From 95008285045d7130c028d6755dcc2bae5387cb22 Mon Sep 17 00:00:00 2001 From: Matteo Bernardini Date: Fri, 3 Jan 2020 23:09:25 +0100 Subject: 20200103.1 global branch merge. Signed-off-by: Matteo Bernardini --- academic/antiprism/antiprism.SlackBuild | 2 +- academic/geda-gaf/geda-gaf.info | 2 +- academic/gelemental/gcc.patch | 12 +++++++++++ academic/gelemental/gelemental.SlackBuild | 3 +++ academic/genius/README | 2 +- academic/genometools/genometools.SlackBuild | 2 +- academic/primer3/primer3.SlackBuild | 4 +--- academic/root/root.SlackBuild | 9 ++++---- academic/root/root.info | 8 ++++---- academic/tophat/make_pair.patch | 24 ++++++++++++++++++++++ academic/tophat/tophat.SlackBuild | 3 +++ .../ugene-1.22.0-dont_hardcode_includes.patch | 24 ++++++++++++++++++++++ academic/ugene/ugene.SlackBuild | 3 +++ academic/veusz/veusz.SlackBuild | 4 ---- 14 files changed, 82 insertions(+), 20 deletions(-) create mode 100644 academic/gelemental/gcc.patch create mode 100644 academic/tophat/make_pair.patch create mode 100644 academic/ugene/ugene-1.22.0-dont_hardcode_includes.patch (limited to 'academic') diff --git a/academic/antiprism/antiprism.SlackBuild b/academic/antiprism/antiprism.SlackBuild index 271184a166..f3c6c291e6 100644 --- a/academic/antiprism/antiprism.SlackBuild +++ b/academic/antiprism/antiprism.SlackBuild @@ -55,7 +55,7 @@ find -L . \ sed "/^docdir/s|= .*|= @docdir@|" -i Makefile.in CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS -fpermissive" \ ./configure \ --prefix=/usr \ --libdir=/usr/lib$LIBDIRSUFFIX \ diff --git a/academic/geda-gaf/geda-gaf.info b/academic/geda-gaf/geda-gaf.info index 3664fa7fb5..1362c53982 100644 --- a/academic/geda-gaf/geda-gaf.info +++ b/academic/geda-gaf/geda-gaf.info @@ -5,6 +5,6 @@ DOWNLOAD="http://ftp.geda-project.org/geda-gaf/stable/v1.8/1.8.2/geda-gaf-1.8.2. MD5SUM="fa8a807615decf47027e22a217dd0ded" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="" +REQUIRES="guile1.8" MAINTAINER="Stephen Van Berg" EMAIL="stephen_van_berg@earlicker.com" diff --git a/academic/gelemental/gcc.patch b/academic/gelemental/gcc.patch new file mode 100644 index 0000000000..eeb16293d9 --- /dev/null +++ b/academic/gelemental/gcc.patch @@ -0,0 +1,12 @@ +diff -Naur gelemental-1.2.0.orig/src/dialogs.cc gelemental-1.2.0/src/dialogs.cc +--- gelemental-1.2.0.orig/src/dialogs.cc 2007-09-25 06:49:33.000000000 +0200 ++++ gelemental-1.2.0/src/dialogs.cc 2017-07-27 21:45:34.356776770 +0200 +@@ -247,7 +247,7 @@ + const Gtk::TreePath& tpath, bool) + { + Gtk::TreeIter iter = store->get_iter (tpath); +- return iter ? iter->get_value (cols.property) : false; ++ return iter ? static_cast(iter->get_value (cols.property)) : false; + } + + diff --git a/academic/gelemental/gelemental.SlackBuild b/academic/gelemental/gelemental.SlackBuild index e4b332e18a..d2ae765eb6 100644 --- a/academic/gelemental/gelemental.SlackBuild +++ b/academic/gelemental/gelemental.SlackBuild @@ -70,6 +70,9 @@ 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 {} \; +# Fix for the newer gcc +patch -p1 -i $CWD/gcc.patch + CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS -std=c++11" \ ./configure \ diff --git a/academic/genius/README b/academic/genius/README index d4a270574c..fa2fa4b67b 100644 --- a/academic/genius/README +++ b/academic/genius/README @@ -7,5 +7,5 @@ or educational tool. The syntax is very intuitive and is designed to mimic how mathematics is usually written. If you would like the GUI interface as well, it requires -libgnomeui and gtksourceview. If you have these dependencies, +libgnomeui, gtksourceview and vte2. If you have these dependencies, pass the variable of GNOME=YES (or anything that isn't NO ;) diff --git a/academic/genometools/genometools.SlackBuild b/academic/genometools/genometools.SlackBuild index f4af4db0f9..117e1bb420 100644 --- a/academic/genometools/genometools.SlackBuild +++ b/academic/genometools/genometools.SlackBuild @@ -76,7 +76,7 @@ find -L . \ sed -i "s:lib/libgenometools:lib${LIBDIRSUFFIX}/libgenometools:g" Makefile sed -i "s:\$(prefix)/lib:\$(prefix)/lib${LIBDIRSUFFIX}:g" Makefile -CFLAGS="$SLKCFLAGS" \ +CFLAGS="$SLKCFLAGS -Wno-error=format-truncation=" \ CXXFLAGS="$SLKCFLAGS" \ make $BUILDARCH \ prefix=/usr diff --git a/academic/primer3/primer3.SlackBuild b/academic/primer3/primer3.SlackBuild index d3ae1b399c..514f65fd23 100644 --- a/academic/primer3/primer3.SlackBuild +++ b/academic/primer3/primer3.SlackBuild @@ -75,13 +75,11 @@ patch -p1 -i $CWD/gcc-7.patch cd ./src # Use our CFLAGS -sed -i "/^CFLAGS/s/=/+=/" Makefile +sed -i -e "s|-O2|$SLKCFLAGS|" -e "s|-g -Wall|-fpermissive|" 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="$SLKCFLAGS" \ make # This is recommended, but the tests take a really long time. Be patient diff --git a/academic/root/root.SlackBuild b/academic/root/root.SlackBuild index bb507f0536..e0ec409dca 100644 --- a/academic/root/root.SlackBuild +++ b/academic/root/root.SlackBuild @@ -18,7 +18,7 @@ # Modified by the slackbuilds.org project PRGNAM=root -VERSION=${VERSION:-5.34.36} +VERSION=${VERSION:-6.10.02} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -79,9 +79,9 @@ fi 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 +cd $PRGNAM-$VERSION chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -134,9 +134,8 @@ mkdir -p $PKG$PYTHONDIR mv \ $PKG$PREFIX/lib$LIBDIRSUFFIX/*.py \ $PKG$PREFIX/lib$LIBDIRSUFFIX/*.pyc \ - $PKG$PREFIX/lib$LIBDIRSUFFIX/python/genreflex \ + $PKG$PREFIX/lib$LIBDIRSUFFIX/*.pyo \ $PKG$PYTHONDIR -rm -fr $PKG$PREFIX/lib$LIBDIRSUFFIX/python find $PKG | xargs file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneded 2> /dev/null || true diff --git a/academic/root/root.info b/academic/root/root.info index 450e1bde00..7df5c81738 100644 --- a/academic/root/root.info +++ b/academic/root/root.info @@ -1,10 +1,10 @@ PRGNAM="root" -VERSION="5.34.36" +VERSION="6.10.02" HOMEPAGE="http://root.cern.ch/drupal/" -DOWNLOAD="https://root.cern.ch/download/root_v5.34.36.source.tar.gz" -MD5SUM="6a1ad549b3b79b10bbb1f116b49067ee" +DOWNLOAD="https://root.cern.ch/download/root_v6.10.02.source.tar.gz" +MD5SUM="19f2285c845a48355db779938fb4db99" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="ftgl" +REQUIRES="ftgl unixODBC" MAINTAINER="Jože Zobec" EMAIL="jozze.zepl@gmail.com" 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(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(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..e3e97fcc85 100644 --- a/academic/tophat/tophat.SlackBuild +++ b/academic/tophat/tophat.SlackBuild @@ -69,6 +69,9 @@ 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 archlinux +patch -p1 < $CWD/make_pair.patch + ./autogen.sh CFLAGS="$SLKCFLAGS" \ diff --git a/academic/ugene/ugene-1.22.0-dont_hardcode_includes.patch b/academic/ugene/ugene-1.22.0-dont_hardcode_includes.patch new file mode 100644 index 0000000000..6bc26e1f19 --- /dev/null +++ b/academic/ugene/ugene-1.22.0-dont_hardcode_includes.patch @@ -0,0 +1,24 @@ +diff -up ugene-1.22.0/src/libs_3rdparty/samtools/samtools.pri.dont_hardcode_includes ugene-1.22.0/src/libs_3rdparty/samtools/samtools.pri +--- ugene-1.22.0/src/libs_3rdparty/samtools/samtools.pri.dont_hardcode_includes 2016-03-31 07:21:56.000000000 -0500 ++++ ugene-1.22.0/src/libs_3rdparty/samtools/samtools.pri 2016-06-02 17:49:02.383069490 -0500 +@@ -3,7 +3,7 @@ UGENE_RELATIVE_DESTDIR = '' + + TEMPLATE = lib + CONFIG +=thread debug_and_release staticlib warn_off +-INCLUDEPATH += src src/samtools ../../include /usr/include ++INCLUDEPATH += src src/samtools ../../include + win32 : INCLUDEPATH += src/samtools/win32 + DEFINES+="_FILE_OFFSET_BITS=64" _LARGEFILE64_SOURCE _USE_KNETFILE + win32 : DEFINES += _USE_MATH_DEFINES "inline=__inline" "__func__=__FUNCTION__" "R_OK=4" "atoll=_atoi64" "alloca=_alloca" +diff -up ugene-1.22.0/src/plugins_3rdparty/variants/variants.pri.dont_hardcode_includes ugene-1.22.0/src/plugins_3rdparty/variants/variants.pri +--- ugene-1.22.0/src/plugins_3rdparty/variants/variants.pri.dont_hardcode_includes 2016-03-31 07:22:09.000000000 -0500 ++++ ugene-1.22.0/src/plugins_3rdparty/variants/variants.pri 2016-06-02 20:26:35.265356432 -0500 +@@ -20,7 +20,7 @@ use_bundled_zlib() { + win32 : LIBS += -lwsock32 + + +-INCLUDEPATH += src ../../include /usr/include ++INCLUDEPATH += src ../../include + INCLUDEPATH += ../../libs_3rdparty/samtools/src/samtools + INCLUDEPATH += ../../libs_3rdparty/samtools/src + INCLUDEPATH += ../../libs_3rdparty/samtools/src/samtools/bcftools diff --git a/academic/ugene/ugene.SlackBuild b/academic/ugene/ugene.SlackBuild index ac95c63b17..1b68d3e510 100644 --- a/academic/ugene/ugene.SlackBuild +++ b/academic/ugene/ugene.SlackBuild @@ -73,6 +73,9 @@ 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 fedora +patch -p1 < $CWD/ugene-1.22.0-dont_hardcode_includes.patch + # Fix libraries and man pages paths sed -i "s:/lib:/lib${LIBDIRSUFFIX}:g" src/ugene_globals.pri sed -i "s:/share/man:/man:g" src/ugene_globals.pri diff --git a/academic/veusz/veusz.SlackBuild b/academic/veusz/veusz.SlackBuild index f3e607ab95..39d3b8fe80 100644 --- a/academic/veusz/veusz.SlackBuild +++ b/academic/veusz/veusz.SlackBuild @@ -69,10 +69,6 @@ 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 {} \; -PYTHONVER=$(python -V 2>&1 | cut -f 2 -d' ' | cut -f 1-2 -d.) -export SIP_EXE=/usr/bin/python2-sip -export SIP_INCLUDE_DIR="/usr/include/python$PYTHONVER/python2-sip" - python setup.py install --root $PKG find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ -- cgit v1.2.3