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author Matteo Bernardini2020-01-03 23:09:25 +0100
committer Matteo Bernardini2020-01-03 23:09:25 +0100
commit95008285045d7130c028d6755dcc2bae5387cb22 (patch)
tree65f9ab22c4711d52dbe2d3a77112b00e4a8e051d /academic
parent66bb71ec178eb531b8a07c19457800341c8f0d9f (diff)
downloadslackbuilds-current-20200103.1.tar.gz
20200103.1 global branch merge.current-20200103.1
Signed-off-by: Matteo Bernardini <ponce@slackbuilds.org>
Diffstat (limited to 'academic')
-rw-r--r--academic/antiprism/antiprism.SlackBuild2
-rw-r--r--academic/geda-gaf/geda-gaf.info2
-rw-r--r--academic/gelemental/gcc.patch12
-rw-r--r--academic/gelemental/gelemental.SlackBuild3
-rw-r--r--academic/genius/README2
-rw-r--r--academic/genometools/genometools.SlackBuild2
-rw-r--r--academic/primer3/primer3.SlackBuild4
-rw-r--r--academic/root/root.SlackBuild9
-rw-r--r--academic/root/root.info8
-rw-r--r--academic/tophat/make_pair.patch24
-rw-r--r--academic/tophat/tophat.SlackBuild3
-rw-r--r--academic/ugene/ugene-1.22.0-dont_hardcode_includes.patch24
-rw-r--r--academic/ugene/ugene.SlackBuild3
-rw-r--r--academic/veusz/veusz.SlackBuild4
14 files changed, 82 insertions, 20 deletions
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<bool>(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="Jo┼że 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, 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..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 \