuit simulator. -Gnucap is designed so it can eventually replace Spice. Today, it can -replace Spice in some applications. There are some significant technical -advantages. It is a work in progress. New features are added regularly -as time and demand permits. +Gnucap is a modern "post-spice" analog and mixed signal circuit +simulator. Gnucap is designed so it can eventually replace +Spice. Today, it can replace Spice in some applications. There are +some significant technical advantages. It is a work in progress. New +features are added regularly as time and demand permits. diff --git a/academic/gnucap/gnucap.SlackBuild b/academic/gnucap/gnucap.SlackBuild index a350ac9121..2cbcce0492 100644 --- a/academic/gnucap/gnucap.SlackBuild +++ b/academic/gnucap/gnucap.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for Gnucap @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=gnucap VERSION=${VERSION:-20091207} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} SRCVER="$( echo $VERSION | sed 's|\(....\)\(..\)\(..\)|\1-\2-\3|' )" @@ -37,7 +40,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -121,4 +131,4 @@ StartupNotify=true EOF cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/gp2fasta/gp2fasta.SlackBuild b/academic/gp2fasta/gp2fasta.SlackBuild index ade5c82653..ce052827b0 100644 --- a/academic/gp2fasta/gp2fasta.SlackBuild +++ b/academic/gp2fasta/gp2fasta.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for gp2fasta @@ -26,26 +26,36 @@ # http://kde-look.org/content/show.php/Fasta+icons?content=54012 # Author is Luis-Miguel Rodriguez. Thank you! +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=gp2fasta VERSION=${VERSION:-0.2} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -76,6 +86,7 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ -exec chmod 644 {} \; +. /etc/profile.d/qt4.sh qmake -project qmake @@ -107,4 +118,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/gp2fasta/gp2fasta.info b/academic/gp2fasta/gp2fasta.info index 04cb8295c4..c4522ea239 100644 --- a/academic/gp2fasta/gp2fasta.info +++ b/academic/gp2fasta/gp2fasta.info @@ -5,6 +5,6 @@ DOWNLOAD="http://gp2fasta.netmark.pl/gp2fasta.zip" MD5SUM="f1124fb098c531154f4e6dcf7c9d174d" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="" +REQUIRES="qt4" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/gplates/README b/academic/gplates/README new file mode 100644 index 0000000000..8ba9347278 --- /dev/null +++ b/academic/gplates/README @@ -0,0 +1,45 @@ +GPlates is free and open source desktop software for the interactive +visualisation of plate tectonics for research, educational, +professional, and other purposes. It is developed by an international +team of researchers and software developers who refer to internal +divisions of the University of Sidney and Caltech (California +Institute of Technology). + +GPlates offers a novel combination of interactive plate tectonic +reconstructions, geographic information system (GIS) functionality and +raster data visualisation. GPlates enables both the visualisation and +the manipulation of plate tectonic reconstructions and associated data +through geological time. +GPlates can be used to handle and visualise data in a variety of +geometries and formats, including raster data, to link plate kinematics +to geodynamic models, to serve as an interactive client in a +grid-computing network, to facilitate the production of high-quality +paleo-geographic maps. + +GPlates requires in runtime pre-packed datasets provided by the project +or other datasets. By default, this slackbuild does not install any +dataset, since the download of project's data source is allowed only by +using a web browser. Standard procedure compliant with curl or wget is +not allowed. + +If you want to install the data source using this slackbuild follow the +download instructions reported in README.SBo file and save the archive +gplates_2.3.0_geodata.zip in the same directory of the slackbuild +script. The slackbuild autodetect this archive and if found will +include the datasets in the installation package. Datasets will be +installed in the directory /usr/share/gplates/GeoData + +Alternative datasets are not handled by this slackbuild. If you want +to use other datasets you have to add them in local or shared +directories and apply them using the tools of the application GUI. + +CGAL library is a required dependency, but the build can also use the +alternative header-only library CGAL5 if installed in your system. + +Published works powered with GPlates should include the following +citation: + +Müller, R. D., Cannon, J., Qin, X., Watson, R. J., Gurnis, M., +Williams, S., et al. 2018. GPlates: Building a virtual Earth through +deep time. Geochemistry, Geophysics, Geosystems, 19. +doi:10.1029/2018GC007584. diff --git a/academic/gplates/README.SBo b/academic/gplates/README.SBo new file mode 100644 index 0000000000..eb20e6214f --- /dev/null +++ b/academic/gplates/README.SBo @@ -0,0 +1,32 @@ +Although this is not strictly required for build GPlates, since +alternative datasets can be used, you would install the data source +provided by EarthByte, the official maintainer of GPlates project at +the same time of the build of GPlates package. +Unfortunately, this dataset is not released in the github repository +of GPlates and can be downloaded only using a Web browser, not with +other applications like curl or wget. + +If you want install this dataset (strongly recommended) please follow +these instructions: + +1. Connect to the webpage: + https://www.earthbyte.org/download-gplates-2-3/ + +2. In the section "Download file links" select the option from the + Download selection list: + gplates_2.3.0_geodata.zip + + (Warning: do not select the application source, because the + tarball will not handled by the slackbuild script. Use the tarball + downloaded from the github repository of GPlates) + +3. Fill the form notifying: + - your name (OPTIONAL: leave empty for anonymous download) + - your email address (OPTIONAL: leave empty for anonymous download) + - select your purposes (REQUIRED) + +4. Click the button "Get download link(s)" + +After the above steps, you will get at the bottom of the page the +hardlink to download the geodata archive. This must be saved in the +same directory of the slackbuild script. diff --git a/academic/gplates/boost-placeholders.patch b/academic/gplates/boost-placeholders.patch new file mode 100644 index 0000000000..aefc26e64f --- /dev/null +++ b/academic/gplates/boost-placeholders.patch @@ -0,0 +1,35 @@ +--- gplates_2.3.0_src/src/gui/TopologyTools.cc 2021-07-05 07:28:32.000000000 +0200 ++++ gplates_2.3.0_src-fixed/src/gui/TopologyTools.cc 2022-04-10 16:00:01.000000000 +0200 +@@ -39,4 +39,6 @@ + #include <boost/none.hpp> + #include <boost/numeric/conversion/cast.hpp> ++#include <boost/bind/placeholders.hpp> ++using namespace boost::placeholders; + + #include <QtDebug> +--- gplates_2.3.0_src/src/qt-widgets/ViewportWindow.cc 2021-08-05 07:40:35.000000000 +0200 ++++ gplates_2.3.0_src-fixed/src/qt-widgets/ViewportWindow.cc 2022-04-10 16:10:01.000000000 +0200 +@@ -37,4 +37,6 @@ + #include <boost/foreach.hpp> + #include <boost/bind/bind.hpp> ++#include <boost/bind/placeholders.hpp> ++using namespace boost::placeholders; + + #include <QActionGroup> +--- gplates_2.3.0_src/src/presentation/ReconstructionGeometryRenderer.cc 2021-08-05 07:40:35.000000000 +0200 ++++ gplates_2.3.0_src-fixed/src/presentation/ReconstructionGeometryRenderer.cc 2022-04-10 16:20:01.000000000 +0200 +@@ -30,4 +30,6 @@ + #include <boost/bind/bind.hpp> + #include <boost/foreach.hpp> ++#include <boost/bind/placeholders.hpp> ++using namespace boost::placeholders; + + #include "ReconstructionGeometryRenderer.h" +--- gplates_2.3.0_src/src/presentation/VisualLayerRegistry.cc 2021-08-05 07:40:35.000000000 +0200 ++++ gplates_2.3.0_src-fixed/src/presentation/VisualLayerRegistry.cc 2022-04-10 16:30:01.000000000 +0200 +@@ -27,4 +27,6 @@ + #include <boost/bind/bind.hpp> + #include <boost/foreach.hpp> ++#include <boost/bind/placeholders.hpp> ++using namespace boost::placeholders; + #include <QPixmap> diff --git a/academic/kile/doinst.sh b/academic/gplates/doinst.sh index aea0f894eb..aea0f894eb 100644 --- a/academic/kile/doinst.sh +++ b/academic/gplates/doinst.sh diff --git a/academic/gplates/gplates.SlackBuild b/academic/gplates/gplates.SlackBuild new file mode 100644 index 0000000000..e237b951ad --- /dev/null +++ b/academic/gplates/gplates.SlackBuild @@ -0,0 +1,156 @@ +#!/bin/bash + +# Slackware build script for gplates + +# Copyright 2022-2024 Giancarlo Dessi, Cagliari, IT +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=gplates +SRCNAM=GPlates-GPlates +VERSION=${VERSION:-2.3} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} +GEODATADIR=GeoData +GEODATAVERSION=$VERSION.0 + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $SRCNAM-$VERSION +rm -rf $GEODATADIR +tar xvf $CWD/$SRCNAM-$VERSION.tar.gz + +# Detect if GeoData archive if present +if [ -f $CWD/gplates_${GEODATAVERSION}_geodata.zip ]; then + echo "*********************************************************" + echo "* GeoData source found! This slackbuild will include in *" + echo "* the install package the official datasets released by *" + echo "* the EarthByte project. *" + echo "* *" + echo "* Remember that you can also use other compatible *" + echo "* datasets. *" + echo "*********************************************************" + + withGeoData=" -DGPLATES_INSTALL_GEO_DATA=true \ + -DGPLATES_INSTALL_GEO_DATA_DIR=$TMP/$GEODATADIR " + unzip $CWD/gplates_${GEODATAVERSION}_geodata.zip -d $TMP + + +else + echo "*********************************************************" + echo "* WARNING! GeoData source released by EarthByte project *" + echo "* not found. This slackbuild will not include datasets *" + echo "* in the install package but only the application. *" + echo "* *" + echo "* Remember that GPlates requires compatible datasets *" + echo "* that you have to use in runtime. *" + echo "*********************************************************" + + withGeoData=" -DGPLATES_INSTALL_GEO_DATA=false " +fi + +cd $SRCNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +# This fix errors given by gcc 11 or earlier compilers +patch -p1 < $CWD/boost-placeholders.patch + +mkdir -p build +cd build + cmake \ + -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + $withGeoData \ + -DCMAKE_BUILD_TYPE=Release .. + make + make install/strip DESTDIR=$PKG +cd .. + +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +mv $PKG/usr/share/man $PKG/usr/man + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +find $PKG/usr/man -type f -exec gzip -9 {} \; +for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done + +# Include application icon and desktop entry +mkdir -p $PKG/usr/share/icons/hicolor/160x160/apps +cp -a src/qt-resources/GPlates-icon-160x160-opaque.png \ + $PKG/usr/share/icons/hicolor/160x160/apps/gplates.png + +mkdir -p $PKG/usr/share/applications +cp -a $CWD/gplates.desktop $PKG/usr/share/applications +chown root:root $PKG/usr/share/applications/gplates.desktop + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a AUTHORS CHANGELOG COPYING CREDITS README $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/gplates/gplates.desktop b/academic/gplates/gplates.desktop new file mode 100644 index 0000000000..249b8af64b --- /dev/null +++ b/academic/gplates/gplates.desktop @@ -0,0 +1,21 @@ +[Desktop Entry] +Type=Application +Name=GPlates +GenericName=Plate tectonics program +GenericName[de]=Programm der Plattentektonik +GenericName[es]=Programa de placas tectónicas +GenericName[fr]=Programme des plaques tectoniques +GenericName[it]=Programma sulle placche tettoniche +GenericName[pt]=Programa de placas tectônicas +Comment=Interactive visualisation of plate tectonics +Comment[de]=Interaktive Visualisierung von tektonischen Platten +Comment[es]=Visualización interactiva de placas tectónicas +Comment[fr]=Visualisation interactive des plaques tectoniques +Comment[it]=Visualizzazione interattiva delle placche tettoniche +Comment[pt]=Visualização interativa de placas tectônicas +Exec=gplates %f +Icon=/usr/share/icons/hicolor/160x160/apps/gplates.png +Terminal=false +Categories=Qt;Education;Science;Geology; +StartupNotify=true +MimeType=application/x-gproj;text/gpml;text/grot; diff --git a/academic/gplates/gplates.info b/academic/gplates/gplates.info new file mode 100644 index 0000000000..c465138289 --- /dev/null +++ b/academic/gplates/gplates.info @@ -0,0 +1,10 @@ +PRGNAM="gplates" +VERSION="2.3" +HOMEPAGE="https://www.gplates.org" +DOWNLOAD="https://github.com/GPlates/GPlates/archive/GPlates-2.3/GPlates-GPlates-2.3.tar.gz" +MD5SUM="f6d3db99c7388615019f05a87d838e1f" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="CGAL gdal python3-numpy qwt" +MAINTAINER="Giancarlo Dessi" +EMAIL="slack@giand.it" diff --git a/academic/gplates/slack-desc b/academic/gplates/slack-desc new file mode 100644 index 0000000000..ec6094b579 --- /dev/null +++ b/academic/gplates/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +gplates: gplates (interactive visualisation of plate tectonics) +gplates: +gplates: GPlates is a desktop application for the interactive visualisation of +gplates: plate tectonics. It offers combination of interactive plate tectonic +gplates: reconstructions, geographic information system (GIS) functionality +gplates: and raster data visualisation. +gplates: +gplates: +gplates: Home page: https://www.gplates.org +gplates: +gplates: diff --git a/academic/gpredict/gpredict.SlackBuild b/academic/gpredict/gpredict.SlackBuild index b3e4f352d8..4f6d1c7981 100644 --- a/academic/gpredict/gpredict.SlackBuild +++ b/academic/gpredict/gpredict.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for gpredict # Yth | Pont-en-Royans, France | yth@ythogtha.org @@ -23,10 +23,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=gpredict -VERSION=${VERSION:-2.3} +VERSION=${VERSION:-2.2.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -36,7 +39,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -50,6 +60,9 @@ elif [ "$ARCH" = "i686" ]; then elif [ "$ARCH" = "x86_64" ]; then SLKCFLAGS="-O2 -fPIC" LIBDIRSUFFIX="64" +elif [ "$ARCH" = "aarch64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" else SLKCFLAGS="-O2" LIBDIRSUFFIX="" @@ -70,11 +83,9 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -./autogen.sh - -CFLAGS="$SLKCFLAGS" \ +CFLAGS="$SLKCFLAGS -w -Wl,--allow-multiple-definition" \ CXXFLAGS="$SLKCFLAGS" \ -./configure \ +./autogen.sh \ --prefix=/usr \ --libdir=/usr/lib${LIBDIRSUFFIX} \ --sysconfdir=/etc \ @@ -104,4 +115,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/gpredict/gpredict.info b/academic/gpredict/gpredict.info index dfafad0f3f..1b08c53140 100644 --- a/academic/gpredict/gpredict.info +++ b/academic/gpredict/gpredict.info @@ -1,8 +1,8 @@ PRGNAM="gpredict" -VERSION="2.3" +VERSION="2.2.1" HOMEPAGE="http://gpredict.oz9aec.net" -DOWNLOAD="https://github.com/csete/gpredict/archive/v2.3/gpredict-2.3.tar.gz" -MD5SUM="58081bc4d55298b941c1f30f334fa6ca" +DOWNLOAD="https://github.com/csete/gpredict/archive/v2.2.1/gpredict-2.2.1.tar.gz" +MD5SUM="1e947f195c7182a52a2984c35594fef8" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="goocanvas2 hamlib" diff --git a/academic/grace/README b/academic/grace/README index 0e60c72cf5..8d1c5d7724 100644 --- a/academic/grace/README +++ b/academic/grace/README @@ -2,10 +2,11 @@ Grace is a WYSIWYG tool to make two-dimensional plots of numerical data. It runs under various (if not all) flavors of Unix with X11 and M*tif (LessTif or Motif). It also runs under VMS, OS/2, and Windows (95/98/NT/2000/XP). Its capabilities are roughly similar to GUI-based -programs like Sigmaplot or Microcal Origin plus script-based tools -like Gnuplot or Genplot. Its strength lies in the fact that it -combines the convenience of a graphical user interface with the power -of a scripting language which enables it to do sophisticated -calculations or perform automated tasks. +programs like Sigmaplot or Microcal Origin plus script-based tools like +Gnuplot or Genplot. Its strength lies in the fact that it combines the +convenience of a graphical user interface with the power of a scripting +language which enables it to do sophisticated calculations or perform +automated tasks. -Grace is derived from Xmgr (a.k.a. ACE/gr), originally written by Paul Turner. +Grace is derived from Xmgr (a.k.a. ACE/gr), originally written by Paul +Turner. diff --git a/academic/grace/grace.SlackBuild b/academic/grace/grace.SlackBuild index a4005d50b9..008415e106 100644 --- a/academic/grace/grace.SlackBuild +++ b/academic/grace/grace.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for grace @@ -23,10 +23,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=grace VERSION=${VERSION:-5.1.25} BUILD=${BUILD:-1} TAG=${TAG:-"_SBo"} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -36,7 +39,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-"/tmp/SBo"} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-"/tmp"} @@ -123,4 +133,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/grace/grace.info b/academic/grace/grace.info index 2ba34f78e3..1784546f10 100644 --- a/academic/grace/grace.info +++ b/academic/grace/grace.info @@ -1,7 +1,7 @@ PRGNAM="grace" VERSION="5.1.25" -HOMEPAGE="http://plasma-gate.weizmann.ac.il/Grace/" -DOWNLOAD="ftp://plasma-gate.weizmann.ac.il/pub/grace/src/grace5/grace-5.1.25.tar.gz" +HOMEPAGE="https://plasma-gate.weizmann.ac.il/Grace/" +DOWNLOAD="https://plasma-gate.weizmann.ac.il/pub/grace/src/grace5/grace-5.1.25.tar.gz" MD5SUM="c0482b1f18b113192946a96f5ff35a4d" DOWNLOAD_x86_64="" MD5SUM_x86_64="" diff --git a/academic/gresistor/gresistor.SlackBuild b/academic/gresistor/gresistor.SlackBuild index a6e2f24a3e..9aba26dce9 100644 --- a/academic/gresistor/gresistor.SlackBuild +++ b/academic/gresistor/gresistor.SlackBuild @@ -1,35 +1,45 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for gresistor # Written by Erwin van Zanten <e.van.zanten.evz@gmail.com> +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=gresistor VERSION=${VERSION:-0.0.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM-$VERSION +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="README" -if [ $ARCH = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" -elif [ $ARCH = "i686" ]; then +elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" LIBDIRSUFFIX="" -elif [ $ARCH = "x86_64" ]; then +elif [ "$ARCH" = "x86_64" ]; then SLKCFLAGS="-O2 -fPIC" LIBDIRSUFFIX="64" else @@ -70,4 +80,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/gretl/gretl.SlackBuild b/academic/gretl/gretl.SlackBuild index 2092c45699..d6a8650813 100644 --- a/academic/gretl/gretl.SlackBuild +++ b/academic/gretl/gretl.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for Gretl @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=gretl -VERSION=${VERSION:-2017c} -BUILD=${BUILD:-1} +VERSION=${VERSION:-2022a} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -80,7 +90,7 @@ CXXFLAGS="$SLKCFLAGS" \ --docdir=/usr/doc/$PRGNAM-$VERSION \ --disable-static \ --build=$ARCH-slackware-linux -make -j1 +make make -j1 install DESTDIR=$PKG find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ @@ -88,14 +98,16 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr mv $PKG/usr/share/man $PKG/usr find $PKG/usr/man -type f -exec gzip -9 {} \; -for i in $( find $PKG/usr/share/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done +for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a README README.audio COPYING INSTALL README.win32 $PKG/usr/doc/$PRGNAM-$VERSION +cp -a README COPYING INSTALL README.win32 $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild cp $CWD/$PRGNAM.png $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.png cp $CWD/*.pdf $PKG/usr/doc/$PRGNAM-$VERSION/ +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/doinst.sh > $PKG/install/doinst.sh cat $CWD/slack-desc > $PKG/install/slack-desc @@ -119,4 +131,4 @@ Categories=Education EOF cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/gretl/gretl.info b/academic/gretl/gretl.info index d2e95b62f3..a46978b95e 100644 --- a/academic/gretl/gretl.info +++ b/academic/gretl/gretl.info @@ -1,14 +1,14 @@ PRGNAM="gretl" -VERSION="2017c" -HOMEPAGE="http://gretl.sourceforge.net/" -DOWNLOAD="http://downloads.sourceforge.net/gretl/gretl-2017c.tar.xz \ - http://ponce.cc/slackware/sources/repo/gretl-ref.pdf \ - http://ponce.cc/slackware/sources/repo/gretl-guide.pdf" -MD5SUM="a785bbdbfce1306a2366235b5659e289 \ - d6adb54ba9247b049a5c3dc7e442b37a \ - f8f058a9b43db33bedefedee4bf461d4" +VERSION="2022a" +HOMEPAGE="https://gretl.sourceforge.net" +DOWNLOAD="https://downloads.sourceforge.net/gretl/gretl-2022a.tar.xz \ + https://ponce.cc/slackware/sources/repo/gretl/2022a/gretl-ref.pdf \ + https://ponce.cc/slackware/sources/repo/gretl/2022a/gretl-guide.pdf" +MD5SUM="21ca11178c3373222944daebdd5f1612 \ + faa9858bb8fb516a882aa28e365e99f8 \ + 2b995eeb8a82b7962e2e279c3a457625" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="gtksourceview3 json-glib lapack unixODBC" +REQUIRES="lapack" MAINTAINER="R. S. Ananda Murthy" EMAIL="rsamurti@gmail.com" diff --git a/academic/gri/gri.SlackBuild b/academic/gri/gri.SlackBuild index 965946ecd2..baa6a4e266 100644 --- a/academic/gri/gri.SlackBuild +++ b/academic/gri/gri.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for gri @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=gri VERSION=${VERSION:-2.12.23} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -114,4 +124,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/gri/gri.info b/academic/gri/gri.info index 4ca61c4974..6e4ee42dde 100644 --- a/academic/gri/gri.info +++ b/academic/gri/gri.info @@ -1,6 +1,6 @@ PRGNAM="gri" VERSION="2.12.23" -HOMEPAGE="https://gri.sourceforge.net/" +HOMEPAGE="https://sourceforge.net/p/gri/wiki/Home/" DOWNLOAD="https://github.com/dankelley/gri/archive/v2.12.23/gri-2.12.23.tar.gz" MD5SUM="7594140fdd1ea1ccf890c2d7ede0e1e9" DOWNLOAD_x86_64="" diff --git a/academic/gromacs/README b/academic/gromacs/README new file mode 100644 index 0000000000..a49f531bd4 --- /dev/null +++ b/academic/gromacs/README @@ -0,0 +1,20 @@ +GROMACS is a versatile package to perform molecular dynamics, i.e. +simulate the Newtonian equations of motion for systems with hundreds +to millions of particles and is a community-driven project. + +It is primarily designed for biochemical molecules like proteins, +lipids and nucleic acids that have a lot of complicated bonded +interactions, but since GROMACS is extremely fast at calculating the +nonbonded interactions (that usually dominate simulations) many groups +are also using it for research on non-biological systems, e.g. +polymers and fluid dynamics. + + +Optional dependences: +For run-time detection of hardware capabilities set HWLOC=yes. This +requires hwloc. +To enable MPI set PARALLEL=yes. This requires a MPI implementation +either openmpi or mpich. +For enabling CUDA set CUDA=yes. This requires the CUDA SDK. +To enable OpenCL set OPENCL=yes. This requires a OpenCL +implementation. diff --git a/academic/gromacs/gromacs.SlackBuild b/academic/gromacs/gromacs.SlackBuild new file mode 100644 index 0000000000..aaa0ac7022 --- /dev/null +++ b/academic/gromacs/gromacs.SlackBuild @@ -0,0 +1,144 @@ +#!/bin/bash + +# Slackware build script for gromacs + +# Copyright 2022 William PC - Seattle (USA) +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=gromacs +VERSION=${VERSION:-2021.6} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION-Source +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +# Enable run-time detection of hardware capabilities +if [ "${HWLOC:-no}" == "yes" ]; then + OPT_DEPS="$OPT_DEPS -DGMX_HWLOC=ON" +fi + +# Use CUDA SDK. +if [ "${CUDA:-no}" == "yes" ]; then + OPT_DEPS="$OPT_DEPS -DGMX_GPU=CUDA" +fi + +# Use an OpenCL implementation. +if [ "${OPENCL:-no}" == "yes" ]; then + OPT_DEPS="$OPT_DEPS -DGMX_GPU=OpenCL" +fi + +CFGSERIAL="-DGMX_MPI=OFF" + +CFGPARALLEL="-DGMX_MPI=ON" + +CFGGROMACS=$CFGSERIAL +BUILDDIR=build-serial + +if [ "${PARALLEL:-no}" == "yes" ]; then + CFGGROMACS=$CFGPARALLEL + BUILDDIR=build-parallel +fi + + rm -fr $BUILDDIR + mkdir -p $BUILDDIR + cd $BUILDDIR + + cmake \ + -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/opt/$PRGNAM \ + $CFGGROMACS \ + $OPT_DEPS \ + -DBUILD_SHARED_LIBS=ON \ + -DCMAKE_BUILD_TYPE=RELEASE .. + + make +# make check + make install DESTDIR=$PKG +cd .. + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +find $PKG -name perllocal.pod -o -name ".packlist" -o -name "*.bs" | xargs rm -f || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a {AUTHORS,COPYING,README} $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/gromacs/gromacs.info b/academic/gromacs/gromacs.info new file mode 100644 index 0000000000..f800414e54 --- /dev/null +++ b/academic/gromacs/gromacs.info @@ -0,0 +1,10 @@ +PRGNAM="gromacs" +VERSION="2021.6" +HOMEPAGE="https://www.gromacs.org" +DOWNLOAD="https://ftp.gromacs.org/gromacs/gromacs-2021.6.tar.gz" +MD5SUM="ed1bdc2a634413dfdd5a7c0be82f6a9d" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/gromacs/slack-desc b/academic/gromacs/slack-desc new file mode 100644 index 0000000000..606601ed62 --- /dev/null +++ b/academic/gromacs/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +gromacs: gromacs (gromacs project) +gromacs: +gromacs: GROMACS is a versatile package to perform molecular dynamics, i.e. +gromacs: simulate the Newtonian equations of motion for systems with hundreds +gromacs: to millions of particles and is a community-driven project. +gromacs: +gromacs: +gromacs: +gromacs: +gromacs: +gromacs: diff --git a/academic/grpn/README b/academic/grpn/README index af0f57f7b3..ebe90d81ce 100644 --- a/academic/grpn/README +++ b/academic/grpn/README @@ -1,9 +1,10 @@ -GRPN is a graphical reverse polish notation (RPN) calculator. -GRPN is written in C and uses the GIMP Toolkit (GTK) on top of X11. GRPN -was developed under Linux but has also been tested under SunOS and Solaris. -It should work with almost any UNIX, though. GRPN works with real numbers -and complex numbers. Numbers can be displayed in 4 different radix modes, -and complex numbers can be displayed in either Cartesian or polar form. +GRPN is a graphical reverse polish notation (RPN) calculator. GRPN is +written in C and uses the GIMP Toolkit (GTK) on top of X11. GRPN was +developed under Linux but has also been tested under SunOS and Solaris. +It should work with almost any UNIX, though. GRPN works with real +numbers and complex numbers. Numbers can be displayed in 4 different +radix modes, and complex numbers can be displayed in either Cartesian +or polar form. -GRPN uses a stack and reverse polish notation to evaluate expressions. The -stack in GRPN is infinite and limited only by available memory. +GRPN uses a stack and reverse polish notation to evaluate expressions. +The stack in GRPN is infinite and limited only by available memory. diff --git a/academic/grpn/grpn.SlackBuild b/academic/grpn/grpn.SlackBuild index 43d21124e1..f0a9c04743 100644 --- a/academic/grpn/grpn.SlackBuild +++ b/academic/grpn/grpn.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for grpn @@ -6,26 +6,36 @@ # Released into the public domain June 6, 2009 +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=grpn VERSION=${VERSION:-1.1.2} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -76,4 +86,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/gspiceui/gspiceui.SlackBuild b/academic/gspiceui/gspiceui.SlackBuild index 5855a4a05e..2b5f7956fb 100644 --- a/academic/gspiceui/gspiceui.SlackBuild +++ b/academic/gspiceui/gspiceui.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for Gspiceui @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=gspiceui -VERSION=${VERSION:-1.2.36} +VERSION=${VERSION:-1.2.87} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -95,4 +105,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/gspiceui/gspiceui.info b/academic/gspiceui/gspiceui.info index a46c540959..223171695c 100644 --- a/academic/gspiceui/gspiceui.info +++ b/academic/gspiceui/gspiceui.info @@ -1,10 +1,10 @@ PRGNAM="gspiceui" -VERSION="1.2.36" +VERSION="1.2.87" HOMEPAGE="http://users.tpg.com.au/micksw012/gspiceui.html" -DOWNLOAD="https://sourceforge.net/projects/gspiceui/files/gSpiceUI/gspiceui-v1.2.36/gspiceui-v1.2.36.tar.gz" -MD5SUM="a385028952ada5aa69acdb7298332c8c" +DOWNLOAD="https://sourceforge.net/projects/gspiceui/files/gSpiceUI/gspiceui-v1.2.87/gspiceui-v1.2.87.tar.gz" +MD5SUM="ae580ac1665674fda3b7029392695157" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="pangox-compat wxPython3" +REQUIRES="pangox-compat wxGTK3" MAINTAINER="R. S. Ananda Murthy" EMAIL="rsamurti@gmail.com" diff --git a/academic/gtkwave/README b/academic/gtkwave/README index fa42f8d4de..6c030894b0 100644 --- a/academic/gtkwave/README +++ b/academic/gtkwave/README @@ -1,2 +1,2 @@ -GTKWave is a fully featured GTK+ based wave viewer which reads LXT, LXT2, -VZT, and GHW files as well as standard Verilog VCD EVCD files. +GTKWave is a fully featured GTK+ based wave viewer which reads LXT, +LXT2, VZT, and GHW files as well as standard Verilog VCD EVCD files. diff --git a/academic/gtkwave/gtkwave.SlackBuild b/academic/gtkwave/gtkwave.SlackBuild index 2fe435439c..1c4fbb4a14 100644 --- a/academic/gtkwave/gtkwave.SlackBuild +++ b/academic/gtkwave/gtkwave.SlackBuild @@ -1,28 +1,38 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for Icarus Verilog compiler # Written by Stephen Van Berg stephen_van_berg@earlicker.com. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=gtkwave -VERSION=${VERSION:-3.3.51} +VERSION=${VERSION:-3.3.111} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -93,4 +103,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/gtkwave/gtkwave.info b/academic/gtkwave/gtkwave.info index c76491fcc6..b027e7ff05 100644 --- a/academic/gtkwave/gtkwave.info +++ b/academic/gtkwave/gtkwave.info @@ -1,8 +1,8 @@ PRGNAM="gtkwave" -VERSION="3.3.51" +VERSION="3.3.111" HOMEPAGE="http://gtkwave.sourceforge.net/" -DOWNLOAD="http://gtkwave.sourceforge.net/gtkwave-3.3.51.tar.gz" -MD5SUM="7214a0358bdeadbbe305dfd6eeced828" +DOWNLOAD="http://gtkwave.sourceforge.net/gtkwave-3.3.111.tar.gz" +MD5SUM="ec9978cc21582ccb89b844e0abfc9b94" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/gtypist/gtypist.SlackBuild b/academic/gtypist/gtypist.SlackBuild index 73df0f076f..b23279fa52 100644 --- a/academic/gtypist/gtypist.SlackBuild +++ b/academic/gtypist/gtypist.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for gtypist # Copyright 2007-2012 Grigorios Bouzakis <grbzks@imap.cc> -# Copyright 2014 Aaditya Bagga <aaditya_gnulinux@zoho.com> +# Copyright 2014 Aaditya <aaditya_gnulinux@zoho.com> # All rights reserved. # # Permission to use, copy, modify, and distribute this software for any purpose @@ -20,26 +20,36 @@ # (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF # THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=gtypist VERSION=${VERSION:-2.9.5} BUILD=${BUILD:-3} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -106,4 +116,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/gtypist/gtypist.info b/academic/gtypist/gtypist.info index 5e318927d7..fbcdbb4e74 100644 --- a/academic/gtypist/gtypist.info +++ b/academic/gtypist/gtypist.info @@ -6,5 +6,5 @@ MD5SUM="010824327ebbc0e01626da2b50b0efaf" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" -MAINTAINER="Aaditya Bagga" +MAINTAINER="Aaditya" EMAIL="aaditya_gnulinux@zoho.com" diff --git a/academic/gwyddion/README b/academic/gwyddion/README index 3b8a4dee6f..06564ec378 100644 --- a/academic/gwyddion/README +++ b/academic/gwyddion/README @@ -1,7 +1,7 @@ Gwyddion is a modular program for SPM (scanning probe microscopy) data visualization and analysis. Primarily it is intended for analysis of height fields obtained by means of scanning probe microscopy techniques -(AFM, MFM, STM, SNOM/NSOM), however it can be generally used for any other -height field and image analysis. +(AFM, MFM, STM, SNOM/NSOM), however it can be generally used for any +other height field and image analysis. -libminizip, libwebp and cfitsio are the optional dependencies. +libunique and hdf5 are the optional dependencies. diff --git a/academic/gwyddion/doinst.sh b/academic/gwyddion/doinst.sh index 36863cab7d..8a5ffa8af5 100644 --- a/academic/gwyddion/doinst.sh +++ b/academic/gwyddion/doinst.sh @@ -1,12 +1,3 @@ -schema_install() { - SCHEMA="$1" - GCONF_CONFIG_SOURCE="xml::etc/gconf/gconf.xml.defaults" \ - chroot . gconftool-2 --makefile-install-rule \ - /etc/gconf/schemas/$SCHEMA \ - 1>/dev/null -} - -schema_install gwyddion-thumbnailer.schemas if [ -x /usr/bin/update-desktop-database ]; then /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 diff --git a/academic/gwyddion/gwyddion.SlackBuild b/academic/gwyddion/gwyddion.SlackBuild index 9537fb157d..5f741433c1 100644 --- a/academic/gwyddion/gwyddion.SlackBuild +++ b/academic/gwyddion/gwyddion.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for gwyddion -# Copyright 2012-2017 Daniil Bratashov <dn2010@gmail.com> +# Copyright 2012-2022 Daniil Bratashov <dn2010@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=gwyddion -VERSION=${VERSION:-2.55} +VERSION=${VERSION:-2.65} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -92,9 +102,11 @@ mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a AUTHORS ChangeLog README $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/gwyddion/gwyddion.info b/academic/gwyddion/gwyddion.info index ab4ec07b9d..6dc1a61df0 100644 --- a/academic/gwyddion/gwyddion.info +++ b/academic/gwyddion/gwyddion.info @@ -1,8 +1,8 @@ PRGNAM="gwyddion" -VERSION="2.55" +VERSION="2.65" HOMEPAGE="http://gwyddion.net" -DOWNLOAD="http://downloads.sourceforge.net/gwyddion/gwyddion-2.55.tar.xz" -MD5SUM="91d7f7cdc2fb46ec639f87349425d3d2" +DOWNLOAD="http://downloads.sourceforge.net/gwyddion/gwyddion-2.65.tar.xz" +MD5SUM="6c55a05fe3040d6e102bd34d46d3da7d" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="gtkglext" diff --git a/academic/h5utils/README b/academic/h5utils/README index 3b0ed29af6..60dcde6366 100644 --- a/academic/h5utils/README +++ b/academic/h5utils/README @@ -1,9 +1,33 @@ -H5utils is is a set of utilities for visualization and -conversion of scientific data in the free, portable HDF5 -format. Besides providing a simple tool for batch -visualization as PNG images, h5utils also includes -programs to convert HDF5 datasets into the formats -required by other free visualization software (e.g. -plain text, Vis5d, and VTK). - -Optional dependencies: libmatheval, octave, hdf, and perhaps Vis5d. +h5utils (visualization and conversion of HDF5 data) + +H5utils is is a set of utilities for visualization and conversion of +scientific data in the free, portable HDF5 format. Besides providing +a simple tool for batch visualization as PNG images, h5utils also +includes programs to convert HDF5 datasets into the formats required +by other free visualization software (e.g. plain text, Vis5d, and +VTK). + +This package requires: hdf5 + +You probably want to preinstall: libmatheval + +You possibly want to install: octave, hdf; and perhaps Vis5d (not on +SBo). + + +Configuration: + +You can add additional options to the command line using the +environment variable SBOPTIONS_H5UTILS; e.g. to enable the hdf4 utils +and not rely on the conversion routines, use + +SBOPTIONS_H5UTILS="--with-hdf4" ./h5utils.Slackbuild + +Alternatively, if building non-interactively (e.g. if using slpkg), +use/create the file /etc/sbo_pkg_options.conf since this slackbuild +script will search it for options. Simply include a line starting +"h5utils:" followed by options, e.g.: + +h5utils: --with-hdf4 + + diff --git a/academic/h5utils/h5utils.SlackBuild b/academic/h5utils/h5utils.SlackBuild index 1f85355f30..1bc4c3a5ef 100644 --- a/academic/h5utils/h5utils.SlackBuild +++ b/academic/h5utils/h5utils.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for h5utils @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=h5utils -VERSION=${VERSION:-1.13.1} +VERSION=${VERSION:-1.13.2} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -54,13 +64,13 @@ else LIBDIRSUFFIX="" fi +set -e + # change annoying underscores into hyphens SVERSION=$(echo $VERSION | tr '_' '-') # make a custom list of doc files in advance DOCFILES="AUTHORS COPYING" -set -e - rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP @@ -75,11 +85,20 @@ find -L . \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; # if there is no configure script, try to build one! -if [ ! -f ./configure ] ; then +if [ ! -f ./configure ] ; then ./autogen.sh fi LOCALCONFIGS= +XDBFILE=/etc/sbo_pkg_options.conf +if [ -f ${XDBFILE} ] ; then + LOCALCONFIGS=${LOCALCONFIGS}" "$(grep "^${PRGNAM}:" ${XDBFILE} | grep -v '^#' | awk -F: '{print$2}') + echo Build options selected by file: LOCALCONFIGS=${LOCALCONFIGS} +fi +if [ -n "${SBOPTIONS_H5UTILS}" ] ; then + LOCALCONFIGS=${LOCALCONFIGS}" "${SBOPTIONS_H5UTILS} + echo Build options selected by environment: LOCALCONFIGS=${LOCALCONFIGS} +fi CFLAGS="$SLKCFLAGS" \ CPPFLAGS="$SLKCFLAGS" \ @@ -91,12 +110,6 @@ CPPFLAGS="$SLKCFLAGS" \ --build=$ARCH-slackware-linux \ $LOCALCONFIGS -# allow parallel makes if this variable is set; -# but always finish with a single make in case -# there is a problem with that -if [ "${JMULTIMAKE}" ] ; then - make -j ${JMULTIMAKE} -fi make make install DESTDIR=$PKG @@ -107,8 +120,11 @@ cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true +find $PKG/usr/man -type f -exec gzip -9 {} \; +for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/h5utils/h5utils.info b/academic/h5utils/h5utils.info index a600f211b9..08f261fe8b 100644 --- a/academic/h5utils/h5utils.info +++ b/academic/h5utils/h5utils.info @@ -1,8 +1,8 @@ PRGNAM="h5utils" -VERSION="1.13.1" +VERSION="1.13.2" HOMEPAGE="https://github.com/NanoComp/h5utils" -DOWNLOAD="https://github.com/NanoComp/h5utils/releases/download/1.13.1/h5utils-1.13.1.tar.gz" -MD5SUM="b116cbb79ea22bbd1640cd8a1290f6f8" +DOWNLOAD="https://github.com/NanoComp/h5utils/releases/download/1.13.2/h5utils-1.13.2.tar.gz" +MD5SUM="32949375c6bfbe5849b940e82a0464dd" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="hdf5" diff --git a/academic/h5utils/slack-desc b/academic/h5utils/slack-desc index 226340b323..2fecfe9c9a 100644 --- a/academic/h5utils/slack-desc +++ b/academic/h5utils/slack-desc @@ -8,7 +8,7 @@ |-----handy-ruler------------------------------------------------------| h5utils: h5utils (visualization and conversion of HDF5 data) h5utils: -h5utils: These utilities provide simple tools for batch visualization of +h5utils: These utilities provide simple tools for batch visualization of h5utils: hdf5 datafiles as PNG images. They also allow conversion from hdf5 h5utils: format into other formats used for visualization, such as plain text, h5utils: Vis5d, and VTK. diff --git a/academic/harminv/README b/academic/harminv/README index fc3c9c0bc7..f574c1996c 100644 --- a/academic/harminv/README +++ b/academic/harminv/README @@ -1,5 +1,14 @@ -Harminv is a program and library that solves the problem of -harmonic inversion. It takes a discrete-time, finite-length -signal, and decomposes it into a sum of finitely-many -sinusoids, determining the frequencies, decay constants, +harminv (harmonic inversion from a time series) + +Harminv is a program and library that solves the problem of +harmonic inversion. It takes a discrete-time, finite-length +signal, and decomposes it into a sum of finitely-many +sinusoids, determining the frequencies, decay constants, amplitudes, and phases of those sinusoids. + +This package requires: lapack + +If the build script can find the ATLAS libraries, it will +adapt the configure options to use them rather than the +default lapack. + diff --git a/academic/harminv/harminv.SlackBuild b/academic/harminv/harminv.SlackBuild index 34d85f200d..7bbd8433bf 100644 --- a/academic/harminv/harminv.SlackBuild +++ b/academic/harminv/harminv.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for harminv @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=harminv -VERSION=${VERSION:-1.4.1} +VERSION=${VERSION:-1.4.2} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -54,13 +64,13 @@ else LIBDIRSUFFIX="" fi +set -e + # change annoying underscores into hyphens SVERSION=$(echo $VERSION | tr '_' '-') # make a custom list of doc files in advance DOCFILES="COPYING COPYRIGHT NEWS.md README.md doc/*.md " -set -e - rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP @@ -79,7 +89,20 @@ if [ ! -f ./configure ] ; then ./autogen.sh fi -LOCALCONFIGS="--enable-shared --with-blas=atlas" + +LOCALCONFIGS="--enable-shared --enable-static=no " + + +# check for the Atlas replacement for blas; if the libraries are found, +# add the configure option accordingly + +if [ -f /usr/lib/libatlas.a ] ; then + if [ -f /usr/lib/libatlas.so ] ; then + echo "NOTICE: libatlas was found, configure --with-blas=atlas" + LOCALCONFIGS=${LOCALCONFIGS}" --with-blas=atlas" + fi +fi + CFLAGS="$SLKCFLAGS" \ CPPFLAGS="$SLKCFLAGS" \ @@ -89,12 +112,14 @@ CPPFLAGS="$SLKCFLAGS" \ --libdir=/usr/lib${LIBDIRSUFFIX} \ --docdir=/usr/doc/$PRGNAM-$VERSION \ --build=$ARCH-slackware-linux \ - --enable-static=no \ $LOCALCONFIGS make make install DESTDIR=$PKG +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true @@ -109,4 +134,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/harminv/harminv.info b/academic/harminv/harminv.info index 4ba38e5070..298d496d12 100644 --- a/academic/harminv/harminv.info +++ b/academic/harminv/harminv.info @@ -1,8 +1,8 @@ PRGNAM="harminv" -VERSION="1.4.1" +VERSION="1.4.2" HOMEPAGE="https://github.com/NanoComp/harminv" -DOWNLOAD="https://github.com/NanoComp/harminv/releases/download/v1.4.1/harminv-1.4.1.tar.gz" -MD5SUM="a1ac921b1b97cd2c0354c35b2d8a77fc" +DOWNLOAD="https://github.com/NanoComp/harminv/releases/download/v1.4.2/harminv-1.4.2.tar.gz" +MD5SUM="0ad9ed9b2b345c2e8c2929f20bdf2492" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="lapack" diff --git a/academic/harminv/slack-desc b/academic/harminv/slack-desc index 63773e4878..7e7a2360d6 100644 --- a/academic/harminv/slack-desc +++ b/academic/harminv/slack-desc @@ -8,9 +8,9 @@ |-----handy-ruler------------------------------------------------------| harminv: harminv (harmonic inversion from a time series) harminv: -harminv: Harminv is a program and library that solves the problem of -harminv: harmonic inversion. It takes a discrete-time, finite-length -harminv: signal, and decomposes it into a sum of finitely-many +harminv: Harminv is a program and library that solves the problem of +harminv: harmonic inversion. It takes a discrete-time, finite-length +harminv: signal, and decomposes it into a sum of finitely-many harminv: sinusoids, dettermining the frequencies, decay constants, harminv: amplitudes, and phases of those sinusoids. harminv: diff --git a/academic/hdfview/README b/academic/hdfview/README new file mode 100644 index 0000000000..70371cc79a --- /dev/null +++ b/academic/hdfview/README @@ -0,0 +1,15 @@ +HDFView Software + +HDFView software consists of the HDFView utility and the Java HDF +Object Package. + +HDFView is a visual tool written in Java for browsing and editing HDF +(HDF5 and HDF4) files. Using HDFView, you can: + +View a file hierarchy in a tree structure +Create new files, add or delete groups and datasets +View and modify the content of a dataset +Add, delete and modify attributes + +HDFView uses the Java HDF Object Package, which implements HDF4 and +HDF5 data objects in an object-oriented form. diff --git a/academic/hdfview/hdfview.SlackBuild b/academic/hdfview/hdfview.SlackBuild new file mode 100644 index 0000000000..bb19668283 --- /dev/null +++ b/academic/hdfview/hdfview.SlackBuild @@ -0,0 +1,112 @@ +#!/bin/bash + +# Slackware build script for hdfview + +# Copyright 2023, Lockywolf +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=hdfview +VERSION=${VERSION:-3.3.1} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +elif [ "$ARCH" = "aarch64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP + +rm -rf $PRGNAM-$VERSION +mkdir $PRGNAM-$VERSION +cd $PRGNAM-$VERSION +#https://support.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdfview-3.1.3/bin/HDFView-3.1.3-fedora33_64.tar.gz" + +tar xvf $CWD/HDFView-$VERSION-centos8_64.tar.gz +rpm2cpio $PRGNAM-$VERSION-1.x86_64.rpm | cpio --extract --make-directories + +chown -R root:root . +# find -L . \ +# \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ +# -o -perm 511 \) -exec chmod 755 {} + -o \ +# \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ +# -o -perm 440 -o -perm 400 \) -exec chmod 644 {} + +find -L . \ + -type d -exec chmod 755 {} + +find -L . \ + -type f -exec chmod 755 {} + + + +install -d -m 755 $PKG/usr/bin + +cp -r ./opt $PKG/ + +echo "#!/bin/bash +exec /opt/$PRGNAM/bin/HDFView \"$@\"" > $PKG/usr/bin/$PRGNAM +chmod +x $PKG/usr/bin/$PRGNAM + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION + +cat README.txt > $PKG/usr/doc/$PRGNAM-$VERSION/README.txt +cat COPYING > $PKG/usr/doc/$PRGNAM-$VERSION/COPYING + +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/hdfview/hdfview.info b/academic/hdfview/hdfview.info new file mode 100644 index 0000000000..ff596fab36 --- /dev/null +++ b/academic/hdfview/hdfview.info @@ -0,0 +1,10 @@ +PRGNAM="hdfview" +VERSION="3.3.1" +HOMEPAGE="https://gephi.org/" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="https://support.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdfview-3.3.1/bin/HDFView-3.3.1-centos8_64.tar.gz" +MD5SUM_x86_64="f54feb3dcd15be989d762320a57753f8" +REQUIRES="" +MAINTAINER="Lockywolf" +EMAIL="for_sbo.gephi_2023-07-18@lockywolf.net" diff --git a/academic/hdfview/slack-desc b/academic/hdfview/slack-desc new file mode 100644 index 0000000000..28e9b7e7d0 --- /dev/null +++ b/academic/hdfview/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +hdfview: hdfview (visual tool written in Java for browsing and editing HDF) +hdfview: +hdfview: HDFView is a visual tool written in Java for browsing and editing HDF +hdfview: (HDF5 and HDF4) files. Using HDFView, you can: +hdfview: View a file hierarchy in a tree structure +hdfview: Create new files, add or delete groups and datasets +hdfview: View and modify the content of a dataset +hdfview: Add, delete and modify attributes +hdfview: HDFView uses the Java HDF Object Package, which implements HDF4 +hdfview: and HDF5 data objects in an object-oriented form. +hdfview: diff --git a/academic/hyphy/README b/academic/hyphy/README index 4405702da1..2aca901dff 100644 --- a/academic/hyphy/README +++ b/academic/hyphy/README @@ -51,6 +51,10 @@ NOTE! The script builds two executables: HYPHYMP, which uses pthreads to do multiprocessing and HYPHYMPI, which uses openmpi (hence the dependency). +HyPhy Vision +To visualise your results produced offline, you can use HyPhy Vision: +http://vision.hyphy.org/ + Citing Sergei L. Kosakovsky Pond, Simon D. W. Frost and Spencer V. Muse (2005) HyPhy: hypothesis testing using phylogenies. diff --git a/academic/hyphy/hyphy.SlackBuild b/academic/hyphy/hyphy.SlackBuild index e22cf3435a..aa4484c239 100644 --- a/academic/hyphy/hyphy.SlackBuild +++ b/academic/hyphy/hyphy.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for hyphy -# Copyright 2017-2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2017-2023 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=hyphy -VERSION=${VERSION:-2.3.14} +VERSION=${VERSION:-2.5.50} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -71,11 +81,18 @@ find -L . \ # Fix the libraries path on 64 systems and use our compiler flags sed -i "s:lib/hyphy:lib${LIBDIRSUFFIX}/hyphy:g" CMakeLists.txt -sed -i "s:-msse3:$SLKCFLAGS:g" CMakeLists.txt -sed -i "s:-march=corei7-avx -mtune=corei7-avx:$SLKCFLAGS:g" CMakeLists.txt -sed -i "s:-mno-avx:$SLKCFLAGS:g" CMakeLists.txt -sed -i "s:-mno-sse3:$SLKCFLAGS:g" CMakeLists.txt -sed -i "s:-fsigned-char -O3:$SLKCFLAGS:g" CMakeLists.txt + +# Use our flags +sed -i "s:-fsigned-char -O3:$SLKCFLAGS -fsigned-char:g" CMakeLists.txt + +# Use _only_ our flags. You may wish to comment out the lines below to +# enable flags automatically set for you architecture. +sed -i "s:-march=native -mtune=native -mavx::g" CMakeLists.txt +sed -i "s:-mavx::g" CMakeLists.txt +sed -i "s:-mfma::g" CMakeLists.txt +sed -i "s:-msse3::g" CMakeLists.txt +sed -i "s:-mno-avx::g" CMakeLists.txt +sed -i "s:-mno-sse3::g" CMakeLists.txt mkdir -p build cd build @@ -83,22 +100,15 @@ cd build -DCMAKE_INSTALL_PREFIX=/usr \ -DCMAKE_BUILD_TYPE=Release .. -# It is actually not necessary anymore to specify here MP and HYPHYMPI, -# as 'make' alone will attempt to build them both. However, let's leave -# them, just in case. - make MP HYPHYMPI + make HYPHYMPI make install DESTDIR=$PKG cd .. find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true -# Include a few examples -mkdir -p $PKG/usr/share/$PRGNAM -cp -a Examples $PKG/usr/share/$PRGNAM - mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a help/*.pdf LICENSE README.md $PKG/usr/doc/$PRGNAM-$VERSION +cp -a LICENSE README.md CONTRIBUTING.md $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References @@ -106,4 +116,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/hyphy/hyphy.info b/academic/hyphy/hyphy.info index 33786b6d6c..b35f93b3bb 100644 --- a/academic/hyphy/hyphy.info +++ b/academic/hyphy/hyphy.info @@ -1,8 +1,8 @@ PRGNAM="hyphy" -VERSION="2.3.14" +VERSION="2.5.50" HOMEPAGE="https://veg.github.io/hyphy-site/" -DOWNLOAD="https://github.com/veg/hyphy/archive/2.3.14/hyphy-2.3.14.tar.gz" -MD5SUM="d82809929d213e236078ed4853ea3962" +DOWNLOAD="https://github.com/veg/hyphy/archive/2.5.50/hyphy-2.5.50.tar.gz" +MD5SUM="c4e02d58025f4d1f129cc2b0c2dc97dd" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="openmpi" diff --git a/academic/iTest/iTest.SlackBuild b/academic/iTest/iTest.SlackBuild index 4d1fb23da1..9ba531b79c 100644 --- a/academic/iTest/iTest.SlackBuild +++ b/academic/iTest/iTest.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for iTest @@ -22,27 +22,37 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=iTest VERSION=${VERSION:-1.4.2_PREVIEW4} SRCVER=$(echo $VERSION | tr _ -) BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -77,6 +87,8 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; +. /etc/profile.d/qt4.sh + cd iTestServer lrelease iTestServer.pro cd .. @@ -137,4 +149,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/iTest/iTest.info b/academic/iTest/iTest.info index 093a59a20d..a4933c1590 100644 --- a/academic/iTest/iTest.info +++ b/academic/iTest/iTest.info @@ -5,6 +5,6 @@ DOWNLOAD="http://sourceforge.net/projects/itest/files/itest-prereleases/iTest-1. MD5SUM="8e4b055c42850ec740cccc18db681bd6" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="" +REQUIRES="qt4" MAINTAINER="R. S. Ananda Murthy" EMAIL="rsamurti@gmail.com" diff --git a/academic/io_lib/io_lib.SlackBuild b/academic/io_lib/io_lib.SlackBuild index 43a72cb84f..2f78cde485 100644 --- a/academic/io_lib/io_lib.SlackBuild +++ b/academic/io_lib/io_lib.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for io_lib -# Copyright 2011-2020 Petar Petrov slackalaxy@gmail.com +# Copyright 2011-2023 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=io_lib -VERSION=${VERSION:-1.14.11} +VERSION=${VERSION:-1.15.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -95,8 +105,10 @@ cp -a \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/io_lib/io_lib.info b/academic/io_lib/io_lib.info index ba3fb88a0c..dc94f30b2b 100644 --- a/academic/io_lib/io_lib.info +++ b/academic/io_lib/io_lib.info @@ -1,8 +1,8 @@ PRGNAM="io_lib" -VERSION="1.14.11" +VERSION="1.15.0" HOMEPAGE="https://github.com/jkbonfield/io_lib" -DOWNLOAD="https://github.com/jkbonfield/io_lib/releases/download/io_lib-1-14-11/io_lib-1.14.11.tar.gz" -MD5SUM="90fa0b6ad125e033a9b2c48b3fe4ac0a" +DOWNLOAD="https://github.com/jkbonfield/io_lib/releases/download/io_lib-1-15-0/io_lib-1.15.0.tar.gz" +MD5SUM="5d0949836d6e235a69f59a9a3b2af022" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/iqtree/README b/academic/iqtree/README new file mode 100644 index 0000000000..00f5a25553 --- /dev/null +++ b/academic/iqtree/README @@ -0,0 +1,62 @@ +iqtree (IQ-TREE): Efficient and versatile phylogenomic software by +maximum likelihood (ML) + +The IQ-TREE software was created as the successor of IQPNNI and TREE- +PUZZLE (thus the name IQ-TREE). IQ-TREE was motivated by the rapid +accumulation of phylogenomic data, leading to a need for efficient +phylogenomic software that can handle a large amount of data and provide +more complex models of sequence evolution. To this end, IQ-TREE can +utilize multicore computers and distributed parallel computing to speed +up the analysis. IQ-TREE automatically performs checkpointing to resume +an interrupted analysis. + +As input IQ-TREE accepts all common sequence alignment formats including +PHYLIP, FASTA, Nexus, Clustal and MSF. As output IQ-TREE will write a +self-readable report file (name suffix .iqtree), a NEWICK tree file +(.treefile) which can be visualized by tree viewer programs such as +FigTree, Dendroscope or iTOL. + +Key features +- Efficient search algorithm: Fast and effective stochastic algorithm to + reconstruct phylogenetic trees by maximum likelihood. IQ-TREE compares + favorably to RAxML and PhyML in terms of likelihood while requiring + similar amount of computing time. +- Ultrafast bootstrap: An ultrafast bootstrap approximation (UFBoot) to + assess branch supports. UFBoot is 10 to 40 times faster than RAxML + rapid bootstrap and obtains less biased support values. +- Ultrafast model selection: An ultrafast and automatic model selection + (ModelFinder) which is 10 to 100 times faster than jModelTest and + ProtTest. ModelFinder also finds best-fit partitioning scheme like + PartitionFinder. +- Big Data Analysis: Supporting huge datasets with thousands of + sequences or millions of alignment sites via checkpointing, safe + numerical and low memory mode. Multicore CPUs and parallel MPI system + are utilized to speedup analysis. +- Phylogenetic testing: Several fast branch tests like SH-aLRT and a + Bayes test and tree topology tests like the approximately unbiased + (AU) test. + +The strength of IQ-TREE is the availability of a wide variety of +phylogenetic models: +- Common models: All common substitution models for DNA, protein, codon, + binary and morphological data with rate heterogeneity among sites and + ascertainment bias correction for e.g. SNP data. +- Partition models: Allowing individual models for different genomic + loci (e.g. genes or codon positions), mixed data types, mixed rate + heterogeneity types, linked or unlinked branch lengths between + partitions. +- Mixture models: fully customizable mixture models and empirical + protein mixture models and. +- Polymorphism-aware models: Accounting for incomplete lineage sorting + to infer species tree from genome-wide population data. + +CITING: +To maintain IQ-TREE, support users and secure fundings, it is important +that you cite the papers, whenever the corresponding features were +applied for your analysis. Note that the paper of Nguyen et al. (2015) +only described the tree search algorithm. Thus, it is not enough to only +cite this paper if you, for example, use partition models, where +Chernomor et al. (2016) should be cited. + +Check the "References" file in the package doc folder, as well as, the +program's web-page. diff --git a/academic/iqtree/References b/academic/iqtree/References new file mode 100644 index 0000000000..37b6382d9c --- /dev/null +++ b/academic/iqtree/References @@ -0,0 +1,35 @@ +How to cite? +To maintain IQ-TREE, support users and secure fundings, it is important for us that you cite the following papers, whenever the corresponding features were applied for your analysis. Note that the paper of Nguyen et al. (2015) only described the tree search algorithm. Thus, it is not enough to only cite this paper if you, for example, use partition models, where Chernomor et al. (2016) should be cited. + +General citation for IQ-TREE 2: +B.Q. Minh, H.A. Schmidt, O. Chernomor, D. Schrempf, M.D. Woodhams, A. von Haeseler, R. Lanfear (2020) IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol., 37:1530-1534. https://doi.org/10.1093/molbev/msaa015 + +When using concordance factors please cite: +B.Q. Minh, M.W. Hahn, R. Lanfear (2020) New methods to calculate concordance factors for phylogenomic datasets. Mol. Biol. Evol. https://doi.org/10.1093/molbev/msaa106 + +When using heterotachy models please cite: +S.M. Crotty, B.Q. Minh, N.G. Bean, B.R. Holland, J. Tuke, L.S. Jermiin, A. von Haeseler (2020) GHOST: Recovering historical signal from heterotachously-evolved sequence alignments. Syst. Biol., 69:249-264. https://doi.org/10.1093/sysbio/syz051 + +When using the tests of symmetry please cite: +S. Naser-Khdour, B.Q. Minh, W. Zhang, E.A. Stone, R. Lanfear (2019) The Prevalence and Impact of Model Violations in Phylogenetic Analysis. Genome Biol. Evol., 11:3341-3352. https://doi.org/10.1093/gbe/evz193 + +When using polymorphism-aware models please cite: +D. Schrempf, B.Q. Minh, A. von Haeseler, C. Kosiol (2019) Polymorphism-aware species trees with advanced mutation models, bootstrap, and rate heterogeneity. Mol. Biol. Evol., 36:1294–1301. https://doi.org/10.1093/molbev/msz043 + +When performing ultrafast bootstrap (UFBoot) please cite: +D.T. Hoang, O. Chernomor, A. von Haeseler, B.Q. Minh, L.S. Vinh (2018) UFBoot2: Improving the ultrafast bootstrap approximation. Mol. Biol. Evol., 35:518–522. https://doi.org/10.1093/molbev/msx281 + +When using posterior mean site frequency model (PMSF) please cite: +H.C. Wang, B.Q. Minh, S. Susko, A.J. Roger (2018) Modeling site heterogeneity with posterior mean site frequency profiles accelerates accurate phylogenomic estimation. Syst. Biol., 67:216–235. https://doi.org/10.1093/sysbio/syx068 + +When using model selection (ModelFinder) please cite: +S. Kalyaanamoorthy, B.Q. Minh, T.K.F. Wong, A. von Haeseler, L.S. Jermiin (2017) ModelFinder: Fast model selection for accurate phylogenetic estimates. Nat. Methods, 14:587-589. https://doi.org/10.1038/nmeth.4285 + +When using partition models please cite: +O. Chernomor, A. von Haeseler, B.Q. Minh (2016) Terrace aware data structure for phylogenomic inference from supermatrices. Syst. Biol., 65:997-1008. https://doi.org/10.1093/sysbio/syw037 + +When using IQ-TREE web server please cite: +J. Trifinopoulos, L.-T. Nguyen, A. von Haeseler, B.Q. Minh (2016) W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis.. Nucleic Acids Res., 44:W232-W235. https://doi.org/10.1093/nar/gkw256 + +For IQ-TREE 1 please cite: +L.-T. Nguyen, H.A. Schmidt, A. von Haeseler, B.Q. Minh (2015) IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies.. Mol. Biol. Evol., 32:268-274. https://doi.org/10.1093/molbev/msu300 diff --git a/academic/iqtree/iqtree.SlackBuild b/academic/iqtree/iqtree.SlackBuild new file mode 100644 index 0000000000..83542b001d --- /dev/null +++ b/academic/iqtree/iqtree.SlackBuild @@ -0,0 +1,86 @@ +#!/bin/bash + +# Slackware build script for <iqtree> + +# Copyright 2022-2023 Petar Petrov slackalaxy at gmail dot com +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=iqtree +VERSION=${VERSION:-2.2.2.7} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION-Linux +tar xvf $CWD/$PRGNAM-$VERSION-Linux.tar.gz +cd $PRGNAM-$VERSION-Linux +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +install -D -m755 bin/iqtree2 $PKG/usr/bin/iqtree2 + +cd $PKG/usr/bin/ +ln -s iqtree2 $PRGNAM +cd - + +mkdir -p $PKG/usr/share/$PRGNAM +cp -a example.* models.nex $PKG/usr/share/$PRGNAM + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/iqtree/iqtree.info b/academic/iqtree/iqtree.info new file mode 100644 index 0000000000..fed2f89662 --- /dev/null +++ b/academic/iqtree/iqtree.info @@ -0,0 +1,10 @@ +PRGNAM="iqtree" +VERSION="2.2.2.7" +HOMEPAGE="http://www.iqtree.org/" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="https://github.com/iqtree/iqtree2/releases/download/v2.2.2.7/iqtree-2.2.2.7-Linux.tar.gz" +MD5SUM_x86_64="8159c4bb33dae900ccd513a19561fd01" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/iqtree/slack-desc b/academic/iqtree/slack-desc new file mode 100644 index 0000000000..cecc57ba48 --- /dev/null +++ b/academic/iqtree/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +iqtree: iqtree (Efficient and versatile phylogenomic software by ML) +iqtree: +iqtree: The IQ-TREE software was created as the successor of IQPNNI and +iqtree: TREE-PUZZLE. IQ-TREE can utilize multicore computers and +iqtree: distributed parallel computing to speed up the analysis. IQ-TREE +iqtree: automatically performs checkpointing to resume an interrupted +iqtree: analysis. +iqtree: +iqtree: http://www.iqtree.org/ +iqtree: https://github.com/Cibiv/IQ-TREE +iqtree: diff --git a/academic/irsim/irsim.SlackBuild b/academic/irsim/irsim.SlackBuild index 898c8c00dc..689040de0d 100644 --- a/academic/irsim/irsim.SlackBuild +++ b/academic/irsim/irsim.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for IRSIM # Written by Mauricio Martinez <eigenfilter {at} gmail [dot] com> @@ -14,10 +14,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=irsim VERSION=${VERSION:-9.7.94} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -27,7 +30,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -89,4 +99,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/isoelectric-point/isoelectric-point.SlackBuild b/academic/isoelectric-point/isoelectric-point.SlackBuild index dc96c2f792..3e9244579b 100644 --- a/academic/isoelectric-point/isoelectric-point.SlackBuild +++ b/academic/isoelectric-point/isoelectric-point.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for isoelectrick-point @@ -22,26 +22,36 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=isoelectric-point VERSION=${VERSION:-1.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -70,6 +80,7 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ -exec chmod 644 {} \; +. /etc/profile.d/qt4.sh cd ./sources qmake -project qmake @@ -101,4 +112,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/isoelectric-point/isoelectric-point.info b/academic/isoelectric-point/isoelectric-point.info index 40ae7acf7a..4d9e2d005d 100644 --- a/academic/isoelectric-point/isoelectric-point.info +++ b/academic/isoelectric-point/isoelectric-point.info @@ -5,6 +5,6 @@ DOWNLOAD="http://ipc.netmark.pl/files/isoelectric-point-linux.tar.gz" MD5SUM="7c2ab92babad116c586f9dc21659d306" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="" +REQUIRES="qt4" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/itex2mml/itex2mml.SlackBuild b/academic/itex2mml/itex2mml.SlackBuild index 6b7423ba23..26f11ba992 100644 --- a/academic/itex2mml/itex2mml.SlackBuild +++ b/academic/itex2mml/itex2mml.SlackBuild @@ -1,13 +1,16 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for itex2mml # Written by David Matthew Jerry Koenig <koenigdavidmj@gmail.com> # Public domain. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=itex2mml VERSION=${VERSION:-1.5.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -17,7 +20,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -85,5 +95,5 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/jalview/README b/academic/jalview/README index ba6e70c2c7..a028e48bcd 100644 --- a/academic/jalview/README +++ b/academic/jalview/README @@ -11,4 +11,7 @@ Jalview Version 2-a multiple sequence alignment editor and analysis workbench. Bioinformatics 25: 1189-1191. NOTE: -The 'source' is hosted at SourceForge by the SlackBuild maintainer. +If you have several jdk-s/jre-s installed, the program may have trouble +starting. If that's the case check the instructions in the wrapper: + +/usr/bin/jalview diff --git a/academic/jalview/jalview b/academic/jalview/jalview index 31813c2c2a..21f9cff3d2 100644..100755 --- a/academic/jalview/jalview +++ b/academic/jalview/jalview @@ -1,16 +1,10 @@ -#!/bin/sh +#!/bin/bash -# This wrapper script is taken from Arch Linux AUR entry of jalview. -# https://aur.archlinux.org/packages/jalview/ -# Maintainer of the PKGBUILD is Stefan Seemayer. +# If you have several jdk-s/jre-s, zulu-openjdk8 may not be the "active" +# one. If that's the case, uncomment the three lines below: -progname="jalview" -mainclass="jalview.bin.Jalview" -basedir="/usr/share/java/$progname" +# export JAVA_HOME=/usr/lib64/zulu-openjdk8 +# export MANPATH="${MANPATH}:${JAVA_HOME}/man" +# export PATH="${JAVA_HOME}/bin:${JAVA_HOME}/jre/bin:${PATH}" -# build classpath: all jars in $basedir -cp=$( ls $basedir/*.jar | xargs echo | sed "s/ /:/g" ); - - -# run jar -"$JAVA_HOME/bin/java" -cp $cp $mainclass +java -jar /usr/share/jalview/jalview diff --git a/academic/jalview/jalview.SlackBuild b/academic/jalview/jalview.SlackBuild index 1ec9acf47f..879740e8fa 100644 --- a/academic/jalview/jalview.SlackBuild +++ b/academic/jalview/jalview.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for jalview -# Copyright 2013-2016 Petar Petrov slackalaxy@gmail.com +# Copyright 2013-2023 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,17 +22,26 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -# With help from the jalview PKGBUILD at Arch linux AUR: -# https://aur.archlinux.org/packages/jalview/ +cd $(dirname $0) ; CWD=$(pwd) PRGNAM=jalview -VERSION=${VERSION:-2.10.0b1} +VERSION=${VERSION:-2.11.2.7} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} ARCH=noarch +JAVA=j1.8 + + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi -CWD=$(pwd) TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -42,27 +51,11 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $PRGNAM-$VERSION -tar xvf $CWD/$PRGNAM-$VERSION.tar.gz -cd $PRGNAM-$VERSION -chown -R root:root . -find -L . \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; - -mkdir -p $PKG/usr/share/java/$PRGNAM -cp -a *.jar $PKG/usr/share/java/$PRGNAM -# The wrapper is from Arch. Thank you! +install -D -m755 $CWD/$PRGNAM-all-$VERSION-$JAVA.jar $PKG/usr/share/$PRGNAM/$PRGNAM install -D -m755 $CWD/$PRGNAM $PKG/usr/bin/$PRGNAM mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a \ - building.html exampleFeatures.txt LICENSE README_IA \ - $PKG/usr/doc/$PRGNAM-$VERSION -cat $CWD/TheJalviewTutorial_screen.pdf > $PKG/usr/doc/$PRGNAM-$VERSION/Tutorial.pdf cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild @@ -76,4 +69,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/jalview/jalview.info b/academic/jalview/jalview.info index 928c20cf89..90b4e3b971 100644 --- a/academic/jalview/jalview.info +++ b/academic/jalview/jalview.info @@ -1,12 +1,10 @@ PRGNAM="jalview" -VERSION="2.10.0b1" +VERSION="2.11.2.7" HOMEPAGE="http://www.jalview.org/" -DOWNLOAD="http://sourceforge.net/projects/sboppetrov/files/JalView/2.10/jalview-2.10.0b1.tar.gz \ - http://sourceforge.net/projects/sboppetrov/files/JalView/TheJalviewTutorial_screen.pdf" -MD5SUM="fb5b30202210e21647ecc7da5242bab3 \ - 5e2f8da8f2528049f055263aecd2f8af" +DOWNLOAD="http://www.jalview.org/getdown/release/jalview-all-2.11.2.7-j1.8.jar" +MD5SUM="15b9f3e9ca81c56050efea28e530a4c1" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="jdk" +REQUIRES="zulu-openjdk8" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/jalview/slack-desc b/academic/jalview/slack-desc index 3afaa82c61..fd372a3f3a 100644 --- a/academic/jalview/slack-desc +++ b/academic/jalview/slack-desc @@ -14,6 +14,6 @@ jalview: It can also work with sequence annotation, secondary structure jalview: information, phylogenetic trees and 3D molecular structures. jalview: jalview: Home: http://www.jalview.org/ -jalview: References: /usr/doc/jalview-2.10.0b1/References +jalview: jalview: jalview: diff --git a/academic/jellyfish_k-mer/jellyfish_k-mer.SlackBuild b/academic/jellyfish_k-mer/jellyfish_k-mer.SlackBuild index e2f2db0ffa..2a13437dd8 100644 --- a/academic/jellyfish_k-mer/jellyfish_k-mer.SlackBuild +++ b/academic/jellyfish_k-mer/jellyfish_k-mer.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for jellyfish -# Copyright 2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2018-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=jellyfish_k-mer VERSION=${VERSION:-1.1.12} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} SRCNAM=jellyfish @@ -37,7 +40,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -97,8 +107,10 @@ cp -a \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/jpicedt/README b/academic/jpicedt/README index ddc93e1dee..2c578cf5bc 100644 --- a/academic/jpicedt/README +++ b/academic/jpicedt/README @@ -1,12 +1,14 @@ -jPicEdt is a software aimed at alleviating the burden of using PSTricks, -eepic or LaTeX's picture environment macros in a LaTeX file. It allows the -user to draw graphical objects using graphic primitives (e.g. splines, -arcs, polygons,...), position them easily with the mouse, and add text -using LaTeX/PSTricks box commands (e.g. dashbox, psframebox,...). +jPicEdt is a software aimed at alleviating the burden of using +PSTricks, eepic or LaTeX's picture environment macros in a LaTeX +file. It allows the user to draw graphical objects using graphic +primitives (e.g. splines, arcs, polygons,...), position them easily +with the mouse, and add text using LaTeX/PSTricks box commands +(e.g. dashbox, psframebox,...). This is a repackaging of the JPicEdt distribution jar archive. -There is a required pstricks-add.{sty,tex} available in add-ons/Tex-macros -of the source. The versions supplied with Slackware's tetex package are -newer and seem to work fine by default; however, if you encounter any problems -with it, you might try using the files supplied with JPicEdt. +There is a required pstricks-add.{sty,tex} available in +add-ons/Tex-macros of the source. The versions supplied with +Slackware's tetex package are newer and seem to work fine by default; +however, if you encounter any problems with it, you might try using the +files supplied with JPicEdt. diff --git a/academic/jpicedt/jpicedt.SlackBuild b/academic/jpicedt/jpicedt.SlackBuild index 66402404c9..799ef4a103 100644 --- a/academic/jpicedt/jpicedt.SlackBuild +++ b/academic/jpicedt/jpicedt.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Copyright 2008 Robert Allen - slacker@slaphappygeeks.com # All rights reserved including Creator Endowed Unalienable Rights. @@ -20,26 +20,36 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=jpicedt VERSION=${VERSION:-1.4.1_03} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -84,4 +94,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG chown -R root:root . -/sbin/makepkg -c n -l y $OUTPUT/${PRGNAM}-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -c n -l y $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/jpicedt/jpicedt.info b/academic/jpicedt/jpicedt.info index 584e475fdf..e67a6ff736 100644 --- a/academic/jpicedt/jpicedt.info +++ b/academic/jpicedt/jpicedt.info @@ -5,6 +5,6 @@ DOWNLOAD="http://downloads.sourceforge.net/jpicedt/jpicedt-install_1_4_1_03_2007 MD5SUM="bc1894efbe41c87e5767fb17c8a21d20" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="jdk" +REQUIRES="zulu-openjdk8" MAINTAINER="Robert Allen" EMAIL="slacker@slaphappygeeks.com" diff --git a/academic/jugglinglab/jugglinglab.SlackBuild b/academic/jugglinglab/jugglinglab.SlackBuild index a43b2b0b0c..1320dcd5da 100644 --- a/academic/jugglinglab/jugglinglab.SlackBuild +++ b/academic/jugglinglab/jugglinglab.SlackBuild @@ -1,17 +1,27 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for Juggling Lab # Petr Kletecka admin@zonglovani.info <2014> +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=jugglinglab VERSION=${VERSION:-0.6.2} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} ARCH=noarch -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -46,4 +56,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/jugglinglab/jugglinglab.info b/academic/jugglinglab/jugglinglab.info index 3f55b9112c..3a72ece5e5 100644 --- a/academic/jugglinglab/jugglinglab.info +++ b/academic/jugglinglab/jugglinglab.info @@ -5,6 +5,6 @@ DOWNLOAD="http://downloads.sourceforge.net/jugglinglab/JugglingLab-0.6.2_other.t MD5SUM="752a399833f0c78c2a2517ef6fffc46b" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="jdk" +REQUIRES="zulu-openjdk8" MAINTAINER="Petr Kletecka" EMAIL="admin@zonglovani.info" diff --git a/academic/kalign/README b/academic/kalign/README new file mode 100644 index 0000000000..23331f54fe --- /dev/null +++ b/academic/kalign/README @@ -0,0 +1,9 @@ +Kalign is a fast multiple sequence alignment program for biological +sequences. + +Kalign expects the input to be a set of unaligned sequences in fasta +format or aligned sequences in aligned fasta, MSF or clustal format. If +the sequences are already aligned, kalign will remove all gap characters +and re-align the sequences. By default, Kalign automatically detects +whether the input sequences are protein or DNA and selects appropriate +alignment parameters. diff --git a/academic/kalign/kalign.SlackBuild b/academic/kalign/kalign.SlackBuild new file mode 100644 index 0000000000..a679082f32 --- /dev/null +++ b/academic/kalign/kalign.SlackBuild @@ -0,0 +1,107 @@ +#!/bin/bash + +# Slackware build script for kalign + +# Copyright 2023 Petar Petrov slackalaxy.com +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=kalign +VERSION=${VERSION:-3.3.5} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +mkdir -p build +cd build + cmake \ + -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DLIB_SUFFIX=${LIBDIRSUFFIX} \ + -DMAN_INSTALL_DIR=/usr/man \ + -DCMAKE_BUILD_TYPE=Release .. + make + make install/strip DESTDIR=$PKG +cd .. + +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + AUTHORS ChangeLog COPYING README.md \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/kalign/kalign.info b/academic/kalign/kalign.info new file mode 100644 index 0000000000..431f1f7bd1 --- /dev/null +++ b/academic/kalign/kalign.info @@ -0,0 +1,10 @@ +PRGNAM="kalign" +VERSION="3.3.5" +HOMEPAGE="https://github.com/TimoLassmann/kalign/" +DOWNLOAD="https://github.com/TimoLassmann/kalign/archive/v3.3.5/kalign-3.3.5.tar.gz" +MD5SUM="4634d95e88ea3bacfbad856afab91685" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/slatec/slack-desc b/academic/kalign/slack-desc index 7265dc6b16..1dac2dad23 100644 --- a/academic/slatec/slack-desc +++ b/academic/kalign/slack-desc @@ -6,14 +6,14 @@ # customary to leave one space after the ':' except on otherwise blank lines. |-----handy-ruler------------------------------------------------------| -slatec: slatec (SLATEC Common Mathematical Library) -slatec: -slatec: SLATEC Common Mathematical Library, is a comprehensive software -slatec: library containing over 1400 general purpose mathematical and -slatec: statistical routines written in Fortran 77. -slatec: -slatec: -slatec: -slatec: -slatec: -slatec: +kalign: kalign (A fast multiple sequence alignment program) +kalign: +kalign: Kalign is a fast multiple sequence alignment program for +kalign: biological sequences. +kalign: +kalign: https://github.com/TimoLassmann/kalign +kalign: +kalign: +kalign: +kalign: +kalign: diff --git a/academic/karma/karma.SlackBuild b/academic/karma/karma.SlackBuild index ff1ae1b500..ff42bd236d 100644 --- a/academic/karma/karma.SlackBuild +++ b/academic/karma/karma.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for karma @@ -22,11 +22,16 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +# 20220318 bkw: Modified by SlackBuilds.org: fix build when ARCH is +# set to i586 in the environment. + +cd $(dirname $0) ; CWD=$(pwd) PRGNAM=karma VERSION=${VERSION:-1.7.25} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -36,21 +41,22 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} set -e -if [ "$ARCH" = "x86_64" ]; then - ARCHDEP="amd64_Linux_libc6.3" -elif [ "$ARCH" = "i686" ]; then - ARCHDEP="i386_Linux_libc6" -else - printf "\n\n$ARCH is not supported... \n" - exit 1 -fi +case "$ARCH" in + x86_64) ARCHDEP="amd64_Linux_libc6.3" ;; + i?86) ARCHDEP="i386_Linux_libc6" ;; + *) printf "\n\n$ARCH is not supported... \n"; exit 1 ;; +esac rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT @@ -69,10 +75,9 @@ rm -R $ARCHDEP chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ + -o -perm 511 \) -exec chmod 755 {} \+ -o \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; - + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \+ # Copy everything to package directory mkdir -p $PKG/opt/$PRGNAM @@ -113,4 +118,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/kile/README b/academic/kile/README deleted file mode 100644 index d083e911fe..0000000000 --- a/academic/kile/README +++ /dev/null @@ -1,4 +0,0 @@ -To build Kile, you will need a Latex distribution like TeTeX or -Tex-Live. Slackware 13.0 (and lower) include the former distribution -and it is available on the installation disk(s) if you did not do a -full install. diff --git a/academic/kile/kile.info b/academic/kile/kile.info deleted file mode 100644 index edc969bd33..0000000000 --- a/academic/kile/kile.info +++ /dev/null @@ -1,10 +0,0 @@ -PRGNAM="kile" -VERSION="2.1.3" -HOMEPAGE="http://kile.sourceforge.net/" -DOWNLOAD="http://downloads.sourceforge.net/kile/kile-2.1.3.tar.bz2" -MD5SUM="f3129e73eea21890c40781de80b44808" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="" -MAINTAINER="Heinz Wiesinger" -EMAIL="pprkut@liwjatan.at" diff --git a/academic/kissat/README b/academic/kissat/README new file mode 100644 index 0000000000..27b8882eb3 --- /dev/null +++ b/academic/kissat/README @@ -0,0 +1,16 @@ +Kissat is a "keep it simple and clean bare metal SAT solver" written +in C. It is a port of CaDiCaL back to C with improved data +structures, better scheduling of inprocessing and optimized +algorithms and implementation. + +Coincidentally "kissat" also means "cats" in Finnish. + +You can get more information about Kissat in the last solver +description for the SAT Competition 2022: + +Armin Biere and Mathias Fleury. Gimsatul, IsaSAT and Kissat entering +the SAT Competition 2022. In Proc. of SAT Competition 2022 - Solver +and Benchmark Descriptions, Tomas Balyo, Marijn Heule, Markus Iser, +Matti Järvisalo, Martin Suda (editors), vol. B-2022-1 of Department +of Computer Science Report Series B, pages 10-11, University of +Helsinki, 2022. diff --git a/academic/kissat/kissat.SlackBuild b/academic/kissat/kissat.SlackBuild new file mode 100644 index 0000000000..6fdda8acf6 --- /dev/null +++ b/academic/kissat/kissat.SlackBuild @@ -0,0 +1,113 @@ +#!/bin/bash + +# Slackware build script for kissat + +# Copyright Caterino Tommaso, T.O.P. 2024 USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=kissat +VERSION=${VERSION:-3.1.1} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +elif [ "$ARCH" = "aarch64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-rel-$VERSION +tar xvf $CWD/$PRGNAM-rel-$VERSION.tar.gz +cd $PRGNAM-rel-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \+ -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \+ + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure + +cd build +make +cd .. + +mkdir -p $PKG/usr/bin $PKG/usr/lib${LIBDIRSUFFIX} +cp -a build/kissat $PKG/usr/bin/ +cp -a build/libkissat.a $PKG/usr/lib${LIBDIRSUFFIX}/ + +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +rm -f $PKG/usr/info/dir + +find $PKG -name perllocal.pod -o -name ".packlist" -o -name "*.bs" | xargs rm -f || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + CONTRIBUTING LICENSE NEWS.md README.md VERSION \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/kissat/kissat.info b/academic/kissat/kissat.info new file mode 100644 index 0000000000..cefa036030 --- /dev/null +++ b/academic/kissat/kissat.info @@ -0,0 +1,10 @@ +PRGNAM="kissat" +VERSION="3.1.1" +HOMEPAGE="https://github.com/arminbiere/kissat" +DOWNLOAD="https://github.com/arminbiere/kissat/archive/refs/tags/rel-3.1.1.tar.gz" +MD5SUM="601d796884d5e9efe2af78dfe77d73ba" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Caterino Tommaso, T.O.P." +EMAIL="alan_NaverOsa@lavSaPbiAtM.com (remove capital letters)" diff --git a/academic/kissat/slack-desc b/academic/kissat/slack-desc new file mode 100644 index 0000000000..02a27e4e5d --- /dev/null +++ b/academic/kissat/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +kissat: kissat (International SAT Competition award-winning SAT solver) +kissat: Kissat is a "keep it simple and clean bare metal SAT solver" written +kissat: in C. It is a port of CaDiCaL back to C with improved data +kissat: structures, better scheduling of inprocessing and optimized +kissat: algorithms and implementation. +kissat: Armin Biere and Mathias Fleury. Gimsatul, IsaSAT and Kissat entering +kissat: the SAT Competition 2022. In Proc. of SAT Competition 2022 - Solver +kissat: and Benchmark Descriptions, Tomas Balyo, Marijn Heule, Markus Iser, +kissat: Matti Jarvisalo, Martin Suda (editors), vol. B-2022-1 of Department +kissat: of Computer Science Report Series B, pages 10-11, University of +kissat: Helsinki, 2022 diff --git a/academic/kiwisolver/README b/academic/kiwisolver/README deleted file mode 100644 index 7773aa35ea..0000000000 --- a/academic/kiwisolver/README +++ /dev/null @@ -1,7 +0,0 @@ -This is an efficient C++ implementation of the Cassowary constraint solving -algorithm. Kiwi(solver) is an implementation of the algorithm based on the -seminal Cassowary paper. It is not a refactoring of the original C++ solver. -Kiwi(solver) has been designed from the ground up to be lightweight and fast. -It ranges from 10x to 500x faster than the original Cassowary solver with -typical use cases gaining a 40x improvement. Memory savings are consistently -> 5x. diff --git a/academic/kiwisolver/kiwisolver.info b/academic/kiwisolver/kiwisolver.info deleted file mode 100644 index 41a6cb3771..0000000000 --- a/academic/kiwisolver/kiwisolver.info +++ /dev/null @@ -1,10 +0,0 @@ -PRGNAM="kiwisolver" -VERSION="1.0.1" -HOMEPAGE="https://pypi.org/project/kiwisolver" -DOWNLOAD="https://files.pythonhosted.org/packages/31/60/494fcce70d60a598c32ee00e71542e52e27c978e5f8219fae0d4ac6e2864/kiwisolver-1.0.1.tar.gz" -MD5SUM="e2a1718b837e2cd001f7c06934616fcd" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="" -MAINTAINER="Serban Udrea" -EMAIL="S.Udrea@gsi.de" diff --git a/academic/kiwisolver/slack-desc b/academic/kiwisolver/slack-desc deleted file mode 100644 index ccdb0a1776..0000000000 --- a/academic/kiwisolver/slack-desc +++ /dev/null @@ -1,19 +0,0 @@ -# HOW TO EDIT THIS FILE: -# The "handy ruler" below makes it easier to edit a package description. -# Line up the first '|' above the ':' following the base package name, and -# the '|' on the right side marks the last column you can put a character in. -# You must make exactly 11 lines for the formatting to be correct. It's also -# customary to leave one space after the ':' except on otherwise blank lines. - - |-----handy-ruler------------------------------------------------------| -kiwisolver: kiwisolver (an implementation of the Cassowary algorithm) -kiwisolver: -kiwisolver: This is an efficient C++ implementation of the Cassowary constraint -kiwisolver: solving algorithm. Kiwi(solver) is an implementation of the algorithm -kiwisolver: based on the seminal Cassowary paper. It is not a refactoring of the -kiwisolver: original C++ solver. Kiwi(solver) has been designed from the ground -kiwisolver: up to be lightweight and fast. -kiwisolver: -kiwisolver: Homepage: https://pypi.org/project/kiwisolver -kiwisolver: -kiwisolver: diff --git a/academic/klavaro/klavaro.SlackBuild b/academic/klavaro/klavaro.SlackBuild index 2ad1b51b30..926705cdc7 100644 --- a/academic/klavaro/klavaro.SlackBuild +++ b/academic/klavaro/klavaro.SlackBuild @@ -1,9 +1,9 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for Klavaro # Copyright 2015 Thibaut Notteboom -# Copyright 2019 Johannes Schoepfer, Germany +# Copyright 2019-2022 Johannes Schoepfer, Germany # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,10 +23,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=klavaro -VERSION=${VERSION:-3.03} +VERSION=${VERSION:-3.14} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -36,7 +39,11 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -82,8 +89,7 @@ CXXFLAGS="$SLKCFLAGS" \ make make install DESTDIR=$PKG -# Don't ship .la files: -#rm -f $PKG/usr/lib${LIBDIRSUFFIX}/*.la +rm -f $PKG/usr/lib${LIBDIRSUFFIX}/*.la find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true @@ -92,7 +98,7 @@ find $PKG/usr/man -type f -exec gzip -9 {} \; for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a ABOUT-NLS AUTHORS ChangeLog COPYING INSTALL NEWS README TODO \ +cp -a ABOUT-NLS AUTHORS ChangeLog COPYING NEWS README TODO \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild @@ -101,4 +107,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/klavaro/klavaro.info b/academic/klavaro/klavaro.info index a7b7be9946..eed8101207 100644 --- a/academic/klavaro/klavaro.info +++ b/academic/klavaro/klavaro.info @@ -1,10 +1,10 @@ PRGNAM="klavaro" -VERSION="3.03" +VERSION="3.14" HOMEPAGE="https://klavaro.sourceforge.io/" -DOWNLOAD="https://downloads.sourceforge.net/project/klavaro/klavaro-3.03.tar.bz2" -MD5SUM="0299f185ed8f9aac3441685fbf7177dc" +DOWNLOAD="https://downloads.sourceforge.net/project/klavaro/klavaro-3.14.tar.bz2" +MD5SUM="68ee70d964b23dc4db97aa066a12f8e2" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="" +REQUIRES="gtkdatabox" MAINTAINER="Johannes Schoepfer" EMAIL="slackbuilds@schoepfer.info" diff --git a/academic/klu/README b/academic/klu/README index fe8941f406..e3da56e0c7 100644 --- a/academic/klu/README +++ b/academic/klu/README @@ -1,7 +1,7 @@ -KLU is a sparse LU factorization algorithm well-suited for use in circuit -simulation. +KLU is a sparse LU factorization algorithm well-suited for use in +circuit simulation. This package is part of SuiteSparse. -CHOLMOD is an optional dependency and will be used if found. -It is primarily used for this package's test suite. +CHOLMOD is an optional dependency and will be used if found. It is +primarily used for this package's test suite. diff --git a/academic/klu/klu.SlackBuild b/academic/klu/klu.SlackBuild index 780ce2daf4..9cabf3f4c0 100644 --- a/academic/klu/klu.SlackBuild +++ b/academic/klu/klu.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for KLU -# Copyright 2013-2020 Kyle Guinn <elyk03@gmail.com> +# Copyright 2013-2021 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,13 +22,16 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=klu SRCNAM=SuiteSparse SUBDIR=KLU VERSION=${VERSION:-1.3.9} -SRCVER=${SRCVER:-5.6.0} -BUILD=${BUILD:-3} +SRCVER=${SRCVER:-5.8.1} +BUILD=${BUILD:-4} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$(uname -m)" in @@ -38,15 +41,22 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM-$VERSION +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="README.txt Doc/ChangeLog Doc/License.txt Doc/lesser.txt" -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" @@ -108,4 +118,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/klu/klu.info b/academic/klu/klu.info index 3865f63f7d..44adddda01 100644 --- a/academic/klu/klu.info +++ b/academic/klu/klu.info @@ -1,10 +1,10 @@ PRGNAM="klu" VERSION="1.3.9" HOMEPAGE="http://faculty.cse.tamu.edu/davis/suitesparse.html" -DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.6.0/SuiteSparse-5.6.0.tar.gz" -MD5SUM="af8b97cbded4cd5c6672e878bc0c37c2" +DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.8.1/SuiteSparse-5.8.1.tar.gz" +MD5SUM="c414679bbc9432a3def01b31ad921140" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="suitesparseconfig amd colamd btf" +REQUIRES="amd colamd btf" MAINTAINER="Kyle Guinn" EMAIL="elyk03@gmail.com" diff --git a/academic/knime/knime.SlackBuild b/academic/knime/knime.SlackBuild index 2f9736914f..7180e12bdb 100644 --- a/academic/knime/knime.SlackBuild +++ b/academic/knime/knime.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for knime # Copyright 2014 Stephen Van Berg USA @@ -23,10 +23,13 @@ # Stephen Van Berg 2014-4-17 # Updated 2015-07-31 for knime version 2.12.0 +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=knime VERSION=${VERSION:-2.12.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -36,7 +39,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -79,4 +89,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/kraken/kraken.SlackBuild b/academic/kraken/kraken.SlackBuild index ab71cb0f0c..4cd7d07008 100644 --- a/academic/kraken/kraken.SlackBuild +++ b/academic/kraken/kraken.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for kraken -# Copyright 2018-2019 Petar Petrov slackalaxy@gmail.com +# Copyright 2018-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=kraken VERSION=${VERSION:-1.1.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -98,4 +108,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/ktikz/ktikz.SlackBuild b/academic/ktikz/ktikz.SlackBuild index 71c10fef06..12d7b45435 100644 --- a/academic/ktikz/ktikz.SlackBuild +++ b/academic/ktikz/ktikz.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for ktikz -# Copyright 2012 Giorgio Peron Campodarsego, PD, Italy +# Copyright 2021 Giorgio Peron <giorgio.peron@gmail.com> Belluno Italy # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,26 +23,36 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=ktikz -VERSION=${VERSION:-0.10} +VERSION=${VERSION:-0.13.2} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -63,36 +73,46 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $PRGNAM -tar xvzf $CWD/$PRGNAM\_$VERSION.tar.gz -cd $PRGNAM +rm -rf $PRGNAM-$VERSION +tar xvzf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION chown -R root:root . find -L . \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; - -# Comedy sed command thanks to Arch :-) -sed -e 's|\\\\\\||g' -i app/CMakeLists.txt - -cmake \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +mkdir -p build{,qt} +cd build +cmake .. \ -DCMAKE_C_FLAGS="$SLKCFLAGS" \ -DCMAKE_CXX_FLAGS="$SLKCFLAGS" \ - -DCMAKE_INSTALL_PREFIX=`kde4-config --prefix` \ + -DCMAKE_INSTALL_PREFIX=/usr \ -DCMAKE_BUILD_TYPE=Release make +cd - +cd buildqt +qmake ../qtikz.pro +make +cd - +cd build make install DESTDIR=$PKG +cd - find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true +mkdir -p $PKG/usr +mv $PKG/usr/share/man $PKG/usr/ find $PKG/usr/man -type f -exec gzip -9 {} \; for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +mv $PKG/usr/share/doc/* $PKG/usr/doc/$PRGNAM-$VERSION/ +rm -rf $PKG/usr/share/doc cp -a \ - Changelog HACKING INSTALL LICENSE.GPL2 README TODO \ + Changelog HACKING INSTALL LICENSE.* README.md TODO \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild @@ -101,4 +121,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/ktikz/ktikz.info b/academic/ktikz/ktikz.info index 888176171c..674d966100 100644 --- a/academic/ktikz/ktikz.info +++ b/academic/ktikz/ktikz.info @@ -1,8 +1,8 @@ PRGNAM="ktikz" -VERSION="0.10" +VERSION="0.13.2" HOMEPAGE="http://www.hackenberger.at/blog/ktikz-editor-for-the-tikz-language/" -DOWNLOAD="http://www.hackenberger.at/ktikz/ktikz_0.10.tar.gz" -MD5SUM="e8f0826cba2447250bcdcd389a71a2ac" +DOWNLOAD="https://github.com/fhackenberger/ktikz/archive/0.13.2/ktikz-0.13.2.tar.gz" +MD5SUM="26cb3537bc5fd501bd37d4ba80a06260" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/kurso/doinst.sh b/academic/kurso/doinst.sh index 65c7e2eeb9..4e8ba7071d 100644 --- a/academic/kurso/doinst.sh +++ b/academic/kurso/doinst.sh @@ -2,8 +2,3 @@ if [ -x /usr/bin/update-desktop-database ]; then /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 fi -if [ -e usr/share/icons/hicolor/icon-theme.cache ]; then - if [ -x /usr/bin/gtk-update-icon-cache ]; then - /usr/bin/gtk-update-icon-cache -f usr/share/icons/hicolor >/dev/null 2>&1 - fi -fi diff --git a/academic/kurso/icons/kurso128.png b/academic/kurso/icons/kurso128.png Binary files differdeleted file mode 100644 index 86b72c8a21..0000000000 --- a/academic/kurso/icons/kurso128.png +++ /dev/null diff --git a/academic/kurso/icons/kurso16.png b/academic/kurso/icons/kurso16.png Binary files differdeleted file mode 100644 index 0ca94f4ca9..0000000000 --- a/academic/kurso/icons/kurso16.png +++ /dev/null diff --git a/academic/kurso/icons/kurso24.png b/academic/kurso/icons/kurso24.png Binary files differdeleted file mode 100644 index 0151c02f30..0000000000 --- a/academic/kurso/icons/kurso24.png +++ /dev/null diff --git a/academic/kurso/icons/kurso256.png b/academic/kurso/icons/kurso256.png Binary files differdeleted file mode 100644 index a62d795335..0000000000 --- a/academic/kurso/icons/kurso256.png +++ /dev/null diff --git a/academic/kurso/icons/kurso32.png b/academic/kurso/icons/kurso32.png Binary files differdeleted file mode 100644 index 5425b260a1..0000000000 --- a/academic/kurso/icons/kurso32.png +++ /dev/null diff --git a/academic/kurso/icons/kurso48.png b/academic/kurso/icons/kurso48.png Binary files differdeleted file mode 100644 index c3cf1f56b8..0000000000 --- a/academic/kurso/icons/kurso48.png +++ /dev/null diff --git a/academic/kurso/icons/kurso64.png b/academic/kurso/icons/kurso64.png Binary files differdeleted file mode 100644 index c63abae818..0000000000 --- a/academic/kurso/icons/kurso64.png +++ /dev/null diff --git a/academic/kurso/kurso b/academic/kurso/kurso index 21a08a19ce..335c8a3ea3 100644 --- a/academic/kurso/kurso +++ b/academic/kurso/kurso @@ -1,4 +1,3 @@ #!/bin/sh - -export QT_PLUGIN_PATH=/usr/lib64/kde4/plugins -/usr/bin/kurso4 +cd /opt/kurso +./kursokape diff --git a/academic/kurso/kurso.SlackBuild b/academic/kurso/kurso.SlackBuild index 13c5777a81..227840e5a1 100644 --- a/academic/kurso/kurso.SlackBuild +++ b/academic/kurso/kurso.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for kurso @@ -22,50 +22,40 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=kurso -VERSION=${VERSION:-4.1.2} -BUILD=${BUILD:-2} +VERSION=${VERSION:-5.2} +BUILD=${BUILD:-1} TAG=${TAG:-_SBo} -SRCTARNAM=kurso4_source -SRCNAM=kurso4 -BINTARNAM=kurso.i386 -BINNAM="kurso-de-esperanto-4" +PKGTYPE=${PKGTYPE:-tgz} +ARCH=$( uname -m ) + +if [ "${ARCH}" != "x86_64" ]; then + echo "Architecture ${ARCH} is not supported." + exit 1 +fi -if [ -z "$ARCH" ]; then - case "$( uname -m )" in - i?86) ARCH=i586 ;; - arm*) ARCH=arm ;; - *) ARCH=$( uname -m ) ;; - esac +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 fi -CWD=$(pwd) TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i586" ]; then - SLKCFLAGS="-O2 -march=i586 -mtune=i686" - LIBDIRSUFFIX="" -elif [ "$ARCH" = "i686" ]; then - SLKCFLAGS="-O2 -march=i686 -mtune=i686" - LIBDIRSUFFIX="" -elif [ "$ARCH" = "x86_64" ]; then - SLKCFLAGS="-O2 -fPIC" - LIBDIRSUFFIX="64" -else - SLKCFLAGS="-O2" - LIBDIRSUFFIX="" -fi - set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $SRCNAM -tar xvf $CWD/$SRCTARNAM.tar.gz -cd $SRCNAM +rm -rf ${PRGNAM}_${ARCH} +tar xvf $CWD/${PRGNAM}_${ARCH}.tar.gz +cd ${PRGNAM}_${ARCH} chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -73,60 +63,12 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -sed -i -e '/.*Loko = QApplication.*/i \ /*\r' \ - -e '/Loko.append.*/a \ */\r\n Loko = "/usr/share/kurso/";\r' \ - main.cpp - -qmake \ - QMAKE_CFLAGS="$SLKCFLAGS" \ - QMAKE_CXXFLAGS="$SLKCFLAGS" - -make - -mkdir -p $PKG/usr/bin -install -m 755 -t $PKG/usr/bin kurso4 -mkdir -p $PKG/usr/share/kurso -# stiloj and tradukoj are embedded into the binary but they aren't -# being called properly, so it will look for them in the data dir. :( -# Patching this isn't worth the effort. -mv -f stiloj $PKG/usr/share/kurso/ -mv -f tradukoj $PKG/usr/share/kurso/ -cd $PKG/usr/share/kurso/tradukoj/kiel -for i in *.html -do - ln -s $i kiel_${i} -done -cd $PKG/usr/share/kurso/tradukoj/kio -for i in *.html -do - ln -s $i kio_${i} -done - -cd $TMP -rm -rf $BINNAM -tar xvf $CWD/$BINTARNAM.tar.gz -cd $BINNAM -chown -R root:root . -find -L . \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 -o -perm 700 \) -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; - -mv -f sonoj $PKG/usr/share/kurso/ -mv -f video $PKG/usr/share/kurso/ - -find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ - | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true - -install -m 755 -t $PKG/usr/bin $CWD/kurso -sed -i "s/64/${LIBDIRSUFFIX}/" $PKG/usr/bin/kurso +mkdir -p $PKG/opt/kurso +cp -a kursokape sonoj video $PKG/opt/kurso/ -for i in 16 24 32 48 64 128 256 -do - install -D -m 0644 $CWD/icons/kurso${i}.png $PKG/usr/share/icons/hicolor/${i}x${i}/apps/kurso.png -done +install -D -m 0644 kurso_256.png $PKG/usr/share/pixmaps/kurso.png install -D -m 0644 $CWD/kurso.desktop $PKG/usr/share/applications/kurso.desktop +install -D -m 0755 $CWD/kurso $PKG/usr/bin/kurso mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild @@ -136,4 +78,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/kurso/kurso.desktop b/academic/kurso/kurso.desktop index bfdc44c3eb..2fed560086 100644 --- a/academic/kurso/kurso.desktop +++ b/academic/kurso/kurso.desktop @@ -6,4 +6,4 @@ Type=Application Exec=kurso Icon=kurso Terminal=false -Categories=Education;Languages;KDE;Qt; +Categories=Education;Languages;Qt; diff --git a/academic/kurso/kurso.info b/academic/kurso/kurso.info index e05c18b257..001428a797 100644 --- a/academic/kurso/kurso.info +++ b/academic/kurso/kurso.info @@ -1,12 +1,10 @@ PRGNAM="kurso" -VERSION="4.1.2" +VERSION="5.2" HOMEPAGE="http://www.kurso.com.br/index.php?en" -DOWNLOAD="http://kurso.com.br/kurso4_source.tar.gz \ - http://kurso.com.br/kurso.i386.tar.gz" -MD5SUM="a92fb13a1ec6734d0d254a8733b610b3 \ - fa580797b4fb2ee34b30dccc79fb4b8d" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="https://ponce.cc/slackware/sources/repo/kurso_x86_64.tar.gz" +MD5SUM_x86_64="ed6cc642b8c7b368516b871377b5af4d" REQUIRES="" MAINTAINER="T3slider" EMAIL="t3slider@gmail.com" diff --git a/academic/labplot2/README b/academic/labplot2/README index d34496e452..11b9ca7430 100644 --- a/academic/labplot2/README +++ b/academic/labplot2/README @@ -3,20 +3,21 @@ labplot2 (interactive graphing and analysis of scientific data) LabPlot is a KDE-application for interactive graphing and analysis of scientific data. -LabPlot provides an easy way to create, manage and edit plots. It allows -you to produce plots based on data from a spreadsheet or on data imported -from external files. Plots can be exported to several pixmap and vector -graphic formats. +LabPlot provides an easy way to create, manage and edit plots. It +allows you to produce plots based on data from a spreadsheet or on +data imported from external files. Plots can be exported to several +pixmap and vector graphic formats. -LabPlot2 is a complete rewrite of LabPlot1 and lacks in the first release -a lot of features available in the predecessor. On the other hand, the -GUI and the usability is more superior as compared to LabPlot1 and there -are several new features that were not available in LabPlot1. +LabPlot2 is a complete rewrite of LabPlot1 and lacks in the first +release a lot of features available in the predecessor. On the other +hand, the GUI and the usability is more superior as compared to +LabPlot1 and there are several new features that were not available +in LabPlot1. optional dependencies: -- LaTeX (to enable LaTeX typesetting in LabPlot) -- fftw - hdf5 - netcdf - cfitsio +- matio +- discount diff --git a/academic/wxmacmolplt/doinst.sh b/academic/labplot2/doinst.sh index 0fb9c8b686..4f83cde390 100644 --- a/academic/wxmacmolplt/doinst.sh +++ b/academic/labplot2/doinst.sh @@ -1,3 +1,4 @@ + if [ -x /usr/bin/update-desktop-database ]; then /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 fi @@ -11,4 +12,3 @@ if [ -e usr/share/icons/hicolor/icon-theme.cache ]; then /usr/bin/gtk-update-icon-cache -f usr/share/icons/hicolor >/dev/null 2>&1 fi fi - diff --git a/academic/labplot2/labplot2.SlackBuild b/academic/labplot2/labplot2.SlackBuild index f10f2442bc..a4b4946d00 100644 --- a/academic/labplot2/labplot2.SlackBuild +++ b/academic/labplot2/labplot2.SlackBuild @@ -1,8 +1,10 @@ -#!/bin/sh +#!/bin/bash # # Slackware build script for LabPlot -# Based on the Slackware 14.1 SlackBuild and AUR PKGBUILD for labplot -# Written by Fellype do Nascimento <fellype(at)gmail.com> +# Based on the Slackware 15.0 SlackBuild and AUR PKGBUILD for labplot +# +# Copyright 2014-2023, Fellype do Nascimento, Guaratingueta - Brazil +# All rights reserved. # # Redistribution and use of this script, with or without modification, is # permitted provided that the following conditions are met: @@ -21,11 +23,14 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) NAME=labplot + PRGNAM=labplot2 -VERSION=${VERSION:-2.4.0} -BUILD=${BUILD:-1} +VERSION=${VERSION:-2.10.1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,17 +40,30 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} if [ "$ARCH" = "i586" ]; then - SLKCFLAGS="-O2 -march=i586 -mtune=i686"; SLKLDFLAGS=""; LIBDIRSUFFIX=""; CHOST=i486 + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then - SLKCFLAGS="-O2 -march=i686 -mtune=i686"; SLKLDFLAGS=""; LIBDIRSUFFIX=""; CHOST=i486 + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" elif [ "$ARCH" = "x86_64" ]; then - SLKCFLAGS="-O2 -fPIC"; SLKLDFLAGS="-L/usr/lib64"; LIBDIRSUFFIX="64" + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" fi set -e @@ -56,6 +74,7 @@ cd $TMP rm -rf $NAME-$VERSION tar -xJf $CWD/$NAME-$VERSION.tar.xz cd $NAME-$VERSION + chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -63,32 +82,48 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -./compile - +mkdir build ( cd build/ -cmake ./ -DCMAKE_INSTALL_PREFIX=/usr -cmake ./ -DCMAKE_BUILD_TYPE=Release -make install DESTDIR=$PKG +cmake -DCMAKE_INSTALL_PREFIX=/usr \ + -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_BUILD_TYPE=Release \ + -DMAN_INSTALL_DIR=/usr/man \ + -DENABLE_READSTAT=OFF \ + -DENABLE_TESTS=OFF \ + -DLOCAL_DBC_PARSER=OFF \ + -DLOCAL_VECTOR_BLF=OFF \ + .. +make +make install/strip DESTDIR=$PKG ) -( cd $PKG -find -L . | xargs -O file | grep "executable" | grep ELF | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true -find -L . | xargs -O file | grep "shared object" | grep ELF | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true -find -L . | xargs -O file | grep "current ar archive" | cut -f 1 -d : | xargs strip -g 2> /dev/null || true -) +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +# no usr/share/doc dir +mkdir -p $PKG/usr/doc +mv $PKG/usr/share/doc/* $PKG/usr/doc +rmdir $PKG/usr/share/doc + +# Leave only one main category in key "Categories" for the .desktop file +sed -i "s:Qt;KDE;Education;Science;Physics;Math;:Science;:" $PKG/usr/share/applications/org.kde.labplot2.desktop + +# Fix permissions in .desktop file +chmod 0644 $PKG/usr/share/applications/org.kde.labplot2.desktop + +find $PKG/usr/man -type f -exec gzip -9 {} \; +for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a AUTHORS ChangeLog COPYING INSTALL README \ +cp -a AUTHORS ChangeLog README.md LICENSES/* \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc - -if [ -e /usr/bin/requiredbuilder ]; then - requiredbuilder -v -y -s $CWD $PKG -fi +cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/labplot2/labplot2.info b/academic/labplot2/labplot2.info index b9af5858f7..fca8ba5bad 100644 --- a/academic/labplot2/labplot2.info +++ b/academic/labplot2/labplot2.info @@ -1,10 +1,10 @@ PRGNAM="labplot2" -VERSION="2.4.0" +VERSION="2.10.1" HOMEPAGE="https://labplot.kde.org/" -DOWNLOAD="http://kde.c3sl.ufpr.br/stable/labplot/2.4.0/labplot-2.4.0.tar.xz" -MD5SUM="ee59c0095190bb3dc100e29e1a00c654" +DOWNLOAD="https://download.kde.org/stable/labplot/labplot-2.10.1.tar.xz" +MD5SUM="b3cdfe029d64fa834e0990e9b5ab446f" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="extra-cmake-modules" +REQUIRES="" MAINTAINER="Fellype do Nascimento" -EMAIL="fellype(at)gmail.com" +EMAIL="fellype (at) gmail (dot) com" diff --git a/academic/ladr/README b/academic/ladr/README index 2bee5905d9..c2fd2fb0fc 100644 --- a/academic/ladr/README +++ b/academic/ladr/README @@ -1,3 +1,4 @@ -LADR includes some mathematical programs like - - prover 9 (automated theorem prover for first-order and equational logic) - - mace4 (search for finite models and counterexamples) +LADR includes some mathematical programs like: + +prover 9 (automated theorem prover for first-order and equational logic) +mace4 (search for finite models and counterexamples) diff --git a/academic/ladr/ladr.SlackBuild b/academic/ladr/ladr.SlackBuild index 1a8d75236a..ef780319ec 100644 --- a/academic/ladr/ladr.SlackBuild +++ b/academic/ladr/ladr.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for ladr -# Copyright 2007-2010 Heinz Wiesinger, Amsterdam, The Netherlands +# Copyright 2007-2021 Heinz Wiesinger, Amsterdam, The Netherlands # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -11,21 +11,24 @@ # 1. Redistributions of this script must retain the above copyright # notice, this list of conditions and the following disclaimer. # -# THIS SOFTWARE IS PROVIDED BY THE AUTHOR ''AS IS'' AND ANY EXPRESS OR IMPLIED -# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF -# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO -# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, -# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, -# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; -# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, -# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR -# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF -# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) PRGNAM=ladr VERSION=${VERSION:-2009_11A} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -80,7 +90,6 @@ XFLAGS="$SLKCFLAGS" make all MAKEFLAGS="-j1" mkdir -p $PKG/usr/{bin,lib$LIBDIRSUFFIX} install -m 0755 ./bin/* $PKG/usr/bin/ -install -m 0755 ./ladr/libladr.la $PKG/usr/lib$LIBDIRSUFFIX/ install -m 0755 ./ladr/.libs/libladr.so.4.0.0 $PKG/usr/lib$LIBDIRSUFFIX/ ln -s /usr/lib$LIBDIRSUFFIX/libladr.so.4.0.0 $PKG/usr/lib$LIBDIRSUFFIX/libladr.so.4 ln -s /usr/lib$LIBDIRSUFFIX/libladr.so.4.0.0 $PKG/usr/lib$LIBDIRSUFFIX/libladr.so @@ -107,4 +116,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/ladr/ladr.info b/academic/ladr/ladr.info index ce229f3444..2754652ed5 100644 --- a/academic/ladr/ladr.info +++ b/academic/ladr/ladr.info @@ -7,4 +7,4 @@ DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" MAINTAINER="Heinz Wiesinger" -EMAIL="pprkut@liwjatan.at" +EMAIL="pprkut@slackbuilds.org" diff --git a/academic/laghos/README b/academic/laghos/README new file mode 100644 index 0000000000..655cace20f --- /dev/null +++ b/academic/laghos/README @@ -0,0 +1,4 @@ + Laghos (LAGrangian High-Order Solver) is a miniapp that solves the +time-dependent Euler equations of compressible gas dynamics in a +moving Lagrangian frame using unstructured high-order finite element +spatial discretization and explicit high-order time-stepping. diff --git a/academic/laghos/laghos.SlackBuild b/academic/laghos/laghos.SlackBuild new file mode 100644 index 0000000000..c0ddd9ffc5 --- /dev/null +++ b/academic/laghos/laghos.SlackBuild @@ -0,0 +1,123 @@ +#!/bin/bash + +# Slackware build script for Laghos + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=laghos +VERSION=${VERSION:-3.1} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +SRCNAM=Laghos + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $SRCNAM-$VERSION +tar xvf $CWD/$SRCNAM-$VERSION.tar.gz +cd $SRCNAM-$VERSION + +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +sed -i 's#config/config.mk#share/mfem-4.5/config.mk#' {.,amr,serial}/makefile +sed -i 's#config/test.mk#share/mfem-4.5/test.mk#' amr/makefile + +# not working keep it or later (do not tell about it at README) +if [ "${PARALLEL:-no}" == "yes" ]; then + make MFEM_DIR=/usr +else + cd serial + make MFEM_DIR=/usr + make MFEM_DIR=/usr checks + cd .. +fi + +install -d $PKG/usr/bin +install -m 0755 serial/laghos $PKG/usr/bin + +install -d $PKG/usr/share/$PRGNAM +cp -av data $PKG/usr/share/$PRGNAM + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +find $PKG -depth -type d -empty -delete || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a CHANGELOG LICENSE NOTICE README.md \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/laghos/laghos.info b/academic/laghos/laghos.info new file mode 100644 index 0000000000..e7f2ae8aed --- /dev/null +++ b/academic/laghos/laghos.info @@ -0,0 +1,10 @@ +PRGNAM="laghos" +VERSION="3.1" +HOMEPAGE="https://math-atlas.sourceforge.net" +DOWNLOAD="https://github.com/CEED/Laghos/archive/v3.1/Laghos-3.1.tar.gz" +MD5SUM="5c2cc3c9fb68985cd9d6fa2c36721f21" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="mfem hypre" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/laghos/slack-desc b/academic/laghos/slack-desc new file mode 100644 index 0000000000..c772f12ebf --- /dev/null +++ b/academic/laghos/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +laghos: laghos (LAGrangian High-Order Solver) +laghos: +laghos: +laghos: Laghos (LAGrangian High-Order Solver) is a miniapp that solves +laghos: the time-dependent Euler equations of compressible gas dynamics +laghos: in a moving Lagrangian frame using unstructured high-order finite +laghos: element spatial discretization and explicit high-order time-stepping. +laghos: +laghos: +laghos: +laghos: diff --git a/academic/lalnview/README b/academic/lalnview/README index e91c30683f..364d8d0378 100644 --- a/academic/lalnview/README +++ b/academic/lalnview/README @@ -5,6 +5,13 @@ similarities between the two sequences. Blocks of similarity between the two sequences are colored according to the degree of identity between segments. +A suitable alignment tool for protein sequences is SIM at ExPASy: +https://web.expasy.org/sim/ + +SIM finds a user-defined number of best non-intersecting alignments +between two protein sequences or within a sequence. Once the alignment +is computed, you can view it using LalnView. + For details and citation: Duret, L., Gasteiger, E. and Perriere, G. (1996) LalnView: a graphical viewer for pairwise sequence alignments. Comput. Applic. diff --git a/academic/lalnview/lalnview.SlackBuild b/academic/lalnview/lalnview.SlackBuild index cb92a3bcc3..7e2e1cfa44 100644 --- a/academic/lalnview/lalnview.SlackBuild +++ b/academic/lalnview/lalnview.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for lalnview -# Copyright 2011-2016 Petar Petrov slackalaxy@gmail.com +# Copyright 2011-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -24,26 +24,38 @@ # Thanks to Niels Horn for correcting the CFLAGS. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=lalnview VERSION=${VERSION:-3.0} -BUILD=${BUILD:-2} +BUILD=${BUILD:-3} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +SRCTAR=sources20050615.tar if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -64,24 +76,24 @@ cd $TMP rm -rf $PRGNAM-$VERSION mkdir $PRGNAM-$VERSION cd $PRGNAM-$VERSION -tar xvf $CWD/sources20050615.tar +tar xvf $CWD/$SRCTAR chown -R root:root . find -L . \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; # Point to the correct place of lalnview.help -sed -i "s:lalnview.help:/usr/doc/$PRGNAM-$VERSION/lalnview.help:" MF_MainWindow.cxx +sed -i "s:$PRGNAM.help:/usr/doc/$PRGNAM-$VERSION/$PRGNAM.help:" MF_MainWindow.cxx OPT="$SLKCFLAGS" make -install -D -m755 lalnview $PKG/usr/bin/$PRGNAM +install -D -m755 $PRGNAM $PKG/usr/bin/$PRGNAM find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true -# Couldn't find an icon, so i made one myself. I know it sucks. +# Couldn't find an icon, so i made one myself. mkdir -p $PKG/usr/share/{applications,pixmaps} cp $CWD/$PRGNAM.desktop $PKG/usr/share/applications cp $CWD/$PRGNAM.png $PKG/usr/share/pixmaps @@ -96,4 +108,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/lalnview/lalnview.png b/academic/lalnview/lalnview.png Binary files differindex f4cc77c61c..f528cc3d46 100644 --- a/academic/lalnview/lalnview.png +++ b/academic/lalnview/lalnview.png diff --git a/academic/lammps/README b/academic/lammps/README new file mode 100644 index 0000000000..2a2f19c3ee --- /dev/null +++ b/academic/lammps/README @@ -0,0 +1,48 @@ +LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel +Simulator. + +It is a classical molecular dynamics simulation code designed to +run efficiently on parallel computers. It was developed at Sandia +National Laboratories, a US Department of Energy facility. + +A basic installation of LAMMPS can be enhanced enabling the build of +internal or external extensions (packages) that add methods and/or +give support to third parts libraries or platforms. + +Dependencies strictly needed to build LAMMPS with most internal +packages enabled are already present in a full installation of +Slackware 15.0 and the slackbuild can be launched without any other +dependency not released with the official Slackware. Only openmpi is +highly recommended since LAMMPS takes advantage of the parallel +computation. Furthermore some packages require it as strictly +dependency. Instead of openmpi LAMMPS can be build with the support +of mpich, although the latter does not support the enabling of a +package (OPENMP). If any MPI platform is found in the system, LAMMPS +will be built anyway but with a reduced functionality. + +Other optional dependencies available in Slackbuilds.org are +autodetected and allow the enabling of some additional packages: HDF5, +OpenBLAS, python3-numpy, voro++, PLUMED, netcdf. Other packages need +third parts libraries given by downloaded extrafile and bundled in +the application during the compilation. The slackbuild prevent the +download during the build, so you have to download these extrafiles +listed in lammps.info. Optional dependencies and the download of +extrafiles are not needed if you do not require the respective +packages. + +Warning: except to GPU, all packages are enabled by default if no +dependencies are required (or they dependencies are found in the +system), but you have to disable the packages that require the +extrafiles listed in lammps.info if you do not download them, +otherwise the build fails during the check of cmake. +For GPU package you can try: + GPU=yes ./lammps.SlackBuild +or + GPU=yes STATIC_OCL=yes ./lammps.SlackBuild +The latter uses an internal static OpenCL loader. + +See README.SBo for a full list of available packages and their +dependencies. + +Some packages available in the source of LAMMPS cannot be enabled for +reasons reported in README.SBo. diff --git a/academic/lammps/README.SBo b/academic/lammps/README.SBo new file mode 100644 index 0000000000..b74f864a25 --- /dev/null +++ b/academic/lammps/README.SBo @@ -0,0 +1,211 @@ +Table of contents + +1. HOW TO DISABLE NOT REQUIRED PACKAGES +2. INTERDEPENDENT PACKAGES +3. EXTERNAL PACKAGES +4. LIST OF PACKAGES AND RELATED REQUIREMENTS +5. PACKAGES NOT AVAILABLE +6. NOTES + +1. HOW TO DISABLE NOT REQUIRED PACKAGES + +Almost all packages that are supported by your system and dependencies +installed (autodetected) are enabled by default. You can disable those +not required in three different ways: +A. edit the code of the slackbuild + for example, a package enabled by default has this condition: + atc="" [ "${ATC:-no}" = "yes" ] && atc="-DPKG_ATC=yes " + if you want to disable it you have to edit as following: + atc="" [ "${ATC:-no}" = "yes" ] && atc="-DPKG_ATC=yes " +B. remove the variables not required from the global $packages at line + 221. The script will not pass the related flags to cmake) + for example, if you want to disable AMOEBA and ATC you have to + remove the strings $amoeba and $atc from packages=$amoeba$asphere... +C. pass to the script the related environment variable as following + AMOEBA=no ATC=no ./lammps.SlackBuild + +2. INTERDEPENDENT PACKAGES + + The enabling of some packages require that also other packages are + enabled. For example, the ATC package require also MANYBODY enabled. + The script or cmake check if this condition is not respected, so all + required additional packages will be enabled automatically + +3. EXTERNAL PACKAGES + + Various packages are build as bundled features that interface LAMMPS + to third part software that it should already installed in your + system. These deps are released with the official Slackware (fftw + for example) or available in Slackbuilds.org. Some packages require + the download of additional sources (listed in lammps.info). Please + make sure to download all required extrafiles if the dependent + package is enable. If you do not do this, the process will fail or + starts the download during the compilation. + +4. LIST OF PACKAGES AND RELATED REQUIREMENTS + + For description of each package see the documentation on line at + https://docs.lammps.org/Packages_list.html + + Dependencies available in the official Slackware are not reported. +----------------------------------------------------------------------- +PACKAGE ; ENV. VARIABLE ; ENABLED ALSO ; EXTERNAL DEPENDENCIES +----------------------------------------------------------------------- +AMOEBA ; AMOEBA ; ; +ASPHERE ; ASPHERE ; ; +ATC ; ATC ; MANYBODY ; +AWPMD ; AWPMD ; ; +BOCS ; BOCS ; ; +BODY ; BODY ; ; +BPM ; BPM ; ; +BROWNIAN ; BROWNIAN ; ; +CG-DNA ; CGDNA ; ASPHERE \ + MOLECULE ; +CG-SPICA ; CGSPICA ; ; +CLASS2 ; CLASS2 ; ; +COLLOID ; COLLOID ; ; +COLVARS ; COLVARS ; ; +COMPRESS ; COMPRESS ; ; +CORESHELL ; CORESHELL ; ; +DIELECTRIC ; DIELECTRIC ; EXTRA-PAIR \ + KSPACE ; +DIFFRACTION ; DIFFRACTION ; ; +DIPOLE ; DIPOLE ; ; +DPD-BASIC ; DPDBASIC ; ; +DPD-MESO ; DPDMESO ; ; +DPD-REACT ; DPDREACT ; ; +DPD-SMOOTH ; DPDSMOOTH ; ; +DRUDE ; DRUDE ; ; +EFF ; EFF ; ; +ELECTRODE ; ELECTRODE ; KSPACE ; OpenBLAS (optional) +EXTRA-COMPUTE ; EXTRACOMPUTE ; ; +EXTRA-DUMP ; EXTRADUMP ; ; +EXTRA-FIX ; EXTRAFIX ; ; +EXTRA-MOLECULE ; EXTRAMOLECULE ; ; +EXTRA-PAIR ; EXTRAPAIR ; ; +FEP ; FEP ; ; +GPU ; GPU ; ; see NOTES +GRANULAR ; GRANULAR ; ; +H5MD ; H5MD ; ; hdf5 (needed) +INTEL ; INTEL ; OPENMP ; see NOTES +INTERLAYER ; INTERLAYER ; ; +KOKKOS ; KOKKOS ; ; see NOTES +KSPACE ; KSPACE ; ; +LATBOLTZ ; LATBOLTZ ; ; see NOTES +LEPTON ; LEPTON ; ; +MACHDYN ; MACHDYN ; ; +MANIFOLD ; MANIFOLD ; ; +MANYBODY ; MANYBODY ; ; +MC ; MC ; ; +MDI ; MDI ; ; download extrasource +MEAM ; MEAM ; ; +MESONT ; MESONT ; MOLECULE ; download data file +MGPT ; MGPT ; ; +MISC ; MISC ; ; +ML-HDNNP ; MLHDNNP ; ; download extrasource +ML-IAP ; MLIAP ; ML-SNAP \ + PYTHON ; python3-numpy (needed) +ML-PACE ; MLPACE ; ; download extrasource +ML-POD ; MLPOD ; ; +ML-RANN ; MLRANN ; ; +ML-SNAP ; MLSNAP ; ; +MOFFF ; MOFFF ; ; +MOLECULE ; MOLECULE ; ; +NETCDF ; NETCDF ; ; netcdf +OPENMP ; OPENMP ; ; openmpi (needed) \ + (mpich not supported) +OPT ; OPT ; ; +ORIENT ; ORIENT ; ; +PERI ; PERI ; ; +PHONON ; PHONON ; KSPACE ; +PLUMED ; PLUMED ; ; PLUMED +POEMS ; POEMS ; ; +PTM ; PTM ; ; +PYTHON ; PYTHON ; ; +QEQ ; QEQ ; ; +QTB ; QTB ; ; +REACTION ; REACTION ; ; +REAXFF ; REAXFF ; ; +REPLICA ; REPLICA ; ; +RIGID ; RIGID ; ; +SCAFACOS ; SCAFACOS ; ; scafacos +SHOCK ; SHOCK ; ; +SMTBQ ; SMTBQ ; ; +SPH ; SPH ; ; +SPIN ; SPIN ; ; +SRD ; SRD ; ; +TALLY ; TALLY ; ; +UEF ; UEF ; ; +YAFF ; YAFF ; ; +----------------------------------------------------------------------- + +5. PACKAGES NOT AVAILABLE + +Some packages, available in the source, are not supported in this +slackbuild for various reasons. These are: +- ADIOS: requires a library not available in Slackware or SBo. +- KIM: requires the download of extrasource during the compilation + which cannot be prevented by a predownload. +- ML-QUIP: the version for non-commercial uses can be downloaded only + during the compilation. A preventive download is allowed + only via git. +- MOLFILE: this package supports the VMD plugin that is must be built + and installed only by sources or packages downloaded after + registration +- MPIIO: this packages is unmantained and it should be enabled with + caution +- MSCG: requires the download of extrasource during the compilation or + the installation in the system. This library is free and open + source but the anonymous download is not permitted. +- QMMM: requires a library that can be built and installed from source + downloaded after registration +- VORONOI: since the required dependency available in this repository + can be build as static library, this package is not compatible + when lammps is built enabling shared libraries, so support to + it is disabled +- VTK: not available at the moment because the build fails. It is + possible that this is caused by the VTK built in my system: the + issue is a conflict with the support of VTK to openmpi in my + built. I have to make some tests to find the problem. + +6. NOTES + +The GPU package supports OpenCL, CUDA and HIP by setting the +appropriate build configuration. See the documentation on line if you +would extend the functionality of LAMMPS adapted to you hardware. This +slackbuild sets a basic configuration build the package with OpenCL. +LAMMPS can be build linking the system OpenCL or using a static +internal OpenCL loader. To enable the build with the internal OpenCL +you have to download the extrasource from the link indicated in +lammps.info and pass the variable STATIC_OCL=yes to the slackbuild. +The enabling of this package gives different results depending on the +hardware/software configurations, so it is disabled by default because +we have to apply additional settings to prevent the issues (build +failures and segmentation faults). With a basic configuration I enabled +it in a Slackware current with a an old Nvidia GPU and driver and +using the system OpenCL (the bundled OpenCL gives segmentation fault). +In other tests (Slackware 15 with older Nvidia GPU and driver, +Slackware 32-bit in virtual machine) the build not works. You could +passing GPU=yes (and eventually STATIC_OCL=yes) to the slackbuild to +try if it works in your system with a basic configuration, but it is no +guaranteed. + +The INTEL package takes advantage in build and runtime of an advanced +configuration using Intel compilers and hardware it should work also +with other with reduced performances. If detected, the build takes +advantage of the parallelism (MPI and tbb, for example). + +KOKKOS is another package that enhances the functionality of LAMMPS +taking advandage of the parallel computation. Since its build requires +resources and a build with a single core seems very long, I set the +enabling by default only for 64-bit architectures because I do not know +how it can be useful in 32-bit systems. + +The LATBOLTZ package must be enabled only if LAMMPS is built with the +support to MPI (openmpi or mpich). The script allows the enabling of +LATBOLTZ if one of these dependencies are found in the system. + +By default, LAMMPS will be built with Python anyway, even if packages +that require it will not be enabled. If you want disable the support +to Python, you have to launch the slackbuild with + PYTHON=no ./lammps.SlackBuild diff --git a/academic/lammps/lammps.SlackBuild b/academic/lammps/lammps.SlackBuild new file mode 100644 index 0000000000..2cf95b7453 --- /dev/null +++ b/academic/lammps/lammps.SlackBuild @@ -0,0 +1,389 @@ +#!/bin/bash + +# Slackware build script for lammps + +# Copyright 2023-2024 Giancarlo Dessi, Cagliari, IT +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=lammps +VERSION=${VERSION:-2023.08.02_update3} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} +SRCNAM=lammps-stable +SRCVERSION=${SRCVERSION:-2Aug2023_update3} +PACEVERSION=v.2023.10.04 +MDIVERSION=1.4.26 +N2P2VERSION=2.2.0 +OCLLVERSION=2022.01.04 + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +# First detect if openmpi or mpich are installed, so we can build LAMMPS with the +# parallel computing and enable some packages +MP="" +mpi="" +if pkg-config --exists ompi; then + MP="openmpi"; + mpi="-DBUILD_OMP=yes " +fi +if pkg-config --exists mpich; then + MP="mpich"; + mpi="-DBUILD_MPI=yes " +fi + +# Detect if some dependencies are installed or extrafile download. +# These are needed conditions to prevent the download of extrafiles +# during the build +scafacos="" +mdi="" +mlpace="" +# External ScaFaCos must be installed in the system +if pkg-config --exists scafacos; then + scafacos="-DPKG_SCAFACOS=yes -DDOWNLOAD_SCAFACOS=OFF " +fi +# lammps-user-pace must be downloaded in $CWD +PACETARBALL=$CWD/lammps-user-pace-$PACEVERSION.tar.gz +if [ -f $PACETARBALL ]; then + mlpace="" ; [ "${MLPACE:-yes}" = "yes" ] && mlpace="-DPKG_ML-PACE=yes " +fi +# MDI_Library must be downloaded in $CWD. Installation of this library +# in the system does not work +MDITARBALL=$CWD/MDI_Library-$MDIVERSION.tar.gz +if [ -f $MDITARBALL ]; then + mdi="" ; [ "${MDI:-yes}" = "yes" ] && mdi="-DPKG_MDI=yes -DDOWNLOAD_MDI=ON " +fi +# N2P2 must be downloaded in $CWD +N2P2=$CWD/n2p2-$N2P2VERSION.tar.gz +if [ -f $MDITARBALL ]; then + mlhdnnp="" ; [ "${MLHDNNP:-yes}" = "yes" ] && mlhdnnp="-DPKG_ML-HDNNP=yes " +fi + + +# These internal packages are enabled by default. +# If you do not require some of them you have to edit the conditions in this block +# otherwise pass the respective environment variables set to "no" to the script +# for each package not desired +# (for example: AMOEBA=no ASPHERE=no ./lammps.SlackBuild) + +amoeba="" [ "${AMOEBA:-yes}" = "yes" ] && amoeba="-DPKG_AMOEBA=yes " +asphere="" ; [ "${ASPHERE:-yes}" = "yes" ] && asphere="-DPKG_ASPHERE=yes " +atc="" ; [ "${ATC:-yes}" = "yes" ] && atc="-DPKG_ATC=yes " +awpmd="" ; [ "${AWPMD:-yes}" = "yes" ] && awpmd="-DPKG_AWPMD=yes " +bocs="" ; [ "${BOCS:-yes}" = "yes" ] && bocs="-DPKG_BOCS=yes " +body="" ; [ "${BODY:-yes}" = "yes" ] && body="-DPKG_BODY=yes " +bpm="" ; [ "${BPM:-yes}" = "yes" ] && bpm="-DPKG_BPM=yes " +brownian="" ; [ "${BROWNIAN:-yes}" = "yes" ] && brownian="-DPKG_BROWNIAN=yes " +cgdna="" ; [ "${CGDNA:-yes}" = "yes" ] && cgdna="-DPKG_CG-DNA=yes " +cgspica="" ; [ "${CGSPICA:-yes}" = "yes" ] && cgspica="-DPKG_CG-SPICA=yes " +class2="" ; [ "${CLASS2:-yes}" = "yes" ] && class2="-DPKG_CLASS2=yes " +colloid="" ; [ "${COLLOID:-yes}" = "yes" ] && colloid="-DPKG_COLLOID=yes " +colvars="" ; [ "${COLVARS:-yes}" = "yes" ] && colvars="-DPKG_COLVARS=yes " +compress="" ; [ "${COMPRESS:-yes}" = "yes" ] && compress="-DPKG_COMPRESS=yes " +coreshell="" ; [ "${CORESHELL:-yes}" = "yes" ] && coreshell="-DPKG_CORESHELL=yes " +dielectric="" ; [ "${DIELECTRIC:-yes}" = "yes" ] && dielectric="-DPKG_DIELECTRIC=yes " +diffraction="" ; [ "${DIFFRACTION:-yes}" = "yes" ] && diffraction="-DPKG_DIFFRACTION=yes " +dipole="" ; [ "${DIPOLE:-yes}" = "yes" ] && dipole="-DPKG_DIPOLE=yes " +dpdbasic="" ; [ "${DPDBASIC:-yes}" = "yes" ] && dpdbasic="-DPKG_DPD-BASIC=yes " +dpdmeso="" ; [ "${DPDMESO:-yes}" = "yes" ] && dpdmeso="-DPKG_DPD-MESO=yes " +dpdreact="" ; [ "${DPDREACT:-yes}" = "yes" ] && dpdreact="-DPKG_DPD-REACT=yes " +dpdsmooth="" ; [ "${DPDSMOOTH:-yes}" = "yes" ] && dpdsmooth="-DPKG_DPD-SMOOTH=yes " +drude="" ; [ "${DRUDE:-yes}" = "yes" ] && drude="-DPKG_DRUDE=yes " +eff="" ; [ "${EFF:-yes}" = "yes" ] && eff="-DPKG_EFF=yes " +electrode="" ; [ "${ELECTRODE:-yes}" = "yes" ] && electrode="-DPKG_ELECTRODE=yes " +extracompute="" ; [ "${EXTRACOMPUTE:-yes}" = "yes" ] && extracompute="-DPKG_EXTRA-COMPUTE=yes " +extradump="" ; [ "${EXTRADUMP:-yes}" = "yes" ] && extradump="-DPKG_EXTRA-DUMP=yes " +extrafix="" ; [ "${EXTRAFIX:-yes}" = "yes" ] && extrafix="-DPKG_EXTRA-FIX=yes " +extramolecule="" ; [ "${EXTRAMOLECULE:-yes}" = "yes" ] && extramolecule="-DPKG_EXTRA-MOLECULE=yes " +extrapair="" ; [ "${EXTRAPAIR:-yes}" = "yes" ] && extrapair="-DPKG_EXTRA-PAIR=yes " +fep="" ; [ "${FEP:-yes}" = "yes" ] && fep="-DPKG_FEP=yes " +granular="" ; [ "${GRANULAR:-yes}" = "yes" ] && granular="-DPKG_GRANULAR=yes " +intel="" ; [ "${INTEL:-yes}" = "yes" ] && intel="-DPKG_INTEL=yes " +interlayer="" ; [ "${INTERLAYER:-yes}" = "yes" ] && interlayer="-DPKG_INTERLAYER=yes " +kspace="" ; [ "${KSPACE:-yes}" = "yes" ] && kspace="-DPKG_KSPACE=yes " +lepton="" ; [ "${LEPTON:-yes}" = "yes" ] && lepton="-DPKG_LEPTON=yes " +machdyn="" ; [ "${MACHDYN:-yes}" = "yes" ] && machdyn="-DPKG_MACHDYN=yes " +manifold="" ; [ "${MANIFOLD:-yes}" = "yes" ] && manifold="-DPKG_MANIFOLD=yes " +manybody="" ; [ "${MANYBODY:-yes}" = "yes" ] && manybody="-DPKG_MANYBODY=yes " +mc="" ; [ "${MC:-yes}" = "yes" ] && mc="-DPKG_MC=yes " +meam="" ; [ "${MEAM:-yes}" = "yes" ] && meam="-DPKG_MEAM=yes " +mesont="" ; [ "${MESONT:-yes}" = "yes" ] && mesont="-DPKG_MESONT=yes " +mgpt="" ; [ "${MGPT:-yes}" = "yes" ] && mgpt="-DPKG_MGPT=yes " +misc="" ; [ "${MISC:-yes}" = "yes" ] && misc="-DPKG_MISC=yes " +mlpod="" ; [ "${MLPOD:-yes}" = "yes" ] && mlpod="-DPKG_ML-POD=yes " +mlrann="" ; [ "${MLRANN:-yes}" = "yes" ] && mlrann="-DPKG_ML-RANN=yes " +mlsnap="" ; [ "${MLSNAP:-yes}" = "yes" ] && mlsnap="-DPKG_ML-SNAP=yes " +mofff="" ; [ "${MOFFF:-yes}" = "yes" ] && mofff="-DPKG_MOFFF=yes " +molecule="" ; [ "${MOLECULE:-yes}" = "yes" ] && molecule="-DPKG_MOLECULE=yes " +opt="" ; [ "${OPT:-yes}" = "yes" ] && opt="-DPKG_OPT=yes " +orient="" ; [ "${ORIENT:-yes}" = "yes" ] && orient="-DPKG_ORIENT=yes " +peri="" ; [ "${PERI:-yes}" = "yes" ] && peri="-DPKG_PERI=yes " +phonon="" ; [ "${PHONON:-yes}" = "yes" ] && phonon="-DPKG_PHONON=yes " +plugin="" ; [ "${PLUGIN:-yes}" = "yes" ] && plugin="-DPKG_PLUGIN=yes " +poems="" ; [ "${POEMS:-yes}" = "yes" ] && poems="-DPKG_POEMS=yes " +ptm="" ; [ "${PTM:-yes}" = "yes" ] && ptm="-DPKG_PTM=yes " +qeq="" ; [ "${QEQ:-yes}" = "yes" ] && qeq="-DPKG_QEQ=yes " +qtb="" ; [ "${QTB:-yes}" = "yes" ] && qtb="-DPKG_QTB=yes " +reaction="" ; [ "${REACTION:-yes}" = "yes" ] && reaction="-DPKG_REACTION=yes " +reaxff="" ; [ "${REAXFF:-yes}" = "yes" ] && reaxff="-DPKG_REAXFF=yes " +replica="" ; [ "${REPLICA:-yes}" = "yes" ] && replica="-DPKG_REPLICA=yes " +rigid="" ; [ "${RIGID:-yes}" = "yes" ] && rigid="-DPKG_RIGID=yes " +shock="" ; [ "${SHOCK:-yes}" = "yes" ] && shock="-DPKG_SHOCK=yes " +smtbq="" ; [ "${SMTBQ:-yes}" = "yes" ] && smtbq="-DPKG_SMTBQ=yes " +sph="" ; [ "${SPH:-yes}" = "yes" ] && sph="-DPKG_SPH=yes " +spin="" ; [ "${SPIN:-yes}" = "yes" ] && spin="-DPKG_SPIN=yes " +srd="" ; [ "${SRD:-yes}" = "yes" ] && srd="-DPKG_SRD=yes " +tally="" ; [ "${TALLY:-yes}" = "yes" ] && tally="-DPKG_TALLY=yes " +uef="" ; [ "${UEF:-yes}" = "yes" ] && uef="-DPKG_UEF=yes " +yaff="" ; [ "${YAFF:-yes}" = "yes" ] && yaff="-DPKG_YAFF=yes " + +# If OpenBLAS is installed ELECTRODE will be enabled using the system LAPACK +# otherwise a bundled linear algebra is used. To force the use of internal +# linear algebra edit the CMake flag setting "-DUSE_INTERNAL_LINALG=yes " +if [ "$electrode" = "-DPKG_ELECTRODE=yes " ]; then + if pkg-config --exists openblas; then + electrode=$electrode"-DUSE_INTERNAL_LINALG=no " + fi +fi + +if [ "${PYTHON:-yes}" = "yes" ]; then + python="-DPKG_PYTHON=yes " + if [ -d /usr/doc/python3-numpy* ]; then + mliap="" ; [ "${MLIAP:-yes}" = "yes" ] && mliap="-DPKG_ML-IAP=yes -DMLIAP_ENABLE_PYTHON=autodetected " + else + mliap="" + fi +else + python="" + mliap="" +fi + +# The GPU package requires some basic settings that may be customized through environment +# variables. For advanced options requiring specific hardware configurations (GPU) see the +# documentation in lammps.org +# This package causes many issues depending on the hardware/software configuration (build +# failure or segmentation fault) that require additional settings to be solved, so it is +# disabled by default. +if [ "${GPU:-no}" = "yes" ]; then + # by default the GPU package is enabled using bundled OpenCL ICD loader library/headers + # but users may prefer the local opencl installed in the system + opencl_loader="yes" ; [ "${STATIC_OCL:-no}" = "no" ] && opencl_loader="no" + gpu="-DPKG_GPU=yes -DGPU_API=opencl -DUSE_STATIC_OPENCL_LOADER=${opencl_loader} " +else + opencl_loader="" + gpu="" +fi + +# Following conditions enable by default all packages that require dependencies if these +# are installed in the system + +latboltz="" +openmp="" +if [ "$MP" = "openmpi" ]; then + latboltz="" ; [ "${LATBOLTZ:-yes}" = "yes" ] && latboltz="-DPKG_LATBOLTZ=yes " + openmp="" ; [ "${OPENMP:-yes}" = "yes" ] && openmp="-DPKG_OPENMP=yes " +fi + +if [ "$MP" = "mpich" ]; then + latboltz="" ; [ "${LATBOLTZ:-yes}" = "yes" ] && latboltz="-DPKG_LATBOLTZ=yes " +fi + +if pkg-config --exists plumed; then + plumed="" ; [ "${PLUMED:-yes}" = "yes" ] && plumed="-DPKG_PLUMED=yes -DDOWNLOAD_PLUMED=no " +else + plumed="" +fi + +netcdf="" +if pkg-config --exists netcdf; then + netcdf="" ; [ "${NETCDF:-yes}" = "yes" ] && netcdf="-DPKG_NETCDF=yes " +fi + +h5md="" +if [ -f /usr/bin/h5cc ]; then + h5md="" ; [ "${H5MD:-yes}" = "yes" ] && h5md="-DPKG_H5MD=yes " +fi + +# This shouldn't need in 32-bit architectures, however it significantly extends the build times +# and absorbs many resources. Openmpi is strictly required. +kokkos="" +if [ "$ARCH" = "x86_64" ]; then + if [ "${KOKKOS:-yes}" = "yes" ] ; then + kokkos="-DPKG_KOKKOS=yes -DKokkos_ARCH_NATIVE=yes -DKokkos_ENABLE_OPENMP=yes " + fi + if [ "$MP" != "openmpi" ]; then + kokkos="" + fi +fi + +# All required cmake flags related to packages are included in a single global variable +packages=$amoeba$asphere$atc$awpmd$bocs$body$bpm$brownian$cgdna$cgspica$class2$colloid\ +$colvars$compress$coreshell$dielectric$diffraction$dipole$dpdbasic$dpdmeso$dpdreact\ +$dpdsmooth$drude$eff$electrode$extracompute$extradump$extrafix$extramolecule$extrapair\ +$fep$gpu$granular$h5md$intel$interlayer$kokkos$kspace$latboltz$lepton$machdyn$manifold\ +$manybody$mc$mdi$meam$mesont$mgpt$misc$mlhdnnp$mliap$mlpod$mlrann$mlsnap$mofff$molecule\ +$netcdf$openmp$opt$orient$peri$phonon$plugin$plumed$poems$ptm$qeq$qtb$reaction\ +$reaxff$replica$rigid$shock$smtbq$sph$spin$srd$tally$uef$yaff + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf ${SRCNAM}_${SRCVERSION} +tar xvf $CWD/${SRCNAM}_${SRCVERSION}.tar.gz +cd ${SRCNAM}_${SRCVERSION} + +if [ "$mesont" != "" ]; then + cp -a $CWD/C_10_10.mesocnt ./potentials + if [ "$molecule" = "" ]; then + echo -e "\n\033[33mYou have enabled the package MESONT. Since this package requires also " + echo -e "the package MOLECULE, the build of MOLECULE will be automatically enabled\033[0m\n" + packages=$packages" -DPKG_MOLECULE=yes " + fi +fi + +if [ "$MP" = "" ]; then + echo -e "\n\033[33m******************** WARNING ********************\n" + echo " no API supporting MPI (mpich or openmpi) are " + echo " installed on your system. This does not affect " + echo " the build and installation of LAMMPS, but some " + echo " packages cannot be enabled and other may work " + echo " not optimally. " + echo -e "\n*************************************************\n\033[0m" +fi + +# Prepare directories to move the extrafiles needed to build some packages +mkdir -p cmake/build + +if [ "$opencl_loader" = "yes" ]; then + mkdir -p cmake/build/_deps + cp -a $CWD/opencl-loader-$OCLLVERSION.tar.gz cmake/build/_deps +fi + +if [ "$mdi" != "" ]; then + mkdir -p cmake/build/mdi_build_ext/src/ + cp -a $CWD/MDI_Library-$MDIVERSION.tar.gz cmake/build/mdi_build_ext/src/v$MDIVERSION.tar.gz +fi + + +if [ "$mlhdnnp" != "" ]; then + mkdir -p cmake/build/n2p2_build-prefix/src/ + cp -a $CWD/n2p2-$N2P2VERSION.tar.gz cmake/build/n2p2_build-prefix/src/v$N2P2VERSION.tar.gz +fi + +if [ "$mlpace" != "" ]; then + cp -a $CWD/lammps-user-pace-$PACEVERSION.tar.gz cmake/build/libpace.tar.gz +fi + +echo -e "\nFLAGS FOR PACKAGES ENABLED:\n "$packages"\n" + +echo -e "FLAGS FOR PYTHON:\n "$python + +echo -e "\nFLAGS FOR MPI:\n "$mpi + +echo -e "\nFLAGS FOR SCAFACOS:\n "$scafacos + +echo -e "\nFLAGS FOR ML-PACE:\n "$mlpace + +echo "" + +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +# The Source has not a CMakeLists.txt file in the root directory we +# need to change in the cmake directory +cd cmake +cd build + cmake \ + -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DCMAKE_BUILD_TYPE=Release \ + -DBUILD_SHARED_LIBS=ON \ + $mpi \ + $scafacos \ + $mdi \ + $python \ + $mlpace \ + $packages \ + .. + make + make install DESTDIR=$PKG +cd .. + +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +#Since the build installs man in /usr/share we move the directory in /usr +mv -v $PKG/usr/share/man $PKG/usr +find $PKG/usr/man -type f -exec gzip -9 {} \; +for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done + +#Since the build installs etc as subfolder of /usr (?), we move it in the root directory +mv -v $PKG/usr/etc $PKG + +cd $TMP/${SRCNAM}_${SRCVERSION} +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a LICENSE README $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/lammps/lammps.info b/academic/lammps/lammps.info new file mode 100644 index 0000000000..8583388823 --- /dev/null +++ b/academic/lammps/lammps.info @@ -0,0 +1,20 @@ +PRGNAM="lammps" +VERSION="2023.08.02_update3" +HOMEPAGE="https://www.lammps.org" +DOWNLOAD="https://github.com/lammps/lammps/archive/stable_2Aug2023_update3/lammps-stable_2Aug2023_update3.tar.gz \ + https://download.lammps.org/potentials/C_10_10.mesocnt \ + https://download.lammps.org/thirdparty/opencl-loader-2022.01.04.tar.gz \ + https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.26/MDI_Library-1.4.26.tar.gz \ + https://github.com/CompPhysVienna/n2p2/archive/v2.2.0/n2p2-2.2.0.tar.gz \ + https://github.com/ICAMS/lammps-user-pace/archive/v.2023.10.04.tar.gz" +MD5SUM="a68cd5d9f70822da73092457bc3ccede \ + 68b5ca26283968fd9889aa0a37f7b7fb \ + 8d3a801e87a2c6653bf0e27707063914 \ + 3124bb85259471e2a53a891f04bf697a \ + a2d9ab7f676b3a74a324fc1eda0a911d \ + 70ff79f4e59af175e55d24f3243ad1ff" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="openmpi scafacos" +MAINTAINER="Giancarlo Dessi" +EMAIL="slack@giand.it" diff --git a/academic/lammps/slack-desc b/academic/lammps/slack-desc new file mode 100644 index 0000000000..c082c858ab --- /dev/null +++ b/academic/lammps/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +lammps: lammps (LAMMPS Molecular Dynamics Simulator) +lammps: +lammps: LAMMPS stands for +lammps: Large-scale Atomic/Molecular Massively Parallel Simulator. +lammps: It was developed at Sandia National Laboratories (US Department of +lammps: Energy) and is designed to run efficiently on parallel computers. +lammps: +lammps: +lammps: Home page: https://www.lamps.org +lammps: +lammps: diff --git a/academic/lapack95/lapack95.SlackBuild b/academic/lapack95/lapack95.SlackBuild index 6a4a9e7815..8d970095c7 100644 --- a/academic/lapack95/lapack95.SlackBuild +++ b/academic/lapack95/lapack95.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for lapack95 -# Written by Pablo Santamaría (pablosantamaria@gmail.com) +# Written by Pablo SantamarÃa (pablosantamaria@gmail.com) # Copyright 2017 Ekin Akoglu, Erdemli, Mersin, Turkey # All rights reserved. # @@ -23,10 +23,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=lapack95 VERSION=${VERSION:-3.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -36,7 +39,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -104,4 +114,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/lapacke/README b/academic/lapacke/README index 56e7a29488..118c2449de 100644 --- a/academic/lapacke/README +++ b/academic/lapacke/README @@ -1,10 +1,12 @@ LAPACKE provides a native C interface to LAPACK routines available at -www.netlib.org/lapack to facilitate usage of LAPACK functionality for C -programmers. +www.netlib.org/lapack to facilitate usage of LAPACK functionality for +C programmers. -This package is intended for use with the Netlib reference LAPACK. It should -also work with other LAPACK implementations that do not already provide a -LAPACKE implementation. +This package is intended for use with the Netlib reference LAPACK. +It should also work with other LAPACK implementations that do not +already provide a LAPACKE implementation. -To build a static library in addition to the shared library, -pass STATIC=yes to the script. +xblas is an optional dependency. + +To build a static library in addition to the shared library, pass +STATIC=yes to the script. diff --git a/academic/lapacke/lapacke.SlackBuild b/academic/lapacke/lapacke.SlackBuild index e0c9fe36d0..61025be61b 100644 --- a/academic/lapacke/lapacke.SlackBuild +++ b/academic/lapacke/lapacke.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for LAPACKE -# Copyright 2016-2020 Kyle Guinn <elyk03@gmail.com> +# Copyright 2016-2024 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,11 +22,14 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=lapacke SRCNAM=lapack -VERSION=${VERSION:-3.9.0} +VERSION=${VERSION:-3.12.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$(uname -m)" in @@ -36,15 +39,19 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM-$VERSION +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="LAPACKE/LICENSE LAPACKE/README DOCS/lapacke.pdf" -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" elif [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" elif [ "$ARCH" = "i686" ]; then @@ -69,6 +76,10 @@ chmod -R u+w,go-w,a+rX-st . # Allow building only the LAPACKE component. patch -p1 < $CWD/patches/cmake-piecewise.diff +if pkg-config --exists xblas; then + use_xblas='-DUSE_XBLAS=ON' +fi + # Avoid adding an RPATH entry to the shared lib. It's unnecessary (except for # running the test suite), and it's broken on 64-bit (needs LIBDIRSUFFIX). mkdir -p shared @@ -82,6 +93,7 @@ cd shared -DUSE_OPTIMIZED_LAPACK=ON \ -DBUILD_LAPACKE=ON \ -DBUILD_DEPRECATED=ON \ + $use_xblas \ -DBUILD_SHARED_LIBS=ON \ -DCMAKE_SKIP_RPATH=YES \ .. @@ -104,6 +116,7 @@ if [ "${STATIC:-no}" != "no" ]; then -DUSE_OPTIMIZED_LAPACK=ON \ -DBUILD_LAPACKE=ON \ -DBUILD_DEPRECATED=ON \ + $use_xblas \ .. make make install/strip DESTDIR=$PKG @@ -118,4 +131,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/lapacke/lapacke.info b/academic/lapacke/lapacke.info index 80f3fc335b..fe7070f8aa 100644 --- a/academic/lapacke/lapacke.info +++ b/academic/lapacke/lapacke.info @@ -1,8 +1,8 @@ PRGNAM="lapacke" -VERSION="3.9.0" -HOMEPAGE="http://www.netlib.org/lapack/lapacke.html" -DOWNLOAD="https://github.com/Reference-LAPACK/lapack/archive/v3.9.0/lapack-3.9.0.tar.gz" -MD5SUM="0b251e2a8d5f949f99b50dd5e2200ee2" +VERSION="3.12.0" +HOMEPAGE="https://www.netlib.org/lapack/lapacke.html" +DOWNLOAD="https://github.com/Reference-LAPACK/lapack/archive/v3.12.0/lapack-3.12.0.tar.gz" +MD5SUM="c1b38bef123584d86a1bd8000784a7b2" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="lapack" diff --git a/academic/lapacke/patches/cmake-piecewise.diff b/academic/lapacke/patches/cmake-piecewise.diff index b1bdfaec1e..37cde2acaa 100644 --- a/academic/lapacke/patches/cmake-piecewise.diff +++ b/academic/lapacke/patches/cmake-piecewise.diff @@ -2,69 +2,37 @@ diff --git a/CBLAS/CMakeLists.txt b/CBLAS/CMakeLists.txt --- a/CBLAS/CMakeLists.txt +++ b/CBLAS/CMakeLists.txt @@ -1,8 +1,6 @@ - message(STATUS "CBLAS enable") + message(STATUS "CBLAS enabled") enable_language(C) --set(LAPACK_INSTALL_EXPORT_NAME cblas-targets) +-set(LAPACK_INSTALL_EXPORT_NAME ${CBLASLIB}-targets) - # Create a header file cblas.h for the routines called in my C programs - include(FortranCInterface) - ## Ensure that the fortran compiler and c compiler specified are compatible -@@ -41,54 +39,8 @@ - add_subdirectory(examples) - endif() - --if(NOT BLAS_FOUND) -- set(ALL_TARGETS ${ALL_TARGETS} blas) --endif() -- --# Export cblas targets from the --# install tree, if any. --set(_cblas_config_install_guard_target "") --if(ALL_TARGETS) -- install(EXPORT cblas-targets -- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/cblas-${LAPACK_VERSION} -- COMPONENT Development -- ) -- # Choose one of the cblas targets to use as a guard for -- # cblas-config.cmake to load targets from the install tree. -- list(GET ALL_TARGETS 0 _cblas_config_install_guard_target) --endif() -- --# Export cblas targets from the build tree, if any. --set(_cblas_config_build_guard_target "") --if(ALL_TARGETS) -- export(TARGETS ${ALL_TARGETS} FILE cblas-targets.cmake) -- -- # Choose one of the cblas targets to use as a guard -- # for cblas-config.cmake to load targets from the build tree. -- list(GET ALL_TARGETS 0 _cblas_config_build_guard_target) --endif() + include(CheckLanguage) + check_language(Fortran) +@@ -54,22 +52,3 @@ + DESTINATION ${PKG_CONFIG_DIR} + COMPONENT Development + ) - -configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cmake/cblas-config-version.cmake.in -- ${LAPACK_BINARY_DIR}/cblas-config-version.cmake @ONLY) +- ${LAPACK_BINARY_DIR}/${CBLASLIB}-config-version.cmake @ONLY) -configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cmake/cblas-config-build.cmake.in -- ${LAPACK_BINARY_DIR}/cblas-config.cmake @ONLY) -- -- - configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cblas.pc.in ${CMAKE_CURRENT_BINARY_DIR}/cblas.pc @ONLY) - install(FILES - ${CMAKE_CURRENT_BINARY_DIR}/cblas.pc - DESTINATION ${PKG_CONFIG_DIR} - ) +- ${LAPACK_BINARY_DIR}/${CBLASLIB}-config.cmake @ONLY) - -configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cmake/cblas-config-install.cmake.in -- ${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/cblas-config.cmake @ONLY) +- ${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/${CBLASLIB}-config.cmake @ONLY) -install(FILES -- ${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/cblas-config.cmake -- ${LAPACK_BINARY_DIR}/cblas-config-version.cmake -- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/cblas-${LAPACK_VERSION} +- ${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/${CBLASLIB}-config.cmake +- ${LAPACK_BINARY_DIR}/${CBLASLIB}-config-version.cmake +- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/${CBLASLIB}-${LAPACK_VERSION} +- COMPONENT Development - ) - --#install(EXPORT cblas-targets --# DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/cblas-${LAPACK_VERSION} --# COMPONENT Development --# ) +-install(EXPORT ${CBLASLIB}-targets +- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/${CBLASLIB}-${LAPACK_VERSION} +- COMPONENT Development +- ) diff --git a/CBLAS/cmake/cblas-config-build.cmake.in b/CBLAS/cmake/cblas-config-build.cmake.in deleted file mode 100644 --- a/CBLAS/cmake/cblas-config-build.cmake.in @@ -76,41 +44,37 @@ deleted file mode 100644 - -# Load lapack targets from the build tree, including lapacke targets. -if(NOT TARGET lapacke) -- include("@LAPACK_BINARY_DIR@/lapack-targets.cmake") +- include("@LAPACK_BINARY_DIR@/@LAPACKLIB@-targets.cmake") -endif() - -# Report cblas header search locations from build tree. -set(CBLAS_INCLUDE_DIRS "@LAPACK_BINARY_DIR@/include") - -# Report cblas libraries. --set(CBLAS_LIBRARIES cblas) +-set(CBLAS_LIBRARIES @CBLASLIB@) diff --git a/CBLAS/cmake/cblas-config-install.cmake.in b/CBLAS/cmake/cblas-config-install.cmake.in deleted file mode 100644 --- a/CBLAS/cmake/cblas-config-install.cmake.in +++ /dev/null -@@ -1,23 +0,0 @@ +@@ -1,19 +0,0 @@ -# Compute locations from <prefix>/@{LIBRARY_DIR@/cmake/lapacke-<v>/<self>.cmake -get_filename_component(_CBLAS_SELF_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH) --get_filename_component(_CBLAS_PREFIX "${_CBLAS_SELF_DIR}" PATH) --get_filename_component(_CBLAS_PREFIX "${_CBLAS_PREFIX}" PATH) --get_filename_component(_CBLAS_PREFIX "${_CBLAS_PREFIX}" PATH) - -# Load the LAPACK package with which we were built. --set(LAPACK_DIR "${_CBLAS_PREFIX}/@CMAKE_INSTALL_LIBDIR@/cmake/lapack-@LAPACK_VERSION@") +-set(LAPACK_DIR "@CMAKE_INSTALL_FULL_LIBDIR@/cmake/@LAPACKLIB@-@LAPACK_VERSION@") -find_package(LAPACK NO_MODULE) - -# Load lapacke targets from the install tree. --if(NOT TARGET cblas) -- include(${_CBLAS_SELF_DIR}/cblas-targets.cmake) +-if(NOT TARGET @CBLASLIB@) +- include(${_CBLAS_SELF_DIR}/@CBLASLIB@-targets.cmake) -endif() - -# Report lapacke header search locations. --set(CBLAS_INCLUDE_DIRS ${_CBLAS_PREFIX}/include) +-set(CBLAS_INCLUDE_DIRS @CMAKE_INSTALL_FULL_INCLUDEDIR@) - -# Report lapacke libraries. --set(CBLAS_LIBRARIES cblas) +-set(CBLAS_LIBRARIES @CBLASLIB@) - --unset(_CBLAS_PREFIX) -unset(_CBLAS_SELF_DIR) diff --git a/CBLAS/cmake/cblas-config-version.cmake.in b/CBLAS/cmake/cblas-config-version.cmake.in deleted file mode 100644 @@ -128,16 +92,16 @@ deleted file mode 100644 diff --git a/CBLAS/src/CMakeLists.txt b/CBLAS/src/CMakeLists.txt --- a/CBLAS/src/CMakeLists.txt +++ b/CBLAS/src/CMakeLists.txt -@@ -120,9 +120,5 @@ - VERSION ${LAPACK_VERSION} - SOVERSION ${LAPACK_MAJOR_VERSION} - ) --target_include_directories(cblas PUBLIC -- $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/../include> +@@ -172,9 +172,5 @@ + if(HAS_ATTRIBUTE_WEAK_SUPPORT) + target_compile_definitions(${CBLASLIB} PRIVATE HAS_ATTRIBUTE_WEAK_SUPPORT) + endif() +-target_include_directories(${CBLASLIB} PUBLIC +- $<BUILD_INTERFACE:${LAPACK_BINARY_DIR}/include> - $<INSTALL_INTERFACE:include> -) - target_link_libraries(cblas PRIVATE ${BLAS_LIBRARIES}) - lapack_install_library(cblas) + target_link_libraries(${CBLASLIB} PUBLIC ${BLAS_LIBRARIES}) + lapack_install_library(${CBLASLIB}) diff --git a/CMAKE/lapack-config-build.cmake.in b/CMAKE/lapack-config-build.cmake.in deleted file mode 100644 --- a/CMAKE/lapack-config-build.cmake.in @@ -146,7 +110,7 @@ deleted file mode 100644 -# Load lapack targets from the build tree if necessary. -set(_LAPACK_TARGET "@_lapack_config_build_guard_target@") -if(_LAPACK_TARGET AND NOT TARGET "${_LAPACK_TARGET}") -- include("@LAPACK_BINARY_DIR@/lapack-targets.cmake") +- include("@LAPACK_BINARY_DIR@/@LAPACKLIB@-targets.cmake") -endif() -unset(_LAPACK_TARGET) - @@ -168,7 +132,7 @@ deleted file mode 100644 -# Load lapack targets from the install tree if necessary. -set(_LAPACK_TARGET "@_lapack_config_install_guard_target@") -if(_LAPACK_TARGET AND NOT TARGET "${_LAPACK_TARGET}") -- include("${_LAPACK_SELF_DIR}/lapack-targets.cmake") +- include("${_LAPACK_SELF_DIR}/@LAPACKLIB@-targets.cmake") -endif() -unset(_LAPACK_TARGET) - @@ -184,11 +148,11 @@ deleted file mode 100644 diff --git a/CMakeLists.txt b/CMakeLists.txt --- a/CMakeLists.txt +++ b/CMakeLists.txt -@@ -112,11 +112,8 @@ - +@@ -155,11 +155,8 @@ + endif() # -------------------------------------------------- --set(LAPACK_INSTALL_EXPORT_NAME lapack-targets) +-set(LAPACK_INSTALL_EXPORT_NAME ${LAPACKLIB}-targets) - macro(lapack_install_library lib) install(TARGETS ${lib} @@ -196,30 +160,8 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} COMPONENT Development LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} COMPONENT RuntimeLibraries RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} COMPONENT RuntimeLibraries -@@ -155,21 +152,6 @@ - include(CheckLAPACKCompilerFlags) - CheckLAPACKCompilerFlags() +@@ -218,8 +215,9 @@ --# -------------------------------------------------- --# Check second function -- --include(CheckTimeFunction) --set(TIME_FUNC NONE ${TIME_FUNC}) --CHECK_TIME_FUNCTION(NONE TIME_FUNC) --CHECK_TIME_FUNCTION(INT_CPU_TIME TIME_FUNC) --CHECK_TIME_FUNCTION(EXT_ETIME TIME_FUNC) --CHECK_TIME_FUNCTION(EXT_ETIME_ TIME_FUNC) --CHECK_TIME_FUNCTION(INT_ETIME TIME_FUNC) --message(STATUS "--> Will use second_${TIME_FUNC}.f and dsecnd_${TIME_FUNC}.f as timing function.") -- --set(SECOND_SRC ${LAPACK_SOURCE_DIR}/INSTALL/second_${TIME_FUNC}.f) --set(DSECOND_SRC ${LAPACK_SOURCE_DIR}/INSTALL/dsecnd_${TIME_FUNC}.f) -- - # deprecated LAPACK and LAPACKE routines - option(BUILD_DEPRECATED "Build deprecated routines" OFF) - message(STATUS "Build deprecated routines: ${BUILD_DEPRECATED}") -@@ -193,8 +175,9 @@ - endif() # -------------------------------------------------- -# Subdirectories that need to be processed @@ -229,7 +171,7 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt # Check the usage of the user provided BLAS libraries if(BLAS_LIBRARIES) -@@ -205,113 +188,108 @@ +@@ -230,59 +228,41 @@ if(BLAS_FOUND) message(STATUS "--> BLAS supplied by user is WORKING, will use ${BLAS_LIBRARIES}.") else() @@ -250,7 +192,7 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt - message(STATUS "Using supplied NETLIB BLAS implementation") - add_subdirectory(BLAS) +elseif(BUILD_BLAS) - set(BLAS_LIBRARIES blas) + set(BLAS_LIBRARIES ${BLASLIB}) -else() - set(CMAKE_EXE_LINKER_FLAGS - "${CMAKE_EXE_LINKER_FLAGS} ${BLAS_LINKER_FLAGS}" @@ -300,21 +242,28 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt # Check the usage of the user provided or automatically found LAPACK libraries if(LAPACK_LIBRARIES) - include(CheckFortranFunctionExists) - set(CMAKE_REQUIRED_LIBRARIES ${LAPACK_LIBRARIES}) - # Check if new routine of 3.4.0 is in LAPACK_LIBRARIES -- CHECK_FORTRAN_FUNCTION_EXISTS("dgeqrt" LATESTLAPACK_FOUND) -+ CHECK_FORTRAN_FUNCTION_EXISTS("dgeqrt" LAPACK_FOUND) - unset(CMAKE_REQUIRED_LIBRARIES) -- if(LATESTLAPACK_FOUND) -+ if(LAPACK_FOUND) - message(STATUS "--> LAPACK supplied by user is WORKING, will use ${LAPACK_LIBRARIES}.") +@@ -293,27 +273,28 @@ + include(CheckFortranFunctionExists) + set(CMAKE_REQUIRED_LIBRARIES ${LAPACK_LIBRARIES}) + # Check if new routine of 3.4.0 is in LAPACK_LIBRARIES +- CHECK_FORTRAN_FUNCTION_EXISTS("dgeqrt" LATESTLAPACK_FOUND) ++ CHECK_FORTRAN_FUNCTION_EXISTS("dgeqrt" LAPACK_FOUND) + unset(CMAKE_REQUIRED_LIBRARIES) +- if(LATESTLAPACK_FOUND) ++ if(LAPACK_FOUND) + message(STATUS "--> LAPACK supplied by user is WORKING, will use ${LAPACK_LIBRARIES}.") + else() +- message(ERROR "--> LAPACK supplied by user is not WORKING or is older than LAPACK 3.4.0, CANNOT USE ${LAPACK_LIBRARIES}.") +- message(ERROR "--> Will use REFERENCE LAPACK (by default)") +- message(ERROR "--> Or Correct your LAPACK_LIBRARIES entry ") +- message(ERROR "--> Or Consider checking USE_OPTIMIZED_LAPACK") ++ message(SEND_ERROR "--> LAPACK supplied by user is NOT WORKING or is older than LAPACK 3.4.0, cannot use ${LAPACK_LIBRARIES}.") + endif() else() -- message(ERROR "--> LAPACK supplied by user is not WORKING or is older than LAPACK 3.4.0, CANNOT USE ${LAPACK_LIBRARIES}.") -- message(ERROR "--> Will use REFERENCE LAPACK (by default)") -- message(ERROR "--> Or Correct your LAPACK_LIBRARIES entry ") -- message(ERROR "--> Or Consider checking USE_OPTIMIZED_LAPACK") -+ message(SEND_ERROR "--> LAPACK supplied by user is NOT WORKING or is older than LAPACK 3.4.0, cannot use ${LAPACK_LIBRARIES}.") + message(STATUS "--> LAPACK supplied by user is ${LAPACK_LIBRARIES}.") + message(STATUS "--> CMake couldn't find a Fortran compiler, so it cannot check if the provided LAPACK library works.") +- set(LATESTLAPACK_FOUND TRUE) ++ set(LAPACK_FOUND TRUE) endif() -endif() @@ -326,24 +275,16 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt + find_package(LAPACK) + +elseif(BUILD_LAPACK) - set(LAPACK_LIBRARIES lapack) + set(LAPACK_LIBRARIES ${LAPACKLIB}) + set(LAPACK_FOUND TRUE) + + set(NEED_BLAS TRUE) -+ -+ # Check second function -+ include(CheckTimeFunction) -+ set(TIME_FUNC NONE ${TIME_FUNC}) -+ CHECK_TIME_FUNCTION(NONE TIME_FUNC) -+ CHECK_TIME_FUNCTION(INT_CPU_TIME TIME_FUNC) -+ CHECK_TIME_FUNCTION(EXT_ETIME TIME_FUNC) -+ CHECK_TIME_FUNCTION(EXT_ETIME_ TIME_FUNC) -+ CHECK_TIME_FUNCTION(INT_ETIME TIME_FUNC) -+ message(STATUS "--> Will use second_${TIME_FUNC}.f and dsecnd_${TIME_FUNC}.f as timing function.") -+ -+ set(SECOND_SRC ${LAPACK_SOURCE_DIR}/INSTALL/second_${TIME_FUNC}.f) -+ set(DSECOND_SRC ${LAPACK_SOURCE_DIR}/INSTALL/dsecnd_${TIME_FUNC}.f) -+ + + enable_language(Fortran) + +@@ -336,67 +317,38 @@ + set(DSECOND_SRC ${LAPACK_SOURCE_DIR}/INSTALL/dsecnd_${TIME_FUNC}.f) + add_subdirectory(SRC) -else() - set(CMAKE_EXE_LINKER_FLAGS @@ -363,9 +304,9 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt + add_subdirectory(TESTING) + endif() + -+ configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapack.pc.in ${CMAKE_CURRENT_BINARY_DIR}/lapack.pc @ONLY) ++ configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapack.pc.in ${CMAKE_CURRENT_BINARY_DIR}/${LAPACKLIB}.pc @ONLY) + install(FILES -+ ${CMAKE_CURRENT_BINARY_DIR}/lapack.pc ++ ${CMAKE_CURRENT_BINARY_DIR}/${LAPACKLIB}.pc + DESTINATION ${PKG_CONFIG_DIR} + COMPONENT Development + ) @@ -381,11 +322,37 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt option(LAPACKE_WITH_TMG "Build LAPACKE with tmglib routines" OFF) if(LAPACKE_WITH_TMG) - set(LAPACKE ON) +-endif() +- +-# TMGLIB +-# Cache export target +-set(LAPACK_INSTALL_EXPORT_NAME_CACHE ${LAPACK_INSTALL_EXPORT_NAME}) +-if(BUILD_TESTING OR LAPACKE_WITH_TMG) +- enable_language(Fortran) +- if(LATESTLAPACK_FOUND AND LAPACKE_WITH_TMG) +- set(CMAKE_REQUIRED_LIBRARIES ${LAPACK_LIBRARIES}) +- # Check if dlatms (part of tmg) is found +- include(CheckFortranFunctionExists) +- CHECK_FORTRAN_FUNCTION_EXISTS("dlatms" LAPACK_WITH_TMGLIB_FOUND) +- unset(CMAKE_REQUIRED_LIBRARIES) +- if(NOT LAPACK_WITH_TMGLIB_FOUND) +- # Build and install TMG as part of LAPACKE targets (as opposed to LAPACK +- # targets) +- set(LAPACK_INSTALL_EXPORT_NAME ${LAPACKELIB}-targets) +- endif() +- endif() +- add_subdirectory(TESTING/MATGEN) + set(BUILD_LAPACKE ON) endif() - if(BUILD_TESTING OR LAPACKE_WITH_TMG) #already included, avoid double inclusion - add_subdirectory(TESTING/MATGEN) - endif() +-# Reset export target +-set(LAPACK_INSTALL_EXPORT_NAME ${LAPACK_INSTALL_EXPORT_NAME_CACHE}) +-unset(LAPACK_INSTALL_EXPORT_NAME_CACHE) +- + +-#------------------------------------- +-# LAPACKE + # Include lapack.h and lapacke_mangling.h even if LAPACKE is not built + add_subdirectory(LAPACKE/include) -if(LAPACKE) +if(BUILD_LAPACKE) @@ -393,8 +360,12 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt add_subdirectory(LAPACKE) endif() -@@ -338,109 +316,12 @@ - _display_cpp_implementation_msg("LAPACK") +- + #------------------------------------- + # BLAS++ / LAPACK++ + option(BLAS++ "Build BLAS++" OFF) +@@ -446,111 +398,16 @@ + ExternalProject_Add_StepDependencies(lapackpp build blaspp ${BLAS_LIBRARIES} ${LAPACK_LIBRARIES}) endif() -# -------------------------------------------------- @@ -411,7 +382,7 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt -set(CPACK_PACKAGE_INSTALL_DIRECTORY "LAPACK") -if(WIN32 AND NOT UNIX) - # There is a bug in NSI that does not handle full unix paths properly. Make -- # sure there is at least one set of four (4) backlasshes. +- # sure there is at least one set of four (4) backslashes. - set(CPACK_NSIS_HELP_LINK "http:\\\\\\\\http://icl.cs.utk.edu/lapack-forum") - set(CPACK_NSIS_URL_INFO_ABOUT "http:\\\\\\\\www.netlib.org/lapack") - set(CPACK_NSIS_CONTACT "lapack@eecs.utk.edu") @@ -430,23 +401,19 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt -# -------------------------------------------------- - -if(NOT BLAS_FOUND) -- set(ALL_TARGETS ${ALL_TARGETS} blas) +- set(ALL_TARGETS ${ALL_TARGETS} ${BLASLIB}) -endif() - -if(NOT LATESTLAPACK_FOUND) -- set(ALL_TARGETS ${ALL_TARGETS} lapack) --endif() -- --if(BUILD_TESTING OR LAPACKE_WITH_TMG) -- set(ALL_TARGETS ${ALL_TARGETS} tmglib) +- set(ALL_TARGETS ${ALL_TARGETS} ${LAPACKLIB}) -endif() - -# Export lapack targets, not including lapacke, from the -# install tree, if any. -set(_lapack_config_install_guard_target "") -if(ALL_TARGETS) -- install(EXPORT lapack-targets -- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/lapack-${LAPACK_VERSION} +- install(EXPORT ${LAPACKLIB}-targets +- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/${LAPACKLIB}-${LAPACK_VERSION} - COMPONENT Development - ) - @@ -457,12 +424,16 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt - -# Include cblas in targets exported from the build tree. -if(CBLAS) -- set(ALL_TARGETS ${ALL_TARGETS} cblas) +- set(ALL_TARGETS ${ALL_TARGETS} ${CBLASLIB}) -endif() - -# Include lapacke in targets exported from the build tree. -if(LAPACKE) -- set(ALL_TARGETS ${ALL_TARGETS} lapacke) +- set(ALL_TARGETS ${ALL_TARGETS} ${LAPACKELIB}) +-endif() +- +-if(NOT LAPACK_WITH_TMGLIB_FOUND AND LAPACKE_WITH_TMG) +- set(ALL_TARGETS ${ALL_TARGETS} ${TMGLIB}) +# Neither user specified or optimized BLAS libraries can be used +if(NEED_BLAS AND NOT BLAS_FOUND) + message(FATAL_ERROR "--> No BLAS library found. Specify BLAS_LIBRARIES or enable USE_OPTIMIZED_BLAS or BUILD_BLAS.") @@ -471,7 +442,7 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt -# Export lapack and lapacke targets from the build tree, if any. -set(_lapack_config_build_guard_target "") -if(ALL_TARGETS) -- export(TARGETS ${ALL_TARGETS} FILE lapack-targets.cmake) +- export(TARGETS ${ALL_TARGETS} FILE ${LAPACKLIB}-targets.cmake) - - # Choose one of the lapack or lapacke targets to use as a guard - # for lapack-config.cmake to load targets from the build tree. @@ -480,84 +451,85 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt +if(NEED_LAPACK AND NOT LAPACK_FOUND) + message(FATAL_ERROR "--> No LAPACK library found. Specify LAPACK_LIBRARIES or enable USE_OPTIMIZED_LAPACK or BUILD_LAPACK.") endif() -- + -configure_file(${LAPACK_SOURCE_DIR}/CMAKE/lapack-config-build.cmake.in -- ${LAPACK_BINARY_DIR}/lapack-config.cmake @ONLY) +- ${LAPACK_BINARY_DIR}/${LAPACKLIB}-config.cmake @ONLY) - - --configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapack.pc.in ${CMAKE_CURRENT_BINARY_DIR}/lapack.pc @ONLY) +-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapack.pc.in ${CMAKE_CURRENT_BINARY_DIR}/${LAPACKLIB}.pc @ONLY) - install(FILES -- ${CMAKE_CURRENT_BINARY_DIR}/lapack.pc +- ${CMAKE_CURRENT_BINARY_DIR}/${LAPACKLIB}.pc - DESTINATION ${PKG_CONFIG_DIR} - COMPONENT Development - ) - -configure_file(${LAPACK_SOURCE_DIR}/CMAKE/lapack-config-install.cmake.in -- ${LAPACK_BINARY_DIR}/CMakeFiles/lapack-config.cmake @ONLY) +- ${LAPACK_BINARY_DIR}/CMakeFiles/${LAPACKLIB}-config.cmake @ONLY) - -include(CMakePackageConfigHelpers) -write_basic_package_version_file( -- ${LAPACK_BINARY_DIR}/lapack-config-version.cmake +- ${LAPACK_BINARY_DIR}/${LAPACKLIB}-config-version.cmake - VERSION ${LAPACK_VERSION} - COMPATIBILITY SameMajorVersion - ) - -install(FILES -- ${LAPACK_BINARY_DIR}/CMakeFiles/lapack-config.cmake -- ${LAPACK_BINARY_DIR}/lapack-config-version.cmake -- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/lapack-${LAPACK_VERSION} +- ${LAPACK_BINARY_DIR}/CMakeFiles/${LAPACKLIB}-config.cmake +- ${LAPACK_BINARY_DIR}/${LAPACKLIB}-config-version.cmake +- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/${LAPACKLIB}-${LAPACK_VERSION} - COMPONENT Development - ) -- -\ No newline at end of file + if (LAPACK++) + install( + DIRECTORY "${LAPACK_BINARY_DIR}/lib/" diff --git a/LAPACKE/CMakeLists.txt b/LAPACKE/CMakeLists.txt --- a/LAPACKE/CMakeLists.txt +++ b/LAPACKE/CMakeLists.txt @@ -1,8 +1,6 @@ - message(STATUS "LAPACKE enable") + message(STATUS "LAPACKE enabled") enable_language(C) --set(LAPACK_INSTALL_EXPORT_NAME lapacke-targets) +-set(LAPACK_INSTALL_EXPORT_NAME ${LAPACKELIB}-targets) - - # Create a header file lapacke_mangling.h for the routines called in my C programs - include(FortranCInterface) - ## Ensure that the fortran compiler and c compiler specified are compatible -@@ -79,14 +77,6 @@ + include_directories(include ${LAPACK_BINARY_DIR}/include) + add_subdirectory(src) + add_subdirectory(utils) +@@ -74,14 +72,6 @@ VERSION ${LAPACK_VERSION} SOVERSION ${LAPACK_MAJOR_VERSION} ) --target_include_directories(lapacke PUBLIC -- $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include> +-target_include_directories(${LAPACKELIB} PUBLIC +- $<BUILD_INTERFACE:${LAPACK_BINARY_DIR}/include> - $<INSTALL_INTERFACE:include> -) -if(WIN32 AND NOT UNIX) -- target_compile_definitions(lapacke PUBLIC HAVE_LAPACK_CONFIG_H LAPACK_COMPLEX_STRUCTURE) +- target_compile_definitions(${LAPACKELIB} PUBLIC HAVE_LAPACK_CONFIG_H LAPACK_COMPLEX_STRUCTURE) - message(STATUS "Windows BUILD") -endif() if(LAPACKE_WITH_TMG) - target_link_libraries(lapacke PRIVATE tmglib) -@@ -111,22 +101,3 @@ + target_link_libraries(${LAPACKELIB} PRIVATE ${TMGLIB}) +@@ -106,22 +96,3 @@ DESTINATION ${PKG_CONFIG_DIR} COMPONENT Development ) - -configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cmake/lapacke-config-version.cmake.in -- ${LAPACK_BINARY_DIR}/lapacke-config-version.cmake @ONLY) +- ${LAPACK_BINARY_DIR}/${LAPACKELIB}-config-version.cmake @ONLY) -configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cmake/lapacke-config-build.cmake.in -- ${LAPACK_BINARY_DIR}/lapacke-config.cmake @ONLY) +- ${LAPACK_BINARY_DIR}/${LAPACKELIB}-config.cmake @ONLY) - -configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cmake/lapacke-config-install.cmake.in -- ${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/lapacke-config.cmake @ONLY) +- ${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/${LAPACKELIB}-config.cmake @ONLY) -install(FILES -- ${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/lapacke-config.cmake -- ${LAPACK_BINARY_DIR}/lapacke-config-version.cmake -- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/lapacke-${LAPACK_VERSION} +- ${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/${LAPACKELIB}-config.cmake +- ${LAPACK_BINARY_DIR}/${LAPACKELIB}-config-version.cmake +- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/${LAPACKELIB}-${LAPACK_VERSION} - COMPONENT Development - ) - --install(EXPORT lapacke-targets -- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/lapacke-${LAPACK_VERSION} +-install(EXPORT ${LAPACKELIB}-targets +- DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/${LAPACKELIB}-${LAPACK_VERSION} - COMPONENT Development - ) diff --git a/LAPACKE/cmake/lapacke-config-build.cmake.in b/LAPACKE/cmake/lapacke-config-build.cmake.in @@ -570,8 +542,8 @@ deleted file mode 100644 -find_package(LAPACK NO_MODULE) - -# Load lapack targets from the build tree, including lapacke targets. --if(NOT TARGET lapacke) -- include("@LAPACK_BINARY_DIR@/lapack-targets.cmake") +-if(NOT TARGET @LAPACKELIB@) +- include("@LAPACK_BINARY_DIR@/@LAPACKLIB@-targets.cmake") -endif() - -# Hint for project building against lapack @@ -581,37 +553,33 @@ deleted file mode 100644 -set(LAPACKE_INCLUDE_DIRS "@LAPACK_BINARY_DIR@/include") - -# Report lapacke libraries. --set(LAPACKE_LIBRARIES lapacke ${LAPACK_LIBRARIES}) +-set(LAPACKE_LIBRARIES @LAPACKELIB@ ${LAPACK_LIBRARIES}) diff --git a/LAPACKE/cmake/lapacke-config-install.cmake.in b/LAPACKE/cmake/lapacke-config-install.cmake.in deleted file mode 100644 --- a/LAPACKE/cmake/lapacke-config-install.cmake.in +++ /dev/null -@@ -1,26 +0,0 @@ +@@ -1,22 +0,0 @@ -# Compute locations from <prefix>/@{LIBRARY_DIR@/cmake/lapacke-<v>/<self>.cmake -get_filename_component(_LAPACKE_SELF_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH) --get_filename_component(_LAPACKE_PREFIX "${_LAPACKE_SELF_DIR}" PATH) --get_filename_component(_LAPACKE_PREFIX "${_LAPACKE_PREFIX}" PATH) --get_filename_component(_LAPACKE_PREFIX "${_LAPACKE_PREFIX}" PATH) - -# Load the LAPACK package with which we were built. --set(LAPACK_DIR "${_LAPACKE_PREFIX}/@CMAKE_INSTALL_LIBDIR@/cmake/lapack-@LAPACK_VERSION@") +-set(LAPACK_DIR "@CMAKE_INSTALL_FULL_LIBDIR@/cmake/@LAPACKLIB@-@LAPACK_VERSION@") -find_package(LAPACK NO_MODULE) - -# Load lapacke targets from the install tree. --if(NOT TARGET lapacke) -- include(${_LAPACKE_SELF_DIR}/lapacke-targets.cmake) +-if(NOT TARGET @LAPACKELIB@) +- include(${_LAPACKE_SELF_DIR}/@LAPACKELIB@-targets.cmake) -endif() - -# Hint for project building against lapack -set(LAPACKE_Fortran_COMPILER_ID ${LAPACK_Fortran_COMPILER_ID}) - -# Report lapacke header search locations. --set(LAPACKE_INCLUDE_DIRS ${_LAPACKE_PREFIX}/include) +-set(LAPACKE_INCLUDE_DIRS @CMAKE_INSTALL_FULL_INCLUDEDIR@) - -# Report lapacke libraries. --set(LAPACKE_LIBRARIES lapacke ${LAPACK_LIBRARIES}) +-set(LAPACKE_LIBRARIES @LAPACKELIB@ ${LAPACK_LIBRARIES}) - --unset(_LAPACKE_PREFIX) -unset(_LAPACKE_SELF_DIR) diff --git a/LAPACKE/cmake/lapacke-config-version.cmake.in b/LAPACKE/cmake/lapacke-config-version.cmake.in deleted file mode 100644 @@ -626,3 +594,20 @@ deleted file mode 100644 - endif() -endif() - +diff --git a/LAPACKE/include/CMakeLists.txt b/LAPACKE/include/CMakeLists.txt +--- a/LAPACKE/include/CMakeLists.txt ++++ b/LAPACKE/include/CMakeLists.txt +@@ -1,5 +1,5 @@ + set(LAPACKE_INCLUDE lapack.h) +-IF(LAPACKE) ++IF(BUILD_LAPACKE) + list(APPEND LAPACKE_INCLUDE lapacke.h lapacke_config.h lapacke_utils.h) + endif() + +@@ -23,4 +23,4 @@ + message(WARNING "Reverting to pre-defined include/lapacke_mangling.h") + configure_file(lapacke_mangling_with_flags.h.in + ${LAPACK_BINARY_DIR}/include/lapacke_mangling.h) +-endif() +\ No newline at end of file ++endif() diff --git a/academic/latex2html/latex2html.SlackBuild b/academic/latex2html/latex2html.SlackBuild index 31b157c4bb..11ba0f8d59 100644 --- a/academic/latex2html/latex2html.SlackBuild +++ b/academic/latex2html/latex2html.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for latex2html @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=latex2html -VERSION=${VERSION:-2019.2} +VERSION=${VERSION:-2020} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then @@ -36,7 +39,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -80,7 +90,9 @@ CXXFLAGS="$SLKCFLAGS" \ --with-perl=/usr/bin/perl \ --enable-eps \ --enable-gif \ - --enable-png \ + --enable-svg \ + --enable-pk \ + --enable-pipes \ --build=$ARCH-slackware-linux \ --host=$ARCH-slackware-linux @@ -101,4 +113,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/latex2html/latex2html.info b/academic/latex2html/latex2html.info index b732075636..199a5829f2 100644 --- a/academic/latex2html/latex2html.info +++ b/academic/latex2html/latex2html.info @@ -1,8 +1,8 @@ PRGNAM="latex2html" -VERSION="2019.2" +VERSION="2020" HOMEPAGE="http://www.latex2html.org" -DOWNLOAD="https://github.com/latex2html/latex2html/archive/v2019.2/latex2html-2019.2.tar.gz" -MD5SUM="e9ca34903ac23a6f51385f05fa63c6eb" +DOWNLOAD="https://github.com/latex2html/latex2html/archive/v2020/latex2html-2020.tar.gz" +MD5SUM="d5e2d765ed2bb4d52bd7331a6420f5be" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/latex2html/manual.pdf b/academic/latex2html/manual.pdf Binary files differindex 28a5159b38..699a2ce464 100644 --- a/academic/latex2html/manual.pdf +++ b/academic/latex2html/manual.pdf diff --git a/academic/ldl/README b/academic/ldl/README index b3628fc188..ce58f1983d 100644 --- a/academic/ldl/README +++ b/academic/ldl/README @@ -1,11 +1,12 @@ LDL is a set of concise routines for factorizing symmetric positive-definite sparse matrices, with some applicability to symmetric -indefinite matrices. Its primary purpose is to illustrate much of the -basic theory of sparse matrix algorithms in as concise a code as possible, -including an elegant new method of sparse symmetric factorization that -computes the factorization row-by-row but stores it column-by-column. +indefinite matrices. Its primary purpose is to illustrate much of +the basic theory of sparse matrix algorithms in as concise a code +as possible, including an elegant new method of sparse symmetric +factorization that computes the factorization row-by-row but stores it +column-by-column. This package is part of SuiteSparse. -AMD is an optional dependency and will be used if found. -It is primarily used for this package's test suite. +AMD is an optional dependency and will be used if found. It is +primarily used for this package's test suite. diff --git a/academic/ldl/ldl.SlackBuild b/academic/ldl/ldl.SlackBuild index b4652d420f..d7b79fb194 100644 --- a/academic/ldl/ldl.SlackBuild +++ b/academic/ldl/ldl.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for LDL -# Copyright 2013-2020 Kyle Guinn <elyk03@gmail.com> +# Copyright 2013-2021 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,13 +22,16 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=ldl SRCNAM=SuiteSparse SUBDIR=LDL VERSION=${VERSION:-2.2.6} -SRCVER=${SRCVER:-5.6.0} -BUILD=${BUILD:-6} +SRCVER=${SRCVER:-5.8.1} +BUILD=${BUILD:-7} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$(uname -m)" in @@ -38,15 +41,22 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM-$VERSION +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="README.txt Doc/ChangeLog Doc/License.txt Doc/lesser.txt" -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" @@ -108,4 +118,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/ldl/ldl.info b/academic/ldl/ldl.info index 5676d5bd4f..9274c84ac9 100644 --- a/academic/ldl/ldl.info +++ b/academic/ldl/ldl.info @@ -1,8 +1,8 @@ PRGNAM="ldl" VERSION="2.2.6" HOMEPAGE="http://faculty.cse.tamu.edu/davis/suitesparse.html" -DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.6.0/SuiteSparse-5.6.0.tar.gz" -MD5SUM="af8b97cbded4cd5c6672e878bc0c37c2" +DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.8.1/SuiteSparse-5.8.1.tar.gz" +MD5SUM="c414679bbc9432a3def01b31ad921140" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="suitesparseconfig" diff --git a/academic/libghemical/libghemical.SlackBuild b/academic/libghemical/libghemical.SlackBuild index 83caa1c70b..21465899c3 100644 --- a/academic/libghemical/libghemical.SlackBuild +++ b/academic/libghemical/libghemical.SlackBuild @@ -1,29 +1,39 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for libghemical # Written by Daniil Bratashov (dn2010@gmail.com) +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=libghemical VERSION=${VERSION:-3.0.0} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -78,8 +88,10 @@ cp -a \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/libqalculate/README b/academic/libqalculate/README deleted file mode 100644 index d67d9a7bd8..0000000000 --- a/academic/libqalculate/README +++ /dev/null @@ -1,4 +0,0 @@ -Qalculate! is a multi-purpose desktop calculator for GNU/Linux (and Mac OS). It -is small and simple to use but with much power and versatility underneath. -Features include customizable functions, units, arbitrary precision, plotting, -and a user-friendly interface (GTK+ and CLI). diff --git a/academic/libqalculate/libqalculate.info b/academic/libqalculate/libqalculate.info deleted file mode 100644 index 0ff5260bd8..0000000000 --- a/academic/libqalculate/libqalculate.info +++ /dev/null @@ -1,10 +0,0 @@ -PRGNAM="libqalculate" -VERSION="3.4.0" -HOMEPAGE="http://qalculate.github.io/" -DOWNLOAD="https://github.com/Qalculate/libqalculate/releases/download/v3.4.0/libqalculate-3.4.0.tar.gz" -MD5SUM="71374cfffa41ccb7721543924dea3f8d" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="" -MAINTAINER="Larry Hajali" -EMAIL="larryhaja[at]gmail[dot]com" diff --git a/academic/libqalculate/slack-desc b/academic/libqalculate/slack-desc deleted file mode 100644 index 84c06b2451..0000000000 --- a/academic/libqalculate/slack-desc +++ /dev/null @@ -1,19 +0,0 @@ -# HOW TO EDIT THIS FILE: -# The "handy ruler" below makes it easier to edit a package description. -# Line up the first '|' above the ':' following the base package name, and -# the '|' on the right side marks the last column you can put a character in. -# You must make exactly 11 lines for the formatting to be correct. It's also -# customary to leave one space after the ':' except on otherwise blank lines. - - |-----handy-ruler------------------------------------------------------| -libqalculate: libqalculate (desktop caculator library) -libqalculate: -libqalculate: Qalculate! is a multi-purpose desktop calculator for GNU/Linux (and -libqalculate: Mac OS). It is small and simple to use but with much power and -libqalculate: versatility underneath. Features include customizable functions, -libqalculate: units, arbitrary precision, plotting, and a user-friendly interface -libqalculate: (GTK+ and CLI). -libqalculate: -libqalculate: Homepage: http://qalculate.github.io/ -libqalculate: -libqalculate: diff --git a/academic/link-grammar/README b/academic/link-grammar/README index f985d7cb61..1250ac3145 100644 --- a/academic/link-grammar/README +++ b/academic/link-grammar/README @@ -1,6 +1,6 @@ -The Link Grammar Parser is a syntactic parser of English, based on link -grammar, an original theory of English syntax. Given a sentence, the system -assigns to it a syntactic structure, which consists of a set of labeled links -connecting pairs of words. The parser also produces a "constituent" (Penn -tree-bank style phrase tree) representation of a sentence (showing noun -phrases, verb phrases, etc.). +The Link Grammar Parser is a syntactic parser of English, based on +link grammar, an original theory of English syntax. Given a sentence, +the system assigns to it a syntactic structure, which consists of a set +of labeled links connecting pairs of words. The parser also produces a +"constituent" (Penn tree-bank style phrase tree) representation of a +sentence (showing noun phrases, verb phrases, etc.). diff --git a/academic/link-grammar/link-grammar.SlackBuild b/academic/link-grammar/link-grammar.SlackBuild index ad94858ddd..a7686f7c7a 100644 --- a/academic/link-grammar/link-grammar.SlackBuild +++ b/academic/link-grammar/link-grammar.SlackBuild @@ -1,30 +1,40 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for link-grammar # Written by Michael Gabilondo <mgabilo{at}gmail{dot}com> # This work is in the public domain +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=link-grammar VERSION=${VERSION:-4.8.0} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -78,8 +88,10 @@ find $PKG | xargs file | grep -e "executable" -e "shared object" | grep ELF \ mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/link-grammar/link-grammar.info b/academic/link-grammar/link-grammar.info index ce4fe11b19..5e493b4686 100644 --- a/academic/link-grammar/link-grammar.info +++ b/academic/link-grammar/link-grammar.info @@ -5,6 +5,6 @@ DOWNLOAD="http://www.abisource.com/downloads/link-grammar/4.8.0/link-grammar-4.8 MD5SUM="218a2ee5ffed258bc52a0718811ca66e" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="apache-ant jdk" +REQUIRES="apache-ant zulu-openjdk8" MAINTAINER="Michael Gabilondo" EMAIL="mgabilo{at}gmail{dot}com" diff --git a/academic/locarna/locarna.SlackBuild b/academic/locarna/locarna.SlackBuild index fdeaea36f9..1e84cfa434 100644 --- a/academic/locarna/locarna.SlackBuild +++ b/academic/locarna/locarna.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for locarna -# Copyright 2019 Rob van Nues <sborg63@disroot.org> +# Copyright 2019-2021 Rob van Nues <sborg63@disroot.org> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,11 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) PRGNAM=locarna VERSION=${VERSION:-1.9.2.3} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -36,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -100,8 +109,10 @@ cp -a \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/loggerpro/README b/academic/loggerpro/README deleted file mode 100644 index 8eba8d50b0..0000000000 --- a/academic/loggerpro/README +++ /dev/null @@ -1,12 +0,0 @@ -Vernier LoggerPro (data-collection and analysis software) - -Vernier Software & Technology is the leader in educational data -collection technology. Since 1981, we have developed affordable, -award-winning interfaces, sensors, software, and standards-based -curriculum. This package installs files to allow either LoggerPro -or LoggerLite to access devices. - -Sadly, this package installs two symlinks into /usr/local/share/ -and one symlink into /usr/local/bin/ - the /usr/local/ directory -is hardcoded into the LoggerPro files somewhere, and I've not -been able to figure out where or how to correct it... diff --git a/academic/loggerpro/loggerpro.SlackBuild b/academic/loggerpro/loggerpro.SlackBuild deleted file mode 100644 index bef9968019..0000000000 --- a/academic/loggerpro/loggerpro.SlackBuild +++ /dev/null @@ -1,156 +0,0 @@ -#!/bin/sh - -# Slackware build script for loggerpro - -# Copyright 2016 Robby Workman, Tuscaloosa, Alabama, USA -# All rights reserved. -# -# Redistribution and use of this script, with or without modification, is -# permitted provided that the following conditions are met: -# -# 1. Redistributions of this script must retain the above copyright -# notice, this list of conditions and the following disclaimer. -# -# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED -# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF -# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO -# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, -# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, -# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; -# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, -# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR -# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF -# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - -PRGNAM=loggerpro -VERSION=${VERSION:-3.8.4.6} -BUILD=${BUILD:-1} -TAG=${TAG:-_SBo} - -if [ -z "$ARCH" ]; then - case "$( uname -m )" in - i?86) ARCH=i586 ;; - arm*) ARCH=arm ;; - *) ARCH=$( uname -m ) ;; - esac -fi - -CWD=$(pwd) -TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM -OUTPUT=${OUTPUT:-/tmp} - -if [ "$ARCH" = "i586" ]; then - SHORTARCH="32" - LIBDIRSUFFIX="" -elif [ "$ARCH" = "i686" ]; then - SHORTARCH="32" - LIBDIRSUFFIX="" -elif [ "$ARCH" = "x86_64" ]; then - SHORTARCH="64" - LIBDIRSUFFIX="64" -else - SHORTARCH="32" - LIBDIRSUFFIX="" -fi - -set -e - -rm -rf $PKG -mkdir -p $TMP $PKG $OUTPUT -cd $TMP -rm -rf $PRGNAM-$VERSION -tar xvf $CWD/LPL-$(printf $VERSION | tr -d .)-$SHORTARCH.tar.gz -ar -x vstdrivers_*.deb -tar xf data.tar.xz -C $PKG -ar -x vstloggerpro_${VERSION}_*.deb -tar xf data.tar.xz -C $PKG - -chown -R root:root $PKG -find -L $PKG \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; - -# /etc/udev goes to /lib/udev -mv $PKG/etc $PKG/lib - -mv $PKG/usr/local/bin/* $PKG/usr/bin - -# Copy over icons first since their presence won't allow a clean move -cp -a $PKG/usr/local/share/icons $PKG/usr/share -rm -rf $PKG/usr/local/share/icons - -# Now move everything else -mv $PKG/usr/local/share/* $PKG/usr/share - -# Move the docs over -mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -mv $PKG/usr/share/doc/* $PKG/usr/doc/$PRGNAM-$VERSION -cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild -rmdir $PKG/usr/share/doc - -# Kill the /usr/local tree and remove empty /usr/sbin dir -rm -rf $PKG/usr/local -rmdir $PKG/usr/sbin - -# Fix libdir -[ "$LIBDIRSUFFIX" = "64" ] && mv $PKG/usr/lib $PKG/usr/lib${LIBDIRSUFFIX} - -# Create library symlinks -ln -s libGoIO.so.2.0.53 $PKG/usr/lib${LIBDIRSUFFIX}/libGoIO.so.2 -ln -s libGoIO.so.2 $PKG/usr/lib${LIBDIRSUFFIX}/libGoIO.so -ln -s libNGIO.so.1.0.0 $PKG/usr/lib${LIBDIRSUFFIX}/libNGIO.so.1 -ln -s libNGIO.so.1 $PKG/usr/lib${LIBDIRSUFFIX}/libNGIO.so - -# Nope, we're not writing to /usr during runtime -mkdir -p \ - $PKG/var/lib/LoggerPro/VSTSupport \ - $PKG/var/lib/LoggerPro/tmp \ - $PKG/var/lib/LoggerLite/tmp -rm -r \ - $PKG/usr/share/LoggerPro/Linux/VSTSupport \ - $PKG/usr/share/LoggerPro/Linux/tmp \ - $PKG/usr/share/LoggerLite/Linux/tmp -ln -s /var/lib/LoggerPro/VSTSupport $PKG/usr/share/LoggerPro/Linux/VSTSupport -ln -s /var/lib/LoggerPro/tmp $PKG/usr/share/LoggerPro/Linux/tmp -ln -s /var/lib/LoggerLite/tmp $PKG/usr/share/LoggerLite/Linux/tmp -chmod 1777 \ - $PKG/var/lib/LoggerPro/VSTSupport \ - $PKG/var/lib/LoggerPro/tmp \ - $PKG/var/lib/LoggerLite/tmp - -# The below points were mentioned to Vernier in their forum: -# http://www.vernier.com/forums/logger-pro-linux/404-packaging-improvements/ -# -# /usr/share/LoggerPro/Experiments/ will remain 0755; only the sysadmin -# should be writing to this. TODO: Contact Vernier about this. -# Thinking to myself here... Would be nice to have a three-tier system maybe, -# e.g. /usr/share/LoggerPro/Experiments/, then check a sysadmin configured -# location (e.g. /data/common/LoggerPro/Experiments/ is something like I -# would have), then $HOME, e.g. $HOME/LoggerPro/Experiments/, with all -# three (if set) being check and the contents merged, and each level -# overrides (e.g. same-named files) the previous levels. -# While I'm writing, for the love of sanity, PLEASE use /tmp or /var/tmp -# or some other place, or at least make it configurable in a systemwide -# config file at e.g. /etc/Vernier/LoggerPro.conf (this would be a good -# place to make the other stuff above configurable too) -# Note the move of udev files to /lib/udev instead of /etc/udev - -# Work around the hardcoding of /usr/local (I can't figure out where it's -# hardcoded or thus how to fix it) -mkdir -p $PKG/usr/local/bin $PKG/usr/local/share -ln -s /usr/bin/loggerpro $PKG/usr/local/bin -ln -s /usr/share/LoggerPro $PKG/usr/local/share -ln -s /usr/share/LoggerLite $PKG/usr/local/share - -find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ - | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true - -mkdir -p $PKG/install -cat $CWD/slack-desc > $PKG/install/slack-desc -cat $CWD/doinst.sh > $PKG/install/doinst.sh - -cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} diff --git a/academic/loggerpro/loggerpro.info b/academic/loggerpro/loggerpro.info deleted file mode 100644 index 66f1151f05..0000000000 --- a/academic/loggerpro/loggerpro.info +++ /dev/null @@ -1,10 +0,0 @@ -PRGNAM="loggerpro" -VERSION="3.8.4.6" -HOMEPAGE="https://www.vernier.com/forums/logger-pro-linux/" -DOWNLOAD="http://www.vernier.com/files/downloads/LPL-3846-32.tar.gz" -MD5SUM="5b088d162258656dd2b83163fd968352" -DOWNLOAD_x86_64="http://www.vernier.com/files/downloads/LPL-3846-64.tar.gz" -MD5SUM_x86_64="3c58a64a2e669a532b119da995c92cb7" -REQUIRES="" -MAINTAINER="Robby Workman" -EMAIL="rworkman@slackbuilds.org" diff --git a/academic/louvain-community/README b/academic/louvain-community/README new file mode 100644 index 0000000000..8a989dc3f4 --- /dev/null +++ b/academic/louvain-community/README @@ -0,0 +1,98 @@ +[License: LGPL v3] [build] + +Multi-criteria community detection library + +This library makes the Louvain community detection system +significantly easier to use. Example code: + + #include "louvain_communities/louvain_communities.h" #include +<iostream> + + int main(int /*argc*/, char** /*argv*/) { LouvainC::Communities +graph; + + //First community graph.add_edge(1, 2, 2L); +graph.add_edge(1, 3, 2L); graph.add_edge(1, 4, 2L); +graph.add_edge(2, 3, 2L); graph.add_edge(2, 4, 2L); +graph.add_edge(3, 4, 2L); + + //Second community graph.add_edge(4, 5, 2L); +graph.add_edge(4, 6, 2L); graph.add_edge(4, 7, 2L); +graph.add_edge(5, 6, 2L); graph.add_edge(5, 7, 2L); +graph.add_edge(6, 7, 2L); + + //Weak connection between 1st and 2nd communities +graph.add_edge(1, 4, 0.1L); + + //Calculate communities gplain.calculate(true); + + //Get community mapping auto r = gplain.get_mapping(); +for(auto& vert_to_comm: r) { std::cout << "Vertext " << +vert_to_comm.first << " is in community " << vert_to_comm.second << +std::endl; } } + +How to build + +To build: + + git clone https://github.com/meelgroup/louvain-community cd +louvain-community mkdir build && cd build cmake .. make -j4 sudo +make install + +In case you are going to use the system in another cmake based +project, you don’t even need to install. In these cases, you can +look for the library in your CMakeLists.txt file via: + + find_package(louvain_communities CONFIG) if +(louvain_communities_FOUND) message(STATUS "Found Louvain +Communities library") message(STATUS "Louvain Communities dynamic +lib: ${LOUVAIN_COMMUNITIES_LIBRARIES}") message(STATUS "Louvain +Communities include dirs: ${LOUVAIN_COMMUNITIES_INCLUDE_DIRS}") +else() message(FATAL_ERROR "Cannot find Louvain Communities +libraries. Please install it! Exiting.") endif() + +To compile a static library simply do: + + git clone https://github.com/meelgroup/louvain-community cd +louvain-community mkdir build && cd build cmake -DSTATICCOMPILE=ON +.. make -j4 sudo make install + +Testing + +To test: + + pip install python-louvain + + git clone https://github.com/jlguillaume/louvain cd louvain make +-j4 + + git clone https://github.com/meelgroup/louvain-community cd +louvain-community mkdir build && cd build ln -s ../scritps/* . ln +-s ../../louvain/louvain . ./mytest.py 50-10-9-q.cnf.gz.no_w.cnf +awk '{print "gplain.add_edge(" $1 ", " $2 ", " $3 "L);"}' graph.txt +> ../src/mygraph.cpp cmake -DENABLE_TESTING=ON .. make -j4 +> ./test.sh 50-10-9-q.cnf.gz.no_w.cnf + +To check how well the communities fit a graph generated via VIG +(“Variable Incidence Graphâ€) graph-generation from a DIMACS CNF and +a layout engine using the spring method: + + pip install python-louvain git clone +https://github.com/meelgroup/louvain-community cd louvain-community +mkdir build && cd build ln -s ../scritps/* . ./mytest.py +50-10-9-q.cnf.gz.no_w.cnf --draw + +References + +Based on Community Detection “Louvainâ€, version 0.3, from +SourceForge + +Based on the article “Fast unfolding of community hierarchies in +large networks†Copyright (C) 2008 V. Blondel, J.-L. Guillaume, R. +Lambiotte, E. Lefebvre + +And based on the article Copyright (C) 2013 R. Campigotto, P. Conde +Céspedes, J.-L. Guillaume + +Authors: E. Lefebvre, adapted by J.-L. Guillaume and R. Campigotto, +Mate Soos diff --git a/academic/louvain-community/louvain-community.SlackBuild b/academic/louvain-community/louvain-community.SlackBuild new file mode 100644 index 0000000000..1afcd20183 --- /dev/null +++ b/academic/louvain-community/louvain-community.SlackBuild @@ -0,0 +1,110 @@ +#!/bin/bash + +# Slackware build script for louvain-community + +# Copyright 2024 Caterino Tommaso, T.O.P. USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=louvain-community +VERSION=${VERSION:-681a711} +FULLHASH=${FULLHASH:-681a711a530ded0b25af72ee4881d453a80ac8ac} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +elif [ "$ARCH" = "aarch64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$FULLHASH +tar xvf $CWD/$PRGNAM-$FULLHASH.tar.gz +cd $PRGNAM-$FULLHASH +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \+ -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \+ + +mkdir -p build +cd build + cmake \ + -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DLIB_SUFFIX=${LIBDIRSUFFIX} \ + -DCMAKE_BUILD_TYPE=Release .. + make + make install/strip DESTDIR=$PKG +cd .. + +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +find $PKG -name perllocal.pod -o -name ".packlist" -o -name "*.bs" | xargs rm -f || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + LICENSE.txt README.md \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/louvain-community/louvain-community.info b/academic/louvain-community/louvain-community.info new file mode 100644 index 0000000000..df40a89ce7 --- /dev/null +++ b/academic/louvain-community/louvain-community.info @@ -0,0 +1,10 @@ +PRGNAM="louvain-community" +VERSION="681a711" +HOMEPAGE="https://github.com/meelgroup/louvain-community" +DOWNLOAD="https://github.com/meelgroup/louvain-community/archive/681a711/louvain-community-681a711a530ded0b25af72ee4881d453a80ac8ac.tar.gz" +MD5SUM="f148a5a439ccf5c47a9795c31350b467" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Caterino Tommaso, T.O.P." +EMAIL="aNOlan_aversa@lavabiSPAMt.com (remove NO and SPAM)" diff --git a/academic/louvain-community/slack-desc b/academic/louvain-community/slack-desc new file mode 100644 index 0000000000..a4fd5d8f82 --- /dev/null +++ b/academic/louvain-community/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +louvain-community: louvain-community (Louvain Community Detection Library) +louvain-community: +louvain-community: This graph algorithms library finds communities in networks. +louvain-community: +louvain-community: It is a requirement for cryptominisat's advanced statistics option. +louvain-community: +louvain-community: +louvain-community: +louvain-community: +louvain-community: +louvain-community: diff --git a/academic/lpsolve/lpsolve.SlackBuild b/academic/lpsolve/lpsolve.SlackBuild index a4cfd84c19..844d7a5aca 100644 --- a/academic/lpsolve/lpsolve.SlackBuild +++ b/academic/lpsolve/lpsolve.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for lp_solve @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=lpsolve VERSION=${VERSION:-5.5.2.5} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -102,4 +112,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/mafft/mafft.SlackBuild b/academic/mafft/mafft.SlackBuild index 77bac2a01d..746a5978c3 100644 --- a/academic/mafft/mafft.SlackBuild +++ b/academic/mafft/mafft.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for mafft -# Copyright 2013-2020 Petar Petrov slackalaxy@gmail.com +# Copyright 2013-2023 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=mafft -VERSION=${VERSION:-7.453} +VERSION=${VERSION:-7.520} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -59,9 +69,9 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $PRGNAM-$VERSION-with-extensions -tar xvf $CWD/$PRGNAM-$VERSION-with-extensions-src.tgz -cd $PRGNAM-$VERSION-with-extensions +rm -rf $PRGNAM-v${VERSION} +tar xvf $CWD/$PRGNAM-v${VERSION}.tar.gz +cd $PRGNAM-v${VERSION} chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -124,7 +134,7 @@ cp -a test $PKG/usr/share/$PRGNAM mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - license readme \ + license license.extensions README.md \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References @@ -136,4 +146,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/mafft/mafft.info b/academic/mafft/mafft.info index 4fae8a0354..5b589bcf11 100644 --- a/academic/mafft/mafft.info +++ b/academic/mafft/mafft.info @@ -1,8 +1,8 @@ PRGNAM="mafft" -VERSION="7.453" +VERSION="7.520" HOMEPAGE="https://mafft.cbrc.jp/alignment/software/" -DOWNLOAD="https://mafft.cbrc.jp/alignment/software/mafft-7.453-with-extensions-src.tgz" -MD5SUM="749a7867831482a75b1a728928ec2a1a" +DOWNLOAD="https://gitlab.com/sysimm/mafft/-/archive/v7.520/mafft-v7.520.tar.gz" +MD5SUM="8d53ef6ecf6822d00c9d356f59f5aabe" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/magic/magic.SlackBuild b/academic/magic/magic.SlackBuild index 31127e136a..73f7640cfc 100644 --- a/academic/magic/magic.SlackBuild +++ b/academic/magic/magic.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for magic # Written by Mauricio Martinez <eigenfilter {at} gmail [dot] com> @@ -14,10 +14,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=magic VERSION=${VERSION:-8.0.211} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -27,7 +30,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -89,4 +99,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/mathics/README b/academic/mathics/README index 89bae8e2a1..59741fe499 100644 --- a/academic/mathics/README +++ b/academic/mathics/README @@ -1,9 +1,22 @@ -Mathics is a free, light-weight alternative to Mathematica. Mathics is -a general-purpose online computer algebra system featuring Mathematica- -compatible syntax and functions. It is backed by highly extensible -Python code, relying on SymPy for most mathematical tasks. +Mathics is a general-purpose computer algebra system (CAS). It is an +open-source alternative to Mathematica. It is free both as in "free +beer" and as in "freedom". +The home page of Mathics is https://mathics.org. -Optional Dependency +Installing and Running +See read the docs guide +https://mathics-development-guide.readthedocs.io/en/latest/ +for instructions on installing +https://mathics-development-guide.readthedocs.io/en/latest/ +and running +https://mathics-development-guide.readthedocs.io/en/latest/running.html -You can install Cython for some extra functionality/optimizations. +Contributing +Please feel encouraged to contribute to Mathics! Create your own fork, +make the desired changes, commit, and make a pull request. + +License + +Mathics is released under the GNU General Public License Version 3 +(GPL3). diff --git a/academic/mathics/mathics.SlackBuild b/academic/mathics/mathics.SlackBuild index fe30f109d5..72870973ea 100644 --- a/academic/mathics/mathics.SlackBuild +++ b/academic/mathics/mathics.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for Mathics @@ -22,10 +22,15 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=mathics -VERSION=${VERSION:-1.0} +VERSION=${VERSION:-4.0.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +SRCNAM=Mathics3 if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +40,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -59,9 +71,9 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf Mathics-$VERSION -tar xvf $CWD/Mathics-$VERSION.tar.gz -cd Mathics-$VERSION +rm -rf $SRCNAM-$VERSION +tar xvf $CWD/$SRCNAM-$VERSION.tar.gz +cd $SRCNAM-$VERSION chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -69,7 +81,7 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -python setup.py install --root=$PKG +python3 setup.py install --root=$PKG find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true @@ -84,4 +96,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/mathics/mathics.info b/academic/mathics/mathics.info index f61f3000c2..4f4c0e7aa2 100644 --- a/academic/mathics/mathics.info +++ b/academic/mathics/mathics.info @@ -1,10 +1,10 @@ PRGNAM="mathics" -VERSION="1.0" +VERSION="4.0.0" HOMEPAGE="http://www.mathics.org/" -DOWNLOAD="https://github.com/mathics/Mathics/archive/v1.0/Mathics-1.0.tar.gz" -MD5SUM="a0a161a1787093b90b21e73b0d44c0fc" +DOWNLOAD="https://files.pythonhosted.org/packages/35/68/72d4ec12fe91c3cf569fe95ba20ae324414e59f624ad3fb3eaf767cf2620/Mathics3-4.0.0.tar.gz" +MD5SUM="f221aaf0ef9a27e2953429a32fe94652" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="colorama mpmath ply python-dateutil python-django-legacy six sympy" +REQUIRES="python2-numpy python2-sympy" MAINTAINER="David Melik" EMAIL="dchmelik@gmail.com" diff --git a/academic/mathics/slack-desc b/academic/mathics/slack-desc index 1578bda0e9..a351c60962 100644 --- a/academic/mathics/slack-desc +++ b/academic/mathics/slack-desc @@ -8,12 +8,12 @@ |-----handy-ruler------------------------------------------------------| mathics: mathics (A free, light-weight alternative to Mathematica) mathics: -mathics: Mathics is a free, general-purpose online computer algebra system -mathics: featuring Mathematica-compatible syntax and functions. It is backed -mathics: by highly extensible Python code, relying on SymPy for most -mathics: mathematical tasks. -mathics: -mathics: http://www.mathics.org/ -mathics: +mathics: Mathics is a general-purpose computer algebra system (CAS). It is an +mathics: open-source alternative to Mathematica. It is free both as in "free +mathics: beer" and as in "freedom". mathics: +mathics: The home page of Mathics is https://mathics.org. mathics: +mathics: Installing and Running +mathics: See https://mathics-development-guide.readthedocs.io/en/latest/ for +mathics: instructions on installing and running. diff --git a/academic/mathjax2/README b/academic/mathjax2/README new file mode 100644 index 0000000000..432f11787d --- /dev/null +++ b/academic/mathjax2/README @@ -0,0 +1,2 @@ +MathJax is an open-source JavaScript display engine for mathematics +that works in all modern browsers. diff --git a/academic/mathjax2/mathjax2.SlackBuild b/academic/mathjax2/mathjax2.SlackBuild new file mode 100644 index 0000000000..fb1d4ce3a2 --- /dev/null +++ b/academic/mathjax2/mathjax2.SlackBuild @@ -0,0 +1,110 @@ +#!/bin/bash + +# Slackware build script for mathjax2 + +# Copyright 2022 Isaac Yu <isaacyu@protonmail.com> +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=mathjax2 +VERSION=${VERSION:-2.7.9} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +SRCNAM=MathJax + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $SRCNAM-$VERSION +tar xvf $CWD/$SRCNAM-$VERSION.tar.gz +cd $SRCNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +# Remove unneeded stuff. Refer to the Arch Linux PKGBUILD: +# https://github.com/archlinux/svntogit-community/blob/packages/mathjax2/trunk/PKGBUILD +rm -r docs test unpacked +rm -r fonts/HTML-CSS/TeX/png +for _format in eot otf svg ; do + find . -type d -name "$_format" -prune -exec rm -rf {} \; +done + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/share/fonts +cp -a ../$SRCNAM-$VERSION $PKG/usr/share/mathjax2 +mv $PKG/usr/share/mathjax2/fonts $PKG/usr/share/fonts/mathjax2 +ln -s /usr/share/fonts/mathjax2 $PKG/usr/share/mathjax2/fonts + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + CONTRIBUTING.md LICENSE README.md \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/mathjax2/mathjax2.info b/academic/mathjax2/mathjax2.info new file mode 100644 index 0000000000..66b659c608 --- /dev/null +++ b/academic/mathjax2/mathjax2.info @@ -0,0 +1,10 @@ +PRGNAM="mathjax2" +VERSION="2.7.9" +HOMEPAGE="https://www.mathjax.org/" +DOWNLOAD="https://github.com/mathjax/MathJax/archive/2.7.9/MathJax-2.7.9.tar.gz" +MD5SUM="9032fe7c1c9dcae7f85c20c67435de23" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Isaac Yu" +EMAIL="isaacyu@protonmail.com" diff --git a/academic/mathjax2/slack-desc b/academic/mathjax2/slack-desc new file mode 100644 index 0000000000..88b8b156bf --- /dev/null +++ b/academic/mathjax2/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +mathjax2: mathjax2 (Beautiful math in all browsers) +mathjax2: +mathjax2: MathJax is an open-source JavaScript display engine for mathematics +mathjax2: that works in all modern browsers. +mathjax2: +mathjax2: +mathjax2: +mathjax2: +mathjax2: +mathjax2: +mathjax2: diff --git a/academic/mathomatic/README b/academic/mathomatic/README index 3c01da81e0..7c3e5292c8 100644 --- a/academic/mathomatic/README +++ b/academic/mathomatic/README @@ -4,11 +4,11 @@ subtraction, multiplication, division, modulo division, and all forms of exponentiation. All arithmetic is double precision floating point with up to 14 decimal digits accuracy. -Mathomatic can symbolically combine and solve equations containing many -variables, completely simplify and compare expressions and equations, do -simple calculus transformations and series, perform standard, complex -number, and polynomial arithmetic, generate optimized C, Java, and Python -language code from simplified equations, carry out quick calculations, and -much more. Plotting with gnuplot is also supported. Not implemented in -Mathomatic are named functions, arbitrary-precision arithmetic, and -matrices. +Mathomatic can symbolically combine and solve equations containing many +variables, completely simplify and compare expressions and equations, +do simple calculus transformations and series, perform standard, +complex number, and polynomial arithmetic, generate optimized C, +Java, and Python language code from simplified equations, carry +out quick calculations, and much more. Plotting with gnuplot is +also supported. Not implemented in Mathomatic are named functions, +arbitrary-precision arithmetic, and matrices. diff --git a/academic/mathomatic/mathomatic.SlackBuild b/academic/mathomatic/mathomatic.SlackBuild index 55b8d42f69..ec96c60228 100644 --- a/academic/mathomatic/mathomatic.SlackBuild +++ b/academic/mathomatic/mathomatic.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for mathomatic @@ -24,26 +24,36 @@ # # Originally written by Dylan Armitage <d.armitage89@gmail.com> +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=mathomatic VERSION=${VERSION:-16.0.5} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -111,4 +121,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/matio/matio.SlackBuild b/academic/matio/matio.SlackBuild index 899061e0b6..9c12742701 100644 --- a/academic/matio/matio.SlackBuild +++ b/academic/matio/matio.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for matio @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=matio -VERSION=${VERSION:-1.5.9} +VERSION=${VERSION:-1.5.23} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -95,8 +105,10 @@ rm -rf $PKG/usr/share/info/ mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/matio/matio.info b/academic/matio/matio.info index a10b48a397..4ceeb67884 100644 --- a/academic/matio/matio.info +++ b/academic/matio/matio.info @@ -1,8 +1,8 @@ PRGNAM="matio" -VERSION="1.5.9" +VERSION="1.5.23" HOMEPAGE="https://sourceforge.net/projects/matio/" -DOWNLOAD="https://sourceforge.net/projects/matio/files/matio/1.5.9/matio-1.5.9.tar.gz" -MD5SUM="aab5b4219a3c0262afe7eeb7bdd2f463" +DOWNLOAD="https://downloads.sf.net/matio/matio-1.5.23.tar.gz" +MD5SUM="25dfaf33af030a170eb9d3814cac1fca" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="hdf5" diff --git a/academic/maxima/README b/academic/maxima/README index 35a04af3fa..d084e4cb04 100644 --- a/academic/maxima/README +++ b/academic/maxima/README @@ -1,7 +1,26 @@ -Maxima is a system for the manipulation of symbolic and numerical -expressions, including differentiation, integration, Taylor series, -Laplace transforms, ordinary differential equations, systems of linear -equations, polynomials, and sets, lists, vectors, matrices, and tensors. -Maxima yields high precision numeric results by using exact fractions, -arbitrary precision integers, and arbitrarily precision floating point -numbers. Maxima can plot functions and data in two and three dimensions. + +Maxima is a GPL computer algebra system based on DOE-MACSYMA. It +is comparable to commercial systems like Mathematica and Maple. It +emphasizes symbolic mathematical computation: algebra, trigonometry, +calculus, and much more. + +For example, Maxima solves x^2-r*x-s^2-r*s=0 giving the symbolic +results [x=r+s, x=-s]. + +Maxima can calculate with exact integers and fractions, native +floating-point and high-precision big floats. + +Maxima has user-friendly front-ends, an on-line manual, plotting +commands, and numerical libraries. Users can write programs in its +native programming language, and many have contributed useful packages +in a variety of areas over the decades. + +Maxima is GPL-licensed and largely written in Common Lisp. Executables +can be downloaded for Windows, Mac, Linux, and Android; source code +is also available. An active community maintains and extends the +system. Maxima is widely used. + +SBo Installation notes: +- The info files are not compressed. +- Two .lisp files install to /usr/info. +These are required for maxima's help facility. diff --git a/academic/maxima/doinst.sh b/academic/maxima/doinst.sh new file mode 100644 index 0000000000..7b028b1845 --- /dev/null +++ b/academic/maxima/doinst.sh @@ -0,0 +1,10 @@ + + +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q /usr/share/applications >/dev/null 2>&1 +fi + +if [ -x /usr/bin/update-mime-database ]; then + /usr/bin/update-mime-database /usr/share/mime >/dev/null 2>&1 +fi + diff --git a/academic/maxima/maxima.SlackBuild b/academic/maxima/maxima.SlackBuild index de32fcbf35..15ba5bebbe 100644 --- a/academic/maxima/maxima.SlackBuild +++ b/academic/maxima/maxima.SlackBuild @@ -1,7 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for maxima +# Copyright 2021-23 Judah Milgram <milgram@cgpp.com> # Copyright 2017 Dhaby Xiloj <slack.dhabyx@gmail.com> # All rights reserved. # Based on work of Robby and others slackers. @@ -30,11 +31,17 @@ # Modified by Ken Milmore 2009 # Modified by Glenn Becker to update to version 5.28.0 # Glenn Becker -> update to version 5.38.1 +# JM -> update version 5.39 -> 5.44 +# JM -> update to version 5.46 +# JM -> update to version 5.47 + +cd $(dirname $0) ; CWD=$(pwd) PRGNAM=maxima -VERSION=${VERSION:-5.39.0} +VERSION=${VERSION:-5.47.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -44,7 +51,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -99,15 +113,15 @@ for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; r # NOTE: Do not compress the info pages; they are needed by Maxima's help facility. rm -rf $PKG/usr/info/dir -# gzip -9 $PKG/usr/info/*.info* mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a AUTHORS COPYING ChangeLog* INSTALL* NEWS README* \ +cp -a AUTHORS COPYING ChangeLog* NEWS README* \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/maxima/maxima.info b/academic/maxima/maxima.info index 676c4f7b56..4bc595b8bc 100644 --- a/academic/maxima/maxima.info +++ b/academic/maxima/maxima.info @@ -1,10 +1,10 @@ PRGNAM="maxima" -VERSION="5.39.0" +VERSION="5.47.0" HOMEPAGE="http://maxima.sourceforge.net/" -DOWNLOAD="https://sourceforge.net/projects/maxima/files/Maxima-source/5.39.0-source/maxima-5.39.0.tar.gz" -MD5SUM="3bccafb512ff1054be700c61601088af" +DOWNLOAD="https://sourceforge.net/projects/maxima/files/Maxima-source/5.47.0-source/maxima-5.47.0.tar.gz" +MD5SUM="8ddf54f90fc36e8773fe47a5a9023106" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" -MAINTAINER="DhabyX" -EMAIL="slack.dhabyx@gmail.com" +MAINTAINER="Judah Milgram" +EMAIL="milgram cgpp com" diff --git a/academic/maxima/slack-desc b/academic/maxima/slack-desc index 360e5737ae..0963a7bfea 100644 --- a/academic/maxima/slack-desc +++ b/academic/maxima/slack-desc @@ -8,11 +8,11 @@ |-----handy-ruler------------------------------------------------------| maxima: maxima (a computer algebra system) maxima: -maxima: Maxima is a system for the manipulation of symbolic and numerical -maxima: expressions, including differentiation, integration, Taylor series, -maxima: Laplace transforms, ordinary differential equations, systems of -maxima: linear equations, polynomials, and sets, lists, vectors, matrices, -maxima: and tensors. +maxima: Maxima is a GPL computer algebra system based on DOE-MACSYMA. +maxima: +maxima: It is comparable to commercial systems like Mathematica and Maple end +maxima: emphasizes symbolic mathematical computation in algebra, trigonometry, +maxima: calculus, and much more. maxima: maxima: Homepage: http://maxima.sourceforge.net/ maxima: diff --git a/academic/meep/README b/academic/meep/README index 9baddd56dd..4bfc8b293b 100644 --- a/academic/meep/README +++ b/academic/meep/README @@ -1,14 +1,46 @@ meep (electromagnetic FDTD solver) -Meep is a free and open-source software package for -electromagnetics simulation via the finite-difference -time-domain (FDTD) method spanning a broad range of -applications. +Meep is a free and open-source software package for electromagnetics +simulation via the finite-difference time-domain (FDTD) method +spanning a broad range of applications. It saves results in hdf5 +format. -You may wish to preinstall: harminv, mpb +This package requires: hdf5, libctl, lapack, mpb + +You probably will also want to preinstall: harminv, openmpi You may wish to also install: h5utils -If the build script can find the ATLAS libraries, it will -adapt the configure options to use them rather than the -default lapack. +You very probably want to build a multi-processor version of this +code by adding the "--with-openmp" configure option. Here, mpb is +specified as a prerequisite since at the present time the python +interface will not build without it. + + + +Configuration: + +If the build script can find the ATLAS libraries, it will adapt the +configure options to use them, rather than the the default choice of +lapack. + +You can add additional options to the command line using the +environment variable SBOPTIONS_MEEP; e.g. to enable MPI (multi- +processor calculation) using openmp, use: + +SBOPTIONS_MEEP="--with-openmp" ./meep.Slackbuild + +Alternatively, if building non-interactively (e.g. if using slpkg), +use/create the file /etc/sbo_pkg_options.conf since this slackbuild +script will search it for options. Simply include a line starting +"meep:" followed by options, e.g.: + +meep: --with-openmp + +Currently, building the python support for meep can be problematic +unless the mpb package is also installed; if you do so, and (e.g.) +use openmp, it is best to build mpb with the same option. You may +also need to install mpi4py using pip. If you do not want python +support, specify "--without-python", and in this case installing mpb +is not necessary. + diff --git a/academic/meep/i386-fix.patch.gz b/academic/meep/i386-fix.patch.gz Binary files differnew file mode 100644 index 0000000000..c5572c316c --- /dev/null +++ b/academic/meep/i386-fix.patch.gz diff --git a/academic/meep/meep.SlackBuild b/academic/meep/meep.SlackBuild index 347fb3f9ae..629d20e14d 100644 --- a/academic/meep/meep.SlackBuild +++ b/academic/meep/meep.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for meep @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=meep -VERSION=${VERSION:-1.12.0} -BUILD=${BUILD:-1} +VERSION=${VERSION:-1.25.0} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -54,19 +64,23 @@ else LIBDIRSUFFIX="" fi +set -e + # change annoying underscores into hyphens SVERSION=$(echo $VERSION | tr '_' '-') # make a custom list of doc files in advance DOCFILES="AUTHORS COPYRIGHT LICENSE TODO NEWS.md" -set -e - rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $PRGNAM-$SVERSION tar xvf $CWD/$PRGNAM-$SVERSION.tar.gz cd $PRGNAM-$SVERSION +# patch 32bit build - thanks debian devs +case "$ARCH" in + i?86) zcat $CWD/i386-fix.patch.gz | patch -p1 ;; +esac chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -74,13 +88,27 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -LOCALCONFIGS=" --without-python --with-mpi " +# if there is no configure script, try to build one! +if [ ! -f ./configure ] ; then + ./autogen.sh +fi + +LOCALCONFIGS= +XDBFILE=/etc/sbo_pkg_options.conf +if [ -f ${XDBFILE} ] ; then + LOCALCONFIGS=${LOCALCONFIGS}" "$(grep "^${PRGNAM}:" ${XDBFILE} | grep -v '^#' | awk -F: '{print$2}') + echo Build options selected by file: LOCALCONFIGS=${LOCALCONFIGS} +fi +if [ -n "${SBOPTIONS_MEEP}" ] ; then + LOCALCONFIGS=${LOCALCONFIGS}" "${SBOPTIONS_MEEP} + echo Build options selected by environment: LOCALCONFIGS=${LOCALCONFIGS} +fi # check for the Atlas replacement for blas; if the libraries are found, # add the configure option accordingly -if [ -f /usr/lib${LIBDIRSUFFIX}/libatlas.a ] ; then - if [ -f /usr/lib${LIBIRSUFFIX}/libatlas.so ] ; then +if [ -f /usr/lib/libatlas.a ] ; then + if [ -f /usr/lib/libatlas.so ] ; then echo "NOTICE: libatlas was found, configure --with-blas=atlas" LOCALCONFIGS=${LOCALCONFIGS}" --with-blas=atlas" fi @@ -88,38 +116,29 @@ fi CFLAGS="$SLKCFLAGS" \ CPPFLAGS="$SLKCFLAGS" \ +PYTHON=/usr/bin/python3 \ ./configure \ --prefix=/usr \ --mandir=/usr/man \ --libdir=/usr/lib${LIBDIRSUFFIX} \ --docdir=/usr/doc/$PRGNAM-$VERSION \ --build=$ARCH-slackware-linux \ - --disable-static \ $LOCALCONFIGS make make install DESTDIR=$PKG - find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true -#find $PKG/usr/man -type f -exec gzip -9 {} \; -#for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done - - mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION install -m 0644 $DOCFILES $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc -###sbolint off -if [ -f $CWD/doinst.sh ] ; then - cat $CWD/doinst.sh > $PKG/install/doinst.sh -fi -###sbolint on - cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/meep/meep.info b/academic/meep/meep.info index 4c77d9c392..e999eb6ae0 100644 --- a/academic/meep/meep.info +++ b/academic/meep/meep.info @@ -1,10 +1,10 @@ PRGNAM="meep" -VERSION="1.12.0" +VERSION="1.25.0" HOMEPAGE="https://github.com/NanoComp/meep" -DOWNLOAD="https://github.com/NanoComp/meep/releases/download/v1.12.0/meep-1.12.0.tar.gz" -MD5SUM="ce2064167a540036f315b5b7b4b8253e" +DOWNLOAD="https://github.com/NanoComp/meep/releases/download/v1.25.0/meep-1.25.0.tar.gz" +MD5SUM="968b8da6c25aae3757457520d1520eb2" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="lapack openmpi hdf5 libctl" +REQUIRES="mpb" MAINTAINER="PaulKinsler" EMAIL="dr.paul@kinsler.org" diff --git a/academic/meep/slack-desc b/academic/meep/slack-desc index aa2462124c..8187e87c47 100644 --- a/academic/meep/slack-desc +++ b/academic/meep/slack-desc @@ -8,7 +8,7 @@ |-----handy-ruler------------------------------------------------------| meep: meep (electromagnetics simulation using FDTD) meep: -meep: Meep is a free and open-source software package for +meep: Meep is a free and open-source software package for meep: electromagnetics simulation via the finite-difference meep: time-domain (FDTD) method spanning a broad range of meep: applications. diff --git a/academic/megax/megax.SlackBuild b/academic/megax/megax.SlackBuild index 4710ababcc..4f20e38180 100644 --- a/academic/megax/megax.SlackBuild +++ b/academic/megax/megax.SlackBuild @@ -1,6 +1,6 @@ -#!/bin/sh +#!/bin/bash -# Slackware build script for megax (formerly 'megacc') +# Slackware build script for megax (formerly 'megacc', called now simply 'mega') # This takes the place of "megacc" in 2018, as it includes also the GUI # of the program (megax) in addition to megacc. @@ -24,37 +24,47 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=megax -VERSION=${VERSION:-10.1.6_1} +VERSION=${VERSION:-11.0.11_1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} +SRCNAM=mega DEBVER=$(echo $VERSION | tr _ -) if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i386 ;; - arm*) ARCH=arm ;; + i?86) ARCH=i586 ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) -TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM -OUTPUT=${OUTPUT:-/tmp} - -if [ "$ARCH" = "i386" ] || [ "$ARCH" = "i486" ] || [ "$ARCH" = "i586" ] || [ "$ARCH" = "i686" ]; then - LIBDIRSUFFIX="" - DEBARCH="i386" -elif [ "$ARCH" = "x86_64" ]; then +if [ "$ARCH" = "x86_64" ]; then LIBDIRSUFFIX="64" DEBARCH="amd64" +elif [[ $ARCH =~ i?86 ]]; then + LIBDIRSUFFIX="" + DEBARCH="i386" else - printf "\n\n$ARCH is not supported... \n" + printf "\n\n$ARCH is not supported... \n" >/dev/stderr exit 1 fi +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + set -e rm -rf $PKG @@ -63,7 +73,7 @@ cd $TMP rm -rf $PRGNAM-$VERSION mkdir $PRGNAM-$VERSION cd $PRGNAM-$VERSION -ar p $CWD/${PRGNAM}_${DEBVER}_${DEBARCH}.deb data.tar.xz | tar xJv +ar p $CWD/${SRCNAM}_${DEBVER}_${DEBARCH}.deb data.tar.xz | tar xJv chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -72,20 +82,23 @@ find -L . \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; # Fix path in runmega.sh for x86_64 -sed -i "s|/usr/lib/megax|/usr/lib${LIBDIRSUFFIX}/megax|g" usr/lib/$PRGNAM/runmega.sh +sed -i "s|/usr/lib/megax|/usr/lib${LIBDIRSUFFIX}/$PRGNAM|g" usr/lib/mega/runmega.sh # Place things in /usr/lib and just create symlinks later. # This is what Debian's and RedHat's packages do. mkdir -p $PKG/usr/lib${LIBDIRSUFFIX} -cp -a usr/lib/$PRGNAM $PKG/usr/lib${LIBDIRSUFFIX} +cp -a usr/lib/mega $PKG/usr/lib${LIBDIRSUFFIX}/$PRGNAM # Copy man pages to their proper place. cp -a usr/local/share/man $PKG/usr +sed -i "s:lib:lib${LIBDIRSUFFIX}:" $PKG/usr/lib${LIBDIRSUFFIX}/$PRGNAM/runmega.sh +sed -i "s:mega:$PRGNAM:" $PKG/usr/lib${LIBDIRSUFFIX}/$PRGNAM/runmega.sh + mkdir -p $PKG/usr/bin cd $PKG/usr/bin ln -s ../lib${LIBDIRSUFFIX}/$PRGNAM/megacc - ln -s ../lib${LIBDIRSUFFIX}/$PRGNAM/runmega.sh megax + ln -s ../lib${LIBDIRSUFFIX}/$PRGNAM/runmega.sh runmega cd - find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ @@ -108,4 +121,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/megax/megax.desktop b/academic/megax/megax.desktop index 336d4eb395..4ec785dbf3 100644 --- a/academic/megax/megax.desktop +++ b/academic/megax/megax.desktop @@ -1,7 +1,7 @@ [Desktop Entry] Categories=Education; Comment=Molecular evolutionary genetics analysis -Exec=megax +Exec=runmega Icon=megax Name=MEGA X StartupNotify=false diff --git a/academic/megax/megax.info b/academic/megax/megax.info index 2f53c52fb5..3d1c83a869 100644 --- a/academic/megax/megax.info +++ b/academic/megax/megax.info @@ -1,10 +1,10 @@ PRGNAM="megax" -VERSION="10.1.6_1" +VERSION="11.0.11_1" HOMEPAGE="http://www.megasoftware.net/" -DOWNLOAD="https://www.megasoftware.net/releases/megax_10.1.6-1_i386.deb" -MD5SUM="04d125f5dc9fd43ee3550cc65c4c7fbd" -DOWNLOAD_x86_64="https://www.megasoftware.net/releases/megax_10.1.6-1_amd64.deb" -MD5SUM_x86_64="3f3d3f937443e6baca0b8530e075fab8" +DOWNLOAD="https://www.megasoftware.net/releases/mega_11.0.11-1_i386.deb" +MD5SUM="087a4673f20aec8fd92f18e11683ebbd" +DOWNLOAD_x86_64="https://www.megasoftware.net/releases/mega_11.0.11-1_amd64.deb" +MD5SUM_x86_64="83a2aa21353eabeaf084f38bce496a23" REQUIRES="" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/meme-db-gomo/meme-db-gomo.SlackBuild b/academic/meme-db-gomo/meme-db-gomo.SlackBuild index ab81c7466f..fecb2a0b4b 100644 --- a/academic/meme-db-gomo/meme-db-gomo.SlackBuild +++ b/academic/meme-db-gomo/meme-db-gomo.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for meme-db-gomo -# Copyright 2020 Petar Petrov slackalaxy@gmail.com +# Copyright 2020-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,16 +22,26 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=meme-db-gomo VERSION=${VERSION:-3.2} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} SRCNAM=gomo_databases ARCH=noarch -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -62,4 +72,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/meme-db-gomo/meme-db-gomo.info b/academic/meme-db-gomo/meme-db-gomo.info index b70eb8f874..d4acb6c1c5 100644 --- a/academic/meme-db-gomo/meme-db-gomo.info +++ b/academic/meme-db-gomo/meme-db-gomo.info @@ -1,7 +1,7 @@ PRGNAM="meme-db-gomo" VERSION="3.2" -HOMEPAGE="http://meme-suite.org/db/gomo" -DOWNLOAD="http://meme-suite.org/meme-software/Databases/gomo/gomo_databases.3.2.tgz" +HOMEPAGE="https://meme-suite.org/db/gomo" +DOWNLOAD="https://meme-suite.org/meme-software/Databases/gomo/gomo_databases.3.2.tgz" MD5SUM="5b8fcf3c541b30e2a66580f289132e97" DOWNLOAD_x86_64="" MD5SUM_x86_64="" diff --git a/academic/meme-db-motif/meme-db-motif.SlackBuild b/academic/meme-db-motif/meme-db-motif.SlackBuild index f0e266d8c8..949df9e2be 100644 --- a/academic/meme-db-motif/meme-db-motif.SlackBuild +++ b/academic/meme-db-motif/meme-db-motif.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for meme-db-motif -# Copyright 2020 Petar Petrov slackalaxy@gmail.com +# Copyright 2020-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,16 +22,26 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=meme-db-motif -VERSION=${VERSION:-12.19} +VERSION=${VERSION:-12.23} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} SRCNAM=motif_databases ARCH=noarch -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -62,4 +72,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/meme-db-motif/meme-db-motif.info b/academic/meme-db-motif/meme-db-motif.info index 549263ca24..21a7543ae0 100644 --- a/academic/meme-db-motif/meme-db-motif.info +++ b/academic/meme-db-motif/meme-db-motif.info @@ -1,8 +1,8 @@ PRGNAM="meme-db-motif" -VERSION="12.19" -HOMEPAGE="http://meme-suite.org/db/motifs" -DOWNLOAD="http://meme-suite.org/meme-software/Databases/motifs/motif_databases.12.19.tgz" -MD5SUM="f5ffcaecc07570ee19dba20b82d7bd73" +VERSION="12.23" +HOMEPAGE="https://meme-suite.org/db/motifs" +DOWNLOAD="https://meme-suite.org/meme/meme-software/Databases/motifs/motif_databases.12.23.tgz" +MD5SUM="4a351edb28e456453c804f2da5889b23" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/meme-db-tgene/meme-db-tgene.SlackBuild b/academic/meme-db-tgene/meme-db-tgene.SlackBuild index 95e75e5a5c..4a29171aca 100644 --- a/academic/meme-db-tgene/meme-db-tgene.SlackBuild +++ b/academic/meme-db-tgene/meme-db-tgene.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for meme-db-tgene -# Copyright 2020 Petar Petrov slackalaxy@gmail.com +# Copyright 2020-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,16 +22,26 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=meme-db-tgene VERSION=${VERSION:-1.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} SRCNAM=tgene_databases ARCH=noarch -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -62,4 +72,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/meme-db-tgene/meme-db-tgene.info b/academic/meme-db-tgene/meme-db-tgene.info index 6c90f7f5d3..246a5d99c9 100644 --- a/academic/meme-db-tgene/meme-db-tgene.info +++ b/academic/meme-db-tgene/meme-db-tgene.info @@ -1,7 +1,7 @@ PRGNAM="meme-db-tgene" VERSION="1.0" -HOMEPAGE="http://meme-suite.org/db/tgene" -DOWNLOAD="http://meme-suite.org/meme-software/Databases/tgene/tgene_databases.1.0.tgz" +HOMEPAGE="https://meme-suite.org/db/tgene" +DOWNLOAD="https://meme-suite.org/meme-software/Databases/tgene/tgene_databases.1.0.tgz" MD5SUM="8a2e467f979a4721e4fb2233bf2b0a04" DOWNLOAD_x86_64="" MD5SUM_x86_64="" diff --git a/academic/meme-suite/meme-suite.SlackBuild b/academic/meme-suite/meme-suite.SlackBuild index acc62dc3a5..e8f7f9c521 100644 --- a/academic/meme-suite/meme-suite.SlackBuild +++ b/academic/meme-suite/meme-suite.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for meme-suite -# Copyright 2017-2020 Petar Petrov slackalaxy@gmail.com +# Copyright 2017-2023 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=meme-suite -VERSION=${VERSION:-5.1.0} +VERSION=${VERSION:-5.5.4} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} SRCNAM=meme @@ -37,7 +40,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -119,4 +129,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/meme-suite/meme-suite.info b/academic/meme-suite/meme-suite.info index 4c8ad796e8..f0d7634d52 100644 --- a/academic/meme-suite/meme-suite.info +++ b/academic/meme-suite/meme-suite.info @@ -1,10 +1,10 @@ PRGNAM="meme-suite" -VERSION="5.1.0" -HOMEPAGE="http://meme-suite.org/" -DOWNLOAD="http://meme-suite.org/meme-software/5.1.0/meme-5.1.0.tar.gz" -MD5SUM="71e357be7bce1686f516858957de3921" +VERSION="5.5.4" +HOMEPAGE="https://meme-suite.org/" +DOWNLOAD="https://meme-suite.org/meme-software/5.5.4/meme-5.5.4.tar.gz" +MD5SUM="eed938a859b551209af3c4adf7e41fa1" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="openmpi perl-HTML-Template perl-JSON python3 meme-db-gomo meme-db-motif meme-db-tgene" +REQUIRES="openmpi perl-HTML-Template perl-JSON meme-db-gomo meme-db-motif meme-db-tgene" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/mendeleydesktop/README b/academic/mendeleydesktop/README index 8e9077e627..cdf14f5692 100644 --- a/academic/mendeleydesktop/README +++ b/academic/mendeleydesktop/README @@ -4,11 +4,3 @@ management tool for desktop and web. Before you use Mendeley, make sure that you agree with the terms and conditions at http://www.mendeley.com/terms/ - -Optional Dependency - -qt5 -- this is highly recommended (replacing Mendeley's bundled qt5) to -be able to access all the functions if you use KDE5. You need to use -the option 'SYSTEM_QT5=yes', for example: - - SYSTEM_QT5=yes ./mendeleydesktop.SlackBuild diff --git a/academic/mendeleydesktop/mendeleydesktop.SlackBuild b/academic/mendeleydesktop/mendeleydesktop.SlackBuild index 6be7008a01..bdc072f10d 100644 --- a/academic/mendeleydesktop/mendeleydesktop.SlackBuild +++ b/academic/mendeleydesktop/mendeleydesktop.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for mendeleydesktop @@ -25,28 +25,34 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=mendeleydesktop VERSION=${VERSION:-1.17.9} BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - LIBDIRSUFFIX="" -elif [ "$ARCH" = "i586" ] || [ "$ARCH" = "i686" ]; then - ARCH="i486" # mendeleydesktop doesn't have i586/i686 pre-builds. +SRCARCH="$ARCH" +if [ "$ARCH" = "i586" ] || [ "$ARCH" = "i686" ]; then + SRCARCH="i486" # mendeleydesktop doesn't have i586/i686 pre-builds. LIBDIRSUFFIX="" elif [ "$ARCH" = "x86_64" ]; then LIBDIRSUFFIX="64" @@ -60,18 +66,18 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $PRGNAM-$VERSION-linux-$ARCH -tar xvf $CWD/$PRGNAM-$VERSION-linux-${ARCH}.tar.bz2 -cd $PRGNAM-$VERSION-linux-$ARCH +rm -rf $PRGNAM-$VERSION-linux-$SRCARCH +tar xvf $CWD/$PRGNAM-$VERSION-linux-${SRCARCH}.tar.bz2 +cd $PRGNAM-$VERSION-linux-$SRCARCH chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ + -o -perm 511 \) -exec chmod 755 {} + -o \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} + # removing QT5 bundled libraries -if [ "${SYSTEM_QT5:-no}" != "no" ]; then +if [ "${SYSTEM_QT5:-yes}" != "no" ]; then rm -rf lib/qt rm bin/qt.conf rm -rf lib/$PRGNAM/plugins @@ -98,7 +104,7 @@ MENDELEY_LIB=lib LD_LIBRARY_PATH=\${LD_LIBRARY_PATH}:\${MENDELEY_BASE}/\${MENDELEY_LIB} export LD_LIBRARY_PATH cd /opt/mendeleydesktop/lib/mendeleydesktop/libexec -./mendeleydesktop.$ARCH \$@ +./mendeleydesktop.$SRCARCH \$@ EOF chmod 755 $PKG/usr/bin/$PRGNAM else @@ -119,4 +125,4 @@ cat $CWD/doinst.sh > $PKG/install/doinst.sh cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/metalwalls/README b/academic/metalwalls/README new file mode 100644 index 0000000000..586416382a --- /dev/null +++ b/academic/metalwalls/README @@ -0,0 +1,9 @@ + MetalWalls (MW) is a molecular dynamics code dedicated to the +modelling of electrochemical systems. Its main originality is the +inclusion of a series of methods allowing to apply a constant +potential within the electrode materials. + + For building the MPI version set the environment variable MPI=yes +this requires a MPI implementation either openmpi or mpich. + + The final executable is metalwalls diff --git a/academic/metalwalls/metalwalls.SlackBuild b/academic/metalwalls/metalwalls.SlackBuild new file mode 100644 index 0000000000..8aaaf8a2ed --- /dev/null +++ b/academic/metalwalls/metalwalls.SlackBuild @@ -0,0 +1,123 @@ +#!/bin/bash + +# Slackware build script for MetalWalls + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=metalwalls +VERSION=${VERSION:-21.06.1} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +cp computers/laptop/config-gnu-linux.mk config.mk +sed -i '4s/$/ -std=legacy/' config.mk + +# the laptop config file requires MPI by default +# here we forces a serial build +if [ ! "${MPI:-no}" == "yes" ]; then + sed -i 's#mpif90#gfortran#' config.mk + sed -i '5s#$# -DMW_SERIAL#' config.mk + # fix double setting for error "Sumbol comm already has basic type" + sed -i '42s/^/!/' src/parallel.F90 +fi + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +make +#make install DESTDIR=$PKG + +mkdir -p $PKG/usr/bin +cp mw $PKG/usr/bin/metalwalls + +# install some examples and tools +mkdir -p $PKG/usr/share/$PRGNAM-$VERSION/tools +cp -a example $PKG/usr/share/$PRGNAM-$VERSION +cp -a tools $PKG/usr/share/$PRGNAM-$VERSION/tools + + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + CONTRIBUTORS LICENSE doc \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/metalwalls/metalwalls.info b/academic/metalwalls/metalwalls.info new file mode 100644 index 0000000000..126a022fc5 --- /dev/null +++ b/academic/metalwalls/metalwalls.info @@ -0,0 +1,10 @@ +PRGNAM="metalwalls" +VERSION="21.06.1" +HOMEPAGE="https://gitlab.com/ampere2/metalwalls" +DOWNLOAD="https://gitlab.com/ampere2/metalwalls/-/archive/21.06.1/metalwalls-21.06.1.tar.gz" +MD5SUM="24e8549490d9d9e5c24659fe50d8276e" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="lapack" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/metalwalls/slack-desc b/academic/metalwalls/slack-desc new file mode 100644 index 0000000000..1e47821fe9 --- /dev/null +++ b/academic/metalwalls/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +metalwalls: metalwalls (A molecular code for modelling electrochemical systems) +metalwalls: +metalwalls: +metalwalls: +metalwalls: metalwalls (MW) is a molecular dynamics code dedicated to the +metalwalls: modelling of electrochemical systems. Its main originality is the +metalwalls: inclusion of a series of methods allowing to apply a constant +metalwalls: potential within the electrode materials. +metalwalls: +metalwalls: +metalwalls: diff --git a/academic/metis/metis.SlackBuild b/academic/metis/metis.SlackBuild index 5bd73be964..a7f2a4926e 100644 --- a/academic/metis/metis.SlackBuild +++ b/academic/metis/metis.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for METIS @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=metis VERSION=${VERSION:-5.1.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$(uname -m)" in @@ -35,15 +38,22 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM-$VERSION +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="Changelog LICENSE.txt manual/manual.pdf" -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" @@ -103,4 +113,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/mfem/README b/academic/mfem/README new file mode 100644 index 0000000000..96f8496889 --- /dev/null +++ b/academic/mfem/README @@ -0,0 +1,16 @@ + MFEM is a free, lightweight, scalable C++ library for finite element +methods. + + + Building options that can be set using the environment variable: + - OMP=yes, use OpenMP. + - MPI=yes, use MPI (requires a MPI implementation either mpich or + openmpi and the hypre and metis package. + - CUDA=yes, requires the CUDA toolkit. + - TESTS=yes, to run the tests. + + Compiling the examples: + # mkdir mfem-examples; cd mfem-examples + # cp -av /usr/share/mfem-4.5/{data,examples} . + # make -C examples + # make diff --git a/academic/mfem/mfem.SlackBuild b/academic/mfem/mfem.SlackBuild new file mode 100644 index 0000000000..f85c2c679d --- /dev/null +++ b/academic/mfem/mfem.SlackBuild @@ -0,0 +1,188 @@ +#!/bin/bash + +# Slackware build script for mfem + +# Copyright 2022 William PC, Seattle (USA) +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=mfem +VERSION=${VERSION:-4.5} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +if [ "${OMP:-no}" == "yes" ]; then + OPT_BUILD="MFEM_USE_OPENMP=YES" +fi + +# this can't be null even without using MPI it has to be set +# to don't throw an error at make +MFEM_MPIEXEC="MFEM_MPIEXEC=mpirun" +if [ "${MPI:-no}" == "yes" ]; then + OPT_BUILD="$OPT_BUILD MFEM_USE_MPI=YES" + OPT_BUILD="$OPT_BUILD MFEM_USE_METIS_5=YES" + # fix hypre location + sed -i 's#^HYPRE_DIR = .*#HYPRE_DIR = /usr#' config/defaults.mk + sed -i 's#$(HYPRE_DIR)/include#&/hypre#' config/defaults.mk + sed -i 's#$(HYPRE_DIR)/lib#&'${LIBDIRSUFFIX}'#' config/defaults.mk + # fix metis location + sed -i 's#METIS_DIR = @MFEM_DIR@/../metis-5.0#METIS_DIR = /usr#' config/defaults.mk + sed -i 's#$(METIS_DIR)/include#&/metis#' config/defaults.mk + sed -i 's#-L$(METIS_DIR)/lib#&'${LIBDIRSUFFIX}'#' config/defaults.mk + # fix for running check with MPI + if pkg-config --exists mpich; then + echo "Using mpich" + MFEM_MPIEXEC="MFEM_MPIEXEC=\"mpirun -host localhost\"" + else + echo "Using openmpi" + export OMPI_ALLOW_RUN_AS_ROOT=1 + export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 + + fi +fi + + +if [ "${CUDA:-no}" == "yes" ]; then + OPT_BUILD="$OPT_BUILD MFEM_USE_CUDA=YES" +fi + +# fix lib and share install location +sed -i 's#$(PREFIX)/lib#&'${LIBDIRSUFFIX}'#' makefile +sed -i 's#$(PREFIX)/share/mfem#&-'${VERSION}'#' makefile + +# "$MFEM_MPIEXEC" \ +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +make config \ + MFEM_STATIC=NO \ + MFEM_SHARED=YES \ + $OPT_BUILD \ + "$MFEM_MPIEXEC" \ + BUILD_DIR=build +cd build +make +make check +if [ "${TESTS:-no}" == "yes" ]; then + make test +fi +make install \ + MFEM_PREFIX=/usr \ + MFEM_INC_DIR="@MFEM_PREFIX@/include" \ + MFEM_LIB_DIR="@MFEM_PREFIX@/lib${LIBDIRSUFFIX}" \ + MFEM_TEST_MK="@MFEM_PREFIX@/share/$PRGNAM-$VERSION/test.mk" \ + PREFIX=$PKG/usr +cd .. + +# fix permissions +find -L $PKG/usr/{include,share} \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +# install data files, examples and miniapps +mkdir -p $PKG/usr/share/$PRGNAM-$VERSION +cp -a {data,examples,miniapps} $PKG/usr/share/$PRGNAM-$VERSION +cp -a config/defaults.mk $PKG/usr/share/$PRGNAM-$VERSION + +# fix examples +sed -i -e 's$# MFEM_INSTALL_DIR = ../mfem$MFEM_INSTALL_DIR = /usr$' \ + -e 's$# CONFIG_MK$CONFIG_MK$' \ + -e 's#share/mfem#&-'$VERSION'#' \ + -e 's/^MFEM_LIB_FILE/#&/' \ + $PKG/usr/share/$PRGNAM-$VERSION/examples/makefile + +# fix miniapps +for file in $(find $PKG/usr/share/$PRGNAM-$VERSION/miniapps -iname makefile); do + sed -i 's$# MFEM_INSTALL_DIR = ../../mfem$MFEM_INSTALL_DIR = /usr$' $file + sed -i 's$# CONFIG_MK$CONFIG_MK$' $file + sed -i 's#share/mfem#&-'$VERSION'#' $file + sed -i 's#^DEFAULTS_MK.*#DEFAULTS_MK = /usr/share/'$PRGNAM-$VERSION'/defaults.mk#' $file +done +sed -i 's#../../general#mfem/general#' $PKG/usr/share/$PRGNAM-$VERSION/miniapps/meshing/{minimal-surface,pminimal-surface}.cpp +sed -i 's#../../general#mfem/general#' $PKG/usr/share/$PRGNAM-$VERSION/miniapps/navier/navier_solver.cpp +sed -i 's#../../linalg#mfem/linalg#' $PKG/usr/share/$PRGNAM-$VERSION/miniapps/autodiff/admfem.hpp + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + CHANGELOG CITATION.cff {CODE_OF_CONDUCT,CONTRIBUTING}.md LICENSE doc \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/mfem/mfem.info b/academic/mfem/mfem.info new file mode 100644 index 0000000000..d39a1518f5 --- /dev/null +++ b/academic/mfem/mfem.info @@ -0,0 +1,10 @@ +PRGNAM="mfem" +VERSION="4.5" +HOMEPAGE="https://mfem.org" +DOWNLOAD="https://github.com/mfem/mfem/archive/v4.5/mfem-4.5.tar.gz" +MD5SUM="1a93d4d9982612f52b9434b93265b979" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/kile/slack-desc b/academic/mfem/slack-desc index a98e5da34c..118db0fce4 100644 --- a/academic/kile/slack-desc +++ b/academic/mfem/slack-desc @@ -6,14 +6,14 @@ # customary to leave one space after the ':' except on otherwise blank lines. |-----handy-ruler------------------------------------------------------| -kile: kile (Latex editor) -kile: -kile: Kile is a user friendly TeX/LaTeX editor for the KDE -kile: desktop environment. -kile: This package is a Beta version for use with KDE 4. -kile: -kile: Homepage: http://kile.sourceforge.net/ -kile: License: GNU General Public License v2 -kile: -kile: -kile: +mfem: mfem (library for finite element methods) +mfem: +mfem: +mfem: +mfem: MFEM is a free, lightweight, scalable C++ library for finite +mfem: element methods. +mfem: +mfem: +mfem: +mfem: +mfem: diff --git a/academic/minorminer/README b/academic/minorminer/README new file mode 100644 index 0000000000..c1d4ef7222 --- /dev/null +++ b/academic/minorminer/README @@ -0,0 +1,12 @@ + minorminer is a heuristic tool for minor embedding: given a minor +and target graph, it tries to find a mapping that embeds the minor +into the target. + minorminer is a tool for finding graph minors, developed to embed +Ising problems onto quantum annealers (QA). Where it can be used to +find minors in arbitrary graphs, it is particularly geared towards +the state of the art in QA: problem graphs of a few to a few hundred +variables, and hardware graphs of a few thousand qubits. + + + Optional building mode set with environment variables: + - TESTS=yes (performs tests, requires gtest) diff --git a/academic/minorminer/minorminer.SlackBuild b/academic/minorminer/minorminer.SlackBuild new file mode 100644 index 0000000000..caa9a029d1 --- /dev/null +++ b/academic/minorminer/minorminer.SlackBuild @@ -0,0 +1,140 @@ +#!/bin/bash + +# Slackware build script for minorminer + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM="minorminer" +VERSION=${VERSION:-0.2.9} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +# fix util.hpp +sed -i '19a#include <memory>' include/find_embedding/util.hpp + +# fix examples and tests CMakeLists.txt +sed -i '11s/ minorminer//' examples/CMakeLists.txt +sed -i '11s/ minorminer//' tests/CMakeLists.txt + +python3 setup.py install --root=$PKG + +if [ "${TESTS:-no}" == "yes" ]; then + cd tests + cmake \ + -DCMAKE_CXX_FLAGS="-I../include" . + make + ./run_tests + cd .. +fi + +# run tests (requires homebase, networkx and several other pkgs) +#for file in $(ls test_*.py); do +# PYTHONPATH=../build/lib.linux-x86_64-3.9 \ +# python3 -c "print ('$file'); exec(open('$file').read())" ; +#done + +# install includes +install -d $PKG/usr/include/minorminer +cp -av include/* $PKG/usr/include/minorminer + +# install examples +mkdir -p $PKG/usr/share/$PRGNAM-$VERSION +cp -a examples $PKG/usr/share/$PRGNAM-$VERSION + +# fix example +sed -i 's#\(../include\)/\(find_embedding\).hpp#/usr/include/minorminer/\2/\2.hpp#' $PKG/usr/share/$PRGNAM-$VERSION/examples/example.cpp + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + LICENSE README.rst docs \ + $PKG/usr/doc/$PRGNAM-$VERSION +# fix broken symlink and copy real file +rm $PKG/usr/doc/$PRGNAM-$VERSION/docs/source/parameter_checklist.txt +cp -av parameter_checklist.txt $PKG/usr/doc/$PRGNAM-$VERSION/docs/source/ + +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/minorminer/minorminer.info b/academic/minorminer/minorminer.info new file mode 100644 index 0000000000..a9ea741a1e --- /dev/null +++ b/academic/minorminer/minorminer.info @@ -0,0 +1,10 @@ +PRGNAM="minorminer" +VERSION="0.2.9" +HOMEPAGE="https://github.com/dwavesystems/minorminer" +DOWNLOAD="https://github.com/dwavesystems/minorminer/archive/0.2.9/minorminer-0.2.9.tar.gz" +MD5SUM="de59a2d16a94ee5853938cbf19d61a6f" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/minorminer/slack-desc b/academic/minorminer/slack-desc new file mode 100644 index 0000000000..125054455f --- /dev/null +++ b/academic/minorminer/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +minorminer: minorminer (heuristic tool for minor embedding) +minorminer: +minorminer: +minorminer: +minorminer: minorminer is a heuristic tool for minor embedding: given a minor +minorminer: and target graph, it tries to find a mapping that embeds the minor +minorminer: into the target. +minorminer: +minorminer: +minorminer: +minorminer: diff --git a/academic/mkDSSP/makefile.patch b/academic/mkDSSP/makefile.patch deleted file mode 100644 index 17563fde9a..0000000000 --- a/academic/mkDSSP/makefile.patch +++ /dev/null @@ -1,76 +0,0 @@ -Description: assorted fixes - [Maarten L. Hekkelman <m.hekkelman@cmbi.ru.nl>] - * DEST_DIR patched to DESTDIR - . - [Laszlo Kajan <lkajan@rostlab.org>] - * stripping is patched out so that it can be done by dh into a debug package - * line echo suppression is removed - * spelling errors in man page fixed - . - Upstream is aware of this patch. -Author: Maarten L. Hekkelman <m.hekkelman@cmbi.ru.nl> -Author: Laszlo Kajan <lkajan@rostlab.org> ---- a/makefile -+++ b/makefile -@@ -11,18 +11,16 @@ - - all: mkdssp - --include make.config -- - VERSION = 2.2.1 - - DEST_DIR ?= /usr/local - LIB_DIR = $(BOOST_LIB_DIR) - INC_DIR = $(BOOST_INC_DIR) --BIN_DIR = $(DEST_DIR)/bin --MAN_DIR = $(DEST_DIR)/man/man1 -+BIN_DIR = $(DESTDIR)$(DEST_DIR)/bin -+MAN_DIR = $(DESTDIR)$(DEST_DIR)/share/man/man1 - --BOOST_LIBS = thread filesystem program_options iostreams system --LIBS = $(BOOST_LIBS:%=boost_%$(BOOST_LIB_SUFFIX)) z bz2 -+BOOST_LIBS = thread program_options iostreams system -+LIBS = $(BOOST_LIBS:%=boost_%$(BOOST_LIB_SUFFIX)) - - DEFINES = USE_COMPRESSION LINUX VERSION='"$(VERSION)"' - CXX = g++ -@@ -49,22 +47,19 @@ - OBJECTS = $(OBJ_DIR)/mkdssp.o $(OBJ_DIR)/dssp.o $(OBJ_DIR)/primitives-3d.o $(OBJ_DIR)/structure.o $(OBJ_DIR)/utils.o $(OBJ_DIR)/mas.o $(OBJ_DIR)/iocif.o - - mkdssp: $(OBJECTS) -- @ echo linking $@ -- @ $(CXX) -static -o $@ $^ $(LDOPTS) -+ $(CXX) -o $@ $^ $(LDOPTS) - --include $(OBJECTS:%.o=%.d) -+-include $(OBJECTS:%.o=%.d) - - $(OBJECTS:.o=.d): - - $(OBJ_DIR): -- @ mkdir -p $(OBJ_DIR) -+ mkdir -p $(OBJ_DIR) - - $(OBJ_DIR)/%.o: %.cpp | $(OBJ_DIR) -- @ echo compiling $@ -- @ $(CXX) -MD -c -o $@ $< $(CFLAGS) -+ $(CXX) -MD -c -o $@ $< $(CPPFLAGS) $(CFLAGS) - - clean: -- install -d $(BIN_DIR) $(MAN_DIR) - rm -rf $(OBJ_DIR)/* mkdssp - - install: mkdssp -@@ -85,11 +80,3 @@ - @ cp doc/mkdssp.1 $(DIST_NAME)/doc/mkdssp.1 - tar czf $(DIST_NAME).tgz $(DIST_NAME) - cp $(DIST_NAME).tgz dssp_$(VERSION).orig.tar.gz -- --make.config: -- @echo "creating empty make.config file" -- @echo "# Set local options for make here" > make.config -- @echo "#BOOST_LIB_SUFFIX = -mt" >> make.config -- @echo "#BOOST_LIB_DIR = $(HOME)/projects/boost/lib" >> make.config -- @echo "#BOOST_INC_DIR = $(HOME)/projects/boost/include" >> make.config -- diff --git a/academic/mkDSSP/mkDSSP.SlackBuild b/academic/mkDSSP/mkDSSP.SlackBuild index 4a0e714a2c..d5461df266 100644 --- a/academic/mkDSSP/mkDSSP.SlackBuild +++ b/academic/mkDSSP/mkDSSP.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for mkDSSP -# Copyright 2013-2016 Petar Petrov slackalaxy@gmail.com +# Copyright 2013-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,27 +22,38 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=mkDSSP -SRCNAM=dssp -VERSION=${VERSION:-2.2.1} +VERSION=${VERSION:-4.0.3} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +SRCNAM=dssp if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -61,7 +72,7 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $SRCNAM-$VERSION -tar xvf $CWD/$SRCNAM-$VERSION.tgz +tar xvf $CWD/$SRCNAM-$VERSION.tar.gz cd $SRCNAM-$VERSION chown -R root:root . find -L . \ @@ -70,19 +81,20 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -# Thanks to Debian for the patches! -patch -p1 -i $CWD/makefile.patch -patch -p1 -i $CWD/thread_include.patch - -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ -BIN_DIR=/usr/bin \ -MAN_DIR=/usr/man/man1 \ -make - -make install DEST_DIR=$PKG \ -BIN_DIR=$PKG/usr/bin \ -MAN_DIR=$PKG/usr/man/man1 +sed -i "s|CMAKE_INSTALL_DATADIR}/man|CMAKE_INSTALL_PREFIX}/man|" CMakeLists.txt + +mkdir -p build +cd build + cmake \ + -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DLIB_SUFFIX=${LIBDIRSUFFIX} \ + -DBUILD_SHARED_LIBS=ON \ + -DCMAKE_BUILD_TYPE=Release .. + make + make install DESTDIR=$PKG +cd .. # Some programs (like aline) expect the binary to be called just "dssp" cd $PKG/usr/bin @@ -97,7 +109,7 @@ for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; r mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - changelog LICENSE_1_0.txt README.txt \ + LICENSE README.md \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References @@ -106,4 +118,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/mkDSSP/mkDSSP.info b/academic/mkDSSP/mkDSSP.info index 3f2ccdf323..494233066f 100644 --- a/academic/mkDSSP/mkDSSP.info +++ b/academic/mkDSSP/mkDSSP.info @@ -1,10 +1,10 @@ PRGNAM="mkDSSP" -VERSION="2.2.1" -HOMEPAGE="http://swift.cmbi.ru.nl/gv/dssp/" -DOWNLOAD="ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.2.1.tgz" -MD5SUM="0faa63ea1f0c69def077530de0cf84c1" +VERSION="4.0.3" +HOMEPAGE="https://swift.cmbi.umcn.nl/gv/dssp/DSSP_3.html" +DOWNLOAD="https://github.com/PDB-REDO/dssp/archive/v4.0.3/dssp-4.0.3.tar.gz" +MD5SUM="fac80f6b2ca0120c414510b420dc5b6a" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="" +REQUIRES="libcifpp" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/mkDSSP/thread_include.patch b/academic/mkDSSP/thread_include.patch deleted file mode 100644 index f0b462b19c..0000000000 --- a/academic/mkDSSP/thread_include.patch +++ /dev/null @@ -1,23 +0,0 @@ -Description: moving boost thread include out of header that does not use it - Patch is not yet forwarded upstream. -Author: Laszlo Kajan <lkajan@rostlab.org> ---- a/src/utils.h -+++ b/src/utils.h -@@ -10,7 +10,6 @@ - #endif - - #include <time.h> --#include <boost/thread.hpp> - #include <boost/lexical_cast.hpp> - #include <boost/format.hpp> - #include <boost/filesystem.hpp> ---- a/src/structure.cpp -+++ b/src/structure.cpp -@@ -18,6 +18,7 @@ - #define foreach BOOST_FOREACH - #include <boost/algorithm/string.hpp> - #include <boost/math/special_functions/round.hpp> -+#include <boost/thread.hpp> - - #include "align-2d.h" - #include "utils.h" diff --git a/academic/molequeue/README b/academic/molequeue/README new file mode 100644 index 0000000000..62e5ed704e --- /dev/null +++ b/academic/molequeue/README @@ -0,0 +1,20 @@ +MoleQueue is an open-source, cross-platform, system-tray resident +desktop application for abstracting, managing, and coordinating the +execution of tasks both locally and on remote computational resources. + +Users can set up local and remote queues that describe where the task +will be executed. Each queue can have programs, with templates to +facilitate the execution of the program. Input files can be staged, +and output files collected using a standard interface. + +It is a subproject of OpenChemistry needed by Avogadro 2. + +By default MoleQueue should be started as a resident service and +launched from a script or a shell command line. If you want to lauch +the Graphic Interface User using a desktop entry pass the variable +DESKTOP=yes to the slackbuild script: + +DESKTOP=yes ./molequeue.SlackBuild + +This may be useful if you want to launch the service only when you +are going to start Avogadro 2. diff --git a/academic/flashqard/doinst.sh b/academic/molequeue/doinst.sh index 4a25de5e6f..65c7e2eeb9 100644 --- a/academic/flashqard/doinst.sh +++ b/academic/molequeue/doinst.sh @@ -7,4 +7,3 @@ if [ -e usr/share/icons/hicolor/icon-theme.cache ]; then /usr/bin/gtk-update-icon-cache -f usr/share/icons/hicolor >/dev/null 2>&1 fi fi - diff --git a/academic/molequeue/molequeue.SlackBuild b/academic/molequeue/molequeue.SlackBuild new file mode 100644 index 0000000000..b1ac314514 --- /dev/null +++ b/academic/molequeue/molequeue.SlackBuild @@ -0,0 +1,136 @@ +#!/bin/bash + +# Slackware build script for molequeue. + +# Copyright 2020-2022 Giancarlo Dessì, Cagliari, IT +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=molequeue +VERSION=${VERSION:-0.9.0} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +mkdir -p build +cd build + cmake \ + -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DCMAKE_BUILD_TYPE=Release \ + -DENABLE_TESTING=OFF \ + -Wno-dev \ + .. + make + make install/strip DESTDIR=$PKG +cd .. + +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +# Remove redundant files installed by make install in /usr/share/doc/Molequeue +rm -rf $PKG/usr/share/doc +mkdir -p $PKG/install + +if [ "${DESKTOP:-no}" = "yes" ]; then + + #Copy application icon and create a desktop entry + + mkdir -p $PKG/usr/share/icons/hicolor/32x32/apps + cp -a $TMP/$PRGNAM-$VERSION/molequeue/app/icons/molequeue.png \ + $PKG/usr/share/icons/hicolor/32x32/apps + + mkdir -p $PKG/usr/share/applications + cat << EOF > $PKG/usr/share/applications/molequeue.desktop +[Desktop Entry] +Type=Application +Name=MoleQueue +GenericName=MoleQueue Server for Avogadro 2 +Comment=Desktop integration of high performance computing resources. +Exec=molequeue +Icon=/usr/share/icons/hicolor/32x32/apps/molequeue.png +Terminal=false +Categories=Qt;Science;Chemistry;Physics;Education; +X-KDE-StartupNotify=false +StartupNotify=false +EOF + cat $CWD/doinst.sh > $PKG/install/doinst.sh +else + rm -rf $PKG/usr/share +fi + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a *.md LICENSE $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/molequeue/molequeue.info b/academic/molequeue/molequeue.info new file mode 100644 index 0000000000..3b3945ec12 --- /dev/null +++ b/academic/molequeue/molequeue.info @@ -0,0 +1,10 @@ +PRGNAM="molequeue" +VERSION="0.9.0" +HOMEPAGE="https://www.openchemistry.org/projects/molequeue/" +DOWNLOAD="https://github.com/OpenChemistry/molequeue/archive/0.9.0/molequeue-0.9.0.tar.gz" +MD5SUM="28e707668bfaf2ebc615da54fc98002f" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Giancarlo Dessì" +EMAIL="slack@giand.it" diff --git a/academic/molequeue/slack-desc b/academic/molequeue/slack-desc new file mode 100644 index 0000000000..dbb89964a6 --- /dev/null +++ b/academic/molequeue/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +molequeue: molequeue (Desktop integration of high quality computing resources) +molequeue: +molequeue: This is an open-source, cross-platform, system-tray resident +molequeue: desktop application for abstracting, managing, and coordinating +molequeue: the execution of tasks both locally and on remote computational +molequeue: resources. +molequeue: MoleQueue is a project of OpenChemistry. +molequeue: +molequeue: https://www.openchemistry.org/projects/molequeue/ +molequeue: +molequeue: diff --git a/academic/mpb/README b/academic/mpb/README new file mode 100644 index 0000000000..4710eced99 --- /dev/null +++ b/academic/mpb/README @@ -0,0 +1,42 @@ +mpb (computes electromagnetic band structures and modes) + +MPB is a free and open-source software package for computing +electromagnetic band structures and modes. It saves results in hdf5 +format. + +This package requires: hdf5, libctl, lapack + +You may wish to also install: h5utils + +You very probably want to build a multi-processor version of this +code by adding the "--with-openmp" configure option. + +Configuration: + +If the build script can find the ATLAS libraries, it will adapt the +configure options to use them rather than the default lapack. + +You can add additional options to the command line using +the environment variable SBOPTIONS_MPB; e.g. to enable MPI +(multi-processor calculation) using openmp, use: + +SBOPTIONS_MPB="--with-openmp" ./mpb.Slackbuild + +Alternatively, if building non-interactively (e.g. if using slpkg), +use/create the file /etc/sbo_pkg_options.conf since this slackbuild +script will search it for options. Simply include a line starting +"mpb:" followed by options, e.g.: + +mpb: --with-openmp + +If you want to use mpich instead of openmp, you will have to recompile +the installed slackware fftw library with two additional configure +options, i.e. not only "--with-mpi" but also "--enable-type-prefix". + +Note: + +This mpb build script does *two* passes. This is so that when +MPI support is enabled, the first compiles the mpb-data utility, +then the second builds the full MPI version. The resulting package +includes both, with any MPI version of the files replacing the non- +MPI version. diff --git a/academic/mpb/mpb.SlackBuild b/academic/mpb/mpb.SlackBuild new file mode 100644 index 0000000000..b1d7ff0ec8 --- /dev/null +++ b/academic/mpb/mpb.SlackBuild @@ -0,0 +1,162 @@ +#!/bin/bash + +# Slackware build script for mpb + +# Copyright 2019,2020 Paul Kinsler, U.K. +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=mpb +VERSION=${VERSION:-1.11.1} +BUILD=${BUILD:-2} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +# change annoying underscores into hyphens +SVERSION=$(echo $VERSION | tr '_' '-') +# make a custom list of doc files in advance +DOCFILES="AUTHORS COPYING COPYRIGHT TODO README.md NEWS.md" + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$SVERSION +tar xvf $CWD/$PRGNAM-$SVERSION.tar.gz +cd $PRGNAM-$SVERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +# if there is no configure script, try to build one! +if [ ! -f ./configure ] ; then + ./autogen.sh +fi + +LOCALCONFIGS= +XDBFILE=/etc/sbo_pkg_options.conf +if [ -f ${XDBFILE} ] ; then + LOCALCONFIGS=${LOCALCONFIGS}" "$(grep "^${PRGNAM}:" ${XDBFILE} | grep -v '^#' | awk -F: '{print$2}') + echo Build options selected by file: LOCALCONFIGS=${LOCALCONFIGS} +fi +if [ -n "${SBOPTIONS_MPB}" ] ; then + LOCALCONFIGS=${LOCALCONFIGS}" "${SBOPTIONS_MPB} + echo Build options selected by environment: LOCALCONFIGS=${LOCALCONFIGS} +fi + +# check for the Atlas replacement for blas; if the libraries are found, +# add the configure option accordingly + +if [ -f /usr/lib/libatlas.a ] ; then + if [ -f /usr/lib/libatlas.so ] ; then + echo "NOTICE: libatlas was found, configure --with-blas=atlas" + LOCALCONFIGS=${LOCALCONFIGS}" --with-blas=atlas" + fi +fi + +# LOCALCONFIGS without any mpi requests so I can do a no-mpi compile. +SPLOCALCONFIGS=$(echo $LOCALCONFIGS | sed s/--with-mpi// | sed s/--with-openmp//) + + +# do two passes; first with no mpi (to get mpb-data), +# then a second *with* mpi + +CFLAGS="$SLKCFLAGS" \ +CPPFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --mandir=/usr/man \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --docdir=/usr/doc/$PRGNAM-$VERSION \ + --build=$ARCH-slackware-linux \ + $SPLOCALCONFIGS + +make +make install DESTDIR=$PKG + +CFLAGS="$SLKCFLAGS" \ +CPPFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --mandir=/usr/man \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --docdir=/usr/doc/$PRGNAM-$VERSION \ + --build=$ARCH-slackware-linux \ + $LOCALCONFIGS + +make +make install DESTDIR=$PKG + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +find $PKG/usr/man -type f -exec gzip -9 {} \; +for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +install -m 0644 $DOCFILES $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +rm -f $PKG/usr/lib*/*.la + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/mpb/mpb.info b/academic/mpb/mpb.info new file mode 100644 index 0000000000..bd24b0e499 --- /dev/null +++ b/academic/mpb/mpb.info @@ -0,0 +1,10 @@ +PRGNAM="mpb" +VERSION="1.11.1" +HOMEPAGE="https://github.com/NanoComp/mpb" +DOWNLOAD="https://github.com/NanoComp/mpb/releases/download/v1.11.1/mpb-1.11.1.tar.gz" +MD5SUM="99afe4e8e11427c62a896d8eadd1c205" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="lapack hdf5 libctl" +MAINTAINER="PaulKinsler" +EMAIL="dr.paul@kinsler.org" diff --git a/academic/mpb/slack-desc b/academic/mpb/slack-desc new file mode 100644 index 0000000000..221d698891 --- /dev/null +++ b/academic/mpb/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +mpb: mpb (computation of electromagnetic band structures and modes) +mpb: +mpb: MPB is a free and open-source software package for +mpb: computing electromagnetic band structures and modes. +mpb: +mpb: Homepage: https://github.com/NanoComp/mpb +mpb: +mpb: +mpb: +mpb: +mpb: diff --git a/academic/mrbayes/mrbayes.SlackBuild b/academic/mrbayes/mrbayes.SlackBuild index 2bf1289cb4..cd1d2a252a 100644 --- a/academic/mrbayes/mrbayes.SlackBuild +++ b/academic/mrbayes/mrbayes.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for mrbayes -# Copyright 2013-2019 Petar Petrov slackalaxy@gmail.com +# Copyright 2013-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,11 +22,14 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=mrbayes SRCNAM=MrBayes VERSION=${VERSION:-3.2.7a} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -36,7 +39,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -108,4 +118,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/mumsa/README b/academic/mumsa/README new file mode 100644 index 0000000000..3fad0cf560 --- /dev/null +++ b/academic/mumsa/README @@ -0,0 +1,17 @@ +Mumsa is a tool for automatic assessment of alignment quality. A number +of alternate (to be compared) multiple alignments have to be generated +and submitted. + +Mumsa computes: +- the average overlap score (AOS), reflecting the difficulty of aligning + the sequences +- multiple overlap score (MOS) indicating the quality of each individual + alignment. + +Both scores range between one and zero. + +CITING +Lassmann T, Sonnhammer EL. Kalign, Kalignvu and Mumsa: web servers for +multiple sequence alignment. Nucleic Acids Res. 2006 Jul 1;34(Web Server +issue): W596-9. doi: 10.1093/nar/gkl191. +PMID: 16845078; PMCID: PMC1538774 diff --git a/academic/mumsa/References.txt b/academic/mumsa/References.txt new file mode 100644 index 0000000000..5dd7f95313 --- /dev/null +++ b/academic/mumsa/References.txt @@ -0,0 +1,4 @@ +Lassmann T, Sonnhammer EL. Kalign, Kalignvu and Mumsa: web servers for +multiple sequence alignment. Nucleic Acids Res. 2006 Jul 1;34(Web Server +issue): W596-9. doi: 10.1093/nar/gkl191. +PMID: 16845078; PMCID: PMC1538774 diff --git a/academic/libqalculate/libqalculate.SlackBuild b/academic/mumsa/mumsa.SlackBuild index 86ade486fc..6d9d8cf01e 100644 --- a/academic/libqalculate/libqalculate.SlackBuild +++ b/academic/mumsa/mumsa.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash -# Slackware build script for libqalculate +# Slackware build script for <mumsa> -# Copyright 2016-2019 Larry Hajali <larryhaja[at]gmail[dot]com> +# Copyright 2022 Petar Petrov slackalaxy at gmail dot com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,14 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -PRGNAM=libqalculate -VERSION=${VERSION:-3.4.0} + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=mumsa +VERSION=${VERSION:-1.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +39,11 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -60,7 +68,7 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $PRGNAM-$VERSION -tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +tar xvf $CWD/$PRGNAM-$VERSION.tgz cd $PRGNAM-$VERSION chown -R root:root . find -L . \ @@ -69,34 +77,26 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; +sed -i "/^CFLAGS/s/=/+=/" Makefile CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ -./configure \ - --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ - --docdir=/usr/doc/$PRGNAM-$VERSION \ - --mandir=/usr/man \ - --disable-silent-rules \ - --enable-static=no \ - --disable-rpath \ - --enable-defs2doc \ - --with-libcurl \ - --with-icu \ - --build=$ARCH-slackware-linux - +PREFIX=/usr make make -make install DESTDIR=$PKG + +install -D -m755 $PRGNAM $PKG/usr/bin/$PRGNAM find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true -find $PKG/usr/man -type f -exec gzip -9 {} \; - -cp -a AUTHORS ChangeLog COPYING NEWS README* TODO $PKG/usr/doc/$PRGNAM-$VERSION +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + COPYING \ + $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +cat $CWD/References.txt > $PKG/usr/doc/$PRGNAM-$VERSION/References.txt mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/mumsa/mumsa.info b/academic/mumsa/mumsa.info new file mode 100644 index 0000000000..86eb69b883 --- /dev/null +++ b/academic/mumsa/mumsa.info @@ -0,0 +1,10 @@ +PRGNAM="mumsa" +VERSION="1.0" +HOMEPAGE="https://msa.sbc.su.se/cgi-bin/msa.cgi" +DOWNLOAD="https://msa.sbc.su.se/downloads/mumsa-1.0.tgz" +MD5SUM="80ad4dbd2dc2e5402ad9753c25cc896b" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/mumsa/slack-desc b/academic/mumsa/slack-desc new file mode 100644 index 0000000000..2f487a6eba --- /dev/null +++ b/academic/mumsa/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +mumsa: mumsa (A tool to assess MSA quality) +mumsa: +mumsa: Mumsa is a tool for automatic assessment of alignment quality. +mumsa: +mumsa: https://msa.sbc.su.se/cgi-bin/msa.cgi +mumsa: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538774/ +mumsa: +mumsa: +mumsa: +mumsa: +mumsa: diff --git a/academic/muscle/README b/academic/muscle/README index 4db82130b5..2a8b2c538d 100644 --- a/academic/muscle/README +++ b/academic/muscle/README @@ -3,7 +3,29 @@ nucleotide sequences. A range of options is provided that give you the choice of optimizing accuracy, speed, or some compromise between the two. -For details and citation: -Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high -accuracy and high throughput. Nucleic Acids Res. 32(5):1792-1797. -doi:10.1093/nar/gkh340 +Fast, accurate and easy to use +MUSCLE is one of the best-performing multiple alignment programs +according to published benchmark tests, with accuracy and speed that +are consistently better than CLUSTALW. MUSCLE can align hundreds of +sequences in seconds. Most users learn everything they need to know +about MUSCLE in a few minutes—only a handful of command-line options +are needed to perform common alignment tasks. + +NOTE about the "-stable" option no longer being supported: +The "-stable" option had a bug, which sometimes resulted in incorrect +alignments to be produced. The author has created a python script to +be used as a workaround. The SlackBuild includes it and its usage is: + + python muscle-stable.py input.fasta aligned.fasta > stable.fasta + +Papers +There are two papers. The first (NAR) introduced the algorithm, and is +the primary citation if you use the program. The second (in BMC Bio- +informatics) gives more technical details, including descriptions of +non-default options. + +Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high +accuracy and high throughput. Nucleic Acids Res. 32(5):1792-1797 + +Edgar, R.C. (2004) MUSCLE: a multiple sequence alignment method with +reduced time and space complexity BMC Bioinformatics, (5) 113 diff --git a/academic/muscle/muscle.1 b/academic/muscle/muscle.1 new file mode 100644 index 0000000000..057c81da47 --- /dev/null +++ b/academic/muscle/muscle.1 @@ -0,0 +1,135 @@ +.\" Title: MUSCLE +.\" Author: Robert Elgar +.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/> +.\" Date: 02/06/2008 +.\" Manual: Muscle Manual +.\" Source: muscle 3.7 +.\" +.TH "MUSCLE" "1" "02/06/2008" "muscle 3.7" "Muscle Manual" +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.SH "NAME" +muscle - Multiple Protein Sequence Alignment +.SH "SYNOPSIS" +.HP 7 +\fBmuscle\fR \fB\-in\ \fR\fB\fIinput\ file\ (fasta)\fR\fR [\fB\-out\ \fR\fB\fIoutput\ file\ (default\ fasta)\fR\fR] [\fB\-diags\fR] [\fB\-log\ \fR\fB\fIlog\ file\fR\fR] [\fB\-maxiters\ \fR\fB\fIn\fR\fR] [\fB\-maxhours\ \fR\fB\fIn\fR\fR] [\fB\-maxmb\ \fR\fB\fIm\fR\fR] [\fB\-html\fR] [\fB\-msf\fR] [\fB\-clw\fR] [\fB\-clwstrict\fR] [\fB\-log[a]\ \fR\fB\fIlogfile\fR\fR] [\fB\-quiet\fR] [\fB\-stable\fR] [\fB\-group\fR] [\fB\-version\fR] +.SH "DESCRIPTION" +.PP +This manual page documents briefly the +\fBmuscle\fR +command\. +.PP +\fBmuscle\fR +aligns protein sequences and is considered superior and faster than Clustal\ W\. +.SH "OPTIONS" +.PP +\fB\-in \fR\fB\fIinput file\fR\fR +.RS 4 +Path to FASTA formatted input file +.RE +.PP +\fB\-out \fR\fB\fIoutput file\fR\fR +.RS 4 +Path to output file, FASTA formatted by default +.RE +.PP +\fB\-diags\fR +.RS 4 +Find diagonals (faster for similar sequences) +.RE +.PP +\fB\-maxiters \fR\fB\fIn\fR\fR +.RS 4 +Maximum number of iterations (integer, default 16) +.RE +.PP +\fB\-maxhours \fR\fB\fIn\fR\fR +.RS 4 +Maximum time to iterate in hours (default no limit) +.RE +.PP +\fB\-maxmb \fR\fB\fIm\fR\fR +.RS 4 +Maximum memory to allocate in Mb (default 80% of RAM) +.RE +.PP +\fB\-html\fR +.RS 4 +Write output in HTML format (default FASTA) +.RE +.PP +\fB\-msf\fR +.RS 4 +Write output in MSF format (default FASTA) +.RE +.PP +\fB\-clw\fR +.RS 4 +Write output in Clustal\ W format (default FASTA) +.RE +.PP +\fB\-clwstrict\fR +.RS 4 +As \-clw, with \'CLUSTAL W (1\.81)\' header +.RE +.PP +\fB\-log[a] \fR\fB\fIlogfile\fR\fR +.RS 4 +Log to file (append if \-loga, overwrite if \-log) +.RE +.PP +\fB\-quiet\fR +.RS 4 +Do not write progress messages to stderr +.RE +.PP +\fB\-stable\fR +.RS 4 +Output sequences in input order (default is \-group) +.RE +.PP +\fB\-group\fR +.RS 4 +Group sequences by similarity (this is the default) +.RE +.PP +\fB\-version\fR +.RS 4 +Display version information and exit +.RE +.SH "SEE ALSO" +.PP + +\fBclustalw\fR(1), +\fBseaview\fR(1), +\fBt_coffee\fR(1)\. +.SH "AUTHORS" +.PP +\fBRobert Elgar\fR +.sp -1n +.IP "" 4 +Wrote Muscle\. +.PP +\fBSteffen Moeller\fR <\&moeller@debian\.org\&> +.sp -1n +.IP "" 4 +Wrote this manpage\. +.PP +\fBCharles Plessy\fR <\&charles\-debian\-nospam@plessy\.org\&> +.sp -1n +.IP "" 4 +Updated this manpage\. +.SH "COPYRIGHT" +Copyright \(co 2003, 2004 Steffen Moeller (manpage) +.br +Copyright \(co 2007, 2008 Charles Plessy (manpage) +.br +.PP +Muscle is in the public domain, and therefore not subjected to copyright\. +.PP +This manual page was written by Steffen Moeller moeller@debian\.org for the +Debian(TM) +system (but may be used by others)\. Permission is granted to copy, distribute and/or modify this document as if it were in public domain\. +.sp diff --git a/academic/muscle/muscle.SlackBuild b/academic/muscle/muscle.SlackBuild index 9e69c5b702..a0e6ea735b 100644 --- a/academic/muscle/muscle.SlackBuild +++ b/academic/muscle/muscle.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for muscle -# Copyright 2011-2019 Petar Petrov slackalaxy@gmail.com +# Copyright 2011-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,15 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=muscle VERSION=${VERSION:-3.8.1551} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +MANUAL=muscle_userguide3.8.pdf if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +40,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -63,6 +75,7 @@ rm -rf ${PRGNAM}-${VERSION} mkdir -p ${PRGNAM}-${VERSION} cd ${PRGNAM}-${VERSION} tar xvf $CWD/${PRGNAM}_src_${VERSION}.tar.gz +tar xvf $CWD/stable.tar.gz chown -R root:root . find -L . \ @@ -78,16 +91,25 @@ CFLAGS="$SLKCFLAGS" \ make install -D -m755 $PRGNAM $PKG/usr/bin/$PRGNAM +install -D -m755 stable.py $PKG/usr/bin/$PRGNAM-stable.py + +# Thanks to Debian for the man page +mkdir -p $PKG/usr/man/man1 +cp $CWD/$PRGNAM.1 $PKG/usr/man/man1/$PRGNAM.1 find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true +find $PKG/usr/man -type f -exec gzip -9 {} \; +for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done + mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +cat $CWD/$MANUAL > $PKG/usr/doc/$PRGNAM-$VERSION/$MANUAL cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/muscle/muscle.info b/academic/muscle/muscle.info index e7671cd1bc..e747bd6443 100644 --- a/academic/muscle/muscle.info +++ b/academic/muscle/muscle.info @@ -1,8 +1,12 @@ PRGNAM="muscle" VERSION="3.8.1551" HOMEPAGE="http://www.drive5.com/muscle/" -DOWNLOAD="http://www.drive5.com/muscle/muscle_src_3.8.1551.tar.gz" -MD5SUM="1b7c9661f275a82d3cf708f923736bf8" +DOWNLOAD="http://www.drive5.com/muscle/muscle_src_3.8.1551.tar.gz \ + http://www.drive5.com/muscle/stable.tar.gz \ + http://www.drive5.com/muscle/muscle_userguide3.8.pdf" +MD5SUM="1b7c9661f275a82d3cf708f923736bf8 \ + fceeab190ff13576bfd681a601e7859b \ + 58bb1b7989cf6f2c197dd46552759a40" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/muscle/slack-desc b/academic/muscle/slack-desc index 5e4e7da441..d3d95c0c28 100644 --- a/academic/muscle/slack-desc +++ b/academic/muscle/slack-desc @@ -13,7 +13,7 @@ muscle: or nucleotide sequences. A range of options is provided that give muscle: you the choice of optimizing accuracy, speed, or some compromise muscle: between the two. muscle: -muscle: Home: http://www.drive5.com/muscle/ -muscle: References: /usr/doc/muscle-3.8.31/References +muscle: http://www.drive5.com/muscle/ +muscle: http://www.drive5.com/muscle/stable.html muscle: muscle: diff --git a/academic/muscle5/README b/academic/muscle5/README new file mode 100644 index 0000000000..bdea0f68e6 --- /dev/null +++ b/academic/muscle5/README @@ -0,0 +1,28 @@ +MUSCLE 5: Next-generation MUSCLE + +Muscle v5 is a major re-write of MUSCLE based on new algorithms. + +* Highest accuracy, scalable to thousands of sequences: +Compared to previous versions, Muscle v5 is much more accurate, is often +faster, and scales to much larger datasets. At the time of writing (late +2021), Muscle v5 has the highest scores on multiple alignment benchmarks +including Balibase, Bralibase, Prefab and Balifam. It can align tens of +thousands of sequences with high accuracy on a low-cost commodity +computer (say, an 8-core Intel CPU with 32 Gb RAM). On large datasets, +Muscle v5 is 20-30% more accurate than MAFFT and Clustal-Omega. + +* Alignment ensembles: +Muscle v5 can generate ensembles of high-accuracy alternative +alignments. All replicates have equal average accuracy on benchmark +test, including the MSA made with default parameters. By comparing +results of downstream analysis (trees, structure prediction...) on +different replicates, you can assess the effects of alignment errors on +your study. + +* Manual: +https://drive5.com/muscle5/manual/ + +* Reference (included in the package) +R.C. Edgar (2021) "MUSCLE v5 enables improved estimates of phylogenetic +tree confidence by ensemble bootstrapping" +https://www.biorxiv.org/content/10.1101/2021.06.20.449169v1.full.pdf diff --git a/academic/muscle5/References b/academic/muscle5/References new file mode 100644 index 0000000000..e11f73531f --- /dev/null +++ b/academic/muscle5/References @@ -0,0 +1,5 @@ +References + +R.C. Edgar (2021) "MUSCLE v5 enables improved estimates of phylogenetic +tree confidence by ensemble bootstrapping" +https://www.biorxiv.org/content/10.1101/2021.06.20.449169v1.full.pdf diff --git a/academic/muscle5/muscle5.1 b/academic/muscle5/muscle5.1 new file mode 100644 index 0000000000..d1c2661ec2 --- /dev/null +++ b/academic/muscle5/muscle5.1 @@ -0,0 +1,93 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.48.5. +.TH MUSCLE "1" "January 2022" "muscle 5.1" "User Commands" +.SH NAME +muscle \- Multiple alignment program of protein sequences +.SH DESCRIPTION +MUSCLE is a multiple alignment program for protein sequences. MUSCLE +stands for multiple sequence comparison by log-expectation. In the +authors tests, MUSCLE achieved the highest scores of all tested +programs on several alignment accuracy benchmarks, and is also one of +the fastest programs out there. +.SH USAGE +.SS "Align FASTA input, write aligned FASTA (AFA) output:" +.IP +muscle \fB\-align\fR input.fa \fB\-output\fR aln.afa +.PP +Align large input using Super5 algorithm if \fB\-align\fR is too expensive, +typically needed with more than a few hundred sequences: +.IP +muscle \fB\-super5\fR input.fa \fB\-output\fR aln.afa +.SS "Single replicate alignment:" +.IP +muscle \fB\-align\fR input.fa \fB\-perm\fR PERM \fB\-perturb\fR SEED \fB\-output\fR aln.afa +muscle \fB\-super5\fR input.fa \fB\-perm\fR PERM \fB\-perturb\fR SEED \fB\-output\fR aln.afa +.IP +PERM is guide tree permutation none, abc, acb, bca (default none). +SEED is perturbation seed 0, 1, 2... (default 0 = don't perturb). +.PP +Ensemble of replicate alignments, output in Ensemble FASTA (EFA) format, +EFA has one aligned FASTA for each replicate with header line "<PERM.SEED": +.IP +muscle \fB\-align\fR input.fa \fB\-stratified\fR \fB\-output\fR stratified_ensemble.efa +muscle \fB\-align\fR input.fa \fB\-diversified\fR \fB\-output\fR diversified_ensemble.afa +.HP +\fB\-replicates\fR N +.IP +Number of replicates, defaults 4, 100, 100 for stratified, +.IP +diversified, resampled. With \fB\-stratified\fR there is one +replicate per guide tree permutation, total is 4 x N. +.PP +Generate resampled ensemble from existing ensemble by sampling columns +with replacement: +.IP +muscle \fB\-resample\fR ensemble.efa \fB\-output\fR resampled.efa +.HP +\fB\-maxgapfract\fR F +.IP +Maximum fraction of gaps in a column (F=0..1, default 0.5). +.HP +\fB\-minconf\fR CC +.IP +Minimum column confidence (CC=0..1, default 0.5). +.PP +If ensemble output filename has @, then one FASTA file is generated +for each replicate where @ is replaced by perm.s, otherwise all replicates +are written to one EFA file. +.SS "Calculate disperson of an ensemble:" +.IP +muscle \fB\-disperse\fR ensemble.efa +.SS "Extract replicate with highest total CC (diversified input recommended):" +.IP +muscle \fB\-maxcc\fR ensemble.efa \fB\-output\fR maxcc.afa +.SS "Extract aligned FASTA files from EFA file:" +.IP +muscle \fB\-efa_explode\fR ensemble.efa +.SS "Convert FASTA to EFA, input has one filename per line:" +.IP +muscle \fB\-fa2efa\fR filenames.txt \fB\-output\fR ensemble.efa +.PP +Update ensemble by adding two sequences of digits to each replicate, digits +are column confidence (CC) values, e.g. "73" means CC=0.73, "++" is CC=1.0: +.IP +muscle \fB\-addconfseqs\fR ensemble.efa \fB\-output\fR ensemble_cc.efa +.PP +Calculate letter confidence (LC) values, \fB\-ref\fR specifies the alignment to +compare against the ensemble (e.g. from \fB\-maxcc\fR), output is in aligned +FASTA format with LC values 0, 1 ... 9 instead of letters: +.IP +muscle \fB\-letterconf\fR ensemble.efa \fB\-ref\fR aln.afa \fB\-output\fR letterconf.afa +.HP +\fB\-html\fR aln.html +.IP +Alignment colored by LC in HTML format. +.HP +\fB\-jalview\fR aln.features +.IP +Jalview feature file with LC values and colors. +.SS "More documentation at:" +.IP +https://drive5.com/muscle +.SH AUTHOR + This manpage was written by Andreas Tille for the Debian distribution and + can be used for any other usage of the program. diff --git a/academic/muscle5/muscle5.SlackBuild b/academic/muscle5/muscle5.SlackBuild new file mode 100644 index 0000000000..541a2182a3 --- /dev/null +++ b/academic/muscle5/muscle5.SlackBuild @@ -0,0 +1,118 @@ +#!/bin/bash + +# Slackware build script for muscle5 + +# Copyright 2022 Petar Petrov slackalaxy@gmail.com +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=muscle5 +VERSION=${VERSION:-5.1} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +SRCNAM=muscle + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $SRCNAM-$VERSION +tar xvf $CWD/$SRCNAM-$VERSION.tar.gz +cd $SRCNAM-$VERSION + +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +cd src + +# do not create static executable +sed -i "s:LDFLAGS += -static:#LDFLAGS += -static:" Makefile +make CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" + +install -D -m755 Linux/$SRCNAM $PKG/usr/bin/$PRGNAM +cd .. + +# Thanks to Debian for the man page +mkdir -p $PKG/usr/man/man1 +cp $CWD/$PRGNAM.1 $PKG/usr/man/man1/$PRGNAM.1 + +# The Makefile strips the binary... +#find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ +# | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +find $PKG/usr/man -type f -exec gzip -9 {} \; +for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + CONTRIBUTING.md LICENSE README.md \ + $PKG/usr/doc/$PRGNAM-$VERSION + +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/muscle5/muscle5.info b/academic/muscle5/muscle5.info new file mode 100644 index 0000000000..1749642b98 --- /dev/null +++ b/academic/muscle5/muscle5.info @@ -0,0 +1,10 @@ +PRGNAM="muscle5" +VERSION="5.1" +HOMEPAGE="https://github.com/rcedgar/muscle" +DOWNLOAD="https://github.com/rcedgar/muscle/archive/v5.1/muscle-5.1.tar.gz" +MD5SUM="99b5ef38a119994e7a8f0ea7a12b5987" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/muscle5/slack-desc b/academic/muscle5/slack-desc new file mode 100644 index 0000000000..bc8ca32705 --- /dev/null +++ b/academic/muscle5/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +muscle5: muscle5 (MUSCLE 5: Next-generation MUSCLE) +muscle5: +muscle5: Muscle v5 is a major re-write of MUSCLE based on new algorithms. +muscle5: Compared to previous versions, Muscle v5 is much more accurate, +muscle5: faster, and scales to much larger datasets. +muscle5: +muscle5: https://drive5.com/muscle5/ +muscle5: https://drive5.com/muscle5/manual/ +muscle5: +muscle5: +muscle5: diff --git a/academic/ncbi-blast+/ncbi-blast+.SlackBuild b/academic/ncbi-blast+/ncbi-blast+.SlackBuild index 8796217010..26a8981142 100644 --- a/academic/ncbi-blast+/ncbi-blast+.SlackBuild +++ b/academic/ncbi-blast+/ncbi-blast+.SlackBuild @@ -1,10 +1,10 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for ncbi-blast+ # This takes the place of ncbi-blast-plus (2013-2019), which just # repackaged the binaries provided by upstream. -# Copyright 2013-2020 Petar Petrov slackalaxy@gmail.com +# Copyright 2013-2023 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -24,10 +24,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=ncbi-blast+ -VERSION=${VERSION:-2.10.0} +VERSION=${VERSION:-2.14.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} DIRNAM=ncbi-blast @@ -39,7 +42,11 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -85,7 +92,7 @@ cd c++ # Do not specify the libraries dir by the default way (--libdir=/lib${LIBDIRSUFFIX}), # because the libs will not be included in the package. CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS -Wno-narrowing" \ ./configure \ --prefix=/usr \ --libdir='${exec_prefix}'/lib${LIBDIRSUFFIX} \ @@ -111,6 +118,16 @@ make prefix=$PKG/usr install find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true +# fix a few permissions +chmod 0644 $PKG/usr/include/ncbi-tools++/algo/dustmask/*.tex +chmod 0644 $PKG/usr/include/ncbi-tools++/objects/gbproj/*.{hpp,h} +chmod 0644 $PKG/usr/include/ncbi-tools++/objects/taxon3/*.hpp +chmod 0644 $PKG/usr/include/ncbi-tools++/objtools/edit/*.hpp +chmod 0755 $PKG/usr/lib${LIBDIRSUFFIX}/*.so + +# remove static libs +rm -rf $PKG/usr/lib${LIBDIRSUFFIX}/*.a + mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild @@ -118,4 +135,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/ncbi-blast+/ncbi-blast+.info b/academic/ncbi-blast+/ncbi-blast+.info index 4c2a4057d1..135aa023f6 100644 --- a/academic/ncbi-blast+/ncbi-blast+.info +++ b/academic/ncbi-blast+/ncbi-blast+.info @@ -1,10 +1,10 @@ PRGNAM="ncbi-blast+" -VERSION="2.10.0" +VERSION="2.14.1" HOMEPAGE="https://blast.ncbi.nlm.nih.gov/" -DOWNLOAD="ftp://ftp.ncbi.nih.gov/blast/executables/blast+/2.10.0/ncbi-blast-2.10.0+-src.tar.gz" -MD5SUM="0be82e26787579c5d14517af63502197" +DOWNLOAD="ftp://ftp.ncbi.nih.gov/blast/executables/blast+/2.14.1/ncbi-blast-2.14.1+-src.tar.gz" +MD5SUM="e931f0821d26326b7493882f135f8f60" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="lmdb" +REQUIRES="" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/ncbi-blast/ncbi-blast.SlackBuild b/academic/ncbi-blast/ncbi-blast.SlackBuild index 72015cf2b0..0adf5cbdae 100644 --- a/academic/ncbi-blast/ncbi-blast.SlackBuild +++ b/academic/ncbi-blast/ncbi-blast.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for ncbi-blast -# Copyright 2013-2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2013-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,33 +22,42 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=ncbi-blast VERSION=${VERSION:-2.2.26} BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} SRCNAM=blast if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i386 ;; - arm*) ARCH=arm ;; + i?86) ARCH=i586 ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +if ! [ "$ARCH" = "x86_64" ] && ! [[ $ARCH =~ i?86 ]]; then + printf "\n\n$ARCH is not supported... \n" >/dev/stderr + exit 1 +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} set -e -if [ "$ARCH" != "i386" ] && [ "$ARCH" != "x86_64" ]; then - printf "\n\n$ARCH is not supported... \n" - exit 1 -fi - # Determine the source arch if [ "$ARCH" = "x86_64" ]; then SRCARCH="x64" @@ -107,4 +116,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/ncbi-edirect/README b/academic/ncbi-edirect/README new file mode 100644 index 0000000000..f318903e06 --- /dev/null +++ b/academic/ncbi-edirect/README @@ -0,0 +1,8 @@ +Entrez Direct: E-utilities on the Unix Command Line + +Entrez Direct (EDirect) provides access to the NCBI's suite of inter- +connected databases (publication, sequence, structure, gene, variation, +expression, etc.) from a Unix terminal window. Search terms are entered +as command-line arguments. Individual operations are connected with Unix +pipes to construct multi-step queries. Selected records can then be +retrieved in a variety of formats. diff --git a/academic/ncbi-edirect/ncbi-edirect.SlackBuild b/academic/ncbi-edirect/ncbi-edirect.SlackBuild new file mode 100644 index 0000000000..19ea8fed86 --- /dev/null +++ b/academic/ncbi-edirect/ncbi-edirect.SlackBuild @@ -0,0 +1,114 @@ +#!/bin/bash + +# Slackware build script for ncbi-edirect + +# Copyright 2023 Petar Petrov, slackalaxy@gmail.com +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=ncbi-edirect +VERSION=${VERSION:-20.5.20231007} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +MANPG=ncbi-entrez-direct_19.0.20230216+dfsg-2.debian.tar.xz + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +if [ "$ARCH" != "x86_64" ]; then + printf "\n$ARCH is not supported... \n" + exit 1 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +mkdir $PRGNAM-$VERSION +cd $PRGNAM-$VERSION + +tar xvf $CWD/edirect-$VERSION.tar.gz +cd edirect +tar xvf $CWD/$MANPG +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +# Move these to their proper place +mkdir -p $PKG/usr/share/$PRGNAM +mv ./{cmd,eutils} $PKG/usr/share/$PRGNAM + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +mv ./{help,readme.pdf,README} $PKG/usr/doc/$PRGNAM-$VERSION + +# remove these +rm -rf ./{CA.pm,cacert.pem,Mozilla-CA.tar.gz} + +# include the binaries +mkdir -p $PKG/usr/bin +gunzip -c $CWD/rchive.Linux.gz > $PKG/usr/bin/rchive.Linux +gunzip -c $CWD/transmute.Linux.gz > $PKG/usr/bin/transmute.Linux +gunzip -c $CWD/xtract.Linux.gz > $PKG/usr/bin/xtract.Linux +chmod 755 $PKG/usr/bin/* + +# thanks Debian for the man pages +mkdir -p $PKG/usr/man/man1 +cp -a debian/man/* $PKG/usr/man/man1 +rm -rf debian + +# move what's left +cp -a * $PKG/usr/bin + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +find $PKG/usr/man -type f -exec gzip -9 {} \; +for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/ncbi-edirect/ncbi-edirect.info b/academic/ncbi-edirect/ncbi-edirect.info new file mode 100644 index 0000000000..6124a85041 --- /dev/null +++ b/academic/ncbi-edirect/ncbi-edirect.info @@ -0,0 +1,18 @@ +PRGNAM="ncbi-edirect" +VERSION="20.5.20231007" +HOMEPAGE="https://www.ncbi.nlm.nih.gov/books/NBK179288/" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/20.5.20231007/edirect-20.5.20231007.tar.gz \ +https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/20.5.20231007/rchive.Linux.gz \ +https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/20.5.20231007/transmute.Linux.gz \ +https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/20.5.20231007/xtract.Linux.gz \ +http://deb.debian.org/debian/pool/main/n/ncbi-entrez-direct/ncbi-entrez-direct_19.0.20230216+dfsg-2.debian.tar.xz" +MD5SUM_x86_64="c86b7a39bf08d4fdcfd4894c2810f35b \ +81d15957b38f37c8896836fffe68cf6d \ +ef7f2ca1ad37685c3adffff5b2b15bce \ +67cdff6edaeef6fa6e3b104126538c55 \ +f640a8d59b75655b411c984c984efef0" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/ncbi-edirect/slack-desc b/academic/ncbi-edirect/slack-desc new file mode 100644 index 0000000000..8cbe8e8cd5 --- /dev/null +++ b/academic/ncbi-edirect/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +ncbi-edirect: ncbi-edirect (E-utilities on the Unix Command Line) +ncbi-edirect: +ncbi-edirect: Entrez Direct (EDirect) provides access to the NCBI's suite of +ncbi-edirect: interconnected databases from a Unix terminal window. +ncbi-edirect: +ncbi-edirect: https://www.ncbi.nlm.nih.gov/books/NBK179288/ +ncbi-edirect: +ncbi-edirect: +ncbi-edirect: +ncbi-edirect: +ncbi-edirect: diff --git a/academic/ncbi-rmblastn/ncbi-rmblastn.SlackBuild b/academic/ncbi-rmblastn/ncbi-rmblastn.SlackBuild index b78a2be545..451486417c 100644 --- a/academic/ncbi-rmblastn/ncbi-rmblastn.SlackBuild +++ b/academic/ncbi-rmblastn/ncbi-rmblastn.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for ncbi-rmblastn -# Copyright 2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2018-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,20 +22,27 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=ncbi-rmblastn VERSION=${VERSION:-2.2.28} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i386 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -43,11 +50,11 @@ OUTPUT=${OUTPUT:-/tmp} set -e # Determine the binary arch -if [ "$ARCH" = "x86_64" ]; then - BINARCH="x64" -else - BINARCH="ia32" -fi +case "$ARCH" in + x86_64) BINARCH="x64" ;; + i?86) BINARCH="ia32" ;; + *) echo "Unsupported ARCH '$ARCH'"; exit 1 ;; +esac rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT @@ -58,17 +65,14 @@ cd $PRGNAM-$VERSION chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ + -o -perm 511 \) -exec chmod 755 {} \+ -o \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \+ cd bin -install -D -m755 rmblastn $PKG/usr/bin/rmblastn +install -s -D -m755 rmblastn $PKG/usr/bin/rmblastn cd .. -find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ - | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true - mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a LICENSE README $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild @@ -77,4 +81,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/nco/README b/academic/nco/README index eebc302ed8..2b1492ef0e 100644 --- a/academic/nco/README +++ b/academic/nco/README @@ -1,9 +1,10 @@ NCO (netCDF Operators Software Stack) -The NCO toolkit manipulates and analyzes data stored in netCDF- accessible -formats, including DAP, HDF4, and HDF5. It exploits the geophysical -expressivity of many CF (Climate & Forecast) metadata conventions, the -flexible description of physical dimensions translated by UDUnits, the network -transparency of OPeNDAP, the storage features (e.g., compression, chunking, -groups) of HDF (the Hierarchical Data Format), and many powerful mathematical -and statistical algorithms of GSL (the GNU Scientific Library). +The NCO toolkit manipulates and analyzes data stored in netCDF- +accessible formats, including DAP, HDF4, and HDF5. It exploits the +geophysical expressivity of many CF (Climate & Forecast) metadata +conventions, the flexible description of physical dimensions translated +by UDUnits, the network transparency of OPeNDAP, the storage features +(e.g., compression, chunking, groups) of HDF (the Hierarchical Data +Format), and many powerful mathematical and statistical algorithms of +GSL (the GNU Scientific Library). diff --git a/academic/nco/doinst.sh b/academic/nco/doinst.sh new file mode 100644 index 0000000000..849153dbfd --- /dev/null +++ b/academic/nco/doinst.sh @@ -0,0 +1,7 @@ +if [ -x /usr/bin/install-info ]; then + /usr/bin/install-info --info-dir=usr/info usr/info/nco.info.gz 1> /dev/null 2>&1 + /usr/bin/install-info --info-dir=usr/info usr/info/nco.info-1.gz 1> /dev/null 2>&1 + /usr/bin/install-info --info-dir=usr/info usr/info/nco.info-1.gz 1> /dev/null 2>&1 + /usr/bin/install-info --info-dir=usr/info usr/info/nco.info-3.gz 1> /dev/null 2>&1 + /usr/bin/install-info --info-dir=usr/info usr/info/nco.info-4.gz 1> /dev/null 2>&1 +fi diff --git a/academic/nco/douninst.sh b/academic/nco/douninst.sh new file mode 100644 index 0000000000..6a6fb6c07b --- /dev/null +++ b/academic/nco/douninst.sh @@ -0,0 +1,9 @@ +if [ -x /usr/bin/install-info -a -d usr/info ]; then + ( + cd usr/info + rm -f dir + for i in *.info*; do + /usr/bin/install-info $i dir 1>/dev/null 2>&1 + done + ) +fi diff --git a/academic/nco/nco.SlackBuild b/academic/nco/nco.SlackBuild index 3a20201103..706e1316ed 100644 --- a/academic/nco/nco.SlackBuild +++ b/academic/nco/nco.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for nco -# Copyright 2020 Gregory J. L. Tourte <artourter@gmail.com> +# Copyright 2020-2024 Gregory J. L. Tourte <artourter@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,10 +23,13 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=nco -VERSION=${VERSION:-4.9.2} +VERSION=${VERSION:-5.2.4} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -36,7 +39,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -55,7 +65,7 @@ else LIBDIRSUFFIX="" fi -set -e # Exit on most errors +set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT @@ -65,10 +75,8 @@ tar xvf $CWD/$PRGNAM-$VERSION.tar.gz cd $PRGNAM-$VERSION chown -R root:root . find -L . \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + -perm /111 -a \! -perm 755 -a -exec chmod 755 {} + -o \ + \! -perm /111 -a \! -perm 644 -a -exec chmod 644 {} + CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ @@ -83,7 +91,6 @@ CXXFLAGS="$SLKCFLAGS" \ --disable-static \ --build=$ARCH-slackware-linux -# Compile the application and install it into the $PKG directory make make install DESTDIR=$PKG @@ -93,20 +100,21 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr find $PKG/usr/man -type f -exec gzip -9 {} \; for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done -# Compress info pages and remove the package's dir file rm -f $PKG/usr/info/dir gzip -9 $PKG/usr/info/*.info* -# Copy program documentation into the package mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a \ - AUTHORS CITATION COPYING COPYRIGHT INSTALL LICENSE README.md \ +cp -aL \ + AUTHORS CITATION COPYING COPYRIGHT ChangeLog LICENSE README.md \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild -# Copy the slack-desc (and a custom doinst.sh if necessary) into ./install +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh +cat $CWD/douninst.sh > $PKG/install/douninst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/nco/nco.info b/academic/nco/nco.info index 3a4b113fb2..b6064e2b16 100644 --- a/academic/nco/nco.info +++ b/academic/nco/nco.info @@ -1,8 +1,8 @@ PRGNAM="nco" -VERSION="4.9.2" +VERSION="5.2.4" HOMEPAGE="http://nco.sf.net" -DOWNLOAD="https://github.com/nco/nco/archive/4.9.2/nco-4.9.2.tar.gz" -MD5SUM="366a949084d404b0380af7426ed94648" +DOWNLOAD="https://github.com/nco/nco/archive/5.2.4/nco-5.2.4.tar.gz" +MD5SUM="b46ed9dcdc1a2c857811cb5698a0460c" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="netcdf udunits antlr2" diff --git a/academic/nco/slack-desc b/academic/nco/slack-desc index 15c846b9c3..a65912dc40 100644 --- a/academic/nco/slack-desc +++ b/academic/nco/slack-desc @@ -9,7 +9,7 @@ nco: nco (netCDF Operators Software Stack) nco: nco: The NCO toolkit manipulates and analyzes data stored in netCDF- -nco: accessible formats, including DAP, HDF4, and HDF5. It exploits the +nco: accessible formats, including DAP, HDF4, and HDF5. It exploits the nco: geophysical expressivity of many CF (Climate & Forecast) metadata nco: conventions, the flexible description of physical dimensions nco: translated by UDUnits, the network transparency of OPeNDAP, the diff --git a/academic/ncview/ncview.SlackBuild b/academic/ncview/ncview.SlackBuild index daa3914316..6cbd65f5a7 100644 --- a/academic/ncview/ncview.SlackBuild +++ b/academic/ncview/ncview.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for: ncview # Copyright (c) 2018 Ekin Akoglu <ekinakoglu@gmail.com> @@ -21,10 +21,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=ncview VERSION=${VERSION:-2.1.8} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -34,7 +37,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -94,4 +104,4 @@ mkdir $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/ngspice/ngspice.SlackBuild b/academic/ngspice/ngspice.SlackBuild index 26525cf138..db12c3aab6 100644 --- a/academic/ngspice/ngspice.SlackBuild +++ b/academic/ngspice/ngspice.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for ngspice and libngspice # Written by B. Jogai <jogaib {at} comcast [dot] net> @@ -6,10 +6,13 @@ # Set initial variables: +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=ngspice -VERSION=${VERSION:-31} -BUILD=${BUILD:-4} +VERSION=${VERSION:-42} +BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -19,7 +22,11 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -55,38 +62,48 @@ find -L . \ # Fix the lib path to the code modules if [ "$ARCH" = "x86_64" ]; then - sed -i "s%/lib/%/lib${LIBDIRSUFFIX}/%g" src/spinit.in + sed -i "s%/lib/%/lib${LIBDIRSUFFIX}/%g" src/spinit.in fi -./configure --prefix=/usr \ - --mandir=/usr/man \ - --infodir=/usr/info \ - --with-readline=yes \ - --enable-xspice \ - --enable-cider \ - --enable-openmp \ - --with-ngshared +mkdir release +cd release + + ../configure \ + --prefix=/usr \ + --mandir=/usr/man \ + --infodir=/usr/info \ + --enable-xspice \ + --enable-cider \ + --enable-openmp \ + --with-x \ + --disable-debug \ + --with-ngshared + make CFLAGS="$SLKCFLAGS" \ - ./configure \ - --prefix=/usr \ - --bindir=/usr/bin \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ - --mandir=/usr/man \ - --infodir=/usr/info \ - --disable-debug \ - --with-readline=yes \ - --enable-xspice \ - --enable-cider \ - --enable-shared \ - --disable-static \ - --enable-ndev \ - --enable-openmp \ - --build=$ARCH-slackware-linux + ../configure --prefix=/usr \ + --bindir=/usr/bin \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --mandir=/usr/man \ + --infodir=/usr/info \ + --disable-debug \ + --enable-xspice \ + --enable-cider \ + --enable-shared \ + --disable-static \ + --enable-ndev \ + --enable-openmp \ + --with-x \ + --build=$ARCH-slackware-linux + make make DESTDIR=$PKG install +# This has installed the configure output file as /usr/include/config.h. + +cd .. + find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true @@ -94,17 +111,32 @@ find $PKG/usr/man -type f -exec gzip -9 {} \; for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION/examples -cp -a ANALYSES AUTHORS BUGS COPYING ChangeLog DEVICES FAQ \ - INSTALL NEWS README* examples/ $PKG/usr/doc/$PRGNAM-$VERSION/ + +cp -a \ + ANALYSES AUTHORS BUGS COPYING ChangeLog DEVICES FAQ \ + NEWS README* examples/ \ + $PKG/usr/doc/$PRGNAM-$VERSION/ + cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild -cat $CWD/$PRGNAM-$VERSION-manual.pdf > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM-$VERSION-manual.pdf +cat $CWD/$PRGNAM-$VERSION-manual.pdf \ + > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM-$VERSION-manual.pdf + +# The shared library enabled by "--with-ngshared" +install -Dm755 ./release/src/.libs/libngspice.so.0.0.9 \ + "$PKG/usr/lib${LIBDIRSUFFIX}/libngspice.so.0.0.9" + +strip -s $PKG/usr/lib${LIBDIRSUFFIX}/libngspice.so.0.0.9 + +ln -s "libngspice.so.0.0.9" "$PKG/usr/lib${LIBDIRSUFFIX}/libngspice.so.0" +ln -s "libngspice.so.0.0.9" "$PKG/usr/lib${LIBDIRSUFFIX}/libngspice.so" -install -Dm755 src/.libs/libngspice.so.0.0.0 "$PKG/usr/lib${LIBDIRSUFFIX}/libngspice.so.0.0.0" -ln -s "libngspice.so.0.0.0" "$PKG/usr/lib${LIBDIRSUFFIX}/libngspice.so.0" -ln -s "libngspice.so.0.0.0" "$PKG/usr/lib${LIBDIRSUFFIX}/libngspice.so" +# The include file needed to use the shared library enabled by "--with-ngshared" +install -Dm644 ./src/include/ngspice/sharedspice.h $PKG/usr/include/ngspice/sharedspice.h +# Move the configure output file. +mv $TMP/$PRGNAM-$VERSION/release/src/include/ngspice/config.h $PKG/usr/include/ngspice/ +chmod 644 $PKG/usr/doc/ngspice-42/examples/klu/Circuits/libraries/*.lib -mkdir -p $PKG/usr/share/icons/hicolor/48x48/apps -install -m644 $CWD/$PRGNAM.png $PKG/usr/share/icons/hicolor/48x48/apps/$PRGNAM.png +install -Dm644 $CWD/$PRGNAM.png $PKG/usr/share/icons/hicolor/48x48/apps/$PRGNAM.png mkdir -p $PKG/usr/share/applications cat $CWD/$PRGNAM.desktop > $PKG/usr/share/applications/$PRGNAM.desktop @@ -114,4 +146,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/ngspice/ngspice.info b/academic/ngspice/ngspice.info index cc47ace1ae..d7fa1f2449 100644 --- a/academic/ngspice/ngspice.info +++ b/academic/ngspice/ngspice.info @@ -1,10 +1,10 @@ PRGNAM="ngspice" -VERSION="31" +VERSION="42" HOMEPAGE="http://ngspice.sourceforge.net/" -DOWNLOAD="https://sourceforge.net/projects/ngspice/files/ng-spice-rework/31/ngspice-31.tar.gz \ - https://sourceforge.net/projects/ngspice/files/ng-spice-rework/31/ngspice-31-manual.pdf" -MD5SUM="f50b4d8c6ecbf01acf121cd9edc3baab \ - cd746e20a1a23889acab51d918cc1f77" +DOWNLOAD="https://sourceforge.net/projects/ngspice/files/ng-spice-rework/42/ngspice-42.tar.gz \ + https://sourceforge.net/projects/ngspice/files/ng-spice-rework/42/ngspice-42-manual.pdf" +MD5SUM="84ab9e67127f9732639195dd63b98a5e \ + f1b1bf8a0bd18af216cbe0ccdbacb47f" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/novocraft/README-manual-download b/academic/novocraft/README-manual-download index c66ccd4c18..a93d14a215 100644 --- a/academic/novocraft/README-manual-download +++ b/academic/novocraft/README-manual-download @@ -1,10 +1,3 @@ The program can only be downloaded from the the novocraft website -This is the most direct way: -1) browse to http://www.novocraft.com/support/download/ -2) click on the plus-sign next to or on the boldline with the version -as given in the novocraft.info or novocraft.Slackbuild ($VERSION; this will be relatively close to the top) -3) click on the 'Novocraft Programs' for X86-64 Linux 3.1 Kernel -(it will link to http://www.novocraft.com/support/download/download.php?filename=V{$VERSION}/novocraftV{$VERSION}.Linux3.10.0.tar.gz) -download the program to your computer and -move it to the local repository of your Slackbuilding program (e.g. /var/cache/sbopkg/ ) +Version V3 is license free; diff --git a/academic/novocraft/novocraft.SlackBuild b/academic/novocraft/novocraft.SlackBuild index 0b09df1622..4a794ff455 100644 --- a/academic/novocraft/novocraft.SlackBuild +++ b/academic/novocraft/novocraft.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for novocraft -# Copyright 2017-19 Rob van Nues +# Copyright 2017-2021 Rob van Nues # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=novocraft VERSION=${VERSION:-3.09.03} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} EXTRAVERSION=${EXTRAVERSION:-Linux3.10.0} SRCNAM="${PRGNAM}V${VERSION}.${EXTRAVERSION}" @@ -38,7 +41,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -82,4 +92,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/octave/README b/academic/octave/README index 2a6c9cc1de..a0f531e127 100644 --- a/academic/octave/README +++ b/academic/octave/README @@ -1,38 +1,36 @@ GNU Octave is a high-level language, primarily intended for numerical -computations. It provides a convenient command line interface for solving -linear and nonlinear problems numerically, and for performing other numerical -experiments using a language that is mostly compatible with Matlab. It may -also be used as a batch-oriented language. +computations. It provides a convenient command line interface for +solving linear and nonlinear problems numerically, and for performing +other numerical experiments using a language that is mostly compatible +with Matlab. It may also be used as a batch-oriented language. + +This requires a BLAS/LAPACK implementation. Choose one of these package +sets: -This requires a BLAS/LAPACK implementation. Choose one of these package sets: * OpenBLAS (includes both a BLAS and a LAPACK implementation) * atlas (includes both a BLAS and a LAPACK implementation) * blas, lapack (the Netlib reference implementations) -If more than one set is installed (assuming there are no packaging conflicts) -then the auto-detection will use the first implementation from this list that -it finds. If in doubt, choose the Netlib reference implementations; other -packages that require a BLAS or LAPACK implementation may not build if they -are not configured to detect/use alternate implementations. -These optional dependencies will be used if found (see INSTALL.OCTAVE, in the -Octave source, for a description of what each dependency offers): -amd, camd, colamd, ccolamd, cholmod, umfpack, cxsparse, glpk, arpack-ng, -qrupdate, sundials, qhull, hdf5, fltk, ftgl, gl2ps, jdk, GraphicsMagick, -portaudio. +If more than one set is installed (assuming there are no packaging +conflicts) then the auto-detection will use the first implementation +from this list that it finds. If in doubt, choose the Netlib +reference implementations; other packages that require a BLAS or +LAPACK implementation may not build if they are not configured to +detect/use alternate implementations. -Octave can use either Qt4 or Qt5, and it will select Qt5 if both are -installed. You can force it to use a particular version by passing QT=4 or -QT=5 to the script. If Qt5 is selected and it does not find a Qt5 version of -QScintilla, then the editor window in the GUI will be disabled. If you need -the editor window and have both Qt versions installed, force it to use Qt4. +These optional dependencies will be used if found (see INSTALL.OCTAVE, +in the Octave source, for a description of what each dependency +offers): amd, camd, colamd, ccolamd, cholmod, umfpack, spqr, cxsparse, +glpk, arpack-ng, qrupdate, sundials, qhull, hdf5, fltk, ftgl, gl2ps, +jdk, GraphicsMagick, portaudio, rapidjson. -Octave can use ImageMagick (part of Slackware) or GraphicsMagick (available -from SBo) for image-reading functionality. If both are installed, -GraphicsMagick will be selected by default, since ImageMagick is not -well-supported by the Octave developers. If you have problems with -ImageMagick, try rebuilding Octave with GraphicsMagick, or pass MAGICK="" to -the script. +Octave can use ImageMagick (part of Slackware) or GraphicsMagick +(available from SBo) for image-reading functionality. If both +are installed, GraphicsMagick will be selected by default, +since ImageMagick is not well-supported by the Octave developers. +If you have problems with ImageMagick, try rebuilding Octave with +GraphicsMagick, or pass MAGICK="" to the script. -If you have arpack installed and the configure script segfaults when trying to -detect arpack, try switching to arpack-ng (which is partly maintained by -Octave developers). +If you have arpack installed and the configure script segfaults when +trying to detect arpack, try switching to arpack-ng (which is partly +maintained by Octave developers). diff --git a/academic/octave/octave.SlackBuild b/academic/octave/octave.SlackBuild index fb2d909a46..7fba88f533 100644 --- a/academic/octave/octave.SlackBuild +++ b/academic/octave/octave.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for octave -# Copyright 2012-2020 Kyle Guinn <elyk03@gmail.com> +# Copyright 2012-2024 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=octave -VERSION=${VERSION:-5.2.0} +VERSION=${VERSION:-8.4.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$(uname -m)" in @@ -35,17 +38,18 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM-$VERSION +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="AUTHORS BUGS CITATION COPYING ChangeLog INSTALL* NEWS README" -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" - LIBDIRSUFFIX="" -elif [ "$ARCH" = "i586" ]; then +if [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then @@ -60,13 +64,17 @@ else fi # Use GraphicsMagick by default. Fall back on ImageMagick from the full -# Slackware install if it's not present. Requires a patch for this bug: -# https://savannah.gnu.org/bugs/?49653 +# Slackware install if it's not present. # # GraphicsMagick is default due to the fact that the Octave devs mainly test # with that, and went several releases before noticing ImageMagick was broken. # If ImageMagick doesn't work, install GraphicsMagick, or set MAGICK="". -MAGICK=${MAGICK-GraphicsMagick} +# +# TODO: ImageMagick may no longer be compatible. The --with-magick argument +# should be the name of a pkg-config file. Documentation suggests +# "ImageMagick++" which does not exist. "ImageMagick" and "Magick++" exist; +# the former does not pass configure checks, the latter fails at compile time. +MAGICK=${MAGICK-GraphicsMagick++} if [ -n "$MAGICK" ] && ! pkg-config --exists $MAGICK; then MAGICK=ImageMagick fi @@ -74,12 +82,6 @@ if [ -n "$MAGICK" ]; then MAGICK="--with-magick=$MAGICK" fi -# Allow forcing a particular version of Qt. Set QT=4 or QT=5. -# If unset, Octave will decide, and it prefers version 5. -if [ -n "$QT" ]; then - QT="--with-qt=$QT" -fi - set -e rm -rf $PKG @@ -91,7 +93,6 @@ cd $PRGNAM-$VERSION chown -R root:root . chmod -R u+w,go-w,a+rX-st . -patch -p1 < $CWD/patches/imagemagick.diff # https://savannah.gnu.org/bugs/?49653 patch -p1 < $CWD/patches/atlas-lib-rename.diff autoreconf -vif @@ -100,30 +101,27 @@ autoreconf -vif # If you live far enough east or west that the date contained in version.texi # does not match that file's timestamp when printed accounting for your # timezone, then the docs get rebuilt with your local date. -# -# The TeX environment in Slackware 14.1 fails to build the DVI and PDF -# targets in Octave 3.8.1. Maybe it works with a recent version of TeXLive? find . -name stamp-vti -exec touch {} + ./configure \ --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ + --libdir=\${exec_prefix}/lib${LIBDIRSUFFIX} \ --sysconfdir=/etc \ --localstatedir=/var \ - --mandir=/usr/man \ - --infodir=/usr/info \ - --docdir=/usr/doc/$PRGNAM-$VERSION \ + --mandir=\${prefix}/man \ + --infodir=\${prefix}/info \ + --docdir=\${prefix}/doc/$PRGNAM-$VERSION \ --disable-dependency-tracking \ --with-openssl=auto \ ${MAGICK} \ - ${QT} \ --build=$ARCH-slackware-linux \ CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ FFLAGS="$SLKCFLAGS" \ make -make check +# TODO: May fail if not all optional deps are installed (gl2ps in particular). +#make check make install-strip DESTDIR=$PKG find $PKG/usr/lib${LIBDIRSUFFIX} -name '*.la' -delete @@ -142,4 +140,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/octave/octave.info b/academic/octave/octave.info index a4ea3e666a..13eccf569d 100644 --- a/academic/octave/octave.info +++ b/academic/octave/octave.info @@ -1,8 +1,8 @@ PRGNAM="octave" -VERSION="5.2.0" +VERSION="8.4.0" HOMEPAGE="https://www.gnu.org/software/octave/" -DOWNLOAD="https://ftp.gnu.org/gnu/octave/octave-5.2.0.tar.lz" -MD5SUM="3c621e85026d4a807f5639901a41ae71" +DOWNLOAD="https://ftpmirror.gnu.org/gnu/octave/octave-8.4.0.tar.lz" +MD5SUM="c7146cef6666200c5c835ecacf950804" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="%README% lapack" diff --git a/academic/octave/patches/imagemagick.diff b/academic/octave/patches/imagemagick.diff deleted file mode 100644 index 7a15122a18..0000000000 --- a/academic/octave/patches/imagemagick.diff +++ /dev/null @@ -1,12 +0,0 @@ -diff --git a/libinterp/corefcn/__magick_read__.cc b/libinterp/corefcn/__magick_read__.cc ---- a/libinterp/corefcn/__magick_read__.cc -+++ b/libinterp/corefcn/__magick_read__.cc -@@ -42,6 +42,8 @@ - #include <Magick++.h> - #include <clocale> - -+using Magick::Quantum; // https://savannah.gnu.org/bugs/?49653 -+ - // In theory, it should be enough to check the class: - // Magick::ClassType - // PseudoClass: diff --git a/academic/openboard/README b/academic/openboard/README new file mode 100644 index 0000000000..75711418bc --- /dev/null +++ b/academic/openboard/README @@ -0,0 +1,7 @@ +OpenBoard is an open source cross-platform teaching software for +interactive whiteboard designed primarily for use in schools and +universities. It can be used both with interactive whiteboards or +in a dual-screen setup with a pen-tablet display and a beamer. + +NOTE: Support for Qt6 is available upstream but not yet tested +by maintainer. diff --git a/academic/openboard/doinst.sh b/academic/openboard/doinst.sh new file mode 100644 index 0000000000..f39d8d4dfa --- /dev/null +++ b/academic/openboard/doinst.sh @@ -0,0 +1,3 @@ +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications +fi diff --git a/academic/openboard/openboard.SlackBuild b/academic/openboard/openboard.SlackBuild new file mode 100644 index 0000000000..d244896916 --- /dev/null +++ b/academic/openboard/openboard.SlackBuild @@ -0,0 +1,112 @@ +#!/bin/bash + +# Slackware build script for openboard + +# Copyright 2021-2023 Willy Sudiarto Raharjo <willysr@slackbuilds.org> +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR ''AS IS'' AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=openboard +SRCNAM=OpenBoard +VERSION=${VERSION:-1.7.0} +SRCVER=$(echo $VERSION | tr _ -) +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2" +else + SLKCFLAGS="-O2" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $SRCNAM-$SRCVER +tar xvf $CWD/$SRCNAM-$SRCVER.tar.gz +cd $SRCNAM-$SRCVER +chown -R root:root . +find . -type d -exec chmod 0755 {} \; +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +# Thanks to ArchLinux for these patches +patch -p1 < $CWD/quazip.patch +sed -i "s|lquazip5|lquazip1-qt5|g" OpenBoard.pro + +# Add changes for current +# Thanks to Robby Workman for the idea +QUAZIPVER=`pkg-config --modversion quazip1-qt5` +sed -i "s|QuaZip-Qt5-1.1|QuaZip-Qt5-$QUAZIPVER|g" OpenBoard.pro plugins/cffadaptor/UBCFFAdaptor.pro + +qmake-qt5 OpenBoard.pro -spec linux-g++ +make + +mkdir -p $PKG/opt/openboard $PKG/usr/share/applications/ $PKG/usr/bin +for i in customizations etc i18n library; do + cp -rp resources/$i $PKG/opt/openboard; +done + +cp -rp resources/images/OpenBoard.png $PKG/opt/openboard/ +cp -rp build/linux/release/product/OpenBoard $PKG/opt/openboard/ + +install -D -m 644 $CWD/openboard.desktop $PKG/usr/share/applications/openboard.desktop +( + cd $PKG/usr/bin + ln -s /opt/openboard/OpenBoard $PKG/usr/bin/openboard +) +strip --strip-unneeded /$PKG/opt/openboard/OpenBoard + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/openboard/openboard.desktop b/academic/openboard/openboard.desktop new file mode 100644 index 0000000000..e6663332ba --- /dev/null +++ b/academic/openboard/openboard.desktop @@ -0,0 +1,10 @@ +[Desktop Entry] +Type=Application +Name=OpenBoard +Comment=OpenBoard, an interactive white board application +Exec=openboard %f +Icon=/opt/openboard/OpenBoard.png +StartupNotify=true +Terminal=false +MimeType=application/ubz +Categories=Education; diff --git a/academic/openboard/openboard.info b/academic/openboard/openboard.info new file mode 100644 index 0000000000..20a8614784 --- /dev/null +++ b/academic/openboard/openboard.info @@ -0,0 +1,10 @@ +PRGNAM="openboard" +VERSION="1.7.0" +HOMEPAGE="https://github.com/OpenBoard-org/OpenBoard/" +DOWNLOAD="https://github.com/OpenBoard-org/OpenBoard/archive/v1.7.0/OpenBoard-1.7.0.tar.gz" +MD5SUM="8e4b9780efffbd1adca5582fa161fd7e" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="libpaper libass x264 libfdk-aac" +MAINTAINER="Willy Sudiarto Raharjo" +EMAIL="willysr@slackbuilds.org" diff --git a/academic/openboard/quazip.patch b/academic/openboard/quazip.patch new file mode 100644 index 0000000000..6a5cb79865 --- /dev/null +++ b/academic/openboard/quazip.patch @@ -0,0 +1,41 @@ +--- OpenBoard-1.6.0a/plugins/cffadaptor/UBCFFAdaptor.pro.orig 2020-04-07 08:26:29.240677360 +0700 ++++ OpenBoard-1.6.0a/plugins/cffadaptor/UBCFFAdaptor.pro 2020-04-07 08:27:03.695993158 +0700 +@@ -39,7 +39,7 @@ + QMAKE_POST_LINK += bash postScript_mac.sh "$$DESTDIR" "$$SANKORE_DIR/$$BUILD_DIR/product/Open-Sankore.app/Contents/MacOS" + } + +-LIBS += "-L$$THIRD_PARTY_PATH/quazip/lib/$$SUB_DIR" "-lquazip" ++LIBS += "-lquazip1-qt5" + + QT += xml xmlpatterns core + QT += gui +@@ -51,10 +51,7 @@ + + INCLUDEPATH += src + +-DEPENDPATH += $$THIRD_PARTY_PATH/quazip/ +-INCLUDEPATH += $$THIRD_PARTY_PATH/quazip/ +-include($$THIRD_PARTY_PATH/quazip/quazip.pri) +- ++INCLUDEPATH += /usr/include/QuaZip-Qt5-1.1/quazip/ + + SOURCES += \ + src/UBCFFAdaptor.cpp +@@ -66,4 +63,4 @@ + src/UBCFFConstants.h + + RESOURCES += \ +- resources/resources.qrc +\ No newline at end of file ++ resources/resources.qrc +--- OpenBoard-1.7.0/OpenBoard.pro.orig 2023-12-10 12:06:17.808153181 +0700 ++++ OpenBoard-1.7.0/OpenBoard.pro 2023-12-10 12:10:09.448432404 +0700 +@@ -470,7 +470,7 @@ + INCLUDEPATH += "/usr/include/quazip6" + } else { + LIBS += -lquazip5 +- INCLUDEPATH += "/usr/include/quazip5" ++ INCLUDEPATH += "/usr/include/QuaZip-Qt5-1.1/quazip" + } + + LIBS += -lpoppler diff --git a/academic/Mnemosyne/slack-desc b/academic/openboard/slack-desc index eaef720461..a3a20c653a 100644 --- a/academic/Mnemosyne/slack-desc +++ b/academic/openboard/slack-desc @@ -6,14 +6,14 @@ # customary to leave one space after the ':' except on otherwise blank lines. |-----handy-ruler------------------------------------------------------| -Mnemosyne: Mnemosyne (A free flash-card tool) -Mnemosyne: -Mnemosyne: It's a free flash-card tool which optimizes your learning process. -Mnemosyne: uses a sophisticated algorithm to schedule the best time for -Mnemosyne: a card to come up for review. Difficult cards that you tend to forget -Mnemosyne: quickly will be scheduled more often, while Mnemosyne won't -Mnemosyne: waste your time on things you remember well. -Mnemosyne: -Mnemosyne: -Mnemosyne: -Mnemosyne: +openboard: openboard (Interactive whiteboard) +openboard: +openboard: OpenBoard is an open source cross-platform teaching software for +openboard: interactive whiteboard designed primarily for use in schools and +openboard: universities. It can be used both with interactive whiteboards or +openboard: in a dual-screen setup with a pen-tablet display and a beamer. +openboard: +openboard: +openboard: +openboard: +openboard: diff --git a/academic/pal2nal/pal2nal.SlackBuild b/academic/pal2nal/pal2nal.SlackBuild index cec2f00e83..6326105755 100644 --- a/academic/pal2nal/pal2nal.SlackBuild +++ b/academic/pal2nal/pal2nal.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for pal2nal -# Copyright 2017-2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2017-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,15 +22,25 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=pal2nal VERSION=${VERSION:-14.1} SRCVER=v14.1 BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} ARCH=noarch -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -65,4 +75,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/paml/LICENSE b/academic/paml/LICENSE deleted file mode 100644 index b58e250862..0000000000 --- a/academic/paml/LICENSE +++ /dev/null @@ -1,3 +0,0 @@ -PAML is maintained and distributed for academic use free of charge by -Ziheng Yang. ANSI C source codes are distributed for UNIX/Linux/Mac -OSX, and executables are provided for MS Windows. diff --git a/academic/paml/paml.SlackBuild b/academic/paml/paml.SlackBuild index 0a6759536a..d27df64db3 100644 --- a/academic/paml/paml.SlackBuild +++ b/academic/paml/paml.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for paml -# Copyright 2013-2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2013-2023 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=paml -VERSION=${VERSION:-4.9h} +VERSION=${VERSION:-4.10.6} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,22 +38,29 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} if [ "$ARCH" = "i586" ]; then - SLKCFLAGS="-O2 -march=i586 -mtune=i686" + SLKCFLAGS="-O2 -march=i586 -mtune=i686 -fcommon" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then - SLKCFLAGS="-O2 -march=i686 -mtune=i686" + SLKCFLAGS="-O2 -march=i686 -mtune=i686 -fcommon" LIBDIRSUFFIX="" elif [ "$ARCH" = "x86_64" ]; then - SLKCFLAGS="-O2 -fPIC" + SLKCFLAGS="-O2 -fPIC -fcommon" LIBDIRSUFFIX="64" else - SLKCFLAGS="-O2" + SLKCFLAGS="-O2 -fcommon" LIBDIRSUFFIX="" fi @@ -59,9 +69,9 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf ${PRGNAM}${VERSION} -tar xvf $CWD/${PRGNAM}${VERSION}.tgz -cd ${PRGNAM}${VERSION} +rm -rf ${PRGNAM}-${VERSION} +tar xvf $CWD/${PRGNAM}-${VERSION}.tar.gz +cd ${PRGNAM}-${VERSION} chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -97,12 +107,10 @@ install -D -m755 evolverNSbranches $PKG/usr/libexec/$PRGNAM/evolverNSbranches install -D -m755 evolverNSbranchsites $PKG/usr/libexec/$PRGNAM/evolverNSbranchsites install -D -m755 evolverNSsites $PKG/usr/libexec/$PRGNAM/evolverNSsites -# Compile and install TreeTime -cc $SLKCFLAGS -o TreeTimeJeff TreeTimeJeff.c tools.c -lm -install -D -m755 TreeTimeJeff $PKG/usr/libexec/$PRGNAM/TreeTimeJeff - -# Rename the local README, so we include it in the package. -mv README.txt README-compiling.txt +# This does not build at the moment, so let's disable it for now +# # Compile and install TreeTime +# cc $SLKCFLAGS -o TreeTimeJeff TreeTimeJeff.c tools.c -lm +# install -D -m755 TreeTimeJeff $PKG/usr/libexec/$PRGNAM/TreeTimeJeff # Compile and install NEB, BEB and BranchSite cd ../Technical/Simulation/Codon @@ -114,38 +122,29 @@ install -D -m755 PositiveSitesBEB $PKG/usr/libexec/$PRGNAM/PositiveSitesBEB install -D -m755 PositiveSitesBS $PKG/usr/libexec/$PRGNAM/PositiveSitesBS install -D -m755 PositiveSitesNEB $PKG/usr/libexec/$PRGNAM/PositiveSitesNEB -# Rename this README too so we include it in the package. -mv README.txt README-codon.txt - # Compile and install Multiruns cd .. cc -o multiruns $SLKCFLAGS multiruns.c -lm install -D -m755 multiruns $PKG/usr/libexec/$PRGNAM/multiruns -cd $TMP/${PRGNAM}${VERSION} +cd $TMP/${PRGNAM}-${VERSION} # Include sample system files and example experimental data. -mkdir -p $PKG/usr/share/$PRGNAM/{aa,codon,ctl,dat,nuc,paup,trees} -cp -a *.dat dat/* $PKG/usr/share/$PRGNAM/dat -cp -a Technical/Simulation/Codon/{codeml.ctl,*.dat} \ - $PKG/usr/share/$PRGNAM/codon +mkdir -p $PKG/usr/share/$PRGNAM/Simulation/Codon +cp -a src/*.ctl dat $PKG/usr/share/$PRGNAM +cp -a Technical/Simulation/Codon/{codeml.ctl,*.dat,README.txt} \ + $PKG/usr/share/$PRGNAM/Simulation/Codon cp -a examples $PKG/usr/share/$PRGNAM -cp -a *.aa $PKG/usr/share/$PRGNAM/aa -cp -a *.ctl $PKG/usr/share/$PRGNAM/ctl -cp -a *.nuc $PKG/usr/share/$PRGNAM/nuc -cp -a paup* $PKG/usr/share/$PRGNAM/paup -cp -a *.trees $PKG/usr/share/$PRGNAM/trees find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a README.txt GeneticCode.txt doc/* src/README-compiling.txt \ - Technical/{Pt/eigenQREV.pdf,Simulation/{multiruns.txt,Codon/README-codon.txt}}\ +cp -a README.md LICENSE doc/* \ $PKG/usr/doc/$PRGNAM-$VERSION -cat $CWD/MCMCtree.Tutorials.pdf > $PKG/usr/doc/$PRGNAM-$VERSION/MCMCtree.Tutorial.pdf +cp Technical/Pt/eigenQREV.pdf $PKG/usr/doc/$PRGNAM-$VERSION +cp $CWD/MCMCtreeDOC.pdf $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild -cat $CWD/LICENSE > $PKG/usr/doc/$PRGNAM-$VERSION/LICENSE # Fix permissions. find $PKG/usr/{doc,share} -type d -exec chmod 755 {} \; -o \ @@ -155,4 +154,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/paml/paml.info b/academic/paml/paml.info index 3617cf5097..38bdd3d6ee 100644 --- a/academic/paml/paml.info +++ b/academic/paml/paml.info @@ -1,10 +1,10 @@ PRGNAM="paml" -VERSION="4.9h" -HOMEPAGE="http://abacus.gene.ucl.ac.uk/software/paml.html" -DOWNLOAD="http://abacus.gene.ucl.ac.uk/software/paml4.9h.tgz \ - http://ponce.cc/slackware/sources/repo/MCMCtree.Tutorials.pdf" -MD5SUM="b45d60cc0a82e4835e8dcda6a4c32040 \ - 29c851d887eea56b949c01ab42cc48fb" +VERSION="4.10.6" +HOMEPAGE="https://github.com/abacus-gene/paml/" +DOWNLOAD="https://github.com/abacus-gene/paml/archive/v4.10.6/paml-4.10.6.tar.gz \ + https://raw.githubusercontent.com/slackalaxy/sources/main/MCMCtreeDOC.pdf" +MD5SUM="4a9b10fd6326f8ec51f1e0e9b6cc0352 \ + 99de7c0241b7152d619d899d72775410" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/pamlX/pamlX.SlackBuild b/academic/pamlX/pamlX.SlackBuild index e25f9f4651..c1a5f1e1cc 100644 --- a/academic/pamlX/pamlX.SlackBuild +++ b/academic/pamlX/pamlX.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for pamlX -# Copyright 2013-2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2013-2023 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=pamlX VERSION=${VERSION:-1.3.1} -BUILD=${BUILD:-6} +BUILD=${BUILD:-8} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -69,13 +79,15 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; +. /etc/profile.d/qt4.sh + # Fix the path where pamlX looks for the paml executables, its config # file (if necessary it should be in your home directory) and the # manuals installed by paml. sed -i 's|QApplication::applicationDirPath()|"/usr"|g' mainwindow.cpp sed -i 's|+= "/pamlx.conf"|= "~/.pamlX/pamlx.conf"|g' mainwindow.cpp -sed -i 's|/doc/|/doc/paml-4.9h/|g' mainwindow.cpp -sed -i 's|/doc/|/doc/paml-4.9h/|g' pamlhistorydialog.cpp +sed -i 's|/doc/|/doc/paml-4.10.6/|g' mainwindow.cpp +sed -i 's|/doc/|/doc/paml-4.10.6/|g' pamlhistorydialog.cpp # If you want the "Help" menu to use something else than Okular for # viewing the PDF documentation, uncomment the appropriate line below @@ -113,4 +125,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/pamlX/pamlX.info b/academic/pamlX/pamlX.info index 7e9ac1b1af..0fc74669f4 100644 --- a/academic/pamlX/pamlX.info +++ b/academic/pamlX/pamlX.info @@ -5,6 +5,6 @@ DOWNLOAD="http://abacus.gene.ucl.ac.uk/software/pamlX1.3.1-src.tgz" MD5SUM="55cd96e17d94a30232fc0cdd1eaeccf4" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="paml" +REQUIRES="paml qt4" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/papi/papi.SlackBuild b/academic/papi/papi.SlackBuild index 171b276dd9..d3f215c777 100644 --- a/academic/papi/papi.SlackBuild +++ b/academic/papi/papi.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # # Slackware build script for papi. # @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=papi -VERSION=${VERSION:-5.5.1} +VERSION=${VERSION:-6.0.0.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -79,7 +89,7 @@ CXXFLAGS="$SLKCFLAGS" \ --sysconfdir=/etc \ --localstatedir=/var \ --mandir=/usr/man \ - --with-static-lib=no \ + --with-static-lib=yes \ --with-shared-lib=yes \ --build=$ARCH-slackware-linux @@ -102,4 +112,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/papi/papi.info b/academic/papi/papi.info index 42d8c1de7b..04a6552694 100644 --- a/academic/papi/papi.info +++ b/academic/papi/papi.info @@ -1,8 +1,8 @@ PRGNAM="papi" -VERSION="5.5.1" +VERSION="6.0.0.1" HOMEPAGE="http://icl.utk.edu/papi/" -DOWNLOAD="http://icl.utk.edu/projects/papi/downloads/papi-5.5.1.tar.gz" -MD5SUM="86a8a6f3d0f34cd83251da3514aae15d" +DOWNLOAD="http://icl.cs.utk.edu/projects/papi/downloads/papi-6.0.0.1.tar.gz" +MD5SUM="34c536f3c4a6ad4b5615de23018503ad" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/pari/README b/academic/pari/README index 6e10ca3d19..b51ae28edf 100644 --- a/academic/pari/README +++ b/academic/pari/README @@ -1,7 +1,7 @@ -PARI/GP is a widely used computer algebra system designed for fast computations -in number theory (factorizations, algebraic number theory, elliptic curves, -modular forms, L functions...), but also contains a large number of other -useful functions to compute with mathematical entities such as matrices, -polynomials, power series, algebraic numbers etc., and a lot of transcendental -functions. PARI is also available as a C library to allow for faster -computations. +PARI/GP is a widely used computer algebra system designed for fast +computations in number theory (factorizations, algebraic number theory, +elliptic curves, modular forms, L functions...), but also contains a +large number of other useful functions to compute with mathematical +entities such as matrices, polynomials, power series, algebraic numbers +etc., and a lot of transcendental functions. PARI is also available as +a C library to allow for faster computations. diff --git a/academic/pari/pari.SlackBuild b/academic/pari/pari.SlackBuild index 09d2450383..89b8f20496 100644 --- a/academic/pari/pari.SlackBuild +++ b/academic/pari/pari.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for pari/gp @@ -30,10 +30,13 @@ # Joachim Kruth -> update to version 2.11.1 # Joachim Kruth -> update to version 2.11.2 +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=pari -VERSION=${VERSION:-2.11.2} +VERSION=${VERSION:-2.13.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -43,7 +46,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -94,8 +104,11 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr find $PKG/usr/man -type f -exec gzip -9 {} \; for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done +mkdir -p $PKG/usr/man/man1 +mv $PKG/usr/man/*gz $PKG/usr/man/man1 + mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a AUTHORS COPYING CHANGES* INSTALL* NEW README* \ +cp -a AUTHORS COPYING CHANGES* NEW README* \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild @@ -103,4 +116,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/pari/pari.info b/academic/pari/pari.info index 4dab289fe4..1da54f9b76 100644 --- a/academic/pari/pari.info +++ b/academic/pari/pari.info @@ -1,8 +1,8 @@ PRGNAM="pari" -VERSION="2.11.2" +VERSION="2.13.1" HOMEPAGE="https://pari.math.u-bordeaux.fr/" -DOWNLOAD="https://pari.math.u-bordeaux.fr/pub/pari/unix/pari-2.11.2.tar.gz" -MD5SUM="6afe748a472c33ae8787a5034d7742a9" +DOWNLOAD="https://pari.math.u-bordeaux.fr/pub/pari/unix/pari-2.13.1.tar.gz" +MD5SUM="826064cf75af268be8a482ade6e27501" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/parmetis/README b/academic/parmetis/README index 018f15ca02..ac2b847cf4 100644 --- a/academic/parmetis/README +++ b/academic/parmetis/README @@ -1,10 +1,10 @@ -ParMETIS (Parallel Graph Partitioning and Fill-reducing Matrix Ordering) +ParMETIS (Parallel Graph Partitioning and Fill-reducing Matrix +Ordering) -ParMETIS is an MPI-based parallel library that implements a variety -of algorithms for partitioning unstructured graphs, meshes, and for +ParMETIS is an MPI-based parallel library that implements a variety +of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. -Set precision type: -DP=yes (for 64-bit, default is 32-bit) +Set precision type: DP=yes (for 64-bit, default is 32-bit) The requirement is a MPI implementation, either mpich or openmpi. diff --git a/academic/parmetis/parmetis.SlackBuild b/academic/parmetis/parmetis.SlackBuild index ee4123af4c..6511e58083 100644 --- a/academic/parmetis/parmetis.SlackBuild +++ b/academic/parmetis/parmetis.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for parmetis @@ -22,28 +22,38 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=parmetis VERSION=${VERSION:-4.0.3} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} SRCNAM="$(printf $PRGNAM | cut -d- -f2-)" if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -119,4 +129,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/patsy/patsy.SlackBuild b/academic/patsy/patsy.SlackBuild index 29a4575da1..43c4ef9040 100644 --- a/academic/patsy/patsy.SlackBuild +++ b/academic/patsy/patsy.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for statsmodels @@ -22,26 +22,36 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=patsy VERSION=${VERSION:-0.3.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -83,4 +93,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/patsy/patsy.info b/academic/patsy/patsy.info index 50822d026e..f7e632560f 100644 --- a/academic/patsy/patsy.info +++ b/academic/patsy/patsy.info @@ -5,6 +5,6 @@ DOWNLOAD="https://pypi.python.org/packages/source/p/patsy/patsy-0.3.0.zip" MD5SUM="7545518b413136ba8343dcebea07e5e2" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="six numpy" +REQUIRES="python2-numpy" MAINTAINER="R. S. Ananda Murthy" EMAIL="rsamurti@gmail.com" diff --git a/academic/pcalc/pcalc.SlackBuild b/academic/pcalc/pcalc.SlackBuild index e3df7b6d89..63468ea986 100644 --- a/academic/pcalc/pcalc.SlackBuild +++ b/academic/pcalc/pcalc.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for pcalc @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=pcalc VERSION=${VERSION:-4} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -87,4 +97,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/pcb/pcb.SlackBuild b/academic/pcb/pcb.SlackBuild index 4088a26fad..16536c0b51 100644 --- a/academic/pcb/pcb.SlackBuild +++ b/academic/pcb/pcb.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for pcb @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=pcb VERSION=${VERSION:-4.0.2} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -104,5 +114,5 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/penaltymodel/README b/academic/penaltymodel/README new file mode 100644 index 0000000000..be84eea915 --- /dev/null +++ b/academic/penaltymodel/README @@ -0,0 +1,14 @@ + One approach to solve a constraint satisfaction problem (CSP) using +an Ising model or a QUBO, is to map each individual constraint in +the CSP to a "small" Ising model or QUBO. This mapping is called +a penalty model. + + Imagine that we want to map an AND clause to a QUBO. In other words, +we want the solutions to the QUBO (the solutions that minimize the +energy) to be exactly the valid configurations of an AND gate. Let z = +AND(x_1, x_2). + + + Optional building mode set with environment variables: + - TESTS=yes, performs tests. Requires: dimod, python3-numpy, + networkx, python3-scipy, homebase, lapack. diff --git a/academic/penaltymodel/penaltymodel.SlackBuild b/academic/penaltymodel/penaltymodel.SlackBuild new file mode 100644 index 0000000000..c29dee1453 --- /dev/null +++ b/academic/penaltymodel/penaltymodel.SlackBuild @@ -0,0 +1,117 @@ +#!/bin/bash + +# Slackware build script for penaltymodel + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM="penaltymodel" +VERSION=${VERSION:-1.0.2} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +python3 setup.py install --root=$PKG + +if [ "${TESTS:-no}" == "yes" ]; then + cd tests + for file in $(ls test_*.py); do + echo -n "$file " + PYTHONPATH=../ python3 $file + if [ "$?" -eq "0" ]; then + echo "OK" + else + echo "fail" + fi + done + cd .. +fi + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + LICENSE README.rst docs \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/penaltymodel/penaltymodel.info b/academic/penaltymodel/penaltymodel.info new file mode 100644 index 0000000000..c04f042084 --- /dev/null +++ b/academic/penaltymodel/penaltymodel.info @@ -0,0 +1,10 @@ +PRGNAM="penaltymodel" +VERSION="1.0.2" +HOMEPAGE="https://github.com/dwavesystems" +DOWNLOAD="https://github.com/dwavesystems/penaltymodel/archive/1.0.2/penaltymodel-1.0.2.tar.gz" +MD5SUM="26c6d33ac5a17620c4d6de76985cc552" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/penaltymodel/slack-desc b/academic/penaltymodel/slack-desc new file mode 100644 index 0000000000..1e20efbea8 --- /dev/null +++ b/academic/penaltymodel/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +penaltymodel: penaltymodel (penalty model solver for Ising model or a QUBO) +penaltymodel: +penaltymodel: +penaltymodel: +penaltymodel: One approach to solve a constraint satisfaction problem (CSP) using +penaltymodel: an Ising model or a QUBO, is to map each individual constraint in +penaltymodel: the CSP to a "small" Ising model or QUBO. This mapping is called +penaltymodel: a penalty model. +penaltymodel: +penaltymodel: +penaltymodel: diff --git a/academic/perlprimer/perlprimer.SlackBuild b/academic/perlprimer/perlprimer.SlackBuild index 105e42f9f0..cd0650b277 100644 --- a/academic/perlprimer/perlprimer.SlackBuild +++ b/academic/perlprimer/perlprimer.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for perlprimer -# Copyright 2011-2019 Petar Petrov slackalaxy@gmail.com +# Copyright 2011-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,15 +22,25 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=perlprimer VERSION=${VERSION:-1.2.4} COMMIT=${COMMIT:-f415ea6d0170f2f62f10c678adac8fdc69a3298f} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} ARCH=noarch -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -69,4 +79,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/pianobooster/README b/academic/pianobooster/README index bbc0a15b05..a191b9f461 100644 --- a/academic/pianobooster/README +++ b/academic/pianobooster/README @@ -1,7 +1,7 @@ pianobooster (educational music software) PianoBooster is a fun way of playing along with a musical accompaniment -and at the same time learning the basics of reading musical notation. The -difference between playing along to a CD or a standard midi file is -that PianoBooster listens and follows what you are playing on a midi -piano keyboard. +and at the same time learning the basics of reading musical +notation. The difference between playing along to a CD or a standard +midi file is that PianoBooster listens and follows what you are playing +on a midi piano keyboard. diff --git a/academic/pianobooster/doinst.sh b/academic/pianobooster/doinst.sh index 5fb28930db..65c7e2eeb9 100644 --- a/academic/pianobooster/doinst.sh +++ b/academic/pianobooster/doinst.sh @@ -1,3 +1,9 @@ if [ -x /usr/bin/update-desktop-database ]; then /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 fi + +if [ -e usr/share/icons/hicolor/icon-theme.cache ]; then + if [ -x /usr/bin/gtk-update-icon-cache ]; then + /usr/bin/gtk-update-icon-cache -f usr/share/icons/hicolor >/dev/null 2>&1 + fi +fi diff --git a/academic/pianobooster/pianobooster.SlackBuild b/academic/pianobooster/pianobooster.SlackBuild index d2527905a8..5850531d06 100644 --- a/academic/pianobooster/pianobooster.SlackBuild +++ b/academic/pianobooster/pianobooster.SlackBuild @@ -1,16 +1,22 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for pianobooster -# Written by B. Watson (yalhcru@gmail.com) +# Written by B. Watson (urchlay@slackware.uk) # Modified by Willy Sudiarto Raharjo <willysr@slackware-id.org> # Licensed under the WTFPL. See http://www.wtfpl.net/txt/copying/ for details. +# 20210802 bkw: update for v1.0.0 and -current. + +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=pianobooster -VERSION=${VERSION:-0.6.4b} -BUILD=${BUILD:-2} +SRCNAM=PianoBooster +VERSION=${VERSION:-1.0.0} +BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -20,7 +26,11 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -44,43 +54,29 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $PRGNAM-src-$VERSION -tar xvf $CWD/$PRGNAM-src-$VERSION.tar.gz -cd $PRGNAM-src-$VERSION +rm -rf $SRCNAM-$VERSION +tar xvf $CWD/$SRCNAM-$VERSION.tar.gz +cd $SRCNAM-$VERSION chown -R root:root . -find -L . \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; - -# remove unneeded flag - sed -i '/mwindows/d' src/CMakeLists.txt +find -L . -perm /111 -a \! -perm 755 -a -exec chmod 755 {} \+ -o \ + \! -perm /111 -a \! -perm 644 -a -exec chmod 644 {} \+ +mkdir -p build cd build cmake \ -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ -DCMAKE_INSTALL_PREFIX=/usr \ -DCMAKE_BUILD_TYPE=Release ../src - - # DSO GL and pthread fix - sed -i "s/$/-lGL -lpthread/" CMakeFiles/pianobooster.dir/link.txt - make VERBOSE=1 make install/strip DESTDIR=$PKG cd .. -# Make the .desktop file validate. -sed -i 's/Education;/&AudioVideo;/' $PKG/usr/share/applications/$PRGNAM.desktop - -# Don't need (will install docs manually below). -rm -rf $PKG/usr/share/doc - mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a \ - README.txt gplv3.txt license.txt \ - $PKG/usr/doc/$PRGNAM-$VERSION +mv $PKG/usr/share/doc/$PRGNAM/* \ + $PKG/usr/share/licenses/$PRGNAM/* \ + $PKG/usr/doc/$PRGNAM-$VERSION +rm -rf $PKG/usr/share/doc/ $PKG/usr/share/licenses/ cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install @@ -88,4 +84,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/pianobooster/pianobooster.info b/academic/pianobooster/pianobooster.info index 91a3ad0c6c..5ce9f314c9 100644 --- a/academic/pianobooster/pianobooster.info +++ b/academic/pianobooster/pianobooster.info @@ -1,10 +1,10 @@ PRGNAM="pianobooster" -VERSION="0.6.4b" -HOMEPAGE="http://pianobooster.sourceforge.net/" -DOWNLOAD="http://downloads.sourceforge.net/pianobooster/pianobooster-src-0.6.4b.tar.gz" -MD5SUM="4c1c34a4b763e6108aa9668be7890696" +VERSION="1.0.0" +HOMEPAGE="https://github.com/pianobooster/PianoBooster" +DOWNLOAD="https://github.com/pianobooster/PianoBooster/archive/v1.0.0/PianoBooster-1.0.0.tar.gz" +MD5SUM="2a4701c18a9e3fb7a1185657d51f1dba" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="" +REQUIRES="ftgl" MAINTAINER="B. Watson" -EMAIL="yalhcru@gmail.com" +EMAIL="urchlay@slackware.uk" diff --git a/academic/plasmidomics/plasmidomics.SlackBuild b/academic/plasmidomics/plasmidomics.SlackBuild index a437ad3637..d2d64c7e1c 100644 --- a/academic/plasmidomics/plasmidomics.SlackBuild +++ b/academic/plasmidomics/plasmidomics.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for plasmidomics -# Copyright 2011-2016 Petar Petrov slackalaxy@gmail.com +# Copyright 2011-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,14 +22,24 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=plasmidomics VERSION=${VERSION:-0.2} BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} ARCH=noarch -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -61,4 +71,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/plus42/README b/academic/plus42/README new file mode 100644 index 0000000000..b23684de4c --- /dev/null +++ b/academic/plus42/README @@ -0,0 +1,19 @@ +Plus42 is an advanced scientific programmable calculator, based on +Free42 (a complete re-implementation of the HP-42S scientific +programmable RPN calculator) and adds: + +- A Larger Display, with 8 rows and 22 columns (131x64 pixels) by + default, which the user may resize at will. + +- Algebraic Expressions modeled after those used on the HP-27S and + HP-17B/19B. + +- Attached Units and unit conversions modeled after those used on the + HP-48/49/50 series. + +- Directories for more organized storage of programs and variables. + +- TVM and amortization tables. + +- Two-dimensional Plotting of functions, with ability to zoom and pan, + and find integrals and roots from points in the plot. diff --git a/academic/avogadro/doinst.sh b/academic/plus42/doinst.sh index 4e8ba7071d..4e8ba7071d 100644 --- a/academic/avogadro/doinst.sh +++ b/academic/plus42/doinst.sh diff --git a/academic/plus42/plus42.SlackBuild b/academic/plus42/plus42.SlackBuild new file mode 100644 index 0000000000..c89279a774 --- /dev/null +++ b/academic/plus42/plus42.SlackBuild @@ -0,0 +1,104 @@ +#!/bin/bash + +# Slackware build script for plus42 + +# Copyright 2023-2024 Antonio Leal, Porto Salvo, Oeiras, Portugal +# Copyright 2022-2023 Juan M. Lasca juanmlasca@gmail.com +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=plus42 +VERSION=${VERSION:-1.1.9} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" +else + SLKCFLAGS="-O2" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz || + tar xvf $CWD/${PRGNAM}desktop-$VERSION.tar.gz +mv ${PRGNAM}desktop-$VERSION $PRGNAM-$VERSION +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +cd gtk +sed -i "s|-g\ |$SLKCFLAGS|" Makefile +make -e BCD_MATH=1 AUDIO_ALSA=1 +cd .. +mkdir -p $PKG/usr/bin $PKG/usr/share/applications $PKG/usr/share/pixmaps + +cp gtk/plus42dec $PKG/usr/bin +cp gtk/icon-128x128.xpm $PKG/usr/share/pixmaps/plus42icon-128x128.xpm +cp $CWD/plus42.desktop $PKG/usr/share/applications +(cd $PKG/usr/bin; ln -s plus42dec plus42) + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + README COPYING HISTORY CREDITS \ + $PKG/usr/doc/$PRGNAM-$VERSION +cp -a gtk/README $PKG/usr/doc/$PRGNAM-$VERSION/README-GTK +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/plus42/plus42.desktop b/academic/plus42/plus42.desktop new file mode 100644 index 0000000000..dfcf2b2c11 --- /dev/null +++ b/academic/plus42/plus42.desktop @@ -0,0 +1,8 @@ +[Desktop Entry] +Comment= +Terminal=false +Name=Plus42 +Exec=/usr/bin/plus42dec +Type=Application +Categories=Utility;Calculator; +Icon=/usr/share/pixmaps/plus42icon-128x128.xpm diff --git a/academic/plus42/plus42.info b/academic/plus42/plus42.info new file mode 100644 index 0000000000..45e08e71d5 --- /dev/null +++ b/academic/plus42/plus42.info @@ -0,0 +1,10 @@ +PRGNAM="plus42" +VERSION="1.1.9" +HOMEPAGE="https://www.thomasokken.com/plus42" +DOWNLOAD="https://github.com/thomasokken/plus42desktop/archive/v1.1.9/plus42-1.1.9.tar.gz" +MD5SUM="a06f497124bc6b0e03d2f46c15097faa" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Antonio Leal" +EMAIL="antonioleal@yahoo.com" diff --git a/academic/plus42/slack-desc b/academic/plus42/slack-desc new file mode 100644 index 0000000000..f4de09afd9 --- /dev/null +++ b/academic/plus42/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +plus42: plus42 (An Enhanced HP-42S Calculator Simulator) +plus42: +plus42: Plus42 is an advanced scientific programmable calculator, based on +plus42: Free42 (a complete re-implementation of the HP-42S scientific +plus42: programmable RPN calculator) +plus42: +plus42: Plus42 builds on Free42 and adds: A Larger Display, with 8 rows and 22 +plus42: columns (131x64 pixels) by default, which the user may resize at will; +plus42: Algebraic Expressions; attached Units and unit conversions; +plus42: Directories; TVM and amortization tables; and two-dimensional Plotting +plus42: of functions. Homepage at https://www.thomasokken.com/plus42 diff --git a/academic/pomoxis/README b/academic/pomoxis/README new file mode 100644 index 0000000000..5214c86dc4 --- /dev/null +++ b/academic/pomoxis/README @@ -0,0 +1,4 @@ + Pomoxis comprises a set of basic bioinformatic tools tailored to +nanopore sequencing. Notably tools are included for generating and +analysing draft assemblies. Many of these tools are used by the +research data analysis group at Oxford Nanopore Technologies. diff --git a/academic/pomoxis/pomoxis.SlackBuild b/academic/pomoxis/pomoxis.SlackBuild new file mode 100644 index 0000000000..6c43667b34 --- /dev/null +++ b/academic/pomoxis/pomoxis.SlackBuild @@ -0,0 +1,102 @@ +#!/bin/bash + +# Slackware build script for pomoxis + +# Copyright 2023 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=pomoxis +VERSION=${VERSION:-0.3.12} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +python3 setup.py install --root=$PKG + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + CHANGELOG.md LICENSE.md docs \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/pomoxis/pomoxis.info b/academic/pomoxis/pomoxis.info new file mode 100644 index 0000000000..e78d77e751 --- /dev/null +++ b/academic/pomoxis/pomoxis.info @@ -0,0 +1,10 @@ +PRGNAM="pomoxis" +VERSION="0.3.12" +HOMEPAGE="https://github.com/nanoporetech/pomoxis" +DOWNLOAD="https://github.com/nanoporetech/pomoxis/archive/v0.3.12/pomoxis-0.3.12.tar.gz" +MD5SUM="a2c01f36a87982962143f8d99648a7f1" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="blas" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/pomoxis/slack-desc b/academic/pomoxis/slack-desc new file mode 100644 index 0000000000..8d2494de50 --- /dev/null +++ b/academic/pomoxis/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +pomoxis: pomoxis (bioinformatics tools for nanopore research) +pomoxis: +pomoxis: +pomoxis: Pomoxis comprises a set of basic bioinformatic tools tailored to +pomoxis: nanopore sequencing. Notably tools are included for generating and +pomoxis: analysing draft assemblies. Many of these tools are used by the +pomoxis: research data analysis group at Oxford Nanopore Technologies. +pomoxis: +pomoxis: +pomoxis: +pomoxis: diff --git a/academic/prank-msa/prank-msa.SlackBuild b/academic/prank-msa/prank-msa.SlackBuild index f9de0b7ec9..a3c6791cdd 100644 --- a/academic/prank-msa/prank-msa.SlackBuild +++ b/academic/prank-msa/prank-msa.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for prank-msa -# Copyright 2017 Petar petrov slackalaxy@gmail.com +# Copyright 2017-2022 Petar petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,11 +22,14 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=prank-msa SRCNAM=prank.source VERSION=${VERSION:-170427} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -36,7 +39,11 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -100,4 +107,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/primer3/README b/academic/primer3/README index 51977f2f12..3b57af159d 100644 --- a/academic/primer3/README +++ b/academic/primer3/README @@ -1,14 +1,24 @@ Primer3 is a widely used program for designing PCR primers (PCR = -"Polymerase Chain Reaction"). PCR is an essential and ubiquitous tool -in genetics and molecular biology. Primer3 can design hybridization -probes and sequencing primers. +"Polymerase Chain Reaction"). PCR is an essential and ubiquitous tool in +genetics and molecular biology. Primer3 can design hybridization probes +and sequencing primers. PCR is used for many different goals. Consequently, primer3 has many different input parameters that you control and that tell primer3 exactly what characteristics make good primers for your goals. -For details and citation: -Steve Rozen and Helen J. Skaletsky (2000) Primer3 on the WWW for -general users and for biologist programmers. In: Krawetz S, Misener S -(eds) Bioinformatics Methods and Protocols: Methods in Molecular -Biology. Humana Press, Totowa, NJ, pp 365-386 +Primer3 picks primers for PCR reactions, considering as criteria: +* oligonucleotide melting temperature, size, GC content and primer-dimer + possibilities, +* PCR product size +* positional constraints within the source (template) sequence +* possibilities for ectopic priming (amplifying the wrong sequence) +* many other constraints. + +All of these criteria are user-specifiable as constraints, and some are +specifiable as terms in an objective function that characterizes an +optimal primer pair. + +manual online: https://primer3.org/manual.html + +For details and citation see "References" in the package's doc folder. diff --git a/academic/primer3/References b/academic/primer3/References index 5009a52a1b..f951635a4d 100644 --- a/academic/primer3/References +++ b/academic/primer3/References @@ -1,4 +1,21 @@ -Steve Rozen and Helen J. Skaletsky (2000) Primer3 on the WWW for general -users and for biologist programmers. In: Krawetz S, Misener S (eds) -Bioinformatics Methods and Protocols: Methods in Molecular Biology. Humana -Press, Totowa, NJ, pp 365-386 +We request but do not require that use of this software be cited in publications as + +* Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M and Rozen SG. +Primer3--new capabilities and interfaces. +Nucleic Acids Res. 2012 Aug 1;40(15):e115. +The paper is available at http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3424584/ + +and + +* Koressaar T and Remm M. +Enhancements and modifications of primer design program Primer3. +Bioinformatics 2007;23(10):1289-1291. +The paper is available at https://www.ncbi.nlm.nih.gov/pubmed/17379693 + +If you use masker function, please cite: +* Koressaar T, Lepamets M, Kaplinski L, Raime K, Andreson R and Remm M. +Primer3_masker: integrating masking of template sequence with primer design software. +Bioinformatics 2018;34(11):1937-1938. +The paper is available at https://www.ncbi.nlm.nih.gov/pubmed/29360956 + +Source code available at https://github.com/primer3-org/primer3. diff --git a/academic/primer3/gcc-7.patch b/academic/primer3/gcc-7.patch deleted file mode 100644 index a92d0e77b7..0000000000 --- a/academic/primer3/gcc-7.patch +++ /dev/null @@ -1,22 +0,0 @@ -Author: Andreas Tille <tille@debian.org> -Last-Update: Sat, 26 Aug 2017 00:32:40 +0200 -Bug-Debian: https://bugs.debian.org/853621 -Description: Fix build with gcc-7 - ---- a/src/thal.c -+++ b/src/thal.c -@@ -426,12 +426,12 @@ thal(const unsigned char *oligo_f, - "Illegal type"); - o->align_end_1 = -1; - o->align_end_2 = -1; -- if ('\0' == oligo_f) { -+ if ('\0' == oligo_f[0]) { - strcpy(o->msg, "Empty first sequence"); - o->temp = 0.0; - return; - } -- if ('\0' == oligo_r) { -+ if ('\0' == oligo_r[0]) { - strcpy(o->msg, "Empty second sequence"); - o->temp = 0.0; - return; diff --git a/academic/primer3/primer3.SlackBuild b/academic/primer3/primer3.SlackBuild index d3ae1b399c..9a4bd6b511 100644 --- a/academic/primer3/primer3.SlackBuild +++ b/academic/primer3/primer3.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for primer3 -# Copyright 2011-2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2011-2023 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=primer3 -VERSION=${VERSION:-2.4.0} +VERSION=${VERSION:-2.6.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,11 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -69,24 +76,19 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -# Thanks to Debian for the patch -patch -p1 -i $CWD/gcc-7.patch - cd ./src # Use our CFLAGS -sed -i "/^CFLAGS/s/=/+=/" Makefile +sed -i -e "s|-O2|$SLKCFLAGS|" Makefile # Look for configuration files in /usr/share instead of /opt sed -i "s:/opt/primer3_config:/usr/share/$PRGNAM/primer3_config:g" thal_main.c primer3_boulder_main.c -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ make # This is recommended, but the tests take a really long time. Be patient # if you uncomment the line below. -# make test +#make test install -D -m755 primer3_core $PKG/usr/bin/primer3_core install -D -m755 ntdpal $PKG/usr/bin/ntdpal @@ -100,7 +102,9 @@ ln -s primer3_core primer32_core # Copy configuration files and settings to /usr/share cd $TMP/$PRGNAM-$VERSION mkdir -p $PKG/usr/share/$PRGNAM -cp -a settings_files src/primer3_config $PKG/usr/share/$PRGNAM +cp -a \ + kmer_lists/readme.txt settings_files example src/primer3_config \ + $PKG/usr/share/$PRGNAM # Copy the man pages from Debian mkdir -p $PKG/usr/man/man1 @@ -114,7 +118,7 @@ for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; r mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - src/{release_notes.txt,primer3_manual.htm} LICENSE example README.md \ + src/{release_notes.txt,primer3_manual.htm} LICENSE README.md \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References @@ -123,4 +127,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/primer3/primer3.info b/academic/primer3/primer3.info index 861eb56e58..5a9c2ffe17 100644 --- a/academic/primer3/primer3.info +++ b/academic/primer3/primer3.info @@ -1,8 +1,8 @@ PRGNAM="primer3" -VERSION="2.4.0" -HOMEPAGE="http://primer3.sourceforge.net/" -DOWNLOAD="http://sourceforge.net/projects/primer3/files/primer3/2.4.0/primer3-2.4.0.tar.gz" -MD5SUM="aed6546bdfb60652cd7eba8d51eae8cc" +VERSION="2.6.1" +HOMEPAGE="https://primer3.org/" +DOWNLOAD="https://github.com/primer3-org/primer3/archive/v2.6.1/primer3-2.6.1.tar.gz" +MD5SUM="d18c095694b586c300c88fab4b116c8c" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/primer3/slack-desc b/academic/primer3/slack-desc index 9e871a4b8c..4e4ce377e2 100644 --- a/academic/primer3/slack-desc +++ b/academic/primer3/slack-desc @@ -13,7 +13,7 @@ primer3: "Polymerase Chain Reaction"). PCR is an essential and primer3: ubiquitous tool in genetics and molecular biology. Primer3 can also primer3: design hybridization probes and sequencing primers. primer3: -primer3: Home: http://primer3.sourceforge.net/ -primer3: References: /usr/doc/primer3-2.3.7/References +primer3: https://primer3.org/manual.html +primer3: primer3: primer3: diff --git a/academic/pspp/pspp.SlackBuild b/academic/pspp/pspp.SlackBuild index d1bc94c53a..17b31eb664 100644 --- a/academic/pspp/pspp.SlackBuild +++ b/academic/pspp/pspp.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for pspp @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=pspp -VERSION=${VERSION:-1.2.0} +VERSION=${VERSION:-2.0.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,11 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -69,7 +76,6 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -LIBS="-ltermcap -lgmp" \ CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ @@ -97,7 +103,7 @@ rm -f $PKG/usr/info/dir gzip -9 $PKG/usr/info/*.info* mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a COPYING README AUTHORS ABOUT-NLS INSTALL NEWS ONEWS THANKS $PKG/usr/doc/$PRGNAM-$VERSION +cp -a COPYING README AUTHORS ABOUT-NLS NEWS ONEWS THANKS $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install @@ -105,4 +111,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/pspp/pspp.info b/academic/pspp/pspp.info index e01ee40783..702e496e28 100644 --- a/academic/pspp/pspp.info +++ b/academic/pspp/pspp.info @@ -1,10 +1,10 @@ PRGNAM="pspp" -VERSION="1.2.0" +VERSION="2.0.0" HOMEPAGE="http://www.gnu.org/software/pspp/" -DOWNLOAD="https://mirrors.up.pt/pub/gnu/pspp/pspp-1.2.0.tar.gz" -MD5SUM="e940d666b586f5bd2f17a2b305fac71f" +DOWNLOAD="http://mirrors.nav.ro/gnu/pspp/pspp-2.0.0.tar.gz" +MD5SUM="11f5949311bfe66a44999b9d7db6c99b" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="gtksourceview3 spread-sheet-widget" +REQUIRES="spread-sheet-widget" MAINTAINER="Vitor Borrego" -EMAIL="vitor@bitarus.allowed.org" +EMAIL="vitor@bitarus.mooo.com" diff --git a/academic/pulseview/pulseview.SlackBuild b/academic/pulseview/pulseview.SlackBuild index afeee1876a..9b3885487e 100644 --- a/academic/pulseview/pulseview.SlackBuild +++ b/academic/pulseview/pulseview.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for PulseView @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=pulseview -VERSION=${VERSION:-0.4.1} +VERSION=${VERSION:-20220225_4efbe9b} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -60,7 +70,7 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $PRGNAM-$VERSION -tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +tar xvf $CWD/$PRGNAM-$VERSION.tar.?z cd $PRGNAM-$VERSION chown -R root:root . find -L . \ @@ -97,4 +107,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/pulseview/pulseview.info b/academic/pulseview/pulseview.info index 631c5fefbc..534e4f0210 100644 --- a/academic/pulseview/pulseview.info +++ b/academic/pulseview/pulseview.info @@ -1,10 +1,10 @@ PRGNAM="pulseview" -VERSION="0.4.1" +VERSION="20220225_4efbe9b" HOMEPAGE="https://sigrok.org/wiki/PulseView" -DOWNLOAD="https://sigrok.org/download/source/pulseview/pulseview-0.4.1.tar.gz" -MD5SUM="6056c6e42cc6eae094110cac2351558a" +DOWNLOAD="http://ponce.cc/slackware/sources/repo/pulseview-20220225_4efbe9b.tar.xz" +MD5SUM="eec6859a8bb32d61c9d5f7eb14fda625" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="qt5 libsigrok libsigrokdecode" +REQUIRES="libsigrok libsigrokdecode" MAINTAINER="Andrzej Telszewski" EMAIL="atelszewski@gmail.com" diff --git a/academic/pyCRAC/MANIFEST_slack.txt b/academic/pyCRAC/MANIFEST_slack.txt deleted file mode 100644 index 95a4931773..0000000000 --- a/academic/pyCRAC/MANIFEST_slack.txt +++ /dev/null @@ -1,69 +0,0 @@ -setup.py -MANIFEST.txt -LICENCE.txt -README.txt -pyCRAC/tests/test.novo -pyCRAC/tests/test.sh -pyCRAC/tests/test_coordinates.txt -pyCRAC/tests/test.gtf -pyCRAC/tests/test_f.fastq -pyCRAC/tests/test_f.fastq.gz -pyCRAC/tests/test_f_dm.fastq -pyCRAC/tests/test_r.fastq -pyCRAC/tests/test_r.fastq.gz -pyCRAC/tests/test_r_dm.fastq -pyCRAC/tests/indexes.txt -pyCRAC/tests/barcodes.txt -pyCRAC/tests/genes.lis -pyCRAC/Classes/NGSFormatWriters.py -pyCRAC/Classes/NGSFormatReaders.py -pyCRAC/Classes/PairedReads.py -pyCRAC/Classes/Pileups.py -pyCRAC/Classes/Aligner.py -pyCRAC/Classes/Motifs.py -pyCRAC/Classes/Barcodes.py -pyCRAC/Classes/Coverage.py -pyCRAC/Classes/Exceptions.py -pyCRAC/Classes/FDR.py -pyCRAC/Classes/Clustering -pyCRAC/db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt -pyCRAC/db/Saccharomyces_cerevisiae.EF2.59.1.0.fa -pyCRAC/db/Saccharomyces_cerevisiae.EF2.59.1.0.fa.tab -pyCRAC/db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf -pyCRAC/kinetic_crac_pipeline/CRAC_pipeline_PE.py -pyCRAC/kinetic_crac_pipeline/CRAC_pipeline_PeakFinder.py -pyCRAC/kinetic_crac_pipeline/CRAC_pipeline_SE.py -pyCRAC/kinetic_crac_pipeline/TrimNucs.py -pyCRAC/scripts/pybed2GTF.py -pyCRAC/scripts/pyGTF2bed.py -pyCRaC/scripts/pyGTF2bedGraph.py -pyCRAC/scripts/pyGTF2sgr.py -pyCRAC/scripts/pyNormalizeIntervalLengths.py -pyCRAC/scripts/pyFastqDuplicateRemover.py -pyCRAC/scripts/pyFastqJoiner.py -pyCRAC/scripts/pyFastqSplitter.py -pyCRAC/scripts/pyGetGeneNamesFromGTF.py -pyCRAC/scripts/pySelectMotifsFromGTF.py -pyCRAC/scripts/pyGetGTFSources.py -pyCRAC/scripts/pyFilterGTF.py -pyCRAC/scripts/pyFasta2tab.py -pyCRAC/scripts/pyAlignment2Tab.py -pyCRAC/scripts/pyExtractLinesFromGTF.py -pyCRAC/scripts/pyCheckGTFfile.py -pyCRAC/scripts/pyCalculateChromosomeLengths.py -pyCRAC/pyClusterReads.py -pyCRAC/pyCalculateFDRs.py -pyCRAC/pyCalculateMutationFrequencies.py -pyCRAC/pyBinCollector.py -pyCRAC/pyMotif.py -pyCRAC/pyPileup.py -pyCRAC/pyReadAligner.py -pyCRAC/pyReadCounters.py -pyCRAC/pyBarcodeFilter.py -pyCRAC/Parsers/Blast.py -pyCRAC/Parsers/GTF2.py -pyCRAC/Parsers/Novoalign.py -pyCRAC/Parsers/ParseAlignments.py -pyCRAC/Parsers/SAM.py -pyCRAC/Parsers/fasta2dict.py -pyCRAC/Parsers/tab2dict.py diff --git a/academic/pyCRAC/README b/academic/pyCRAC/README index 1583f3e62c..b9b74fd37b 100644 --- a/academic/pyCRAC/README +++ b/academic/pyCRAC/README @@ -5,11 +5,11 @@ data generated by CLIP or CRAC protocols). It can be used to remove duplicate reads,tackles directional libraries and reports sense and anti-sense hits. -Included is the pipeline used for the analysis of a group of CRAC data -sets. +A pipeline that streamlines the analysis of a group of CRAC datasets +is available at https://git.ecdf.ed.ac.uk/sgrannem/crac_pipelines and +depends on the python package 'ruffus', also at slackbuilds.org. + -An R-function used for kinetic CRAC analysis can be found in -/usr/share/pyCRAC-$VERSION/kinetic_crac_pipeline References @@ -25,23 +25,3 @@ A, Langford A, Franklin R, Iosub I, Wadsworth P, Sanguinetti G, Granneman S. If you want to run the test suite after installation, see README.tests. - -Note on the Crac pipelines: - -The CRAC_pipeline_PE.py and CRAC_pipeline_SE.py scripts now ONLY work -with pyCRAC version 1.3.3 and Flexbar version 3.4.0 and later(!) -Use the -h flag to get a detailed help menu. - -The CRAC_pipeline_PE.py script needs to be run from the folder that -contains the fastq files - -The barcode list file should contain two tab-separated columns in which -the first column is the barcode sequence and the second column is the -name of the experiment - -The file containing the adapter sequences should be in the fasta format. - -The chromosome_lengths file should contain two tab-separated columns in -which the first column has the chromosome name and the second the -chromosome length. - diff --git a/academic/pyCRAC/README.tests b/academic/pyCRAC/README.tests index ee98d3fdaa..e1b634e6a3 100644 --- a/academic/pyCRAC/README.tests +++ b/academic/pyCRAC/README.tests @@ -1,7 +1,7 @@ To test the pyCRAC scripts after installing the package on Slackware: cp -R /usr/share/pyCRAC-$VERSION <path-to-your-work-directory>/ - cd <path-to-your-work-directory>/pyCRAC/tests + cd <path-to-your-work-directory>/pyCRAC-$VERSION/tests sh test.sh If all tests complete without an error, the package is working. diff --git a/academic/pyCRAC/pyCRAC.SlackBuild b/academic/pyCRAC/pyCRAC.SlackBuild index f94cec426b..038db738b1 100644 --- a/academic/pyCRAC/pyCRAC.SlackBuild +++ b/academic/pyCRAC/pyCRAC.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for pyCRAC -# Copyright 2017 Rob van Nues +# Copyright 2017-2023 Rob van Nues # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,23 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=pyCRAC -VERSION=${VERSION:-1.4.6} +VERSION=${VERSION:-1.5.2} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} - -# pyCRAC works with python2 as well as python3; -# Note that python2 is being phased out; therefore python3 is set as default. -# This is the same for the python pyCrac dependencies - -#set which python version to install it for -PYTHON2=false -PYTHON3=true - - -PIPENAM=kinetic_crac_pipeline -PIPEVER=${PIPEVER:-ffe91cc6bf7a} -PIPETAG=sgrann +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -48,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -73,20 +70,12 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $PRGNAM-$VERSION -rm -rf $PIPETAG-$PIPENAM-$PIPEVER tar xvf $CWD/$PRGNAM-$VERSION.tar.gz cd $PRGNAM-$VERSION -mkdir $PRGNAM/$PIPENAM - -if [[ -f $CWD/$PIPETAG-$PIPENAM-$PIPEVER.tar.gz ]]; then - tar xvf $CWD/$PIPETAG-$PIPENAM-$PIPEVER.tar.gz -C $PRGNAM/$PIPENAM --strip-components=1 -elif [[ -f $CWD/$PIPEVER.tar.gz ]]; then - tar xvf $CWD/$PIPEVER.tar.gz -C $PRGNAM/$PIPENAM --strip-components=1 -fi #replace setup.py; test.sh -rm setup.py +mv setup.py setup.py.ORIG cp $CWD/setup_slack.py setup.py rm tests/test.sh cp $CWD/test_slack.sh tests/test.sh @@ -98,32 +87,24 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -if $PYTHON2; then - python setup.py install --root=$PKG -fi -if $PYTHON3; then - python3 setup.py install --root=$PKG -fi +python3 setup.py install --root=$PKG find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true -# The pipeline-R script -mkdir -p $PKG/usr/share/$PRGNAM-$VERSION/$PIPENAM -cp $PRGNAM/$PIPENAM/gaussianProcessAnalysis.R $PKG/usr/share/$PRGNAM-$VERSION/$PIPENAM - # the manual etc. mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ README.md \ + setup.py.ORIG \ + The_pyCRAC_Manual.pdf \ $CWD/README.tests $CWD/setup_slack.py \ $CWD/README \ $PKG/usr/doc/$PRGNAM-$VERSION -cp -a $PRGNAM/$PIPENAM/README.md $PKG/usr/doc/$PRGNAM-$VERSION/$PIPENAM-README.md cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/pyCRAC/pyCRAC.info b/academic/pyCRAC/pyCRAC.info index 8048dd69ec..8fcdeffd60 100644 --- a/academic/pyCRAC/pyCRAC.info +++ b/academic/pyCRAC/pyCRAC.info @@ -1,12 +1,10 @@ PRGNAM="pyCRAC" -VERSION="1.4.6" -HOMEPAGE="http://sandergranneman.bio.ed.ac.uk/pycrac-software" -DOWNLOAD="https://pypi.python.org/packages/source/p/pyCRAC/pyCRAC-1.4.6.tar.gz \ - https://bitbucket.org/sgrann/kinetic_crac_pipeline/get/ffe91cc6bf7a.tar.gz" -MD5SUM="ddbfbd08a5d8a178082056ef3efc99a8 \ - 8c19a15c439941cc5ae17e083f52143a" +VERSION="1.5.2" +HOMEPAGE="https://git.ecdf.ed.ac.uk/sgrannem/pycrac" +DOWNLOAD="https://pypi.python.org/packages/source/p/pyCRAC/pyCRAC-1.5.2.tar.gz" +MD5SUM="f2bbb5dbcbe2b17051b8843a7e4d519f" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="python3 flexbar novocraft numpy3 pysam scipy3 pandas ruffus" +REQUIRES="flexbar novocraft pysam python3-scipy python3-pandas" MAINTAINER="Rob van Nues" EMAIL="sborg63@disroot.org" diff --git a/academic/pyCRAC/setup_slack.py b/academic/pyCRAC/setup_slack.py index 421d43bebe..db5c30751f 100644 --- a/academic/pyCRAC/setup_slack.py +++ b/academic/pyCRAC/setup_slack.py @@ -1,10 +1,10 @@ #!/usr/bin/python __author__ = "Sander Granneman" -__copyright__ = "Copyright 2019" -__version__ = "1.4.6" -__credits__ = ["Sander Granneman","Hywell Dunn Davies"] -__maintainer__ = ["Sander Granneman","Rob van Nues via SlackBuilds.org"] +__copyright__ = "Copyright 2021" +__version__ = "1.5.2" +__credits__ = ["Sander Granneman","Grzegorz Kudla","Hywell Dunn Davies"] +__maintainer__ = ["Sander Granneman","Rob van Nues for SlackBuilds.org"] __email__ = ["sgrannem@staffmail.ed.ac.uk", "sborg63@disroot.org"] __status__ = "Production" @@ -25,7 +25,7 @@ setup(name='pyCRAC', description='Python NextGen sequencing data processing software', author='Sander Granneman', author_email='sgrannem@staffmail.ed.ac.uk', - url='http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html', + url='https://git.ecdf.ed.ac.uk/sgrannem/pycrac', packages=['pyCRAC','pyCRAC.Parsers','pyCRAC.Classes','pyCRAC.Methods'], install_requires=['numpy >= 1.5.1', 'cython >=0.19', 'pysam >= 0.6','six >= 1.9.0'], scripts=[ @@ -55,9 +55,6 @@ setup(name='pyCRAC', 'pyCRAC/scripts/pyGTF2bedGraph.py', 'pyCRAC/scripts/pyFilterGTF.py', 'pyCRAC/scripts/pyNormalizeIntervalLengths.py', - 'pyCRAC/kinetic_crac_pipeline/CRAC_pipeline_PE.py', - 'pyCRAC/kinetic_crac_pipeline/CRAC_pipeline_PeakFinder.py', - 'pyCRAC/kinetic_crac_pipeline/CRAC_pipeline_SE.py', ], classifiers=[ 'Development Status :: 5 - Production/Stable', 'Environment :: Console', @@ -92,6 +89,3 @@ setup(name='pyCRAC', 'tests/genes.list']) ] ) - - - diff --git a/academic/pyfits/README b/academic/pyfits/README deleted file mode 100644 index 89eac1e478..0000000000 --- a/academic/pyfits/README +++ /dev/null @@ -1,3 +0,0 @@ -PyFITS provides an interface to FITS formatted files in the Python -scripting language. PyFITS is a development project of the Science -Software Branch at the Space Telescope Science Institute. diff --git a/academic/pyfits/pyfits.SlackBuild b/academic/pyfits/pyfits.SlackBuild deleted file mode 100644 index 0c4e98b2d7..0000000000 --- a/academic/pyfits/pyfits.SlackBuild +++ /dev/null @@ -1,56 +0,0 @@ -#!/bin/sh - -# Slackware build script for PyFITS. - -# Written by Nicky Chorley <nick.chorley@gmail.com>, but heavily -# based on the NumPy SlackBuild by Aleksandar Samardzic. - -PRGNAM=pyfits -VERSION=${VERSION:-3.1.2} -BUILD=${BUILD:-1} -TAG=${TAG:-_SBo} - -if [ -z "$ARCH" ]; then - case "$( uname -m )" in - i?86) ARCH=i486 ;; - arm*) ARCH=arm ;; - *) ARCH=$( uname -m ) ;; - esac -fi - -CWD=$(pwd) -TMP=${TMP:-/tmp/SBo} -PKG=${PKG:-$TMP/package-$PRGNAM} -OUTPUT=${OUTPUT:-/tmp} - -set -e - -rm -rf $PKG -mkdir -p $TMP $PKG $OUTPUT -cd $TMP -rm -rf $PRGNAM-$VERSION -tar xvf $CWD/$PRGNAM-$VERSION.tar.gz -cd $PRGNAM-$VERSION -chown -R root:root . -find -L . \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; - -python setup.py install --root $PKG - -find $PKG | xargs file | grep -e "executable" -e "shared object" | grep ELF \ - | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true - -mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a CHANGES.txt LICENSE.txt README.txt\ - $PKG/usr/doc/$PRGNAM-$VERSION -cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild -find $PKG/usr/doc -type f -exec chmod 0644 {} \; - -mkdir -p $PKG/install -cat $CWD/slack-desc > $PKG/install/slack-desc - -cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} diff --git a/academic/pyfits/pyfits.info b/academic/pyfits/pyfits.info deleted file mode 100644 index 501d73913c..0000000000 --- a/academic/pyfits/pyfits.info +++ /dev/null @@ -1,10 +0,0 @@ -PRGNAM="pyfits" -VERSION="3.1.2" -HOMEPAGE="https://github.com/spacetelescope/PyFITS" -DOWNLOAD="https://pypi.python.org/packages/source/p/pyfits/pyfits-3.1.2.tar.gz" -MD5SUM="d0f1dce1719170b0c9777bbb15bbd8b3" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="python-stsci.distutils numpy" -MAINTAINER="Nicky Chorley" -EMAIL="nick.chorley@gmail.com" diff --git a/academic/pysam/pysam.SlackBuild b/academic/pysam/pysam.SlackBuild index 1145e63733..17d0db3198 100644 --- a/academic/pysam/pysam.SlackBuild +++ b/academic/pysam/pysam.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for pysam -# Copyright 2017 Rob van Nues +# Copyright 2017-2023 Rob van Nues # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,15 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) PRGNAM=pysam -VERSION=${VERSION:-0.15.4} +VERSION=${VERSION:-0.21.0} BUILD=${BUILD:-2} TAG=${TAG:-_SBo} - -#set which python version to install it for -PYTHON2=false -PYTHON3=true +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -40,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -75,21 +80,12 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -###When pysam gets linked to htslib-1.10 this can be done again: -##use system htslib instead: -#export HTSLIB_LIBRARY_DIR=/usr/lib$LIBDIRSUFFIX -#export HTSLIB_INCLUDE_DIR=/usr/include +# pysam linked to htslib-1.17; SBo-htslib is at 1.18 #the source does not allow 'read' to 'other', which could cause a problem on reloading a Jupyter-notebook chmod 644 pysam.egg-info/* - -if $PYTHON2; then - python setup.py install --root=$PKG -fi -if $PYTHON3; then - python3 setup.py install --root=$PKG -fi +python3 setup.py install --root=$PKG find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true @@ -105,4 +101,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/pysam/pysam.info b/academic/pysam/pysam.info index 8e87762f0f..d71c4d96bd 100644 --- a/academic/pysam/pysam.info +++ b/academic/pysam/pysam.info @@ -1,10 +1,10 @@ PRGNAM="pysam" -VERSION="0.15.4" +VERSION="0.21.0" HOMEPAGE="https://github.com/pysam-developers/pysam" -DOWNLOAD="https://pypi.python.org/packages/source/p/pysam/pysam-0.15.4.tar.gz" -MD5SUM="fed157466d6e267e32593119c05247b2" +DOWNLOAD="https://pypi.python.org/packages/source/p/pysam/pysam-0.21.0.tar.gz" +MD5SUM="dca7fb36d2cf69ef887fe05ddd726998" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="python3-Cython" +REQUIRES="" MAINTAINER="Rob van Nues" EMAIL="sborg63@disroot.org" diff --git a/academic/python2-kiwisolver/README b/academic/python2-kiwisolver/README new file mode 100644 index 0000000000..5a37c5dfc8 --- /dev/null +++ b/academic/python2-kiwisolver/README @@ -0,0 +1,8 @@ +This is an efficient C++ implementation of the Cassowary constraint +solving algorithm. Kiwi(solver) is based on the seminal Cassowary +paper. It is not a refactoring of the original C++ solver, but has been +designed from the ground up to be lightweight and fast. It ranges from +10x to 500x faster than the original Cassowary solver with typical use +cases gaining a 40x improvement. Memory savings are consistently > 5x. + +Version 1.1.0 is the last one with support for python2. diff --git a/academic/kiwisolver/kiwisolver.SlackBuild b/academic/python2-kiwisolver/python2-kiwisolver.SlackBuild index 06b213b486..01e961c82e 100644 --- a/academic/kiwisolver/kiwisolver.SlackBuild +++ b/academic/python2-kiwisolver/python2-kiwisolver.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for kiwisolver -# Copyright 2018 Serban Udrea <s.udrea@gsi.de> +# Copyright 2018-2022 Serban Udrea <s.udrea@gsi.de> # All rights reserved. # # Redistribution and use of this script, with or without modification, @@ -23,10 +23,14 @@ # IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE # POSSIBILITY OF SUCH DAMAGE. -PRGNAM=kiwisolver -VERSION=${VERSION:-1.0.1} +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=python2-kiwisolver +SRCNAM=kiwisolver +VERSION=${VERSION:-1.1.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -36,9 +40,16 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} -PKG=${PKG:-$TMP/package-$PRGNAM} +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} set -e @@ -46,9 +57,9 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $PRGNAM-$VERSION -tar xvf $CWD/$PRGNAM-$VERSION.tar.gz -cd $PRGNAM-$VERSION +rm -rf $SRCNAM-$VERSION +tar xvf $CWD/$SRCNAM-$VERSION.tar.gz +cd $SRCNAM-$VERSION chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -56,17 +67,17 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -python setup.py install --root $PKG +python2 setup.py install --root $PKG find $PKG | xargs file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a COPYING.txt PKG-INFO README.rst $PKG/usr/doc/$PRGNAM-$VERSION +cp -a releasenotes.rst PKG-INFO README.rst $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/python2-kiwisolver/python2-kiwisolver.info b/academic/python2-kiwisolver/python2-kiwisolver.info new file mode 100644 index 0000000000..875281ea80 --- /dev/null +++ b/academic/python2-kiwisolver/python2-kiwisolver.info @@ -0,0 +1,10 @@ +PRGNAM="python2-kiwisolver" +VERSION="1.1.0" +HOMEPAGE="https://pypi.org/project/kiwisolver" +DOWNLOAD="https://files.pythonhosted.org/packages/16/e7/df58eb8868d183223692d2a62529a594f6414964a3ae93548467b146a24d/kiwisolver-1.1.0.tar.gz" +MD5SUM="fc8a614367f7ba0d34a02fd08c535afc" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Serban Udrea" +EMAIL="S.Udrea@gsi.de" diff --git a/academic/python2-kiwisolver/slack-desc b/academic/python2-kiwisolver/slack-desc new file mode 100644 index 0000000000..ecf6335078 --- /dev/null +++ b/academic/python2-kiwisolver/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +python2-kiwisolver: python2-kiwisolver (an implementation of the Cassowary algorithm) +python2-kiwisolver: +python2-kiwisolver: This is an efficient C++ implementation of the Cassowary constraint +python2-kiwisolver: solving algorithm. Kiwi(solver) is based on the seminal Cassowary +python2-kiwisolver: paper. It is not a refactoring of the original C++ solver, but has +python2-kiwisolver: been designed from the ground up to be lightweight and fast. +python2-kiwisolver: +python2-kiwisolver: Homepage: https://pypi.org/project/kiwisolver +python2-kiwisolver: +python2-kiwisolver: Version 1.1.0 is the last one with support for python2. +python2-kiwisolver: diff --git a/academic/python2-scipy/README b/academic/python2-scipy/README new file mode 100644 index 0000000000..aa007f4f7d --- /dev/null +++ b/academic/python2-scipy/README @@ -0,0 +1,25 @@ +SciPy (pronounced "Sigh Pie") is open-source software for mathematics, +science, and engineering. + +The SciPy library is built to work with NumPy arrays, and provides +many user-friendly and efficient numerical routines such as routines +for numerical integration and optimization. Together, they run on +all popular operating systems, are quick to install, and are free of +charge. NumPy and SciPy are easy to use, but powerful enough to be +depended upon by some of the world's leading scientists and engineers. + +matplotlib and ipython are nice to have in connection with scipy, but +scipy does not depend on them. Be aware that ipython gets installed just +for python3. + +Since ver. 0.14.0 scipy uses SuperLU instead of UMFPACK for solving +unsymmetric sparse linear systems. If you want to use UMFPACK you +must install it in advance of numpy and build numpy accordingly (see +the README to numpy's SlackBuild). Moreover, after installing scipy, +you have to install scikit-umfpack. + +If you need to build scipy for debugging, set DEBUG=y. + +NOTE: Version 1.2.3 is the last one with python2 support. If you'd like + to use a newer scipy version you have to switch to using python3 + and install scipy with the scipy3 SlackBuild. diff --git a/academic/scipy3/scipy3.SlackBuild b/academic/python2-scipy/python2-scipy.SlackBuild index 22cbb37f31..683c91db3d 100644 --- a/academic/scipy3/scipy3.SlackBuild +++ b/academic/python2-scipy/python2-scipy.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash -# Build script for the Python SciPy package to be used with python 3 +# Build script for the Python SciPy package -# Copyright 2016-2019 Serban Udrea <s.udrea@gsi.de> +# Copyright 2011-2022 Serban Udrea <s.udrea@gsi.de> # All rights reserved. # # Redistribution and use of this script, with or without modification, @@ -25,14 +25,18 @@ # Written by Eugene Suter <easuter@gmail.com> # Updated to 0.7.2 by João Felipe Santos <joao.eel@gmail.com> -# Updated up to 1.1.0 by Serban Udrea <S.Udrea@gsi.de> +# Updated to 1.2.2 by Matteo Bernardini <ponce@slackbuilds.org> +# Updated up to 1.1.0 and to 1.2.3 by Serban Udrea <S.Udrea@gsi.de> # Added support for building with debugging symbols (S. Udrea) -PRGNAM="scipy3" -SRCNAM="scipy" -VERSION=${VERSION:-1.1.0} +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=python2-scipy +SRCNAM=scipy +VERSION=${VERSION:-1.2.3} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -42,9 +46,16 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} -PKG=${PKG:-$TMP/package-$PRGNAM} +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} set -e @@ -52,9 +63,9 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf "$SRCNAM-$VERSION" +rm -rf $SRCNAM-$VERSION tar xvf $CWD/$SRCNAM-$VERSION.tar.gz -cd "$SRCNAM-$VERSION" +cd $SRCNAM-$VERSION chown -R root:root . find -L . \ @@ -63,17 +74,19 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ -exec chmod 644 {} \; +export FFLAGS="-fallow-argument-mismatch -fPIC" + DEBUG=${DEBUG:-no} DEBUG=$(echo "$DEBUG"|cut -b 1|tr a-z A-Z) if [ "$DEBUG" = "N" ] then - python3 setup.py install --root $PKG + python2 setup.py install --root $PKG find $PKG | xargs file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true else - python3 setup.py build --debug - python3 setup.py install --root $PKG + python2 setup.py build --debug + python2 setup.py install --root $PKG fi mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION @@ -86,4 +99,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/python2-scipy/python2-scipy.info b/academic/python2-scipy/python2-scipy.info new file mode 100644 index 0000000000..801dab6c3c --- /dev/null +++ b/academic/python2-scipy/python2-scipy.info @@ -0,0 +1,10 @@ +PRGNAM="python2-scipy" +VERSION="1.2.3" +HOMEPAGE="https://www.scipy.org/" +DOWNLOAD="https://files.pythonhosted.org/packages/62/4f/7e95c5000c411164d5ca6f55ac54cda5d200a3b6719dafd215ee0bd61578/scipy-1.2.3.tar.gz" +MD5SUM="43b42a507472dfa1dff4c91d58a6543f" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="python2-numpy lapack" +MAINTAINER="Serban Udrea" +EMAIL="S.Udrea@gsi.de" diff --git a/academic/python2-scipy/slack-desc b/academic/python2-scipy/slack-desc new file mode 100644 index 0000000000..040202c817 --- /dev/null +++ b/academic/python2-scipy/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +python2-scipy: python2-scipy (python library for math, science, and engineering) +python2-scipy: +python2-scipy: The SciPy library is built to work with NumPy arrays, and provides +python2-scipy: many user-friendly and efficient numerical routines such as routines +python2-scipy: for numerical integration and optimization. NumPy and SciPy are easy +python2-scipy: to use, but powerful enough to be depended upon by some of the world's +python2-scipy: leading scientists and engineers. +python2-scipy: Version 1.2.3 is the last with support for python2. +python2-scipy: +python2-scipy: https://www.scipy.org/ +python2-scipy: diff --git a/academic/python3-ase/README b/academic/python3-ase/README new file mode 100644 index 0000000000..b37a13ecf8 --- /dev/null +++ b/academic/python3-ase/README @@ -0,0 +1,7 @@ + The Atomic Simulation Environment (ASE) is a set of tools and Python +modules for setting up, manipulating, running, visualizing and +analyzing atomistic simulations. The code is freely available under +the GNU LGPL license. + + + Optional dependence autodetected, matplotlib diff --git a/academic/python3-ase/python3-ase.SlackBuild b/academic/python3-ase/python3-ase.SlackBuild new file mode 100644 index 0000000000..d8f092e024 --- /dev/null +++ b/academic/python3-ase/python3-ase.SlackBuild @@ -0,0 +1,111 @@ +#!/bin/bash + +# Slackware build script for ASE (Atomic Simulation Environment) + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=python3-ase +VERSION=${VERSION:-3.22.1} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +SRCNAM="ase" + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $SRCNAM-$VERSION +tar xvf $CWD/$SRCNAM-$VERSION.tar.gz +cd $SRCNAM-$VERSION + +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +python3 setup.py build +[ "${TEST:-no}" == "yes" ] && PYTHONPATH=$PYTHONPATH:. ./bin/ase test +PYTHONPATH=$PYTHONPATH:. ./bin/ase info; sleep 2 +python3 setup.py install --root=$PKG + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +find $PKG -depth -type d -empty -delete || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + {CHANGELOG,CONTRIBUTING,README}.rst \ + COPYING COPYING.LESSER LICENSE PKG-INFO doc \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/python3-ase/python3-ase.info b/academic/python3-ase/python3-ase.info new file mode 100644 index 0000000000..c23706b96f --- /dev/null +++ b/academic/python3-ase/python3-ase.info @@ -0,0 +1,10 @@ +PRGNAM="python3-ase" +VERSION="3.22.1" +HOMEPAGE="https://wiki.fysik.dtu.dk/ase" +DOWNLOAD="https://pypi.org/packages/source/a/ase/ase-3.22.1.tar.gz" +MD5SUM="8173c8b598faf995ff11cbceafacedc1" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="python3-scipy" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/python3-ase/slack-desc b/academic/python3-ase/slack-desc new file mode 100644 index 0000000000..59d1cf5415 --- /dev/null +++ b/academic/python3-ase/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +python3-ase: python3-ase (Atomic Simulation Environment (ASE)) +python3-ase: +python3-ase: +python3-ase: +python3-ase: The Atomic Simulation Environment (ASE) is a set of tools and +python3-ase: Python modules for setting up, manipulating, running, visualizing +python3-ase: and analyzing atomistic simulations. The code is freely available +python3-ase: under the GNU LGPL license. +python3-ase: +python3-ase: +python3-ase: diff --git a/academic/python3-scipy/README b/academic/python3-scipy/README new file mode 100644 index 0000000000..c4b1d1d862 --- /dev/null +++ b/academic/python3-scipy/README @@ -0,0 +1,26 @@ +SciPy (pronounced "Sigh Pie") is open-source software for mathematics, +science, and engineering. + +The SciPy library is built to work with NumPy arrays, and provides +many user-friendly and efficient numerical routines such as routines +for numerical integration and optimization. Together, they run on +all popular operating systems, are quick to install, and are free of +charge. NumPy and SciPy are easy to use, but powerful enough to be +depended upon by some of the world's leading scientists and engineers. + +matplotlib and ipython are nice to have in connection with scipy, but +scipy does not depend on them. + +Since ver. 0.14.0 scipy uses SuperLU instead of UMFPACK for solving +unsymmetric sparse linear systems. If you want to use UMFPACK you +must install it in advance of numpy and build numpy accordingly (see +the README to numpy's SlackBuild). Moreover, after installing scipy, +you have to install scikit-umfpack. + +If you need to build scipy for debugging, set DEBUG=YES. + +NOTE: this is for Python 3. If you need Python 2 support, install +python2-scipy. + +ADDITIONAL NOTE: Unable to support newer versions than 1.12.0 due to +requiring a newer Cython than included in Slackware (needs 3.0.8). diff --git a/academic/scipy/scipy.SlackBuild b/academic/python3-scipy/python3-scipy.SlackBuild index 043194c101..7586beabdc 100644 --- a/academic/scipy/scipy.SlackBuild +++ b/academic/python3-scipy/python3-scipy.SlackBuild @@ -1,8 +1,10 @@ -#!/bin/sh +#!/bin/bash -# Build script for the Python SciPy package +# Build script for the Python SciPy package to be used with python 3 -# Copyright 2011-2018 Serban Udrea <s.udrea@gsi.de> +# Copyright 2016-2019 Serban Udrea <s.udrea@gsi.de> +# Copyright 2022 Isaac Yu <isaacyu@protonmail.com> +# Copyright 2023-2024 Jeremy Hansen <jebrhansen+SBo@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, @@ -28,10 +30,14 @@ # Updated up to 1.1.0 by Serban Udrea <S.Udrea@gsi.de> # Added support for building with debugging symbols (S. Udrea) -PRGNAM=scipy -VERSION=${VERSION:-1.1.0} -BUILD=${BUILD:-2} +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM="python3-scipy" +SRCNAM="scipy" +VERSION=${VERSION:-1.12.0} +BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -41,9 +47,13 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} -PKG=${PKG:-$TMP/package-$PRGNAM} +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} set -e @@ -51,38 +61,42 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf "$PRGNAM-$VERSION" -tar xvf $CWD/$PRGNAM-$VERSION.tar.gz -cd "$PRGNAM-$VERSION" +rm -rf "$SRCNAM-$VERSION" +tar xvf $CWD/$SRCNAM-$VERSION.tar.gz +cd "$SRCNAM-$VERSION" chown -R root:root . find -L . \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; - -DEBUG=${DEBUG:-no} -DEBUG=$(echo "$DEBUG"|cut -b 1|tr a-z A-Z) - -if [ "$DEBUG" = "N" ] -then - python setup.py install --root $PKG - find $PKG | xargs file | grep -e "executable" -e "shared object" | grep ELF \ - | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true -else - python setup.py build --debug - python setup.py install --root $PKG + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \+ -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \+ + +# Allow our version of numpy and pythran to work +sed -i 's|numpy==1.22.4|numpy>=1.22.4|' pyproject.toml +sed -i 's|numpy==1.23.2|numpy>=1.23.2|' pyproject.toml +sed -i 's|pythran>=0.15.0,<0.16.0|pythran|' pyproject.toml + +# needs newer meson +PYVER=$(python3 -c 'import sys; print("%d.%d" % sys.version_info[:2])') +export PYTHONPATH=/opt/python$PYVER/site-packages/ + +python3 -m build --wheel --no-isolation +python3 -m installer --destdir "$PKG" dist/*.whl + +# Skip stripping symbols if DEBUG is YES +if [ "${DEBUG:-NO}" == "NO" ]; then + find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true fi mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a LICENSE.txt THANKS.txt INSTALL.rst.txt HACKING.rst.txt PKG-INFO \ +cp -a CONTRIBUTING.rst LICENSE.txt LICENSES_bundled.txt README.rst PKG-INFO \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild -find $PKG/usr/doc -type f -exec chmod 0644 {} \; mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/python3-scipy/python3-scipy.info b/academic/python3-scipy/python3-scipy.info new file mode 100644 index 0000000000..b2043cced7 --- /dev/null +++ b/academic/python3-scipy/python3-scipy.info @@ -0,0 +1,10 @@ +PRGNAM="python3-scipy" +VERSION="1.12.0" +HOMEPAGE="https://www.scipy.org/" +DOWNLOAD="https://github.com/scipy/scipy/releases/download/v1.12.0/scipy-1.12.0.tar.gz" +MD5SUM="22683fcf9a411f0a5254b7509bea0a6b" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="pybind11 python3-pythran OpenBLAS" +MAINTAINER="Jeremy Hansen" +EMAIL="jebrhansen+SBo@gmail.com" diff --git a/academic/python3-scipy/slack-desc b/academic/python3-scipy/slack-desc new file mode 100644 index 0000000000..92ab6f1d7a --- /dev/null +++ b/academic/python3-scipy/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +python3-scipy: python3-scipy (python library for math, science, and engineering) +python3-scipy: +python3-scipy: The SciPy library is built to work with NumPy arrays, and provides +python3-scipy: many user-friendly and efficient numerical routines such as routines +python3-scipy: for numerical integration and optimization. Together, they run on all +python3-scipy: popular operating systems, are quick to install, and are free of +python3-scipy: charge. NumPy and SciPy are easy to use, but powerful enough to be +python3-scipy: depended upon by some of the world's leading scientists and engineers. +python3-scipy: +python3-scipy: https://www.scipy.org/ +python3-scipy: diff --git a/academic/qalculate-gtk/qalculate-gtk.SlackBuild b/academic/qalculate-gtk/qalculate-gtk.SlackBuild index 569baa8084..d7eee6b209 100644 --- a/academic/qalculate-gtk/qalculate-gtk.SlackBuild +++ b/academic/qalculate-gtk/qalculate-gtk.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for qalculate-gtk -# Copyright 2016-2019 Larry Hajali <larryhaja[at]gmail[dot]com> +# Copyright 2016-2020 Larry Hajali <larryhaja[at]gmail[dot]com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=qalculate-gtk -VERSION=${VERSION:-3.4.0} +VERSION=${VERSION:-3.10.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -95,4 +105,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/qalculate-gtk/qalculate-gtk.info b/academic/qalculate-gtk/qalculate-gtk.info index e3b8170127..86c67f3cd1 100644 --- a/academic/qalculate-gtk/qalculate-gtk.info +++ b/academic/qalculate-gtk/qalculate-gtk.info @@ -1,10 +1,10 @@ PRGNAM="qalculate-gtk" -VERSION="3.4.0" -HOMEPAGE="http://qalculate.github.io/" -DOWNLOAD="https://github.com/Qalculate/qalculate-gtk/releases/download/v3.4.0/qalculate-gtk-3.4.0.tar.gz" -MD5SUM="58a8670ce4f3e692acbd2f27d104f82e" +VERSION="3.10.0" +HOMEPAGE="https://qalculate.github.io/" +DOWNLOAD="https://github.com/Qalculate/qalculate-gtk/releases/download/v3.10.0/qalculate-gtk-3.10.0.tar.gz" +MD5SUM="5880b40c4a5beb9da290b28a54eb4f46" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="libqalculate" +REQUIRES="" MAINTAINER="Larry Hajali" EMAIL="larryhaja[at]gmail[dot]com" diff --git a/academic/qcl/qcl.SlackBuild b/academic/qcl/qcl.SlackBuild index 535b4f9aba..342310dfcd 100644 --- a/academic/qcl/qcl.SlackBuild +++ b/academic/qcl/qcl.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for qcl @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=qcl VERSION=${VERSION:-0.6.4} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -91,4 +101,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/qhull/qhull.SlackBuild b/academic/qhull/qhull.SlackBuild index ec8f8a6b1b..feabf1cb97 100644 --- a/academic/qhull/qhull.SlackBuild +++ b/academic/qhull/qhull.SlackBuild @@ -1,9 +1,12 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for qhull # Copyright 2012 Chris Abela, Malta # Copyright 2014 Ryan P.C. McQuen, ryanpcmcquen@member.fsf.org, WA +# Copyright 2023, Lockywolf +# Contributed 2024, Kyle Guinn + # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,11 +26,17 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=qhull -VERSION=${VERSION:-2015.2} -BUILD_VERSION=${BUILD_VERSION:-7.2.0} -BUILD=${BUILD:-1} +VERSION=${VERSION:-8.0.2} +BUILD_VERSION=${BUILD_VERSION:-2020} +BUILD_VERSION_PATCH=${BUILD_VERSION_PATCH:-2} + +BUILD=${BUILD:-2} + TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -37,7 +46,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -61,9 +77,11 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $PRGNAM-$VERSION -tar xvf $CWD/$PRGNAM-${VERSION%.*}-src-${BUILD_VERSION}.tgz -cd $PRGNAM-$VERSION + +rm -rf $PRGNAM-$BUILD_VERSION.$BUILD_VERSION_PATCH +tar xvf $CWD/$PRGNAM-${BUILD_VERSION}-src-${VERSION}.tgz +cd $PRGNAM-$BUILD_VERSION.$BUILD_VERSION_PATCH + chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -71,26 +89,28 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; +sed -i \ + -e '/ConfigPackageLocation/s/lib/${LIB_INSTALL_DIR}/' \ + -e '/PkgConfigLocation/s/lib/${LIB_INSTALL_DIR}/' \ + CMakeLists.txt + mkdir -p build cd build cmake \ -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ -DCMAKE_INSTALL_PREFIX=/usr \ - -DBIN_INSTALL_DIR=/usr/bin \ - -DLIB_INSTALL_DIR=/usr/lib${LIBDIRSUFFIX} \ - -DINCLUDE_INSTALL_DIR=/usr/include \ - -DMAN_INSTALL_DIR=/usr/man/man1 \ - -DDOC_INSTALL_DIR=/usr/doc/$PRGNAM-$VERSION \ + -DLIB_INSTALL_DIR=lib${LIBDIRSUFFIX} \ + -DMAN_INSTALL_DIR=man/man1 \ + -DDOC_INSTALL_DIR=doc/$PRGNAM-$VERSION \ + -DCMAKE_SKIP_RPATH=YES \ + -DCMAKE_CXX_COMPILER_LAUNCHER=ccache \ + -DCMAKE_C_COMPILER_LAUNCHER=ccache \ -DCMAKE_BUILD_TYPE=Release .. make make install DESTDIR=$PKG cd .. -# Let octave find us -ln -s libqhull $PKG/usr/include/qhull -ln -s libqhull.h $PKG/usr/include/libqhull/qhull.h - find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true @@ -104,4 +124,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/qhull/qhull.info b/academic/qhull/qhull.info index 2124edbf51..f296e70bab 100644 --- a/academic/qhull/qhull.info +++ b/academic/qhull/qhull.info @@ -1,10 +1,10 @@ PRGNAM="qhull" -VERSION="2015.2" +VERSION="8.0.2" HOMEPAGE="http://www.qhull.org/" -DOWNLOAD="http://www.qhull.org/download/qhull-2015-src-7.2.0.tgz" -MD5SUM="e6270733a826a6a7c32b796e005ec3dc" +DOWNLOAD="http://www.qhull.org/download/qhull-2020-src-8.0.2.tgz" +MD5SUM="295f7332269a38279478f555cc185296" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" -MAINTAINER="Jason Graham" -EMAIL="jgraha8@gmail.com" +MAINTAINER="Lockywolf" +EMAIL="for_sbo.qhull2020_2023-11-19@lockywolf.net" diff --git a/academic/qrupdate/README b/academic/qrupdate/README index e5979003d8..ec5b475e39 100644 --- a/academic/qrupdate/README +++ b/academic/qrupdate/README @@ -1,12 +1,16 @@ qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions. -This requires a BLAS/LAPACK implementation. Choose one of these package sets: +This requires a BLAS/LAPACK implementation. Choose one of these package +sets: + * OpenBLAS (includes both a BLAS and a LAPACK implementation) * atlas (includes both a BLAS and a LAPACK implementation) * blas, lapack (the Netlib reference implementations) -If more than one set is installed (assuming there are no packaging conflicts) -then the auto-detection will use the first implementation from this list that -it finds. If in doubt, choose the Netlib reference implementations; other -packages that require a BLAS or LAPACK implementation may not build if they -are not configured to detect/use alternate implementations. + +If more than one set is installed (assuming there are no packaging +conflicts) then the auto-detection will use the first implementation +from this list that it finds. If in doubt, choose the Netlib reference +implementations; other packages that require a BLAS or LAPACK +implementation may not build if they are not configured to detect/use +alternate implementations. diff --git a/academic/qrupdate/qrupdate.SlackBuild b/academic/qrupdate/qrupdate.SlackBuild index 6e3f11d2b8..859089ed67 100644 --- a/academic/qrupdate/qrupdate.SlackBuild +++ b/academic/qrupdate/qrupdate.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for qrupdate @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=qrupdate VERSION=${VERSION:-1.1.2} BUILD=${BUILD:-4} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$(uname -m)" in @@ -35,15 +38,22 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM-$VERSION +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="COPYING ChangeLog README" -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" @@ -84,7 +94,7 @@ autoreconf -vif --docdir=/usr/doc/$PRGNAM-$VERSION \ --disable-dependency-tracking \ --build=$ARCH-slackware-linux \ - FFLAGS="$SLKCFLAGS" \ + FFLAGS="$SLKCFLAGS -fallow-argument-mismatch" \ make make check @@ -100,4 +110,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/qrupdate/qrupdate.info b/academic/qrupdate/qrupdate.info index 22d6ccbd7f..b61013c4db 100644 --- a/academic/qrupdate/qrupdate.info +++ b/academic/qrupdate/qrupdate.info @@ -5,6 +5,6 @@ DOWNLOAD="https://sourceforge.net/projects/qrupdate/files/qrupdate/1.2/qrupdate- MD5SUM="6d073887c6e858c24aeda5b54c57a8c4" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="blas lapack" +REQUIRES="lapack" MAINTAINER="Kyle Guinn" EMAIL="elyk03@gmail.com" diff --git a/academic/qucs-s/README b/academic/qucs-s/README new file mode 100644 index 0000000000..c6b002c25d --- /dev/null +++ b/academic/qucs-s/README @@ -0,0 +1,8 @@ +Qucs-S is a spin-off of the Qucs circuit simulator. The "S" letter +indicates SPICE. It merges the power of SPICE and the simplicity of +the Qucs GUI. Qucs-S is not a simulator by itself, but it requires +to use a simulation backend with it. The schematic document format of +Qucs and Qucs-S are fully compatible. Qucs-S allows to use the following +simulation kernels: + +Ngspice(recommended optional dependency), XYCE and SpiceOpus. diff --git a/academic/loggerpro/doinst.sh b/academic/qucs-s/doinst.sh index 0fb9c8b686..65c7e2eeb9 100644 --- a/academic/loggerpro/doinst.sh +++ b/academic/qucs-s/doinst.sh @@ -2,13 +2,8 @@ if [ -x /usr/bin/update-desktop-database ]; then /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 fi -if [ -x /usr/bin/update-mime-database ]; then - /usr/bin/update-mime-database usr/share/mime >/dev/null 2>&1 -fi - if [ -e usr/share/icons/hicolor/icon-theme.cache ]; then if [ -x /usr/bin/gtk-update-icon-cache ]; then /usr/bin/gtk-update-icon-cache -f usr/share/icons/hicolor >/dev/null 2>&1 fi fi - diff --git a/academic/qucs-s/qucs-s.SlackBuild b/academic/qucs-s/qucs-s.SlackBuild new file mode 100644 index 0000000000..75d71ab548 --- /dev/null +++ b/academic/qucs-s/qucs-s.SlackBuild @@ -0,0 +1,110 @@ +#!/bin/bash + +# Slackware build script for qucs-s + +# Copyright 2023-2024 Johannes Schoepfer, Germany +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=qucs-s +VERSION=${VERSION:-24.2.1} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" +else + SLKCFLAGS="-O2" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} + -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} + + +# Avoid dependency on dos2unix +sed -i qucsator_rf/src/CMakeLists.txt \ + -e "s/COMMAND \${gperfappgen_exe}.*/COMMAND \${gperfappgen_exe} | fromdos > \${CMAKE_CURRENT_BINARY_DIR}\/gperfapphash.gph/" + +mkdir -p build +cd build + cmake \ + -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -Wno-dev \ + -DCMAKE_BUILD_TYPE=Release .. + make + make install/strip DESTDIR=$PKG +cd .. + +sed \ + -e "/^Encoding/d" \ + -e "/^$/d" \ + -i $PKG/usr/share/applications/qucs-s.desktop + +mv $PKG/usr/share/man $PKG/usr +find $PKG/usr/man -type f -exec gzip -9 {} + +for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a AUTHORS README* COPYING RELEASE ChangeLog THANKS TODO NEWS* VERSION \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/qucs-s/qucs-s.info b/academic/qucs-s/qucs-s.info new file mode 100644 index 0000000000..1feeb476ca --- /dev/null +++ b/academic/qucs-s/qucs-s.info @@ -0,0 +1,10 @@ +PRGNAM="qucs-s" +VERSION="24.2.1" +HOMEPAGE="https://ra3xdh.github.io" +DOWNLOAD="https://github.com/ra3xdh/qucs_s/releases/download/24.2.1/qucs-s-24.2.1.tar.gz" +MD5SUM="6af848a8184e13d3aa9f0c61c7b18845" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Johannes Schoepfer" +EMAIL="slackbuilds@schoepfer.info" diff --git a/academic/qucs-s/slack-desc b/academic/qucs-s/slack-desc new file mode 100644 index 0000000000..85d183826f --- /dev/null +++ b/academic/qucs-s/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +qucs-s: qucs-s (circuit simulator) +qucs-s: +qucs-s: Qucs-S is a spin-off of the Qucs circuit simulator. The "S" letter +qucs-s: indicates SPICE. It merges the power of SPICE and the simplicity of +qucs-s: the Qucs GUI. Qucs-S is not a simulator by itself, but it requires to +qucs-s: use a simulation backend with it. The schematic document format of +qucs-s: Qucs and Qucs-S are fully compatible. These backends are supported: +qucs-s: +qucs-s: Ngspice(recommended, available on SBo), XYCE and SpiceOpus. +qucs-s: +qucs-s: https://ra3xdh.github.io diff --git a/academic/qucs/doinst.sh b/academic/qucs/doinst.sh index 5fb28930db..65c7e2eeb9 100644 --- a/academic/qucs/doinst.sh +++ b/academic/qucs/doinst.sh @@ -1,3 +1,9 @@ if [ -x /usr/bin/update-desktop-database ]; then /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 fi + +if [ -e usr/share/icons/hicolor/icon-theme.cache ]; then + if [ -x /usr/bin/gtk-update-icon-cache ]; then + /usr/bin/gtk-update-icon-cache -f usr/share/icons/hicolor >/dev/null 2>&1 + fi +fi diff --git a/academic/qucs/qucs.SlackBuild b/academic/qucs/qucs.SlackBuild index dd8b555edb..1cf3b6d6ca 100644 --- a/academic/qucs/qucs.SlackBuild +++ b/academic/qucs/qucs.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for Qucs @@ -13,21 +13,24 @@ # 1. Redistributions of this script must retain the above copyright # notice, this list of conditions and the following disclaimer. # -# THIS SOFTWARE IS PROVIDED BY THE AUTHOR ''AS IS'' AND ANY EXPRESS OR IMPLIED -# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF -# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO -# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, -# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, -# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; -# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, -# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR -# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF -# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) PRGNAM=qucs VERSION=${VERSION:-0.0.19} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -37,23 +40,38 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} if [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" SPEC="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" SPEC="" elif [ "$ARCH" = "x86_64" ]; then SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" SPEC="-spec linux-g++-64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" + SPEC="" fi set -e +source /etc/profile.d/qt4.sh rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT @@ -64,22 +82,26 @@ cd $PRGNAM-$VERSION chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --localstatedir=/var \ --mandir=/usr/man \ --disable-doc \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ --build=$ARCH-slackware-linux make make install DESTDIR=$PKG +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + find $PKG/usr/man -type f -exec gzip -9 {} \; for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done @@ -97,4 +119,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/qucs/qucs.info b/academic/qucs/qucs.info index fd2e34b3ab..2d17c1db1f 100644 --- a/academic/qucs/qucs.info +++ b/academic/qucs/qucs.info @@ -5,6 +5,6 @@ DOWNLOAD="http://downloads.sourceforge.net/qucs/qucs-0.0.19.tar.gz" MD5SUM="321b22b88099c6c8ac42ee8b7ab637a8" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="adms" +REQUIRES="adms qt4" MAINTAINER="Fellype do Nascimento" EMAIL="fellype (at) gmail (dot) com" diff --git a/academic/ramulator/README b/academic/ramulator/README new file mode 100644 index 0000000000..fbc6c1077a --- /dev/null +++ b/academic/ramulator/README @@ -0,0 +1,6 @@ +Ramulator is a fast and cycle-accurate DRAM simulator that supports a +wide array of commercial, as well as academic, DRAM standards. + + +Support files are installed at: /usr/share/ramulator-VERSION +Test files are at: /usr/libexec/ramulator diff --git a/academic/ramulator/ramulator.SlackBuild b/academic/ramulator/ramulator.SlackBuild new file mode 100644 index 0000000000..1f1d5112e8 --- /dev/null +++ b/academic/ramulator/ramulator.SlackBuild @@ -0,0 +1,139 @@ +#!/bin/bash + +# Slackware build script for ramulator + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=ramulator +VERSION=${VERSION:-20220503} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +COMMIT=743b940b70a8e18bcffb14eec22d2ed731059540 + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$COMMIT +tar xvf $CWD/$PRGNAM-$COMMIT.tar.gz +cd $PRGNAM-$COMMIT +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +# make rule for libramulator.so +sed -i '39alibramulator.so: $(SRCS) $(SRCDIR)/*.h' Makefile +sed -i '40a\\t$(CXX) -c $(CXXFLAGS) -fpic -DRAMULATOR -o libramulator.o $<' Makefile +sed -i '41a\\t$(CXX) -shared -o libramulator.so libramulator.o' Makefile + +# update other files +sed -i '19,20s#./#/usr/share/'$PRGNAM-$VERSION'/#' test_ramulator.py +sed -i '26s/^/#/' test_ramulator.py +sed -i '27s#./#/usr/share/'$PRGNAM-$VERSION'/#' test_ramulator.py +sed -i '32s#./##' test_ramulator.py +sed -i '24s#./##' test_ddr3.py +sed -i '24s#configs/#/usr/share/'$PRGNAM-$VERSION'/&#' test_ddr3.py + + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +make ramulator libramulator.so + +# installing +install -d $PKG/usr/{bin,include/ramulator,lib${LIBDIRSUFFIX}} +install -m 755 ramulator $PKG/usr/bin +install -m 644 src/*.h $PKG/usr/include/ramulator +install -m 755 libramulator.so $PKG/usr/lib${LIBDIRSUFFIX} + +# install other files +mkdir -p $PKG/usr/share/$PRGNAM-$VERSION +cp -av configs mappings $PKG/usr/share/$PRGNAM-$VERSION +mkdir -p $PKG/usr/share/$PRGNAM-$VERSION/cputraces +find cputraces/ -type f \ + -size -2M -exec cp -av '{}' $PKG/usr/share/$PRGNAM-$VERSION/cputraces \; + +mkdir -p $PKG/usr/libexec/$PRGNAM +cp -av test_ramulator.py $PKG/usr/libexec/$PRGNAM +cp -av test_ddr3.py $PKG/usr/libexec/$PRGNAM +cp -av plot.py $PKG/usr/libexec/$PRGNAM + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + LICENSE README.md \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/ramulator/ramulator.info b/academic/ramulator/ramulator.info new file mode 100644 index 0000000000..1be349e32f --- /dev/null +++ b/academic/ramulator/ramulator.info @@ -0,0 +1,10 @@ +PRGNAM="ramulator" +VERSION="20220503" +HOMEPAGE="https://github.com/CMU-SAFARI/ramulator" +DOWNLOAD="https://github.com/CMU-SAFARI/ramulator/archive/743b940b70a8e18bcffb14eec22d2ed731059540/ramulator-743b940b70a8e18bcffb14eec22d2ed731059540.tar.gz" +MD5SUM="c8eb022ef2465831704bc8551bfa1a36" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/loggerpro/slack-desc b/academic/ramulator/slack-desc index 085a65e8ef..ab7d81704f 100644 --- a/academic/loggerpro/slack-desc +++ b/academic/ramulator/slack-desc @@ -6,14 +6,14 @@ # customary to leave one space after the ':' except on otherwise blank lines. |-----handy-ruler------------------------------------------------------| -loggerpro: loggerpro (data-collection and analysis software) -loggerpro: -loggerpro: Vernier Software & Technology is the leader in educational data -loggerpro: collection technology. Since 1981, we have developed affordable, -loggerpro: award-winning interfaces, sensors, software, and standards-based -loggerpro: curriculum. This package installs files to allow either LoggerPro -loggerpro: or LoggerLite to access devices. -loggerpro: -loggerpro: -loggerpro: -loggerpro: +ramulator: ramulator (a fast and cycle-accurate DRAM simulator) +ramulator: +ramulator: +ramulator: +ramulator: Ramulator is a fast and cycle-accurate DRAM simulator that +ramulator: supports a wide array of commercial, as well as academic, +ramulator: DRAM standards. +ramulator: +ramulator: +ramulator: +ramulator: diff --git a/academic/rbio/rbio.SlackBuild b/academic/rbio/rbio.SlackBuild index 54bfe33088..ba45380aac 100644 --- a/academic/rbio/rbio.SlackBuild +++ b/academic/rbio/rbio.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for RBio -# Copyright 2013-2020 Kyle Guinn <elyk03@gmail.com> +# Copyright 2013-2021 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,13 +22,16 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=rbio SRCNAM=SuiteSparse SUBDIR=RBio VERSION=${VERSION:-2.2.6} -SRCVER=${SRCVER:-5.6.0} -BUILD=${BUILD:-6} +SRCVER=${SRCVER:-5.8.1} +BUILD=${BUILD:-7} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$(uname -m)" in @@ -38,15 +41,22 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM-$VERSION +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="README.txt Doc/ChangeLog Doc/License.txt Doc/gpl.txt" -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" @@ -105,4 +115,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/rbio/rbio.info b/academic/rbio/rbio.info index a2a2652e08..0e914776cd 100644 --- a/academic/rbio/rbio.info +++ b/academic/rbio/rbio.info @@ -1,8 +1,8 @@ PRGNAM="rbio" VERSION="2.2.6" HOMEPAGE="http://faculty.cse.tamu.edu/davis/suitesparse.html" -DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.6.0/SuiteSparse-5.6.0.tar.gz" -MD5SUM="af8b97cbded4cd5c6672e878bc0c37c2" +DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.8.1/SuiteSparse-5.8.1.tar.gz" +MD5SUM="c414679bbc9432a3def01b31ad921140" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="suitesparseconfig" diff --git a/academic/reduce-algebra/README b/academic/reduce-algebra/README index 5b6e1afcff..863d14a3ad 100644 --- a/academic/reduce-algebra/README +++ b/academic/reduce-algebra/README @@ -4,8 +4,8 @@ interactively for simple calculations but also provides a flexible and expressive user programming language. The development of the REDUCE computer algebra system was started in the -1960s by Anthony C. Hearn. Since then, many scientists from all over the -world have contributed to its development. REDUCE has a long and +1960s by Anthony C. Hearn. Since then, many scientists from all over +the world have contributed to its development. REDUCE has a long and distinguished place in the history of computer algebra systems. Other systems that address some of the same issues but sometimes with rather different emphasis are Axiom, Derive, Macsyma (Maxima), Maple, diff --git a/academic/reduce-algebra/reduce-algebra.SlackBuild b/academic/reduce-algebra/reduce-algebra.SlackBuild index 83786cf637..b561aa0c5e 100644 --- a/academic/reduce-algebra/reduce-algebra.SlackBuild +++ b/academic/reduce-algebra/reduce-algebra.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for reduce-algebra @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=reduce-algebra -VERSION=${VERSION:-20200301svn5286} +VERSION=${VERSION:-20201007svn5424} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} SRCNAM=Reduce-${VERSION:8}-src @@ -39,7 +42,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -165,4 +175,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/reduce-algebra/reduce-algebra.info b/academic/reduce-algebra/reduce-algebra.info index a5f168bf25..46f79d0bcb 100644 --- a/academic/reduce-algebra/reduce-algebra.info +++ b/academic/reduce-algebra/reduce-algebra.info @@ -1,10 +1,10 @@ PRGNAM="reduce-algebra" -VERSION="20200301svn5286" +VERSION="20201007svn5424" HOMEPAGE="https://reduce-algebra.sourceforge.io" -DOWNLOAD="https://downloads.sourceforge.net/reduce-algebra/snapshot_2020-03-01/Reduce-svn5286-src.tar.gz \ - https://downloads.sourceforge.net/reduce-algebra/snapshot_2020-03-01/linux64/reduce-common_5286_all.tgz" -MD5SUM="28fa5a23835e5ec1474844e18bf29855 \ - 6a3b2b2e3243ff0894bef9f336597164" +DOWNLOAD="https://downloads.sourceforge.net/reduce-algebra/snapshot_2020-10-07/Reduce-svn5424-src.tar.gz \ + https://downloads.sourceforge.net/reduce-algebra/snapshot_2020-10-07/linux64/reduce-common_5424_all.tgz" +MD5SUM="46eb107df176f965a2bd011c95451382 \ + 325258e8a864bb1098940ed82e9d17b8" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/root/README b/academic/root/README index c8beb68da7..3f7a5201e2 100644 --- a/academic/root/README +++ b/academic/root/README @@ -1,20 +1,36 @@ ROOT - A data analysis framework. -ROOT is a data analysis framework used mostly, but not limited to, -high energy physics. It was written in C++ by the techs at CERN to -explore the benefits of object oriented programming in physics data -analysis. It consists of libraries, CINT or cling interpreter for -C/C++, plotting interface and powerful parellel processing support. -It is the preferred choice in many laboratories. - -It comes with A LOT of different options for compilation. And it +ROOT provides a set of frameworks with the functionality needed to +handle and analyze large amounts of data in an efficient way. It +includes specialized storage methods such as histograms, curve +fitting, function evaluation, minimization, graphics, visualization +classes; the C++ interpreter cling for fast prototyping; and powerful +parallel processing support. + +It comes with a lot of different options for compilation. And it seems impossible to stress all of them in this one script. Therefore -the potential user is strongly advised to check the configure -script. +the potential user is strongly advised to check the cmake command +arguments. + +Compilation takes quite a while, thus consider to build ROOT like that: +# MAKEFLAGS=-j5 ./root.SlackBuild + +REQUIREMENTS: gl2ps libAfterImage python3-numpy tbb ftgl + +NOTES: + - ROOT's python TMVA requires python3-numpy being built over blas. -For mathmore support, run the SlackBuild script with MATHMORE=yes, and -for QT support, run the SlackBuild script with QT=yes, for example + - This SlackBuild sets the root7 build option to ON in order to + prepare the migration to the new ROOT 7 release. More on the ROOT 7 + features you can find here: + https://root.cern/for_developers/root7 - MATHMORE=yes ./root.SlackBuild + - Starting from ROOT version 6.26/00 it uses the web-based version for + the TBrowser if it is build with the root7 option being ON. You can + switch back to the Win95-looking TBrowser by adding the following + line to your $HOME/.rootrc file: + Browser.Name: TRootBrowser -Compilation takes quite a while. + - Starting from ROOT 6.28/00 version, one can use rootssh script for + automatic configuration of ssh tunnel, necessary for web widgets: + rootssh username@remotenode diff --git a/academic/root/root.SlackBuild b/academic/root/root.SlackBuild index bb507f0536..1dc6bb4194 100644 --- a/academic/root/root.SlackBuild +++ b/academic/root/root.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for ROOT @@ -17,148 +17,244 @@ # Modified by the slackbuilds.org project +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=root -VERSION=${VERSION:-5.34.36} +VERSION=${VERSION:-6.28.08} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" - LIBDIRSUFFIX="" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-march=i586 -mtune=i686" elif [ "$ARCH" = "i686" ]; then - SLKCFLAGS="-O2 -march=i686 -mtune=i686" - LIBDIRSUFFIX="" + SLKCFLAGS="-march=i686 -mtune=i686" elif [ "$ARCH" = "x86_64" ]; then - SLKCFLAGS="-O2 -fPIC" - LIBDIRSUFFIX="64" -else - SLKCFLAGS="-O2" - LIBDIRSUFFIX="" -fi - -set -e - -if [ ${GSL:-yes} = "no" ]; then - GSL_FLAGS="--disable-gsl-shared" + SLKCFLAGS="-fPIC" else - GSL_FLAGS="--enable-gsl-shared \ - --with-gsl-incdir=/usr/include \ - --with-gsl-libdir=/usr/lib${LIBDIRSUFFIX}" - if [ "$MATHMORE" = "yes" ]; then - GSL_FLAGS="$GSL_FLAGS --enable-mathmore" - fi + SLKCFLAGS="" fi -if [ ${FFTW:-yes} = "no" ]; then - FFTW_FLAGS="--disable-fftw3" -else - FFTW_FLAGS="--enable-fftw3 \ - --with-fftw3-incdir=/usr/include \ - --with-fftw3-libdir=/usr/lib${LIBDIRSUFFIX}" -fi +CXXSTD=${CXXSTD:-17} -if [ ${QT:-no} = "no" ]; then - QT_FLAGS="--disable-qt" -else - QT_FLAGS="--enable-qt" -fi +set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $PRGNAM +rm -rf $PRGNAM-$VERSION tar xvf $CWD/$PRGNAM\_v$VERSION.source.tar.gz -cd $PRGNAM +mv root-$VERSION src +mkdir -p $PRGNAM-$VERSION +mv src $PRGNAM-$VERSION +cd $PRGNAM-$VERSION + chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ + -o -perm 511 \) -exec chmod 755 {} \+ -o \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; - -# Make sure we use system libs and headers -rm -r graf3d/ftgl/{inc,src} -rm -r graf2d/freetype/src -rm -r graf3d/glew/{inc,src} -rm -r core/pcre/src -LANG=C LC_ALL=C find core/zip -type f -name "[a-z]*" -print0 | xargs -0 rm -f -rm -r core/lzma/src/*.tar.gz + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \+ # prefix where to install stuff -PREFIX=/opt/ROOT - -# Use --with-clang to avoid gcc-5.3 internal compiler error on i586 +PREFIX=/opt/ROOT-${VERSION} +mkdir -p build +cd build CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ -./configure \ - --with-clang \ - --prefix=$PREFIX \ - --libdir=$PREFIX/lib${LIBDIRSUFFIX} \ - --incdir=$PREFIX/include \ - --mandir=$PREFIX/man/man1 \ - --etcdir=$PREFIX/etc/root \ - --docdir=/usr/doc/$PRGNAM-$VERSION \ - --enable-roofit \ - --enable-unuran \ - --disable-builtin-freetype \ - --disable-builtin-ftgl \ - --disable-builtin-glew \ - --disable-builtin-pcre \ - --disable-builtin-zlib \ - --disable-builtin-lzma \ - $GSL_FLAGS \ - $FFTW_FLAGS \ - $QT_FLAGS \ - --enable-shared \ - --build=$ARCH-slackware-linux - +cmake ../src \ + -DCMAKE_INSTALL_PREFIX=$PREFIX \ + -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_STANDARD=${CXXSTD} \ + -DCMAKE_INSTALL_PYTHONDIR=lib \ + -DMAN_INSTALL_DIR=$PREFIX/man \ + -Dbuiltin_cfitsio=OFF \ + -Dbuiltin_davix=OFF \ + -Dbuiltin_fftw3=OFF \ + -Dbuiltin_gsl=OFF \ + -Dbuiltin_gtest=OFF \ + -Dbuiltin_openssl=OFF \ + -Dbuiltin_tbb=OFF \ + -Dbuiltin_vc=OFF \ + -Dbuiltin_vdt=OFF \ + -Dbuiltin_veccore=OFF \ + -Dclad=OFF \ + -Dalien=OFF \ + -Dall=OFF \ + -Darrow=OFF \ + -Dassan=OFF \ + -Dasserts=OFF \ + -Dbuiltin_freetype=OFF \ + -Dfftw3=ON \ + -Dbuiltin_glew=OFF \ + -Dbuiltin_clang=ON \ + -Dbuiltin_cling=ON \ + -Dbuiltin_llvm=ON \ + -Dbuiltin_lz4=OFF \ + -Dbuiltin_lzma=OFF \ + -Dbuiltin_nlohmannjson=ON \ + -Dbuiltin_openui5=ON \ + -Dbuiltin_pcre=OFF \ + -Dbuiltin_unuran=OFF \ + -Dbuiltin_xrootd=OFF \ + -Dbuiltin_xxhash=OFF \ + -Dbuiltin_zlib=OFF \ + -Dbuiltin_zstd=OFF \ + -Dccache=OFF \ + -Dcefweb=OFF \ + -Dclingtest=OFF \ + -Dcocoa=OFF \ + -Dcompression_default=zlib \ + -Dcoverage=OFF \ + -Dcuda=OFF \ + -Dcudnn=OFF \ + -Dcxx_modules=OFF \ + -Ddataframe=ON \ + -Ddavix=OFF \ + -Ddcache=OFF \ + -Ddev=OFF \ + -Ddistcc=OFF \ + -Dexceptions=ON \ + -Dfail-on-missing=ON \ + -Dfcgi=OFF \ + -Dfitsio=ON \ + -Dfortran=ON \ + -Dgdml=ON \ + -Dgfal=OFF \ + -Dgminimal=OFF \ + -Dgnuinstall=OFF \ + -Dgsl_shared=ON \ + -Dmathmore=ON \ + -Dgviz=OFF \ + -Dhttp=ON \ + -Djemalloc=OFF \ + -Dlibcxx=OFF \ + -Dmacos_native=OFF \ + -Dmemory_termination=OFF \ + -Dminimal=OFF \ + -Dminuit2=ON \ + -Dmlp=ON \ + -Dmonalisa=OFF \ + -Dmpi=OFF \ + -Dmysql=OFF \ + -Dodbc=OFF \ + -Dopengl=ON \ + -Doracle=OFF \ + -Dpgsql=OFF \ + -Dpyroot=ON \ + -Dpyroot_legacy=OFF \ + -Dpythia6=OFF \ + -Dpythia6_nolink=OFF \ + -Dpythia8=OFF \ + -Dqt5web=OFF \ + -Dr=OFF \ + -Droofit=ON \ + -Droot7=ON \ + -Drootbench=OFF \ + -Droottest=OFF \ + -Drpath=OFF \ + -Druntime_cxxmodules=ON \ + -Dshadowpw=OFF \ + -Dshared=ON \ + -Dsoversion=ON \ + -Dspectrum=ON \ + -Dsqlite=OFF \ + -Dssl=ON \ + -Dtcmalloc=OFF \ + -Dtest_distrdf_pyspark=OFF \ + -Dtesting=OFF \ + -Dtmva=ON \ + -Dtmva-cpu=ON \ + -Dtmva-gpu=OFF \ + -Dtmva-pymva=ON \ + -Dtmva-rmva=OFF \ + -Dunuran=OFF \ + -During=OFF \ + -Dvc=OFF \ + -Dvdt=OFF \ + -Dveccore=OFF \ + -Dvmc=OFF \ + -Dwebgui=ON \ + -Dwin_broken_tests=OFF \ + -Dwinrtdebug=OFF \ + -Dx11=ON \ + -Dxml=ON \ + -Dxproofd=OFF \ + -Dxrootd=OFF \ + -DCMAKE_BUILD_TYPE=Release ../src make -make install DESTDIR=$PKG - -# Move some python stuff in the proper place -PYTHONDIR=$(python -c "import sys, os; print os.path.join('/usr/lib${LIBDIRSUFFIX}', 'python%s' % sys.version[:3], 'site-packages')")/ -mkdir -p $PKG$PYTHONDIR -mv \ - $PKG$PREFIX/lib$LIBDIRSUFFIX/*.py \ - $PKG$PREFIX/lib$LIBDIRSUFFIX/*.pyc \ - $PKG$PREFIX/lib$LIBDIRSUFFIX/python/genreflex \ - $PKG$PYTHONDIR -rm -fr $PKG$PREFIX/lib$LIBDIRSUFFIX/python +make install/strip DESTDIR=$PKG find $PKG | xargs file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneded 2> /dev/null || true find $PKG$PREFIX/man -type f -exec gzip -9 {} \; +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +# We are still in build directory +# Copy documentation to system; also to ROOTSYS (ROOT expects it there) +cp -a README/ README.md LICENSE LGPL2_1.txt ../src/CONTRIBUTING.md \ + $PKG/usr/doc/$PRGNAM-$VERSION +find $PKG/usr/doc/$PRGNAM-$VERSION -type f -exec chmod 644 {} \; +cp -a README/ LICENSE \ + $PKG$PREFIX +# README is a directory +find $PKG$PREFIX/README -type d -exec chmod 755 {} \; +find $PKG$PREFIX/README -type f -exec chmod 644 {} \; +chmod -R 644 $PKG$PREFIX/LICENSE +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + # Install some profile.d scripts to use the right paths mkdir -p $PKG/etc/profile.d -echo "set path = ( \$path $PREFIX/bin )" > $PKG/etc/profile.d/root.csh -echo "setenv MANPATH \${MANPATH}:$PREFIX/man" >> $PKG/etc/profile.d/root.csh -echo "PATH=\$PATH:$PREFIX/bin" > $PKG/etc/profile.d/root.sh -echo "MANPATH=\$MANPATH:$PREFIX/man" >> $PKG/etc/profile.d/root.sh +# Start with tcsh +echo "setenv ROOTSYS $PREFIX" > $PKG/etc/profile.d/root.csh +echo "set path = ( \$path $PREFIX/bin )" >> $PKG/etc/profile.d/root.csh +echo "setenv MANPATH \${MANPATH}:$PREFIX/man" >> $PKG/etc/profile.d/root.csh +echo "if ( ! \$?PYTHONPATH ) then" >> $PKG/etc/profile.d/root.csh +echo "setenv PYTHONPATH $PREFIX/lib" >> $PKG/etc/profile.d/root.csh +echo "else" >> $PKG/etc/profile.d/root.csh +echo "if ( \"\$PYTHONPATH\" != \"\") then" >> $PKG/etc/profile.d/root.csh +echo "setenv PYTHONPATH \$PYTHONPATH:$PREFIX/lib">> $PKG/etc/profile.d/root.csh +echo "else" >> $PKG/etc/profile.d/root.csh +echo "setenv PYTHONPATH $PREFIX/lib" >> $PKG/etc/profile.d/root.csh +echo "endif" >> $PKG/etc/profile.d/root.csh +echo "endif" >> $PKG/etc/profile.d/root.csh +# And bash +echo "ROOTSYS=$PREFIX" > $PKG/etc/profile.d/root.sh +echo "PATH=\$PATH:$PREFIX/bin" >> $PKG/etc/profile.d/root.sh +echo "MANPATH=\$MANPATH:$PREFIX/man" >> $PKG/etc/profile.d/root.sh +echo "if [ -z \"\${PYTHONPATH}\" ]; then" >> $PKG/etc/profile.d/root.sh +echo " export PYTHONPATH=$PREFIX/lib" >> $PKG/etc/profile.d/root.sh +echo "else" >> $PKG/etc/profile.d/root.sh +echo " export PYTHONPATH=\$PYTHONPATH:$PREFIX/lib" \ + >> $PKG/etc/profile.d/root.sh +echo "fi" >> $PKG/etc/profile.d/root.sh chmod +x $PKG/etc/profile.d/root.* -cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +mkdir -p $PKG/etc/ld.so.conf.d +echo "$PREFIX/lib" > $PKG/etc/ld.so.conf.d/root.conf mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc -sed \ - -e "s|@LIBDIRSUFFIX@|$LIBDIRSUFFIX|" \ - -e "s|@PREFIX@|$PREFIX|" \ - $CWD/doinst.sh > $PKG/install/doinst.sh +cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/root/root.info b/academic/root/root.info index 450e1bde00..9343758408 100644 --- a/academic/root/root.info +++ b/academic/root/root.info @@ -1,10 +1,10 @@ PRGNAM="root" -VERSION="5.34.36" -HOMEPAGE="http://root.cern.ch/drupal/" -DOWNLOAD="https://root.cern.ch/download/root_v5.34.36.source.tar.gz" -MD5SUM="6a1ad549b3b79b10bbb1f116b49067ee" +VERSION="6.28.08" +HOMEPAGE="https://root.cern" +DOWNLOAD="https://root.cern/download/root_v6.28.08.source.tar.gz" +MD5SUM="3eca7fadb7867232fa74a7262644b05d" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="ftgl" -MAINTAINER="Jože Zobec" -EMAIL="jozze.zepl@gmail.com" +REQUIRES="gl2ps libAfterImage python3-numpy tbb ftgl" +MAINTAINER="Andrei Rabusov" +EMAIL="arabusov@gmail.com" diff --git a/academic/root/slack-desc b/academic/root/slack-desc index 50c68b3ed0..8dfe3a9ded 100644 --- a/academic/root/slack-desc +++ b/academic/root/slack-desc @@ -1,5 +1,5 @@ # HOW TO EDIT THIS FILE: -# The "handy ruler" below makes it easier to edit a package description. +# The handy ruler below makes it easier to edit a package description. # Line up the first '|' above the ':' following the base package name, and # the '|' on the right side marks the last column you can put a character in. # You must make exactly 11 lines for the formatting to be correct. It's also @@ -8,12 +8,12 @@ |-----handy-ruler------------------------------------------------------| root: root (data analysis framework) root: -root: ROOT is a data analysis framework used mostly, but not limited to, -root: high energy physics. It was written in C++ by the techs at CERN to -root: explore the benefits of object oriented programming in physics data -root: analysis. It consists of libraries, CINT or cling interpreter for -root: C/C++, plotting interface and powerful parellel processing support. -root: It is the preferred choice in many laboratories. +root: ROOT provides a set of frameworks with the functionality needed to +root: handle and analyze large amounts of data in an efficient way. It +root: includes specialized storage methods such as histograms, curve +root: fitting, function evaluation, minimization, graphics, visualization +root: classes; the C++ interpreter cling for fast prototyping; and powerful +root: parallel processing support. root: -root: Homepage: http://root.cern.ch/drupal/ +root: Homepage: https://root.cern root: diff --git a/academic/rpy2/README b/academic/rpy2/README new file mode 100644 index 0000000000..3685736766 --- /dev/null +++ b/academic/rpy2/README @@ -0,0 +1,24 @@ +Python interface to the R language. + +rpy2 is running an embedded R, providing access to it +from Python using R's own C-API through either: + +1) a high-level interface making R functions and objects +just like Python functions and providing a seamless +conversion to numpy and pandas data structures + +2) a low-level interface closer to the C-API + +It is also providing features for when working with +jupyter notebooks or ipython. + +NOTE: +R needs to be compiled with the shared library flag, +thus: build R on SBo with R_SHLIB=yes and BLAS_SHLIB=yes +(See also the notes in the rpy2.Slackbuild) + +Remove installed rpy2 before building and upgrading to a new version. + + +home:https://rpy2.github.io/ +documentation:https://rpy2.github.io/doc/latest/html/index.html diff --git a/academic/rpy2/Rlibs.conf b/academic/rpy2/Rlibs.conf new file mode 100644 index 0000000000..cd1ea265b7 --- /dev/null +++ b/academic/rpy2/Rlibs.conf @@ -0,0 +1,2 @@ +##placed as rpy2 cannot load R without "export LD_LIBRARY_PATH=/usr/lib64/R/lib/" +/usr/lib64/R/lib
\ No newline at end of file diff --git a/academic/rpy2/doinst.sh b/academic/rpy2/doinst.sh new file mode 100644 index 0000000000..bf984ccfe4 --- /dev/null +++ b/academic/rpy2/doinst.sh @@ -0,0 +1,2 @@ +#load the path to the R libraries to enable linking +ldconfig diff --git a/academic/rpy2/rpy2.SlackBuild b/academic/rpy2/rpy2.SlackBuild new file mode 100644 index 0000000000..ea640b1291 --- /dev/null +++ b/academic/rpy2/rpy2.SlackBuild @@ -0,0 +1,124 @@ +#!/bin/bash +# +# SlackBuild for rpy2 +# +# Copyright 2020-2024 Rob van Nues (sborg63@disroot.org) +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR ''AS IS'' AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=rpy2 +VERSION=${VERSION:-3.5.16} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +## make sure there is R +if ! [ -x "$(command -v R)" ]; then + echo 'Error: R is not installed.' >&2 + exit 1 +fi + +## make sure that R has been compiled with +## --enable-R-shlib +## --enable-BLAS-shlib +RHOMLIB=$(R RHOME) +echo Found R libs: +echo $RHOMLIB/lib/* + +if ! [ "$(readelf -h $RHOMLIB/lib/libR*.so | grep DYN)" ]; then + echo "Error: R is not compiled with shared libraries." >&2 + exit 1 +fi + +## this removes an error message from setup.py +## https://github.com/rpy2/rpy2/issues/675 +export LD_LIBRARY_PATH="${RHOMLIB}/lib:${LD_LIBRARY_PATH}" +echo "LD_LIBRARY_PATH set to ${LD_LIBRARY_PATH}" + +# replace deprecated `python3 setup.py build install --root=$PKG` +# thanks to fourtysixandtwo +PYVER=$(python3 -c 'import sys; print("%d.%d" % sys.version_info[:2])') +export PYTHONPATH=/opt/python$PYVER/site-packages/ + +python3 -m build --no-isolation +python3 -m installer -d "$PKG" dist/*.whl + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a AUTHORS gpl-2.0.txt NEWS README* $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +## to facilitate dynamic linking with R, +## libR.so and libRblas.so still need to be found +## https://github.com/rpy2/rpy2/issues/675 +mkdir -p $PKG/etc/ld.so.conf.d/ +cat $CWD/Rlibs.conf > $PKG/etc/ld.so.conf.d/Rlibs.conf + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/rpy2/rpy2.info b/academic/rpy2/rpy2.info new file mode 100644 index 0000000000..2c3adced95 --- /dev/null +++ b/academic/rpy2/rpy2.info @@ -0,0 +1,10 @@ +PRGNAM="rpy2" +VERSION="3.5.16" +HOMEPAGE="https://rpy2.github.io/" +DOWNLOAD="https://pypi.python.org/packages/source/r/rpy2/rpy2-3.5.16.tar.gz" +MD5SUM="be5385a5547673f5b1b64e245dcd7f13" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="R cffi python3-pytest tzlocal python3-setuptools-scm-opt" +MAINTAINER="Rob van Nues" +EMAIL="sborg63@disroot.org" diff --git a/academic/rpy2/slack-desc b/academic/rpy2/slack-desc new file mode 100644 index 0000000000..4b6f260ede --- /dev/null +++ b/academic/rpy2/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +rpy2: rpy2 (R in Python) +rpy2: +rpy2: rpy2 is an interface to R running embedded in a Python process. +rpy2: The project is mature, stable, documented, and widely used +rpy2: +rpy2: It is also providing features for when working +rpy2: with jupyter notebooks or ipython. +rpy2: +rpy2: home:https://rpy2.github.io/ +rpy2: https://rpy2.github.io/doc/latest/html/index.html +rpy2: diff --git a/academic/sage-bin/9.4.patch b/academic/sage-bin/9.4.patch new file mode 100644 index 0000000000..307a558acb --- /dev/null +++ b/academic/sage-bin/9.4.patch @@ -0,0 +1,258 @@ +--- opt/SageMath/local/lib/python3.9/site-packages/sage/combinat/posets/poset_examples.py.bu 2021-08-22 19:12:42.000000000 +1000 ++++ opt/SageMath/local/lib/python3.9/site-packages/sage/combinat/posets/poset_examples.py 2022-01-02 13:10:42.447658457 +1100 +@@ -155,7 +155,7 @@ + + @staticmethod + def BooleanLattice(n, facade=None, use_subsets=False): +- """ ++ r""" + Return the Boolean lattice containing `2^n` elements. + + - ``n`` -- integer; number of elements will be `2^n` +--- opt/SageMath/local/lib/python3.9/site-packages/traitlets/config/loader.py.bu 2021-08-22 22:00:01.000000000 +1000 ++++ opt/SageMath/local/lib/python3.9/site-packages/traitlets/config/loader.py 2022-01-11 11:39:00.600018177 +1100 +@@ -792,7 +792,7 @@ + nargs = '?' + else: + nargs = None +- if len(key) is 1: ++ if len(key) == 1: + paa('-'+key, '--'+key, type=text_type, dest=value, nargs=nargs) + else: + paa('--'+key, type=text_type, dest=value, nargs=nargs) +@@ -801,7 +801,7 @@ + # + self.alias_flags[self.aliases[key]] = value + continue +- if len(key) is 1: ++ if len(key) == 1: + paa('-'+key, '--'+key, action='append_const', dest='_flags', const=value) + else: + paa('--'+key, action='append_const', dest='_flags', const=value) +--- opt/SageMath/local/lib/python3.9/site-packages/psutil/_pslinux.py.bu 2021-08-22 21:58:18.000000000 +1000 ++++ opt/SageMath/local/lib/python3.9/site-packages/psutil/_pslinux.py 2022-01-11 12:14:46.007349527 +1100 +@@ -548,7 +548,7 @@ + # https://github.com/giampaolo/psutil/issues/200 + # try to parse /proc/stat as a last resort + if num == 0: +- search = re.compile('cpu\d') ++ search = re.compile(r'cpu\d') + with open_text('%s/stat' % get_procfs_path()) as f: + for line in f: + line = line.split(' ')[0] +@@ -1465,9 +1465,9 @@ + @wrap_exceptions + def memory_full_info( + self, +- _private_re=re.compile(b"Private.*:\s+(\d+)"), +- _pss_re=re.compile(b"Pss.*:\s+(\d+)"), +- _swap_re=re.compile(b"Swap.*:\s+(\d+)")): ++ _private_re=re.compile(br"Private.*:\s+(\d+)"), ++ _pss_re=re.compile(br"Pss.*:\s+(\d+)"), ++ _swap_re=re.compile(br"Swap.*:\s+(\d+)")): + basic_mem = self.memory_info() + # Note: using 3 regexes is faster than reading the file + # line by line. +@@ -1580,7 +1580,7 @@ + raise + + @wrap_exceptions +- def num_ctx_switches(self, _ctxsw_re=re.compile(b'ctxt_switches:\t(\d+)')): ++ def num_ctx_switches(self, _ctxsw_re=re.compile(br'ctxt_switches:\t(\d+)')): + data = self._read_status_file() + ctxsw = _ctxsw_re.findall(data) + if not ctxsw: +@@ -1593,7 +1593,7 @@ + return _common.pctxsw(int(ctxsw[0]), int(ctxsw[1])) + + @wrap_exceptions +- def num_threads(self, _num_threads_re=re.compile(b'Threads:\t(\d+)')): ++ def num_threads(self, _num_threads_re=re.compile(br'Threads:\t(\d+)')): + # Note: on Python 3 using a re is faster than iterating over file + # line by line. On Python 2 is the exact opposite, and iterating + # over a file on Python 3 is slower than on Python 2. +@@ -1649,7 +1649,7 @@ + return cext.proc_cpu_affinity_get(self.pid) + + def _get_eligible_cpus( +- self, _re=re.compile(b"Cpus_allowed_list:\t(\d+)-(\d+)")): ++ self, _re=re.compile(br"Cpus_allowed_list:\t(\d+)-(\d+)")): + # See: https://github.com/giampaolo/psutil/issues/956 + data = self._read_status_file() + match = _re.findall(data) +@@ -1811,13 +1811,13 @@ + return int(self._parse_stat_file()[2]) + + @wrap_exceptions +- def uids(self, _uids_re=re.compile(b'Uid:\t(\d+)\t(\d+)\t(\d+)')): ++ def uids(self, _uids_re=re.compile(br'Uid:\t(\d+)\t(\d+)\t(\d+)')): + data = self._read_status_file() + real, effective, saved = _uids_re.findall(data)[0] + return _common.puids(int(real), int(effective), int(saved)) + + @wrap_exceptions +- def gids(self, _gids_re=re.compile(b'Gid:\t(\d+)\t(\d+)\t(\d+)')): ++ def gids(self, _gids_re=re.compile(br'Gid:\t(\d+)\t(\d+)\t(\d+)')): + data = self._read_status_file() + real, effective, saved = _gids_re.findall(data)[0] + return _common.pgids(int(real), int(effective), int(saved)) +./opt/SageMath/local/lib/python3.9/site-packages/sage/symbolic/RCS +diff -u -r1.1 expression_conversions.py +--- opt/SageMath/local/lib/python3.9/site-packages/sage/symbolic/expression_conversions.py 2021/08/22 09:12:43 1.1 ++++ opt/SageMath/local/lib/python3.9/site-packages/sage/symbolic/expression_conversions.py 2022/01/28 02:07:09 +@@ -969,7 +969,7 @@ + super(FriCASConverter, self).__init__(sage.interfaces.fricas.fricas) + + def pyobject(self, ex, obj): +- """ ++ r""" + Return a string which, when evaluated by FriCAS, returns the + object as an expression. + +./opt/SageMath/local/lib/python3.9/site-packages/IPython/core/RCS +diff -u -r1.1 oinspect.py +./opt/SageMath/local/lib/python3.9/site-packages/requests/RCS +diff -u -r1.1 api.py +--- opt/SageMath/local/lib/python3.9/site-packages/requests/api.py 2021/08/22 11:52:24 1.1 ++++ opt/SageMath/local/lib/python3.9/site-packages/requests/api.py 2022/01/28 00:49:42 +@@ -57,7 +57,7 @@ + + + def get(url, params=None, **kwargs): +- """Sends a GET request. ++ r"""Sends a GET request. + + :param url: URL for the new :class:`Request` object. + :param params: (optional) Dictionary or bytes to be sent in the query string for the :class:`Request`. +@@ -71,7 +71,7 @@ + + + def options(url, **kwargs): +- """Sends a OPTIONS request. ++ r"""Sends a OPTIONS request. + + :param url: URL for the new :class:`Request` object. + :param \*\*kwargs: Optional arguments that ``request`` takes. +@@ -84,7 +84,7 @@ + + + def head(url, **kwargs): +- """Sends a HEAD request. ++ r"""Sends a HEAD request. + + :param url: URL for the new :class:`Request` object. + :param \*\*kwargs: Optional arguments that ``request`` takes. +@@ -97,7 +97,7 @@ + + + def post(url, data=None, json=None, **kwargs): +- """Sends a POST request. ++ r"""Sends a POST request. + + :param url: URL for the new :class:`Request` object. + :param data: (optional) Dictionary, bytes, or file-like object to send in the body of the :class:`Request`. +@@ -111,7 +111,7 @@ + + + def put(url, data=None, **kwargs): +- """Sends a PUT request. ++ r"""Sends a PUT request. + + :param url: URL for the new :class:`Request` object. + :param data: (optional) Dictionary, bytes, or file-like object to send in the body of the :class:`Request`. +@@ -125,7 +125,7 @@ + + + def patch(url, data=None, **kwargs): +- """Sends a PATCH request. ++ r"""Sends a PATCH request. + + :param url: URL for the new :class:`Request` object. + :param data: (optional) Dictionary, bytes, or file-like object to send in the body of the :class:`Request`. +@@ -139,7 +139,7 @@ + + + def delete(url, **kwargs): +- """Sends a DELETE request. ++ r"""Sends a DELETE request. + + :param url: URL for the new :class:`Request` object. + :param \*\*kwargs: Optional arguments that ``request`` takes. +diff -u -r1.1 models.py +--- opt/SageMath/local/lib/python3.9/site-packages/requests/models.py 2021/08/22 11:52:24 1.1 ++++ opt/SageMath/local/lib/python3.9/site-packages/requests/models.py 2022/01/28 00:45:51 +@@ -840,7 +840,7 @@ + return content + + def json(self, **kwargs): +- """Returns the json-encoded content of a response, if any. ++ r"""Returns the json-encoded content of a response, if any. + + :param \*\*kwargs: Optional arguments that ``json.loads`` takes. + :raises ValueError: If the response body does not contain valid json. +diff -u -r1.1 sessions.py +--- opt/SageMath/local/lib/python3.9/site-packages/requests/sessions.py 2021/08/22 11:52:24 1.1 ++++ opt/SageMath/local/lib/python3.9/site-packages/requests/sessions.py 2022/01/28 01:00:24 +@@ -490,7 +490,7 @@ + return resp + + def get(self, url, **kwargs): +- """Sends a GET request. Returns :class:`Response` object. ++ r"""Sends a GET request. Returns :class:`Response` object. + + :param url: URL for the new :class:`Request` object. + :param \*\*kwargs: Optional arguments that ``request`` takes. +@@ -501,7 +501,7 @@ + return self.request('GET', url, **kwargs) + + def options(self, url, **kwargs): +- """Sends a OPTIONS request. Returns :class:`Response` object. ++ r"""Sends a OPTIONS request. Returns :class:`Response` object. + + :param url: URL for the new :class:`Request` object. + :param \*\*kwargs: Optional arguments that ``request`` takes. +@@ -512,7 +512,7 @@ + return self.request('OPTIONS', url, **kwargs) + + def head(self, url, **kwargs): +- """Sends a HEAD request. Returns :class:`Response` object. ++ r"""Sends a HEAD request. Returns :class:`Response` object. + + :param url: URL for the new :class:`Request` object. + :param \*\*kwargs: Optional arguments that ``request`` takes. +@@ -523,7 +523,7 @@ + return self.request('HEAD', url, **kwargs) + + def post(self, url, data=None, json=None, **kwargs): +- """Sends a POST request. Returns :class:`Response` object. ++ r"""Sends a POST request. Returns :class:`Response` object. + + :param url: URL for the new :class:`Request` object. + :param data: (optional) Dictionary, bytes, or file-like object to send in the body of the :class:`Request`. +@@ -535,7 +535,7 @@ + return self.request('POST', url, data=data, json=json, **kwargs) + + def put(self, url, data=None, **kwargs): +- """Sends a PUT request. Returns :class:`Response` object. ++ r"""Sends a PUT request. Returns :class:`Response` object. + + :param url: URL for the new :class:`Request` object. + :param data: (optional) Dictionary, bytes, or file-like object to send in the body of the :class:`Request`. +@@ -546,7 +546,7 @@ + return self.request('PUT', url, data=data, **kwargs) + + def patch(self, url, data=None, **kwargs): +- """Sends a PATCH request. Returns :class:`Response` object. ++ r"""Sends a PATCH request. Returns :class:`Response` object. + + :param url: URL for the new :class:`Request` object. + :param data: (optional) Dictionary, bytes, or file-like object to send in the body of the :class:`Request`. +@@ -557,7 +557,7 @@ + return self.request('PATCH', url, data=data, **kwargs) + + def delete(self, url, **kwargs): +- """Sends a DELETE request. Returns :class:`Response` object. ++ r"""Sends a DELETE request. Returns :class:`Response` object. + + :param url: URL for the new :class:`Request` object. + :param \*\*kwargs: Optional arguments that ``request`` takes. diff --git a/academic/sage-bin/9.4_sh b/academic/sage-bin/9.4_sh new file mode 100644 index 0000000000..7e29552a0d --- /dev/null +++ b/academic/sage-bin/9.4_sh @@ -0,0 +1,6 @@ +cp -a opt/SageMath/local/lib/python3.9/site-packages/sage/combinat/posets/poset_examples.py opt/SageMath/src/sage/combinat/posets +cp -a opt/SageMath/local/lib/python3.9/site-packages/sage/combinat/posets/poset_examples.py opt/SageMath/pkgs/sagemath-standard/build/lib.linux-x86_64-3.9/sage/combinat/posets +tar xf $CWD/debian_binaries-11.2.tar.xz -U -C opt/SageMath/local/lib64/gcc/x86_64-pc-linux-gnu/10.3.0 +tar xf $CWD/debian_libraries-11.2.tar.xz -U -C opt/SageMath/local/lib +mkdir -p usr/lib64 +mv opt/SageMath/local/lib/libbrotlicommon.so* usr/lib64/ diff --git a/academic/sage-bin/sage-bin.SlackBuild b/academic/sage-bin/sage-bin.SlackBuild index 90c381a894..2ff263c6dd 100644 --- a/academic/sage-bin/sage-bin.SlackBuild +++ b/academic/sage-bin/sage-bin.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for sage-bin @@ -22,11 +22,16 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=sage-bin -VERSION=${VERSION:-8.3} -DEBVERSION=${DEBVERSION:-9} +VERSION=${VERSION:-9.4} +DEBVERSION=${DEBVERSION:-11} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} +SLK_VERSION=${SLK_VERSION:-$(cat /etc/slackware-version|cut -d' ' -f2)} +[ $SLK_VERSION = 14.2 ] && PYTHON=python || PYTHON=python2 if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -36,7 +41,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -53,6 +65,8 @@ mkdir -p $TMP $PKG $OUTPUT cd $PKG mkdir root proc opt tar xvf $CWD/sage-$VERSION-Debian_GNU_Linux_$DEBVERSION-$ARCH.tar.bz2 -C $PKG/opt +[ ! -r $CWD/$VERSION.patch ] || patch -p0 < $CWD/$VERSION.patch +[ ! -r $CWD/${VERSION}_sh ] || . $CWD/${VERSION}_sh chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -61,8 +75,9 @@ find -L . \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; mkchroot . -addchroot . python sed util-linux +addchroot . $PYTHON sed util-linux chroot . <<//// +export SAGE_BANNER=bare mount -t proc proc proc opt/SageMath/sage < /dev/null # Run sage patch system umount proc @@ -74,6 +89,7 @@ rm -rf Tools bin dev etc lib64 proc root sbin usr # and other junk rm -rf $PKG/opt/SageMath/.git +mkdir -p $PKG/etc/profile.d install -D -m0755 $CWD/profile.d/sage.sh $PKG/etc/profile.d install -D -m0755 $CWD/profile.d/sage.csh $PKG/etc/profile.d @@ -93,8 +109,9 @@ for res in 16x16 32x32 64x64 128x128 ; do $PKG/usr/share/icons/hicolor/$res/mimetypes done -find $PKG/opt/SageMath/local/share/man -type f -exec gzip -9 {} \; -for i in $( find $PKG/opt/SageMath/local/share/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done +# Some man pages and their symlinks are already gzipped +find $PKG/opt/SageMath/local/share/man -type f ! -name '*.gz' -exec gzip -9 {} \; +for i in $( find $PKG/opt/SageMath/local/share/man -type l ! -name '*.gz' ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a opt/SageMath/*.{md,txt} $PKG/usr/doc/$PRGNAM-$VERSION @@ -105,4 +122,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/sage-bin/sage-bin.info b/academic/sage-bin/sage-bin.info index eddc8fbee5..9d85b66d3b 100644 --- a/academic/sage-bin/sage-bin.info +++ b/academic/sage-bin/sage-bin.info @@ -1,10 +1,14 @@ PRGNAM="sage-bin" -VERSION="8.3" -HOMEPAGE="http://www.sagemath.org" +VERSION="9.4" +HOMEPAGE="https://www.sagemath.org" DOWNLOAD="UNSUPPORTED" MD5SUM="" -DOWNLOAD_x86_64="http://mirrors.mit.edu/sage/linux/64bit/sage-8.3-Debian_GNU_Linux_9-x86_64.tar.bz2" -MD5SUM_x86_64="a97ff237de39d74faedc06b9f4e1fbcc" +DOWNLOAD_x86_64="https://mirrors.mit.edu/sage/linux/64bit/sage-9.4-Debian_GNU_Linux_11-x86_64.tar.bz2 \ + https://sourceforge.net/projects/slackbuildsdirectlinks/files/sage-bin/debian_binaries-11.2.tar.xz \ + https://sourceforge.net/projects/slackbuildsdirectlinks/files/sage-bin/debian_libraries-11.2.tar.xz" +MD5SUM_x86_64="3128ef3530f514932cabcaf62b78030a \ + dc0f1b19c9b73821865599e1cefe66b6 \ + 9380db91d6afbbc4e5a23ba13553d616" REQUIRES="mkchroot" MAINTAINER="Duncan Roe" EMAIL="duncan_roe@optusnet.com.au" diff --git a/academic/sage/README b/academic/sage/README index 6c308c8cce..6772d6b5d3 100644 --- a/academic/sage/README +++ b/academic/sage/README @@ -14,17 +14,17 @@ redefine $TMP and/or $OUTPUT. Note that the build will likely spit out many "zero length file" errors, which can safely be ignored. -See README.BUILDOPTS for additional (important) information about -build options and such. Specifically, if you do not move the installation -directory via a specification of SAGEROOT, you may need to do something -like +See README.BUILDOPTS for additional (important) information +about build options and such. Specifically, if you do not move the +installation directory via a specification of SAGEROOT, you may need +to do something like source /etc/profile.d/sage.ch so make sure the binary is in your path. -This package does not include the doc files. Those can be found at doc.sagemath.org. +This package does not include the doc files. Those can be found at +doc.sagemath.org. -NOTE: -If you have ATOM processors, you need to run this command prior building: -export OPENBLAS_CONFIGURE="TARGET=ATOM" +NOTE: If you have ATOM processors, you need to run this command prior +building: export OPENBLAS_CONFIGURE="TARGET=ATOM" diff --git a/academic/sage/pynac.patch b/academic/sage/pynac.patch deleted file mode 100644 index c8a0cdc26b..0000000000 --- a/academic/sage/pynac.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- build/pkgs/pynac/spkg-install.orig 2014-08-11 20:52:14.220516400 +0700 -+++ build/pkgs/pynac/spkg-install 2014-08-11 20:52:27.906551659 +0700 -@@ -31,6 +31,7 @@ - - build_pynac() - { -+ chmod -R g-w ${PYNACDIR} - cd ${PYNACDIR} - PKG_CONFIG_PATH=${SAGE_LOCAL}/lib/pkgconfig; export PKG_CONFIG_PATH - ./configure --disable-static --prefix=${SAGE_LOCAL} --libdir="$SAGE_LOCAL/lib" diff --git a/academic/sage/sage-build-root.patch b/academic/sage/sage-build-root.patch deleted file mode 100644 index 0daaca9c33..0000000000 --- a/academic/sage/sage-build-root.patch +++ /dev/null @@ -1,24 +0,0 @@ ---- sage-6.10/configure.old 2015-12-19 08:15:37.404497471 +0700 -+++ sage-6.10/configure 2015-12-19 08:15:55.691461292 +0700 -@@ -2965,21 +2965,6 @@ - - #--------------------------------------------------------- - --{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for root user" >&5 --$as_echo_n "checking for root user... " >&6; } -- --uid=`id -u` --if test "x$uid" == "x0"; then -- { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 --$as_echo "yes" >&6; } -- as_fn_error $? "You cannot build Sage as root, switch to an unpriviledged user" "$LINENO" 5 --else -- { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 --$as_echo "no" >&6; } -- --fi; -- -- - # Check whether we are on a supported platform - # Make sure we can run config.sub. - $SHELL "$ac_aux_dir/config.sub" sun4 >/dev/null 2>&1 || diff --git a/academic/sage/sage.SlackBuild b/academic/sage/sage.SlackBuild index 2ee5996dc9..d70c643c99 100644 --- a/academic/sage/sage.SlackBuild +++ b/academic/sage/sage.SlackBuild @@ -1,8 +1,10 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for sage # Written by Jack Maddox <jack@auburn.edu> # Currently maintained by Christopher L Duston <christopher.duston@protonmail.com> +# Last update June 2023. +# # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +24,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=sage -VERSION=${VERSION:-9.0} +VERSION=${VERSION:-10.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -36,17 +41,28 @@ if [ -z "$ARCH" ]; then fi #### These lines are to ensure the build can happen on multilib systems. -if [ "$ARCH" = "i586" ]; then -LIBDIRSUFFIX="" +if [ "$ARCH" = "i586" ] || [ "$ARCH" = "i686" ]; then + LIBDIRSUFFIX="" elif [ "$ARCH" = "x86_64" ]; then -LIBDIRSUFFIX="64" + LIBDIRSUFFIX="64" else -LIBDIRSUFFIX="" + LIBDIRSUFFIX="" fi #### -CWD=$(pwd) -TMP=${TMP:-/tmp/SBo} +# SAGE_ROOT/bin/sage points to the build directory, which can't be +# in the /tmp folder if we want it to remain after installation. +# So we'll put it in /var/tmp. Maybe just sticking it in /usr is better. + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/var/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -63,29 +79,17 @@ cd $PRGNAM-$VERSION chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; mkdir -p $PKG/$SAGEROOT $PKG/usr/share/{applications,pixmaps} \ $PKG/usr/doc/$PRGNAM-$VERSION $PKG/etc/profile.d -# Added freeBSD patch to build as root, thanks to Heinz for pointing it -patch -p0 < $CWD/pynac.patch - -# Added more patch to build as root. -patch -p1 < $CWD/sage-build-root.patch - -# Thanks to Philip Lacroix <slackph@posteo.de> -rm build/pkgs/python2/patches/sys_path_security-issue_16202.patch - -# Test Fix - this did not work. -# sed -i "s|/lib|/lib${LIBDIRSUFFIX}|" build/pkgs/iml/spkg-install - - - # The docs do not build correctly, so instead of make, do the following: LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}" \ + ./configure \ + --enable-build-as-root make build # test all examples in the documentation (over 93,000 line of input) @@ -128,12 +132,15 @@ if [ "${INSTALLSCRIPTS:-no}" = "yes" ]; then fi sed "s%SAGEROOT%${SAGEROOT}%" $CWD/$PRGNAM-notebook.desktop > $PKG/usr/share/applications/$PRGNAM-notebook.desktop -cp src/doc/common/themes/sage/static/sageicon.png $PKG/usr/share/pixmaps/ +#cp src/doc/common/themes/sage/static/sageicon.png $PKG/usr/share/pixmaps/ # Put a line here which *actually* adds sage to the path +# Gotta source that .sh script, that works fine (see README) + # install sagetex to a location that is accessible to the system TeX installation -cp -a local/share/texmf $PKG/usr/share +cp -a local/var/lib/sage/venv-python3.9/share/texmf $PKG/usr/share + cp -a COPYING.txt README.md $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild @@ -143,4 +150,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc sed "s%SAGEROOT%${SAGEROOT}%" $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -p -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -p -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/sage/sage.info b/academic/sage/sage.info index c88eea8153..70070f617e 100644 --- a/academic/sage/sage.info +++ b/academic/sage/sage.info @@ -1,8 +1,8 @@ PRGNAM="sage" -VERSION="9.0" +VERSION="10.1" HOMEPAGE="http://www.sagemath.org" -DOWNLOAD="http://mirrors.mit.edu/sage/src/sage-9.0.tar.gz" -MD5SUM="b864b8c19d376193e70eb2c8084bbd50" +DOWNLOAD="http://mirrors.mit.edu/sage/src/sage-10.1.tar.gz" +MD5SUM="53a3ea057086eca87102eedb4efa9722" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/samtools-legacy/samtools-legacy.SlackBuild b/academic/samtools-legacy/samtools-legacy.SlackBuild index 2e89ec4ff7..8797efd9e8 100644 --- a/academic/samtools-legacy/samtools-legacy.SlackBuild +++ b/academic/samtools-legacy/samtools-legacy.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for samtools-legacy -# Copyright 2013-2019 Petar Petrov slackalaxy@gmail.com +# Copyright 2013-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,10 +25,13 @@ # With help about the install paths from Arch Linux AUR: # https://aur.archlinux.org/packages/sa/samtools/PKGBUILD +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=samtools-legacy VERSION=${VERSION:-0.1.19} BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} SRCNAM=samtools SUFFIX=legacy @@ -41,7 +44,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -141,4 +151,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/samtools/README b/academic/samtools/README index 857bfbeaa7..d8e2540720 100644 --- a/academic/samtools/README +++ b/academic/samtools/README @@ -1,16 +1,16 @@ -SAM (Sequence Alignment/Map) format is a generic format for storing large -nucleotide sequence alignments. The original samtools package has been split -into three separate but tightly coordinated projects: htslib (C library for -handling high-throughput sequencing data), samtools (for handling SAM, BAM, -CRAM), and bcftools (for handling VCF and BCF). +SAM (Sequence Alignment/Map) format is a generic format for storing +large nucleotide sequence alignments. The original samtools package has +been split into three separate but tightly coordinated projects: htslib +(C library for handling high-throughput sequencing data), samtools (for +handling SAM, BAM, CRAM), and bcftools (for handling VCF and BCF). -Samtools is now distributed as an individual package. Installation is set up -so that the code uses an external HTSlib (also at SBo). Although deprecated -upstream, in the case that people need parts of samtools-legacy (e.g header -files or libbam) these can be installed from this package by modifying the -samtools.Slackbuild. Note that the sam.h of htslib differs from sam.h coming -with samtools. +Samtools is now distributed as an individual package. Installation is +set up so that the code uses an external HTSlib (also at SBo). Although +deprecated upstream, in the case that people need parts of +samtools-legacy (e.g header files or libbam) these can be installed from +this package by modifying the samtools.Slackbuild. Note that the sam.h +of htslib differs from sam.h coming with samtools. -Prior to the introduction of HTSlib, SAMtools and BCFtools were distributed -in a single samtools-0.1.x package. This old version remains available from -SBo as samtools-legacy. +Prior to the introduction of HTSlib, SAMtools and BCFtools were +distributed in a single samtools-0.1.x package. This old version remains +available from SBo as samtools-legacy. diff --git a/academic/samtools/samtools.SlackBuild b/academic/samtools/samtools.SlackBuild index 4a7efb30d8..7efbaf3288 100644 --- a/academic/samtools/samtools.SlackBuild +++ b/academic/samtools/samtools.SlackBuild @@ -1,9 +1,9 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for samtools # Copyright 2013-2016 Petar Petrov slackalaxy@gmail.com -# Copyright 2017-2020 Rob van Nues # All rights reserved. +# Copyright 2017-2024 Rob van Nues # All rights reserved. # # Redistribution and use of this script, with or without modification, is # permitted provided that the following conditions are met: @@ -22,13 +22,17 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -PRGNAM=samtools -VERSION=${VERSION:-1.10} +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=samtools +VERSION=${VERSION:-1.19.2} +HTSLIBV=${HTSLIBV:-1.19.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} -# Some applications still rely on the legacy samtools API instead of using htslib -# exclusively, in that case, install the headers in /usr/include/bam and the static +# Some applications still rely on the legacy samtools API instead of using htslib +# exclusively, in that case, install the headers in /usr/include/bam and the static # libbam library as well by declaring (uncommenting): #SAMLIB="yes" # and commenting out: @@ -47,7 +51,11 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -81,7 +89,7 @@ find -L . \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; # force linking to installed htslib -rm -r htslib-$VERSION +rm -r htslib-$HTSLIBV CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ @@ -115,13 +123,13 @@ for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; r mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - AUTHORS LICENSE README INSTALL NEWS examples \ + AUTHORS LICENSE README NEWS.md examples \ $PKG/usr/doc/$PRGNAM-$VERSION -cp $CWD/README.references $PKG/usr/doc/$PRGNAM-$VERSION +cp $CWD/README $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/samtools/samtools.info b/academic/samtools/samtools.info index 05fe9a33a0..eef9473b1e 100644 --- a/academic/samtools/samtools.info +++ b/academic/samtools/samtools.info @@ -1,8 +1,8 @@ PRGNAM="samtools" -VERSION="1.10" +VERSION="1.19.2" HOMEPAGE="http://www.htslib.org" -DOWNLOAD="https://github.com/samtools/samtools/releases/download/1.10/samtools-1.10.tar.bz2" -MD5SUM="506b0b9b2628e1f3bbedd77855b4c709" +DOWNLOAD="https://github.com/samtools/samtools/releases/download/1.19.2/samtools-1.19.2.tar.bz2" +MD5SUM="318492d95f5d8cef697442d1be996b77" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="htslib" diff --git a/academic/scidavis/README b/academic/scidavis/README index a9cfc5d263..3f0de3cf1c 100644 --- a/academic/scidavis/README +++ b/academic/scidavis/README @@ -7,13 +7,5 @@ features such as scriptability and extensibility. SciDAVis started as a fork of QtiPlot. -Optional dependencies, after installation, are scipy and pygsl (to -improve python scripting). - -Note for Slackware-current - -Since version 1.23 it is possible to build/use SciDAVis with Python 3 -- just use PYTHON3=yes before executing scidavis.SlackBuild. Default is -to use python 2 (PYTHON3=no). -*** It does not build using Python 3 in Slackware 14.2 or previous -because the shipped PyQt was not built with Python 3 support. *** +Optional dependencies at runtime are scipy and pygsl (to improve +python scripting) diff --git a/academic/scidavis/scidavis.SlackBuild b/academic/scidavis/scidavis.SlackBuild index a6d3f7b75a..6ebdd91a51 100644 --- a/academic/scidavis/scidavis.SlackBuild +++ b/academic/scidavis/scidavis.SlackBuild @@ -1,9 +1,9 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for SciDAVis -# Based on the Slackware 14.2 SlackBuild +# Based on the Slackware 15.0 SlackBuild # -# Copyright 2017-2019, Fellype do Nascimento, Campinas - Brazil +# Copyright 2017-2022, Fellype do Nascimento, Guaratingueta - Brazil # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,10 +23,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=scidavis -VERSION=${VERSION:-1.26} +VERSION=${VERSION:-2.9.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -36,20 +39,30 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} if [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" - SPEC="" + LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" - SPEC="" + LIBDIRSUFFIX="" elif [ "$ARCH" = "x86_64" ]; then SLKCFLAGS="-O2 -fPIC" - SPEC="-spec linux-g++-64" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" fi rm -rf $PKG @@ -58,6 +71,18 @@ cd $TMP rm -rf $PRGNAM-$VERSION tar xvf $CWD/$PRGNAM-$VERSION.tar.gz cd $PRGNAM-$VERSION + +rmdir 3rdparty/qwt5-qt5/ +rmdir 3rdparty/qwtplot3d/ +rmdir 3rdparty/liborigin/ + +tar xvf $CWD/qwt5-qt5-f7519200f102676fb04fb7bd0be555e0a419d378.tar.gz -C 3rdparty/ +mv 3rdparty/qwt5-qt5-f7519200f102676fb04fb7bd0be555e0a419d378 3rdparty/qwt5-qt5 +tar xvf $CWD/qwtplot3d-b2655743d30ed3185f3c0e2626b33a1d29655216.tar.gz -C 3rdparty/ +mv 3rdparty/qwtplot3d-b2655743d30ed3185f3c0e2626b33a1d29655216 3rdparty/qwtplot3d +tar xvf $CWD/liborigin-a92f26f28e531f64684b66a2731dd617bea3cb45.tar.gz -C 3rdparty/ +mv 3rdparty/liborigin-a92f26f28e531f64684b66a2731dd617bea3cb45 3rdparty/liborigin + chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -65,45 +90,41 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -# Correct the manpage path -sed -i -e 's#share/man#man#' scidavis/scidavis.pro +PYVER=$(python3 -c 'import sys; print("%d.%d" % sys.version_info[:2])') -# Since version 1.23 it is possible to build/use SciDAVis with Python 3 - just use -# PYTHON3=yes before execute scidavis.SlackBuild. Default is to use python 2 (PYTHON3=no). -# *** It does not build using Python 3 in Slackware 14.2 or previous because PyQt was not built with -# Python 3 support. I'm adding this here because I know it will be useful in the future and for the -# tests currently done in -current -if [ "${PYTHON3:-no}" = "yes" ]; then - export PYTHON=python3 -else - export PYTHON=python2 -fi +# Set the correct python paths - code based on scidavis.spec for Fedora by Alexander Ploumistos +sed -i "s:set(PYTHON_SCRIPTDIR etc:set(PYTHON_SCRIPTDIR lib$LIBDIRSUFFIX/python$PYVER/site-packages/scidavis:" scidavis/CMakeLists.txt +sed -i "s:FILES scidavisrc.py \${CMAKE_CURRENT_BINARY_DIR}/\$<CONFIG>/scidavisrc.pyc DESTINATION:FILES scidavisrc.py DESTINATION:" scidavis/CMakeLists.txt +sed -i "s:FILES scidavisrc.py \${CMAKE_CURRENT_BINARY_DIR}/scidavisrc.pyc DESTINATION:FILES scidavisrc.py DESTINATION:" scidavis/CMakeLists.txt +sed -i "s:FILES scidavisUtil.py DESTINATION share/scidavis:FILES scidavisUtil.py DESTINATION \${PYTHON_SCRIPTDIR}:" scidavis/CMakeLists.txt +sed -i "s:PYTHON_CONFIG_PATH=\"\${CMAKE_INSTALL_PREFIX}/etc\":PYTHON_CONFIG_PATH=\"/usr/lib$LIBDIRSUFFIX/python$PYVER/site-packages/scidavis\":" libscidavis/CMakeLists.txt +sed -i "s:PYTHON_UTIL_PATH=\"\${CMAKE_INSTALL_PREFIX}/share/scidavis\":PYTHON_UTIL_PATH=\"/usr/lib$LIBDIRSUFFIX/python$PYVER/site-packages/scidavis\":" libscidavis/CMakeLists.txt + +export PYTHON=python3 -## For some unknown reason, to build in Slackware we need to run qmake twice in order to get the app icons working properly -## See https://sourceforge.net/p/scidavis/scidavis-bugs/259/ -qmake -qmake \ - CONFIG+="liborigin python" \ - PRESET=linux_package \ - QMAKE_CFLAGS+="$SLKCFLAGS" \ - QMAKE_CXXFLAGS+="$SLKCFLAGS" \ - $SPEC +mkdir build && cd build +cmake .. -DSEARCH_FOR_UPDATES=OFF \ + -DDOWNLOAD_LINKS=OFF \ + -DORIGIN_IMPORT=ON \ + -DSCRIPTING_PYTHON=ON \ + -DCMAKE_INSTALL_PREFIX=/usr \ + .. make -make install INSTALL_ROOT=$PKG +make install DESTDIR=$PKG find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true -## Sometimes 'make install' fails to install the translation files -mkdir -p $PKG/usr/share/scidavis/translations -install -m 0644 scidavis/translations/*.qm $PKG/usr/share/scidavis/translations +# Move manpage to a more appropriated dir +mkdir -p $PKG/usr/man/man1/ +mv $PKG/usr/share/man/man1/scidavis.1 $PKG/usr/man/man1/scidavis.1 +rm -rf $PKG/usr/share/man/ find $PKG/usr/man -type f -exec gzip -9 {} \; for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a README.md LICENSE $PKG/usr/doc/$PRGNAM-$VERSION cp -a $PKG/usr/share/doc/scidavis/*.* $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild rm -rf $PKG/usr/share/doc @@ -113,4 +134,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/scidavis/scidavis.info b/academic/scidavis/scidavis.info index 526fd3b7f9..7904927c3f 100644 --- a/academic/scidavis/scidavis.info +++ b/academic/scidavis/scidavis.info @@ -1,10 +1,16 @@ PRGNAM="scidavis" -VERSION="1.26" +VERSION="2.9.0" HOMEPAGE="http://scidavis.sourceforge.net/" -DOWNLOAD="https://ufpr.dl.sourceforge.net/project/scidavis/SciDAVis/1.26/scidavis-1.26.tar.gz" -MD5SUM="a3e6158c9607dbbaab193941836259bf" +DOWNLOAD="https://github.com/SciDAVis/scidavis/archive/2.9.0/scidavis-2.9.0.tar.gz \ + https://github.com/SciDAVis/qwt5-qt5/archive/f751920/qwt5-qt5-f7519200f102676fb04fb7bd0be555e0a419d378.tar.gz \ + https://github.com/SciDAVis/qwtplot3d/archive/b265574/qwtplot3d-b2655743d30ed3185f3c0e2626b33a1d29655216.tar.gz \ + https://github.com/SciDAVis/liborigin/archive/a92f26f/liborigin-a92f26f28e531f64684b66a2731dd617bea3cb45.tar.gz" +MD5SUM="fc80267e26c4ba75490d7baa9dfdf93f \ + da7c360266e318948919ab2ddc8a2c4b \ + aefa1c98e1a0df67418304b66d810b3d \ + 8baa9dffeacc1fedeb94ffa8d35eae2c" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="muParser qwt5 qwtplot3d" +REQUIRES="muParser" MAINTAINER="Fellype do Nascimento" -EMAIL="fellype(at)gmail.com" +EMAIL="fellype (at) gmail (dot) com" diff --git a/academic/scilab/README b/academic/scilab/README index 300aaf1edf..9c9b1b0fd5 100644 --- a/academic/scilab/README +++ b/academic/scilab/README @@ -11,3 +11,10 @@ to run the updated profile scripts. If you have issues on upgrading/reinstalling or changing desktop environments, try delete/rename $HOME/.Scilab to resolve. + +zulu-openjdk8, openjdk8 or jdk are optional. Scilab will use the +system-wide installed java if found. Otherwise, scilab will use +its own internal jre. + +*NOTE* the tarball url is not wget-friendly: you might need a browser +to download it. diff --git a/academic/scilab/scilab.SlackBuild b/academic/scilab/scilab.SlackBuild index dba3c52491..5d3927f85c 100644 --- a/academic/scilab/scilab.SlackBuild +++ b/academic/scilab/scilab.SlackBuild @@ -1,9 +1,9 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for Scilab # Copyright 2011-2015 Fridrich von Stauffenberg <cancellor2@gmail.com> -# Copyright 2018-2019 Edward W. Koenig ,kingbeowulf@gmail.com> +# Copyright 2018-2022 Edward W. Koenig ,kingbeowulf@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,10 +23,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=scilab -VERSION=${VERSION:-6.0.2} +VERSION=${VERSION:-6.1.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -36,7 +39,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -70,13 +80,14 @@ mv $PKG/opt/$PRGNAM/lib/pkgconfig $PKG/usr/lib${LIBDIRSUFFIX} mv $PKG/opt/$PRGNAM/share/mime $PKG/usr/share mv $PKG/opt/$PRGNAM/share/icons $PKG/usr/share -# Fix an issue reported here: -#https://www.linuxquestions.org/questions/slackware-14/how-recover-from-damage-from-slackpkg-%27upgrade%27-scilab-4175656261/page3.html#post6009411 -# Slackware's versions should be plenty new enough. -mv $PKG/opt/$PRGNAM/lib/thirdparty/redist $PKG/opt/$PRGNAM/lib/thirdparty/NONWORKING_redist +# Remove conflicting libs (esp. for current) +rm -f $PKG/opt/$PRGNAM/lib/thirdparty/redist/libncurses.so +rm -f /$PKG/opt/$PRGNAM/lib/thirdparty/redist/libncurses.so.5 +rm -f $PKG/opt/$PRGNAM/lib/thirdparty/redist/libncurses.so.5.7 # fix issues with .desktop files due to upstream bugs -rm -rf $PKG/opt/$PRGNAM/share/applications +rm -rf $PKG/opt/$PRGNAM/share/applications +mkdir -p $PKG/usr/share/applications cp -a $CWD/*.desktop $PKG/usr/share/applications mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION @@ -88,4 +99,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/scilab/scilab.info b/academic/scilab/scilab.info index 2e04b16077..470c724c40 100644 --- a/academic/scilab/scilab.info +++ b/academic/scilab/scilab.info @@ -1,10 +1,10 @@ PRGNAM="scilab" -VERSION="6.0.2" +VERSION="6.1.1" HOMEPAGE="http://www.scilab.org" -DOWNLOAD="http://www.scilab.org/download/6.0.2/scilab-6.0.2.bin.linux-i686.tar.gz" -MD5SUM="ace129667674a7292511a242fe6b921d" -DOWNLOAD_x86_64="http://www.scilab.org/download/6.0.2/scilab-6.0.2.bin.linux-x86_64.tar.gz" -MD5SUM_x86_64="667cb0789c365beab5c2b0a675ffe98d" -REQUIRES="jdk" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="http://www.scilab.org/download/6.1.1/scilab-6.1.1.bin.linux-x86_64.tar.gz" +MD5SUM_x86_64="406a6346866a4decdaea8127c27ea936" +REQUIRES="" MAINTAINER="Edward W. Koenig" -EMAIL="kingbeowulf@gmail.com" +EMAIL="kingbeowulf@lnuxgalaxy.org" diff --git a/academic/scipy/README b/academic/scipy/README deleted file mode 100644 index 730af33108..0000000000 --- a/academic/scipy/README +++ /dev/null @@ -1,24 +0,0 @@ -SciPy (pronounced "Sigh Pie") is open-source software for mathematics, -science, and engineering. - -The SciPy library is built to work with NumPy arrays, and provides many -user-friendly and efficient numerical routines such as routines for -numerical integration and optimization. Together, they run on all popular -operating systems, are quick to install, and are free of charge. NumPy -and SciPy are easy to use, but powerful enough to be depended upon by -some of the world's leading scientists and engineers. - -matplotlib and ipython are nice to have in connection with scipy, but scipy -does not depend on them. - -Since ver. 0.14.0 scipy uses SuperLU instead of UMFPACK for solving unsymmetric -sparse linear systems. If you want to use UMFPACK you must install it in advance -of numpy and build numpy accordingly (see the README to numpy's SlackBuild). -Moreover, after installing scipy, you have to install scikit-umfpack, which -presently is not available on SlackBuilds.org. - -If you need to build scipy for debugging, set DEBUG=y. - -NOTE: If you use this SlackBuild scipy will run with the python version - provided by Slackware Linux, which is presently 2.7.xx. If you'd like to - use python 3.x then you have to install scipy with the scipy3 SlackBuild. diff --git a/academic/scipy/scipy.info b/academic/scipy/scipy.info deleted file mode 100644 index 0dfd4507f6..0000000000 --- a/academic/scipy/scipy.info +++ /dev/null @@ -1,10 +0,0 @@ -PRGNAM="scipy" -VERSION="1.1.0" -HOMEPAGE="https://www.scipy.org/" -DOWNLOAD="https://github.com/scipy/scipy/releases/download/v1.1.0/scipy-1.1.0.tar.gz" -MD5SUM="aa6bcc85276b6f25e17bcfc4dede8718" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="numpy lapack" -MAINTAINER="Serban Udrea" -EMAIL="S.Udrea@gsi.de" diff --git a/academic/scipy/slack-desc b/academic/scipy/slack-desc deleted file mode 100644 index 9dd00a3d2c..0000000000 --- a/academic/scipy/slack-desc +++ /dev/null @@ -1,19 +0,0 @@ -# HOW TO EDIT THIS FILE: -# The "handy ruler" below makes it easier to edit a package description. -# Line up the first '|' above the ':' following the base package name, and -# the '|' on the right side marks the last column you can put a character in. -# You must make exactly 11 lines for the formatting to be correct. It's also -# customary to leave one space after the ':' except on otherwise blank lines. - - |-----handy-ruler------------------------------------------------------| -scipy: scipy (python library for math, science, and engineering) -scipy: -scipy: The SciPy library is built to work with NumPy arrays, and provides -scipy: many user-friendly and efficient numerical routines such as routines -scipy: for numerical integration and optimization. Together, they run on all -scipy: popular operating systems, are quick to install, and are free of -scipy: charge. NumPy and SciPy are easy to use, but powerful enough to be -scipy: depended upon by some of the world's leading scientists and engineers. -scipy: -scipy: https://www.scipy.org/ -scipy: diff --git a/academic/scipy3/README b/academic/scipy3/README deleted file mode 100644 index 5a72b73476..0000000000 --- a/academic/scipy3/README +++ /dev/null @@ -1,25 +0,0 @@ -SciPy (pronounced "Sigh Pie") is open-source software for mathematics, -science, and engineering. - -The SciPy library is built to work with NumPy arrays, and provides many -user-friendly and efficient numerical routines such as routines for -numerical integration and optimization. Together, they run on all popular -operating systems, are quick to install, and are free of charge. NumPy -and SciPy are easy to use, but powerful enough to be depended upon by -some of the world's leading scientists and engineers. - -matplotlib and ipython are nice to have in connection with scipy, but scipy -does not depend on them. - -Since ver. 0.14.0 scipy uses SuperLU instead of UMFPACK for solving unsymmetric -sparse linear systems. If you want to use UMFPACK you must install it in advance -of numpy and build numpy accordingly (see the README to numpy's SlackBuild). -Moreover, after installing scipy, you have to install scikit-umfpack, which -presently is not available on SlackBuilds.org. - -If you need to build scipy for debugging, set DEBUG=y. - -NOTE: If you use this SlackBuild scipy will run with the python 3 version - installed on your system. If you'd like to use python 2.7.xx as - provided by Slackware Linux then you have to install it with the scipy - SlackBuild. diff --git a/academic/scipy3/scipy3.info b/academic/scipy3/scipy3.info deleted file mode 100644 index afdc113a2e..0000000000 --- a/academic/scipy3/scipy3.info +++ /dev/null @@ -1,10 +0,0 @@ -PRGNAM="scipy3" -VERSION="1.1.0" -HOMEPAGE="https://www.scipy.org/" -DOWNLOAD="https://github.com/scipy/scipy/releases/download/v1.1.0/scipy-1.1.0.tar.gz" -MD5SUM="aa6bcc85276b6f25e17bcfc4dede8718" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="numpy3 lapack" -MAINTAINER="Serban Udrea" -EMAIL="S.Udrea@gsi.de" diff --git a/academic/scipy3/slack-desc b/academic/scipy3/slack-desc deleted file mode 100644 index 2e586787e1..0000000000 --- a/academic/scipy3/slack-desc +++ /dev/null @@ -1,19 +0,0 @@ -# HOW TO EDIT THIS FILE: -# The "handy ruler" below makes it easier to edit a package description. -# Line up the first '|' above the ':' following the base package name, and -# the '|' on the right side marks the last column you can put a character in. -# You must make exactly 11 lines for the formatting to be correct. It's also -# customary to leave one space after the ':' except on otherwise blank lines. - - |-----handy-ruler------------------------------------------------------| -scipy3: scipy3 (python library for math, science, and engineering) -scipy3: -scipy3: The SciPy library is built to work with NumPy arrays, and provides -scipy3: many user-friendly and efficient numerical routines such as routines -scipy3: for numerical integration and optimization. Together, they run on all -scipy3: popular operating systems, are quick to install, and are free of -scipy3: charge. NumPy and SciPy are easy to use, but powerful enough to be -scipy3: depended upon by some of the world's leading scientists and engineers. -scipy3: -scipy3: https://www.scipy.org/ -scipy3: diff --git a/academic/scmutils/README b/academic/scmutils/README new file mode 100644 index 0000000000..1b97071fd6 --- /dev/null +++ b/academic/scmutils/README @@ -0,0 +1,4 @@ +scmutils is a mit-scheme library for classical mechanics. + +It is used as part of the course 6946 in MIT, +"Classical Mechanics: A Computational Approach". diff --git a/academic/scmutils/scmutils.SlackBuild b/academic/scmutils/scmutils.SlackBuild new file mode 100644 index 0000000000..ec734392d0 --- /dev/null +++ b/academic/scmutils/scmutils.SlackBuild @@ -0,0 +1,82 @@ +#!/bin/bash + +# Slackware build script for scmutils + +# Copyright 2023, Lockywolf +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=scmutils +VERSION=${VERSION:-20230902} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +target="$PKG/$(mit-scheme --batch-mode --no-init-file --eval "(write-string (->namestring (system-library-directory-pathname)))" "(exit)")" +install -Dm644 mechanics.com "$target/mechanics.com" +for src in $(find * -type f -name '*.bci'); do + install -Dm644 $src "$target/$src" +done +install -Dm755 mechanics.sh "$PKG/usr/bin/mechanics" + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + README COPYING \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/scmutils/scmutils.info b/academic/scmutils/scmutils.info new file mode 100644 index 0000000000..fad299a360 --- /dev/null +++ b/academic/scmutils/scmutils.info @@ -0,0 +1,10 @@ +PRGNAM="scmutils" +VERSION="20230902" +HOMEPAGE="http://mitpress.mit.edu/sicm/" +DOWNLOAD="https://groups.csail.mit.edu/mac/users/gjs/6946/mechanics-system-installation/native-code/scmutils-20230902.tar.gz" +MD5SUM="12b7723c14219f7a3677cc88ec7b8429" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="mit-scheme" +MAINTAINER="Lockywolf" +EMAIL="for_sbo.scmutils_2023-11-27@lockywolf.net" diff --git a/academic/scmutils/slack-desc b/academic/scmutils/slack-desc new file mode 100644 index 0000000000..6ce8862d2d --- /dev/null +++ b/academic/scmutils/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +scmutils: scmutils (numerical and algebraic packages, written in Scheme) +scmutils: +scmutils: Scmutils is a set of mathematical subroutines used for the course +scmutils: in Classical Mechanics in MIT. +scmutils: +scmutils: +scmutils: +scmutils: +scmutils: +scmutils: +scmutils: diff --git a/academic/seaview/README b/academic/seaview/README index e72249f563..2fd0c66479 100644 --- a/academic/seaview/README +++ b/academic/seaview/README @@ -14,7 +14,6 @@ sequence alignment and molecular phylogeny. Features: of evolutionary distances, maximum likelihood, driving program PhyML - Can use the Transfer Bootstrap Expectation method to compute the bootstrap support of PhyML and distance trees. -- Uses the Treerecs method to reconcile gene and species trees. - Prints and draws phylogenetic trees on screen, SVG, PDF or PostScript files. - Allows to download sequences from EMBL / GenBank / UniProt. diff --git a/academic/seaview/seaview.SlackBuild b/academic/seaview/seaview.SlackBuild index 522170872c..327d7df737 100644 --- a/academic/seaview/seaview.SlackBuild +++ b/academic/seaview/seaview.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for seaview -# Copyright 2011-2020 Petar Petrov slackalaxy@gmail.com +# Copyright 2011-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,10 +25,13 @@ # Thanks to Niels Horn for correcting the CFLAGS. # Thanks to developer Dr. Manolo Gouy for all his help. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=seaview -VERSION=${VERSION:-5.0} -BUILD=${BUILD:-1} +VERSION=${VERSION:-5.0.5} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -38,7 +41,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -87,8 +97,8 @@ sed -i "s:#HELPFILE:HELPFILE:" Makefile sed -i "s:/share/doc/seaview:/doc/$PRGNAM-$VERSION/:" Makefile sed -i "s:#PHYMLNAME:PHYMLNAME:" Makefile -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ +CFLAGS="$SLKCFLAGS -fcommon" \ +CXXFLAGS="$SLKCFLAGS -fcommon" \ make install -D -m755 $PRGNAM $PKG/usr/bin/$PRGNAM @@ -114,4 +124,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/seaview/seaview.info b/academic/seaview/seaview.info index fc329f3fd3..d1968b049b 100644 --- a/academic/seaview/seaview.info +++ b/academic/seaview/seaview.info @@ -1,8 +1,8 @@ PRGNAM="seaview" -VERSION="5.0" +VERSION="5.0.5" HOMEPAGE="http://doua.prabi.fr/software/seaview/" -DOWNLOAD="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_5.0.tar.gz" -MD5SUM="d9f1a97672efb3fd24850cf542326915" +DOWNLOAD="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_5.0.5.tar.gz" +MD5SUM="09f6800973308a91316bb820c4331cb0" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="fltk PDFlib-Lite Gblocks PhyML clustalo muscle treerecs" diff --git a/academic/seqkit/README b/academic/seqkit/README new file mode 100644 index 0000000000..d78d8069cd --- /dev/null +++ b/academic/seqkit/README @@ -0,0 +1,26 @@ +SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file +manipulation + +FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide +and protein sequences. Common manipulations of FASTA/Q file include +converting, searching, filtering, deduplication, splitting, shuffling, +and sampling. Existing tools only implement some of these manipulations, +and not particularly efficiently, and some are only available for +certain operating systems. Furthermore, the complicated installation +process of required packages and running environments can render these +programs less user friendly. + +This project describes a cross-platform ultrafast comprehensive toolkit +for FASTA/Q processing. SeqKit provides executable binary files for all +major operating systems, including Windows, Linux, and Mac OS X, and can +be directly used without any dependencies or pre-configurations. SeqKit +demonstrates competitive performance in execution time and memory usage +compared to similar tools. The efficiency and usability of SeqKit enable +researchers to rapidly accomplish common FASTA/Q file manipulations. + +Note: This just repackages the binaries provided from upstream. + +Please cite: +Wei Shen,Shuai Le,Yan Li ,Fuquan Hu. SeqKit: A Cross-Platform and +Ultrafast Toolkit for FASTA/Q File Manipulation. October 5, 2016 +https://doi.org/10.1371/journal.pone.0163962 diff --git a/academic/seqkit/seqkit.SlackBuild b/academic/seqkit/seqkit.SlackBuild new file mode 100644 index 0000000000..d460717784 --- /dev/null +++ b/academic/seqkit/seqkit.SlackBuild @@ -0,0 +1,86 @@ +#!/bin/bash + +# Slackware build script for seqkit + +# Copyright 2020-2023 Petar Petrov slackalaxy@gmail.com +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=seqkit +VERSION=${VERSION:-2.5.1} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +case "$ARCH" in + i?86) + BINARCH="386" + ;; + x86_64) + BINARCH="amd64" + ;; + *) + printf "\n\n%s\n" "$ARCH is not supported." >/dev/stderr + exit 1 + ;; +esac + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +mkdir $PRGNAM-$VERSION +tar xvf $CWD/${PRGNAM}_linux_${BINARCH}.tar.gz + +install -D -m755 $PRGNAM $PKG/usr/bin/$PRGNAM + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/seqkit/seqkit.info b/academic/seqkit/seqkit.info new file mode 100644 index 0000000000..8888b7bef9 --- /dev/null +++ b/academic/seqkit/seqkit.info @@ -0,0 +1,10 @@ +PRGNAM="seqkit" +VERSION="2.5.1" +HOMEPAGE="https://bioinf.shenwei.me/seqkit/" +DOWNLOAD="https://github.com/shenwei356/seqkit/releases/download/v2.5.1/seqkit_linux_386.tar.gz" +MD5SUM="0357a5347d5c86677c542b3c6e6cf88f" +DOWNLOAD_x86_64="https://github.com/shenwei356/seqkit/releases/download/v2.5.1/seqkit_linux_amd64.tar.gz" +MD5SUM_x86_64="b90ee92597254007b93b57980528b2b4" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/seqkit/slack-desc b/academic/seqkit/slack-desc new file mode 100644 index 0000000000..5cbf1904cb --- /dev/null +++ b/academic/seqkit/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +seqkit: seqkit (Ultrafast toolkit for FASTA/Q file manipulation) +seqkit: +seqkit: A cross-platform ultrafast comprehensive toolkit for FASTA/Q +seqkit: processing. +seqkit: +seqkit: https://bioinf.shenwei.me/seqkit/ +seqkit: https://github.com/shenwei356/seqkit +seqkit: https://doi.org/10.1371/journal.pone.0163962 +seqkit: +seqkit: +seqkit: diff --git a/academic/sequence-analysis/sequence-analysis.SlackBuild b/academic/sequence-analysis/sequence-analysis.SlackBuild index 2db816ff72..40eaff150e 100644 --- a/academic/sequence-analysis/sequence-analysis.SlackBuild +++ b/academic/sequence-analysis/sequence-analysis.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for sequence-analysis -# Copyright 2011-2016 Petar Petrov slackalaxy@gmail.com +# Copyright 2011-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,14 +22,24 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=sequence-analysis VERSION=${VERSION:-1.7.2} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} ARCH=noarch -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -55,4 +65,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/sequence-analysis/sequence-analysis.info b/academic/sequence-analysis/sequence-analysis.info index d5e7228042..b022257ddb 100644 --- a/academic/sequence-analysis/sequence-analysis.info +++ b/academic/sequence-analysis/sequence-analysis.info @@ -5,6 +5,6 @@ DOWNLOAD="http://sourceforge.net/projects/sboppetrov/files/sequence-analysis/1.7 MD5SUM="815c7e6a8717a9e2a7fedc9ed94fbd0e" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="jdk" +REQUIRES="zulu-openjdk11" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/sigrok-cli/sigrok-cli.SlackBuild b/academic/sigrok-cli/sigrok-cli.SlackBuild index 2409d136e3..acf3296360 100644 --- a/academic/sigrok-cli/sigrok-cli.SlackBuild +++ b/academic/sigrok-cli/sigrok-cli.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for sigrok-cli @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=sigrok-cli -VERSION=${VERSION:-0.7.1} +VERSION=${VERSION:-20220222_525f481} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -60,7 +70,7 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $PRGNAM-$VERSION -tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +tar xvf $CWD/$PRGNAM-$VERSION.tar.?z cd $PRGNAM-$VERSION chown -R root:root . find -L . \ @@ -69,6 +79,7 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; +./autogen.sh CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ @@ -89,7 +100,7 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr gzip -9 $PKG/usr/man/man1/sigrok-cli.1 mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a AUTHORS ChangeLog COPYING INSTALL NEWS README $PKG/usr/doc/$PRGNAM-$VERSION +cp -a AUTHORS COPYING HACKING NEWS README $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install @@ -97,4 +108,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/sigrok-cli/sigrok-cli.info b/academic/sigrok-cli/sigrok-cli.info index 513cb7e46c..afb44f0e69 100644 --- a/academic/sigrok-cli/sigrok-cli.info +++ b/academic/sigrok-cli/sigrok-cli.info @@ -1,8 +1,8 @@ PRGNAM="sigrok-cli" -VERSION="0.7.1" +VERSION="20220222_525f481" HOMEPAGE="https://sigrok.org/wiki/Sigrok-cli" -DOWNLOAD="https://sigrok.org/download/source/sigrok-cli/sigrok-cli-0.7.1.tar.gz" -MD5SUM="3f45ce664bad529d8b3f78a61b017d75" +DOWNLOAD="https://ponce.cc/slackware/sources/repo/sigrok-cli-20220222_525f481.tar.xz" +MD5SUM="047f3b75b01a17b94e736601f169f022" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="libsigrok" diff --git a/academic/sim/README b/academic/sim/README new file mode 100644 index 0000000000..b8dec9d5ba --- /dev/null +++ b/academic/sim/README @@ -0,0 +1,9 @@ +SIM - Local similarity program + +SIM finds k best non-intersecting alignments between two sequences or +within a sequence using dynamic programming techniques. The alignments +are reported in order of decreasing similarity score and share no +aligned pairs. + +Once the alignment is computed, you can view it using "lalnview", a +graphical viewer program for pairwise alignments, available at SBo. diff --git a/academic/sim/References b/academic/sim/References new file mode 100644 index 0000000000..6e829c7445 --- /dev/null +++ b/academic/sim/References @@ -0,0 +1,3 @@ +Xiaoquin Huang and Webb Miller: +"A Time-Efficient, Linear-Space Local Similarity Algorithm" +Advances in Applied Mathematics, vol. 12 (1991), pp. 337-357. diff --git a/academic/sim/sim.SlackBuild b/academic/sim/sim.SlackBuild new file mode 100644 index 0000000000..6fb9c1b34e --- /dev/null +++ b/academic/sim/sim.SlackBuild @@ -0,0 +1,91 @@ +#!/bin/bash + +# Slackware build script for sim + +# Copyright 2023 Petar Petrov, slackalaxy@gmail.com +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=sim +VERSION=${VERSION:-204} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" +else + SLKCFLAGS="-O2" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +mkdir $PRGNAM-$VERSION +cd $PRGNAM-$VERSION +cp $CWD/${PRGNAM}* . +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +cc $SLKCFLAGS -o $PRGNAM ${PRGNAM}${VERSION}.c -lm +install -D -m 755 $PRGNAM $PKG/usr/bin/$PRGNAM + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a $PRGNAM.doc $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/sim/sim.info b/academic/sim/sim.info new file mode 100644 index 0000000000..c1026b3e92 --- /dev/null +++ b/academic/sim/sim.info @@ -0,0 +1,12 @@ +PRGNAM="sim" +VERSION="204" +HOMEPAGE="https://web.expasy.org/sim/" +DOWNLOAD="ftp://pbil.univ-lyon1.fr/pub/logiciel/lalnview/sim/sim204.c \ +ftp://pbil.univ-lyon1.fr/pub/logiciel/lalnview/sim/sim.doc" +MD5SUM="69edf7f5aa1c58bb3ad37ad761a289c2 \ +70f4bf9be3b16369dc21467d15cc7b48" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/sim/slack-desc b/academic/sim/slack-desc new file mode 100644 index 0000000000..c38253a06f --- /dev/null +++ b/academic/sim/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +sim: sim (Local similarity program) +sim: +sim: SIM finds k best non-intersecting alignments between two sequences +sim: or within a sequence using dynamic programming techniques. The +sim: alignments are reported in order of decreasing similarity score and +sim: share no aligned pairs. Once the alignment is computed, you can view +sim: it using "lalnview" +sim: +sim: +sim: +sim: diff --git a/academic/siril/README b/academic/siril/README index 3e9ef4ac5e..bdd99c4b52 100644 --- a/academic/siril/README +++ b/academic/siril/README @@ -1,7 +1,9 @@ SIRIL is an astronomical image processing tool. -SIRIL is an image processing tool specially tailored for noise reduction and -improving the signal/noise ratio of an image from multiple captures as -required in astronomy. -SIRIL can align automatically or manually, stack and enhance pictures from -various file formats, even images sequences (movies and SER files). +SIRIL is an image processing tool specially tailored for noise +reduction and improving the signal/noise ratio of an image +from multiple captures as required in astronomy. SIRIL can align +automatically or manually, stack and enhance pictures from various file +formats, even images sequences (movies and SER files). + +libheif is an optional dependency. diff --git a/academic/siril/siril.SlackBuild b/academic/siril/siril.SlackBuild index 03073692f2..2da99a2d8e 100644 --- a/academic/siril/siril.SlackBuild +++ b/academic/siril/siril.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for siril @@ -22,10 +22,14 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=siril -VERSION=${VERSION:-0.9.6} +VERSION=${VERSION:-1.0.0_rc2} +SRCVER=$(echo $VERSION | tr _ - ) BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +39,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -59,9 +70,10 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $PRGNAM-$VERSION -tar xvf $CWD/$PRGNAM-$VERSION.tar.bz2 -cd $PRGNAM-$VERSION +rm -rf $PRGNAM-$SRCVER +mkdir -p $PRGNAM-$SRCVER +cd $PRGNAM-$SRCVER +tar xvf $CWD/$PRGNAM-$SRCVER.tar.bz2 chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -69,21 +81,21 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -sh ./autogen.sh - -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ -./configure \ - --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ - --sysconfdir=/etc \ - --localstatedir=/var \ - --mandir=/usr/man \ - --docdir=/usr/doc/$PRGNAM-$VERSION \ - --build=$ARCH-slackware-linux - -make -make DESTDIR=$PKG install +mkdir compile +cd compile + CFLAGS="$SLKCFLAGS" \ + CXXFLAGS="$SLKCFLAGS" \ + meson .. \ + --buildtype=release \ + --infodir=/usr/info \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --localstatedir=/var \ + --mandir=/usr/man \ + --prefix=/usr \ + --sysconfdir=/etc \ + -Dstrip=true + DESTDIR=$PKG "${NINJA:=ninja}" install +cd .. find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true @@ -91,12 +103,13 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr find $PKG/usr/man -type f -exec gzip -9 {} \; for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done +rm -fR $PKG/usr/share/doc mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a AUTHORS README.md ChangeLog NEWS LICENSE COPYING $PKG/usr/doc/$PRGNAM-$VERSION +cp -a AUTHORS README.md ChangeLog NEWS LICENSE* $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/siril/siril.info b/academic/siril/siril.info index 77bd63b367..743f994968 100644 --- a/academic/siril/siril.info +++ b/academic/siril/siril.info @@ -1,10 +1,10 @@ PRGNAM="siril" -VERSION="0.9.6" -HOMEPAGE="https://free-astro.org/index.php?title=Main_Page" -DOWNLOAD="https://free-astro.org/download/siril-0.9.6.tar.bz2" -MD5SUM="aaa649ba5a57738ab8fb8c4223ed83dd" +VERSION="1.0.0_rc2" +HOMEPAGE="https://siril.org" +DOWNLOAD="https://free-astro.org/download/siril-1.0.0-rc2.tar.bz2" +MD5SUM="764767e35ea835fe2206d2dadf79dee6" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="cfitsio libconfig" +REQUIRES="libconfig" MAINTAINER="Daniel Jordan" EMAIL="daniel.budd.j+SBo@gmail.com" diff --git a/academic/slatec/README b/academic/slatec/README deleted file mode 100644 index 09230ef34f..0000000000 --- a/academic/slatec/README +++ /dev/null @@ -1,5 +0,0 @@ -SLATEC Common Mathematical Library - -SLATEC Common Mathematical Library, is a comprehensive software -library containing over 1400 general purpose mathematical and -statistical routines written in Fortran 77. diff --git a/academic/slatec/makedoc.sed b/academic/slatec/makedoc.sed deleted file mode 100644 index a80bccdf2d..0000000000 --- a/academic/slatec/makedoc.sed +++ /dev/null @@ -1,81 +0,0 @@ -# By Giuseppe Borzi' - my first sed scriptfile -# cancels lines after the proglogue -# Modified by Pablo Santamaria for section 3 of manual pages -1,/END\ PROLOGUE/!d -1,/END\ PROLOGUE/{ -# defines and print the title -/^\*DECK/{ -s/^\*DECK *\(.*\)/.TH \1 3/ -p -s/.*/.SH SYNOPSIS/ -} -s/^ *// -# The hell ! -/^C\*\*\*BEGIN PROLOGUE/{ -# convert to lowercase for use in NAME -y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/ -# append next line -N -s/^c\*\*\*begin prologue *\([a-z0-9]*\)\nC\*\*\*PURPOSE *\(.*\)/\1 \\- \2/ -t nosubsidiary -s/\nC\*\*\*SUBSIDIARY// -N -s/^c\*\*\*begin prologue *\([a-z0-9]*\)\nC\*\*\*PURPOSE *\(.*\)/\1 \\- \2/ -:nosubsidiary -h -# print NAME heading -s/.*/.SH NAME/ -p -# retrieve original line from hold space and rewrite -x -} -# cancels END PROLOGUE -s/^C\*\*\*END PROLOGUE.*// -# change each C*** to a roff section heading -s/^C\*\*\*/.SH / -# builds headings formed by two or more words -/\.SH ROUTINES CALLED/{ -h -s/\(\.SH ROUTINES CALLED\).*/\1/ -p -x -s/\.SH ROUTINES CALLED *\(.*\)/\1/ -} -/\.SH REVISION HISTORY (YYMMDD)/{ -h -s/\(\.SH REVISION HISTORY (YYMMDD)\).*/\1/ -p -s/\(\.SH REVISION HISTORY (YYMMDD)\).*/.PD 0/ -p -x -s/\.SH REVISION HISTORY (YYMMDD) *\(.*\)/\1/ -} -/\.SH COMMON BLOCKS/{ -h -s/\(\.SH COMMON BLOCKS\).*/\1/ -p -x -s/\.SH COMMON BLOCKS *\(.*\)/\1/ -} -/\.SH SEE ALSO/{ -h -s/\(\.SH SEE ALSO\).*/\1/ -p -x -s/\.SH SEE ALSO *\(.*\)/\1/ -} -# builds headings formed by one word -/\.SH/{ -h -s/\(\.SH *[A-Z]*\).*/\1/ -p -x -s/\.SH *[A-Z]* *\(.*\)/\1/ -} -# strip initial C and eventually spaces -s/^C *// -s/^C$// -# this is Y2K compliant ! -/[0789][0-9][01][0-9][0-3][0-9]/i\ -.P -} diff --git a/academic/slatec/slatec.SlackBuild b/academic/slatec/slatec.SlackBuild deleted file mode 100644 index e0fd8c5169..0000000000 --- a/academic/slatec/slatec.SlackBuild +++ /dev/null @@ -1,98 +0,0 @@ -#!/bin/sh - -# Slackware build script for slatec - -# Written by Pablo Santamaria (pablosantamaria@gmail.com) - -PRGNAM=slatec -VERSION=${VERSION:-4.1} -BUILD=${BUILD:-1} -TAG=${TAG:-_SBo} - -SRCVERSION=${VERSION}-4 - -if [ -z "$ARCH" ]; then - case "$( uname -m )" in - i?86) ARCH=i486 ;; - arm*) ARCH=arm ;; - *) ARCH=$( uname -m ) ;; - esac -fi - -CWD=$(pwd) -TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM -OUTPUT=${OUTPUT:-/tmp} - -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" - LIBDIRSUFFIX="" -elif [ "$ARCH" = "i686" ]; then - SLKCFLAGS="-O2 -march=i686 -mtune=i686" - LIBDIRSUFFIX="" -elif [ "$ARCH" = "x86_64" ]; then - SLKCFLAGS="-O2 -fPIC" - LIBDIRSUFFIX="64" -else - SLKCFLAGS="-O2" - LIBDIRSUFFIX="" -fi - -set -e - -rm -rf $PKG -mkdir -p $TMP $PKG $OUTPUT -cd $TMP -rm -rf ${PRGNAM}_$SRCVERSION -tar xvf $CWD/${PRGNAM}_${SRCVERSION}.tar.gz -cd $PRGNAM-$VERSION -chown -R root:root . -find -L . \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; - -# Compile static and dynamic library. -v1=$(echo $VERSION | cut -d. -f1) -v2=$VERSION -make MA_N=${v1} MI_N=${v2} OPT="$SLKCFLAGS -std=legacy" F77="gfortran" CC="gcc" - -mkdir -p $PKG/usr/lib${LIBDIRSUFFIX} -cp -a libslatec.a $PKG/usr/lib${LIBDIRSUFFIX} -cp -a libslatec.so.$v2 $PKG/usr/lib${LIBDIRSUFFIX} -( cd $PKG/usr/lib${LIBDIRSUFFIX} - ln -s libslatec.so.$v2 libslatec.so.$v1 - ln -s libslatec.so.$v2 libslatec.so -) - -# Create manpages. -mkdir -p $PKG/usr/man/man3 -for f in $(find -name "*.f") ; do - sed -f $CWD/makedoc.sed $f > $PKG/usr/man/man3/$(basename $f .f).3 -done - -# Let's not overwrite manpages that are already on the system -for i in \ - acosh asinh atanh cacos cacosh carg casin casinh catan catanh cbrt ccosh \ - clog10 csinh ctan ctanh des erf erfc gamma rand ; do - mv $PKG/usr/man/man3/$i.3 $PKG/usr/man/man3/$i-slatec.3 ; -done - -find $PKG | xargs file | grep -e "executable" -e "shared object" | grep ELF \ - | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true - -( cd $PKG/usr/man - find . -type f -exec gzip -9 {} \; - for i in $( find . -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done -) - -mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a readme $PKG/usr/doc/$PRGNAM-$VERSION -cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild - -mkdir -p $PKG/install -cat $CWD/slack-desc > $PKG/install/slack-desc - -cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} diff --git a/academic/slatec/slatec.info b/academic/slatec/slatec.info deleted file mode 100644 index 60069da341..0000000000 --- a/academic/slatec/slatec.info +++ /dev/null @@ -1,10 +0,0 @@ -PRGNAM="slatec" -VERSION="4.1" -HOMEPAGE="http://www.netlib.org/slatec/" -DOWNLOAD="http://devernay.free.fr/hacks/netlibs/slatec_4.1-4.tar.gz" -MD5SUM="fee6fcc5755ad7135261de5dc8400da9" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="" -MAINTAINER="Pablo Santamaria" -EMAIL="pablosantamaria@gmail.com" diff --git a/academic/smath-studio/README b/academic/smath-studio/README index 8871582bea..55547a2d61 100644 --- a/academic/smath-studio/README +++ b/academic/smath-studio/README @@ -12,3 +12,8 @@ Among its capabilities are: - Numeric integration - Simple multiline looped programs - User defined functions + + To download, you may need to go to the website URL + https://en.smath.com/view/SMathStudio/download + or try + wget --referer=https://en.smath.com/view/SMathStudio/download ... diff --git a/academic/smath-studio/smath-studio.SlackBuild b/academic/smath-studio/smath-studio.SlackBuild index 961bc97f33..4b26c719c3 100644 --- a/academic/smath-studio/smath-studio.SlackBuild +++ b/academic/smath-studio/smath-studio.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for SMath Studio @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=smath-studio -VERSION=${VERSION:-0.97.5346} +VERSION=${VERSION:-1.0.8348} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} ORIG_PRGNAM=SMathStudio ORIG_VERSION=$(sed 's/\./_/g' <<< $VERSION) @@ -33,7 +36,14 @@ ORIG_FILENAME=${ORIG_PRGNAM}Desktop.$ORIG_VERSION.Mono.tar.gz ARCH=noarch -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -69,4 +79,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/smath-studio/smath-studio.info b/academic/smath-studio/smath-studio.info index d8e41f4084..bc40d92965 100644 --- a/academic/smath-studio/smath-studio.info +++ b/academic/smath-studio/smath-studio.info @@ -1,12 +1,12 @@ PRGNAM="smath-studio" -VERSION="0.97.5346" -HOMEPAGE="http://smath.info" -DOWNLOAD="http://ponce.cc/slackware/sources/repo/SMathStudioDesktop.0_97_5346.Mono.tar.gz \ +VERSION="1.0.8348" +HOMEPAGE="https://smath.info" +DOWNLOAD="https://smath.com/file/Lw2xA/SMathStudioDesktop.1_0_8348.Mono.tar.gz \ http://ponce.cc/slackware/sources/repo/SMathStudio.Icons.zip" -MD5SUM="cb922fa31fca89d347df6468d421eb52 \ +MD5SUM="4ae9109f910c0085eeb8c193f3ad1c10 \ 1dd3ff0477b5c3c57fb815320a387643" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="mono" MAINTAINER="Edward W. Koenig" -EMAIL="kingbeowulf@gmail.com" +EMAIL="kingbeowulf@linuxgalaxy.org" diff --git a/academic/snpEff/snpEff.SlackBuild b/academic/snpEff/snpEff.SlackBuild index 0b0d9d09cd..ec1346b235 100644 --- a/academic/snpEff/snpEff.SlackBuild +++ b/academic/snpEff/snpEff.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for snpEff -# Copyright 2015-2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2015-2022 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,15 +22,25 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=snpEff VERSION=${VERSION:-4.3t} SRCVER=${SRCVER:-v4_3t} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} ARCH=noarch -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -40,7 +50,9 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $PRGNAM +rm -rf $PRGNAM-$VERSION +mkdir -p $PRGNAM-$VERSION +cd $PRGNAM-$VERSION unzip $CWD/${PRGNAM}_${SRCVER}_core.zip cd $PRGNAM chown -R root:root . @@ -50,8 +62,10 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -mkdir -p $PKG/usr/share/java/$PRGNAM -cp -a examples galaxy scripts $PRGNAM.config $PRGNAM.jar SnpSift.jar \ +install -D -m755 $PRGNAM.jar $PKG/usr/share/java/$PRGNAM/$PRGNAM.jar +install -D -m755 SnpSift.jar $PKG/usr/share/java/$PRGNAM/SnpSift.jar + +cp -a examples galaxy scripts $PRGNAM.config \ $PKG/usr/share/java/$PRGNAM mkdir -p $PKG/usr/bin @@ -71,4 +85,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/snpEff/snpEff.info b/academic/snpEff/snpEff.info index ab5b87f4e8..deace26fa8 100644 --- a/academic/snpEff/snpEff.info +++ b/academic/snpEff/snpEff.info @@ -5,6 +5,6 @@ DOWNLOAD="https://sourceforge.net/projects/snpeff/files/snpEff_v4_3t_core.zip" MD5SUM="1fa84a703580a423e27f1e14a945901c" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="jdk" +REQUIRES="zulu-openjdk11" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/solfege/solfege.SlackBuild b/academic/solfege/solfege.SlackBuild index dff0e2386b..4b69490ae4 100644 --- a/academic/solfege/solfege.SlackBuild +++ b/academic/solfege/solfege.SlackBuild @@ -1,28 +1,38 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for solfege # Written by Phillip Warner <pc_warner@yahoo.com> +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=solfege VERSION=${VERSION:-3.22.2} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -90,4 +100,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/spades/spades.SlackBuild b/academic/spades/spades.SlackBuild index 9111d7444e..c6e75b0411 100644 --- a/academic/spades/spades.SlackBuild +++ b/academic/spades/spades.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for spades -# Copyright 2015-2020 Petar Petrov slackalaxy@gmail.com +# Copyright 2015-2023 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=spades -VERSION=${VERSION:-3.14.0} +VERSION=${VERSION:-3.15.5} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} SRCNAM=SPAdes @@ -37,7 +40,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -89,6 +99,8 @@ cd build make install DESTDIR=$PKG cd .. +chmod 755 $PKG/usr/bin/spades_init.py + find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true @@ -103,4 +115,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/spades/spades.info b/academic/spades/spades.info index 34c460730b..3c72751ee4 100644 --- a/academic/spades/spades.info +++ b/academic/spades/spades.info @@ -1,10 +1,10 @@ PRGNAM="spades" -VERSION="3.14.0" +VERSION="3.15.5" HOMEPAGE="http://cab.spbu.ru/software/spades/" DOWNLOAD="UNSUPPORTED" MD5SUM="" -DOWNLOAD_x86_64="http://cab.spbu.ru/files/release3.14.0/SPAdes-3.14.0.tar.gz" -MD5SUM_x86_64="e809eeb822fd103461a27eed39b6e709" +DOWNLOAD_x86_64="http://cab.spbu.ru/files/release3.15.5/SPAdes-3.15.5.tar.gz" +MD5SUM_x86_64="e181bf668ee96971458fb50cbfdaf604" REQUIRES="" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/speedcrunch/speedcrunch.SlackBuild b/academic/speedcrunch/speedcrunch.SlackBuild index a728cc46dd..813dc8292d 100644 --- a/academic/speedcrunch/speedcrunch.SlackBuild +++ b/academic/speedcrunch/speedcrunch.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for speedcrunch @@ -22,12 +22,15 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=speedcrunch SRCNAM=SpeedCrunch VERSION=${VERSION:-0.12.0} COMMIT=${COMMIT:-ea93b21f9498} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -37,7 +40,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -100,4 +110,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/speedcrunch/speedcrunch.info b/academic/speedcrunch/speedcrunch.info index 54723631aa..5763a7ef2e 100644 --- a/academic/speedcrunch/speedcrunch.info +++ b/academic/speedcrunch/speedcrunch.info @@ -5,6 +5,6 @@ DOWNLOAD="https://bitbucket.org/heldercorreia/speedcrunch/get/release-0.12.0.tar MD5SUM="f294f00d9ab8153ad4f2bebaaa93176c" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="qt5" +REQUIRES="" MAINTAINER="Larry Hajali" EMAIL="larryhaja[at]gmail[dot]com" diff --git a/academic/spiceopus/spiceopus.SlackBuild b/academic/spiceopus/spiceopus.SlackBuild index ea63f086d0..74e9e2517e 100644 --- a/academic/spiceopus/spiceopus.SlackBuild +++ b/academic/spiceopus/spiceopus.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for SpiceOpus @@ -22,28 +22,38 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=spiceopus VERSION=${VERSION:-2.3} SRCDIR=spice_opus23_linux_18.Jan.2010_08.57 PROGNAME=spice_opus23_linux BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -120,4 +130,4 @@ cat $CWD/doinst.sh > $PKG/install/doinst.sh cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/spidey/spidey.SlackBuild b/academic/spidey/spidey.SlackBuild index e9ea109df7..09928e95bb 100644 --- a/academic/spidey/spidey.SlackBuild +++ b/academic/spidey/spidey.SlackBuild @@ -1,6 +1,6 @@ -#!/bin/sh +#!/bin/bash -# Copyright 2011-2016 Petar Petrov slackalaxy@gmail.com +# Copyright 2011-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -20,30 +20,38 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=spidey VERSION=${VERSION:-20060601} # Keep the date of the 32bit binary as version. BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i386 ;; - arm*) ARCH=arm ;; + i?86) ARCH=i586 ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) -TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM -OUTPUT=${OUTPUT:-/tmp} - - -if [ "$ARCH" != "i386" ] && [ "$ARCH" != "x86_64" ]; then +if ! [[ $ARCH =~ i?86 ]] && ! [ "$ARCH" = "x86_64" ]; then printf "\n\n$ARCH is not supported... \n" exit 1 fi +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + # Determine the source arch. Many thanks to the Ugene project for the # 64bit executable! if [ "$ARCH" = "x86_64" ]; then @@ -63,7 +71,7 @@ cd $PRGNAM-$VERSION gunzip -c $CWD/$PRGNAM.linux${SRCARCH}.gz > spidey -install -D -m755 spidey $PKG/usr/bin/spidey +install -D -m 755 spidey $PKG/usr/bin/spidey mkdir -p $PKG/usr/man/man1 cp $CWD/$PRGNAM.1 $PKG/usr/man/man1/$PRGNAM.1 @@ -81,4 +89,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/spqr/README b/academic/spqr/README index 051977e0e6..8bb80aef4f 100644 --- a/academic/spqr/README +++ b/academic/spqr/README @@ -1,18 +1,22 @@ SuiteSparseQR is an implementation of the multifrontal sparse QR -factorization method. Parallelism is exploited both in the BLAS and -across different frontal matrices using Intel's Threading Building Blocks, -a shared-memory programming model for modern multicore +factorization method. Parallelism is exploited both in the BLAS and +across different frontal matrices using Intel's Threading Building +Blocks, a shared-memory programming model for modern multicore architectures. It can obtain a substantial fraction of the theoretical peak performance of a multicore computer. This package is part of SuiteSparse. -This requires a BLAS/LAPACK implementation. Choose one of these package sets: +This requires a BLAS/LAPACK implementation. Choose one of these package +sets: + * OpenBLAS (includes both a BLAS and a LAPACK implementation) * atlas (includes both a BLAS and a LAPACK implementation) * blas, lapack (the Netlib reference implementations) -If more than one set is installed (assuming there are no packaging conflicts) -then the auto-detection will use the first implementation from this list that -it finds. If in doubt, choose the Netlib reference implementations; other -packages that require a BLAS or LAPACK implementation may not build if they -are not configured to detect/use alternate implementations. + +If more than one set is installed (assuming there are no packaging +conflicts) then the auto-detection will use the first implementation +from this list that it finds. If in doubt, choose the Netlib reference +implementations; other packages that require a BLAS or LAPACK +implementation may not build if they are not configured to detect/use +alternate implementations. diff --git a/academic/spqr/patches/autoconfiscate.diff b/academic/spqr/patches/autoconfiscate.diff index ffd9eb9657..8fff318251 100644 --- a/academic/spqr/patches/autoconfiscate.diff +++ b/academic/spqr/patches/autoconfiscate.diff @@ -463,7 +463,7 @@ diff --git a/m4/ax_blas.m4 b/m4/ax_blas.m4 new file mode 100644 --- /dev/null +++ b/m4/ax_blas.m4 -@@ -0,0 +1,238 @@ +@@ -0,0 +1,241 @@ +# =========================================================================== +# https://www.gnu.org/software/autoconf-archive/ax_blas.html +# =========================================================================== @@ -502,6 +502,7 @@ new file mode 100644 +# LICENSE +# +# Copyright (c) 2008 Steven G. Johnson <stevenj@alum.mit.edu> ++# Copyright (c) 2019 Geoffrey M. Oxberry <goxberry@gmail.com> +# +# This program is free software: you can redistribute it and/or modify it +# under the terms of the GNU General Public License as published by the @@ -529,7 +530,7 @@ new file mode 100644 +# modified version of the Autoconf Macro, you may extend this special +# exception to the GPL to apply to your modified version as well. + -+#serial 16 ++#serial 17 + +AU_ALIAS([ACX_BLAS], [AX_BLAS]) +AC_DEFUN([AX_BLAS], [ @@ -543,7 +544,9 @@ new file mode 100644 +case $with_blas in + yes | "") ;; + no) ax_blas_ok=disable ;; -+ -* | */* | *.a | *.so | *.so.* | *.o) BLAS_LIBS="$with_blas" ;; ++ -* | */* | *.a | *.so | *.so.* | *.dylib | *.dylib.* | *.o) ++ BLAS_LIBS="$with_blas" ++ ;; + *) BLAS_LIBS="-l$with_blas" ;; +esac + @@ -982,7 +985,7 @@ diff --git a/m4/ax_lapack.m4 b/m4/ax_lapack.m4 new file mode 100644 --- /dev/null +++ b/m4/ax_lapack.m4 -@@ -0,0 +1,131 @@ +@@ -0,0 +1,134 @@ +# =========================================================================== +# https://www.gnu.org/software/autoconf-archive/ax_lapack.html +# =========================================================================== @@ -1022,6 +1025,7 @@ new file mode 100644 +# LICENSE +# +# Copyright (c) 2009 Steven G. Johnson <stevenj@alum.mit.edu> ++# Copyright (c) 2019 Geoffrey M. Oxberry <goxberry@gmail.com> +# +# This program is free software: you can redistribute it and/or modify it +# under the terms of the GNU General Public License as published by the @@ -1049,7 +1053,7 @@ new file mode 100644 +# modified version of the Autoconf Macro, you may extend this special +# exception to the GPL to apply to your modified version as well. + -+#serial 9 ++#serial 10 + +AU_ALIAS([ACX_LAPACK], [AX_LAPACK]) +AC_DEFUN([AX_LAPACK], [ @@ -1061,7 +1065,9 @@ new file mode 100644 +case $with_lapack in + yes | "") ;; + no) ax_lapack_ok=disable ;; -+ -* | */* | *.a | *.so | *.so.* | *.o) LAPACK_LIBS="$with_lapack" ;; ++ -* | */* | *.a | *.so | *.so.* | *.dylib | *.dylib.* | *.o) ++ LAPACK_LIBS="$with_lapack" ++ ;; + *) LAPACK_LIBS="-l$with_lapack" ;; +esac + diff --git a/academic/spqr/spqr.SlackBuild b/academic/spqr/spqr.SlackBuild index 576fb608ee..a99c21b3d7 100644 --- a/academic/spqr/spqr.SlackBuild +++ b/academic/spqr/spqr.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for SPQR -# Copyright 2013-2020 Kyle Guinn <elyk03@gmail.com> +# Copyright 2013-2023 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,13 +22,16 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=spqr SRCNAM=SuiteSparse SUBDIR=SPQR VERSION=${VERSION:-2.0.9} -SRCVER=${SRCVER:-5.6.0} -BUILD=${BUILD:-2} +SRCVER=${SRCVER:-5.8.1} +BUILD=${BUILD:-4} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$(uname -m)" in @@ -38,17 +41,18 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM-$VERSION +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="README.txt Doc/ChangeLog Doc/License.txt Doc/gpl.txt" -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" - LIBDIRSUFFIX="" -elif [ "$ARCH" = "i586" ]; then +if [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then @@ -92,6 +96,7 @@ touch Doc/spqr_user_guide.pdf --infodir=/usr/info \ --docdir=/usr/doc/$PRGNAM-$VERSION \ --disable-dependency-tracking \ + --without-tbb \ --build=$ARCH-slackware-linux \ CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ @@ -110,4 +115,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/spqr/spqr.info b/academic/spqr/spqr.info index 2bab1e6903..eff7ce4d4d 100644 --- a/academic/spqr/spqr.info +++ b/academic/spqr/spqr.info @@ -1,10 +1,10 @@ PRGNAM="spqr" VERSION="2.0.9" HOMEPAGE="http://faculty.cse.tamu.edu/davis/suitesparse.html" -DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.6.0/SuiteSparse-5.6.0.tar.gz" -MD5SUM="af8b97cbded4cd5c6672e878bc0c37c2" +DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.8.1/SuiteSparse-5.8.1.tar.gz" +MD5SUM="c414679bbc9432a3def01b31ad921140" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="blas lapack suitesparseconfig cholmod tbb" +REQUIRES="cholmod" MAINTAINER="Kyle Guinn" EMAIL="elyk03@gmail.com" diff --git a/academic/squizz/squizz.SlackBuild b/academic/squizz/squizz.SlackBuild index 363c2f9c7c..dfe2237f5c 100644 --- a/academic/squizz/squizz.SlackBuild +++ b/academic/squizz/squizz.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for squizz -# Copyright 2013-2017 Petar Petrov slackalaxy@gmail.com +# Copyright 2013-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=squizz VERSION=${VERSION:-0.99d} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -95,8 +105,10 @@ cp -a \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/staden/README b/academic/staden/README index 0d8a67c590..aa36fdbcd8 100644 --- a/academic/staden/README +++ b/academic/staden/README @@ -1,20 +1,40 @@ The programs part of the Staden package provide an excellent and fully developed set of DNA sequence assembly, editing, analysis and more. - Some of its features include: -GAP4 - Performs assembly, contig joining, assembly checking, repeat - search, experiment suggestion, read pair analysis and contig - editing. -GAP5 - The new development version of Gap4, designed to work with the - large volumes of data attainable through the newer sequencing - technologies. -PREGAP4 - Provides a graphical user interface to set up the processing - required to prepare trace data for assembly or analysis. -SPIN - Compares pairs of sequences in many ways, often presenting its - results graphically and has a sliding sequence window linked to - the plots. -TREV - A rapid and flexible viewer and editor for ABI, ALF or SCF - trace files. +* GAP4: Performs assembly, contig joining, assembly checking, repeat + search, experiment suggestion, read pair analysis and contig editing. + +* GAP5: The new development version of Gap4, designed to work with large + volumes of data attainable through the newer sequencing technologies. + +* PREGAP4: Provides a graphical user interface to set up the processing + required to prepare trace data for assembly or analysis. + +* SPIN: Compares pairs of sequences in many ways, often presenting its + results graphically and has a sliding sequence window linked to the + plots. + +* TREV: A rapid and flexible viewer and editor for ABI, ALF or SCF trace + files. + +NOTE: Xfce submenus +For XFCE, if you want to have the menu entries grouped in a submenu +folder (multilevel menu entry), do: + + SUBMENU="YES" ./staden.SlackBuild + +NOTE: Staden and EMBOSS: +Staden used to provide a GUI for (at least part of) the programs from +EMBOSS. To give it a try, run this after install (of course you need to +have installed EMBOSS, too): + + create_emboss_files + +This will create some files in: + + /usr/share/staden/tcl/spin_emboss/acdtcl/ + +CITING For more information and citing, visit Staden's web page and check the "References" file in the documentation. diff --git a/academic/staden/desktop/staden.directory b/academic/staden/desktop/staden.directory new file mode 100644 index 0000000000..2623e56005 --- /dev/null +++ b/academic/staden/desktop/staden.directory @@ -0,0 +1,4 @@ +[Desktop Entry] +Type=Directory +Name=Staden Package +Icon=folder diff --git a/academic/staden/desktop/staden.menu b/academic/staden/desktop/staden.menu new file mode 100644 index 0000000000..3f5ba10187 --- /dev/null +++ b/academic/staden/desktop/staden.menu @@ -0,0 +1,20 @@ +<!DOCTYPE Menu PUBLIC "-//freedesktop//DTD Menu 1.0//EN" +"http://www.freedesktop.org/standards/menu-spec/menu-1.0.dtd"> +<Menu> + <Name>Applications</Name> + <Menu> + <Name>Education</Name> + <Directory>xfce4-education.directory</Directory> + <Menu> + <Name>Staden Package</Name> + <Directory>staden.directory</Directory> + <Include> + <Filename>gap4.desktop</Filename> + <Filename>gap5.desktop</Filename> + <Filename>pregap4.desktop</Filename> + <Filename>trev.desktop</Filename> + <Filename>spin.desktop</Filename> + </Include> + </Menu> + </Menu> +</Menu> diff --git a/academic/staden/staden.SlackBuild b/academic/staden/staden.SlackBuild index 72d19c745a..4c16f47019 100644 --- a/academic/staden/staden.SlackBuild +++ b/academic/staden/staden.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for staden -# Copyright 2011-2016 Petar Petrov slackalaxy@gmail.com +# Copyright 2011-2023 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=staden VERSION=${VERSION:-2.0.0b11} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -37,7 +40,14 @@ fi TKLIB=tklib0.6 # Folder name of TKLIB -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -87,6 +97,11 @@ CXXFLAGS="$SLKCFLAGS" \ --with-tklib=/usr/lib${LIBDIRSUFFIX}/$TKLIB \ --build=$ARCH-slackware-linux +# Point to the right place of the EMBOSS .acd and data files. This is +# needed if the "create_emboss_files" script is run after install. +sed -i "133 c set acd_dir /usr/share/EMBOSS/acd" spin_emboss/create_emboss_files.tcl +sed -i "73 a EMBOSS_DATA=/usr/share/EMBOSS/data; export EMBOSS_DATA" spin/spin + make make install DESTDIR=$PKG @@ -101,6 +116,21 @@ mkdir -p $PKG/usr/share/{applications,pixmaps} cp $CWD/desktop/*.desktop $PKG/usr/share/applications cp $CWD/desktop/*.png $PKG/usr/share/pixmaps +# Do we want a submenu? For more info: +# https://slackalaxy.com/2021/08/08/xfce-multilevel-menu/ +if [ $SUBMENU = "YES" ]; then + # Use a separate "Staden Package" menu entry within "Education" + mkdir -p $PKG/etc/xdg/menus/applications-merged + cp $CWD/desktop/$PRGNAM.menu $PKG/etc/xdg/menus/applications-merged + + # Menu directory structure + mkdir -p $PKG/usr/share/desktop-directories + cp $CWD/desktop/$PRGNAM.directory $PKG/usr/share/desktop-directories + + # The category in the .desktop files is commented out to avoid duplication in menus + sed -i "s:Categories:#Categories:" $PKG/usr/share/applications/*.desktop +fi + mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a ChangeLog LICENCE.txt NEWS README.build \ $PKG/usr/doc/$PRGNAM-$VERSION @@ -112,4 +142,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/stellarium/README b/academic/stellarium/README index c4a3136eca..09942222a2 100644 --- a/academic/stellarium/README +++ b/academic/stellarium/README @@ -5,5 +5,5 @@ projectors. Just set your coordinates and go. For reasonable performance, you will want to have some kind of 3D acceleration. -gpsd is an optional dependency for enabling location detection through a GPS -device. +gpsd is an optional dependency for enabling location detection through +a GPS device. diff --git a/academic/stellarium/stellarium.SlackBuild b/academic/stellarium/stellarium.SlackBuild index 4c7e1ff99e..18b68389b1 100644 --- a/academic/stellarium/stellarium.SlackBuild +++ b/academic/stellarium/stellarium.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for stellarium # Copyright 2008 Alan Alberghini <414N@slacky.it> @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=stellarium -VERSION=${VERSION:-0.18.1} +VERSION=${VERSION:-23.4} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -60,7 +70,7 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $PRGNAM-$VERSION -tar -xzvf $CWD/$PRGNAM-$VERSION.tar.gz +tar xvf $CWD/$PRGNAM-$VERSION.tar.xz cd $PRGNAM-$VERSION chown -R root:root . find -L . \ @@ -69,25 +79,70 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -mkdir build && cd build - cmake -DCMAKE_INSTALL_PREFIX=/usr \ - -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ +# CPM dependency retrieval lifting: prepare a cache dir in the format +# expected by CPM with pre-downloaded sources. + +# CPM normally puts downloaded deps under this dir +CPM_CACHE_DIR=$TMP/$PRGNAM-$VERSION/build/_deps + +CPM_SHOWMYSKY_VERSION=v0.3.1 +CPM_QXSLX_VERSION=1.4.6 +CPM_INDI_VERSION=1.8.5 +CPM_GLM_VERSION=0.9.9.8 +CPM_NLOPT_VERSION=v2.7.1 + +# We need to match dependencies names used in cmake files with the +# actual dependency tarball names +declare -A CPM_SOURCE CPM_DEST +CPM_SOURCE["SHOWMYSKY"]="$CWD/CalcMySky-$CPM_SHOWMYSKY_VERSION.tar.gz" +CPM_SOURCE["QXLSX"]="$CWD/QXlsx-v$CPM_QXSLX_VERSION.tar.gz" +CPM_SOURCE["INDI"]="$CWD/indi-$CPM_INDI_VERSION.zip" +CPM_SOURCE["GLM"]="$CWD/glm-$CPM_GLM_VERSION.7z" +CPM_SOURCE["NLOPT"]="$CWD/nlopt-$CPM_NLOPT_VERSION.tar.gz" +CPM_DEST["SHOWMYSKY"]="$CPM_CACHE_DIR/showmysky-qt5-subbuild/showmysky-qt5-populate-prefix/src/$CPM_SHOWMYSKY_VERSION.tar.gz" +CPM_DEST["QXLSX"]="$CPM_CACHE_DIR/qxlsxqt5-subbuild/qxlsxqt5-populate-prefix/src/v$CPM_QXSLX_VERSION.tar.gz" +CPM_DEST["INDI"]="$CPM_CACHE_DIR/indiclient-subbuild/indiclient-populate-prefix/src/v$CPM_INDI_VERSION.zip" +CPM_DEST["GLM"]="$CPM_CACHE_DIR/glm-subbuild/glm-populate-prefix/src/glm-$CPM_GLM_VERSION.7z" +CPM_DEST["NLOPT"]="$CPM_CACHE_DIR/nlopt-subbuild/nlopt-populate-prefix/src/$CPM_NLOPT_VERSION.tar.gz" + +for dep in "${!CPM_SOURCE[@]}" +do + mkdir -p "$(dirname "${CPM_DEST[$dep]}")" + ln -s "${CPM_SOURCE[$dep]}" "${CPM_DEST[$dep]}" +done + +# End of CPM deps management + +mkdir -p build +cd build + cmake \ -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ - -DCMAKE_BUILD_TYPE="release" \ - .. + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DPYTHON_EXECUTABLE=/usr/bin/python3 \ + -DCMAKE_INSTALL_LIBDIR=/usr/lib${LIBDIRSUFFIX} \ + -DCMAKE_INSTALL_MANDIR=/usr/man \ + -DPREFER_SYSTEM_INDILIB=NO \ + -DCMAKE_BUILD_TYPE=Release .. make make install DESTDIR=$PKG cd - +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true -mv $PKG/usr/share/man $PKG/usr +# upstream doesn't honor the CMAKE_INSTALL_MANDIR. Move files manually, for now +mv $PKG/usr/share/man $PKG/usr/ find $PKG/usr/man -type f -exec gzip -9 {} \; for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a CREDITS.md COPYING ChangeLog README.md $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + CREDITS.md COPYING ChangeLog README.md \ + $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install @@ -95,4 +150,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/stellarium/stellarium.info b/academic/stellarium/stellarium.info index 35dd774260..df1c008e58 100644 --- a/academic/stellarium/stellarium.info +++ b/academic/stellarium/stellarium.info @@ -1,10 +1,20 @@ PRGNAM="stellarium" -VERSION="0.18.1" +VERSION="23.4" HOMEPAGE="http://www.stellarium.org" -DOWNLOAD="https://github.com/Stellarium/stellarium/releases/download/v0.18.1/stellarium-0.18.1.tar.gz" -MD5SUM="1eb0098db83f0543b44877a8e72acbb6" +DOWNLOAD="https://github.com/Stellarium/stellarium/releases/download/v23.4/stellarium-23.4.tar.xz \ +https://github.com/10110111/CalcMySky/archive/refs/tags/v0.3.1/CalcMySky-v0.3.1.tar.gz \ +https://github.com/QtExcel/QXlsx/archive/refs/tags/v1.4.6/QXlsx-v1.4.6.tar.gz \ +https://github.com/indilib/indi/archive/v1.8.5/indi-1.8.5.zip \ +https://github.com/g-truc/glm/releases/download/0.9.9.8/glm-0.9.9.8.7z \ +https://github.com/stevengj/nlopt/archive/refs/tags/v2.7.1/nlopt-v2.7.1.tar.gz" +MD5SUM="c44271c128de0f2830ce465574e28ce8 \ +88def58da627a30135cd1871fffa5577 \ +fdc7a2bf239bd0ff84f6058694dcd9f9 \ +14a092a9eb2117e5c51ba3302197e097 \ +c8342552801ebeb31497288192c4e793 \ +ed1a3000a1c8c248d51df126dfcfaa78" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="qt5" +REQUIRES="" MAINTAINER="Alan Alberghini" EMAIL="414N@slacky.it" diff --git a/academic/stringtie/stringtie.SlackBuild b/academic/stringtie/stringtie.SlackBuild index 91f7fe98f8..62c1a9eece 100644 --- a/academic/stringtie/stringtie.SlackBuild +++ b/academic/stringtie/stringtie.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for stringtie -# Copyright 2018-2019 Petar Petrov slackalaxy@gmail.com +# Copyright 2018-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=stringtie VERSION=${VERSION:-1.3.6} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -87,4 +97,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/suitesparse/README b/academic/suitesparse/README index 7eb56aa16e..4704b3906b 100644 --- a/academic/suitesparse/README +++ b/academic/suitesparse/README @@ -1,5 +1,5 @@ -suitesparse is a collection of libraries for computations involving sparse -matrices. The package includes the following libraries: +suitesparse is a collection of libraries for computations involving +sparse matrices. The package includes the following libraries: AMD: approximate minimum degree ordering. CAMD: constrained approximate minimum degree ordering. @@ -25,4 +25,7 @@ by default. SlackBuilds.org also has all the parts of this suite as individual builds - DO NOT try and install the individual parts and the suite; -pick one or the other. +choose one or the other. + +For Slackware 15.0, suitesparse's version is being held at 5.13.0. +Later versions are not compatible with 15.0 supplied version of cmake. diff --git a/academic/suitesparse/suitesparse.SlackBuild b/academic/suitesparse/suitesparse.SlackBuild index 938a5758fd..774fbc1a19 100644 --- a/academic/suitesparse/suitesparse.SlackBuild +++ b/academic/suitesparse/suitesparse.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for suitesparse -# Copyright 2017-2019 Christoph Willing, Brisbane Australia +# Copyright 2017-2023 Christoph Willing, Brisbane Australia # All rights reserved. # Thanks to Pablo Santamaria for previous versions # @@ -23,11 +23,14 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=suitesparse SRCNAM=SuiteSparse -VERSION=${VERSION:-5.4.0} -BUILD=${BUILD:-1} +VERSION=${VERSION:-5.13.0} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -37,7 +40,11 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -63,7 +70,7 @@ mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $SRCNAM tar xvf $CWD/$SRCNAM-$VERSION.tar.gz -cd $SRCNAM +cd $SRCNAM-$VERSION chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -75,6 +82,7 @@ mkdir -p $PKG/usr/include/suitesparse mkdir -p $PKG/usr/lib$LIBDIRSUFFIX mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +export BLAS="$(pkg-config --libs openblas)" make make install \ INSTALL_INCLUDE=$PKG/usr/include/suitesparse \ @@ -93,11 +101,11 @@ done find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true -cp -a LICENSE.txt CONTRIBUTOR-LICENSE.txt README.txt $PKG/usr/doc/$PRGNAM-$VERSION +cp -a LICENSE.txt CONTRIBUTOR-LICENSE.txt README.md $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/suitesparse/suitesparse.info b/academic/suitesparse/suitesparse.info index 9e33539498..929ec6e26f 100644 --- a/academic/suitesparse/suitesparse.info +++ b/academic/suitesparse/suitesparse.info @@ -1,8 +1,8 @@ PRGNAM="suitesparse" -VERSION="5.4.0" +VERSION="5.13.0" HOMEPAGE="http://faculty.cse.tamu.edu/davis/suitesparse.html" -DOWNLOAD="http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-5.4.0.tar.gz" -MD5SUM="4a6d4e74fc44c503f52996ae95cad03a" +DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.13.0/SuiteSparse-5.13.0.tar.gz" +MD5SUM="e9e7bc594b77ae4b58d943cdc286d679" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="lapack OpenBLAS chrpath" diff --git a/academic/suitesparseconfig/README b/academic/suitesparseconfig/README index 1832b9d60e..88061d2d50 100644 --- a/academic/suitesparseconfig/README +++ b/academic/suitesparseconfig/README @@ -1,5 +1,6 @@ -SuiteSparse_config is a common configuration library for the SuiteSparse -family of sparse matrix packages, including SuiteSparseQR, AMD, CAMD, COLAMD, -CCOLAMD, CHOLMOD, KLU, BTF, LDL, CXSparse, RBio, and UMFPACK. +SuiteSparse_config is a common configuration library for the +SuiteSparse family of sparse matrix packages, including SuiteSparseQR, +AMD, CAMD, COLAMD, CCOLAMD, CHOLMOD, KLU, BTF, LDL, CXSparse, RBio, +and UMFPACK. This library was formerly named UFconfig. diff --git a/academic/suitesparseconfig/patches/autoconfiscate.diff b/academic/suitesparseconfig/patches/autoconfiscate.diff index a6a40926ee..80b550a08a 100644 --- a/academic/suitesparseconfig/patches/autoconfiscate.diff +++ b/academic/suitesparseconfig/patches/autoconfiscate.diff @@ -34,7 +34,7 @@ new file mode 100644 +# Process this file with autoconf to produce a configure script. + +AC_PREREQ([2.69]) -+AC_INIT([SuiteSparse_config],[5.6.0],[https://github.com/DrTimothyAldenDavis/SuiteSparse],[suitesparseconfig],[http://www.suitesparse.com/]) ++AC_INIT([SuiteSparse_config],[5.8.1],[https://github.com/DrTimothyAldenDavis/SuiteSparse],[suitesparseconfig],[http://www.suitesparse.com/]) +AC_CONFIG_SRCDIR([SuiteSparse_config.c]) +AC_CONFIG_AUX_DIR([build-aux]) +AC_CONFIG_MACRO_DIR([m4]) diff --git a/academic/suitesparseconfig/suitesparseconfig.SlackBuild b/academic/suitesparseconfig/suitesparseconfig.SlackBuild index f228f534cc..8ebbedcfc1 100644 --- a/academic/suitesparseconfig/suitesparseconfig.SlackBuild +++ b/academic/suitesparseconfig/suitesparseconfig.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for SuiteSparse_config -# Copyright 2013-2020 Kyle Guinn <elyk03@gmail.com> +# Copyright 2013-2021 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,13 +22,16 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=suitesparseconfig SRCNAM=SuiteSparse SUBDIR=SuiteSparse_config -VERSION=${VERSION:-5.6.0} -SRCVER=${SRCVER:-5.6.0} +VERSION=${VERSION:-5.8.1} +SRCVER=${SRCVER:-5.8.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$(uname -m)" in @@ -38,15 +41,22 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM-$VERSION +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="README.txt" -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" @@ -106,4 +116,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/suitesparseconfig/suitesparseconfig.info b/academic/suitesparseconfig/suitesparseconfig.info index 34bb7ee90f..17cea1c0bf 100644 --- a/academic/suitesparseconfig/suitesparseconfig.info +++ b/academic/suitesparseconfig/suitesparseconfig.info @@ -1,8 +1,8 @@ PRGNAM="suitesparseconfig" -VERSION="5.6.0" +VERSION="5.8.1" HOMEPAGE="http://faculty.cse.tamu.edu/davis/suitesparse.html" -DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.6.0/SuiteSparse-5.6.0.tar.gz" -MD5SUM="af8b97cbded4cd5c6672e878bc0c37c2" +DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.8.1/SuiteSparse-5.8.1.tar.gz" +MD5SUM="c414679bbc9432a3def01b31ad921140" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/sundials/sundials.SlackBuild b/academic/sundials/sundials.SlackBuild index 67f7922291..3fb0a5fab5 100644 --- a/academic/sundials/sundials.SlackBuild +++ b/academic/sundials/sundials.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for sundials @@ -24,10 +24,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=sundials -VERSION=${VERSION:-3.1.1} +VERSION=${VERSION:-5.6.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -37,7 +40,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -82,6 +92,8 @@ sed -i \ src/*/CMakeLists.txt \ src/*/*/CMakeLists.txt +export PATH=/opt/cmake-202x/bin:$PATH + mkdir -p build cd build cmake \ @@ -108,4 +120,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/sundials/sundials.info b/academic/sundials/sundials.info index 609a18e7f3..23d1a73b71 100644 --- a/academic/sundials/sundials.info +++ b/academic/sundials/sundials.info @@ -1,8 +1,8 @@ PRGNAM="sundials" -VERSION="3.1.1" +VERSION="5.6.1" HOMEPAGE="https://computation.llnl.gov/projects/sundials" -DOWNLOAD="https://computation.llnl.gov/projects/sundials/download/sundials-3.1.1.tar.gz" -MD5SUM="e63f4de0be5be97f750b30b0fa11ef34" +DOWNLOAD="https://github.com/LLNL/sundials/releases/download/v5.6.1/sundials-5.6.1.tar.gz" +MD5SUM="a945bf3fa606fb6676ec025723688f15" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/sword-data-kjv/README b/academic/sword-data-kjv/README index d4dc4c01ad..7f1f855900 100644 --- a/academic/sword-data-kjv/README +++ b/academic/sword-data-kjv/README @@ -1,6 +1,6 @@ -sword-data-kjv is a data package containing the king james with strongs -dictionarys for sword. -This packages the King James Version bible with strongs refereneces +sword-data-kjv is a data package containing the King James bible with +Strongs dictionaries. +This packages the King James Version bible with strongs references and the strongs Hebrew and Greek dictionaries for use with the sword engine/library V1.7.0 or higher. This and many other bibles and dictionaries can be downloaded from the www.crosswire.org web site. As @@ -10,12 +10,14 @@ Go to www.crosswire.org/sword/modules/ to find more texts, dictionaries, commentaries and other related stuff which can be used by the sword engine. -wget has problems using the urls directly at www.crosswire.org/sword/modules -allthough a browser such as firefox works fine. See the .info file for an -example of url location when using wget. +wget has problems using the urls directly at +www.crosswire.org/sword/modules allthough a browser such as firefox +works fine. See the .info file for an example of url location when using +wget. -most sword based bible programs, such as bibletime or xiphos (gnomesword) -have a facility to download more content using their gui. +most sword based bible programs, such as bibletime or xiphos +(previously called gnomesword) have a facility to download more content +using their gui. Please Note: you need at least sword 1.7.0 or higher to read this data. -It has been tested with sword 1.7.0 1.7.5a1 and 1.8.1 +It has been tested with sword 1.7.0 1.7.5a1 1.8.1 and 1.9.0 diff --git a/academic/sword-data-kjv/sword-data-kjv.SlackBuild b/academic/sword-data-kjv/sword-data-kjv.SlackBuild index 4b41aacc36..198bb6bc89 100644 --- a/academic/sword-data-kjv/sword-data-kjv.SlackBuild +++ b/academic/sword-data-kjv/sword-data-kjv.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for sword-data-kjv -# Copyright 2015/6/8 Tim Dickson, email: tim at googlemail.com +# Copyright 2015-2023 Tim Dickson, email: tim at googlemail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,15 +22,25 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=sword-data-kjv -VERSION=${VERSION:-1.8.1} -BUILD=${BUILD:-1} +VERSION=${VERSION:-1.9.0_2} +BUILD=${BUILD:-3} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} #this is a data package, architecture is irrelevant ARCH=noarch -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -43,7 +53,7 @@ cd $TMP rm -rf $PRGNAM-$VERSION #check if sword is installed and get data location, otherwise use default -DATADEST="/usr/shared/sword/" +DATADEST="/usr/share/sword/" if [ -e /etc/sword.conf ]; then DATADEST=`cat /etc/sword.conf|grep DataPath|awk -F"=" '{print $2}'` if [ "x$DATADEST" = "x" ]||[ "x$DATDEST" = "x/" ]; then @@ -57,10 +67,10 @@ fi mkdir -p $PKG${DATADEST} cd $PKG${DATADEST} -chown -R root:root . unzip $CWD/KJV.zip unzip $CWD/StrongsGreek.zip unzip $CWD/StrongsHebrew.zip +chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ -o -perm 511 \) -exec chmod 755 {} \; -o \ @@ -74,4 +84,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/sword-data-kjv/sword-data-kjv.info b/academic/sword-data-kjv/sword-data-kjv.info index d58f037e03..11c62693b1 100644 --- a/academic/sword-data-kjv/sword-data-kjv.info +++ b/academic/sword-data-kjv/sword-data-kjv.info @@ -1,11 +1,11 @@ PRGNAM="sword-data-kjv" -VERSION="1.8.1" +VERSION="1.9.0_2" HOMEPAGE="http://www.crosswire.org/sword/modules/" DOWNLOAD="http://www.crosswire.org/ftpmirror/pub/sword/packages/rawzip/KJV.zip \ http://www.crosswire.org/ftpmirror/pub/sword/packages/rawzip/StrongsGreek.zip \ http://www.crosswire.org/ftpmirror/pub/sword/packages/rawzip/StrongsHebrew.zip" -MD5SUM="43b84512562a6b2406b34abf46fca4fa \ - 2acde501e6a33e84feeeaa62f8e53d89 \ +MD5SUM="f55dab4fb1515c1b0b229148319d074d \ + 5b2816b8b424033a72850eb64355f104 \ 3cbbc69d7410efc9d1d7f6f6b30e3415" DOWNLOAD_x86_64="" MD5SUM_x86_64="" diff --git a/academic/sword/README b/academic/sword/README index 2de1d80d89..a9972f2fae 100644 --- a/academic/sword/README +++ b/academic/sword/README @@ -1,13 +1,19 @@ -The SWORD Project is an effort to create an ever expanding software package -for research and study of God and His Word. The SWORD Bible Framework allows -easy manipulation of Bible texts, commentaries, lexicons, dictionaries, etc. -Many frontends are build using this framework. An installed module set may -be shared between any frontend using the framework. +The SWORD Project is an effort to create an ever expanding software +package for research and study of God and His Word. The SWORD Bible +Framework allows easy manipulation of Bible texts, commentaries, +lexicons,dictionaries, etc. +Many frontends are build using this framework. An installed module set +may be shared between any frontend using the framework. This engine/library needs data to operate on to be usefull. -A sword-data-kjv package is available on sbo to provide a basic bible with -strongs and Greek and Hebrew dictionaries for use with this library. Many -more bibles, commentries etc. can be found on the crosswire.org website. +A sword-data-kjv package is available on sbo to provide a basic bible +with strongs and Greek and Hebrew dictionaries for use with this +library. Many more bibles, commentries etc. can be found on the +crosswire.org website. + modules can be downloaded in raw format (zip) and extracted into the /usr/share/sword directory. + +You will also need a frontend, such as xiphos or bibletime (both on sbo) +to view the bible data. diff --git a/academic/sword/sword.SlackBuild b/academic/sword/sword.SlackBuild index ffdff4fc6a..7ec9c9c693 100644 --- a/academic/sword/sword.SlackBuild +++ b/academic/sword/sword.SlackBuild @@ -1,11 +1,11 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for sword # Copyright 2008-2011 Heinz Wiesinger, Amsterdam, The Netherlands # All rights reserved. # -# changes updating to v1.7.5a1 and v1.8.1 Copyright 2015-2018 Tim Dickson, Scotland +# changes updating to v1.7.5a1 and v1.8.1 Copyright 2015-2020 Tim Dickson, Scotland # # Redistribution and use of this script, with or without modification, is # permitted provided that the following conditions are met: @@ -24,10 +24,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=sword -VERSION=${VERSION:-1.8.1} -BUILD=${BUILD:-2} +VERSION=${VERSION:-1.9.0} +BUILD=${BUILD:-3} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -37,7 +40,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -72,11 +82,10 @@ find -L . \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; #now patch the automake stuff so it doesn't error on slackware's newer version -#thanks to aur.archlinux.org for the information... -#since update to 1.8.1 first patch has to be commented out. we will get a bunch of -#warnings, but at least the library compiles -#sed -i 's/AM_INIT_AUTOMAKE$/AM_INIT_AUTOMAKE\(\[subdir\-objects\]\)/g' configure.ac sed -i 's/ftemplate-depth-25/ftemplate-depth\=125/g' configure.ac +#patch to remove subdir-objects warnings +sed -i 's/1.6/1.6 subdir-objects/g' lib/Makefile.am + ./autogen.sh #add workaround for compiling with more recent (>=61) versions of icu4c CFLAGS="$SLKCFLAGS -DU_USING_ICU_NAMESPACE=1" \ @@ -98,9 +107,11 @@ cp -a AUTHORS ChangeLog CODINGSTYLE COPYING INSTALL LICENSE NEWS README \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +rm -f $PKG/usr/lib*/*.la + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/sword/sword.info b/academic/sword/sword.info index bafb795e6c..8417f0c7ec 100644 --- a/academic/sword/sword.info +++ b/academic/sword/sword.info @@ -1,8 +1,8 @@ PRGNAM="sword" -VERSION="1.8.1" +VERSION="1.9.0" HOMEPAGE="http://www.crosswire.org/sword" -DOWNLOAD="http://crosswire.org/ftpmirror/pub/sword/source/v1.8/sword-1.8.1.tar.gz" -MD5SUM="ddab24192104b15cbec72e569145ccd1" +DOWNLOAD="http://crosswire.org/ftpmirror/pub/sword/source/v1.9/sword-1.9.0.tar.gz" +MD5SUM="7b86ab627993ef295307e3729d8edef2" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/t_coffee/README b/academic/t_coffee/README index f5f6689f7d..a52a9692f0 100644 --- a/academic/t_coffee/README +++ b/academic/t_coffee/README @@ -8,6 +8,8 @@ to combine sequence information with protein structural information 3D-Coffee/Expresso), profile information (PSI-Coffee) or RNA secondary structures (R-Coffee). +examples are installed in /usr/share/t_coffee/ + For detailed information and citation: T-Coffee: A novel method for multiple sequence alignments. Notredame, Higgins,Heringa,JMB,302(205-217)2000 diff --git a/academic/t_coffee/t_coffee.SlackBuild b/academic/t_coffee/t_coffee.SlackBuild index e54497f7a9..94d3e3918d 100644 --- a/academic/t_coffee/t_coffee.SlackBuild +++ b/academic/t_coffee/t_coffee.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for t_coffee -# Copyright 2013-2020 Petar Petrov slackalaxy@gmail.com +# Copyright 2013-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,13 +22,15 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=t_coffee -VERSION=${VERSION:-13.41.0_git28bdc39} +VERSION=${VERSION:-13.45.58.c355d11} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} -TARNAM=tcoffee -COMMIT=28bdc39911d10d8597db8513f9515fb2ed7a9158 +TARNAM=T-COFFEE_distribution_Version if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -38,7 +40,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -62,9 +71,9 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf ${TARNAM}-${COMMIT} -tar xvf $CWD/${TARNAM}-${COMMIT}.tar.gz -cd ${TARNAM}-${COMMIT} +rm -rf ${TARNAM}_${VERSION} +tar xvf $CWD/${TARNAM}_${VERSION}.tar.gz +cd ${TARNAM}_${VERSION} chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -73,17 +82,20 @@ find -L . \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; # Use our CFLAGS -sed -i "/^CFLAGS/s/=/+=/" t_coffee/src/makefile +sed -i "s|-O3 -Wno-write-strings|$SLKCFLAGS|" t_coffee_source/makefile + +CFLAGS="$SLKCFLAGS" make t_coffee -C t_coffee_source +install -D -m755 t_coffee_source/$PRGNAM $PKG/usr/bin/$PRGNAM -CFLAGS="$SLKCFLAGS" make t_coffee -C t_coffee/src -install -D -m755 t_coffee/src/$PRGNAM $PKG/usr/bin/$PRGNAM +mkdir -p $PKG/usr/share/t_coffee +cp -a example $PKG/usr/share/t_coffee/ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - HOW_BUILD_WORKS.md README.md docs/*.rst \ + README doc license.txt \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References @@ -92,4 +104,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/t_coffee/t_coffee.info b/academic/t_coffee/t_coffee.info index ec75e49f23..355fa22ca2 100644 --- a/academic/t_coffee/t_coffee.info +++ b/academic/t_coffee/t_coffee.info @@ -1,8 +1,8 @@ PRGNAM="t_coffee" -VERSION="13.41.0_git28bdc39" +VERSION="13.45.58.c355d11" HOMEPAGE="http://www.tcoffee.org/" -DOWNLOAD="https://github.com/cbcrg/tcoffee/archive/28bdc39/tcoffee-28bdc39911d10d8597db8513f9515fb2ed7a9158.tar.gz" -MD5SUM="3392d55a2817575ce90c1c3e94e08c0b" +DOWNLOAD="https://ponce.cc/slackware/sources/repo/T-COFFEE_distribution_Version_13.45.58.c355d11.tar.gz" +MD5SUM="8b5d42142b531f913429dd9c2d4c8b27" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/tabix-legacy/tabix-legacy.SlackBuild b/academic/tabix-legacy/tabix-legacy.SlackBuild index d20dc5ade9..afca1c6f11 100644 --- a/academic/tabix-legacy/tabix-legacy.SlackBuild +++ b/academic/tabix-legacy/tabix-legacy.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for tabix-legacy -# Copyright 2013-2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2013-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=tabix-legacy VERSION=${VERSION:-0.2.6} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} SRCNAM=tabix SUFFIX=legacy @@ -38,7 +41,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -103,4 +113,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/tiemu/README b/academic/tiemu/README new file mode 100644 index 0000000000..83497217ab --- /dev/null +++ b/academic/tiemu/README @@ -0,0 +1,7 @@ +TiEmu is a multi-platform emulator for TI89 / TI89 Titanium / TI92 / +TI92+ / V200PLT hand-helds. + +TiEmu does not emulate TI82, 83, ... hand-helds but TiLem does. + +TiEmu requires a ROM for your calculator. A GPL'd ROM called PedroM +is included. diff --git a/academic/tiemu/doinst.sh b/academic/tiemu/doinst.sh new file mode 100644 index 0000000000..65c7e2eeb9 --- /dev/null +++ b/academic/tiemu/doinst.sh @@ -0,0 +1,9 @@ +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 +fi + +if [ -e usr/share/icons/hicolor/icon-theme.cache ]; then + if [ -x /usr/bin/gtk-update-icon-cache ]; then + /usr/bin/gtk-update-icon-cache -f usr/share/icons/hicolor >/dev/null 2>&1 + fi +fi diff --git a/academic/tiemu/patches/01-build-fix.patch b/academic/tiemu/patches/01-build-fix.patch new file mode 100644 index 0000000000..7660b69430 --- /dev/null +++ b/academic/tiemu/patches/01-build-fix.patch @@ -0,0 +1,487 @@ +# This patch is based on the Ubuntu patch for TiEmu 3.02, see +# http://packages.ubuntu.com/de/oneiric/tiemu + + +diff -purN tiemu-3.03.orig/src/gui/calc/calc.c tiemu-3.03/src/gui/calc/calc.c +--- tiemu-3.03.orig/src/gui/calc/calc.c 2007-12-16 16:29:16.000000000 +0100 ++++ tiemu-3.03/src/gui/calc/calc.c 2011-11-04 23:11:40.000000000 +0100 +@@ -313,7 +313,7 @@ on_drawingarea1_expose_event ( + { + gdk_draw_pixmap( + widget->window, +- widget->style->fg_gc[GTK_WIDGET_STATE (widget)], ++ widget->style->fg_gc[gtk_widget_get_state (widget)], + pixmap, + event->area.x, event->area.y, + event->area.x, event->area.y, +@@ -586,7 +586,7 @@ int hid_init(void) + + // Install LCD refresh: 100 FPS (10 ms) + tid = g_timeout_add((params.lcd_rate == -1) ? 50 : params.lcd_rate, +- (GtkFunction)hid_refresh, NULL); ++ (GSourceFunc)hid_refresh, NULL); + + explicit_destroy = 0; + gtk_widget_show(main_wnd); // show wnd here +@@ -640,7 +640,7 @@ void hid_lcd_rate_set(void) + g_source_remove(tid); + + tid = g_timeout_add((params.lcd_rate == -1) ? 50 : params.lcd_rate, +- (GtkFunction)hid_refresh, NULL); ++ (GSourceFunc)hid_refresh, NULL); + } + + int hid_switch_with_skin(void) +diff -purN tiemu-3.03.orig/src/gui/calc/popup.c tiemu-3.03/src/gui/calc/popup.c +--- tiemu-3.03.orig/src/gui/calc/popup.c 2009-05-08 22:43:47.000000000 +0200 ++++ tiemu-3.03/src/gui/calc/popup.c 2011-11-04 22:45:28.000000000 +0100 +@@ -26,7 +26,9 @@ + # include <config.h> + #endif + ++#undef GTK_DISABLE_DEPRECATED + #include <gtk/gtk.h> ++#define GTK_DISABLE_DEPRECATED + #include <glade/glade.h> + #include <stdlib.h> + #include <string.h> +diff -purN tiemu-3.03.orig/src/gui/calc/screen.c tiemu-3.03/src/gui/calc/screen.c +--- tiemu-3.03.orig/src/gui/calc/screen.c 2006-11-06 18:18:51.000000000 +0100 ++++ tiemu-3.03/src/gui/calc/screen.c 2011-11-04 23:12:09.000000000 +0100 +@@ -187,7 +187,7 @@ void redraw_skin(void) + skin_infos.image = gdk_pixbuf_scale_simple(skin_infos.raw, wr.wr.w, wr.wr.h, GDK_INTERP_NEAREST); + + // and draw image into pixmap (next, into window on expose event) +- gdk_draw_pixbuf(pixmap, main_wnd->style->fg_gc[GTK_WIDGET_STATE(main_wnd)], ++ gdk_draw_pixbuf(pixmap, main_wnd->style->fg_gc[gtk_widget_get_state(main_wnd)], + skin_infos.image, 0, 0, 0, 0, -1, -1, GDK_RGB_DITHER_NONE, 0, 0); + gdk_window_invalidate_rect(main_wnd->window, &wr.gr, FALSE); + } +@@ -204,7 +204,7 @@ void redraw_lcd(void) + gdk_pixbuf_scale_simple(skin_infos.raw, sr.w, sr.h, GDK_INTERP_NEAREST); + + // and draw +- gdk_draw_pixbuf(pixmap, main_wnd->style->fg_gc[GTK_WIDGET_STATE(main_wnd)], ++ gdk_draw_pixbuf(pixmap, main_wnd->style->fg_gc[gtk_widget_get_state(main_wnd)], + skin_infos.image, ls.x, ls.y, lr.x, lr.y, lr.w, lr.h, GDK_RGB_DITHER_NONE, 0, 0); + gtk_widget_queue_draw_area(area, lr.x, lr.y, lr.w, lr.h); + } +@@ -324,7 +324,7 @@ int hid_update_lcd(void) + skin_infos.image = gdk_pixbuf_scale_simple(lcd, lr.w, lr.h, GDK_INTERP_NEAREST); + + // and draw image into pixmap (next, into window on expose event) +- gdk_draw_pixbuf(pixmap, main_wnd->style->fg_gc[GTK_WIDGET_STATE(main_wnd)], ++ gdk_draw_pixbuf(pixmap, main_wnd->style->fg_gc[gtk_widget_get_state(main_wnd)], + skin_infos.image, src.x, src.y, lr.x, lr.y, src.w, src.h, + GDK_RGB_DITHER_NONE, 0, 0); + gtk_widget_queue_draw_area(area, lr.x, lr.y, src.w, src.h); +@@ -332,7 +332,7 @@ int hid_update_lcd(void) + else + { + // and draw image into pixmap (next, into window on expose event) +- gdk_draw_pixbuf(pixmap, main_wnd->style->fg_gc[GTK_WIDGET_STATE(main_wnd)], ++ gdk_draw_pixbuf(pixmap, main_wnd->style->fg_gc[gtk_widget_get_state(main_wnd)], + lcd_mem, src.x, src.y, lr.x, lr.y, src.w, src.h, + GDK_RGB_DITHER_NONE, 0, 0); + gtk_widget_queue_draw_area(area, lr.x, lr.y, src.w, src.h); +diff -purN tiemu-3.03.orig/src/gui/debugger/dbg_all.c tiemu-3.03/src/gui/debugger/dbg_all.c +--- tiemu-3.03.orig/src/gui/debugger/dbg_all.c 2009-05-08 12:56:40.000000000 +0200 ++++ tiemu-3.03/src/gui/debugger/dbg_all.c 2011-11-04 22:46:29.000000000 +0100 +@@ -90,21 +90,21 @@ void gtk_debugger_refresh(void) + { + WND_TMR_START(); + +- if(options3.dbg_dock || GTK_WIDGET_VISIBLE(dbgw.regs)) ++ if(options3.dbg_dock || gtk_widget_get_visible(dbgw.regs)) + dbgregs_refresh_window(); +- if(options3.dbg_dock || GTK_WIDGET_VISIBLE(dbgw.mem)) ++ if(options3.dbg_dock || gtk_widget_get_visible(dbgw.mem)) + dbgmem_refresh_window(); +- if(options3.dbg_dock || GTK_WIDGET_VISIBLE(dbgw.bkpts)) ++ if(options3.dbg_dock || gtk_widget_get_visible(dbgw.bkpts)) + dbgbkpts_refresh_window(); +- if(options3.dbg_dock || GTK_WIDGET_VISIBLE(dbgw.pclog)) ++ if(options3.dbg_dock || gtk_widget_get_visible(dbgw.pclog)) + dbgpclog_refresh_window(); +- if(options3.dbg_dock || GTK_WIDGET_VISIBLE(dbgw.code)) ++ if(options3.dbg_dock || gtk_widget_get_visible(dbgw.code)) + dbgcode_refresh_window(); +- if(options3.dbg_dock || GTK_WIDGET_VISIBLE(dbgw.stack)) ++ if(options3.dbg_dock || gtk_widget_get_visible(dbgw.stack)) + dbgstack_refresh_window(); +- if(options3.dbg_dock || GTK_WIDGET_VISIBLE(dbgw.heap)) ++ if(options3.dbg_dock || gtk_widget_get_visible(dbgw.heap)) + dbgheap_refresh_window(); +- if(options3.dbg_dock || GTK_WIDGET_VISIBLE(dbgw.iop)) ++ if(options3.dbg_dock || gtk_widget_get_visible(dbgw.iop)) + dbgiop_refresh_window(); + + WND_TMR_STOP("Debugger Refresh Time"); +@@ -163,7 +163,7 @@ int gtk_debugger_enter(int context) + gtk_debugger_refresh(); + + // enable the debugger if GDB disabled it +- if (!options3.dbg_dock && !GTK_WIDGET_SENSITIVE(dbgw.regs)) ++ if (!options3.dbg_dock && !gtk_widget_get_sensitive(dbgw.regs)) + gtk_debugger_enable(); + + // handle automatic debugging requests +@@ -180,7 +180,7 @@ int gtk_debugger_enter(int context) + + ti68k_bkpt_get_pgmentry_offset(id, &handle, &offset); + ti68k_bkpt_del_pgmentry(handle); +- if(options3.dbg_dock || GTK_WIDGET_VISIBLE(dbgw.bkpts)) ++ if(options3.dbg_dock || gtk_widget_get_visible(dbgw.bkpts)) + dbgbkpts_refresh_window(); + + delete_command(NULL, 0); +diff -purN tiemu-3.03.orig/src/gui/debugger/dbg_bkpts.c tiemu-3.03/src/gui/debugger/dbg_bkpts.c +--- tiemu-3.03.orig/src/gui/debugger/dbg_bkpts.c 2009-05-06 21:48:47.000000000 +0200 ++++ tiemu-3.03/src/gui/debugger/dbg_bkpts.c 2011-11-04 22:46:29.000000000 +0100 +@@ -388,7 +388,7 @@ GtkWidget* dbgbkpts_display_window(void) + gtk_window_iconify(GTK_WINDOW(wnd)); + #endif + +- if(!GTK_WIDGET_VISIBLE(dbgw.bkpts) && !options3.bkpts.closed) ++ if(!gtk_widget_get_visible(dbgw.bkpts) && !options3.bkpts.closed) + gtk_widget_show(wnd); + + return wnd; +diff -purN tiemu-3.03.orig/src/gui/debugger/dbg_code.c tiemu-3.03/src/gui/debugger/dbg_code.c +--- tiemu-3.03.orig/src/gui/debugger/dbg_code.c 2009-05-06 21:48:47.000000000 +0200 ++++ tiemu-3.03/src/gui/debugger/dbg_code.c 2011-11-04 22:46:29.000000000 +0100 +@@ -1117,7 +1117,7 @@ void gdbcallback_refresh_debugger(void) + + int dbgcode_quit_enabled(void) + { +- return GTK_WIDGET_SENSITIVE(mi.m8); ++ return gtk_widget_get_sensitive(mi.m8); + } + + static int close_debugger_wrapper(gpointer data) +diff -purN tiemu-3.03.orig/src/gui/debugger/dbg_dock.c tiemu-3.03/src/gui/debugger/dbg_dock.c +--- tiemu-3.03.orig/src/gui/debugger/dbg_dock.c 2008-05-26 18:48:30.000000000 +0200 ++++ tiemu-3.03/src/gui/debugger/dbg_dock.c 2011-11-04 23:05:02.000000000 +0100 +@@ -151,22 +151,22 @@ void dbgdock_set_sensitivity(int state) +
+ void dbgdock_show_all(int all)
+ {
+- if(!GTK_WIDGET_VISIBLE(dbgw.dock) && all)
++ if(!gtk_widget_get_visible(dbgw.dock) && all)
+ gtk_widget_show(dbgw.dock);
+
+- if(GTK_WIDGET_VISIBLE(dbgw.iop))
++ if(gtk_widget_get_visible(dbgw.iop))
+ gtk_window_iconify(GTK_WINDOW(dbgw.iop));
+- if(GTK_WIDGET_VISIBLE(dbgw.pclog))
++ if(gtk_widget_get_visible(dbgw.pclog))
+ gtk_window_iconify(GTK_WINDOW(dbgw.pclog));
+ }
+
+ void dbgdock_hide_all(int all)
+ {
+- if(GTK_WIDGET_VISIBLE(dbgw.dock) && all)
++ if(gtk_widget_get_visible(dbgw.dock) && all)
+ gtk_widget_hide(dbgw.dock);
+
+- if(GTK_WIDGET_VISIBLE(dbgw.pclog))
++ if(gtk_widget_get_visible(dbgw.pclog))
+ gtk_widget_hide(dbgw.pclog);
+- if(GTK_WIDGET_VISIBLE(dbgw.iop))
++ if(gtk_widget_get_visible(dbgw.iop))
+ gtk_widget_hide(dbgw.iop);
+ }
+diff -purN tiemu-3.03.orig/src/gui/debugger/dbg_heap.c tiemu-3.03/src/gui/debugger/dbg_heap.c +--- tiemu-3.03.orig/src/gui/debugger/dbg_heap.c 2009-05-06 21:48:47.000000000 +0200 ++++ tiemu-3.03/src/gui/debugger/dbg_heap.c 2011-11-04 22:46:29.000000000 +0100 +@@ -171,7 +171,7 @@ GtkWidget* dbgheap_display_window(void) + gtk_window_iconify(GTK_WINDOW(dbgw.heap)); + #endif + +- if(!GTK_WIDGET_VISIBLE(dbgw.heap) && !options3.heap.closed) ++ if(!gtk_widget_get_visible(dbgw.heap) && !options3.heap.closed) + gtk_widget_show(dbgw.heap); + + return dbgw.heap; +diff -purN tiemu-3.03.orig/src/gui/debugger/dbg_iop.c tiemu-3.03/src/gui/debugger/dbg_iop.c +--- tiemu-3.03.orig/src/gui/debugger/dbg_iop.c 2009-05-02 21:46:04.000000000 +0200 ++++ tiemu-3.03/src/gui/debugger/dbg_iop.c 2011-11-04 22:46:29.000000000 +0100 +@@ -455,7 +455,7 @@ GtkWidget* dbgiop_display_window(void) + gtk_window_iconify(GTK_WINDOW(dbgw.iop)); + #endif + +- if(!GTK_WIDGET_VISIBLE(dbgw.iop) && !options3.iop.closed) ++ if(!gtk_widget_get_visible(dbgw.iop) && !options3.iop.closed) + gtk_widget_show(dbgw.iop); + + return dbgw.iop; +diff -purN tiemu-3.03.orig/src/gui/debugger/dbg_mem.c tiemu-3.03/src/gui/debugger/dbg_mem.c +--- tiemu-3.03.orig/src/gui/debugger/dbg_mem.c 2009-05-06 21:48:47.000000000 +0200 ++++ tiemu-3.03/src/gui/debugger/dbg_mem.c 2011-11-04 22:46:29.000000000 +0100 +@@ -435,7 +435,7 @@ GtkWidget* dbgmem_display_window(void) + gtk_window_iconify(GTK_WINDOW(dbgw.mem)); + #endif + +- if(!GTK_WIDGET_VISIBLE(dbgw.mem) && !options3.mem.closed) ++ if(!gtk_widget_get_visible(dbgw.mem) && !options3.mem.closed) + gtk_widget_show(dbgw.mem); + + return dbgw.mem; +@@ -605,7 +605,7 @@ dbgmem_button6_clicked + + GLADE_CB void + on_notebook1_switch_page (GtkNotebook *notebook, +- GtkNotebookPage *page, ++ gpointer *page, + guint page_num, + gpointer user_data) + { +diff -purN tiemu-3.03.orig/src/gui/debugger/dbg_pclog.c tiemu-3.03/src/gui/debugger/dbg_pclog.c +--- tiemu-3.03.orig/src/gui/debugger/dbg_pclog.c 2009-05-02 21:46:04.000000000 +0200 ++++ tiemu-3.03/src/gui/debugger/dbg_pclog.c 2011-11-04 22:46:29.000000000 +0100 +@@ -163,7 +163,7 @@ GtkWidget* dbgpclog_display_window(void) + gtk_window_iconify(GTK_WINDOW(dbgw.pclog)); + #endif + +- if(!GTK_WIDGET_VISIBLE(dbgw.pclog) && !options3.pclog.closed) ++ if(!gtk_widget_get_visible(dbgw.pclog) && !options3.pclog.closed) + gtk_widget_show(dbgw.pclog); + + return dbgw.pclog; +diff -purN tiemu-3.03.orig/src/gui/debugger/dbg_regs.c tiemu-3.03/src/gui/debugger/dbg_regs.c +--- tiemu-3.03.orig/src/gui/debugger/dbg_regs.c 2009-05-06 21:48:47.000000000 +0200 ++++ tiemu-3.03/src/gui/debugger/dbg_regs.c 2011-11-04 22:46:29.000000000 +0100 +@@ -302,7 +302,7 @@ GtkWidget* dbgregs_display_window(void) + gtk_window_iconify(GTK_WINDOW(dbgw.regs)); + #endif + +- if(!GTK_WIDGET_VISIBLE(dbgw.regs) && !options3.regs.closed) ++ if(!gtk_widget_get_visible(dbgw.regs) && !options3.regs.closed) + gtk_widget_show(dbgw.regs); + + return dbgw.regs; +diff -purN tiemu-3.03.orig/src/gui/debugger/dbg_romcall.c tiemu-3.03/src/gui/debugger/dbg_romcall.c +--- tiemu-3.03.orig/src/gui/debugger/dbg_romcall.c 2007-07-05 13:36:10.000000000 +0200 ++++ tiemu-3.03/src/gui/debugger/dbg_romcall.c 2011-11-04 22:46:29.000000000 +0100 +@@ -29,7 +29,9 @@ + # include <config.h> + #endif + +-#include <gtk/gtk.h> ++#undef GTK_DISABLE_DEPRECATED ++ #include <gtk/gtk.h> ++#define GTK_DISABLE_DEPRECATED + #include <glade/glade.h> + #include <string.h> + +diff -purN tiemu-3.03.orig/src/gui/debugger/dbg_stack.c tiemu-3.03/src/gui/debugger/dbg_stack.c +--- tiemu-3.03.orig/src/gui/debugger/dbg_stack.c 2009-05-06 21:48:47.000000000 +0200 ++++ tiemu-3.03/src/gui/debugger/dbg_stack.c 2011-11-04 22:46:29.000000000 +0100 +@@ -197,7 +197,7 @@ GtkWidget* dbgstack_display_window(void) + gtk_window_iconify(GTK_WINDOW(dbgw.stack)); + #endif + +- if(!GTK_WIDGET_VISIBLE(dbgw.stack) && !options3.stack.closed) ++ if(!gtk_widget_get_visible(dbgw.stack) && !options3.stack.closed) + gtk_widget_show(dbgw.stack); + + return dbgw.stack; +diff -purN tiemu-3.03.orig/src/gui/debugger/dbg_wnds.c tiemu-3.03/src/gui/debugger/dbg_wnds.c +--- tiemu-3.03.orig/src/gui/debugger/dbg_wnds.c 2009-05-07 09:18:02.000000000 +0200 ++++ tiemu-3.03/src/gui/debugger/dbg_wnds.c 2011-11-04 23:07:54.000000000 +0100 +@@ -74,21 +74,21 @@ void dbgwnds_minimize_all(int all) + if(options3.dbg_dock)
+ return;
+
+- if(GTK_WIDGET_VISIBLE(dbgw.regs))
++ if(gtk_widget_get_visible(dbgw.regs))
+ gtk_window_iconify(GTK_WINDOW(dbgw.regs));
+- if(GTK_WIDGET_VISIBLE(dbgw.bkpts))
++ if(gtk_widget_get_visible(dbgw.bkpts))
+ gtk_window_iconify(GTK_WINDOW(dbgw.bkpts));
+- if(GTK_WIDGET_VISIBLE(dbgw.mem))
++ if(gtk_widget_get_visible(dbgw.mem))
+ gtk_window_iconify(GTK_WINDOW(dbgw.mem));
+- if(GTK_WIDGET_VISIBLE(dbgw.pclog))
++ if(gtk_widget_get_visible(dbgw.pclog))
+ gtk_window_iconify(GTK_WINDOW(dbgw.pclog));
+- if(GTK_WIDGET_VISIBLE(dbgw.code) & all)
++ if(gtk_widget_get_visible(dbgw.code) & all)
+ gtk_window_iconify(GTK_WINDOW(dbgw.code));
+- if(GTK_WIDGET_VISIBLE(dbgw.stack))
++ if(gtk_widget_get_visible(dbgw.stack))
+ gtk_window_iconify(GTK_WINDOW(dbgw.stack));
+- if(GTK_WIDGET_VISIBLE(dbgw.heap))
++ if(gtk_widget_get_visible(dbgw.heap))
+ gtk_window_iconify(GTK_WINDOW(dbgw.heap));
+- if(GTK_WIDGET_VISIBLE(dbgw.iop))
++ if(gtk_widget_get_visible(dbgw.iop))
+ gtk_window_iconify(GTK_WINDOW(dbgw.iop));
+ }
+
+@@ -98,21 +98,21 @@ void dbgwnds_unminimize_all(int all) + if(options3.dbg_dock)
+ return;
+
+- if(GTK_WIDGET_VISIBLE(dbgw.regs))
++ if(gtk_widget_get_visible(dbgw.regs))
+ gtk_window_deiconify(GTK_WINDOW(dbgw.regs));
+- if(GTK_WIDGET_VISIBLE(dbgw.bkpts))
++ if(gtk_widget_get_visible(dbgw.bkpts))
+ gtk_window_deiconify(GTK_WINDOW(dbgw.bkpts));
+- if(GTK_WIDGET_VISIBLE(dbgw.mem))
++ if(gtk_widget_get_visible(dbgw.mem))
+ gtk_window_deiconify(GTK_WINDOW(dbgw.mem));
+- if(GTK_WIDGET_VISIBLE(dbgw.pclog))
++ if(gtk_widget_get_visible(dbgw.pclog))
+ gtk_window_deiconify(GTK_WINDOW(dbgw.pclog));
+- if(GTK_WIDGET_VISIBLE(dbgw.code) & all)
++ if(gtk_widget_get_visible(dbgw.code) & all)
+ gtk_window_deiconify(GTK_WINDOW(dbgw.code));
+- if(GTK_WIDGET_VISIBLE(dbgw.stack))
++ if(gtk_widget_get_visible(dbgw.stack))
+ gtk_window_deiconify(GTK_WINDOW(dbgw.stack));
+- if(GTK_WIDGET_VISIBLE(dbgw.heap))
++ if(gtk_widget_get_visible(dbgw.heap))
+ gtk_window_deiconify(GTK_WINDOW(dbgw.heap));
+- if(GTK_WIDGET_VISIBLE(dbgw.iop))
++ if(gtk_widget_get_visible(dbgw.iop))
+ gtk_window_deiconify(GTK_WINDOW(dbgw.iop));
+ }
+
+@@ -122,21 +122,21 @@ void dbgwnds_show_all(int all) + if(options3.dbg_dock)
+ return;
+
+- if(!GTK_WIDGET_VISIBLE(dbgw.regs))
++ if(!gtk_widget_get_visible(dbgw.regs))
+ gtk_widget_show(dbgw.regs);
+- if(!GTK_WIDGET_VISIBLE(dbgw.bkpts))
++ if(!gtk_widget_get_visible(dbgw.bkpts))
+ gtk_widget_show(dbgw.bkpts);
+- if(!GTK_WIDGET_VISIBLE(dbgw.mem))
++ if(!gtk_widget_get_visible(dbgw.mem))
+ gtk_widget_show(dbgw.mem);
+- if(!GTK_WIDGET_VISIBLE(dbgw.pclog))
++ if(!gtk_widget_get_visible(dbgw.pclog))
+ gtk_widget_show(dbgw.pclog);
+- if(!GTK_WIDGET_VISIBLE(dbgw.code) && all)
++ if(!gtk_widget_get_visible(dbgw.code) && all)
+ gtk_widget_show(dbgw.code);
+- if(!GTK_WIDGET_VISIBLE(dbgw.stack))
++ if(!gtk_widget_get_visible(dbgw.stack))
+ gtk_widget_show(dbgw.stack);
+- if(!GTK_WIDGET_VISIBLE(dbgw.heap))
++ if(!gtk_widget_get_visible(dbgw.heap))
+ gtk_widget_show(dbgw.heap);
+- if(!GTK_WIDGET_VISIBLE(dbgw.iop))
++ if(!gtk_widget_get_visible(dbgw.iop))
+ gtk_widget_show(dbgw.iop);
+ }
+
+@@ -146,21 +146,21 @@ void dbgwnds_hide_all(int all) + if(options3.dbg_dock)
+ return;
+
+- if(GTK_WIDGET_VISIBLE(dbgw.regs))
++ if(gtk_widget_get_visible(dbgw.regs))
+ gtk_widget_hide(dbgw.regs);
+- if(GTK_WIDGET_VISIBLE(dbgw.bkpts))
++ if(gtk_widget_get_visible(dbgw.bkpts))
+ gtk_widget_hide(dbgw.bkpts);
+- if(GTK_WIDGET_VISIBLE(dbgw.mem))
++ if(gtk_widget_get_visible(dbgw.mem))
+ gtk_widget_hide(dbgw.mem);
+- if(GTK_WIDGET_VISIBLE(dbgw.pclog))
++ if(gtk_widget_get_visible(dbgw.pclog))
+ gtk_widget_hide(dbgw.pclog);
+- if(GTK_WIDGET_VISIBLE(dbgw.code) && all)
++ if(gtk_widget_get_visible(dbgw.code) && all)
+ gtk_widget_hide(dbgw.code);
+- if(GTK_WIDGET_VISIBLE(dbgw.stack))
++ if(gtk_widget_get_visible(dbgw.stack))
+ gtk_widget_hide(dbgw.stack);
+- if(GTK_WIDGET_VISIBLE(dbgw.heap))
++ if(gtk_widget_get_visible(dbgw.heap))
+ gtk_widget_hide(dbgw.heap);
+- if(GTK_WIDGET_VISIBLE(dbgw.iop))
++ if(gtk_widget_get_visible(dbgw.iop))
+ gtk_widget_hide(dbgw.iop);
+ }
+
+@@ -338,7 +338,7 @@ void update_submenu(GtkWidget *widget, g + if(!options3.dbg_dock)
+ {
+ g_signal_handlers_block_by_func(GTK_OBJECT(item), on_registers1_activate, NULL);
+- gtk_check_menu_item_set_active(item, GTK_WIDGET_VISIBLE(dbgw.regs));
++ gtk_check_menu_item_set_active(item, gtk_widget_get_visible(dbgw.regs));
+ g_signal_handlers_unblock_by_func(GTK_OBJECT(item), on_registers1_activate, NULL);
+ }
+ else
+@@ -350,7 +350,7 @@ void update_submenu(GtkWidget *widget, g + if(!options3.dbg_dock)
+ {
+ g_signal_handlers_block_by_func(GTK_OBJECT(item), on_breakpoints1_activate, NULL);
+- gtk_check_menu_item_set_active(item, GTK_WIDGET_VISIBLE(dbgw.bkpts));
++ gtk_check_menu_item_set_active(item, gtk_widget_get_visible(dbgw.bkpts));
+ g_signal_handlers_unblock_by_func(GTK_OBJECT(item), on_breakpoints1_activate, NULL);
+ }
+ else
+@@ -362,7 +362,7 @@ void update_submenu(GtkWidget *widget, g + if(!options3.dbg_dock)
+ {
+ g_signal_handlers_block_by_func(GTK_OBJECT(item), on_memory1_activate, NULL);
+- gtk_check_menu_item_set_active(item, GTK_WIDGET_VISIBLE(dbgw.mem));
++ gtk_check_menu_item_set_active(item, gtk_widget_get_visible(dbgw.mem));
+ g_signal_handlers_unblock_by_func(GTK_OBJECT(item), on_memory1_activate, NULL);
+ }
+ else
+@@ -372,7 +372,7 @@ void update_submenu(GtkWidget *widget, g + elt = g_list_nth(list, 3);
+ item = GTK_CHECK_MENU_ITEM(elt->data);
+ g_signal_handlers_block_by_func(GTK_OBJECT(item), on_pc_log1_activate, NULL);
+- gtk_check_menu_item_set_active(item, GTK_WIDGET_VISIBLE(dbgw.pclog));
++ gtk_check_menu_item_set_active(item, gtk_widget_get_visible(dbgw.pclog));
+ g_signal_handlers_unblock_by_func(GTK_OBJECT(item), on_pc_log1_activate, NULL);
+
+ // stack
+@@ -381,7 +381,7 @@ void update_submenu(GtkWidget *widget, g + if(!options3.dbg_dock)
+ {
+ g_signal_handlers_block_by_func(GTK_OBJECT(item), on_stack_frame1_activate, NULL);
+- gtk_check_menu_item_set_active(item, GTK_WIDGET_VISIBLE(dbgw.stack));
++ gtk_check_menu_item_set_active(item, gtk_widget_get_visible(dbgw.stack));
+ g_signal_handlers_unblock_by_func(GTK_OBJECT(item), on_stack_frame1_activate, NULL);
+ }
+ else
+@@ -393,7 +393,7 @@ void update_submenu(GtkWidget *widget, g + if(!options3.dbg_dock)
+ {
+ g_signal_handlers_block_by_func(GTK_OBJECT(item), on_heap_frame1_activate, NULL);
+- gtk_check_menu_item_set_active(item, GTK_WIDGET_VISIBLE(dbgw.heap));
++ gtk_check_menu_item_set_active(item, gtk_widget_get_visible(dbgw.heap));
+ g_signal_handlers_unblock_by_func(GTK_OBJECT(item), on_heap_frame1_activate, NULL);
+ }
+ else
+@@ -403,7 +403,7 @@ void update_submenu(GtkWidget *widget, g + elt = g_list_nth(list, 6);
+ item = GTK_CHECK_MENU_ITEM(elt->data);
+ g_signal_handlers_block_by_func(GTK_OBJECT(item), on_ioports_frame1_activate, NULL);
+- gtk_check_menu_item_set_active(item, GTK_WIDGET_VISIBLE(dbgw.iop));
++ gtk_check_menu_item_set_active(item, gtk_widget_get_visible(dbgw.iop));
+ g_signal_handlers_unblock_by_func(GTK_OBJECT(item), on_ioports_frame1_activate, NULL);
+
+ // dock/multi mode
+diff -purN tiemu-3.03.orig/src/gui/filesel.c tiemu-3.03/src/gui/filesel.c +--- tiemu-3.03.orig/src/gui/filesel.c 2007-12-16 16:54:33.000000000 +0100 ++++ tiemu-3.03/src/gui/filesel.c 2011-11-04 22:45:28.000000000 +0100 +@@ -41,7 +41,9 @@ + + #include <stdio.h> + #include <stdlib.h> ++#undef GTK_DISABLE_DEPRECATED + #include <gtk/gtk.h> ++#define GTK_DISABLE_DEPRECATED + #include <string.h> + + #ifdef __WIN32__ diff --git a/academic/tiemu/patches/sysdeps.patch b/academic/tiemu/patches/sysdeps.patch new file mode 100644 index 0000000000..8a4addb76e --- /dev/null +++ b/academic/tiemu/patches/sysdeps.patch @@ -0,0 +1,15 @@ +--- sysdeps.h.orig 2018-10-18 19:48:03.258705538 -0700 ++++ tiemu-3.03/src/core/uae/sysdeps.h 2018-10-18 19:48:34.178704986 -0700 +@@ -137,12 +137,6 @@ + #define ENUMDECL typedef enum + #define ENUMNAME(name) name + +-/* While we're here, make abort more useful. */ +-#define abort() \ +- do { \ +- fprintf (stderr, "UAE: Internal error; file %s, line %d\n", __FILE__, __LINE__); \ +- (abort) (); \ +-} while (0) + #else + #define ENUMDECL enum + #define ENUMNAME(name) ; typedef int name diff --git a/academic/tiemu/slack-desc b/academic/tiemu/slack-desc new file mode 100644 index 0000000000..36e348bc0a --- /dev/null +++ b/academic/tiemu/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +tiemu: tiemu (TI-89/92/V200 emulator for linux) +tiemu: +tiemu: TiEmu emulates Texas Instruments calculators TI-89/92/92+/V200PLT +tiemu: (no GDB). +tiemu: +tiemu: Homepage: http://lpg.ticalc.org/prj_tiemu/ +tiemu: +tiemu: +tiemu: +tiemu: +tiemu: diff --git a/academic/tiemu/tiemu.SlackBuild b/academic/tiemu/tiemu.SlackBuild new file mode 100644 index 0000000000..85b1e0094f --- /dev/null +++ b/academic/tiemu/tiemu.SlackBuild @@ -0,0 +1,116 @@ +#!/bin/bash + +# Slackbuild for tiemu + +# Written by shelldweller <email removed> +# Now maintained by B. Watson <urchlay@slackware.uk> +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +# 20230224 bkw: BUILD=2 +# - new maintainer. +# - remove INSTALL and ABOUT-NLS from doc dir (generic, useless). + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=tiemu +VERSION=${VERSION:-3.03} +BUILD=${BUILD:-2} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION-nogdb.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . -perm /111 -a \! -perm 755 -a -exec chmod 755 {} \+ -o \ + \! -perm /111 -a \! -perm 644 -a -exec chmod 644 {} \+ + +# A few necessary patches +# https://aur.archlinux.org/packages/tiemu/#comment-667308 +patch -p1 < $CWD/patches/01-build-fix.patch +patch -p1 < $CWD/patches/sysdeps.patch + +OPT_CFLAGS="" \ +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --mandir=/usr/man \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --build=$ARCH-slackware-linux \ + --without-kde \ + --disable-gdb + +make +make install DESTDIR=$PKG +strip $PKG/usr/bin/$PRGNAM +gzip -9 $PKG/usr/man/man*/* + +PKGDOC=$PKG/usr/doc/$PRGNAM-$VERSION +mkdir -p $PKGDOC +cp -a AUTHORS BUGS COPYING ChangeLog LICENSES NEWS \ + README RELEASE TODO docs/ \ + $PKGDOC +cat $CWD/$PRGNAM.SlackBuild > $PKGDOC/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/tiemu/tiemu.info b/academic/tiemu/tiemu.info new file mode 100644 index 0000000000..5f6b445bdc --- /dev/null +++ b/academic/tiemu/tiemu.info @@ -0,0 +1,10 @@ +PRGNAM="tiemu" +VERSION="3.03" +HOMEPAGE="http://lpg.ticalc.org/prj_tiemu/" +DOWNLOAD="http://download.sourceforge.net/project/gtktiemu/tiemu-linux/TIEmu%203.03/tiemu-3.03-nogdb.tar.gz" +MD5SUM="2736440d717a0ee97cdb35189814fc93" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="libticalcs2" +MAINTAINER="B. Watson" +EMAIL="urchlay@slackware.uk" diff --git a/academic/tilem/tilem.SlackBuild b/academic/tilem/tilem.SlackBuild index dfd9468239..cbff9b3731 100644 --- a/academic/tilem/tilem.SlackBuild +++ b/academic/tilem/tilem.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackbuild for tilem @@ -20,10 +20,13 @@ # see fit. Or as I see fit. Or as I fit. Although # that is unlikely, as I am rather tall. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=tilem VERSION=${VERSION:-0.973} BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -33,7 +36,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -66,7 +76,7 @@ find -L . \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -p \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ -exec chmod 644 {} \; -CFLAGS="$SLKCFLAGS" \ +CFLAGS="$SLKCFLAGS -w -Wl,--allow-multiple-definition" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ --prefix=/usr \ @@ -91,4 +101,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/tilem2/tilem2.SlackBuild b/academic/tilem2/tilem2.SlackBuild index 44510828a7..f108b86cdc 100644 --- a/academic/tilem2/tilem2.SlackBuild +++ b/academic/tilem2/tilem2.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackbuild for tilem2 @@ -22,11 +22,14 @@ # see fit. Or as I see fit. Or as I fit. Although # that is unlikely, as I am rather tall. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=tilem2 SRCNAM=tilem VERSION=${VERSION:-2.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -36,7 +39,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -110,4 +120,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/tkgate/tkgate.SlackBuild b/academic/tkgate/tkgate.SlackBuild index a51cc6af0b..cbcf6001b4 100644 --- a/academic/tkgate/tkgate.SlackBuild +++ b/academic/tkgate/tkgate.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for tkgate @@ -22,27 +22,37 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=tkgate VERSION=${VERSION:-2.0_b10} SRCVERSION=$(echo $VERSION | tr _ -) BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -151,4 +161,4 @@ EOF (cd $PKG/usr/share/tkgate; chown -R root:root .) cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/topdraw/topdraw.SlackBuild b/academic/topdraw/topdraw.SlackBuild index 1a48ba94fa..5a14bcb0d9 100644 --- a/academic/topdraw/topdraw.SlackBuild +++ b/academic/topdraw/topdraw.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for topdraw -# Copyright 2013-2016 Petar Petrov slackalaxy@gmail.com +# Copyright 2013-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,14 +22,24 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=topdraw VERSION=${VERSION:-sep2002} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} ARCH=noarch -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -60,4 +70,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/topdraw/topdraw.info b/academic/topdraw/topdraw.info index caaad940bb..8080d97ea6 100644 --- a/academic/topdraw/topdraw.info +++ b/academic/topdraw/topdraw.info @@ -1,7 +1,7 @@ PRGNAM="topdraw" VERSION="sep2002" HOMEPAGE="http://crystal.scb.uwa.edu.au/charlie/software/topdraw/" -DOWNLOAD="http://crystal.scb.uwa.edu.au/charlie/software/topdraw/topdraw.zip" +DOWNLOAD="https://slackware.uk/sbosrcarch/by-name/academic/topdraw/topdraw.zip" MD5SUM="9827abf8ea33ea7f0811873661565925" DOWNLOAD_x86_64="" MD5SUM_x86_64="" diff --git a/academic/tophat/make_pair.patch b/academic/tophat/make_pair.patch new file mode 100644 index 0000000000..44b71d1059 --- /dev/null +++ b/academic/tophat/make_pair.patch @@ -0,0 +1,24 @@ +diff -uBw -aur tophat-2.1.1/src/juncs_db.cpp tophat-2.1.1-patched/src/juncs_db.cpp +--- tophat-2.1.1/src/juncs_db.cpp 2016-02-14 19:21:17.354079000 +0100 ++++ tophat-2.1.1-patched/src/juncs_db.cpp 2016-06-02 11:26:34.097425159 +0200 +@@ -338,7 +338,7 @@ + uint32_t left_coord = atoi(scan_left_coord); + uint32_t right_coord = atoi(scan_right_coord); + bool antisense = *orientation == '-'; +- junctions.insert(make_pair<Junction, JunctionStats>(Junction(ref_id, left_coord, right_coord, antisense), JunctionStats())); ++ junctions.insert(make_pair(Junction(ref_id, left_coord, right_coord, antisense), JunctionStats())); + } + } + +diff -uBw -aur tophat-2.1.1/src/tophat_reports.cpp tophat-2.1.1-patched/src/tophat_reports.cpp +--- tophat-2.1.1/src/tophat_reports.cpp 2016-02-23 22:20:44.320710000 +0100 ++++ tophat-2.1.1-patched/src/tophat_reports.cpp 2016-06-02 11:26:22.057239478 +0200 +@@ -2705,7 +2705,7 @@ + junction_stat.gtf_match = true; + junction_stat.accepted = true; + +- gtf_junctions.insert(make_pair<Junction, JunctionStats>(Junction(ref_id, left_coord, right_coord, antisense), junction_stat)); ++ gtf_junctions.insert(make_pair(Junction(ref_id, left_coord, right_coord, antisense), junction_stat)); + } + } + fprintf(stderr, "Loaded %d GFF junctions from %s.\n", (int)(gtf_junctions.size()), gtf_juncs.c_str()); diff --git a/academic/tophat/tophat.SlackBuild b/academic/tophat/tophat.SlackBuild index f32fb590f5..22d1b532bf 100644 --- a/academic/tophat/tophat.SlackBuild +++ b/academic/tophat/tophat.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for tophat -# Copyright 2013-2019 Petar Petrov slackalaxy@gmail.com +# Copyright 2013-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=tophat VERSION=${VERSION:-2.1.2} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -69,10 +79,14 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; +# Thanks archlinux +patch -p1 < $CWD/make_pair.patch + ./autogen.sh CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ +CPPFLAGS="$SLKCFLAGS -std=c++14" \ ./configure \ --prefix=/usr \ --libdir=/usr/lib${LIBDIRSUFFIX} \ @@ -99,4 +113,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/treebest-ensembl/README b/academic/treebest-ensembl/README index b6639d304d..f91a651be9 100644 --- a/academic/treebest-ensembl/README +++ b/academic/treebest-ensembl/README @@ -10,16 +10,18 @@ TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group. -This is the Ensembl Compara modifications version. The main new features -are: +This is the Ensembl Compara modifications version. The main new +features are: 1) -s option in treebest sdi, to allow a user-defined species tree. T node-tag in the NHX output: a bit-field listing the input trees 2) that support the node. 3) -I option in treebest nj, to carry on the T tags from the input tree -4) -Z option in treebest best, to redefine the PhyML variable MIN_DIFF_LK -5) -X option in treebest best, to give a higher weight to the likelihood - that comes from the reconciliation with the species tree (default 1) +4) -Z option in treebest best, to redefine the PhyML variable + MIN_DIFF_LK +5) -X option in treebest best, to give a higher weight to the + likelihood that comes from the reconciliation with the species tree + (default 1) 6) -I option in treebest best, to start from the input tree instead of building one 7) Species-intersection scores are now also reported as floating-point diff --git a/academic/treebest-ensembl/treebest-ensembl.SlackBuild b/academic/treebest-ensembl/treebest-ensembl.SlackBuild index b3a8844539..fe29931646 100644 --- a/academic/treebest-ensembl/treebest-ensembl.SlackBuild +++ b/academic/treebest-ensembl/treebest-ensembl.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for treebest -# Copyright 2020 Petar Petrov slackalaxy@gmail.com +# Copyright 2020-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=treebest-ensembl VERSION=${VERSION:-1.9.2_git347fa82} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} SRCNAM=treebest COMMIT=347fa82a0ce1c169849053fdc9ff7d19d221f290 @@ -38,7 +41,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -76,10 +86,10 @@ find -L . \ sed -i "/^CFLAGS/s/=/+=/" Makefile # Make the CLI treebest and the FLTK GUI -CFLAGS="$SLKCFLAGS" \ +CFLAGS="$SLKCFLAGS -fcommon" \ make -CFLAGS="$SLKCFLAGS" \ +CFLAGS="$SLKCFLAGS -fcommon" \ make fltreebest install -D -m755 treebest $PKG/usr/bin/treebest @@ -109,4 +119,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/treerecs/README b/academic/treerecs/README index cd3794ca26..283164480a 100644 --- a/academic/treerecs/README +++ b/academic/treerecs/README @@ -28,3 +28,11 @@ Bio++ use. 2) genetreeEditor: a small program which provides editing of gene names using species names and format conversion (Newick, Nhx or PhyloXML) . + +For more information, see preprint at bioRxiv: +Treerecs: an integrated phylogenetic tool, from sequences to +reconciliations. Nicolas Comte, Benoit Morel, Damir Hasic, Laurent +Guéguen, Bastien Boussau, Vincent Daubin, Simon Penel, Celine +Scornavacca, Manolo Gouy, Alexandros Stamatakis, Eric Tannier. +View ORCID ProfileDavid P. Parsons +https://www.biorxiv.org/content/10.1101/782946v1 diff --git a/academic/treerecs/treerecs.SlackBuild b/academic/treerecs/treerecs.SlackBuild index 4bff8e9c09..14e1cebfe0 100644 --- a/academic/treerecs/treerecs.SlackBuild +++ b/academic/treerecs/treerecs.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for treerecs -# Copyright 2020 Petar Petrov slackalaxy@gmail.com +# Copyright 2020-2023 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,17 +22,16 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +# Thanks to David Parsons for clarifications about the scipt and suggestions! + +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=treerecs -VERSION=${VERSION:-1.1_gitd1c1bfaf} +SRCNAM=Treerecs +VERSION=${VERSION:-1.2} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} - -COMMIT=d1c1bfaf3e6f072436661c80346dee9ae54b3310 - -# Depending on whether you clicked or used wget to download, the tarball -# name is different. Bleh... -WGETNAME=archive -CLICKNAME=Treerecs-master +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -42,7 +41,11 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -66,15 +69,9 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $CLICKNAME-$COMMIT - -if [ -e $CWD/$WGETNAME.tar.gz ]; then - tar xvf $CWD/$WGETNAME.tar.gz -else - tar xvf $CWD/$CLICKNAME-$COMMIT.tar.gz -fi - -cd $CLICKNAME-$COMMIT +rm -rf $SRCNAM-v${VERSION} +tar xvf $CWD/$SRCNAM-v${VERSION}.tar.gz +cd $SRCNAM-v${VERSION} chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -82,17 +79,22 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; +# GCC 12 explicitly requires these +# https://stackoverflow.com/a/68149587 +sed -i "45i #include <limits>" ext/bpp/bpp-core/src/Bpp/Graph/GlobalGraph.cpp +sed -i "26i #include <utility>" src/treerecs/containers/AbstractGrid.h + mkdir -p build cd build cmake \ -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ - -DCMAKE_BUILD_TYPE=MinSizeRel .. + -DCMAKE_BUILD_TYPE=Release .. make cd .. # This is the program executable. Using "make install DESTDIR=$PKG" -# works, but is simply puts the treerecs in /usr/local/bin and that's it +# works, but it simply puts treerecs in /usr/local/bin and that's it install -D -m755 build/bin/$PRGNAM $PKG/usr/bin/$PRGNAM # Include the extra binaries @@ -115,6 +117,7 @@ cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/treerecs/treerecs.info b/academic/treerecs/treerecs.info index 12feb2eed3..f6a81aa05b 100644 --- a/academic/treerecs/treerecs.info +++ b/academic/treerecs/treerecs.info @@ -1,8 +1,8 @@ PRGNAM="treerecs" -VERSION="1.1_gitd1c1bfaf" +VERSION="1.2" HOMEPAGE="https://project.inria.fr/treerecs/" -DOWNLOAD="https://gitlab.inria.fr/Phylophile/Treerecs/repository/archive.tar.gz" -MD5SUM="1a378daca947481f08071b51950e021e" +DOWNLOAD="https://gitlab.inria.fr/Phylophile/Treerecs/-/archive/v1.2/Treerecs-v1.2.tar.gz" +MD5SUM="a85d2dc0047278bfb0017c2b69824b56" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/treeviewx/treeviewx.SlackBuild b/academic/treeviewx/treeviewx.SlackBuild index 5929e48f2d..fbb5126bc7 100644 --- a/academic/treeviewx/treeviewx.SlackBuild +++ b/academic/treeviewx/treeviewx.SlackBuild @@ -1,11 +1,11 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for treeviewx # Renamed to from "treeview" to "treeviewx" in 2018 to avoid confusion # with Michael Eisen's TreeView for matrix-like display of expression data. -# Copyright 2011-2020 Petar Petrov slackalaxy@gmail.com +# Copyright 2011-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,6 +25,8 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=treeviewx SRCNAM=tv SRCVER=0.5 @@ -32,6 +34,7 @@ VERSION=${VERSION:-0.5.1_20100723} SRCDATE=20100823 BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -41,7 +44,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -121,4 +131,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/treeviewx/treeviewx.info b/academic/treeviewx/treeviewx.info index 8de22d44fb..14ab2567b3 100644 --- a/academic/treeviewx/treeviewx.info +++ b/academic/treeviewx/treeviewx.info @@ -1,7 +1,7 @@ PRGNAM="treeviewx" VERSION="0.5.1_20100723" HOMEPAGE="https://github.com/rdmpage" -DOWNLOAD="http://deb.debian.org/debian/pool/main/t/treeviewx/treeviewx_0.5.1+20100823.orig.tar.gz" +DOWNLOAD="https://slackware.uk/sbosrcarch/by-name/academic/treeviewx/treeviewx_0.5.1+20100823.orig.tar.gz" MD5SUM="8059a306b723e6fb4d3befcf302b2920" DOWNLOAD_x86_64="" MD5SUM_x86_64="" diff --git a/academic/trfind/trfind.SlackBuild b/academic/trfind/trfind.SlackBuild index 76783294e3..245927edac 100644 --- a/academic/trfind/trfind.SlackBuild +++ b/academic/trfind/trfind.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for trfind -# Copyright 2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2018-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,54 +22,97 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=trfind -VERSION=${VERSION:-4.09} -BUILD=${BUILD:-2} +VERSION=${VERSION:-4.09.1} +BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} -SRCNAM=trf -BINVER=409 +SRCNAM=TRF if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i386 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -set -e - -if [ "$ARCH" != "i386" ] && [ "$ARCH" != "x86_64" ]; then - printf "\n\n$ARCH is not supported... \n" - exit 1 -fi - -# Determine binary architecture -if [ "$ARCH" = "x86_64" ]; then - BINARCH="linux64" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" else - BINARCH="linux32" + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" fi +set -e + rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP +rm -rf $SRCNAM-$VERSION +tar xvf $CWD/$SRCNAM-$VERSION.tar.gz +cd $SRCNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +CFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --mandir=/usr/man \ + --docdir=/usr/doc/$PRGNAM-$VERSION \ + --build=$ARCH-slackware-linux + +make + +# "make install" works, but it is simpler this way +install -D -m755 src/trf $PKG/usr/bin/trf + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true -install -D -m755 $CWD/${SRCNAM}${BINVER}.${BINARCH} $PKG/usr/bin/$SRCNAM +# Include FASTA examples, but let's compress the file first +mkdir -p $PKG/usr/share/$PRGNAM +gzip test_seqs.fasta +cp test_seqs.fasta.gz $PKG/usr/share/$PRGNAM mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + README.md COPYING INSTALL history.txt \ + $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References -cat $CWD/LICENSE > $PKG/usr/doc/$PRGNAM-$VERSION/LICENSE mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/trfind/trfind.info b/academic/trfind/trfind.info index 2dfb07986d..adaf4da150 100644 --- a/academic/trfind/trfind.info +++ b/academic/trfind/trfind.info @@ -1,10 +1,10 @@ PRGNAM="trfind" -VERSION="4.09" +VERSION="4.09.1" HOMEPAGE="https://tandem.bu.edu/trf/trf.html" -DOWNLOAD="http://tandem.bu.edu/trf/downloads/trf409.linux32" -MD5SUM="285478f16f417d6e9c9700f556373e43" -DOWNLOAD_x86_64="http://tandem.bu.edu/trf/downloads/trf409.linux64" -MD5SUM_x86_64="0c594fe666e0332db1df9d160d7fabc8" +DOWNLOAD="https://github.com/Benson-Genomics-Lab/TRF/archive/v4.09.1/TRF-4.09.1.tar.gz" +MD5SUM="8569300f69776b65e22ad12caa682ab8" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" REQUIRES="" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/trimmomatic/trimmomatic.SlackBuild b/academic/trimmomatic/trimmomatic.SlackBuild index 1ed26bf60e..6f901f5be1 100644 --- a/academic/trimmomatic/trimmomatic.SlackBuild +++ b/academic/trimmomatic/trimmomatic.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for trimmomatic -# Copyright trimmomatic Petar Petrov slackalaxy@gmail.com +# Copyright 2020-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,15 +22,25 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=trimmomatic ZIPNAM=Trimmomatic -VERSION=${VERSION:-0.38} +VERSION=${VERSION:-0.39} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} ARCH=noarch -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -64,4 +74,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/trimmomatic/trimmomatic.info b/academic/trimmomatic/trimmomatic.info index b16aab676e..9572a0f8fb 100644 --- a/academic/trimmomatic/trimmomatic.info +++ b/academic/trimmomatic/trimmomatic.info @@ -1,10 +1,10 @@ PRGNAM="trimmomatic" -VERSION="0.38" +VERSION="0.39" HOMEPAGE="http://www.usadellab.org/cms/?page=trimmomatic" -DOWNLOAD="http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.38.zip" -MD5SUM="4b3df3caf7fe803ca54c79db1a99c464" +DOWNLOAD="http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.39.zip" +MD5SUM="271ed9dca91132eee0c960e0ae487bcd" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="jdk" +REQUIRES="zulu-openjdk11" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmailc.com" diff --git a/academic/tuxmath/0001-src-menu_lan.c-Remove-unused-duplicate-lan_player_in.patch b/academic/tuxmath/0001-src-menu_lan.c-Remove-unused-duplicate-lan_player_in.patch new file mode 100644 index 0000000000..ee192e9470 --- /dev/null +++ b/academic/tuxmath/0001-src-menu_lan.c-Remove-unused-duplicate-lan_player_in.patch @@ -0,0 +1,26 @@ +From c471e2a94798787afbad4e547a1e2485ef9835db Mon Sep 17 00:00:00 2001 +From: Adrian Bunk <bunk@debian.org> +Date: Sun, 3 Jan 2021 14:22:29 +0200 +Subject: src/menu_lan.c: Remove unused duplicate lan_player_info definition + +This broke the build with gcc 10: +https://bugs.debian.org/976513 +--- + src/menu_lan.c | 1 - + 1 file changed, 1 deletion(-) + +diff --git a/src/menu_lan.c b/src/menu_lan.c +index 4512eb1..d85f2c6 100644 +--- a/src/menu_lan.c ++++ b/src/menu_lan.c +@@ -37,7 +37,6 @@ along with this program. If not, see <http://www.gnu.org/licenses/>. */ + + + /* lan_player_type now defined in network.h */ +-lan_player_type lan_player_info[MAX_CLIENTS]; + + /* Local function prototypes: ------------------- */ + void draw_player_table(void); +-- +2.20.1 + diff --git a/academic/tuxmath/0002-rename-blits-to-tmblits.patch b/academic/tuxmath/0002-rename-blits-to-tmblits.patch new file mode 100644 index 0000000000..c5b5108acf --- /dev/null +++ b/academic/tuxmath/0002-rename-blits-to-tmblits.patch @@ -0,0 +1,54 @@ +Bug-Debian: https://bugs.debian.org/986623 +Forwarded: no +Last-Update: 2021-04-20 + +--- tuxmath-2.0.3.orig/src/titlescreen.c ++++ tuxmath-2.0.3/src/titlescreen.c +@@ -55,7 +55,7 @@ struct blit { + SDL_Rect *srcrect; + SDL_Rect *dstrect; + unsigned char type; +-} blits[MAX_UPDATES]; ++} tmblits[MAX_UPDATES]; + + // Lessons available for play + char **lesson_list_titles = NULL; +@@ -1019,8 +1019,8 @@ void init_blits(void) { + int i; + + for (i = 0; i < MAX_UPDATES; ++i) { +- blits[i].srcrect = &srcupdate[i]; +- blits[i].dstrect = &dstupdate[i]; ++ tmblits[i].srcrect = &srcupdate[i]; ++ tmblits[i].dstrect = &dstupdate[i]; + } + } + +@@ -1032,14 +1032,14 @@ void update_screen(int *frame) { + + /* -- First erase everything we need to -- */ + for (i = 0; i < numupdates; i++) +- if (blits[i].type == 'E') +- SDL_LowerBlit(blits[i].src, blits[i].srcrect, screen, blits[i].dstrect); ++ if (tmblits[i].type == 'E') ++ SDL_LowerBlit(tmblits[i].src, tmblits[i].srcrect, screen, tmblits[i].dstrect); + // SNOW_erase(); + + /* -- then draw -- */ + for (i = 0; i < numupdates; i++) +- if (blits[i].type == 'D') +- SDL_BlitSurface(blits[i].src, blits[i].srcrect, screen, blits[i].dstrect); ++ if (tmblits[i].type == 'D') ++ SDL_BlitSurface(tmblits[i].src, tmblits[i].srcrect, screen, tmblits[i].dstrect); + // SNOW_draw(); + + /* -- update the screen only where we need to! -- */ +@@ -1067,7 +1067,7 @@ void add_rect(SDL_Rect* src, SDL_Rect* d + return; + } + +- update = &blits[numupdates++]; ++ update = &tmblits[numupdates++]; + + update->srcrect->x = src->x; + update->srcrect->y = src->y; diff --git a/academic/tuxmath/README b/academic/tuxmath/README index 6f0d31eb6c..c41e37853f 100644 --- a/academic/tuxmath/README +++ b/academic/tuxmath/README @@ -1,4 +1,4 @@ -"Tux, of Math Command" (aka. tuxmath) is a math drill game starring Tux, -the Linux Penguin. Lessons are included from simple number typing through -addition, subtraction, multiplication, and division of positive and -negative numbers. It is intended for kids ~4-10. +"Tux, of Math Command" (aka. tuxmath) is a math drill game starring +Tux, the Linux Penguin. Lessons are included from simple number typing +through addition, subtraction, multiplication, and division of positive +and negative numbers. It is intended for kids ~4-10. diff --git a/academic/tuxmath/tuxmath.SlackBuild b/academic/tuxmath/tuxmath.SlackBuild index 21f4afe6e3..8128007c5e 100644 --- a/academic/tuxmath/tuxmath.SlackBuild +++ b/academic/tuxmath/tuxmath.SlackBuild @@ -1,29 +1,39 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for tuxmath # Written by Larry Hajali <larryhaja[at]gmail[dot]com> +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=tuxmath VERSION=${VERSION:-2.0.3} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" elif [ "$ARCH" = "x86_64" ]; then @@ -48,7 +58,11 @@ find -L . \ # Fix .desktop. sed -i -e '/^##/d' -e '/^X/d' -e 's|Math;||' $PRGNAM.desktop -CFLAGS="$SLKCFLAGS" \ +patch -p1 < $CWD/0001-src-menu_lan.c-Remove-unused-duplicate-lan_player_in.patch +patch -p1 < $CWD/0002-rename-blits-to-tmblits.patch + +LDFLAGS="-std=gnu11" \ +CFLAGS="$SLKCFLAGS -std=gnu11 -fcommon" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ --prefix=/usr \ @@ -80,4 +94,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/tuxtype2/tuxtype2.SlackBuild b/academic/tuxtype2/tuxtype2.SlackBuild index c4db983a51..ad7e5240be 100644 --- a/academic/tuxtype2/tuxtype2.SlackBuild +++ b/academic/tuxtype2/tuxtype2.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for Tux Typing 2 @@ -22,27 +22,37 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=tuxtype2 VERSION=${VERSION:-1.8.1} SRCPATH=tuxtype_w_fonts BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -95,4 +105,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/ucsc-blat/ucsc-blat.SlackBuild b/academic/ucsc-blat/ucsc-blat.SlackBuild index c2a01b480f..5529adc0ac 100644 --- a/academic/ucsc-blat/ucsc-blat.SlackBuild +++ b/academic/ucsc-blat/ucsc-blat.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for ucsc-blat -# Copyright 2013-2016 Petar Petrov slackalaxy@gmail.com +# Copyright 2013-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,33 +22,42 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=ucsc-blat VERSION=${VERSION:-34} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} SRCNAM=blatSuite if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i386 ;; - arm*) ARCH=arm ;; + i?86) ARCH=i586 ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +if ! [ "$ARCH" = "x86_64" ] && ! [[ $ARCH =~ i?86 ]]; then + printf "\n\n$ARCH is not supported... \n" + exit 1 +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} set -e -if [ "$ARCH" != "i386" ] && [ "$ARCH" != "x86_64" ]; then - printf "\n\n$ARCH is not supported... \n" - exit 1 -fi - rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP @@ -90,4 +99,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/ucsc-blat/ucsc-blat.info b/academic/ucsc-blat/ucsc-blat.info index c2b6884091..6f97e59c99 100644 --- a/academic/ucsc-blat/ucsc-blat.info +++ b/academic/ucsc-blat/ucsc-blat.info @@ -1,9 +1,9 @@ PRGNAM="ucsc-blat" VERSION="34" HOMEPAGE="https://users.soe.ucsc.edu/~kent/" -DOWNLOAD="http://hgwdev.cse.ucsc.edu/~kent/exe/linux/blatSuite.34.zip" +DOWNLOAD="https://hgwdev.cse.ucsc.edu/~kent/exe/linux/blatSuite.34.zip" MD5SUM="ec9fbe02fed2f15051893001da5db767" -DOWNLOAD_x86_64="http://hgwdev.cse.ucsc.edu/~kent/exe/opteron/blatSuite.34.zip" +DOWNLOAD_x86_64="https://hgwdev.cse.ucsc.edu/~kent/exe/opteron/blatSuite.34.zip" MD5SUM_x86_64="bf9042aa85a04ce85b24cef11011faee" REQUIRES="" MAINTAINER="Petar Petrov" diff --git a/academic/ugene/README b/academic/ugene/README index a75fc649e8..181b318651 100644 --- a/academic/ugene/README +++ b/academic/ugene/README @@ -38,30 +38,27 @@ program. All of them are available at SlackBuilds.org: - bowtie2 (A tool for aligning sequencing reads) - bwa (Burrows-Wheeler Aligner) - cap3 (CAP3: A DNA sequence assembly program) -- cistrome-CEAS (CEAS: Cis-regulatory Element Annotation System) -- cistrome-conductGO (Find the top-n highest expressed TFs) -- cistrome-extra (Cistrome Applications Harvard extra apps) -- cistrome-MACS (MACS: Model-based Analysis of ChIP-Seq) -- cistrome-mdseqpos (Cistrome Applications Harvard mdseqpos) -- clark-ugene (Ugene's forked CLAssifier based on Reduced K-mers) - clustalo (Clustal Omega) - clustalw (Multiple Sequence Alignment) - cufflinks (A reference-guided assembler for RNA-Seq experiments) - cutadapt (Trim adapters from high-throughput sequencing reads) -- diamond (A sequence aligner for protein and translated DNA) - fastqc (A quality control tool for high throughput sequence data) +- FastTree (Infers approximately-ML phylogenetic trees) - HMMER (Biosequence analysis using profile hidden Markov models) -- kraken (Assign taxonomic labels to short DNA sequences) +- iqtree (Efficient and versatile phylogenomic software by ML) +- kalign (A fast multiple sequence alignment program) - MetaPhlAn2 (Metagenomic Phylogenetic Analysis) -- ncbi-blast (BLAST: Basic Local Alignment Search Tool) +- mafft (A multiple sequence alignment program) +- mrbayes (MrBayes: Bayesian Inference of Phylogeny) - ncbi-blast+ (BLAST+ Command Line Applications) - PhyML (Phylogenetic estimation using Maximum Likelihood) - samtools-legacy (Sequence Alignment/Map Tools) - snpEff (Genetic variant annotation and effect prediction toolbox) - spades (SPAdes Genome Assembler) - spidey (mRNA-to-genomic alignment) +- stringtie (Assembler of RNA-Seq alignments) - t_coffee (A multiple sequence alignment program) -- tabix-legacy (Generic indexer for TAB-delimited genome position files ) +- tabix-legacy (Generic indexer for TAB-delimited genome position files) - tophat (Splice junction mapper for RNA-Seq reads) - trimmomatic (A flexible read trimming tool for Illumina NGS data) - vcftools (A program package designed for working with VCF files) diff --git a/academic/ugene/ugene.SlackBuild b/academic/ugene/ugene.SlackBuild index c9c8a749b1..3a6f9ff280 100644 --- a/academic/ugene/ugene.SlackBuild +++ b/academic/ugene/ugene.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for ugene -# Copyright 2013-2020 Petar Petrov slackalaxy@gmail.com +# Copyright 2013-2023 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=ugene -VERSION=${VERSION:-33.0} +VERSION=${VERSION:-48.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,11 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -74,21 +81,52 @@ find -L . \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; # Fix libraries and man pages paths -sed -i "s:/lib:/lib${LIBDIRSUFFIX}:g" src/ugene_globals.pri -sed -i "s:/share/man:/man:g" src/ugene_globals.pri +#sed -i "s:/lib:/lib${LIBDIRSUFFIX}:g" src/ugene_globals.pri +#sed -i "s:/share/man:/man:g" src/ugene_globals.pri +#sed -i "s:Werror=maybe-uninitialized:Wno-error=maybe-uninitialized:g +# s:Werror=uninitialized:Wno-error=uninitialized:g" \ +# src/ugene_globals.pri + +qmake-qt5 $QMAKECONFIG -r PREFIX=/usr/lib${LIBDIRSUFFIX}/$PRGNAM \ +QMAKE_CFLAGS="$SLKCFLAGS" \ +QMAKE_CXXFLAGS="$SLKCFLAGS -std=c++11" \ +UGENE_EXCLUDE_LIST_ENABLED=1 +make -qmake-qt5 $QMAKECONFIG -r \ +# Apparently, this has to be done twice to generate the right installation files +# https://github.com/ugeneunipro/ugene/issues/683#issuecomment-1046370388 +qmake-qt5 $QMAKECONFIG -r PREFIX=/usr/lib${LIBDIRSUFFIX}/$PRGNAM \ QMAKE_CFLAGS="$SLKCFLAGS" \ -QMAKE_CXXFLAGS="$SLKCFLAGS" +QMAKE_CXXFLAGS="$SLKCFLAGS -std=c++11" \ +UGENE_EXCLUDE_LIST_ENABLED=1 make + make install INSTALL_ROOT=$PKG +mkdir -p $PKG/usr/share/{applications,pixmaps} +mv $PKG/usr/lib${LIBDIRSUFFIX}/$PRGNAM/$PRGNAM.desktop $PKG/usr/share/applications +mv $PKG/usr/lib${LIBDIRSUFFIX}/$PRGNAM/$PRGNAM.png $PKG/usr/share/pixmaps + +mkdir -p $PKG/usr/man/man1 +mv $PKG/usr/lib${LIBDIRSUFFIX}/$PRGNAM/$PRGNAM.1.gz $PKG/usr/man/man1 + +mkdir -p $PKG/usr/bin +cd $PKG/usr/bin +ln -s ../lib${LIBDIRSUFFIX}/$PRGNAM/$PRGNAM . +cd - + +# Do not associate with my fasta files... +sed -i '/MimeType/d' $PKG/usr/share/applications/$PRGNAM.desktop + +# use just one categiry +sed -i "s:Education;Science:Education:" $PKG/usr/share/applications/$PRGNAM.desktop + find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - build.txt README.md LICENSE.txt LICENSE.3rd_party.txt \ + README.md LICENSE.txt LICENSE.3rd_party.txt \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild @@ -98,4 +136,4 @@ cat $CWD/doinst.sh > $PKG/install/doinst.sh cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/ugene/ugene.info b/academic/ugene/ugene.info index 6bacb212b0..8f9bf4bdf6 100644 --- a/academic/ugene/ugene.info +++ b/academic/ugene/ugene.info @@ -1,10 +1,10 @@ PRGNAM="ugene" -VERSION="33" +VERSION="48.1" HOMEPAGE="http://ugene.net/" -DOWNLOAD="https://github.com/ugeneunipro/ugene/archive/33.0/ugene-33.0.tar.gz" -MD5SUM="d4314b2294d0bd48c26deba7101250e3" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="qt5-webkit" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="https://github.com/ugeneunipro/ugene/archive/48.1/ugene-48.1.tar.gz" +MD5SUM_x86_64="5662a9e58d6ad19a8be7410f12139072" +REQUIRES="" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/umfpack/README b/academic/umfpack/README index 954cb8b964..921b1dcd4b 100644 --- a/academic/umfpack/README +++ b/academic/umfpack/README @@ -3,12 +3,16 @@ systems, Ax=b, using the Unsymmetric MultiFrontal method. This package is part of SuiteSparse. -This requires a BLAS implementation. Choose one of these package sets: +This requires a BLAS implementation. Choose one of these package +sets: + * OpenBLAS * atlas * blas (the Netlib reference implementation) -If more than one set is installed (assuming there are no packaging conflicts) -then the auto-detection will use the first implementation from this list that -it finds. If in doubt, choose the Netlib reference implementations; other -packages that require a BLAS or LAPACK implementation may not build if they -are not configured to detect/use alternate implementations. + +If more than one set is installed (assuming there are no packaging +conflicts) then the auto-detection will use the first implementation +from this list that it finds. If in doubt, choose the Netlib reference +implementations; other packages that require a BLAS or LAPACK +implementation may not build if they are not configured to detect/use +alternate implementations. diff --git a/academic/umfpack/patches/autoconfiscate.diff b/academic/umfpack/patches/autoconfiscate.diff index b902c15281..de66ade417 100644 --- a/academic/umfpack/patches/autoconfiscate.diff +++ b/academic/umfpack/patches/autoconfiscate.diff @@ -866,7 +866,7 @@ diff --git a/m4/ax_blas.m4 b/m4/ax_blas.m4 new file mode 100644 --- /dev/null +++ b/m4/ax_blas.m4 -@@ -0,0 +1,238 @@ +@@ -0,0 +1,241 @@ +# =========================================================================== +# https://www.gnu.org/software/autoconf-archive/ax_blas.html +# =========================================================================== @@ -905,6 +905,7 @@ new file mode 100644 +# LICENSE +# +# Copyright (c) 2008 Steven G. Johnson <stevenj@alum.mit.edu> ++# Copyright (c) 2019 Geoffrey M. Oxberry <goxberry@gmail.com> +# +# This program is free software: you can redistribute it and/or modify it +# under the terms of the GNU General Public License as published by the @@ -932,7 +933,7 @@ new file mode 100644 +# modified version of the Autoconf Macro, you may extend this special +# exception to the GPL to apply to your modified version as well. + -+#serial 16 ++#serial 17 + +AU_ALIAS([ACX_BLAS], [AX_BLAS]) +AC_DEFUN([AX_BLAS], [ @@ -946,7 +947,9 @@ new file mode 100644 +case $with_blas in + yes | "") ;; + no) ax_blas_ok=disable ;; -+ -* | */* | *.a | *.so | *.so.* | *.o) BLAS_LIBS="$with_blas" ;; ++ -* | */* | *.a | *.so | *.so.* | *.dylib | *.dylib.* | *.o) ++ BLAS_LIBS="$with_blas" ++ ;; + *) BLAS_LIBS="-l$with_blas" ;; +esac + diff --git a/academic/umfpack/umfpack.SlackBuild b/academic/umfpack/umfpack.SlackBuild index c87f06711a..3da82b0df8 100644 --- a/academic/umfpack/umfpack.SlackBuild +++ b/academic/umfpack/umfpack.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for UMFPACK -# Copyright 2013-2020 Kyle Guinn <elyk03@gmail.com> +# Copyright 2013-2021 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,13 +22,16 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=umfpack SRCNAM=SuiteSparse SUBDIR=UMFPACK VERSION=${VERSION:-5.7.9} -SRCVER=${SRCVER:-5.6.0} -BUILD=${BUILD:-1} +SRCVER=${SRCVER:-5.8.1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$(uname -m)" in @@ -38,15 +41,22 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM-$VERSION +PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="README.txt Doc/ChangeLog Doc/License.txt Doc/gpl.txt" -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" @@ -111,4 +121,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/umfpack/umfpack.info b/academic/umfpack/umfpack.info index 283dfdc4cb..003572719c 100644 --- a/academic/umfpack/umfpack.info +++ b/academic/umfpack/umfpack.info @@ -1,10 +1,10 @@ PRGNAM="umfpack" VERSION="5.7.9" HOMEPAGE="http://faculty.cse.tamu.edu/davis/suitesparse.html" -DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.6.0/SuiteSparse-5.6.0.tar.gz" -MD5SUM="af8b97cbded4cd5c6672e878bc0c37c2" +DOWNLOAD="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.8.1/SuiteSparse-5.8.1.tar.gz" +MD5SUM="c414679bbc9432a3def01b31ad921140" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="blas suitesparseconfig amd cholmod" +REQUIRES="cholmod" MAINTAINER="Kyle Guinn" EMAIL="elyk03@gmail.com" diff --git a/academic/units/doinst.sh b/academic/units/doinst.sh new file mode 100644 index 0000000000..40e776ac68 --- /dev/null +++ b/academic/units/doinst.sh @@ -0,0 +1,3 @@ +if [ -x /usr/bin/install-info ]; then + /usr/bin/install-info --info-dir=usr/info usr/info/units.info.gz 1> /dev/null 2>&1 +fi diff --git a/academic/units/douninst.sh b/academic/units/douninst.sh new file mode 100644 index 0000000000..0273142e5c --- /dev/null +++ b/academic/units/douninst.sh @@ -0,0 +1,9 @@ +if [ -x /usr/bin/install-info -a -d usr/info ]; then + ( + cd usr/info + rm -f dir + for i in *.info*; do + /usr/bin/install-info $i dir 1>/dev/null 2>&1 + done + ) +fi diff --git a/academic/units/units.SlackBuild b/academic/units/units.SlackBuild index 3897551a24..e9586ecb36 100644 --- a/academic/units/units.SlackBuild +++ b/academic/units/units.SlackBuild @@ -1,9 +1,9 @@ -#!/bin/sh +#!/bin/bash # vim: et ts=2 sw=2 # Slackware build script for gnu units -# Copyright (c) 2010 Gregory J.L. Tourte <artourter@gmail.com> +# Copyright (c) 2010-2024 Gregory J. L. Tourte <artourter@gmail.com> # Previously maintained by Yalla-One <yallaone@gmail.com> # All rights reserved. # @@ -24,10 +24,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=units -VERSION=${VERSION:-2.19} +VERSION=${VERSION:-2.23} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -37,7 +40,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -66,11 +76,10 @@ tar xvf $CWD/$PRGNAM-$VERSION.tar.gz cd $PRGNAM-$VERSION chown -R root:root . find -L . \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + -perm /111 -a \! -perm 755 -a -exec chmod 755 {} + -o \ + \! -perm /111 -a \! -perm 644 -a -exec chmod 644 {} + +PYTHON=/usr/bin/python3 \ CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ @@ -81,9 +90,11 @@ CXXFLAGS="$SLKCFLAGS" \ --infodir=/usr/info \ --localstatedir=/var \ --datadir=/usr/share \ + --sharedstatedir=/usr/share \ --build=$ARCH-slackware-linux make +make units_cur_inst make install DESTDIR=$PKG find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ @@ -96,11 +107,13 @@ rm -f $PKG/usr/info/dir gzip -9 $PKG/usr/info/*.info* mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a INSTALL COPYING ChangeLog NEWS README $PKG/usr/doc/$PRGNAM-$VERSION +cp -a COPYING NEWS README units.pdf $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install -cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh +cat $CWD/douninst.sh > $PKG/install/douninst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/units/units.info b/academic/units/units.info index 679d03f203..cab93752fb 100644 --- a/academic/units/units.info +++ b/academic/units/units.info @@ -1,8 +1,8 @@ PRGNAM="units" -VERSION="2.19" +VERSION="2.23" HOMEPAGE="https://www.gnu.org/software/units/" -DOWNLOAD="https://ftpmirror.gnu.org/units/units-2.19.tar.gz" -MD5SUM="f38468b31a55baa926b449dfdaacc8aa" +DOWNLOAD="https://ftpmirror.gnu.org/units/units-2.23.tar.gz" +MD5SUM="2cb4f754dcde5b2409e656f5d8d4a474" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="Unidecode" diff --git a/academic/vCAPS_coevolution/01_caps_verbose.patch b/academic/vCAPS_coevolution/01_caps_verbose.patch new file mode 100644 index 0000000000..7f64d80f34 --- /dev/null +++ b/academic/vCAPS_coevolution/01_caps_verbose.patch @@ -0,0 +1,114 @@ +diff -pruN orig/caps.cpp new/caps.cpp +--- orig/caps.cpp 2012-12-15 17:13:23.000000000 +0200 ++++ new/caps.cpp 2020-09-09 23:07:46.080566000 +0300 +@@ -14,7 +14,7 @@ + #include <gsl/gsl_statistics.h> + #include<sys/time.h> + #include<iomanip> +- ++#include <bits/stdc++.h> + + + +@@ -69,6 +69,8 @@ + const gsl_rng_type * T; + gsl_rng *r; + ++vector<double> totaltempnew; ++double alphathresh = 0; + int main(int argc, char *argv[]){ + + +@@ -543,16 +545,27 @@ int main(int argc, char *argv[]){ + + + print_splash(output); ++ OUTPUT << "\n\File1: " << files[i] << endl; + vec1.print_to_fasta(output.c_str()); ++ OUTPUT << "\n\nFile2: " << files[j] << endl; + vec2.print_to_fasta(output.c_str()); + int length1 = vec1.sequences[0].length(); + int length2 = vec2.sequences[0].length(); + ++ OUTPUT << "\n\nLength1: " << length1 << endl; ++ OUTPUT << "Length2: " << length2 << endl; + + + if(tree_in ==0){ + tree1 = create_input_tree(vec1.names, vec1.sequences); + tree2 = create_input_tree(vec2.names, vec2.sequences); ++ ++ // Output the CAPS generated trees to the .out file of each pair ++ string temptre1 = TreeTemplateTools::treeToParenthesis(*tree1, true); ++ string temptre2 = TreeTemplateTools::treeToParenthesis(*tree2, true); ++ OUTPUT << "\n" << endl; ++ OUTPUT << "CAPS generated tree 1: " << temptre1 << endl; ++ OUTPUT << "CAPS generated tree 2: " << temptre2 << endl; + }/*else if(tree_in ==1 && variable==1){ + + std::auto_ptr<DistanceMatrix> DS; +@@ -666,6 +679,7 @@ int main(int argc, char *argv[]){ + int value = floor(((totaltemp.size())*(1-(threshval))))+1; + + threshold = totaltemp[value]; ++ totaltempnew = totaltemp; + + + /*=======================================================*/ +@@ -870,6 +884,30 @@ int Chi_squared (int num_pairs, int num_ + + } /* ----- end of function Chi_squared ----- */ + ++/* ++ * === FUNCTION ====================================================================== ++ * Name: find_alpha ++ * Description: Find the index of an element in a vector totaltemp ++ * Help from: https://www.geeksforgeeks.org/how-to-find-index-of-a-given-element-in-a-vector-in-cpp/ ++ * https://stackoverflow.com/questions/8647635/elegant-way-to-find-closest-value-in-a-vector-from-above ++ * Author: Petar Petrov, University of Turku (Finland); pebope@utu.fi ++ * ===================================================================================== ++ */ ++double getIndex(std::vector<double> const& v, double K) ++{ ++ auto const it = std::lower_bound(v.begin(), v.end(), fabs(K)); ++ //auto it = std::upper_bound(v.begin(), v.end(), fabs(K)); ++ ++ if (it != v.end()) { ++ int index = distance(v.begin(), it); ++ alphathresh = (((int)1+(double)v.size()-(int)index)/(double)v.size()); ++ return alphathresh; ++ //cerr << index << "\t" << alphathresh << endl; ++ } ++ else { ++ cerr << "ELEMENT NOT FOUND!" << endl; ++ } ++} + + + +@@ -890,9 +928,9 @@ int print_inter(vector<double>& Correl1, + output << endl << endl; + + output << "Coevolving Pairs of amino acid sites\n"; +- output << "=============================================================================\n"; +- output << "Col1(real)\tCol2(real)\tDmean1\t\tDmean2\t\tCorrelation\tBootstrap value\n\n"; +- output << "=============================================================================\n"; ++ output << "================================================================================================================================\n"; ++ output << "Col1(real)\tCol2(real)\tDmean1\t\tDmean2\t\tCorrelation\tBootstrap value\tP-value1\tP-value2\tMean P-value\tCorrelation1\tCorrelation2\n\n"; ++ output << "================================================================================================================================\n"; + + //double mean = average_vec<double>(Correl); + //double SD = SD_vf(Correl, mean); +@@ -951,9 +989,11 @@ int print_inter(vector<double>& Correl1, + + // } + ++ double Alpha1 = getIndex(totaltempnew, Correl1[cor]); ++ double Alpha2 = getIndex(totaltempnew, Correl2[cor]); + //if(bootval>=bootcut && re1<=8 && re2<=8 ){ + if(bootval>=bootcut){ +- output << i+1 << "(" << i-gaps1+1 << ")\t\t" << j+1 << "(" << (j+1)-gaps2 << ")\t\t" << averDi << "\t\t" << averDj << "\t\t" << (Correl1[cor]+Correl2[cor])/2 << "\t" << bootval << endl; ++ output << i+1 << "(" << i-gaps1+1 << ")\t\t" << j+1 << "(" << (j+1)-gaps2 << ")\t\t" << averDi << "\t\t" << averDj << "\t" << (Correl1[cor]+Correl2[cor])/2 << "\t" << bootval << "\t" << Alpha1 << "\t" << Alpha2 << "\t" << (Alpha1+Alpha2)/2 << "\t" << Correl1[cor] << "\t" << Correl2[cor] << endl; + signif.push_back(((Correl1[cor]+Correl2[cor])/2)); + ++pairs; + vector<int> tem; diff --git a/academic/vCAPS_coevolution/02_caps_sort_input.patch b/academic/vCAPS_coevolution/02_caps_sort_input.patch new file mode 100644 index 0000000000..917bca7cab --- /dev/null +++ b/academic/vCAPS_coevolution/02_caps_sort_input.patch @@ -0,0 +1,38 @@ +diff -pruN old/caps.cpp new/caps.cpp +--- old/caps.cpp 2022-01-20 09:30:24.409886691 +0200 ++++ new/caps.cpp 2022-01-20 09:39:10.669845265 +0200 +@@ -1,4 +1,5 @@ + #include<iostream> ++#include <algorithm> + #include<fstream> + #include"BCFasta.h" + #include"file_manip.h" +@@ -15,7 +16,7 @@ + #include<sys/time.h> + #include<iomanip> + #include <bits/stdc++.h> +- ++#include <vector> + + + #include <Seq/SequenceApplicationTools.h> +@@ -69,6 +70,10 @@ + const gsl_rng_type * T; + gsl_rng *r; + ++// make sure filenames are sorted! ++// https://stackoverflow.com/a/34757557 ++bool compareFunction (std::string a, std::string b) {return a<b;} ++ + vector<double> totaltempnew; + double alphathresh = 0; + int main(int argc, char *argv[]){ +@@ -189,6 +194,8 @@ int main(int argc, char *argv[]){ + + vector<string> files; + files = Folder_to_vector(mystring.c_str()); ++ // make sure filenames are sorted! ++ std::sort(files.begin(),files.end(),compareFunction); + + Fasta_vector file; + file.ref_num=0; diff --git a/academic/vCAPS_coevolution/README b/academic/vCAPS_coevolution/README new file mode 100644 index 0000000000..b8b4a71a4b --- /dev/null +++ b/academic/vCAPS_coevolution/README @@ -0,0 +1,33 @@ +vCAPS: (verbose) Coevolution Analysis using Protein Sequences + +CAPS is aimed at measuring the coevolution between amino acid sites +belonging to the same protein (intra-molecular coevolution) or to two +functionally or physically interacting proteins (inter-molecular +coevolution). The Software implements an improved method to detect +intra-molecular coevolution as published in Genetics (Fares and Travers, +2006) and also inter-protein coevolution analysis. The improved scoring +of amino acid sites is obtained by maximum likelihood ancestral state +reconstruction along with simulations to assess significance. + +This is a modified version of "CAPS_coevolution", used in the AutoCoEv +pipeline: +https://github.com/mattilalab/autocoev + +It applies two _unofficial_ patches: +- 01_caps_verbose: makes the program output its generated trees, as well + as the p-value for each correlated amino acid pair +- 02_caps_sort_input: introduce a function to sort input file names + +The produced executable is called "vCAPS" and can be installed along +"caps" from CAPS_coevolution. Building CAPS from source requires the +Bio++ 1.9 suite libraries, but make sure the current versions of the +bppsuite (and its dependencies) are NOT installed at build time. + +Citing CAPS: +CAPS: coevolution analysis using protein sequences. Fares MA, McNally D. +Bioinformatics. 2006 Nov 15;22(22):2821-2. PMID: 17005535 + +The mathematical model has been described separately: +A novel method for detecting intramolecular coevolution: adding a +further dimension to selective constraints analyses. Fares MA, Travers +SA. Genetics. 2006 May;173(1):9-23. PMID: 16547113 diff --git a/academic/vCAPS_coevolution/References b/academic/vCAPS_coevolution/References new file mode 100644 index 0000000000..e8236cd282 --- /dev/null +++ b/academic/vCAPS_coevolution/References @@ -0,0 +1,14 @@ +If you use CAPS in your research, please include the following citations: + +CAPS: coevolution analysis using protein sequences. +Fares MA, McNally D. +Bioinformatics. 2006 Nov 15;22(22):2821-2. +PMID: 17005535 +https://www.ncbi.nlm.nih.gov/pubmed/17005535 + +The mathematical model has been described separately: +A novel method for detecting intramolecular coevolution: adding a further dimension to selective constraints analyses. +Fares MA, Travers SA. +Genetics. 2006 May;173(1):9-23. +PMID: 16547113 +https://www.ncbi.nlm.nih.gov/pubmed/16547113 diff --git a/academic/vCAPS_coevolution/slack-desc b/academic/vCAPS_coevolution/slack-desc new file mode 100644 index 0000000000..5cd78f0770 --- /dev/null +++ b/academic/vCAPS_coevolution/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +vCAPS_coevolution: vCAPS_coevolution (Coevolution Analysis using Protein Sequences) +vCAPS_coevolution: +vCAPS_coevolution: CAPS is aimed at measuring the coevolution between amino acid +vCAPS_coevolution: sites belonging to the same protein (intra-molecular coevolution) +vCAPS_coevolution: or to two functionally or physically interacting proteins (inter- +vCAPS_coevolution: molecular coevolution). In addition, a test which assesses +vCAPS_coevolution: whether two proteins are interacting is implemented. +vCAPS_coevolution: +vCAPS_coevolution: Home: http://bioinf.gen.tcd.ie/~faresm/software/software.html +vCAPS_coevolution: +vCAPS_coevolution: diff --git a/academic/vCAPS_coevolution/vCAPS_coevolution.SlackBuild b/academic/vCAPS_coevolution/vCAPS_coevolution.SlackBuild new file mode 100644 index 0000000000..f00aea698e --- /dev/null +++ b/academic/vCAPS_coevolution/vCAPS_coevolution.SlackBuild @@ -0,0 +1,129 @@ +#!/bin/bash + +# Slackware build script for vCAPS_coevolution + +# Copyright 2020-2022 Petar Petrov slackalaxy@gmail.com +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=vCAPS_coevolution +VERSION=${VERSION:-2.0_2UN} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +SRCNAM=caps +SRCVER=2.0 +BINNAM=vCAPS + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +LIBDIRPATH="-Wl,-rpath,/usr/lib${LIBDIRSUFFIX}/Bpp1.9" + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf ${SRCNAM}${SRCVER}_src +unzip $CWD/${SRCNAM}2_src.zip +cd ${SRCNAM}${SRCVER}_src +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +# This is needed for gcc in Slackware 14.2 +sed -i "s:CC=g++ -g:CC=g++-5 -g -std=c++11:" Makefile + +# Use our CFLAGS and the custom (legacy) lib path +sed -i "s:CFLAGS=:CFLAGS=$SLKCFLAGS $LIBDIRPATH:" Makefile + +# Find the legacy bpp libraries +sed -i "s:-lbpp-phyl:-L/usr/lib${LIBDIRSUFFIX}/Bpp1.9 -lbpp-phyl:g" Makefile +sed -i "s:-lbpp-numcalc:-L/usr/lib64${LIBDIRSUFFIX}/Bpp1.9 -lbpp-numcalc:g" Makefile +sed -i "s:-lbpp-utils:-L/usr/lib64${LIBDIRSUFFIX}/Bpp1.9 -lbpp-utils:g" Makefile +sed -i "s:-lbpp-seq:-L/usr/lib64${LIBDIRSUFFIX}/Bpp1.9 -lbpp-seq:g" Makefile + +# Rename the produced executable +sed -i "s:-o caps:-o $BINNAM:" Makefile + +# Use our patches +patch -p1 -i $CWD/01_caps_verbose.patch +patch -p1 -i $CWD/02_caps_sort_input.patch + +# we already specified g++-5 above, so no need for this +#source /etc/profile.d/gcc5.sh + +make all + +# Install the binary produced from our patched source, as "vCAPS" +install -D -m755 $BINNAM $PKG/usr/bin/$BINNAM + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/share/$PRGNAM +cp -a sample structures trees TLR1.fa.out $PKG/usr/share/$PRGNAM + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + caps_manual.pdf \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/vCAPS_coevolution/vCAPS_coevolution.info b/academic/vCAPS_coevolution/vCAPS_coevolution.info new file mode 100644 index 0000000000..48545099b1 --- /dev/null +++ b/academic/vCAPS_coevolution/vCAPS_coevolution.info @@ -0,0 +1,10 @@ +PRGNAM="vCAPS_coevolution" +VERSION="2.0_2UN" +HOMEPAGE="http://bioinf.gen.tcd.ie/caps/home.html" +DOWNLOAD="https://raw.githubusercontent.com/slackalaxy/sources/main/caps2_src.zip" +MD5SUM="0914007c32ed22a9cb8a47b55cd18a39" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="bpp1.9-phyl" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/vcftools/vcftools.SlackBuild b/academic/vcftools/vcftools.SlackBuild index 9a3bda873b..4f0ca9920f 100644 --- a/academic/vcftools/vcftools.SlackBuild +++ b/academic/vcftools/vcftools.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for vcftools -# Copyright 2013-2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2013-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=vcftools VERSION=${VERSION:-0.1.16} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -102,4 +112,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/velocyto/README b/academic/velocyto/README new file mode 100644 index 0000000000..24fd05629e --- /dev/null +++ b/academic/velocyto/README @@ -0,0 +1,2 @@ + Velocyto is a library for the analysis of RNA velocity. It includes +a command line tool and an analysis pipeline. diff --git a/academic/velocyto/slack-desc b/academic/velocyto/slack-desc new file mode 100644 index 0000000000..58988e9bed --- /dev/null +++ b/academic/velocyto/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +velocyto: velocyto (library for the analysis of RNA velocity) +velocyto: +velocyto: +velocyto: +velocyto: Velocyto is a library for the analysis of RNA velocity. It includes +velocyto: a command line tool and an analysis pipeline. +velocyto: +velocyto: +velocyto: +velocyto: +velocyto: diff --git a/academic/velocyto/velocyto.SlackBuild b/academic/velocyto/velocyto.SlackBuild new file mode 100644 index 0000000000..145f7344ee --- /dev/null +++ b/academic/velocyto/velocyto.SlackBuild @@ -0,0 +1,107 @@ +#!/bin/bash + +# Slackware build script for velocyto + +# Copyright 2023 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=velocyto +VERSION=${VERSION:-0.17.17} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +SRCNAM=$PRGNAM.py + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $SRCNAM-$VERSION +tar xvf $CWD/$SRCNAM-$VERSION.tar.gz +cd $SRCNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +python3 setup.py build +python3 setup.py install --root=$PKG + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + LICENSE doc \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/velocyto/velocyto.info b/academic/velocyto/velocyto.info new file mode 100644 index 0000000000..ea72fc71d8 --- /dev/null +++ b/academic/velocyto/velocyto.info @@ -0,0 +1,10 @@ +PRGNAM="velocyto" +VERSION="0.17.17" +HOMEPAGE="https://velocyto.org" +DOWNLOAD="https://github.com/velocyto-team/velocyto.py/archive/0.17.17/velocyto.py-0.17.17.tar.gz" +MD5SUM="e85f92edf103fdaf51fbc998c4e1701d" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="python3-numpy" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/verilator/slack-desc b/academic/verilator/slack-desc index 1bb74ecb6d..9cdfb77535 100644 --- a/academic/verilator/slack-desc +++ b/academic/verilator/slack-desc @@ -8,12 +8,12 @@ |-----handy-ruler------------------------------------------------------| verilator: verilator (the fastest free Verilog HDL simulator) verilator: -verilator: Verilator is invoked with parameters similar to GCC or Synopsys’s VCS. -verilator: It "Verilates" the specified synthesizable Verilog or SystemVerilog -verilator: code by reading it, performing lint checks, and optionally inserting -verilator: assertion checks and coverage-analysis points. It outputs single- or -verilator: multi-threaded .cpp and .h files, the "Verilated" code. +verilator: Verilator is invoked with parameters similar to GCC or Synopsys's +verilator: VCS. It "Verilates" the specified synthesizable Verilog or +verilator: SystemVerilog code by reading it, performing lint checks, and +verilator: optionally inserting assertion checks and coverage-analysis points. +verilator: It outputs single- or verilator: multi-threaded .cpp and .h files, +verilator: the "Verilated" code. verilator: verilator: homepage: https://www.veripool.org/wiki/verilator verilator: -verilator: diff --git a/academic/verilator/verilator.SlackBuild b/academic/verilator/verilator.SlackBuild index 3b410de54d..4db86c835f 100644 --- a/academic/verilator/verilator.SlackBuild +++ b/academic/verilator/verilator.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for verilator @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=verilator -VERSION=${VERSION:-4.030} +VERSION=${VERSION:-4.218} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -60,7 +70,7 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $PRGNAM-$VERSION -tar xvf $CWD/$PRGNAM-$VERSION.tgz +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz cd $PRGNAM-$VERSION chown -R root:root . find -L . \ @@ -69,6 +79,8 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; +autoconf -f + CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ @@ -91,7 +103,7 @@ for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; r mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - LICENSE Changes Artistic README.adoc verilator.txt verilator.pdf \ + LICENSE Changes Artistic README.rst \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild @@ -99,4 +111,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/verilator/verilator.info b/academic/verilator/verilator.info index b67785a98d..22dccf1cf7 100644 --- a/academic/verilator/verilator.info +++ b/academic/verilator/verilator.info @@ -1,10 +1,10 @@ PRGNAM="verilator" -VERSION="4.030" +VERSION="4.218" HOMEPAGE="https://www.veripool.org/wiki/verilator" -DOWNLOAD="https://www.veripool.org/ftp/verilator-4.030.tgz" -MD5SUM="f412f817a8eeb142f6d27684e5fd4809" +DOWNLOAD="https://github.com/verilator/verilator/archive/v4.218/verilator-4.218.tar.gz" +MD5SUM="b237c0524327fc82aa4f3af93ecb9371" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="python3" +REQUIRES="verilog" MAINTAINER="Charles Daniels" EMAIL="charles [at] cdaniels [dot] net" diff --git a/academic/verilog/README b/academic/verilog/README index c8ebda2ee7..9df78abc32 100644 --- a/academic/verilog/README +++ b/academic/verilog/README @@ -1,5 +1,6 @@ -Icarus Verilog is a Verilog simulation and synthesis tool. It operates as -a compiler, compiling source code written in Verilog (IEEE-1364) into some -target format. For batch simulation, the compiler can generate an intermediate -form called vvp assembly. This intermediate form is executed by the 'vvp' -command. For synthesis, the compiler generates netlists in the desired format. +Icarus Verilog is a Verilog simulation and synthesis tool. It operates +as a compiler, compiling source code written in Verilog (IEEE-1364) +into some target format. For batch simulation, the compiler can +generate an intermediate form called vvp assembly. This intermediate +form is executed by the 'vvp' command. For synthesis, the compiler +generates netlists in the desired format. diff --git a/academic/verilog/verilog.SlackBuild b/academic/verilog/verilog.SlackBuild index 8de6a9a6a6..797f1bcf9b 100644 --- a/academic/verilog/verilog.SlackBuild +++ b/academic/verilog/verilog.SlackBuild @@ -1,28 +1,38 @@ -#!/bin/sh +#!/bin/bash #Slackware build script for Icarus Verilog compiler #Written by Stephen Van Berg stephen_van_berg@earlicker.com. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=verilog -VERSION=${VERSION:-0.9.7} +VERSION=${VERSION:-11.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -59,6 +69,8 @@ CXXFLAGS="$SLKCFLAGS" \ --localstatedir=/var \ --mandir=/usr/man \ --docdir=/usr/doc/$PRGNAM-$VERSION \ + --enable-shared \ + --disable-static \ --build=$ARCH-slackware-linux make -j1 @@ -80,4 +92,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/verilog/verilog.info b/academic/verilog/verilog.info index 3386e5387d..a78c9fe87d 100644 --- a/academic/verilog/verilog.info +++ b/academic/verilog/verilog.info @@ -1,8 +1,8 @@ PRGNAM="verilog" -VERSION="0.9.7" +VERSION="11.0" HOMEPAGE="http://iverilog.icarus.com/" -DOWNLOAD="ftp://icarus.com/pub/eda/verilog/v0.9/verilog-0.9.7.tar.gz" -MD5SUM="1a8c3f13360078a5e266a0c852bbec57" +DOWNLOAD="https://jaist.dl.sourceforge.net/project/iverilog/iverilog/11.0/verilog-11.0.tar.gz" +MD5SUM="a3f7a618a4f499244ec6ee928574f03d" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/veusz/README b/academic/veusz/README index f09808ca55..f8e783a6ac 100644 --- a/academic/veusz/README +++ b/academic/veusz/README @@ -10,13 +10,13 @@ SAMP interfaces to its plotting facilities. It also allows for manipulation and editing of datasets. Data can be captured from external sources such as Internet sockets or other programs. -See the complete release notes for Veusz 3.2.1 at -https://veusz.github.io/releasenotes/3.2.1.txt +See the complete release notes for Veusz 3.3.1 at +https://veusz.github.io/releasenotes/3.3.1.txt Sphinx is an optional dependency (used to rebuild the manual). **** Note: The veusz.SlackBuild script moved from Python2 to Python3 in version -3.2.1. Please, check the dependencies. +3.3.1. Please, check the dependencies. **** diff --git a/academic/veusz/veusz.SlackBuild b/academic/veusz/veusz.SlackBuild index d4f6b1b28b..0687b9c384 100644 --- a/academic/veusz/veusz.SlackBuild +++ b/academic/veusz/veusz.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for veusz # Based on Slackware 14.2 SlackBuild and Andrea Sciucca's SlackBuild for veusz # -# Copyright 2016-2020, Fellype do Nascimento, Campinas - Brazil +# Copyright 2016-2020, Fellype do Nascimento, Guaratingueta - Brazil # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=veusz -VERSION=${VERSION:-3.2.1} +VERSION=${VERSION:-3.3.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -69,8 +79,7 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -PYTHONVER=$(python -V 2>&1 | cut -f 2 -d' ' | cut -f 1-2 -d.) -export SIP_EXE=/usr/bin/python3-sip +export SIP_EXE=/usr/bin/sip3 python3 setup.py install --root $PKG @@ -78,7 +87,7 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a AUTHORS ChangeLog COPYING INSTALL README VERSION $PKG/usr/doc/$PRGNAM-$VERSION +cp -a AUTHORS ChangeLog COPYING INSTALL README.md VERSION $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild cp Documents/manual/pdf/veusz.pdf $PKG/usr/doc/$PRGNAM-$VERSION @@ -93,8 +102,11 @@ done install -m 644 -p -D veusz.svg $PKG/usr/share/icons/hicolor/scalable/apps/veusz.svg cd - -# Installing desktop menu file +# Install support files install -m 644 -p -D support/veusz.desktop $PKG/usr/share/applications/veusz.desktop +install -m 644 -p -D support/veusz.appdata.xml $PKG/usr/share/appdata/veusz.appdata.xml +install -m 644 -p -D support/veusz.xml $PKG/usr/share/mime/packages/veusz.xml + mkdir -p $PKG/usr/man/man1 gzip Documents/man-page/veusz.1 > $PKG/usr/man/man1/veusz.1.gz @@ -105,4 +117,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/veusz/veusz.info b/academic/veusz/veusz.info index bef4efb40d..4b02fb8b23 100644 --- a/academic/veusz/veusz.info +++ b/academic/veusz/veusz.info @@ -1,10 +1,10 @@ PRGNAM="veusz" -VERSION="3.2.1" +VERSION="3.3.1" HOMEPAGE="https://veusz.github.io/" -DOWNLOAD="https://github.com/veusz/veusz/releases/download/veusz-3.2.1/veusz-3.2.1.tar.gz" -MD5SUM="f341ea793208818088926612bde53d09" +DOWNLOAD="https://github.com/veusz/veusz/releases/download/veusz-3.3.1/veusz-3.3.1.tar.gz" +MD5SUM="1c7d42d6f87ea3b98fafc8dc52dbbc58" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="numpy3 python3-PyQt5" +REQUIRES="python3-numpy" MAINTAINER="Fellype do Nascimento" -EMAIL="fellype(at)gmail(dot)com" +EMAIL="fellype (at) gmail (dot) com" diff --git a/academic/voro++/README b/academic/voro++/README new file mode 100644 index 0000000000..886a2a1030 --- /dev/null +++ b/academic/voro++/README @@ -0,0 +1,7 @@ + Voro++ is a software library for carrying out three-dimensional +computations of the Voronoi tessellation. A distinguishing feature of +the Voro++ library is that it carries out cell-based calculations, +computing the Voronoi cell for each particle individually. It is +particularly well-suited for applications that rely on cell-based +statistics, where features of Voronoi cells (eg. volume, centroid, +number of faces) can be used to analyze a system of particles. diff --git a/academic/voro++/slack-desc b/academic/voro++/slack-desc new file mode 100644 index 0000000000..a0482548d5 --- /dev/null +++ b/academic/voro++/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +voro++: voro++ (A 3D Voronoi cell software library) +voro++: +voro++: Voro++ is a software library for carrying out three-dimensional +voro++: computations of the Voronoi tessellation. A distinguishing feature of +voro++: the Voro++ library is that it carries out cell-based calculations, +voro++: computing the Voronoi cell for each particle individually. It is +voro++: particularly well-suited for applications that rely on cell-based +voro++: statistics, where features of Voronoi cells (eg. volume, centroid, +voro++: number of faces) can be used to analyze a system of particles. +voro++: +voro++: diff --git a/academic/voro++/voro++.SlackBuild b/academic/voro++/voro++.SlackBuild new file mode 100644 index 0000000000..563f9f3e56 --- /dev/null +++ b/academic/voro++/voro++.SlackBuild @@ -0,0 +1,118 @@ +#!/bin/bash + +# Slackware build script for voro++ + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=voro++ +VERSION=${VERSION:-0.4.6} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +# the default make build the examples +# let's keep source only +sed -i '15s/^/#/;24s/^/#/' Makefile + +# comment the include line of example's Makefiles +# then add the right path for include files +sed -i 's/^include ../#&/; /#include/aE_INC=-I/usr/include/voro++' examples/*/Makefile + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +make +make install PREFIX=$PKG/usr + +mkdir -p $PKG/usr/share/$PRGNAM-$VERSION +cp -a examples $PKG/usr/share/$PRGNAM-$VERSION +cp -a scripts $PKG/usr/share/$PRGNAM-$VERSION + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +find $PKG/usr/man -type f -exec gzip -9 {} \; +for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + LICENSE html \ + $PKG/usr/doc/$PRGNAM-$VERSION +chmod 755 $PKG/usr/doc/$PRGNAM-$VERSION/html +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/voro++/voro++.info b/academic/voro++/voro++.info new file mode 100644 index 0000000000..0bfd5007a7 --- /dev/null +++ b/academic/voro++/voro++.info @@ -0,0 +1,10 @@ +PRGNAM="voro++" +VERSION="0.4.6" +HOMEPAGE="https://crd.lbl.gov/divisions/amcr/mathematics-dept/math/software/voro-a-three-dimensional-voronoi-library-in-c/" +DOWNLOAD="https://math.lbl.gov/voro++/download/dir/voro++-0.4.6.tar.gz" +MD5SUM="2338b824c3b7b25590e18e8df5d68af9" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/wcalc/README b/academic/wcalc/README new file mode 100644 index 0000000000..c1522dce07 --- /dev/null +++ b/academic/wcalc/README @@ -0,0 +1,13 @@ +wcalc (command-line scientific calculator) + +Wcalc is a very capable command-line calculator. It has standard +functions (sin, asinh, and sqrt for example, in either radians or +degrees), many pre-defined constants (pi, e, c, G, etc.), support +for using variables, "active" variables, a command history, +hex/octal/binary input and output, unit conversions, embedded +comments, and the ability to save history to a file and load it +from a file. Wcalc evaluates expressions using the standard order of +operations. + +Wcalc uses intuitive expressions. For example, Wcalc will evaluate +5sin 4!-7*2(4%6)^2 to be -221.96631678. diff --git a/academic/wcalc/doinst.sh b/academic/wcalc/doinst.sh new file mode 100644 index 0000000000..65c7e2eeb9 --- /dev/null +++ b/academic/wcalc/doinst.sh @@ -0,0 +1,9 @@ +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 +fi + +if [ -e usr/share/icons/hicolor/icon-theme.cache ]; then + if [ -x /usr/bin/gtk-update-icon-cache ]; then + /usr/bin/gtk-update-icon-cache -f usr/share/icons/hicolor >/dev/null 2>&1 + fi +fi diff --git a/academic/wcalc/icons/128.png b/academic/wcalc/icons/128.png Binary files differnew file mode 100644 index 0000000000..cafefc348c --- /dev/null +++ b/academic/wcalc/icons/128.png diff --git a/academic/wcalc/icons/16.png b/academic/wcalc/icons/16.png Binary files differnew file mode 100644 index 0000000000..ab6bf4aba0 --- /dev/null +++ b/academic/wcalc/icons/16.png diff --git a/academic/wcalc/icons/32.png b/academic/wcalc/icons/32.png Binary files differnew file mode 100644 index 0000000000..5077cee603 --- /dev/null +++ b/academic/wcalc/icons/32.png diff --git a/academic/wcalc/icons/48.png b/academic/wcalc/icons/48.png Binary files differnew file mode 100644 index 0000000000..e188f42fa7 --- /dev/null +++ b/academic/wcalc/icons/48.png diff --git a/academic/wcalc/slack-desc b/academic/wcalc/slack-desc new file mode 100644 index 0000000000..f7e41e97e1 --- /dev/null +++ b/academic/wcalc/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +wcalc: wcalc (command-line scientific calculator) +wcalc: +wcalc: Wcalc is a very capable command-line calculator. It has standard +wcalc: functions (sin, asinh, and sqrt for example, in either radians or +wcalc: degrees), many pre-defined constants (pi, e, c, G, etc.), support +wcalc: for using variables, "active" variables, a command history, +wcalc: hex/octal/binary input and output, unit conversions, embedded +wcalc: comments, and the ability to save history to a file and load it +wcalc: from a file. Wcalc evaluates expressions using the standard order of +wcalc: operations. +wcalc: diff --git a/academic/wcalc/wcalc.SlackBuild b/academic/wcalc/wcalc.SlackBuild new file mode 100644 index 0000000000..21bd7932cd --- /dev/null +++ b/academic/wcalc/wcalc.SlackBuild @@ -0,0 +1,103 @@ +#!/bin/bash + +# Slackware build script for wcalc + +# Written by B. Watson (urchlay@slackware.uk) + +# Licensed under the WTFPL. See http://www.wtfpl.net/txt/copying/ for details. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=wcalc +VERSION=${VERSION:-2.5} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +# the * in the next line is in case '?viasf=1' is appended to the filename... +tar xvf $CWD/$PRGNAM-$VERSION.tar.bz2* +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . -perm /111 -a \! -perm 755 -a -exec chmod 755 {} + -o \ + \! -perm /111 -a \! -perm 644 -a -exec chmod 644 {} + + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --mandir=/usr/man \ + --docdir=/usr/doc/$PRGNAM-$VERSION \ + --disable-static \ + --build=$ARCH-slackware-linux + +make +make install-strip DESTDIR=$PKG +gzip -9 $PKG/usr/man/man*/* + +# Icons extracted from graphics/TheW.icns in the source. +for i in $CWD/icons/*.png; do + px="$( basename $i .png )" + sz="${px}x${px}" + dir=$PKG/usr/share/icons/hicolor/$sz/apps + mkdir -p $dir + cat $i > $dir/$PRGNAM.png +done + +mkdir -p $PKG/usr/share/pixmaps +ln -s ../icons/hicolor/48x48/apps/$PRGNAM.png $PKG/usr/share/pixmaps/$PRGNAM.png + +# .desktop file written by SlackBuild author. +mkdir -p $PKG/usr/share/applications +cat $CWD/$PRGNAM.desktop > $PKG/usr/share/applications/$PRGNAM.desktop + +PKGDOC=$PKG/usr/doc/$PRGNAM-$VERSION +mkdir -p $PKGDOC +cp -a AUTHORS COPYRIGHT ChangeLog NEWS README $PKGDOC +cat $CWD/$PRGNAM.SlackBuild > $PKGDOC/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/wcalc/wcalc.desktop b/academic/wcalc/wcalc.desktop new file mode 100644 index 0000000000..a47430d238 --- /dev/null +++ b/academic/wcalc/wcalc.desktop @@ -0,0 +1,10 @@ +[Desktop Entry] +Version=1.0 +Type=Application +Name=WCalc +Comment=Scientific Calculator +Exec=wcalc +Icon=wcalc +Terminal=true +StartupNotify=false +Categories=Science;Math diff --git a/academic/wcalc/wcalc.info b/academic/wcalc/wcalc.info new file mode 100644 index 0000000000..12bcbc0131 --- /dev/null +++ b/academic/wcalc/wcalc.info @@ -0,0 +1,10 @@ +PRGNAM="wcalc" +VERSION="2.5" +HOMEPAGE="https://w-calc.sourceforge.net/" +DOWNLOAD="https://downloads.sourceforge.net/project/w-calc/Wcalc/2.5/wcalc-2.5.tar.bz2" +MD5SUM="45b02ba339a813ffc65f154d1e54a04b" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="B. Watson" +EMAIL="urchlay@slackware.uk" diff --git a/academic/wehi-cellsymphony/wehi-cellsymphony.SlackBuild b/academic/wehi-cellsymphony/wehi-cellsymphony.SlackBuild index 67a0093fc0..17b701b38f 100644 --- a/academic/wehi-cellsymphony/wehi-cellsymphony.SlackBuild +++ b/academic/wehi-cellsymphony/wehi-cellsymphony.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for wehi-cellsymphony -# Copyright 2016 Petar Petrov slackalaxy@gmail.com +# Copyright 2016-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,15 +22,25 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=wehi-cellsymphony VERSION=${VERSION:-20130721} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} ARCH=noarch SRCNAM=CellSymphony -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -55,4 +65,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/wehi-cellsymphony/wehi-cellsymphony.info b/academic/wehi-cellsymphony/wehi-cellsymphony.info index a6a5e7c3b2..e6a94638b3 100644 --- a/academic/wehi-cellsymphony/wehi-cellsymphony.info +++ b/academic/wehi-cellsymphony/wehi-cellsymphony.info @@ -5,6 +5,6 @@ DOWNLOAD="http://www.frankbattye.com.au/downloads/CellSymphony.jar" MD5SUM="d7c3b806491f7922742271a4dfcdb58c" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="jdk" +REQUIRES="zulu-openjdk11" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/wehi-deid/wehi-deid.SlackBuild b/academic/wehi-deid/wehi-deid.SlackBuild index af6a31c284..b74c193e14 100644 --- a/academic/wehi-deid/wehi-deid.SlackBuild +++ b/academic/wehi-deid/wehi-deid.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for wehi-deid -# Copyright 2016 Petar Petrov slackalaxy@gmail.com +# Copyright 2016-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,15 +22,25 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=wehi-deid VERSION=${VERSION:-20130720} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} ARCH=noarch SRCNAM=DeID -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -55,4 +65,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/wehi-deid/wehi-deid.info b/academic/wehi-deid/wehi-deid.info index ce613b6662..6b465458a5 100644 --- a/academic/wehi-deid/wehi-deid.info +++ b/academic/wehi-deid/wehi-deid.info @@ -5,6 +5,6 @@ DOWNLOAD="http://www.frankbattye.com.au/downloads/DeID.jar" MD5SUM="bd938d07b0471cf9ed9f32b778ded63d" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="jdk" +REQUIRES="zulu-openjdk11" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/wehi-hackit/wehi-hackit.SlackBuild b/academic/wehi-hackit/wehi-hackit.SlackBuild index b24aa12991..a67065af5b 100644 --- a/academic/wehi-hackit/wehi-hackit.SlackBuild +++ b/academic/wehi-hackit/wehi-hackit.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for wehi-hackit -# Copyright 2016 Petar Petrov slackalaxy@gmail.com +# Copyright 2016-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,15 +22,25 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=wehi-hackit VERSION=${VERSION:-20050203} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} ARCH=noarch SRCNAM=Hackit -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -56,4 +66,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/wehi-hackit/wehi-hackit.info b/academic/wehi-hackit/wehi-hackit.info index 962314eea7..043df91eec 100644 --- a/academic/wehi-hackit/wehi-hackit.info +++ b/academic/wehi-hackit/wehi-hackit.info @@ -5,6 +5,6 @@ DOWNLOAD="http://www.frankbattye.com.au/downloads/Hackit.jar" MD5SUM="1b498994d569b147a461b698633078e1" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="jdk" +REQUIRES="zulu-openjdk11" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/wehi-weasel/wehi-weasel b/academic/wehi-weasel/wehi-weasel index 994a389f76..f086e18ce9 100644 --- a/academic/wehi-weasel/wehi-weasel +++ b/academic/wehi-weasel/wehi-weasel @@ -3,4 +3,4 @@ # This starts the program jar file. The -Xmx1024m value indicates the # amount of RAM allocated to the program. You may wish to change this. -java -jar -Xmx1024m /usr/share/java/wehi-weasel/Weasel.jar +java -jar -Xmx2048m /opt/wehi-weasel/Weasel.jar diff --git a/academic/wehi-weasel/wehi-weasel.SlackBuild b/academic/wehi-weasel/wehi-weasel.SlackBuild index 5a8de5b25c..17332d1bb0 100644 --- a/academic/wehi-weasel/wehi-weasel.SlackBuild +++ b/academic/wehi-weasel/wehi-weasel.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for wehi-weasel -# Copyright 2017-2020 Petar Petrov slackalaxy@gmail.com +# Copyright 2017-2023 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,21 +22,31 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=wehi-weasel -VERSION=${VERSION:-3.6.11.8} +VERSION=${VERSION:-3.8.0.18} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} ARCH=noarch -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} SRCNAM=wsl JARNAM=Weasel -SRCVER=36118 +SRCVER=38018 SRCDIST=unix LICENSE=WeaselLicence.doc @@ -57,10 +67,10 @@ find -L . \ # Copy the jar file and the icons. I am not sure the icons are needed # by the program at runtime, but it will not hurt to have them there. -mkdir -p $PKG/usr/share/java/$PRGNAM +mkdir -p $PKG/opt/$PRGNAM cp -a \ $JARNAM.jar WeaselIcon16.gif WeaselIcon32.gif WeaselIcon.ico \ - $PKG/usr/share/java/$PRGNAM + $PKG/opt/$PRGNAM # You may wish to check this simple wrapper for the amount of RAM that # is allocated to the program. @@ -83,4 +93,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/wehi-weasel/wehi-weasel.info b/academic/wehi-weasel/wehi-weasel.info index fd10edf09c..a73a47e760 100644 --- a/academic/wehi-weasel/wehi-weasel.info +++ b/academic/wehi-weasel/wehi-weasel.info @@ -1,10 +1,10 @@ PRGNAM="wehi-weasel" -VERSION="3.6.11.8" +VERSION="3.8.0.18" HOMEPAGE="http://www.frankbattye.com.au/Weasel/" DOWNLOAD="http://www.frankbattye.com.au/Weasel/WeaselDownload.html" -MD5SUM="d13a157935311839de4a8b582389f809" +MD5SUM="f7dfb4363b6d60a7781a212b06afbc98" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="jdk" +REQUIRES="zulu-openjdk11" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/wise/README b/academic/wise/README new file mode 100644 index 0000000000..6fe23af5ad --- /dev/null +++ b/academic/wise/README @@ -0,0 +1,7 @@ +Wise compares a protein sequence to a genomic DNA sequence, allowing for +introns and frameshifting errors. + +The Wise package is now a rather stately bioinformatics package that has +been around for a while. Its key programs are genewise, a program for +aligning proteins or protein HMMs to DNA, and dynamite a rather cranky +"macro language" which automates the production of dynamic programming. diff --git a/academic/wise/patches/01_welcome-csh.patch b/academic/wise/patches/01_welcome-csh.patch new file mode 100644 index 0000000000..3a9057e062 --- /dev/null +++ b/academic/wise/patches/01_welcome-csh.patch @@ -0,0 +1,22 @@ +Author: Philipp Benner <mail@philipp-benner.de> +Description: Avoid dependency from csh + +--- wise-2.4.1.orig/src/makefile ++++ wise-2.4.1/src/makefile +@@ -109,7 +109,7 @@ + bin : + mkdir bin + cp models/pswdb models/psw models/genewisedb models/estwisedb models/estwise models/genewise models/dba models/dnal models/promoterwise network/scanwise_server models/scanwise ./bin +- csh welcome.csh ++ ./welcome.csh + + libs : + (cd base ; $(MAKE) CC="$(CC)" CFLAGS="$(CFLAGS)" libwisebase.a ) +--- wise-2.4.1.orig/src/welcome.csh ++++ wise-2.4.1/src/welcome.csh +@@ -1,4 +1,4 @@ +-#!/bin/tcsh -f ++#!/bin/sh + + echo "" + echo "Welcome to Wise2.4" diff --git a/academic/wise/patches/02_isnumber.patch b/academic/wise/patches/02_isnumber.patch new file mode 100644 index 0000000000..a6ae90856d --- /dev/null +++ b/academic/wise/patches/02_isnumber.patch @@ -0,0 +1,14 @@ +Author: Philipp Benner <mail@philipp-benner.de> +Description: Replace isnumber() (which does not exist on linux) by isdigit(). + +--- wise-2.4.1.orig/src/models/phasemodel.c ++++ wise-2.4.1/src/models/phasemodel.c +@@ -20,7 +20,7 @@ + if( line[0] == '#' ) { + continue; + } +- if( !isnumber(line[0]) ) { ++ if( !isdigit(line[0]) ) { + warn("Bad looking line in intron file, %s",line); + continue; + } diff --git a/academic/wise/patches/03_doc-nodycache.patch b/academic/wise/patches/03_doc-nodycache.patch new file mode 100644 index 0000000000..6fe7b1893c --- /dev/null +++ b/academic/wise/patches/03_doc-nodycache.patch @@ -0,0 +1,15 @@ +Author Philipp Benner <mail@philipp-benner.de> +Description: Documentation bugfix. + +--- wise-2.4.1.orig/docs/wise2.tex ++++ wise-2.4.1/docs/wise2.tex +@@ -1617,7 +1617,8 @@ + \item[-hithelp] more detailed help on hitlist formats + \item[-dymem] memory style [default/linear/explicit] + \item[-kbyte] memory amount to use [4000] +-\item[-\[no\]dycache] implicitly cache dy matrix usage (default yes) ++\item[-dycache] implicitly cache dy matrix usage (default) ++\item[-nodycache] do not implicitly cache dy matrix usage + \item[-dydebug] drop into dynamite dp matrix debugger + \item[-paldebug] print PackAln after debugger run if used + \item[-help] show help options diff --git a/academic/wise/patches/04_wise2-pdflatex-update.patch b/academic/wise/patches/04_wise2-pdflatex-update.patch new file mode 100644 index 0000000000..bbaf2861d7 --- /dev/null +++ b/academic/wise/patches/04_wise2-pdflatex-update.patch @@ -0,0 +1,38 @@ +Author Philipp Benner <mail@philipp-benner.de> +Description: Make wise2.tex pdflatex compatible. + +--- wise-2.4.1.orig/docs/wise2.tex ++++ wise-2.4.1/docs/wise2.tex +@@ -1,6 +1,7 @@ + + \documentclass{article} +-\usepackage{epsfig} ++%\usepackage{epsfig} ++\usepackage{graphicx} + + \begin{document} + \newcommand{\programtext}[1]{{\tt #1}} +@@ -707,8 +708,9 @@ + \begin{figure} + \begin{center} + \leavevmode +-\epsfxsize 300pt +-\epsfbox{genewise21.eps} ++%\epsfxsize 300pt ++%\epsfbox{genewise21.eps} ++%\includegraphics[scale=0.75]{genewise21.pdf} + \newline + \caption{GeneWise21:93 Algorithm. The dark circles represent states, and the + arrows between them transitions. Black transitions are standard +@@ -898,8 +900,9 @@ + \begin{figure} + \begin{center} + \leavevmode +-\epsfxsize 300pt +-\epsfbox{genewise6.eps} ++%\epsfxsize 300pt ++%\epsfbox{genewise6.eps} ++%\includegraphics[scale=0.75]{genewise6.pdf} + \newline + \caption{GeneWise6:23} + \label{Figure:genewise623} diff --git a/academic/wise/patches/05_glib2.patch b/academic/wise/patches/05_glib2.patch new file mode 100644 index 0000000000..908506524a --- /dev/null +++ b/academic/wise/patches/05_glib2.patch @@ -0,0 +1,703 @@ +Author: Barry deFreese <bdefreese@debian.org> +Description: To build wise2 with the Glib version 2.0 instead of 1.2. +Forwarded: birney@sanger.ac.uk +--- wise-2.4.1.orig/src/makefile ++++ wise-2.4.1/src/makefile +@@ -31,13 +31,13 @@ + + + # Intel icc flags +-# CFLAGS = -c -O3 -axWK -ipo `glib-config --cflags` ++# CFLAGS += -c -axWK -ipo `pkg-config --cflags glib-2.0` + + # alpha flags (-pthread) +-# CFLAGS = -c -O3 -pthread `glib-config --cflags` ++# CFLAGS += -c -pthread `pkg-config --cflags glib-2.0` + + # normal linux/bsd/mac flags +-CFLAGS = -c -O3 `glib-config --cflags` ++CFLAGS += $(CPPFLAGS) -c `pkg-config --cflags glib-2.0` + + + EXTRALIBS = -lm +--- wise-2.4.1.orig/src/snp/makefile ++++ wise-2.4.1/src/snp/makefile +@@ -5,9 +5,9 @@ + CC = cc + #CFLAGS = -c -O2 -pg -I../base/ -I../dynlibsrc/ + #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ -I. +-CFLAGS = -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `glib-config --cflags` ++CFLAGS += $(CPPFLAGS) -c -g3 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config --cflags glib-2.0` + +-LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lpthread -lm ++LDFLAGS += -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lpthread -lm + AR_OPTIONS = ru + + RANLIB_NEEDED = 0 +@@ -16,7 +16,7 @@ + $(CC) $(CFLAGS) $(INCFLAGS) $? + + test_est : test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o +- $(CC) -o test_est test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o ../dynlibsrc/libdyna.a ../base/libwisebase.a $(LFLAGS) ++ $(CC) -o test_est test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o ../dynlibsrc/libdyna.a ../base/libwisebase.a $(LDFLAGS) + + INCFLAGS = -I../base/ -I../dynlibsrc/ + DFLAGS = -l -D -n Wise2_ -a _api.h -b _api.t -pthreads -dbtrace 5 -nocwarn +--- wise-2.4.1.orig/src/corba/makefile ++++ wise-2.4.1/src/corba/makefile +@@ -3,9 +3,9 @@ + CC = cc + INCFLAGS = -I../base/ -I../dynlibsrc + #gCFLAGS = -Wall -g -pedantic -c -DUNIX -I../base/ +-#CFLAGS = -O2 -c -DUNIX -I../base/ `glib-config --cflags` -I/usr/local/include/orbit-1.0/ +-CFLAGS = -pthread -c -DUNIX -I../base/ -I../dynlibsrc `orbit-config --cflags client` +-LFLAGS = -L../base/ -lm -lpthread ++#CFLAGS += -c -DUNIX -I../base/ `pkg-config --cflags glib-2.0` -I/usr/local/include/orbit-1.0/ ++CFLAGS += $(CPPFLAGS) -pthread -c -DUNIX -I../base/ -I../dynlibsrc `orbit-config --cflags client` ++LDFLAGS += -L../base/ -lm -lpthread + AR_OPTIONS = ru + + +@@ -14,18 +14,18 @@ + orbit-idl hspscan_corba.idl + + test_server : test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o +- cc -g -o test_server test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o ../dynlibsrc/libdyna_glib.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread ++ cc -g -o test_server test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o ../dynlibsrc/libdyna_glib.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread + + scanwise_protein_index : scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o +- cc -o scanwise_protein_index scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna_glib.a ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread ++ cc -o scanwise_protein_index scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna_glib.a ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread + + + test_client : test_client.o hspscan_corba-common.o hspscan_corba-stubs.o +- cc -g -o test_client test_client.o hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread ++ cc -g -o test_client test_client.o hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread + + + test_wrapper : test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o hspscan_corba_wrapper.o corba_singleton.o +- cc -g -o test_wrapper test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o corba_singleton.o hspscan_corba_wrapper.o ../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread ++ cc -g -o test_wrapper test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o corba_singleton.o hspscan_corba_wrapper.o ../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread + + .c.o : + $(CC) $(CFLAGS) $(INCFLAGS) $? +--- wise-2.4.1.orig/src/models/makefile ++++ wise-2.4.1/src/models/makefile +@@ -62,46 +62,46 @@ + # $(CC) $(CFLAGS) -I../HMMer2/ $(INCFLAGS) wise2xhmmer2.c + + testgenestat : testgenestat.o genestats.o pwmdna.o +- $(CC) -o testgenestat testgenestat.o genestats.o pwmdna.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o testgenestat testgenestat.o genestats.o pwmdna.o -ldyna -lwisebase $(LDFLAGS) + + test_aligng : test_aligng.o aligngenemodel.o pwmdna.o +- $(CC) -o test_aligng test_aligng.o aligngenemodel.o pwmdna.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o test_aligng test_aligng.o aligngenemodel.o pwmdna.o -ldyna -lwisebase $(LDFLAGS) + + makepwm : makepwm.o pwmdna.o +- $(CC) -o makepwm makepwm.o pwmdna.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o makepwm makepwm.o pwmdna.o -ldyna -lwisebase $(LDFLAGS) + + testwise2xhmmer2.o : testwise2xhmmer2.c + $(CC) $(CFLAGS) -I../HMMer2/ $(INCFLAGS) testwise2xhmmer2.c + + testwise2xhmmer2 : testwise2xhmmer2.o threestatemodel.o threestatedb.o pfamhmmer1db.o +- $(CC) -o testwise2xhmmer2 wise2xhmmer2.o testwise2xhmmer2.o threestatemodel.o threestatedb.o pfamhmmer1db.o -ldyna -lwisebase -lhmmer $(LFLAGS) ++ $(CC) -o testwise2xhmmer2 wise2xhmmer2.o testwise2xhmmer2.o threestatemodel.o threestatedb.o pfamhmmer1db.o -ldyna -lwisebase -lhmmer $(LDFLAGS) + + plan7test.o : plan7test.c + $(CC) $(CFLAGS) -I../HMMer2/ plan7test.c + + plan7test : plan7test.o plan7.o wise2xhmmer2.o threestatemodel.o threestatedb.o pfamhmmer1db.o +- $(CC) -o plan7test plan7test.o plan7.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o -ldyna -lwisebase -lhmmer $(LFLAGS) ++ $(CC) -o plan7test plan7test.o plan7.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o -ldyna -lwisebase -lhmmer $(LDFLAGS) + + seqstat : seqstat.o +- $(CC) -o seqstat seqstat.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o seqstat seqstat.o -ldyna -lwisebase $(LDFLAGS) + + mutatedna : mutatedna.o +- $(CC) -o mutatedna mutatedna.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o mutatedna mutatedna.o -ldyna -lwisebase $(LDFLAGS) + + revcomp : revcomp.o +- $(CC) -o revcomp revcomp.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o revcomp revcomp.o -ldyna -lwisebase $(LDFLAGS) + + stupid_motif_scan : stupid_motif_scan.o +- $(CC) -o stupid_motif_scan stupid_motif_scan.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o stupid_motif_scan stupid_motif_scan.o -ldyna -lwisebase $(LDFLAGS) + + seqtrunc : seqtrunc.o +- $(CC) -o seqtrunc seqtrunc.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o seqtrunc seqtrunc.o -ldyna -lwisebase $(LDFLAGS) + + seqlist : seqlist.o +- $(CC) -o seqlist seqlist.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o seqlist seqlist.o -ldyna -lwisebase $(LDFLAGS) + + testpwm : testpwm.o pwmdna.o +- $(CC) -o testpwm testpwm.o pwmdna.o -ldyna -lwisebase $(LFLAGS) -lefence ++ $(CC) -o testpwm testpwm.o pwmdna.o -ldyna -lwisebase $(LDFLAGS) -lefence + + + threestate : $(MODELOBJ) +@@ -111,29 +111,29 @@ + pwise : $(MODELOBJ) threestatemat.o threestatedisplay.o + + test : test.o proteinsw.o protprotdis.o +- $(CC) -o test test.o proteinsw.o protprotdis.o -ldyna_glib -ldyna -lwisebase ../dynlibsrc/matrix.o $(LFLAGS) ++ $(CC) -o test test.o proteinsw.o protprotdis.o -ldyna_glib -ldyna -lwisebase ../dynlibsrc/matrix.o $(LDFLAGS) + + testanc : testanc.o proteinsw.o abc.o pba.o sw_wrap.o +- $(CC) -o testanc testanc.o proteinsw.o abc.o pba.o sw_wrap.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o testanc testanc.o proteinsw.o abc.o pba.o sw_wrap.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + test_tf : test_transfactor.o transfactor.o pwmdna.o +- $(CC) -o test_tf test_transfactor.o transfactor.o pwmdna.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o test_tf test_transfactor.o transfactor.o pwmdna.o $(LDFLAGS) -ldyna -lwisebase + + motifwise : motifwise.o transfactor.o transregion.o pwmdna.o transregiondp.o +- $(CC) -o motifwise motifwise.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o motifwise motifwise.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LDFLAGS) -ldyna -lwisebase + + motifcluster : motifcluster.o transfactor.o transregion.o pwmdna.o transregiondp.o +- $(CC) -o motifcluster motifcluster.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o motifcluster motifcluster.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LDFLAGS) -ldyna -lwisebase + + motifdiff : motifdiff.o transfactor.o transregion.o pwmdna.o transregiondp.o +- $(CC) -o motifdiff motifdiff.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o motifdiff motifdiff.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LDFLAGS) -ldyna -lwisebase + + + cdtest : cdtest.o cdna2genomic.o d2d_display.o +- $(CC) -o cdtest cdtest.o cdna2genomic.o d2d_display.o -ldyna_glib -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o cdtest cdtest.o cdna2genomic.o d2d_display.o -ldyna_glib -ldyna -lwisebase $(LDFLAGS) + + prob2bits : prob2bits.o +- $(CC) -o prob2bits $(LFLAGS) -ldyna_glib -ldyna -lwisebase ++ $(CC) -o prob2bits $(LDFLAGS) -ldyna_glib -ldyna -lwisebase + + quick : + cc -O -c -I../dynlibsrc/ -I../base/ genewise6.c +@@ -180,161 +180,161 @@ + $(CC) $(CFLAGS) fivestarscan.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. + + oldpostwise : oldpostwise.o $(NEWG) +- $(CC) -g -o oldpostwise oldpostwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase ++ $(CC) -g -o oldpostwise oldpostwise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase + + testdna : testdna.o dnaalign.o seqaligndisplay.o +- $(CC) -o testdna testdna.o dnaalign.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o testdna testdna.o dnaalign.o seqaligndisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + dnal : dnal.o dnaalign.o seqaligndisplay.o +- $(CC) -o dnal dnal.o dnaalign.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o dnal dnal.o dnaalign.o seqaligndisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + psw : psw.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o +- $(CC) -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + scanwisep.o : scanwisep.c +- $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `glib-config --cflags` $? ++ $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `pkg-config --cflags glib-2.0` $? + + hsp2aln_sw.o : hsp2aln_sw.c +- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $? ++ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config --cflags glib-2.0` $? + + scanwisep_mysql.o : scanwisep.c + $(CC) $(CFLAGS) -DSCAN_MYSQL -I../corba -I../external/mott -I../mysql/protein_index/ -I/usr/local/mysql/include scanwisep.c + + scanwisep_mysql : scanwisep_mysql.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o +- $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../mysql/protein_index/mysql_protein_index.o $(LFLAGS) -L../external/mott -L/usr/local/mysql/lib -ldyna_glib -ldyna ott -lwisebase -lmysqlclient -lm $(EXTRALIBS) -lpthread -lZ ++ $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../mysql/protein_index/mysql_protein_index.o $(LDFLAGS) -L../external/mott -L/usr/local/mysql/lib -ldyna_glib -ldyna ott -lwisebase -lmysqlclient -lm $(EXTRALIBS) $(LDFLAGS) -lpthread -lZ + + + scanwisep_corba.o : scanwisep.c + $(CC) $(CFLAGS) -DSCAN_CORBA -I../corba -I../external/mott `orbit-config --cflags server` scanwisep.c + + scanwisep_corba : scanwisep_corba.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o +- $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../corba/hspscan_corba-common.o ../corba/hspscan_corba-stubs.o ../corba/corba_singleton.o ../corba/hspscan_corba_wrapper.o $(LFLAGS) -L../external/mott -ldyna_glib -ldyna -lmott -lwisebase $(EXTRALIBS) `orbit-config --libs server` -lpthread ++ $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../corba/hspscan_corba-common.o ../corba/hspscan_corba-stubs.o ../corba/corba_singleton.o ../corba/hspscan_corba_wrapper.o $(LDFLAGS) -L../external/mott -ldyna_glib -ldyna -lmott -lwisebase $(EXTRALIBS) `orbit-config --libs server` -lpthread + + + scanwisep_wiseserver.o : scanwisep.c + $(CC) $(CFLAGS) $(INCFLAGS) -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c + + scanwise : scanwisep_wiseserver.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o +- $(CC) -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o ../network/client_multihspscan.o $(LFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread ++ $(CC) -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o ../network/client_multihspscan.o $(LDFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread + + scanwisep_compress.o : scanwisep.c + $(CC) $(CFLAGS) -DSCAN_COMPRESS -I../dnaindex -I../network -I../socket -I../external/mott scanwisep.c + + scanwisep_compress : scanwisep_compress.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o +- $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../dnaindex/compressed_protein_index.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o ../dnaindex/kmer_index_interface.o $(LFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread ++ $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../dnaindex/compressed_protein_index.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o ../dnaindex/kmer_index_interface.o $(LDFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread + + + + scanwisep : scanwisep.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o +- $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o $(LFLAGS) -L../external/mott -lmott -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `glib-config --libs` -lpthread ++ $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o $(LDFLAGS) -L../external/mott -lmott -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread + + test_gwhsp : test_gwhsp.o genewisehsp.o +- $(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `glib-config --libs` -lpthread ++ $(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LDFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread + + localcishit.o : localcishit.c +- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $? ++ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config --cflags glib-2.0` $? + + promoterwise.o : promoterwise.c +- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $? ++ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config --cflags glib-2.0` $? + + promoterwise : promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o +- $(CC) -g -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `glib-config --libs` -lpthread ++ $(CC) -g -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread + + test_deng : test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o +- $(CC) -o test_deng test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `glib-config --libs` -lpthread ++ $(CC) -o test_deng test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread + + promotercluster : promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o +- $(CC) -o promotercluster promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `glib-config --libs` -lpthread ++ $(CC) -o promotercluster promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread + + dnawise : dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o +- $(CC) -o dnawise dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lpthread ++ $(CC) -o dnawise dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase -lpthread + + pswdb : pswdb.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o +- $(CC) -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + efpswdb : pswdb.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o +- $(CC) -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lefence $(EXTRALIBS) ++ $(CC) -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase -lefence $(EXTRALIBS) + + dba : dbac.o dba.o slimdba.o bigdba.o dbadisplay.o +- $(CC) -o dba dbac.o dba.o slimdba.o bigdba.o dbadisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o dba dbac.o dba.o slimdba.o bigdba.o dbadisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + lba : lba.o largeblockdp.o seqaligndisplay.o +- $(CC) -o lba lba.o largeblockdp.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o lba lba.o largeblockdp.o seqaligndisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + + fastdba : fastdba.o dba.o slimdba.o bigdba.o dbadisplay.o +- $(CC) -o fastdba fastdba.o dba.o slimdba.o bigdba.o dbadisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o fastdba fastdba.o dba.o slimdba.o bigdba.o dbadisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + evopairwise : evopairwise.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o +- $(CC) -o evopairwise evopairwise.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o evopairwise evopairwise.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + test_threestatehsp : test_threestatehsp.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o threestatehsp.o +- $(CC) -o test_threestatehsp test_threestatehsp.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o seqaligndisplay.o threestatehsp.o wise2xhmmer2.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o test_threestatehsp test_threestatehsp.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o seqaligndisplay.o threestatehsp.o wise2xhmmer2.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + makerandomdb : makerandomdb.o +- $(CC) -o makerandomdb makerandomdb.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o makerandomdb makerandomdb.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + genewise : genewise.o $(NEWG) +- $(CC) -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o genewise genewise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + cdnawise : cdnawise.o $(NEWG) cdnawise10.o +- $(CC) -g -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + fivestar : fivestar.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o +- $(CC) -g -o fivestar fivestar.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o fivestar fivestar.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + + fivestarsearch : fivestarsearch.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o +- $(CC) -g -o fivestarsearch fivestarsearch.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o fivestarsearch fivestarsearch.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + fivestarscan : fivestarscan.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o +- $(CC) -g -o fivestarscan fivestarscan.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o fivestarscan fivestarscan.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + + editdist : editdist.o editdistdp.o standardout.o seqaligndisplay.o +- $(CC) -g -o editdist editdist.o editdistdp.o standardout.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase ++ $(CC) -g -o editdist editdist.o editdistdp.o standardout.o seqaligndisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase + + + efgw : genewise.o $(NEWG) +- $(CC) -g -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -lefence ++ $(CC) -g -o genewise genewise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -lefence + + + genewisedb : genewisedb.o $(NEWG) +- $(CC) -g -o genewisedb genewisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o genewisedb genewisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + estwisedb : estwisedb.o $(NEWG) +- $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + edb : estwisedb.o $(NEWG) +- $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -lefence ++ $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -lefence + + estwise : estwise.o $(NEWG) +- $(CC) -g -o estwise estwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o estwise estwise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + + amplimer_resolver : amplimer_resolver.o dnaalign.o dnamatcher.o +- $(CC) -g -o amplimer_resolver amplimer_resolver.o dnamatcher.o dnaalign.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o amplimer_resolver amplimer_resolver.o dnamatcher.o dnaalign.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + genomewise : genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneutil.o geneoutput.o +- $(CC) -g -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + sywise : sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o geneutil.o standardout.o +- $(CC) -g -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + alignwise : alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o +- $(CC) -g -o alignwise alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o alignwise alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + test_splice : test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o +- $(CC) -g -o test_splice test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o test_splice test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + statwise : statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o +- $(CC) -g -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + pseudowise : pseudowise.o pseudowise7.o $(NEWG) +- $(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + clonewise : clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o +- $(CC) -g -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + + HMMER_LIBS = ../HMMer2/ +@@ -345,11 +345,11 @@ + CC = cc + #CFLAGS = -c -O2 -pg -I../base/ -I../dynlibsrc/ + #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ -I. +-CFLAGS = -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `glib-config --cflags` +-#CFLAGS = -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `glib-config --cflags` +-#LFLAGS = -L../base/ -L../dynlibsrc/ -L../HMMer2/ ++CFLAGS += -c -g3 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config --cflags glib-2.0` ++#CFLAGS += -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` ++#LDFLAGS = -L../base/ -L../dynlibsrc/ -L../HMMer2/ + +-LFLAGS = -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `glib-config --libs` ++LDFLAGS += -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `pkg-config --libs glib-2.0` + AR_OPTIONS = ru + + RANLIB_NEEDED = 0 +@@ -360,7 +360,7 @@ + + + #test : test.o libwisedb.a +-# $(CC) -o test test.o libwisedb.a -lprob -ldyn -lwisebase $(LFLAGS) ++# $(CC) -o test test.o libwisedb.a -lprob -ldyn -lwisebase $(LDFLAGS) + + + # +--- wise-2.4.1.orig/src/dnaindex/makefile ++++ wise-2.4.1/src/dnaindex/makefile +@@ -27,53 +27,53 @@ + + + kwise : kwise.o $(ASSEMBLY_OBJ) +- $(CC) -o kwise kwise.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs` ++ $(CC) -o kwise kwise.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `pkg-config --libs glib-2.0` + + arraymatcher : arraymatcher.o $(ASSEMBLY_OBJ) +- $(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs` ++ $(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `pkg-config --libs glib-2.0` + + + findbad_kmer : findbad_kmer.o $(ASSEMBLY_OBJ) +- $(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs` ++ $(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `pkg-config --libs glib-2.0` + + make_shotgun : make_shotgun.o shotgun.o +- $(CC) -o make_shotgun make_shotgun.o shotgun.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o make_shotgun make_shotgun.o shotgun.o -ldyna -lwisebase $(LDFLAGS) + + test_dnanumber : test_dnanumber.o dnanumber.o +- $(CC) -o test_dnanumber test_dnanumber.o dnanumber.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o test_dnanumber test_dnanumber.o dnanumber.o -ldyna -lwisebase $(LDFLAGS) + + test_linkindex : test_linkindex.o linkindex.o dnanumber.o +- $(CC) -o test_linkindex test_linkindex.o linkindex.o dnanumber.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o test_linkindex test_linkindex.o linkindex.o dnanumber.o -ldyna -lwisebase $(LDFLAGS) + + test_forwardindex : test_forwardindex.o forwardindex.o +- $(CC) -o test_forwardindex test_forwardindex.o forwardindex.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o test_forwardindex test_forwardindex.o forwardindex.o -ldyna -lwisebase $(LDFLAGS) + + test_euler : test_euler.o eulerindex.o singleseqspace.o +- $(CC) -o test_euler test_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o test_euler test_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LDFLAGS) + + test_kmer : test_kmer.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o kmer_assembly_untangler.o kmer_assembly_contig.o kmer_assembly_error.o assembly.o +- $(CC) -o test_kmer test_kmer.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o kmer_assembly_untangler.o kmer_assembly_error.o kmer_assembly_contig.o assembly.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o test_kmer test_kmer.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o kmer_assembly_untangler.o kmer_assembly_error.o kmer_assembly_contig.o assembly.o -ldyna -lwisebase $(LDFLAGS) + + kmer_stat : kmer_stat.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o +- $(CC) -o kmer_stat kmer_stat.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o kmer_stat kmer_stat.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o -ldyna -lwisebase $(LDFLAGS) + + test_compara : test_compara.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o +- $(CC) -o test_compara test_compara.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o test_compara test_compara.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o -ldyna -lwisebase $(LDFLAGS) + + bigseqwise : bigseqwise.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o +- $(CC) -o bigseqwise bigseqwise.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o bigseqwise bigseqwise.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o -ldyna -lwisebase $(LDFLAGS) + + + + + show_euler : show_euler.o eulerindex.o singleseqspace.o +- $(CC) -o show_euler show_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o show_euler show_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LDFLAGS) + + CC = cc +-CFLAGS = -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `glib-config --cflags` ++CFLAGS += $(CPPFLAGS) -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` + + +-LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lm ++LDFLAGS += -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lm + + + .c.o : +--- wise-2.4.1.orig/src/dnaindex/assembly/makefile ++++ wise-2.4.1/src/dnaindex/assembly/makefile +@@ -3,33 +3,33 @@ + .SUFFIXES : .dy + + test_basegraph : test_basegraph.o basegraph.o +- $(CC) -o test_basegraph test_basegraph.o basegraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o test_basegraph test_basegraph.o basegraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o $(LDFLAGS) -ldyna -lwisebase + + test_assemblygraph : test_assemblygraph.o assemblygraph.o assemblystats.o basegraph.o +- $(CC) -o test_assemblygraph test_assemblygraph.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o test_assemblygraph test_assemblygraph.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LDFLAGS) -ldyna -lwisebase + + + test_graphtangle : test_graphtangle.o assemblygraph.o assemblystats.o basegraph.o graphtangle.o assemblypath.o +- $(CC) -o test_graphtangle test_graphtangle.o assemblystats.o basegraph.o assemblygraph.o graphtangle.o assemblypath.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o ../kmer_hash.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o test_graphtangle test_graphtangle.o assemblystats.o basegraph.o assemblygraph.o graphtangle.o assemblypath.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o ../kmer_hash.o $(LDFLAGS) -ldyna -lwisebase + + + pathwise : pathwise.o supertangle.o assemblygraph.o assemblystats.o basegraph.o graphtangle.o assemblypath.o grapherror.o graphmanager.o depthmanager.o +- $(CC) -o pathwise pathwise.o supertangle.o depthmanager.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o graphtangle.o assemblypath.o grapherror.o graphmanager.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o ../assembly_sanger_project.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o pathwise pathwise.o supertangle.o depthmanager.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o graphtangle.o assemblypath.o grapherror.o graphmanager.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o ../assembly_sanger_project.o $(LDFLAGS) -ldyna -lwisebase + + + badkmer : badkmer.o assemblygraph.o assemblystats.o basegraph.o +- $(CC) -o badkmer badkmer.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o badkmer badkmer.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LDFLAGS) -ldyna -lwisebase + + arraymatcher : arraymatcher.o assemblygraph.o assemblystats.o basegraph.o +- $(CC) -o arraymatcher arraymatcher.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o arraymatcher arraymatcher.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LDFLAGS) -ldyna -lwisebase + + + + CC = cc +-CFLAGS = -Wall -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `glib-config --cflags` ++CFLAGS += $(CPPFLAGS) -Wall -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `pkg-config --cflags glib-2.0` + + +-LFLAGS = -g -L../../base/ -L../../dynlibsrc/ -lpthread `glib-config --libs` -lm ++LDFLAGS += -g -L../../base/ -L../../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lm + + + .c.o : +--- wise-2.4.1.orig/src/dynlibsrc/makefile ++++ wise-2.4.1/src/dynlibsrc/makefile +@@ -84,11 +84,11 @@ + CC = cc + INCFLAGS = -I../base/ + #CFLAGS = -Wall -g -pedantic -c -DUNIX -I../base/ +-CFLAGS = -Wall -pthread -g3 -DCOMPILE_VERBOSITY -DPTHREAD -O2 -c -DUNIX -I../base/ `glib-config --cflags` +-#CFLAGS = -Wall -g3 -pg -DPTHREAD -O2 -c -DUNIX -I../base/ `glib-config --cflags` +-#CFLAGS = -O2 -c -pthread -DUNIX -I../base/ `glib-config --cflags` ++CFLAGS += $(CPPFLAGS) -Wall -pthread -g3 -DCOMPILE_VERBOSITY -DPTHREAD -c -DUNIX -I../base/ `pkg-config --cflags glib-2.0` ++#CFLAGS += -Wall -g3 -pg -DPTHREAD -c -DUNIX -I../base/ `pkg-config --cflags glib-2.0` ++#CFLAGS += -c -pthread -DUNIX -I../base/ `pkg-config --cflags glib-2.0` + #CFLAGS = -O -c -DUNIX -DNOERROR -I../base/ +-LFLAGS = -g -L../base/ -lm ++LDFLAGS += -g -L../base/ -lm + AR_OPTIONS = ru + + RANLIB_NEEDED = 0 +@@ -133,47 +133,47 @@ + # + + test_genomic : genomic.o test_genomic.o sequence.o codon.o +- $(CC) -o test_genomic test_genomic.o genomic.o sequence.o codon.o ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS)-o test_genomic test_genomic.o genomic.o sequence.o codon.o ../base/libwisebase.a -lm + + test_tree : tree.o test_tree.o +- $(CC) -o test_tree test_tree.o tree.o libdyna.a ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -o test_tree test_tree.o tree.o libdyna.a ../base/libwisebase.a -lm + + test_intallocator : intallocator.o test_intallocator.o +- $(CC) -o test_intallocator intallocator.o test_intallocator.o ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -o test_intallocator intallocator.o test_intallocator.o ../base/libwisebase.a -lm + + test_psi : test_psi.o proteinstreamedindex.o +- $(CC) -o test_psi test_psi.o proteinstreamedindex.o ./libdyna.a ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -o test_psi test_psi.o proteinstreamedindex.o ./libdyna.a ../base/libwisebase.a -lm + + test_shadowindex : test_shadowindex.o shadowseqindex.o shadowseq.o libdyna.a +- $(CC) -g -o test_shadowindex test_shadowindex.o shadowseqindex.o shadowseq.o ./libdyna.a ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -g -o test_shadowindex test_shadowindex.o shadowseqindex.o shadowseq.o ./libdyna.a ../base/libwisebase.a -lm + + test_seqhash : test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a +- $(CC) -g -o test_seqhash `glib-config --libs` test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -g -o test_seqhash `pkg-config --libs glib-2.0` test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a ../base/libwisebase.a -lm + + test_hsp : test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o +- $(CC) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `glib-config --libs` ++ $(CC) $(LDFLAGS) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `pkg-config --libs glib-2.0` + + test_topscore : test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o +- $(CC) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `glib-config --libs` ++ $(CC) $(LDFLAGS) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `pkg-config --libs glib-2.0` + + + testgendb : probability.o genomicdb.o genomic.o testgendb.o sequence.o codon.o sequencedb.o complexsequence.o complexevalset.o +- $(CC) -o testgendb probability.o genomicdb.o genomic.o testgendb.o sequence.o codon.o sequencedb.o complexsequence.o complexevalset.o ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -o testgendb probability.o genomicdb.o genomic.o testgendb.o sequence.o codon.o sequencedb.o complexsequence.o complexevalset.o ../base/libwisebase.a -lm + + testseqalign : seqalign.o testseqalign.o sequence.o codon.o +- $(CC) -o testseqalign testseqalign.o seqalign.o sequence.o codon.o ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -o testseqalign testseqalign.o seqalign.o sequence.o codon.o ../base/libwisebase.a -lm + + testanc : libdyna.a +- $(CC) -o testanc ../models/testanc.o ../models/proteinsw.o ../models/abc.o ../models/pba.o ../models/sw_wrap.o libdyna.a ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -o testanc ../models/testanc.o ../models/proteinsw.o ../models/abc.o ../models/pba.o ../models/sw_wrap.o libdyna.a ../base/libwisebase.a -lm + + testdb : testdb.o sequencedb.o sequence.o codon.o probability.o +- $(CC) -o testdb testdb.o sequencedb.o sequence.o codon.o probability.o ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -o testdb testdb.o sequencedb.o sequence.o codon.o probability.o ../base/libwisebase.a -lm + + testpdb : testpdb.o protein.o proteindb.o complexevalset.o complexsequence.o sequencedb.o sequence.o codon.o probability.o randomdb.o randommodel.o histogram.o +- $(CC) -o testpdb testpdb.o protein.o proteindb.o complexsequence.o sequencedb.o sequence.o codon.o probability.o randomdb.o randommodel.o complexevalset.o histogram.o ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -o testpdb testpdb.o protein.o proteindb.o complexsequence.o sequencedb.o sequence.o codon.o probability.o randomdb.o randommodel.o complexevalset.o histogram.o ../base/libwisebase.a -lm + + testpb : testpairbase.o pairbase.o pairbaseseq.o sequence.o seqalign.o codon.o probability.o complexsequence.o complexevalset.o +- $(CC) -g -o testpb testpairbase.o pairbase.o pairbaseseq.o sequence.o codon.o seqalign.o probability.o complexsequence.o complexevalset.o ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -g -o testpb testpairbase.o pairbase.o pairbaseseq.o sequence.o codon.o seqalign.o probability.o complexsequence.o complexevalset.o ../base/libwisebase.a -lm + + .c.o : + $(CC) $(CFLAGS) $(INCFLAGS) $? +--- wise-2.4.1.orig/src/network/makefile ++++ wise-2.4.1/src/network/makefile +@@ -3,8 +3,8 @@ + + CC = cc + INCFLAGS = -I../base/ -I../socket -I../dynlibsrc -I../dnaindex +-CFLAGS = -O2 -c -pthread -DUNIX -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `glib-config --cflags` +-LFLAGS = -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `glib-config --libs` ++CFLAGS += $(CPPFLAGS) -c -pthread -DUNIX -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `pkg-config --cflags glib-2.0` ++LDFLAGS += -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config --libs glib-2.0` + AR_OPTIONS = ru + + RANLIB_NEEDED = 0 +@@ -13,7 +13,7 @@ + + + scanwise_server : wise_proteinindex_server.o net_hspscan.o ../dynlibsrc/libdyna.a ../dynlibsrc/libdyna_glib.a ../dnaindex/compressed_protein_index.o ../dnaindex/kmer_index_interface.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o +- $(CC) -g -o scanwise_server wise_proteinindex_server.o net_hspscan.o ../dnaindex/compressed_protein_index.o ../dnaindex/kmer_index_interface.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o -ldyna_glib -ldyna -lwisesocket -lwisebase $(LFLAGS) -lpthread ++ $(CC) -g -o scanwise_server wise_proteinindex_server.o net_hspscan.o ../dnaindex/compressed_protein_index.o ../dnaindex/kmer_index_interface.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o -ldyna_glib -ldyna -lwisesocket -lwisebase $(LDFLAGS) -lpthread + + + .c.o : +--- wise-2.4.1.orig/src/other_programs/makefile ++++ wise-2.4.1/src/other_programs/makefile +@@ -3,8 +3,8 @@ + .SUFFIXES : .dy + + CC = cc +-CFLAGS = -O2 -g3 -c -pthread -DUNIX -I../base/ -I../dynlibsrc `glib-config --cflags` +-LFLAGS = -g -L../base/ -L../dynlibsrc -lm `glib-config --libs` ++CFLAGS += $(CPPFLAGS) -g3 -c -pthread -DUNIX -I../base/ -I../dynlibsrc `pkg-config --cflags glib-2.0` ++LDFLAGS += -g -L../base/ -L../dynlibsrc -lm `pkg-config --libs glib-2.0` + AR_OPTIONS = ru + + RANLIB_NEEDED = 0 +--- wise-2.4.1.orig/src/base/makefile ++++ wise-2.4.1/src/base/makefile +@@ -19,9 +19,9 @@ + + + +-#CFLAGS = -c -g -DUNIX -DWISE_MEMORY_WATCH +-CFLAGS = -c -O2 -DUNIX -pthread +-LFLAGS = -g -lm ++#CFLAGS += -c -g -DUNIX -DWISE_MEMORY_WATCH ++CFLAGS += $(CPPFLAGS) -c -DUNIX -pthread ++LDFLAGS += -g -lm + DFLAGS = -n Wise2_ -a _api.h -b _api.t -l -D + AR_OPTIONS = ru + +--- wise-2.4.1.orig/src/HMMer2/Makefile ++++ wise-2.4.1/src/HMMer2/Makefile +@@ -13,7 +13,7 @@ + ## your compiler and compiler flags + # + CC = cc +-CFLAGS = -g ++CFLAGS += $(CPPFLAGS) -g + + ## machine specific definitions + # +@@ -75,25 +75,25 @@ + all: $(PROGS) + + hmmalign: $(OBJ) hmmalign.o +- $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmalign.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmalign.o $(OBJ) $(LIBS) + + hmmbuild: $(OBJ) hmmbuild.o +- $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmbuild.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmbuild.o $(OBJ) $(LIBS) + + hmmcalibrate: $(OBJ) hmmcalibrate.o +- $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmcalibrate.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmcalibrate.o $(OBJ) $(LIBS) + + hmmconvert: $(OBJ) hmmconvert.o +- $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmconvert.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmconvert.o $(OBJ) $(LIBS) + + hmmemit: $(OBJ) hmmemit.o +- $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmemit.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmemit.o $(OBJ) $(LIBS) + + hmmpfam: $(OBJ) hmmpfam.o +- $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmpfam.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmpfam.o $(OBJ) $(LIBS) + + hmmsearch: $(OBJ) hmmsearch.o +- $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmsearch.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmsearch.o $(OBJ) $(LIBS) + + ####### + ## Target used in making Shiva test suite diff --git a/academic/wise/patches/06_getline.patch b/academic/wise/patches/06_getline.patch new file mode 100644 index 0000000000..341cdae82e --- /dev/null +++ b/academic/wise/patches/06_getline.patch @@ -0,0 +1,305 @@ +Author: Philipp Benner <philipp@debian.org> +Last-Update: Sat, 31 Oct 2009 21:25:52 +0000 +Bug-Debian: http://bugs.debian.org/552821 +Description: Fixed conflicting definitions of getline(). + +--- wise-2.4.1.orig/src/HMMer2/sqio.c ++++ wise-2.4.1/src/HMMer2/sqio.c +@@ -213,7 +213,7 @@ + } + } + +-/* Function: getline() ++/* Function: getline_() + * Date: SRE, Tue Mar 3 08:30:01 1998 [St. Louis] + * + * Purpose: read a line from a sequence file into V->sbuffer. +@@ -229,7 +229,7 @@ + * Returns: (void) + */ + static void +-getline(struct ReadSeqVars *V) ++getline_(struct ReadSeqVars *V) + { + char *cp; + +@@ -299,7 +299,7 @@ + V->seqlen = 0; + if (addfirst) addseq(V->sbuffer, V); + do { +- getline(V); ++ getline_(V); + /* feof() alone is a bug; files not necessarily \n terminated */ + if (*(V->sbuffer) == '\0' && feof(V->f)) + done = TRUE; +@@ -327,7 +327,7 @@ + char *sptr; + /* load first line of entry */ + while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0) +- getline(V); ++ getline_(V); + if (feof(V->f)) return; + + if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL) +@@ -336,7 +336,7 @@ + SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID); + } + do { +- getline(V); ++ getline_(V); + if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0) + SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC); + else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0) +@@ -345,7 +345,7 @@ + SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC); + } + } while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0)); +- getline(V); /* skip next line, coords */ ++ getline_(V); /* skip next line, coords */ + + readLoop(0, endPIR, V); + +@@ -359,7 +359,7 @@ + /* get next line + */ + while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0) +- getline(V); ++ getline_(V); + } + + +@@ -377,7 +377,7 @@ + char *nm; + /* position past ';' comments */ + do { +- getline(V); ++ getline_(V); + } while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) )); + + if (!feof(V->f)) +@@ -389,7 +389,7 @@ + } + + while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';')))) +- getline(V); ++ getline_(V); + } + + static int +@@ -411,7 +411,7 @@ + if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL) + SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME); + } +- getline(V); ++ getline_(V); + } + + if (! feof(V->f)) +@@ -420,7 +420,7 @@ + /* load next line + */ + while ((!feof(V->f)) && (*V->sbuffer != ';')) +- getline(V); ++ getline_(V); + } + + +@@ -438,7 +438,7 @@ + int in_definition; + + while (strncmp(V->sbuffer, "LOCUS", 5) != 0) +- getline(V); ++ getline_(V); + + if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL) + { +@@ -449,7 +449,7 @@ + in_definition = FALSE; + while (! feof(V->f)) + { +- getline(V); ++ getline_(V); + if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer) + { + if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL) +@@ -482,11 +482,11 @@ + + + while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer)))) +- getline(V); ++ getline_(V); + /* SRE: V->s now holds "//", so sequential + reads are wedged: fixed Tue Jul 13 1993 */ + while (!feof(V->f) && strstr(V->sbuffer, "LOCUS ") != V->sbuffer) +- getline(V); ++ getline_(V); + } + + static int +@@ -515,7 +515,7 @@ + Die("bogus GCGdata format? %s", V->sbuffer); + + /* second line contains free text description */ +- getline(V); ++ getline_(V); + SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC); + + if (binary) { +@@ -535,7 +535,7 @@ + else readLoop(0, endGCGdata, V); + + while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>')))) +- getline(V); ++ getline_(V); + } + + static int +@@ -555,12 +555,12 @@ + if ((sptr = strtok(NULL, "\n")) != NULL) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC); + /* workaround for long NCBI NR lines */ +- while (V->longline && ! feof(V->f)) getline(V); ++ while (V->longline && ! feof(V->f)) getline_(V); + + readLoop(0, endPearson, V); + + while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>')))) +- getline(V); ++ getline_(V); + } + + +@@ -587,7 +587,7 @@ + + /* make sure we have first line */ + while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0) +- getline(V); ++ getline_(V); + + if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL) + { +@@ -596,7 +596,7 @@ + } + + do { +- getline(V); ++ getline_(V); + if (!feof(V->f) && strstr(V->sbuffer, "AC ") == V->sbuffer) + { + if ((sptr = strtok(V->sbuffer+5, "; \t\n")) != NULL) +@@ -620,7 +620,7 @@ + + /* load next record's ID line */ + while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0) +- getline(V); ++ getline_(V); + } + + +@@ -636,7 +636,7 @@ + { + char *sptr; + +- getline(V); /*s == "seqLen seqid string..."*/ ++ getline_(V); /*s == "seqLen seqid string..."*/ + + if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); +@@ -647,7 +647,7 @@ + readLoop(0, endZuker, V); + + while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '(')))) +- getline(V); ++ getline_(V); + } + + static void +@@ -669,7 +669,7 @@ + + do { + done = feof(V->f); +- getline(V); ++ getline_(V); + if (! done) addseq(V->sbuffer, V); + } while (!done); + } +@@ -681,7 +681,7 @@ + char *sptr; + int dostruc = FALSE; + +- while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V); ++ while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline_(V); + + if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); +@@ -689,7 +689,7 @@ + /*CONSTCOND*/ + while (1) + { +- getline(V); ++ getline_(V); + if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; } + + if (strncmp(V->sbuffer, "SRC ", 4) == 0) +@@ -721,14 +721,14 @@ + while (1) + { + /* sequence line */ +- getline(V); ++ getline_(V); + if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0) + break; + addseq(V->sbuffer, V); + /* structure line */ + if (dostruc) + { +- getline(V); ++ getline_(V); + if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; } + addstruc(V->sbuffer, V); + } +@@ -736,7 +736,7 @@ + + + while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0) +- getline(V); ++ getline_(V); + } + + +@@ -816,7 +816,7 @@ + + /* Load the first line. + */ +- getline(dbfp); ++ getline_(dbfp); + + return dbfp; + } +@@ -833,7 +833,7 @@ + Die("SeqfilePosition() failed: in a nonrewindable data file or stream"); + + fseek(sqfp->f, offset, SEEK_SET); +- getline(sqfp); ++ getline_(sqfp); + } + + +@@ -853,7 +853,7 @@ + if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0; + else { + rewind(sqfp->f); +- getline(sqfp); ++ getline_(sqfp); + } + } + +@@ -949,7 +949,7 @@ + do { /* skip leading comments on GCG file */ + gotuw = (strstr(V->sbuffer,"..") != NULL); + if (gotuw) readUWGCG(V); +- getline(V); ++ getline_(V); + } while (! feof(V->f)); + break; + diff --git a/academic/wise/patches/07_ld--as-needed.patch b/academic/wise/patches/07_ld--as-needed.patch new file mode 100644 index 0000000000..51ee254370 --- /dev/null +++ b/academic/wise/patches/07_ld--as-needed.patch @@ -0,0 +1,52 @@ +Description: Fix FTBFS with ld --as-needed. +Bug-Ubuntu: https://bugs.launchpad.net/ubuntu/+source/wise/+bug/832935 + +--- wise-2.4.1.orig/src/models/makefile ++++ wise-2.4.1/src/models/makefile +@@ -215,7 +215,7 @@ + $(CC) $(CFLAGS) $(INCFLAGS) -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c + + scanwise : scanwisep_wiseserver.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o +- $(CC) -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o ../network/client_multihspscan.o $(LDFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread ++ $(CC) -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o ../network/client_multihspscan.o $(LDFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread $(LDFLAGS) + + scanwisep_compress.o : scanwisep.c + $(CC) $(CFLAGS) -DSCAN_COMPRESS -I../dnaindex -I../network -I../socket -I../external/mott scanwisep.c +@@ -275,7 +275,7 @@ + $(CC) -o makerandomdb makerandomdb.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + genewise : genewise.o $(NEWG) +- $(CC) -o genewise genewise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o genewise genewise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) $(LDFLAGS) + + cdnawise : cdnawise.o $(NEWG) cdnawise10.o + $(CC) -g -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) +@@ -300,16 +300,16 @@ + + + genewisedb : genewisedb.o $(NEWG) +- $(CC) -g -o genewisedb genewisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o genewisedb genewisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) $(LDFLAGS) + + estwisedb : estwisedb.o $(NEWG) +- $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) $(LDFLAGS) + + edb : estwisedb.o $(NEWG) + $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -lefence + + estwise : estwise.o $(NEWG) +- $(CC) -g -o estwise estwise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o estwise estwise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) $(LDFLAGS) + + + amplimer_resolver : amplimer_resolver.o dnaalign.o dnamatcher.o +@@ -331,7 +331,7 @@ + $(CC) -g -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + pseudowise : pseudowise.o pseudowise7.o $(NEWG) +- $(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) $(LDFLAGS) + + clonewise : clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o + $(CC) -g -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) diff --git a/academic/wise/patches/08_mayhem.patch b/academic/wise/patches/08_mayhem.patch new file mode 100644 index 0000000000..c54c7c66ab --- /dev/null +++ b/academic/wise/patches/08_mayhem.patch @@ -0,0 +1,103 @@ +Author: Philipp Benner <philipp@debian.org> +Last-Update: Sun, 07 Jul 2013 13:33:01 +0200 +Description: Fix run time errors detected by Mayhem + +--- wise-2.4.1.orig/src/models/dbac.c ++++ wise-2.4.1/src/models/dbac.c +@@ -535,8 +535,12 @@ + * + */ + +- one = read_fasta_file_Sequence(*argv++); +- two = read_fasta_file_Sequence(*argv++); ++ if( (one = read_fasta_file_Sequence(*argv++)) == NULL ) { ++ fatal("Unable to read the sequence in file"); ++ } ++ if( (two = read_fasta_file_Sequence(*argv++)) == NULL ) { ++ fatal("Unable to read the sequence in file"); ++ } + + uppercase_Sequence(one); + uppercase_Sequence(two); +--- wise-2.4.1.orig/src/models/estwise.c ++++ wise-2.4.1/src/models/estwise.c +@@ -313,7 +313,7 @@ + } + } + +- if( reverse == TRUE ) { ++ if( cdna && reverse == TRUE ) { + if( tstart > tend ) { + warn("You have already reversed the DNA by using %d - %d truncation. Re-reversing",tstart,tend); + } +@@ -323,7 +323,7 @@ + cdna = cdna_temp; + } + +- if( target_abs == TRUE ) { ++ if( cdna && target_abs == TRUE ) { + cdna->baseseq->offset = 1; + cdna->baseseq->end = strlen(cdna->baseseq->seq); + } +@@ -472,8 +472,11 @@ + } + + cp = flat_cDNAParser(indel_error); +- cm = flat_CodonMapper(ct); +- sprinkle_errors_over_CodonMapper(cm,subs_error); ++ ++ if( ct ) { ++ cm = flat_CodonMapper(ct); ++ sprinkle_errors_over_CodonMapper(cm,subs_error); ++ } + + return ret; + +--- wise-2.4.1.orig/src/models/genewise.c ++++ wise-2.4.1/src/models/genewise.c +@@ -550,8 +550,10 @@ + ret = FALSE; + } + +- gen->baseseq->offset = 1; +- gen->baseseq->end = strlen(gen->baseseq->seq); ++ if ( gen ) { ++ gen->baseseq->offset = 1; ++ gen->baseseq->end = strlen(gen->baseseq->seq); ++ } + } + + if( alg_str != NULL ) { +--- wise-2.4.1.orig/src/models/estwisedb.c ++++ wise-2.4.1/src/models/estwisedb.c +@@ -688,8 +688,11 @@ + + + cps = flat_cDNAParser(indel_error); +- cm = flat_CodonMapper(ct); +- sprinkle_errors_over_CodonMapper(cm,subs_error); ++ ++ if( ct ) { ++ cm = flat_CodonMapper(ct); ++ sprinkle_errors_over_CodonMapper(cm,subs_error); ++ } + + return ret; + +--- wise-2.4.1.orig/src/models/promoterwise.c ++++ wise-2.4.1/src/models/promoterwise.c +@@ -147,8 +147,12 @@ + + lchs = standard_LocalCisHitScore(NMaskType_VARIABLE); + +- query = read_fasta_file_Sequence(argv[1]); +- target = read_fasta_file_Sequence(argv[2]); ++ if( (query = read_fasta_file_Sequence(argv[1])) == NULL ) { ++ fatal("Unable to read the sequence in query file"); ++ } ++ if( (target = read_fasta_file_Sequence(argv[2])) == NULL ) { ++ fatal("Unable to read the sequence in target file"); ++ } + + for(i=0;i<query->len;i++) { + query->seq[i] = toupper(query->seq[i]); diff --git a/academic/wise/patches/09_dnal-add-return-statement.patch b/academic/wise/patches/09_dnal-add-return-statement.patch new file mode 100644 index 0000000000..62931ed624 --- /dev/null +++ b/academic/wise/patches/09_dnal-add-return-statement.patch @@ -0,0 +1,17 @@ +Author: Dejan Latinovic <Dejan.Latinovic@imgtec.com> +Last-Update: Mon, 4 Aug 2014 17:10:38 +0000 +Bug-Debian: http://bugs.debian.org/751277 +Description: Make sure dnal has a valid return value + This affects a bug reported against python-biopython. + +--- wise-2.4.1.orig/src/models/dnal.c ++++ wise-2.4.1/src/models/dnal.c +@@ -75,6 +75,8 @@ + + if( show_alb == TRUE ) + dump_ascii_AlnBlock(alb,stdout); ++ ++ return 0; + } + + diff --git a/academic/wise/patches/10_fix_path_to_data_files.patch b/academic/wise/patches/10_fix_path_to_data_files.patch new file mode 100644 index 0000000000..f437241cd1 --- /dev/null +++ b/academic/wise/patches/10_fix_path_to_data_files.patch @@ -0,0 +1,337 @@ +Author: Andreas Tille <tille@debian.org> +Last-Update: Mon, 04 Aug 2014 19:25:58 +0200 +Description: Brute force patch to fix the PATH to the data files to make the + tools finding the needed data for the test suite + . + In principle the PATH should be configurable and the test suite script even + contains a parameter (-cf) for this - but this seems to be ignored. + . + The correct way to deal with this would be a configuration option but I had + no intend to spend to much time into some software that was declared to be + orphaned (superseded by exonerate). So this primitive patch works to run + the test suite successfully (which is not the case without the patch). + +--- a/src/models/estwise.c ++++ b/src/models/estwise.c +@@ -484,8 +484,8 @@ boolean build_objects(void) + + void build_defaults(void) + { +- codon_file = "codon.table"; +- matrix_file = "BLOSUM62.bla"; ++ codon_file = "/usr/share/wise/codon.table"; ++ matrix_file = "/usr/share/wise/BLOSUM62.bla"; + + + +--- a/src/models/estwisedb.c ++++ b/src/models/estwisedb.c +@@ -78,7 +78,7 @@ char * qend_str = NULL; + int qend = -1; + + +-char * matrix_file = "BLOSUM62.bla"; ++char * matrix_file = "/usr/share/wise/BLOSUM62.bla"; + CompMat * mat = NULL; + + char * gap_str = "12"; +@@ -849,8 +849,8 @@ void show_version(FILE * ofp) + + void build_defaults(void) + { +- codon_file = "codon.table"; +- matrix_file = "BLOSUM62.bla"; ++ codon_file = "/usr/share/wise/codon.table"; ++ matrix_file = "/usr/share/wise/BLOSUM62.bla"; + + + } +--- a/src/models/pswdb.c ++++ b/src/models/pswdb.c +@@ -40,7 +40,7 @@ int max_desc = 500; + + char * querydb = NULL; + char * targetdb = NULL; +-char * matrix_file = "BLOSUM62.bla"; ++char * matrix_file = "/usr/share/wise/BLOSUM62.bla"; + char * output_file = "-"; + + char * cutoff_str = NULL; +@@ -65,7 +65,7 @@ void show_help(FILE * ofp) + fprintf(ofp,"\npswdb <options> <query_db> <target_db>\nSeqs in fasta format\n" + "\t-g gap penalty (default 12)\n" + "\t-e ext penatly (default 2)\n" +- "\t-m comp matrix (default BLOSUM62.bla)\n" ++ "\t-m comp matrix (default /usr/share/wise/BLOSUM62.bla)\n" + "\t-abc use the abc model\n" + "\t-a a penalty for above (default 120)\n" + "\t-b b penalty for above (default 10)\n" +@@ -397,7 +397,7 @@ int main(int argc,char *argv[]) + + matrix_file = strip_out_assigned_argument(&argc,argv,"m"); + if( matrix_file == NULL) +- matrix_file = "BLOSUM62.bla"; ++ matrix_file = "/usr/share/wise/BLOSUM62.bla"; + + /* database implementation stuff */ + dbsi = new_DBSearchImpl_from_argv(&argc,argv); +--- a/src/models/genewisedb.c ++++ b/src/models/genewisedb.c +@@ -77,7 +77,7 @@ int qend = -1; + char * gene_file = NULL; + GeneFrequency21 * gf = NULL; + +-char * matrix_file = "BLOSUM62.bla"; ++char * matrix_file = "/usr/share/wise/BLOSUM62.bla"; + CompMat * mat = NULL; + + char * gap_str = "12"; +@@ -1015,9 +1015,9 @@ void show_version(FILE * ofp) + + void build_defaults(void) + { +- gene_file = "human.gf"; +- codon_file = "codon.table"; +- matrix_file = "BLOSUM62.bla"; ++ gene_file = "/usr/share/wise/human.gf"; ++ codon_file = "/usr/share/wise/codon.table"; ++ matrix_file = "/usr/share/wise/BLOSUM62.bla"; + + + } +--- a/src/models/genewise.c ++++ b/src/models/genewise.c +@@ -749,10 +749,10 @@ boolean build_objects(void) + + void build_defaults(void) + { +- gene_file = "human.gf"; +- new_gene_file = "gene.stat"; +- codon_file = "codon.table"; +- matrix_file = "BLOSUM62.bla"; ++ gene_file = "/usr/share/wise/human.gf"; ++ new_gene_file = "/usr/share/wise/gene.stat"; ++ codon_file = "/usr/share/wise/codon.table"; ++ matrix_file = "/usr/share/wise/BLOSUM62.bla"; + + + } +--- a/src/models/scanwisep.c ++++ b/src/models/scanwisep.c +@@ -157,7 +157,7 @@ ScanWiseHSPImpl * new_ScanWiseHSPImpl_fr + out->use_multiscan = FALSE; + out->ior_file = NULL; + out->direct_sequence = NULL; +- out->matrix_file = "BLOSUM62.bla"; ++ out->matrix_file = "/usr/share/wise/BLOSUM62.bla"; + out->step = 32; + out->host = "localhost"; + out->port = 4050; +@@ -546,7 +546,7 @@ int main(int argc,char ** argv) + + /* ugly, but we don't want to bounce matrices around the network... */ + +- mat = read_Blast_file_CompMat("BLOSUM62.bla"); ++ mat = read_Blast_file_CompMat("/usr/share/wise/BLOSUM62.bla"); + + erroroff(REPORT); + +--- a/src/models/psw.c ++++ b/src/models/psw.c +@@ -24,7 +24,7 @@ void show_help(FILE * ofp) + "\tOPTIONS\n" + "\t-g gap penalty (default 12)\n" + "\t-e ext penatly (default 2)\n" +- "\t-m comp matrix (default BLOSUM62.bla)\n" ++ "\t-m comp matrix (default /usr/share/wise/BLOSUM62.bla)\n" + "\t-abc use the abc model\n" + "\t-a a penalty for above (default 120)\n" + "\t-b b penalty for above (default 10)\n" +@@ -126,7 +126,7 @@ int main(int argc,char ** argv) + + comp_file = strip_out_assigned_argument(&argc,argv,"m"); + if( comp_file == NULL) +- comp_file = "BLOSUM62.bla"; ++ comp_file = "/usr/share/wise/BLOSUM62.bla"; + + if( (temp = strip_out_assigned_argument(&argc,argv,"dpenv")) != NULL ) { + dpenv = read_DPEnvelope_file(temp); +--- a/src/test/basic_cdna.out ++++ b/src/test/basic_cdna.out +@@ -3,13 +3,13 @@ This program is freely distributed under + Copyright (c) GRL limited: portions of the code are from separate copyrights + + Query protein: roa1_drome +-Comp Matrix: BLOSUM62.bla ++Comp Matrix: /usr/share/wise/BLOSUM62.bla + Gap open: 12 + Gap extension: 2 + Start/End default + Target Sequence HSHNCPA1 + Strand: both +-Codon Table: codon.table ++Codon Table: /usr/share/wise/codon.table + Subs error: 1e-05 + Indel error: 1e-05 + Algorithm 333 +--- a/src/test/basic_genomic.out ++++ b/src/test/basic_genomic.out +@@ -3,17 +3,17 @@ This program is freely distributed under + Copyright (c) GRL limited: portions of the code are from separate copyright + + Query protein: roa1_drome +-Comp Matrix: BLOSUM62.bla ++Comp Matrix: /usr/share/wise/BLOSUM62.bla + Gap open: 12 + Gap extension: 2 + Start/End default + Target Sequence HSHNCPA1 + Strand: forward + Start/End (protein) default +-Gene Parameter file: gene.stat ++Gene Parameter file: /usr/share/wise/gene.stat + Splice site model: GT/AG only + GT/AG bits penalty -9.96 +-Codon Table: codon.table ++Codon Table: /usr/share/wise/codon.table + Subs error: 1e-06 + Indel error: 1e-06 + Null model syn +--- a/src/test/pswdb.out ++++ b/src/test/pswdb.out +@@ -12,7 +12,7 @@ Gap open: 12 + Gap extension: 2 + Query info from: road.pep + Database info from: pep.fa +-Comp Matrix: BLOSUM62.bla ++Comp Matrix: /usr/share/wise/BLOSUM62.bla + [Warning: Can't fit histogram to a db smaller than 1,000] + + +--- a/src/models/genestats.c ++++ b/src/models/genestats.c +@@ -22,7 +22,7 @@ void show_help_GeneModelParam(FILE * ofp + fprintf(ofp," -splice_score_offset [%.1f] score offset for splice sites\n",DEFAULT_SPLICE_OFFSET_SCORE); + fprintf(ofp," -[no]splice_gtag make just gtag splice sites (default is gtag, ie no model)\n"); + fprintf(ofp," -splice_gtag_prob [0.001] probability for gt/ag \n"); +- fprintf(ofp," -genestats [gene.stat]\n"); ++ fprintf(ofp," -genestats [/usr/share/wise/gene.stat]\n"); + + } + +@@ -270,7 +270,7 @@ GeneModelParam * std_GeneModelParam(void + out->min_collar = -5.0; + out->max_collar = +5.0; + out->score_offset = DEFAULT_SPLICE_OFFSET_SCORE; +- out->gene_stats_file = stringalloc("gene.stat"); ++ out->gene_stats_file = stringalloc("/usr/share/wise/gene.stat"); + out->use_gtag_splice = TRUE; + + out->prob_for_gtag = 0.001; +--- a/src/models/genestats.dy ++++ b/src/models/genestats.dy +@@ -103,7 +103,7 @@ void show_help_GeneModelParam(FILE * ofp + fprintf(ofp," -splice_score_offset [%.1f] score offset for splice sites\n",DEFAULT_SPLICE_OFFSET_SCORE); + fprintf(ofp," -[no]splice_gtag make just gtag splice sites (default is gtag, ie no model)\n"); + fprintf(ofp," -splice_gtag_prob [0.001] probability for gt/ag \n"); +- fprintf(ofp," -genestats [gene.stat]\n"); ++ fprintf(ofp," -genestats [/usr/share/wise/gene.stat]\n"); + + } + +@@ -290,7 +290,7 @@ GeneModelParam * std_GeneModelParam(void + out->min_collar = -5.0; + out->max_collar = +5.0; + out->score_offset = DEFAULT_SPLICE_OFFSET_SCORE; +- out->gene_stats_file = stringalloc("gene.stat"); ++ out->gene_stats_file = stringalloc("/usr/share/wise/gene.stat"); + out->use_gtag_splice = TRUE; + + out->prob_for_gtag = 0.001; +--- a/src/models/testgenestat.c ++++ b/src/models/testgenestat.c +@@ -23,7 +23,7 @@ int main(int argc,char ** argv) + + seq = read_fasta_file_Sequence("../../test_data/human.genomic"); + +- ifp = openfile("gene.stat","r"); ++ ifp = openfile("/usr/share/wise/gene.stat","r"); + + st = read_GeneStats(ifp); + +--- a/src/test/hmm_genomic.out ++++ b/src/test/hmm_genomic.out +@@ -7,10 +7,10 @@ Start/End local + Target Sequence HSHNCPA1 + Strand: forward + Start/End (protein) local +-Gene Parameter file: gene.stat ++Gene Parameter file: /usr/share/wise/gene.stat + Splice site model: GT/AG only + GT/AG bits penalty -9.96 +-Codon Table: codon.table ++Codon Table: /usr/share/wise/codon.table + Subs error: 1e-06 + Indel error: 1e-06 + Null model syn +--- a/src/test/hmm_cdna.out ++++ b/src/test/hmm_cdna.out +@@ -6,7 +6,7 @@ Query model: unnamed + Start/End default + Target Sequence HSHNCPA1 + Strand: both +-Codon Table: codon.table ++Codon Table: /usr/share/wise/codon.table + Subs error: 1e-05 + Indel error: 1e-05 + Algorithm 333L +--- a/src/test/genewise-db.out ++++ b/src/test/genewise-db.out +@@ -12,8 +12,8 @@ Search mode: Single protein vs + Protein info from: rrm.HMM + Dna info from: dna.db + Start/End (protein) global +-Gene Paras: human.gf +-Codon Table: codon.table ++Gene Paras: /usr/share/wise/human.gf ++Codon Table: /usr/share/wise/codon.table + Subs error: 1e-05 + Indel error: 1e-05 + Model splice? model +--- a/src/test/genewise-db-lite.out ++++ b/src/test/genewise-db-lite.out +@@ -12,8 +12,8 @@ Search mode: Single protein vs + Protein info from: rrm.HMM + Dna info from: dna.db + Start/End (protein) global +-Gene Paras: human.gf +-Codon Table: codon.table ++Gene Paras: /usr/share/wise/human.gf ++Codon Table: /usr/share/wise/codon.table + Subs error: 1e-05 + Indel error: 1e-05 + Model splice? model +--- a/src/test/estwise-db.out ++++ b/src/test/estwise-db.out +@@ -13,7 +13,7 @@ Search mode: Single protein vs + Protein info from: rrm.HMM + Dna info from: dna.db + Start/End local +-Codon Table: codon.table ++Codon Table: /usr/share/wise/codon.table + Subs error: 0.01 + Indel error: 0.01 + Null model: synchronous +--- a/src/test/genewisedb-pfam.out ++++ b/src/test/genewisedb-pfam.out +@@ -12,8 +12,8 @@ Search mode: Single genomic vs + Protein info from: rrm.HMM + Dna info from: short.dna + Start/End (protein) default +-Gene Paras: human.gf +-Codon Table: codon.table ++Gene Paras: /usr/share/wise/human.gf ++Codon Table: /usr/share/wise/codon.table + Subs error: 1e-05 + Indel error: 1e-05 + Model splice? model diff --git a/academic/wise/patches/11_consistent_manual_dates.patch b/academic/wise/patches/11_consistent_manual_dates.patch new file mode 100644 index 0000000000..eaea1eec90 --- /dev/null +++ b/academic/wise/patches/11_consistent_manual_dates.patch @@ -0,0 +1,53 @@ +Description: Use fixed dates for manuals. + These make the build reproducible. I have picked the file modificatin dates of + the corresponding source .tex files. +Author: Sascha Steinbiss <sascha@steinbiss.name> +--- a/docs/dynamite.tex ++++ b/docs/dynamite.tex +@@ -1,4 +1,5 @@ + \documentstyle{article} ++\pdftrailerid{} + \begin{document} + + \newcommand{\programtext}[1]{{\tt #1}} +@@ -10,6 +11,7 @@ + Hinxton, Cambridge CB10 1SA,\\ + England.\\ + Email: birney@sanger.ac.uk} ++\date{18/6/2001} + + \maketitle + +--- a/docs/wise2.tex ++++ b/docs/wise2.tex +@@ -1,5 +1,6 @@ + + \documentclass{article} ++\pdftrailerid{} + %\usepackage{epsfig} + \usepackage{graphicx} + +@@ -13,6 +14,7 @@ + Hinxton, Cambridge CB10 1SD,\\ + England.\\ + Email: birney@ebi.ac.uk} ++\date{18/6/2001} + + \maketitle + +--- a/docs/wise2api.tex ++++ b/docs/wise2api.tex +@@ -1,4 +1,5 @@ + \documentstyle{article} ++\pdftrailerid{} + \begin{document} + + \newcommand{\programtext}[1]{{\tt #1}} +@@ -10,6 +11,7 @@ + Hinxton, Cambridge CB10 1SA,\\ + England.\\ + Email: birney@sanger.ac.uk} ++\date{18/6/2001} + + \maketitle + diff --git a/academic/wise/patches/cross.patch b/academic/wise/patches/cross.patch new file mode 100644 index 0000000000..f6da1363d0 --- /dev/null +++ b/academic/wise/patches/cross.patch @@ -0,0 +1,266 @@ +Date: Sat, 18 Apr 2020 11:59:09 +0200 +From: Helmut Grohne <helmut@subdivi.de> +Bug-Debian: https://bugs.debian.org/958094 +Description: Do not hard code the build architecture pkg-config + +--- a/src/corba/makefile ++++ b/src/corba/makefile +@@ -1,9 +1,10 @@ + + + CC = cc ++PKG_CONFIG ?= pkg-config + INCFLAGS = -I../base/ -I../dynlibsrc + #gCFLAGS = -Wall -g -pedantic -c -DUNIX -I../base/ +-#CFLAGS += -c -DUNIX -I../base/ `pkg-config --cflags glib-2.0` -I/usr/local/include/orbit-1.0/ ++#CFLAGS += -c -DUNIX -I../base/ `$(PKG_CONFIG) --cflags glib-2.0` -I/usr/local/include/orbit-1.0/ + CFLAGS += $(CPPFLAGS) -pthread -c -DUNIX -I../base/ -I../dynlibsrc `orbit-config --cflags client` + LDFLAGS += -L../base/ -lm -lpthread + AR_OPTIONS = ru +@@ -14,18 +15,18 @@ hspscan_corba.c : hspscan_corba.idl + orbit-idl hspscan_corba.idl + + test_server : test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o +- cc -g -o test_server test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o ../dynlibsrc/libdyna_glib.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread ++ cc -g -o test_server test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o ../dynlibsrc/libdyna_glib.a `$(PKG_CONFIG) --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread + + scanwise_protein_index : scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o +- cc -o scanwise_protein_index scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna_glib.a ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread ++ cc -o scanwise_protein_index scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna_glib.a ../dynlibsrc/libdyna.a ../base/libwisebase.a `$(PKG_CONFIG) --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread + + + test_client : test_client.o hspscan_corba-common.o hspscan_corba-stubs.o +- cc -g -o test_client test_client.o hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread ++ cc -g -o test_client test_client.o hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `$(PKG_CONFIG) --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread + + + test_wrapper : test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o hspscan_corba_wrapper.o corba_singleton.o +- cc -g -o test_wrapper test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o corba_singleton.o hspscan_corba_wrapper.o ../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread ++ cc -g -o test_wrapper test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o corba_singleton.o hspscan_corba_wrapper.o ../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `$(PKG_CONFIG) --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread + + .c.o : + $(CC) $(CFLAGS) $(INCFLAGS) $? +--- a/src/dnaindex/assembly/makefile ++++ b/src/dnaindex/assembly/makefile +@@ -26,10 +26,11 @@ arraymatcher : arraymatcher.o assemblygr + + + CC = cc +-CFLAGS += $(CPPFLAGS) -Wall -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `pkg-config --cflags glib-2.0` ++PKG_CONFIG ?= pkg-config ++CFLAGS += $(CPPFLAGS) -Wall -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `$(PKG_CONFIG) --cflags glib-2.0` + + +-LDFLAGS += -g -L../../base/ -L../../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lm ++LDFLAGS += -g -L../../base/ -L../../dynlibsrc/ -lpthread `$(PKG_CONFIG) --libs glib-2.0` -lm + + + .c.o : +--- a/src/dnaindex/makefile ++++ b/src/dnaindex/makefile +@@ -27,14 +27,14 @@ all: $(ASSEMBLY_OBJ) + + + kwise : kwise.o $(ASSEMBLY_OBJ) +- $(CC) -o kwise kwise.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `pkg-config --libs glib-2.0` ++ $(CC) -o kwise kwise.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `$(PKG_CONFIG) --libs glib-2.0` + + arraymatcher : arraymatcher.o $(ASSEMBLY_OBJ) +- $(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `pkg-config --libs glib-2.0` ++ $(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `$(PKG_CONFIG) --libs glib-2.0` + + + findbad_kmer : findbad_kmer.o $(ASSEMBLY_OBJ) +- $(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `pkg-config --libs glib-2.0` ++ $(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `$(PKG_CONFIG) --libs glib-2.0` + + make_shotgun : make_shotgun.o shotgun.o + $(CC) -o make_shotgun make_shotgun.o shotgun.o -ldyna -lwisebase $(LDFLAGS) +@@ -70,10 +70,11 @@ show_euler : show_euler.o eulerindex.o s + $(CC) -o show_euler show_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LDFLAGS) + + CC = cc +-CFLAGS += $(CPPFLAGS) -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` ++PKG_CONFIG ?= pkg-config ++CFLAGS += $(CPPFLAGS) -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `$(PKG_CONFIG) --cflags glib-2.0` + + +-LDFLAGS += -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lm ++LDFLAGS += -g -L../base/ -L../dynlibsrc/ -lpthread `$(PKG_CONFIG) --libs glib-2.0` -lm + + + .c.o : +--- a/src/dynlibsrc/makefile ++++ b/src/dynlibsrc/makefile +@@ -82,11 +82,12 @@ DYNHELPEROBJ = packaln.o \ + + + CC = cc ++PKG_CONFIG ?= pkg-config + INCFLAGS = -I../base/ + #CFLAGS = -Wall -g -pedantic -c -DUNIX -I../base/ +-CFLAGS += $(CPPFLAGS) -Wall -pthread -g3 -DCOMPILE_VERBOSITY -DPTHREAD -c -DUNIX -I../base/ `pkg-config --cflags glib-2.0` +-#CFLAGS += -Wall -g3 -pg -DPTHREAD -c -DUNIX -I../base/ `pkg-config --cflags glib-2.0` +-#CFLAGS += -c -pthread -DUNIX -I../base/ `pkg-config --cflags glib-2.0` ++CFLAGS += $(CPPFLAGS) -Wall -pthread -g3 -DCOMPILE_VERBOSITY -DPTHREAD -c -DUNIX -I../base/ `$(PKG_CONFIG) --cflags glib-2.0` ++#CFLAGS += -Wall -g3 -pg -DPTHREAD -c -DUNIX -I../base/ `$(PKG_CONFIG) --cflags glib-2.0` ++#CFLAGS += -c -pthread -DUNIX -I../base/ `$(PKG_CONFIG) --cflags glib-2.0` + #CFLAGS = -O -c -DUNIX -DNOERROR -I../base/ + LDFLAGS += -g -L../base/ -lm + AR_OPTIONS = ru +@@ -148,13 +149,13 @@ test_shadowindex : test_shadowindex.o sh + $(CC) $(LDFLAGS) -g -o test_shadowindex test_shadowindex.o shadowseqindex.o shadowseq.o ./libdyna.a ../base/libwisebase.a -lm + + test_seqhash : test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a +- $(CC) $(LDFLAGS) -g -o test_seqhash `pkg-config --libs glib-2.0` test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -g -o test_seqhash `$(PKG_CONFIG) --libs glib-2.0` test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a ../base/libwisebase.a -lm + + test_hsp : test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o +- $(CC) $(LDFLAGS) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `pkg-config --libs glib-2.0` ++ $(CC) $(LDFLAGS) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `$(PKG_CONFIG) --libs glib-2.0` + + test_topscore : test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o +- $(CC) $(LDFLAGS) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `pkg-config --libs glib-2.0` ++ $(CC) $(LDFLAGS) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `$(PKG_CONFIG) --libs glib-2.0` + + + testgendb : probability.o genomicdb.o genomic.o testgendb.o sequence.o codon.o sequencedb.o complexsequence.o complexevalset.o +--- a/src/makefile ++++ b/src/makefile +@@ -23,6 +23,7 @@ + # Most likely you have a non ANSI C compiler + # CC = /opt/intel_cc_80/bin/icc + CC = cc ++PKG_CONFIG ?= pkg-config + + # These are the CFLAGS to use. These days Wise2 is inherently + # pthreaded, and everything is compiled with threads. However +@@ -31,13 +32,13 @@ CC = cc + + + # Intel icc flags +-# CFLAGS += -c -axWK -ipo `pkg-config --cflags glib-2.0` ++# CFLAGS += -c -axWK -ipo `$(PKG_CONFIG) --cflags glib-2.0` + + # alpha flags (-pthread) +-# CFLAGS += -c -pthread `pkg-config --cflags glib-2.0` ++# CFLAGS += -c -pthread `$(PKG_CONFIG) --cflags glib-2.0` + + # normal linux/bsd/mac flags +-CFLAGS += $(CPPFLAGS) -c `pkg-config --cflags glib-2.0` ++CFLAGS += $(CPPFLAGS) -c `$(PKG_CONFIG) --cflags glib-2.0` + + + EXTRALIBS = -lm +--- a/src/models/makefile ++++ b/src/models/makefile +@@ -192,10 +192,10 @@ psw : psw.o seqaligndisplay.o proteinsw. + $(CC) -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + scanwisep.o : scanwisep.c +- $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `pkg-config --cflags glib-2.0` $? ++ $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `$(PKG_CONFIG) --cflags glib-2.0` $? + + hsp2aln_sw.o : hsp2aln_sw.c +- $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config --cflags glib-2.0` $? ++ $(CC) $(CFLAGS) $(INCFLAGS) `$(PKG_CONFIG) --cflags glib-2.0` $? + + scanwisep_mysql.o : scanwisep.c + $(CC) $(CFLAGS) -DSCAN_MYSQL -I../corba -I../external/mott -I../mysql/protein_index/ -I/usr/local/mysql/include scanwisep.c +@@ -226,25 +226,25 @@ scanwisep_compress : scanwisep_compress. + + + scanwisep : scanwisep.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o +- $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o $(LDFLAGS) -L../external/mott -lmott -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread ++ $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o $(LDFLAGS) -L../external/mott -lmott -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `$(PKG_CONFIG) --libs glib-2.0` -lpthread + + test_gwhsp : test_gwhsp.o genewisehsp.o +- $(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LDFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread ++ $(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LDFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `$(PKG_CONFIG) --libs glib-2.0` -lpthread + + localcishit.o : localcishit.c +- $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config --cflags glib-2.0` $? ++ $(CC) $(CFLAGS) $(INCFLAGS) `$(PKG_CONFIG) --cflags glib-2.0` $? + + promoterwise.o : promoterwise.c +- $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config --cflags glib-2.0` $? ++ $(CC) $(CFLAGS) $(INCFLAGS) `$(PKG_CONFIG) --cflags glib-2.0` $? + + promoterwise : promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o +- $(CC) -g -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread ++ $(CC) -g -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `$(PKG_CONFIG) --libs glib-2.0` -lpthread + + test_deng : test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o +- $(CC) -o test_deng test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread ++ $(CC) -o test_deng test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `$(PKG_CONFIG) --libs glib-2.0` -lpthread + + promotercluster : promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o +- $(CC) -o promotercluster promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread ++ $(CC) -o promotercluster promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `$(PKG_CONFIG) --libs glib-2.0` -lpthread + + dnawise : dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o + $(CC) -o dnawise dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase -lpthread +@@ -343,13 +343,14 @@ HMMER_DEFINE = + + + CC = cc ++PKG_CONFIG ?= pkg-config + #CFLAGS = -c -O2 -pg -I../base/ -I../dynlibsrc/ + #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ -I. +-CFLAGS += -c -g3 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config --cflags glib-2.0` +-#CFLAGS += -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` ++CFLAGS += -c -g3 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `$(PKG_CONFIG) --cflags glib-2.0` ++#CFLAGS += -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `$(PKG_CONFIG) --cflags glib-2.0` + #LDFLAGS = -L../base/ -L../dynlibsrc/ -L../HMMer2/ + +-LDFLAGS += -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `pkg-config --libs glib-2.0` ++LDFLAGS += -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `$(PKG_CONFIG) --libs glib-2.0` + AR_OPTIONS = ru + + RANLIB_NEEDED = 0 +--- a/src/network/makefile ++++ b/src/network/makefile +@@ -2,9 +2,10 @@ + .SUFFIXES : .dy + + CC = cc ++PKG_CONFIG ?= pkg-config + INCFLAGS = -I../base/ -I../socket -I../dynlibsrc -I../dnaindex +-CFLAGS += $(CPPFLAGS) -c -pthread -DUNIX -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `pkg-config --cflags glib-2.0` +-LDFLAGS += -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config --libs glib-2.0` ++CFLAGS += $(CPPFLAGS) -c -pthread -DUNIX -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `$(PKG_CONFIG) --cflags glib-2.0` ++LDFLAGS += -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `$(PKG_CONFIG) --libs glib-2.0` + AR_OPTIONS = ru + + RANLIB_NEEDED = 0 +--- a/src/other_programs/makefile ++++ b/src/other_programs/makefile +@@ -3,8 +3,9 @@ + .SUFFIXES : .dy + + CC = cc +-CFLAGS += $(CPPFLAGS) -g3 -c -pthread -DUNIX -I../base/ -I../dynlibsrc `pkg-config --cflags glib-2.0` +-LDFLAGS += -g -L../base/ -L../dynlibsrc -lm `pkg-config --libs glib-2.0` ++PKG_CONFIG ?= pkg-config ++CFLAGS += $(CPPFLAGS) -g3 -c -pthread -DUNIX -I../base/ -I../dynlibsrc `$(PKG_CONFIG) --cflags glib-2.0` ++LDFLAGS += -g -L../base/ -L../dynlibsrc -lm `$(PKG_CONFIG) --libs glib-2.0` + AR_OPTIONS = ru + + RANLIB_NEEDED = 0 +--- a/src/snp/makefile ++++ b/src/snp/makefile +@@ -3,11 +3,12 @@ + + + CC = cc ++PKG_CONFIG ?= pkg-config + #CFLAGS = -c -O2 -pg -I../base/ -I../dynlibsrc/ + #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ -I. +-CFLAGS += $(CPPFLAGS) -c -g3 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config --cflags glib-2.0` ++CFLAGS += $(CPPFLAGS) -c -g3 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `$(PKG_CONFIG) --cflags glib-2.0` + +-LDFLAGS += -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lpthread -lm ++LDFLAGS += -g -L../base/ -L../dynlibsrc/ -lpthread `$(PKG_CONFIG) --libs glib-2.0` -lpthread -lm + AR_OPTIONS = ru + + RANLIB_NEEDED = 0 diff --git a/academic/wise/patches/spelling.patch b/academic/wise/patches/spelling.patch new file mode 100644 index 0000000000..cb46f070ce --- /dev/null +++ b/academic/wise/patches/spelling.patch @@ -0,0 +1,702 @@ +Author: Andreas Tille <tille@debian.org> +Last-Update: Fri, 22 Sep 2017 09:18:47 +0200 +Description: Fix spelling issues + +--- a/src/dynlibsrc/hscore.c ++++ b/src/dynlibsrc/hscore.c +@@ -413,7 +413,7 @@ DataScore * new_DataScore_from_storage(H + if( hs->st_len == 0 ) { + new = new_DataScoreStorage(); + if( new == NULL ) { +- warn("could not make inital data score storage!"); ++ warn("could not make initial data score storage!"); + return NULL; + } + add_st_Hscore(hs,new); +--- a/src/dynlibsrc/hscore.dy ++++ b/src/dynlibsrc/hscore.dy +@@ -422,7 +422,7 @@ DataScore * new_DataScore_from_storage(H + if( hs->st_len == 0 ) { + new = new_DataScoreStorage(); + if( new == NULL ) { +- warn("could not make inital data score storage!"); ++ warn("could not make initial data score storage!"); + return NULL; + } + add_st_Hscore(hs,new); +--- a/docs/dynamite.tex ++++ b/docs/dynamite.tex +@@ -2839,7 +2839,7 @@ needs at least one offset to be non zero + Once all the semantics of the Dynamite blueprint is ok, the compiler then turns its + attention to the calc lines. This is like a mini-parser operating inside the dynamite + parser, but unlike the dynamite parser, this once was written in yacc/lex and is +-a more vanilla parser enviroment. ++a more vanilla parser environment. + + \subsubsection{Parser Syntax error on calc line} + +--- a/docs/wise2.tex ++++ b/docs/wise2.tex +@@ -121,7 +121,7 @@ Warning Error + Could not read a GeneFrequency file in human.gf + ... + \end{verbatim} +-This means that the enviroment variable WISECONFIGDIR has not been ++This means that the environment variable WISECONFIGDIR has not been + set up correctly. You need to find where the distribution was downloaded + to (a directory called something like wise2.1.16b) and inside that + directory should be the configuration directory wisecfg. You need to +@@ -427,7 +427,7 @@ sequence flag) as well. An example run w + \begin{verbatim} + genewisedb -pfam Pfam -dnas myseq.fa + \end{verbatim} +-If you have set up the HMMER package to work with Pfam using the enviroment ++If you have set up the HMMER package to work with Pfam using the environment + variable HMMERDB, Wise2 will also pick that up as well. + + +@@ -675,7 +675,7 @@ mathematically it is almost that easy: t + of the probability. + + Perhaps a better known example is the relationship between the old +-profile technology, as developped by Gribskov and Gibson along with ++profile technology, as developed by Gribskov and Gibson along with + others, and its probabilistic partner, profile Hidden Markov Models + (profile HMMs). In terms of the actual algorithm these two methods + are very similar: it is simply that the profile HMM has a strong +@@ -1639,7 +1639,7 @@ Of course there are many options to chan + \subsection{dba - Dna Block Aligner} + \label{sec:dba} + +-dba - standing for Dna Block Aligner, was developped by Niclas Jareborg, ++dba - standing for Dna Block Aligner, was developed by Niclas Jareborg, + Richard Durbin and Ewan Birney for characterising shared regulatory regions + of genomic DNA, either in upstream regions or introns of genes + +--- a/src/base/wisefile.c ++++ b/src/base/wisefile.c +@@ -329,7 +329,7 @@ FILE * openfile(const char * filename,co + * + * + * +- * Arg: envname [READ ] enviroment variable to read from [NullString] ++ * Arg: envname [READ ] environment variable to read from [NullString] + * Arg: filename [UNKN ] Undocumented argument [char *] + * Arg: name [READ ] filename to open [NullString] + * Arg: env [UNKN ] Undocumented argument [char *] +@@ -344,17 +344,17 @@ FILE * envopenfile(char * filename,char + char path [512]; + + if( filename == NULL || env == NULL ) { +- warn("Passed a NULL filename or enviroment name into Envfile. Should trap this elsewhere"); ++ warn("Passed a NULL filename or environment name into Envfile. Should trap this elsewhere"); + return NULL; + } + + if( (envp = getenv(env)) == NULL ) { +- /* fail gracefully - somebody might query a number of enviroment variables */ ++ /* fail gracefully - somebody might query a number of environment variables */ + return NULL; + } + + if( strlen(filename) + strlen(envp) < 490 ) { +- warn("Really long filename/enviroment variables [%s] [%s] Can't cope!",filename,envp); ++ warn("Really long filename/environment variables [%s] [%s] Can't cope!",filename,envp); + return NULL; + } + sprintf(path,"%s/%s",filename,envp); +--- a/src/base/wisefile.dy ++++ b/src/base/wisefile.dy +@@ -302,7 +302,7 @@ in HMMer2. You call it as + + %arg + name r filename to open +-envname r enviroment variable to read from ++envname r environment variable to read from + return a valid file pointer or NULL + %% + FILE * envopenfile(char * filename,char * env) +@@ -311,17 +311,17 @@ FILE * envopenfile(char * filename,char + char path [512]; + + if( filename == NULL || env == NULL ) { +- warn("Passed a NULL filename or enviroment name into Envfile. Should trap this elsewhere"); ++ warn("Passed a NULL filename or environment name into Envfile. Should trap this elsewhere"); + return NULL; + } + + if( (envp = getenv(env)) == NULL ) { +- /* fail gracefully - somebody might query a number of enviroment variables */ ++ /* fail gracefully - somebody might query a number of environment variables */ + return NULL; + } + + if( strlen(filename) + strlen(envp) < 490 ) { +- warn("Really long filename/enviroment variables [%s] [%s] Can't cope!",filename,envp); ++ warn("Really long filename/environment variables [%s] [%s] Can't cope!",filename,envp); + return NULL; + } + sprintf(path,"%s/%s",filename,envp); +--- a/src/base/wisefile.h ++++ b/src/base/wisefile.h +@@ -143,7 +143,7 @@ FILE * Wise2_openfile(const char * filen + * + * + * +- * Arg: envname [READ ] enviroment variable to read from [NullString] ++ * Arg: envname [READ ] environment variable to read from [NullString] + * Arg: filename [UNKN ] Undocumented argument [char *] + * Arg: name [READ ] filename to open [NullString] + * Arg: env [UNKN ] Undocumented argument [char *] +--- a/LICENSE ++++ b/LICENSE +@@ -19,7 +19,7 @@ an acknowledgement of the authorship nee + + The HMMer2 libaries (Sean Eddy's HMM package) and the models directory + (The algorithms for the Wise2 package, and final executable programs) +-are both distributed under a Gnu General Public License (GPL). This ++are both distributed under a GNU General Public License (GPL). This + means that the entire package as it is distributed with these portions + in is also licensed under GPL, due to the 'infectious' nature of the + GPL. +--- a/docs/wise3arch.tex ++++ b/docs/wise3arch.tex +@@ -49,7 +49,7 @@ clear up a considerable amount of confus + + \subsection{Committment to open source, freely available code} + +-The Wise2 package has been licensed under the Gnu Public License since ++The Wise2 package has been licensed under the GNU General Public License since + its inception. In addition, parts of the package has even less + restrictive Licenses. I have a strong committment to keep Wise a + freely available, open source package. The aim of the open +--- a/src/corba/scanwise_protein_index.c ++++ b/src/corba/scanwise_protein_index.c +@@ -19,7 +19,7 @@ char * program_name = "scanwise_protein_ + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/dnaindex/assembly/badkmer.c ++++ b/src/dnaindex/assembly/badkmer.c +@@ -25,7 +25,7 @@ void show_help(FILE * ofp) + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EBI 2003\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/dnaindex/assembly/pathwise.c ++++ b/src/dnaindex/assembly/pathwise.c +@@ -40,7 +40,7 @@ void show_help(FILE * ofp) + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EBI 2003\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/dnaindex/bigseqwise.c ++++ b/src/dnaindex/bigseqwise.c +@@ -10,7 +10,7 @@ char * program_name = "bigseqwise"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/dnaindex/findbad_kmer.c ++++ b/src/dnaindex/findbad_kmer.c +@@ -13,7 +13,7 @@ char * program_name = "findbad_kmer"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/dnaindex/kwise.c ++++ b/src/dnaindex/kwise.c +@@ -15,7 +15,7 @@ char * program_name = "kwise"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/alignwise.c ++++ b/src/models/alignwise.c +@@ -61,7 +61,7 @@ void show_Gene_debug(AlnBlock * alb,Sequ + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/amplimer_resolver.c ++++ b/src/models/amplimer_resolver.c +@@ -10,7 +10,7 @@ char * program_name = "amplimer_resolver + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/cdnawise.c ++++ b/src/models/cdnawise.c +@@ -15,7 +15,7 @@ void show_version(FILE * ofp) + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); + + +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL (2001) and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/clonewise.c ++++ b/src/models/clonewise.c +@@ -25,7 +25,7 @@ int mismatch_score = -1; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/dbac.c ++++ b/src/models/dbac.c +@@ -363,7 +363,7 @@ void show_version(FILE * ofp) + fprintf(ofp," Released %s\n",RELEASE_DAY); + fprintf(ofp," Compiled %s\n",COMPILE_DATE); + fprintf(ofp,"dba was written by Niclas Jareborg, Ewan Birney and Richard Durbin\n"); +- fprintf(ofp,"Copyright (c) 1998,1999,2000,2001 GRL ltd. It is distributed under a Gnu Public License\n"); ++ fprintf(ofp,"Copyright (c) 1998,1999,2000,2001 GRL ltd. It is distributed under a GNU General Public License\n"); + fprintf(ofp,"See GNULICENSE in source directory for more information\n"); + } + +--- a/src/models/dnal.c ++++ b/src/models/dnal.c +@@ -104,7 +104,7 @@ void show_short_help(FILE * ofp) + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) GRL 1998 and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/dnawise.c ++++ b/src/models/dnawise.c +@@ -8,7 +8,7 @@ char * program_name = "dnawise"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/editdist.c ++++ b/src/models/editdist.c +@@ -8,7 +8,7 @@ char * program_name = "editdist"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/estwise.c ++++ b/src/models/estwise.c +@@ -557,7 +557,7 @@ void show_help(FILE * ofp) + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) GRL 1998 and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/estwisedb.c ++++ b/src/models/estwisedb.c +@@ -807,7 +807,7 @@ boolean show_header(FILE * ofp) + fprintf(ofp,"-------------------------------------------------------------\n"); + fprintf(ofp,"Wise2 - database searching mode\n"); + fprintf(ofp,"Program: %s version: %s released: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY); +- fprintf(ofp,"This program is freely distributed under a Gnu Public License.\n"); ++ fprintf(ofp,"This program is freely distributed under a GNU General Public License.\n"); + fprintf(ofp," See -version for more info on copyright\n"); + fprintf(ofp,"Bugs and credits to Ewan Birney <birney@sanger.ac.uk>\n"); + fprintf(ofp,"-------------------------------------------------------------\n\n"); +@@ -836,7 +836,7 @@ boolean show_header(FILE * ofp) + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) GRL 1998 and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/evopairwise.c ++++ b/src/models/evopairwise.c +@@ -15,7 +15,7 @@ char * program_name = "evopairwise"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/fivestar.c ++++ b/src/models/fivestar.c +@@ -14,7 +14,7 @@ char * program_name = "fivestar"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/fivestarscan.c ++++ b/src/models/fivestarscan.c +@@ -14,7 +14,7 @@ char * program_name = "fivestarscan"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/fivestarsearch.c ++++ b/src/models/fivestarsearch.c +@@ -12,7 +12,7 @@ char * program_name = "fivestarsearch"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/genewise.c ++++ b/src/models/genewise.c +@@ -858,7 +858,7 @@ void show_help(FILE * ofp) + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) GRL 1998 and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/genewisedb.c ++++ b/src/models/genewisedb.c +@@ -505,7 +505,7 @@ boolean show_header(FILE * ofp) + { + fprintf(ofp,"Wise2 - database searching mode\n"); + fprintf(ofp,"Program: %s version: %s released: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY); +- fprintf(ofp,"This program is freely distributed under a Gnu Public License.\n"); ++ fprintf(ofp,"This program is freely distributed under a GNU General Public License.\n"); + fprintf(ofp," See -version for more info on copyright\n"); + fprintf(ofp,"Bugs and credits to Ewan Birney <birney@sanger.ac.uk>\n"); + fprintf(ofp,"-----------------------------------------------------\n\n"); +@@ -1003,7 +1003,7 @@ void show_help(FILE * ofp) + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) GRL 1998 and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/genomewise.c ++++ b/src/models/genomewise.c +@@ -16,7 +16,7 @@ void show_utr_exon_genomewise(AlnBlock * + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/lba.c ++++ b/src/models/lba.c +@@ -8,7 +8,7 @@ char * program_name = "lba"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/motifcluster.c ++++ b/src/models/motifcluster.c +@@ -8,7 +8,7 @@ char * program_name = "motifcluster"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/motifdiff.c ++++ b/src/models/motifdiff.c +@@ -8,7 +8,7 @@ char * program_name = "motifdiff"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/motifwise.c ++++ b/src/models/motifwise.c +@@ -8,7 +8,7 @@ char * program_name = "motifwise"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/oldpostwise.c ++++ b/src/models/oldpostwise.c +@@ -375,7 +375,7 @@ void show_help(char * help_arg) + void show_version(void) + { + fprintf(stdout,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(stdout,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(stdout,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(stdout,"The source code is copyright (c) GRL 1998 and others\n"); + fprintf(stdout,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(stdout,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/promotercluster.c ++++ b/src/models/promotercluster.c +@@ -7,7 +7,7 @@ char * program_name = "promotercluster"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/promoterwise.c ++++ b/src/models/promoterwise.c +@@ -15,7 +15,7 @@ char * program_name = "promoterwise"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/pseudowise.c ++++ b/src/models/pseudowise.c +@@ -13,7 +13,7 @@ char * program_name = "pseudowise"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/psw.c ++++ b/src/models/psw.c +@@ -259,7 +259,7 @@ int main(int argc,char ** argv) + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) GRL 1998 and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/pswdb.c ++++ b/src/models/pswdb.c +@@ -95,7 +95,7 @@ void show_help(FILE * ofp) + void show_version(void) + { + fprintf(stdout,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(stdout,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(stdout,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(stdout,"The source code is copyright (c) EMBL 1998 and others\n"); + fprintf(stdout,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(stdout,"For more information read the GNULICENSE file in the distribution\n\n"); +@@ -347,7 +347,7 @@ boolean show_header(FILE * ofp) + fprintf(ofp,"-------------------------------------------------------------\n"); + fprintf(ofp,"Wise2 - Protein vs. Protein\n"); + fprintf(ofp,"Program: %s version: %s released: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY); +- fprintf(ofp,"This program is freely distributed under a Gnu Public License.\n"); ++ fprintf(ofp,"This program is freely distributed under a GNU General Public License.\n"); + fprintf(ofp," See -version for more info on copyright\n"); + fprintf(ofp,"Bugs and credits to: Richard Copley <copley@embl-heidelberg.de>\n"); + fprintf(ofp," Ewan Birney <birney@sanger.ac.uk>\n"); +--- a/src/models/scanwisep.c ++++ b/src/models/scanwisep.c +@@ -421,7 +421,7 @@ HitList * HitList_from_HSP_HSP2HitListIm + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/statwise.c ++++ b/src/models/statwise.c +@@ -11,7 +11,7 @@ char * codon_table = "codon.table"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/sywise.c ++++ b/src/models/sywise.c +@@ -12,7 +12,7 @@ char * codon_table = "codon.table"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/network/wise_proteinindex_server.c ++++ b/src/network/wise_proteinindex_server.c +@@ -26,7 +26,7 @@ char * program_name = "scanwise_server"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/test/estwise-db.out ++++ b/src/test/estwise-db.out +@@ -1,7 +1,7 @@ + ------------------------------------------------------------- + Wise2 - database searching mode + Program: estwisedb version: $Name: wise2-4-1 $ released: unreleased +-This program is freely distributed under a Gnu Public License. ++This program is freely distributed under a GNU General Public License. + See -version for more info on copyright + Bugs and credits to Ewan Birney <birney@sanger.ac.uk> + ------------------------------------------------------------- +--- a/src/test/genewise-db-lite.out ++++ b/src/test/genewise-db-lite.out +@@ -1,6 +1,6 @@ + Wise2 - database searching mode + Program: genewisedb version: $Name: wise2-4-1 $ released: unreleased +-This program is freely distributed under a Gnu Public License. ++This program is freely distributed under a GNU General Public License. + See -version for more info on copyright + Bugs and credits to Ewan Birney <birney@sanger.ac.uk> + ----------------------------------------------------- +--- a/src/test/genewise-db.out ++++ b/src/test/genewise-db.out +@@ -1,6 +1,6 @@ + Wise2 - database searching mode + Program: genewisedb version: $Name: wise2-4-1 $ released: unreleased +-This program is freely distributed under a Gnu Public License. ++This program is freely distributed under a GNU General Public License. + See -version for more info on copyright + Bugs and credits to Ewan Birney <birney@sanger.ac.uk> + ----------------------------------------------------- +--- a/src/test/genewisedb-pfam.out ++++ b/src/test/genewisedb-pfam.out +@@ -1,6 +1,6 @@ + Wise2 - database searching mode + Program: genewisedb version: $Name: wise2-4-1 $ released: unreleased +-This program is freely distributed under a Gnu Public License. ++This program is freely distributed under a GNU General Public License. + See -version for more info on copyright + Bugs and credits to Ewan Birney <birney@sanger.ac.uk> + ----------------------------------------------------- +--- a/src/test/pswdb.out ++++ b/src/test/pswdb.out +@@ -1,7 +1,7 @@ + ------------------------------------------------------------- + Wise2 - Protein vs. Protein + Program: pswdb version: $Name: wise2-4-1 $ released: unreleased +-This program is freely distributed under a Gnu Public License. ++This program is freely distributed under a GNU General Public License. + See -version for more info on copyright + Bugs and credits to: Richard Copley <copley@embl-heidelberg.de> + Ewan Birney <birney@sanger.ac.uk> +--- a/src/models/genefrequency.c ++++ b/src/models/genefrequency.c +@@ -636,7 +636,7 @@ double double_from_line(char * buffer) + ret = strtod(runner,&end); + + if( end == runner || isalnum((int)*end) ) { +- warn("Bad conversion of string [%s] to double [%f] occured",runner,ret); ++ warn("Bad conversion of string [%s] to double [%f] occurred",runner,ret); + } + + return ret; +--- a/src/models/genefrequency.dy ++++ b/src/models/genefrequency.dy +@@ -597,7 +597,7 @@ double double_from_line(char * buffer) + ret = strtod(runner,&end); + + if( end == runner || isalnum((int)*end) ) { +- warn("Bad conversion of string [%s] to double [%f] occured",runner,ret); ++ warn("Bad conversion of string [%s] to double [%f] occurred",runner,ret); + } + + return ret; +--- a/src/models/seqerror.dy ++++ b/src/models/seqerror.dy +@@ -42,7 +42,7 @@ Sequence * seq + SequenceErrorSet * ses + %info + This holds a sequence and what +-errors have occured in it. ++errors have occurred in it. + %% + + +--- a/src/models/seqerror.h ++++ b/src/models/seqerror.h +@@ -72,7 +72,7 @@ typedef struct Wise2_SequenceErrorSet Wi + /* Object ErrorSequence + * + * Descrip: This holds a sequence and what +- * errors have occured in it. ++ * errors have occurred in it. + * + * + */ diff --git a/academic/wise/slack-desc b/academic/wise/slack-desc new file mode 100644 index 0000000000..c99b9025f0 --- /dev/null +++ b/academic/wise/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +wise: wise (Compare protein to DNA sequence) +wise: +wise: Wise compares a protein sequence to a genomic DNA sequence, +wise: allowing for introns and frameshifting errors. +wise: +wise: https://www.ebi.ac.uk/~birney/wise2/ +wise: https://www.ebi.ac.uk/Tools/psa/genewise/ +wise: +wise: +wise: +wise: diff --git a/academic/wise/wise.SlackBuild b/academic/wise/wise.SlackBuild new file mode 100644 index 0000000000..84230832be --- /dev/null +++ b/academic/wise/wise.SlackBuild @@ -0,0 +1,131 @@ +#!/bin/bash + +# Slackware build script for <wise> + +# Copyright 2023 Petar Petrov, slackalaxy@gmail.com +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=wise +VERSION=${VERSION:-2.4.1} +BUILD=${BUILD:-2} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" +else + SLKCFLAGS="-O2" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/${PRGNAM}_${VERSION}.orig.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +patch -p1 -i $CWD/patches/01_welcome-csh.patch +patch -p1 -i $CWD/patches/02_isnumber.patch +patch -p1 -i $CWD/patches/03_doc-nodycache.patch +patch -p1 -i $CWD/patches/04_wise2-pdflatex-update.patch +patch -p1 -i $CWD/patches/05_glib2.patch +patch -p1 -i $CWD/patches/06_getline.patch +patch -p1 -i $CWD/patches/07_ld--as-needed.patch +patch -p1 -i $CWD/patches/08_mayhem.patch +patch -p1 -i $CWD/patches/09_dnal-add-return-statement.patch +patch -p1 -i $CWD/patches/10_fix_path_to_data_files.patch +patch -p1 -i $CWD/patches/11_consistent_manual_dates.patch +patch -p1 -i $CWD/patches/spelling.patch +patch -p1 -i $CWD/patches/cross.patch + +# This prevents some weird build breaks. Thanks to Urchlay. His explanation: +# +# The .c files that are in the tarball, were already built from the .dy +# files. However, some of them get patched, e.g. wisefile.c and wisefile.dy +# both have a modification time of the current time/date, which is why make +# thinks it needs to rebuild the wisefile.c. When make is run, it looks at +# the timestamps and decided wisefile.c is older than wisefile.dy (which it +# is, ever so slightly, assuming the filesystem's timestamp resolution is +# fine enough). What the solution does is force the timestamp on all the +# .dy files to be older than the generated .c files, so make won't think it +# needs to run dyc to generate the .c files. +find src -name \*.dy -print0 | xargs -0 touch -d '2000-01-01' + +cd src +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +make all + +mkdir -p $PKG/usr/bin +mkdir -p $PKG/usr/share/$PRGNAM + +cd bin +for i in * ; do + install -m 755 $i $PKG/usr/bin/$i +done + +cd ../.. +cp -a test_data wisecfg/* $PKG/usr/share/$PRGNAM + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + LICENSE README docs/{*.tex,*.eps,papers} \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/wise/wise.info b/academic/wise/wise.info new file mode 100644 index 0000000000..1aafd927ee --- /dev/null +++ b/academic/wise/wise.info @@ -0,0 +1,10 @@ +PRGNAM="wise" +VERSION="2.4.1" +HOMEPAGE="https://www.ebi.ac.uk/Tools/psa/genewise/" +DOWNLOAD="http://deb.debian.org/debian/pool/main/w/wise/wise_2.4.1.orig.tar.gz" +MD5SUM="9e90132c19a653831ce63b5af7f08302" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/wmcalc/README b/academic/wmcalc/README index 6b8bee5461..b898b6bfce 100644 --- a/academic/wmcalc/README +++ b/academic/wmcalc/README @@ -1,6 +1,6 @@ wmcalc (calculator dockapp for windowmaker) -wmcalc is a program designed to act as a simple four-function calculator. -It is different from other calculator programs, however in that it is -designed to take up very little desktop space. As such, it can be left -running on the desktop at all times. +wmcalc is a program designed to act as a simple four-function +calculator. It is different from other calculator programs, however +in that it is designed to take up very little desktop space. As such, +it can be left running on the desktop at all times. diff --git a/academic/wmcalc/doinst.sh b/academic/wmcalc/doinst.sh index 2cb6861d40..f79396baf0 100644 --- a/academic/wmcalc/doinst.sh +++ b/academic/wmcalc/doinst.sh @@ -1,3 +1,7 @@ +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 +fi + if [ -e usr/share/icons/hicolor/icon-theme.cache ]; then if [ -x /usr/bin/gtk-update-icon-cache ]; then /usr/bin/gtk-update-icon-cache usr/share/icons/hicolor >/dev/null 2>&1 diff --git a/academic/wmcalc/wmcalc.SlackBuild b/academic/wmcalc/wmcalc.SlackBuild index 0b75dc766c..7cab2d19df 100644 --- a/academic/wmcalc/wmcalc.SlackBuild +++ b/academic/wmcalc/wmcalc.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for wmcalc # @@ -25,8 +25,9 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -# Now maintained by B. Watson <yalhcru@gmail.com> +# Now maintained by B. Watson <urchlay@slackware.uk> +# 20221226 bkw: add missing update-desktop-database to doinst.sh, BUILD=2. # 20180911 bkw: update for v0.7. # 20160816 bkw: @@ -43,10 +44,13 @@ # - version bump, BUILD=1 # - previous version installed man page in wrong place +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=wmcalc VERSION=${VERSION:-0.7} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -56,7 +60,11 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -111,4 +119,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/wmcalc/wmcalc.info b/academic/wmcalc/wmcalc.info index 09b7df1b66..2894313a5b 100644 --- a/academic/wmcalc/wmcalc.info +++ b/academic/wmcalc/wmcalc.info @@ -7,4 +7,4 @@ DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" MAINTAINER="B. Watson" -EMAIL="yalhcru@gmail.com" +EMAIL="urchlay@slackware.uk" diff --git a/academic/wxMaxima/slack-desc b/academic/wxMaxima/slack-desc index 9ae6f3b3ff..5fe290b31d 100644 --- a/academic/wxMaxima/slack-desc +++ b/academic/wxMaxima/slack-desc @@ -11,7 +11,7 @@ wxMaxima: wxMaxima: wxMaxima is a cross platform GUI for the computer algebra system wxMaxima: Maxima based on wxWidgets. wxMaxima: -wxMaxima: Homepage: https://andrejv.github.io/wxmaxima/ +wxMaxima: Homepage: https://wxmaxima-developers.github.io/wxmaxima/ wxMaxima: wxMaxima: wxMaxima: diff --git a/academic/wxMaxima/wxMaxima.SlackBuild b/academic/wxMaxima/wxMaxima.SlackBuild index fb42b15df6..feb51615b1 100644 --- a/academic/wxMaxima/wxMaxima.SlackBuild +++ b/academic/wxMaxima/wxMaxima.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for wxMaxima @@ -22,37 +22,45 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +# 20230627 bkw: Modified by SlackBuilds.org, BUILD=2: +# - use DESTDIR properly, to avoid baking $PKG into the binary. + +# Mar 2021 - updated for v. 21.01, Judah Milgram, milgram at cgpp com + +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=wxMaxima SRCNAM=wxmaxima -VERSION=${VERSION:-16.04.2} -BUILD=${BUILD:-1} +VERSION=${VERSION:-21.01.0} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" - LIBDIRSUFFIX="" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" - LIBDIRSUFFIX="" elif [ "$ARCH" = "x86_64" ]; then SLKCFLAGS="-O2 -fPIC" - LIBDIRSUFFIX="64" else SLKCFLAGS="-O2" - LIBDIRSUFFIX="" fi set -e @@ -60,57 +68,46 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $SRCNAM-$VERSION -tar xvf $CWD/$SRCNAM-$VERSION.tar.gz -cd $SRCNAM-$VERSION +rm -rf $SRCNAM-Version-$VERSION +tar xvf $CWD/$SRCNAM-Version-$VERSION.tar.gz +cd $SRCNAM-Version-$VERSION chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ + -o -perm 511 \) -exec chmod 755 {} + -o \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; - -# Fix man directory. -sed -i '/^mandatadir/s|=.*|= \$(mandir)|' data/Makefile* -#Fix end-of-line encoding. -for i in art/*.txt; do - sed -e 's/\r//' $i > ${i}.new - touch -r $i ${i}.new - mv ${i}.new $i -done - -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ -./configure \ - --prefix=/usr \ - --mandir=/usr/man \ - --infodir=/usr/info \ - --docdir=/usr/doc/$PRGNAM-$VERSION \ - --disable-dependency-tracking \ - --disable-silent-rules \ - --enable-printing \ - --build=$ARCH-slackware-linux - -make -make allmo -make install DESTDIR=$PKG + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} + + +BUILDDIR=build +mkdir -p $BUILDDIR + +export PATH="/opt/cmake-202x/bin:$PATH" +cmake \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DCMAKE_BUILD_TYPE=Release \ + -G Ninja -S . -B $BUILDDIR +cmake --build $BUILDDIR +DESTDIR=$PKG cmake --install $BUILDDIR find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true +mv $PKG/usr/share/man $PKG/usr find $PKG/usr/man -type f -exec gzip -9 {} \; +for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done -rm -f $PKG/usr/info/dir -gzip -9 $PKG/usr/info/*.info* - -mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a AUTHORS ChangeLog COPYING README.md art/*.txt $PKG/usr/doc/$PRGNAM-$VERSION -rm -f $PKG/usr/share/$PRGNAM/{COPYING,README} +mkdir $PKG/usr/doc +mv $PKG/usr/share/doc/$SRCNAM $PKG/usr/doc/$PRGNAM-$VERSION +rmdir $PKG/usr/share/doc cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION/examples +cp -a examples/*.wxm $PKG/usr/doc/$PRGNAM-$VERSION/examples + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/wxMaxima/wxMaxima.info b/academic/wxMaxima/wxMaxima.info index 2c1f2c97d3..b1cffd86c3 100644 --- a/academic/wxMaxima/wxMaxima.info +++ b/academic/wxMaxima/wxMaxima.info @@ -1,8 +1,8 @@ PRGNAM="wxMaxima" -VERSION="16.04.2" -HOMEPAGE="https://andrejv.github.io/wxmaxima/" -DOWNLOAD="http://downloads.sourceforge.net/wxmaxima/wxmaxima-16.04.2.tar.gz" -MD5SUM="6d98324d70115615e7b4f7413b594dd5" +VERSION="21.01.0" +HOMEPAGE="https://wxmaxima-developers.github.io/wxmaxima/" +DOWNLOAD="https://github.com/wxMaxima-developers/wxmaxima/archive/Version-21.01.0/wxmaxima-Version-21.01.0.tar.gz" +MD5SUM="2c9b97c786806172aa6ed000784e995e" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="maxima wxGTK3" diff --git a/academic/wxmacmolplt/README b/academic/wxmacmolplt/README deleted file mode 100644 index 803f99ea8b..0000000000 --- a/academic/wxmacmolplt/README +++ /dev/null @@ -1,8 +0,0 @@ -The MacMolPlt molecular visualization program - -MacMolPlt is designed to display the input and output of the GAMESS(US) -and patched to support PCGAMESS/Firefly quantum chemistry packages. -It produces animations and/or publication quality output from a variety -of input file formats. - -It can be built with wxGTK3 instead of wxPython. diff --git a/academic/wxmacmolplt/wxmacmolplt-7.2.1-raman.patch b/academic/wxmacmolplt/wxmacmolplt-7.2.1-raman.patch deleted file mode 100644 index 6845b0bdaa..0000000000 --- a/academic/wxmacmolplt/wxmacmolplt-7.2.1-raman.patch +++ /dev/null @@ -1,33 +0,0 @@ -diff -Nru wxmacmolplt-7.2.1.orig/src/Frame.cpp wxmacmolplt-7.2.1/src/Frame.cpp ---- wxmacmolplt-7.2.1.orig/src/Frame.cpp 2008-04-10 01:04:51.000000000 +0400 -+++ wxmacmolplt-7.2.1/src/Frame.cpp 2009-03-09 10:59:11.000000000 +0300 -@@ -1896,6 +1896,29 @@ - } else tVib = icol; - } - } -+ if (Buffer->LocateKeyWord("RAMAN ACTIVITY:", 15, Buffer->GetFilePos()+132)) { -+ Buffer->GetLine(LineText); -+ LinePos = 16; -+ if ((imode == NumVibs)&&(lVibs->RamanIntensity.empty())) { -+ lVibs->RamanIntensity.reserve(NumModes); -+ } -+ LineLength = strlen(LineText); -+ long tVib = NumVibs; -+ float raman; -+ for (long icol=0; icol<tVib; icol++) { -+ if (LinePos<LineLength) { -+ test = sscanf(&(LineText[LinePos]), "%s%n", &token, &nchar); -+ LinePos += nchar; -+ if (test) { -+ if (token[0] != '*') { -+ test = sscanf(token, "%f", &raman); -+ if (test) -+ lVibs->RamanIntensity.push_back(raman); -+ } else lVibs->RamanIntensity.push_back(10000.0); -+ } else tVib = icol; -+ } else tVib = icol; -+ } -+ } - if (Buffer->LocateKeyWord("DEPOLARIZATION:", 15, Buffer->GetFilePos()+132)) { - Buffer->GetLine(LineText); - LinePos = 16; diff --git a/academic/wxmacmolplt/wxmacmolplt-7.4-firefly.patch b/academic/wxmacmolplt/wxmacmolplt-7.4-firefly.patch deleted file mode 100644 index 540ec0bb5c..0000000000 --- a/academic/wxmacmolplt/wxmacmolplt-7.4-firefly.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- a/src/BFiles.cpp 2009-11-13 06:42:20.000000000 +0300 -+++ b/src/BFiles.cpp 2009-12-09 21:08:16.000000000 +0300 -@@ -294,6 +294,8 @@ - while ((ByteCount <= FileSize)&&(Type == kUnknown)) { - if (LocateKeyWord("GAMESS VERSION", 14, -1)) - Type = kGAMESSlogType; -+ else if (LocateKeyWord("Firefly (PC GAMESS) version", 27, -1)) -+ Type = kGAMESSlogType; - else if (LocateKeyWord("===== IRC DATA PACKET", 21, -1)) - Type = kGAMESSTRJType; - else if (LocateKeyWord("===== DRC DATA PACKET", 21, -1)) diff --git a/academic/wxmacmolplt/wxmacmolplt-7.4.4-files.patch b/academic/wxmacmolplt/wxmacmolplt-7.4.4-files.patch deleted file mode 100644 index e02e4ae7e6..0000000000 --- a/academic/wxmacmolplt/wxmacmolplt-7.4.4-files.patch +++ /dev/null @@ -1,22 +0,0 @@ ---- src/Files.cpp.orig 2012-12-30 22:55:10.000000000 +0400 -+++ src/Files.cpp 2013-01-20 22:10:48.000000000 +0400 -@@ -2420,7 +2420,8 @@ - // } - std::vector<std::pair <std::string, int> > OptKeywords; //search tokens for optimizations - OptKeywords.push_back(make_pair (std::string("BEGINNING GEOMETRY SEARCH POINT"), 0)); -- OptKeywords.push_back(make_pair (std::string("1NSERCH"), 1)); -+ OptKeywords.push_back(make_pair (std::string("1NSERCH"), 1)); -+ OptKeywords.push_back(make_pair (std::string("COORDINATES OF ALL ATOMS ARE (ANGS)"), 2)); - - if (Append) { - Buffer->LocateKeyWord("RUN TITLE", 9); //find and skip over run title since -@@ -3921,7 +3921,9 @@ - sscanf(&(LineText[6]), "%d", &temp); - SetDiag(temp); - } -+ Buffer->SetFilePos(EndPos); - } -+ - long MolDisplayWin::OpenGAMESSTRJ(BufferFile * Buffer, bool Append, long flip, float offset) - { - TypeOfRun runType=InvalidRunType; diff --git a/academic/wxmacmolplt/wxmacmolplt.info b/academic/wxmacmolplt/wxmacmolplt.info deleted file mode 100644 index f936a7beb7..0000000000 --- a/academic/wxmacmolplt/wxmacmolplt.info +++ /dev/null @@ -1,10 +0,0 @@ -PRGNAM="wxmacmolplt" -VERSION="7.7" -HOMEPAGE="http://brettbode.github.io/wxmacmolplt/" -DOWNLOAD="https://uofi.box.com/shared/static/7pzccnku3uv0mmf6il6yiqghf4b34lc7.gz" -MD5SUM="e4c8ec2b47532423c5e5f67aa62c2af7" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="ming wxPython" -MAINTAINER="Daniil Bratashov" -EMAIL="dn2010@gmail.com" diff --git a/academic/x48/README b/academic/x48/README new file mode 100644 index 0000000000..b5cd057318 --- /dev/null +++ b/academic/x48/README @@ -0,0 +1,5 @@ +x48 is a vintage emulator capable of providing a faithful replication +of the HP48 Calculator. It requires a copy of the ROM software. + +The user can initialize an HP48GX(r) ROM in $HOME/.hp48 with: +x48 -initialize -reset -rom /usr/doc/x48-0.6.4/gxrom-r diff --git a/academic/x48/slack-desc b/academic/x48/slack-desc new file mode 100644 index 0000000000..80dc45794a --- /dev/null +++ b/academic/x48/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +x48: x48 (HP48 Calculator emulator) +x48: +x48: x48 is a vintage emulator capable of providing a faithful replication +x48: of the HP48 Calculator. It requires a copy of the ROM software. +x48: +x48: The user can initialize an HP48GX(r) ROM in $HOME/.hp48 with: +x48: x48 -initialize -reset -rom /usr/doc/x48-0.6.4/gxrom-r +x48: +x48: http://www.hpcc.org/calculators/hp48.html +x48: +x48: diff --git a/academic/coq/coq.SlackBuild b/academic/x48/x48.SlackBuild index afa9d5f58f..84e9c4207f 100644 --- a/academic/coq/coq.SlackBuild +++ b/academic/x48/x48.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash -# Slackware build script for coq +# Slackware build script for x48 -# Copyright 2020 Nick Smallbone <nick@smallbone.se>, Gothenburg, Sweden +# Copyright 2022 Lorenzo Trevisan, Caorle, Venice, Italy # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -PRGNAM=coq -VERSION=${VERSION:-8.9.0} +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=x48 +VERSION=${VERSION:-0.6.4} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,18 +38,26 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" LIBDIRSUFFIX="64" else + SLKCFLAGS="-O2" LIBDIRSUFFIX="" fi @@ -56,8 +67,9 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $PRGNAM-$VERSION -tar xvf $CWD/$PRGNAM-$VERSION.tar.gz -cd $PRGNAM-$VERSION +mkdir $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.bz2 -C $PRGNAM-$VERSION + chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -65,29 +77,19 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -# Configure findlib so it can find camlp5. -cp /etc/findlib.conf . -sed -i "s@path=\"@path=\"/usr/lib${LIBDIRSUFFIX}/ocaml:@" findlib.conf -export OCAMLFIND_CONF=$(pwd)/findlib.conf +cd $PRGNAM-$VERSION -CONFIG_ARGS= -if [ z$COQIDE = zyes ];then - CONFIG_ARGS+=" -coqide opt" -else - CONFIG_ARGS+=" -coqide no" -fi +sed -i -e '698s=inline int=static inline int=' ./src/emulate.c +./autogen.sh ./configure \ - -prefix /usr \ - -libdir /usr/lib${LIBDIRSUFFIX}/$PRGNAM \ - -configdir /etc/xdg/$PRGNAM \ - -mandir /usr/man \ - -docdir /usr/doc/$PRGNAM-$VERSION \ - -arch $ARCH \ - $CONFIG_ARGS + --prefix=/usr \ + --mandir=/usr/man make -make install COQINSTALLPREFIX=$PKG +make install DESTDIR=$PKG + +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true @@ -97,12 +99,15 @@ for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; r mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - CHANGES.md CONTRIBUTING.md CREDITS INSTALL LICENSE README.md \ + README ChangeLog AUTHORS \ $PKG/usr/doc/$PRGNAM-$VERSION +cp $CWD/hp48g-qsg-en.pdf $PKG/usr/doc/$PRGNAM-$VERSION +cp $CWD/hp48g-ug-en.pdf $PKG/usr/doc/$PRGNAM-$VERSION +bunzip2 -k -c $CWD/gxrom-r.bz2 > $PKG/usr/doc/$PRGNAM-$VERSION/gxrom-r cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/x48/x48.info b/academic/x48/x48.info new file mode 100644 index 0000000000..d6301da61e --- /dev/null +++ b/academic/x48/x48.info @@ -0,0 +1,16 @@ +PRGNAM="x48" +VERSION="0.6.4" +HOMEPAGE="http://www.hpcc.org/calculators/hp48.html" +DOWNLOAD="https://sourceforge.net/projects/x48.berlios/files/x48-0.6.4.tar.bz2 \ + https://sourceforge.net/projects/x48.berlios/files/gxrom-r.bz2 \ + https://literature.hpcalc.org/community/hp48g-qsg-en.pdf \ + https://literature.hpcalc.org/community/hp48g-ug-en.pdf" +MD5SUM="700e631f8924a991b35d8a86ce60aab7 \ + a08249c9a75d52671045dbb9c35321fa \ + 1e91e669ed5bc126049f35f43e12805a \ + 9efd58fc89b6ea89bc00d6dbff6812a3" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Lorenzo Trevisan" +EMAIL="lorenzo.trevisan@gmail.com" diff --git a/academic/xcircuit/README b/academic/xcircuit/README index b8eca76d61..0dba86217d 100644 --- a/academic/xcircuit/README +++ b/academic/xcircuit/README @@ -1,5 +1,4 @@ -XCircuit is a UNIX/X11 (and Windows, if you have an X-Server running, -or Windows API, if not) program for drawing publishable-quality +XCircuit is a program for drawing publishable-quality electrical circuit schematic diagrams and related figures, and produce circuit netlists through schematic capture. XCircuit regards circuits as inherently hierarchical, and writes both hierarchical PostScript @@ -8,3 +7,5 @@ in and retrieved from libraries which are fully editable. XCircuit does not separate artistic expression from circuit drawing; it maintains flexiblity in style without compromising the power of schematic capture. + +ngspice is an optional dependency diff --git a/academic/xcircuit/slack-desc b/academic/xcircuit/slack-desc index 8d83821bbe..dc34decbd6 100644 --- a/academic/xcircuit/slack-desc +++ b/academic/xcircuit/slack-desc @@ -6,9 +6,9 @@ # customary to leave one space after the ':' except on otherwise blank lines. |-----handy-ruler------------------------------------------------------| -xcircuit: xcircuit (circuit design tool) -xcircuit: XCircuit is a UNIX/X11 (and Windows, if you have an X-Server running, -xcircuit: or Windows API, if not) program for drawing publishable-quality +xcircuit: xcircuit (Circuit drawing and schematic capture program) +xcircuit: +xcircuit: XCircuit is a UNIX/X11 program for drawing publishable-quality xcircuit: electrical circuit schematic diagrams and related figures, and xcircuit: produce circuit netlists through schematic capture. XCircuit regards xcircuit: circuits as inherently hierarchical, and writes both hierarchical diff --git a/academic/xcircuit/xcircuit.SlackBuild b/academic/xcircuit/xcircuit.SlackBuild index 2336153e6c..9429418716 100644 --- a/academic/xcircuit/xcircuit.SlackBuild +++ b/academic/xcircuit/xcircuit.SlackBuild @@ -1,28 +1,55 @@ -#!/bin/sh +#!/bin/bash + +# Slackware build script for xcircuit -# Slackware build script for grace # Written by B. Jogai <jogaib {at} comcast [dot] net> +# Copyright 2023 Johannes Schoepfer, Germany +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) PRGNAM=xcircuit -VERSION=${VERSION:-3.7.54} +VERSION=${VERSION:-3.10.30} BUILD=${BUILD:-1} TAG=${TAG:-"_SBo"} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -45,10 +72,10 @@ tar xvf $CWD/$PRGNAM-$VERSION.tgz cd $PRGNAM-$VERSION chown -R root:root . find -L . \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; CFLAGS="$SLKCFLAGS" \ ./configure \ @@ -56,27 +83,28 @@ CFLAGS="$SLKCFLAGS" \ --bindir=/usr/bin \ --libdir=/usr/lib${LIBDIRSUFFIX} \ --mandir=/usr/man \ - --with-x \ + --with-cairo \ --with-ngspice \ --with-tcl=/usr/lib${LIBDIRSUFFIX} \ + --with-tk=/usr/lib${LIBDIRSUFFIX} \ --build=$ARCH-slackware-linux \ make make DESTDIR=$PKG install +[ "$ARCH" = "x86_64" ] && mv $PKG/usr/lib $PKG/usr/lib$LIBDIRSUFFIX + find $PKG | xargs file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true # Add desktop menu entries -mkdir -p $PKG/usr/share/{applications,pixmaps} -cat $CWD/xcircuit.png > $PKG/usr/share/pixmaps/xcircuit.png -cat $CWD/xcircuit.desktop > $PKG/usr/share/applications/xcircuit.desktop - -# Copy the man pages from the lib to the man directory. -# Don't move it in case the program needs it there for some reason. -rm -rf $PKG/usr/man -mkdir -p $PKG/usr/man/man1 -cp $PKG/usr/lib$LIBDIRSUFFIX/$PRGNAM-3.7/man/*.1 $PKG/usr/man/man1 +mkdir -p $PKG/usr/share/{applications,icons} +convert $PKG/usr/lib$LIBDIRSUFFIX/$PRGNAM-*.*/pixmaps/$PRGNAM.gif \ + $PKG/usr/share/icons/$PRGNAM.png +cat $CWD/$PRGNAM.desktop > $PKG/usr/share/applications/$PRGNAM.desktop + +mkdir $PKG/usr/man +mv $PKG/usr/lib$LIBDIRSUFFIX/$PRGNAM-*.*/man $PKG/usr/man/man1 find $PKG/usr/man -type f -exec gzip -9 {} \; mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION @@ -89,4 +117,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/xcircuit/xcircuit.desktop b/academic/xcircuit/xcircuit.desktop index f687451b21..8ff88e11c3 100644 --- a/academic/xcircuit/xcircuit.desktop +++ b/academic/xcircuit/xcircuit.desktop @@ -1,8 +1,9 @@ [Desktop Entry] Type=Application Exec=xcircuit -Name=xcircuit -GenericName=Circuit drawing program +Name=Xcircuit +Comment=A program for drawing publishable-quality electrical circuit schematic diagrams Icon=xcircuit Terminal=false -Categories=Qt;KDE;Graphics;Development; +StartupNotify=false +Categories=Development; diff --git a/academic/xcircuit/xcircuit.info b/academic/xcircuit/xcircuit.info index 02b589bf38..e7e79a3d25 100644 --- a/academic/xcircuit/xcircuit.info +++ b/academic/xcircuit/xcircuit.info @@ -1,10 +1,10 @@ PRGNAM="xcircuit" -VERSION="3.7.54" +VERSION="3.10.30" HOMEPAGE="http://opencircuitdesign.com/xcircuit/" -DOWNLOAD="http://opencircuitdesign.com/xcircuit/archive/xcircuit-3.7.54.tgz" -MD5SUM="25e60837e5db6b4ff71615505493a481" +DOWNLOAD="http://opencircuitdesign.com/xcircuit/archive/xcircuit-3.10.30.tgz" +MD5SUM="f83be9d40d5bea00f27391b979bb1f76" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" -MAINTAINER="Glenn Becker" -EMAIL="glenn.becker@gmail.com" +MAINTAINER="Johannes Schoepfer" +EMAIL="slackbuilds@schoepfer.info" diff --git a/academic/xcircuit/xcircuit.png b/academic/xcircuit/xcircuit.png Binary files differdeleted file mode 100644 index 85cc4da406..0000000000 --- a/academic/xcircuit/xcircuit.png +++ /dev/null diff --git a/academic/xephem/README b/academic/xephem/README index ab546d369a..fb0bde75c4 100644 --- a/academic/xephem/README +++ b/academic/xephem/README @@ -1,6 +1,7 @@ xephem - Astronomy program -xephem is a scientific-grade interactive astronomical ephemeris software -package for UNIX-like* systems. +xephem is a scientific-grade interactive astronomical ephemeris +software package for UNIX-like* systems. -Note that this is not free software: read the license agreement carefully. +Note that this is not free software: read the license agreement +carefully. diff --git a/academic/xephem/slack-desc b/academic/xephem/slack-desc index 7af4a92da3..6a8ac39af8 100644 --- a/academic/xephem/slack-desc +++ b/academic/xephem/slack-desc @@ -8,11 +8,11 @@ |-----handy-ruler------------------------------------------------------| xephem: xephem (Astronomy program) xephem: -xephem: The scientific-grade interactive astronomical ephemeris -xephem: software package for UNIX-like* systems. -xephem: -xephem: Note that this is not free software: read the license -xephem: agreement carefully. +xephem: XEphem is an interactive astronomy program for all UNIX platforms. +xephem: Originally written by Elwood Downey in the 1990s, it has graciously +xephem: been released under the MIT License. It is now maintained by an +xephem: MIT License. It is now maintained by an "XEphem" organization, +xephem: with its source code residing at https://github.com/XEphem/XEphem. xephem: xephem: xephem: diff --git a/academic/xephem/xephem.SlackBuild b/academic/xephem/xephem.SlackBuild index 6e37dde398..8747d3db80 100644 --- a/academic/xephem/xephem.SlackBuild +++ b/academic/xephem/xephem.SlackBuild @@ -1,13 +1,17 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for xephem # Written by Dario Nicodemi dario.sbo@gmail.com +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=xephem -VERSION=${VERSION:-3.7.7} +VERSION=${VERSION:-4.1.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} +SRCNAM="XEphem" if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -17,7 +21,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -41,9 +52,9 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $PRGNAM-$VERSION -tar xvf $CWD/$PRGNAM-$VERSION.tgz -cd $PRGNAM-$VERSION +rm -rf $SRCNAM-$VERSION +tar xvf $CWD/$SRCNAM-$VERSION.tar.gz +cd $SRCNAM-$VERSION chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \ @@ -57,7 +68,7 @@ sed -i 's/^CFLAGS =/override CFLAGS +=/g' GUI/xephem/Makefile cd GUI/xephem patch -p3 < $CWD/00_trailmenu.patch - make -j1 CFLAGS="$SLKCFLAGS" CLDFLAGS="" MOTIFL="/usr/lib$LIBDIRSUFFIX" || exit 1 + make -j1 CFLAGS="$SLKCFLAGS" CLDFLAGS="" MOTIFL="/usr/lib$LIBDIRSUFFIX" mkdir -p $PKG/usr/{bin,man/man1,share/xephem} cp xephem $PKG/usr/bin cp XEphem.png $PKG/usr/share/xephem @@ -90,7 +101,7 @@ find $PKG | xargs file | grep -e "executable" -e "shared object" | grep ELF \ mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - Copyright INSTALL README \ + INSTALL LICENSE README.md \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild @@ -99,4 +110,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/xephem/xephem.info b/academic/xephem/xephem.info index 4a17ddb0d2..69028f4e5b 100644 --- a/academic/xephem/xephem.info +++ b/academic/xephem/xephem.info @@ -1,8 +1,8 @@ PRGNAM="xephem" -VERSION="3.7.7" -HOMEPAGE="http://www.clearskyinstitute.com/xephem/" -DOWNLOAD="http://www.clearskyinstitute.com/xephem/xephem-3.7.7.tgz" -MD5SUM="27c67061a89085bf2b0d4e9deb758a79" +VERSION="4.1.0" +HOMEPAGE="https://xephem.github.io/XEphem/Site/xephem.html" +DOWNLOAD="https://github.com/XEphem/XEphem/archive/4.1.0/XEphem-4.1.0.tar.gz" +MD5SUM="14b5aafd6d8cbfe3d261fc4661e04caa" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/xflr5/README b/academic/xflr5/README index 1521ecb74b..628905a5a5 100644 --- a/academic/xflr5/README +++ b/academic/xflr5/README @@ -1,6 +1,6 @@ -XFLR5 is an analysis tool for airfoils, wings, and planes operating at low -Reynolds numbers. It includes: +XFLR5 is an analysis tool for airfoils, wings, and planes operating at +low Reynolds numbers. It includes: 1. XFoil's Direct and Inverse analysis capabilities -2. Wing design and analysis capabilities based on Lifting Line Theory, on the - Vortex Lattice Method, and on a 3D Panel Method +2. Wing design and analysis capabilities based on Lifting Line Theory, + on the Vortex Lattice Method, and on a 3D Panel Method diff --git a/academic/xflr5/link_directly.patch b/academic/xflr5/link_directly.patch deleted file mode 100644 index 722a238556..0000000000 --- a/academic/xflr5/link_directly.patch +++ /dev/null @@ -1,13 +0,0 @@ ---- xflr5-gui/xflr5-gui.pro 2019-12-26 23:06:50.168628145 -0500 -+++ xflr5-gui/xflr5-gui.pro.new 2019-12-26 23:07:01.925796901 -0500 -@@ -128,8 +128,8 @@ - QMAKE_CFLAGS_WARN_ON -= -W3 - QMAKE_CFLAGS_WARN_ON += -W4 - --LIBS += -L../xflr5-engine -lxflr5-engine --LIBS += -L../XFoil-lib -lXFoil -+LIBS += ../xflr5-engine/libxflr5-engine.so -+LIBS += ../XFoil-lib/libXFoil.so - - include(xflr5v6.pri) - diff --git a/academic/xflr5/link_directly.patch.gz b/academic/xflr5/link_directly.patch.gz Binary files differnew file mode 100644 index 0000000000..232529802f --- /dev/null +++ b/academic/xflr5/link_directly.patch.gz diff --git a/academic/xflr5/xflr5.SlackBuild b/academic/xflr5/xflr5.SlackBuild index 48a6186c63..8bfc0a4705 100644 --- a/academic/xflr5/xflr5.SlackBuild +++ b/academic/xflr5/xflr5.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for xflr5 -# Copyright 2020 Daniel Prosser, Lexington Park, MD, USA +# Copyright 2020-2023 Daniel Prosser, Lexington Park, MD, USA # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=xflr5 -VERSION=${VERSION:-6.47} +VERSION=${VERSION:-6.61} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -59,9 +69,9 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $PRGNAM -tar xvf $CWD/${PRGNAM}_v${VERSION}_src.tar.gz -cd $PRGNAM +rm -rf ${PRGNAM}-${VERSION} +tar -xzvf $CWD/${PRGNAM}-${VERSION}.tar.gz +cd ${PRGNAM}-${VERSION} chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -72,11 +82,15 @@ find -L . \ # Change default path for libraries installation sed -i "s/target\.path = \$\$PREFIX\/lib/target\.path = \$\$PREFIX\/lib${LIBDIRSUFFIX}/g" \ XFoil-lib/XFoil-lib.pro -sed -i "s/target\.path = \$\$PREFIX\/lib/target\.path = \$\$PREFIX\/lib${LIBDIRSUFFIX}/g" \ - xflr5-engine/xflr5-engine.pro -# Fix linking -patch -p0 < $CWD/link_directly.patch +# Fix some hardcoded paths in launcher +sed -i "s/Exec=\/usr\/local\/bin\/xflr5/Exec=\/usr\/bin\/xflr5/g" linux/xflr5.desktop +sed -i "s/Icon=\/usr\/local\/share\/xflr5\/xflr5.png/Icon=xflr5/g" linux/xflr5.desktop + +# Fix linking XFoil-lib +# Note: this patch *must* be gzipped, as it contain a mix of \n and \r\n +# line endings, and git would strip the \r's. +zcat $CWD/link_directly.patch.gz | patch -p0 qmake-qt5 \ PREFIX=/usr \ @@ -91,11 +105,11 @@ make install INSTALL_ROOT=$PKG find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true -mkdir -p $PKG/usr/share/icons/hicolor/64x64/apps -cp -a xflr5-gui/images/xflr5_64.png $PKG/usr/share/icons/hicolor/64x64/apps +mkdir -p $PKG/usr/share/icons/hicolor/128x128/apps +cp -a res/xflr5.png $PKG/usr/share/icons/hicolor/128x128/apps mkdir -p $PKG/usr/share/applications -cp -a $CWD/xflr5.desktop $PKG/usr/share/applications +cp -a linux/xflr5.desktop $PKG/usr/share/applications mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a License.txt $PKG/usr/doc/$PRGNAM-$VERSION @@ -106,4 +120,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/xflr5/xflr5.desktop b/academic/xflr5/xflr5.desktop deleted file mode 100644 index 4559ab869f..0000000000 --- a/academic/xflr5/xflr5.desktop +++ /dev/null @@ -1,10 +0,0 @@ -[Desktop Entry] -Comment=an analysis tool for airfoils, wings, and planes -Exec=xflr5 -GenericName=Aircraft analysis tool -Icon=xflr5_64 -Name=xflr5 -StartupNotify=true -Terminal=false -Type=Application -Categories=Education;Science; diff --git a/academic/xflr5/xflr5.info b/academic/xflr5/xflr5.info index 8fff4322ae..947ad8f4ea 100644 --- a/academic/xflr5/xflr5.info +++ b/academic/xflr5/xflr5.info @@ -1,10 +1,10 @@ PRGNAM="xflr5" -VERSION="6.47" +VERSION="6.61" HOMEPAGE="http://www.xflr5.com/xflr5.htm" -DOWNLOAD="https://ayera.dl.sourceforge.net/project/xflr5/6.47/xflr5_v6.47_src.tar.gz" -MD5SUM="272484cc3fe077af31bbe2ad7ef4205b" +DOWNLOAD="http://sourceforge.net/projects/slackbuildsdirectlinks/files/xflr5/xflr5-6.61.tar.gz" +MD5SUM="ddedf9a123e67dfbf206901f6d6d59f1" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="qt5" +REQUIRES="" MAINTAINER="Daniel Prosser" EMAIL="dpross1100@msn.com" diff --git a/academic/xfoil/Makefile_patches/Makefile.xfoil.patch b/academic/xfoil/Makefile_patches/Makefile.xfoil.patch index e8e0b413e3..4fca1643f1 100644 --- a/academic/xfoil/Makefile_patches/Makefile.xfoil.patch +++ b/academic/xfoil/Makefile_patches/Makefile.xfoil.patch @@ -105,7 +105,7 @@ FC = gfortran CHK = -CHK = -fbounds-check -finit-real=inf -ffpe-trap=invalid,zero -+#CHK = -fbounds-check -finit-real=inf -ffpe-trap=invalid,zero,denormal ++CHK = -std=legacy DBL = -fdefault-real-8 -FFLAGS = -O $(CHK) $(DBL) -FFLOPT = -O $(CHK) $(DBL) diff --git a/academic/xfoil/README b/academic/xfoil/README index c9bb85dfea..6eb218961a 100644 --- a/academic/xfoil/README +++ b/academic/xfoil/README @@ -1,7 +1,8 @@ -XFOIL is an interactive program for the design and analysis of subsonic isolated -airfoils. It consists of a collection of menu-driven routines which perform -various useful functions, such as viscous (or inviscid) analysis of an existing -airfoil, airfoil design and redesign by interactive modification of surface -speed distributions or geometric parameters, blending of airfoils, writing and -reading of airfoil coordinates and polar save files, and plotting of geometry, -pressure distributions, and multiple polars. +XFOIL is an interactive program for the design and analysis of subsonic +isolated airfoils. It consists of a collection of menu-driven routines +which perform various useful functions, such as viscous (or inviscid) +analysis of an existing airfoil, airfoil design and redesign by +interactive modification of surface speed distributions or geometric +parameters, blending of airfoils, writing and reading of airfoil +coordinates and polar save files, and plotting of geometry, pressure +distributions, and multiple polars. diff --git a/academic/xfoil/xfoil.SlackBuild b/academic/xfoil/xfoil.SlackBuild index 16775a3064..5d7e719d29 100644 --- a/academic/xfoil/xfoil.SlackBuild +++ b/academic/xfoil/xfoil.SlackBuild @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for xfoil @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=xfoil VERSION=${VERSION:-6.99} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -106,4 +116,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/xiphos/README b/academic/xiphos/README index 1860dba832..e430c8f0fe 100644 --- a/academic/xiphos/README +++ b/academic/xiphos/README @@ -2,27 +2,5 @@ xiphos (formerly gnomesword. A bible study application) Xiphos is a bible study program for GNOME. Xiphos is based on the Sword project by the CrossWire Bible Society. -computer reading of the text using festival has not been tested. -if it works let me know, and i'll remove these two lines from the readme. - -if you pass the variable WK2=yes to the build script, the dependencies -change slightly. instead of webkitgtk3, webkit2gtk and gtkhtml (v4) are -required. - -note: End program differences between webkit and webkit2 versions. -webkit: - studypad is missing the image for the "bold" text button (but it works) - reported not to work with current -webkit2: - studypad has an "add emoticon" button, but the images included are not -found, so an empty imagebox is added in the text if you try to add an icon. - a few warnings shown on compile (but seems to work just fine). - try this one for current. if it works, let me know, and I might change - the default to WK2 :-). - -For both versions, there is an issue where if the previewer is in the sidebar, -text is offset to the left, so you can't see the first 2 characters of each -line. This can be fixed by making the sidebar a little bit wider. - -Note. xiphos version 4.1.0 requires sword v1.8 or higher -and biblesync v1.2 or higher +computer reading of the text using festival has not been tested. if +it works let me know, and i'll remove these two lines from the readme. diff --git a/academic/xiphos/xiphos.SlackBuild b/academic/xiphos/xiphos.SlackBuild index cd9533ba6f..3471341e36 100644 --- a/academic/xiphos/xiphos.SlackBuild +++ b/academic/xiphos/xiphos.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for xiphos -# Copyright 2015-2018 Tim Dickson, email: dickson.tim@googlemail.com +# Copyright 2015-2023 Tim Dickson, email: dickson.tim@googlemail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,13 +22,15 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +#note: webkit2gtk is a dep, but is already included as a dep of yelp. + +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=xiphos -VERSION=${VERSION:-4.1.0} -BUILD=${BUILD:-1} +VERSION=${VERSION:-4.2.1} +BUILD=${BUILD:-5} TAG=${TAG:-_SBo} - -#if WK2 is yes use webkit2. this requires webkit2gtk and gtkhtml (v4) instead of webkitgtk3 -WK2=${WK2:-no} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -38,7 +40,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -65,6 +74,8 @@ cd $TMP rm -rf $PRGNAM-$VERSION tar xvf $CWD/$PRGNAM-$VERSION.tar.gz cd $PRGNAM-$VERSION + +#sane permissions for everything chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -72,38 +83,32 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -./waf distclean - -# patch navbar_versekey.gtkbuilder to work with gtk shipped with slackware 14.2 -# patch won't be needed for slackware 15 -sed -i "s/3.20/3.14/g" ui/navbar_versekey.gtkbuilder - -if [ "x$WK2" = "xyes" ]; then - CFLAGS="$SLKCFLAGS" \ - CXXFLAGS="$SLKCFLAGS" \ - ./waf configure \ - --prefix=/usr \ - --enable-webkit2 \ - --gtk=3 - # --disable-dbus - # --gtk=2 doesn't work with webkitgtk as gtk2 is disabled -else - CFLAGS="$SLKCFLAGS" \ - CXXFLAGS="$SLKCFLAGS" \ - ./waf configure \ - --prefix=/usr \ - --enable-webkit-editor \ - --gtk=3 - # --disable-dbus - # --gtk=2 doesn't work with webkitgtk as gtk2 is disabled -fi - -./waf build -./waf install --destdir=$PKG - +#patch to make work with newer glib +echo "#define GLIB_VERSION_MIN_REQUIRED (GLIB_VERSION_2_26)" >>cmake/config.h.cmake.in +mkdir -p build +cd build +cmake -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DLIB_SUFFIX=${LIBDIRSUFFIX} \ + -DCMAKE_INSTALL_MANDIR=man \ + -DHTMLHELP=ON \ + -DCMAKE_BUILD_TYPE=Release \ + -DDBUS=OFF -DSTRIP=ON -DPOSTINST=OFF -DGTKHTML=ON .. + +#cmake should have created make file so restore PATH +make +make install DESTDIR=$PKG +cd .. + +#output should be stripped but we just make sure.. find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true +#compress man pages. +find $PKG/usr/man -type f -exec gzip -9 {} \; +for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done + mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION mv $PKG/usr/share/doc/$PRGNAM/* $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild @@ -114,4 +119,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/xiphos/xiphos.info b/academic/xiphos/xiphos.info index d2cd894617..70245d07d3 100644 --- a/academic/xiphos/xiphos.info +++ b/academic/xiphos/xiphos.info @@ -1,10 +1,10 @@ PRGNAM="xiphos" -VERSION="4.1.0" -HOMEPAGE="http://xiphos.org" -DOWNLOAD="https://github.com/crosswire/xiphos/releases/download/4.1.0/xiphos-4.1.0.tar.gz" -MD5SUM="f40c5b249c50a49af71de94420ee720d" +VERSION="4.2.1" +HOMEPAGE="https://xiphos.org" +DOWNLOAD="https://github.com/crosswire/xiphos/releases/download/4.2.1/xiphos-4.2.1.tar.gz" +MD5SUM="77d8a99c063433bea3006954710b2fd5" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="sword webkitgtk3 biblesync rarian %README%" +REQUIRES="sword biblesync rarian gtkhtml libminizip appstream-glib yelp" MAINTAINER="Tim Dickson" EMAIL="dickson.tim@googlemail.com" diff --git a/academic/xoscope/README b/academic/xoscope/README index 0f1c14e952..828260ac2d 100644 --- a/academic/xoscope/README +++ b/academic/xoscope/README @@ -2,7 +2,7 @@ xoscope is a digital real-time oscilloscope. It graphically displays signal amplitude or bit logic as a function of time. Signals may be displayed, saved, recalled, and manipulated by math functions. -Signal input devices currently include ALSA, ESD, and COMEDI. +Signal input devices currently include ALSA and COMEDI. If you use your sound card as the input, consider building this buffer circuit to protect it from overvoltage: diff --git a/academic/xoscope/xoscope.SlackBuild b/academic/xoscope/xoscope.SlackBuild index b0f9ff77e8..3e29b53dd8 100644 --- a/academic/xoscope/xoscope.SlackBuild +++ b/academic/xoscope/xoscope.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for xoscope -# Copyright 2015-2016 Kyle Guinn <elyk03@gmail.com>, USA +# Copyright 2015-2021 Kyle Guinn <elyk03@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=xoscope -VERSION=${VERSION:-2.2} +VERSION=${VERSION:-2.3} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$(uname -m)" in @@ -35,15 +38,22 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} DOCS="AUTHORS COPYING ChangeLog INSTALL NEWS README TODO* hardware" -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i586" ]; then SLKCFLAGS="-O2 -march=i586 -mtune=i686" @@ -97,4 +107,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/xoscope/xoscope.info b/academic/xoscope/xoscope.info index 7583dc5f8f..23fbc760a8 100644 --- a/academic/xoscope/xoscope.info +++ b/academic/xoscope/xoscope.info @@ -1,8 +1,8 @@ PRGNAM="xoscope" -VERSION="2.2" +VERSION="2.3" HOMEPAGE="http://xoscope.sourceforge.net/" -DOWNLOAD="http://downloads.sourceforge.net/xoscope/xoscope-2.2.tar.gz" -MD5SUM="468ff79d38b5645f9033b564091bfecd" +DOWNLOAD="https://sourceforge.net/projects/xoscope/files/xoscope/2.3/xoscope-2.3.tar.gz" +MD5SUM="737504856797fb0eac6f9c768446a184" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="gtkdatabox" diff --git a/academic/xschem/README b/academic/xschem/README new file mode 100644 index 0000000000..9af371c59b --- /dev/null +++ b/academic/xschem/README @@ -0,0 +1,18 @@ +Xschem is a schematic capture program, it allows creation of +hierarchical representation of circuits with a top down approach . By +focusing on interfaces, hierarchy and instance properties a complex +system can be described in terms of simpler building blocks. A VHDL +or Verilog or Spice netlist can be generated from the drawn schematic, +allowing the simulation of the circuit. Key feature of the program is +its drawing engine written in C and using directly the Xlib drawing +primitives; this gives very good speed performance, even on very big +circuits. The user interface is built with the Tcl-Tk toolkit, tcl is +also the extension language used. - hierarchical schematic drawings, +no limits on size - any object in the schematic can have any sort of +properties (generics in VHDL, parameters in Spice or Verilog) - new +Spice/Verilog primitives can be created, and the netlist format can +be defined by the user -tcl extension language allows the creation +of scripts; any user command in the drawing window has an associated +tcl comand - VHDL / Verilog / Spice netlist, ready for simulation - +Behavioral VHDL / Verilog code can be embedded as one of the properties +of the schematic block. diff --git a/academic/xschem/doinst.sh b/academic/xschem/doinst.sh new file mode 100644 index 0000000000..5fb28930db --- /dev/null +++ b/academic/xschem/doinst.sh @@ -0,0 +1,3 @@ +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 +fi diff --git a/academic/xschem/slack-desc b/academic/xschem/slack-desc new file mode 100644 index 0000000000..cf6956bfb7 --- /dev/null +++ b/academic/xschem/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +xschem: xschem (schematic capture program) +xschem: +xschem: It support various simulators, build it waveform viewer and it can +xschem: connect with other waveform viewer like gaw and BeSpice +xschem: +xschem: +xschem: +xschem: +xschem: +xschem: +xschem: diff --git a/academic/xschem/xschem.SlackBuild b/academic/xschem/xschem.SlackBuild new file mode 100644 index 0000000000..1c513ac5c2 --- /dev/null +++ b/academic/xschem/xschem.SlackBuild @@ -0,0 +1,113 @@ +#!/bin/bash + +# Slackware build script for xschem + +# Copyright 2023 Alfredo USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=xschem +VERSION=${VERSION:-3.4.4} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +elif [ "$ARCH" = "aarch64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + +make install PREFIX=/usr DESTDIR=$PKG + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mv $PKG/usr/share/man $PKG/usr/ + +find $PKG/usr/man -type f -exec gzip -9 {} \; +for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done + +mkdir -p $PKG/usr/share/applications +mkdir -p $PKG/usr/share/pixmaps/$PRGNAM/ +cp $CWD/$PRGNAM.desktop $PKG/usr/share/applications/ +cp $CWD/$PRGNAM.png $PKG/usr/share/pixmaps/$PRGNAM/ + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +mv $PKG/usr/share/doc/$PRGNAM/* $PKG/usr/doc/$PRGNAM-$VERSION/ +rmdir $PKG/usr/share/doc/$PRGNAM/ +rmdir $PKG/usr/share/doc/ +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/xschem/xschem.desktop b/academic/xschem/xschem.desktop new file mode 100644 index 0000000000..8706de83a2 --- /dev/null +++ b/academic/xschem/xschem.desktop @@ -0,0 +1,11 @@ +[Desktop Entry] +Exec=/usr/bin/xschem +InitialPreference=2 +MimeType=application/xscheme; +Name=xscheme +Comment=Schematic capture +Icon=/usr/share/pixmaps/xschem/xschem.png +Terminal=false +Type=Application +Categories=Graphics; +Keywords=CAD;simualtion;design;drawing; diff --git a/academic/xschem/xschem.fig b/academic/xschem/xschem.fig new file mode 100644 index 0000000000..79265fe77e --- /dev/null +++ b/academic/xschem/xschem.fig @@ -0,0 +1,10 @@ +#FIG 3.2 Produced by xfig version 3.2.8b +Landscape +Center +Inches +Letter +100.00 +Single +-2 +1200 2 +4 0 4 50 -1 18 16 0.0000 4 210 1185 225 600 XSCHEM\001 diff --git a/academic/xschem/xschem.info b/academic/xschem/xschem.info new file mode 100644 index 0000000000..7a6abe4add --- /dev/null +++ b/academic/xschem/xschem.info @@ -0,0 +1,10 @@ +PRGNAM="xschem" +VERSION="3.4.4" +HOMEPAGE="https://xschem.sourceforge.io/stefan/index.html" +DOWNLOAD="https://sourceforge.net/projects/xschem/files/xschem-3.4.4.tar.gz" +MD5SUM="d9dbdce18579fb6dc4c08ac942dd8001" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="A. Tomasini" +EMAIL="alto dot tom at gmail dot com" diff --git a/academic/xschem/xschem.png b/academic/xschem/xschem.png Binary files differnew file mode 100644 index 0000000000..9892fbaf2f --- /dev/null +++ b/academic/xschem/xschem.png diff --git a/academic/xsimd/README b/academic/xsimd/README new file mode 100644 index 0000000000..bd2c62b1bb --- /dev/null +++ b/academic/xsimd/README @@ -0,0 +1,11 @@ +SIMD (Single Instruction, Multiple Data) is a feature of microprocessors +that has been available for many years. SIMD instructions perform a +single operation on a batch of values at once, and thus provide a way +to significantly accelerate code execution. However, these instructions +differ between microprocessor vendors and compilers. + +xsimd provides a unified means for using these features for library +authors. Namely, it enables manipulation of batches of numbers with +the same arithmetic operators as for single values. It also provides +accelerated implementation of common mathematical functions operating +on batches. diff --git a/academic/xsimd/slack-desc b/academic/xsimd/slack-desc new file mode 100644 index 0000000000..cea4fc827a --- /dev/null +++ b/academic/xsimd/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +xsimd: xsimd (C++ wrappers for SIMD intrinsics) +xsimd: +xsimd: xsimd provides a unified means for using SIMD features for library +xsimd: authors. Namely, it enables manipulation of batches of numbers with +xsimd: the same arithmetic operators as for single values. It also provides +xsimd: accelerated implementation of common mathematical functions operating +xsimd: on batches. +xsimd: +xsimd: +xsimd: +xsimd: diff --git a/academic/kile/kile.SlackBuild b/academic/xsimd/xsimd.SlackBuild index 8b054abe8f..f15fa4eb2b 100644 --- a/academic/kile/kile.SlackBuild +++ b/academic/xsimd/xsimd.SlackBuild @@ -1,8 +1,9 @@ -#!/bin/sh +#!/bin/bash -# Slackware build script for Kile +# Slackware build script for xsimd -# Copyright 2012 Heinz Wiesinger, Amsterdam, The Netherlands +# Copyright 2022-2023 Isaac Yu <isaacyu@protonmail.com> +# Copyright 2023 Jeremy Hansen <jebrhansen+SBo@gmail.com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,36 +23,39 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -PRGNAM=kile -VERSION=${VERSION:-2.1.3} +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=xsimd +VERSION=${VERSION:-11.1.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" - LIBDIRSUFFIX="" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" - LIBDIRSUFFIX="" elif [ "$ARCH" = "x86_64" ]; then SLKCFLAGS="-O2 -fPIC" - LIBDIRSUFFIX="64" else SLKCFLAGS="-O2" - LIBDIRSUFFIX="" fi set -e @@ -60,37 +64,36 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $PRGNAM-$VERSION -tar xvf $CWD/$PRGNAM-$VERSION.tar.bz2 +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz cd $PRGNAM-$VERSION chown -R root:root . find -L . \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -mkdir build && cd build +mkdir build +cd build cmake \ - -DCMAKE_C_FLAGS="$SLKCFLAGS" \ - -DCMAKE_CXX_FLAGS="$SLKCFLAGS" \ + -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ -DCMAKE_INSTALL_PREFIX=/usr \ - -DLIB_SUFFIX="$LIBDIRSUFFIX" \ - .. + -DBUILD_TESTS=yes \ + -DCMAKE_BUILD_TYPE=Release .. make make install DESTDIR=$PKG -cd - +cd .. -find $PKG | xargs file | grep -e "executable" -e "shared object" | grep ELF \ +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a AUTHORS ChangeLog COPYING* README* \ - $PKG/usr/doc/$PRGNAM-$VERSION/ +cp -a LICENSE README.md $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc -cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/xsimd/xsimd.info b/academic/xsimd/xsimd.info new file mode 100644 index 0000000000..8a24d36307 --- /dev/null +++ b/academic/xsimd/xsimd.info @@ -0,0 +1,10 @@ +PRGNAM="xsimd" +VERSION="11.1.0" +HOMEPAGE="https://github.com/QuantStack/xsimd" +DOWNLOAD="https://github.com/QuantStack/xsimd/archive/11.1.0/xsimd-11.1.0.tar.gz" +MD5SUM="29ffd841d6491fddfbfaedeffc637f02" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="doctest" +MAINTAINER="Jeremy Hansen" +EMAIL="jebrhansen+SBo@gmail.com" diff --git a/academic/yices2/README b/academic/yices2/README new file mode 100644 index 0000000000..65774f7f8c --- /dev/null +++ b/academic/yices2/README @@ -0,0 +1,14 @@ + Yices 2 is an SMT solver that decides the satisfiability of formulas +containing uninterpreted function symbols with equality, real and +integer arithmetic, bitvectors, scalar types, and tuples. Yices 2 +supports both linear and nonlinear arithmetic. + + Yices 2 can process input written in the SMT-LIB notation (both +versions 2.0 and 1.2 are supported). Alternatively, you can write +specifications using Yices 2's own specification language, which +includes tuples and scalar types. You can also use Yices 2 as a +library in your software. + + + If you want to enable non-linear real and integer arithmetic +set MCSAT=yes, this requires libpoly and libcudd. diff --git a/academic/yices2/slack-desc b/academic/yices2/slack-desc new file mode 100644 index 0000000000..a575d6fc35 --- /dev/null +++ b/academic/yices2/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +yices2: yices2 (Satisfiability modulo theories solver) +yices2: +yices2: +yices2: +yices2: Yices 2 is an SMT solver that decides the satisfiability of +yices2: formulas containing uninterpreted function symbols with equality, +yices2: real and integer arithmetic, bitvectors, scalar types, and tuples. +yices2: Yices 2 supports both linear and nonlinear arithmetic. +yices2: +yices2: +yices2: diff --git a/academic/wxmacmolplt/wxmacmolplt.SlackBuild b/academic/yices2/yices2.SlackBuild index 8a40559843..7d80ee1a9e 100644 --- a/academic/wxmacmolplt/wxmacmolplt.SlackBuild +++ b/academic/yices2/yices2.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash -# Slackware build script for wxmacmolplt +# Slackware build script for yices2 -# Copyright 2012 Daniil Bratashov <dn2010@gmail.com> +# Copyright 2022 William PC - Seattle, USA # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,26 +22,39 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -PRGNAM=wxmacmolplt -VERSION=${VERSION:-7.7} + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=yices2 +VERSION=${VERSION:-2.6.4} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +SRCNAM=yices-$VERSION-src if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -59,15 +72,9 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $PRGNAM-$VERSION - -if [ -f $CWD/$PRGNAM-$VERSION.tar.gz ]; then - tar xvf $CWD/$PRGNAM-$VERSION.tar.gz -elif [ -f $CWD/7pzccnku3uv0mmf6il6yiqghf4b34lc7.gz ]; then - tar xvf $CWD/7pzccnku3uv0mmf6il6yiqghf4b34lc7.gz -fi - -cd $PRGNAM-$VERSION +rm -rf $PRGNAM-Yices-$VERSION +tar xvf $CWD/$SRCNAM.tar.gz +cd $PRGNAM-Yices-$VERSION chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -75,16 +82,12 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -# Fix for PCGAMESS new raman activities format -patch -p1 < $CWD/wxmacmolplt-7.2.1-raman.patch - -# Fix for Firefly format autodetection -patch -p1 < $CWD/wxmacmolplt-7.4-firefly.patch -# Fix for endless loop in system group read -# Fix for energy plot with firefly 8 -patch -p0 < $CWD/wxmacmolplt-7.4.4-files.patch +if [ "${MCSAT:-no}" == "yes" ]; then + OPT="--enable-mcsat" +fi +autoconf CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ @@ -93,31 +96,36 @@ CXXFLAGS="$SLKCFLAGS" \ --sysconfdir=/etc \ --localstatedir=/var \ --mandir=/usr/man \ - --docdir=/usr/doc/$PRGNAM-$VERSION \ - --build=$ARCH-slackware-linux + $OPT \ + --docdir=/usr/doc/$PRGNAM-$VERSION make make install DESTDIR=$PKG -find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ - | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true +# install docs and fix permissions +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -av doc/*.* $PKG/usr/doc/$PRGNAM-$VERSION +find $PKG/usr/doc/$PRGNAM-$VERSION -type d -exec chmod 755 '{}' \; -find $PKG/usr/man -type f -exec gzip -9 {} \; -for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done +# installing examples +mkdir -p $PKG/usr/share/$PRGNAM-$VERSION +cp -a examples $PKG/usr/share/$PRGNAM-$VERSION -mkdir -p $PKG/usr/share/icons/hicolor/128x128/apps -cp resources/wxmacmolplt.png $PKG/usr/share/icons/hicolor/128x128/apps -mkdir -p $PKG/usr/share/applications -cp resources/wxmacmolplt.desktop $PKG/usr/share/applications + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION -cp -a INSTALL LICENSE README $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + LICENSE.txt README.md \ + $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild -( cd $PKG/usr/doc/$PRGNAM-$VERSION ; ln -s ../../share/$PRGNAM misc ) mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc -cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/yices2/yices2.info b/academic/yices2/yices2.info new file mode 100644 index 0000000000..2811b191e2 --- /dev/null +++ b/academic/yices2/yices2.info @@ -0,0 +1,10 @@ +PRGNAM="yices2" +VERSION="2.6.4" +HOMEPAGE="https://yices.csl.sri.com" +DOWNLOAD="https://yices.csl.sri.com/releases/2.6.4/yices-2.6.4-src.tar.gz" +MD5SUM="6863fb6c44345e4b72490d16a7ee9f27" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/z3/README b/academic/z3/README index a1f132277a..a1c4c5a806 100644 --- a/academic/z3/README +++ b/academic/z3/README @@ -1,12 +1,8 @@ Z3 is an automated theorem prover and satisfiability modulo theories -(SMT) solver. Given a formula in first-order logic, it attempts to -either prove the formula or find a counterexample. Z3 supports +(SMT) solver. Given a formula in first-order logic, it attempts +to either prove the formula or find a counterexample. Z3 supports arithmetic, reasoning about arrays, and several other built-in theories. Input problems are written in SMT-LIB format. -This package includes the z3 program as well as the C++ and -Python APIs. By default the Python 2 version of the API is built; -if you also want the Python 3 version, run the SlackBuild with -PYTHON3=yes, like so: - - PYTHON3=yes ./z3.SlackBuild +This package includes the z3 program as well as the C++, Python2, and +Python3 APIs. diff --git a/academic/z3/z3.SlackBuild b/academic/z3/z3.SlackBuild index 741a7c6e4a..af9aa52dad 100644 --- a/academic/z3/z3.SlackBuild +++ b/academic/z3/z3.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for z3 -# Copyright 2019 Nick Smallbone, Gothenburg, Sweden +# Copyright 2019-2022 Nick Smallbone, Gothenburg, Sweden # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,10 +22,13 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=z3 -VERSION=${VERSION:-4.8.7} +VERSION=${VERSION:-4.11.2} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,11 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -60,14 +67,14 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $PRGNAM-$PRGNAM-$VERSION -tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +tar xvf $CWD/$PRGNAM-$PRGNAM-$VERSION.tar.gz cd $PRGNAM-$PRGNAM-$VERSION chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ + -o -perm 511 \) -exec chmod 755 {} \+ -o \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \+ CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ @@ -83,25 +90,24 @@ cd ../doc python mk_api_doc.py cd .. -if [ z$PYTHON3 = zyes ]; then - # Copy the Python bindings to python3.X/site-packages. - PYTHON_VERSION=$(python3 -c 'import sys; print("%d.%d" % sys.version_info[:2])') - PYLIB=$PKG/usr/lib${LIBDIRSUFFIX}/python${PYTHON_VERSION}/site-packages - mkdir -p $PYLIB - cp -a build/python/z3 $PYLIB/z3 - find $PYLIB/z3 -name '*.pyc' -delete -fi +# The Python bindings are installed for Python2 by default but work on +# Python3 too. Copy them to python3.X/site-packages. +PYTHON_VERSION=$(python3 -c 'import sys; print("%d.%d" % sys.version_info[:2])') +PYLIB=$PKG/usr/lib${LIBDIRSUFFIX}/python${PYTHON_VERSION}/site-packages +mkdir -p $PYLIB +cp -a build/python/z3 $PYLIB/z3 +find $PYLIB/z3 -name '*.pyc' -delete find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - README.md RELEASE_NOTES LICENSE.txt \ + README.md RELEASE_NOTES.md LICENSE.txt Parameters.md \ $PKG/usr/doc/$PRGNAM-$VERSION mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION/examples cp -a \ - examples/c examples/c++ examples/maxsat examples/python examples/tptp \ + examples/c examples/c++ examples/maxsat examples/python examples/tptp examples/SMT-LIB2 \ $PKG/usr/doc/$PRGNAM-$VERSION/examples find $PKG/usr/doc/$PRGNAM-$VERSION/examples -name CMakeLists.txt -delete cp -a \ @@ -113,4 +119,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/z3/z3.info b/academic/z3/z3.info index 71512a125f..b3b6178ae5 100644 --- a/academic/z3/z3.info +++ b/academic/z3/z3.info @@ -1,8 +1,8 @@ PRGNAM="z3" -VERSION="4.8.7" +VERSION="4.11.2" HOMEPAGE="https://github.com/Z3Prover/z3/wiki" -DOWNLOAD="https://github.com/Z3Prover/z3/archive/z3-4.8.7.tar.gz" -MD5SUM="18e7332ab136c1d8686ea719ed7107ed" +DOWNLOAD="https://github.com/Z3Prover/z3/archive/z3-4.11.2/z3-z3-4.11.2.tar.gz" +MD5SUM="35afb5c6658bc07c11d73ef7f08ff272" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/zotero-gtk2/README b/academic/zotero-gtk2/README new file mode 100644 index 0000000000..ca62239484 --- /dev/null +++ b/academic/zotero-gtk2/README @@ -0,0 +1,35 @@ +This is the last GTK2 version of Zotero. It will conflict with the +latest one, so don't install both. + +Zotero is a free, easy-to-use tool to help you collect, organize, +cite, and share research. + +Zotero is the only software that automatically senses research on +the web. Need an article from JSTOR or a preprint from arXiv.org? +A news story from the New York Times or a book from a library? +Zotero has you covered, everywhere. + +Zotero helps you organize your research any way you want. You can +sort items into collections and tag them with keywords. Or create +saved searches that automatically fill with relevant materials as +you work. + +Zotero instantly creates references and bibliographies for any +text editor, and directly inside Word, LibreOffice, and Google +Docs. With support for over 100,000 citation styles, you can +format your work to match any style guide or publication. + +Zotero can optionally synchronize your data across devices, +keeping your notes, files, and bibliographic records seamlessly +up to date. If you decide to sync, you can also always access +your research from any web browser. + +Zotero lets you co-write a paper with a colleague, distribute +course materials to students, or build a collaborative +bibliography. You can share a Zotero library with as many +people you like, at no cost. + +Zotero is open source and developed by an independent, +nonprofit organization that has no financial interest in your +private information. With Zotero, you always stay in control +of your own data. diff --git a/academic/zotero-gtk2/doinst.sh b/academic/zotero-gtk2/doinst.sh new file mode 100644 index 0000000000..65c7e2eeb9 --- /dev/null +++ b/academic/zotero-gtk2/doinst.sh @@ -0,0 +1,9 @@ +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 +fi + +if [ -e usr/share/icons/hicolor/icon-theme.cache ]; then + if [ -x /usr/bin/gtk-update-icon-cache ]; then + /usr/bin/gtk-update-icon-cache -f usr/share/icons/hicolor >/dev/null 2>&1 + fi +fi diff --git a/academic/zotero-gtk2/slack-desc b/academic/zotero-gtk2/slack-desc new file mode 100644 index 0000000000..fa0f527cb5 --- /dev/null +++ b/academic/zotero-gtk2/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +zotero-gtk2: zotero-gtk2 (Collect, organize, cite, and share research sources) +zotero-gtk2: +zotero-gtk2: Zotero is a free, easy-to-use tool to help you collect, organize, +zotero-gtk2: cite, and share research. This is the last GTK2 version of Zotero. +zotero-gtk2: If you are looking for the newest one, install "zotero", instead. +zotero-gtk2: +zotero-gtk2: Homepage: https://www.zotero.org/ +zotero-gtk2: +zotero-gtk2: +zotero-gtk2: +zotero-gtk2: diff --git a/academic/zotero-gtk2/zotero-gtk2.SlackBuild b/academic/zotero-gtk2/zotero-gtk2.SlackBuild new file mode 100644 index 0000000000..a758a63504 --- /dev/null +++ b/academic/zotero-gtk2/zotero-gtk2.SlackBuild @@ -0,0 +1,93 @@ +#!/bin/bash + +# Slackware build script for <zotero-gtk2> + +# Copyright 2023 Petar Petrov slackalaxy at gmail dot com +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=zotero-gtk2 +SRCNAM=Zotero +VERSION=${VERSION:-4.0.28} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i686 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +set -e + +if [ "$ARCH" != "i686" ] && [ "$ARCH" != "x86_64" ]; then + printf "\n\n$ARCH is not supported... \n" + exit 1 +fi + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $SRCNAM-${VERSION}_linux-$ARCH +tar xvf $CWD/$SRCNAM-${VERSION}_linux-$ARCH.tar.bz2 +cd ${SRCNAM}_linux-$ARCH +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +sed -i -e 's:MOZ_PROGRAM="":MOZ_PROGRAM="/opt/zotero/zotero":g' run-zotero.sh + +mkdir -p $PKG/opt/zotero +cp -a * $PKG/opt/zotero + +mkdir -p $PKG/usr/bin +cd $PKG/usr/bin +ln -s ../../opt/zotero/run-zotero.sh zotero + +mkdir -p $PKG/usr/share/{applications,pixmaps} +cp $CWD/zotero.desktop $PKG/usr/share/applications +cp $CWD/zotero.png $PKG/usr/share/pixmaps + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/zotero-gtk2/zotero-gtk2.info b/academic/zotero-gtk2/zotero-gtk2.info new file mode 100644 index 0000000000..2feff911d9 --- /dev/null +++ b/academic/zotero-gtk2/zotero-gtk2.info @@ -0,0 +1,10 @@ +PRGNAM="zotero-gtk2" +VERSION="4.0.28" +HOMEPAGE="https://www.zotero.org/" +DOWNLOAD="https://download.zotero.org/client/release/4.0.28/Zotero-4.0.28_linux-i686.tar.bz2" +MD5SUM="a5cb40b79b26dbe4fb29b8e9fdb61a9f" +DOWNLOAD_x86_64="https://download.zotero.org/client/release/4.0.28/Zotero-4.0.28_linux-x86_64.tar.bz2" +MD5SUM_x86_64="55f743aa7c08ca16d933e91faf43a2fc" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy at gmail dot com" diff --git a/academic/zotero-gtk2/zotero.desktop b/academic/zotero-gtk2/zotero.desktop new file mode 100644 index 0000000000..24e542f951 --- /dev/null +++ b/academic/zotero-gtk2/zotero.desktop @@ -0,0 +1,7 @@ +[Desktop Entry] +Type=Application +Name=Zotero Standalone +Icon=zotero +Exec=zotero %f +Categories=Office +Terminal=false diff --git a/academic/zotero/zotero.png b/academic/zotero-gtk2/zotero.png Binary files differindex fe80851fb3..fe80851fb3 100644 --- a/academic/zotero/zotero.png +++ b/academic/zotero-gtk2/zotero.png diff --git a/academic/zotero/README b/academic/zotero/README index 5979cc3be2..90a652ecda 100644 --- a/academic/zotero/README +++ b/academic/zotero/README @@ -1,15 +1,32 @@ -Zotero [zoh-TAIR-oh] is a free, easy-to-use tool to help you collect, -organize, cite, and share your research sources. - -Zotero collects all your research in a single, searchable interface. -You can add PDFs, images, audio / video files, snapshots of web pages, -and really anything else. Zotero automatically indexes the full-text -content of your library, enabling you to find exactly what you are -looking for with just a few keystrokes. - -Zotero is the only research tool that automatically senses content in -your web browser, allowing you to add it to your personal library with -a single click. Whether you're searching for a preprint on arXiv.org, -a journal article from JSTOR, a news story from the New York Times, or -a book from your university library catalog, Zotero has you covered -with support for thousands of sites. +Zotero is a free, easy-to-use tool to help you collect, organize, +cite, and share research. + +Zotero is the only software that automatically senses research on +the web. Need an article from JSTOR or a preprint from arXiv.org? +A news story from the New York Times or a book from a library? +Zotero has you covered, everywhere. + +Zotero helps you organize your research any way you want. You can +sort items into collections and tag them with keywords. Or create +saved searches that automatically fill with relevant materials as +you work. + +Zotero instantly creates references and bibliographies for any +text editor, and directly inside Word, LibreOffice, and Google +Docs. With support for over 100,000 citation styles, you can +format your work to match any style guide or publication. + +Zotero can optionally synchronize your data across devices, +keeping your notes, files, and bibliographic records seamlessly +up to date. If you decide to sync, you can also always access +your research from any web browser. + +Zotero lets you co-write a paper with a colleague, distribute +course materials to students, or build a collaborative +bibliography. You can share a Zotero library with as many +people you like, at no cost. + +Zotero is open source and developed by an independent, +nonprofit organization that has no financial interest in your +private information. With Zotero, you always stay in control +of your own data. diff --git a/academic/zotero/doinst.sh b/academic/zotero/doinst.sh index 5fb28930db..65c7e2eeb9 100644 --- a/academic/zotero/doinst.sh +++ b/academic/zotero/doinst.sh @@ -1,3 +1,9 @@ if [ -x /usr/bin/update-desktop-database ]; then /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 fi + +if [ -e usr/share/icons/hicolor/icon-theme.cache ]; then + if [ -x /usr/bin/gtk-update-icon-cache ]; then + /usr/bin/gtk-update-icon-cache -f usr/share/icons/hicolor >/dev/null 2>&1 + fi +fi diff --git a/academic/zotero/slack-desc b/academic/zotero/slack-desc index d051f78252..fc426aba92 100644 --- a/academic/zotero/slack-desc +++ b/academic/zotero/slack-desc @@ -8,12 +8,12 @@ |-----handy-ruler------------------------------------------------------| zotero: zotero (Collect, organize, cite, and share research sources) zotero: -zotero: Zotero automatically senses content in your web browser, allowing -zotero: you to add it to your personal library. Zotero collects all your -zotero: research in a single, searchable interface. You can add PDFs, -zotero: images, audio / video files, snapshots of web pages, and really -zotero: anything else. Zotero automatically indexes the full-text content -zotero: of your library, enabling you to find exactly what you are looking -zotero: for with just a few keystrokes. +zotero: Zotero is a free, easy-to-use tool to help you collect, organize, +zotero: cite, and share research. +zotero: +zotero: +zotero: +zotero: zotero: zotero: Homepage: https://www.zotero.org/ +zotero: diff --git a/academic/zotero/zotero.SlackBuild b/academic/zotero/zotero.SlackBuild index 8ad1d6a014..db10f91ca6 100644 --- a/academic/zotero/zotero.SlackBuild +++ b/academic/zotero/zotero.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for zotero -# Copyright 2018-2020 Andrew Payne phalange@komputermatrix.com +# Copyright 2018-2024 Andrew Payne phalange@komputermatrix.com # Copyright 2014-2018 Petar Petrov slackalaxy@gmail.com # All rights reserved. # @@ -23,11 +23,14 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=zotero SRCNAM=Zotero -VERSION=${VERSION:-5.0.85} +VERSION=${VERSION:-6.0.35} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -37,7 +40,14 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -66,19 +76,31 @@ mkdir -p $PKG/{usr/bin,opt/$PRGNAM} cp -a * $PKG/opt/$PRGNAM ln -s /opt/$PRGNAM/zotero $PKG/usr/bin/$PRGNAM +# put the icons in the right place +mkdir -p $PKG/usr/share/icons/hicolor/{16x16,32x32,48x48,256x256,scalable}/apps +cp $PKG/opt/$PRGNAM/chrome/icons/default/default16.png \ + $PKG/usr/share/icons/hicolor/16x16/apps/zotero.png +cp $PKG/opt/$PRGNAM/chrome/icons/default/default32.png \ + $PKG/usr/share/icons/hicolor/32x32/apps/zotero.png +cp $PKG/opt/$PRGNAM/chrome/icons/default/default48.png \ + $PKG/usr/share/icons/hicolor/48x48/apps/zotero.png +cp $PKG/opt/$PRGNAM/chrome/icons/default/default256.png \ + $PKG/usr/share/icons/hicolor/256x256/apps/zotero.png +cp $PKG/opt/$PRGNAM/chrome/icons/default/main-window.ico \ + $PKG/usr/share/icons/hicolor/scalable/apps/zotero.ico + find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild -mkdir -p $PKG/usr/share/{applications,pixmaps} -cp $CWD/$PRGNAM.desktop $PKG/usr/share/applications -cp $CWD/$PRGNAM.png $PKG/usr/share/pixmaps/$PRGNAM.png +mkdir -p $PKG/usr/share/applications +cat $CWD/$PRGNAM.desktop > $PKG/usr/share/applications/$PRGNAM.desktop mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/zotero/zotero.desktop b/academic/zotero/zotero.desktop index 24e542f951..277ba1f7aa 100644 --- a/academic/zotero/zotero.desktop +++ b/academic/zotero/zotero.desktop @@ -1,6 +1,6 @@ [Desktop Entry] Type=Application -Name=Zotero Standalone +Name=Zotero Icon=zotero Exec=zotero %f Categories=Office diff --git a/academic/zotero/zotero.info b/academic/zotero/zotero.info index 564a6702dd..ef23199303 100644 --- a/academic/zotero/zotero.info +++ b/academic/zotero/zotero.info @@ -1,10 +1,10 @@ PRGNAM="zotero" -VERSION="5.0.85" +VERSION="6.0.35" HOMEPAGE="https://www.zotero.org/" -DOWNLOAD="https://download.zotero.org/client/release/5.0.85/Zotero-5.0.85_linux-i686.tar.bz2" -MD5SUM="196d758dc19a658a54d30877fe0c41b2" -DOWNLOAD_x86_64="https://download.zotero.org/client/release/5.0.85/Zotero-5.0.85_linux-x86_64.tar.bz2" -MD5SUM_x86_64="6509c159079ed59c2c95ac0132dc2328" +DOWNLOAD="https://download.zotero.org/client/release/6.0.35/Zotero-6.0.35_linux-i686.tar.bz2" +MD5SUM="2fc1598b9221cfd545913b97061661d7" +DOWNLOAD_x86_64="https://download.zotero.org/client/release/6.0.35/Zotero-6.0.35_linux-x86_64.tar.bz2" +MD5SUM_x86_64="9fe5026af4b30da8a50b40f576602704" REQUIRES="" MAINTAINER="Andrew Payne" EMAIL="phalange@komputermatrix.com" |
