diff options
author | Matteo Bernardini | 2017-08-07 16:31:24 +0200 |
---|---|---|
committer | Matteo Bernardini | 2017-08-07 16:31:24 +0200 |
commit | 16f7c508bb21dabaf5d8068454a31ca6f3d6c979 (patch) | |
tree | e3aea401c8004362cc89daa2db7b308fcb12598f /academic | |
parent | 5e5132bde843b256dd4833682296e363a01f78c2 (diff) | |
download | old.slackbuilds-830af7984ec508e7fc1739d7af30add2a3a15d7b.tar.gz |
20170807.1 global branch merge.current-20170807.1
Signed-off-by: Matteo Bernardini <ponce@slackbuilds.org>
Diffstat (limited to 'academic')
-rw-r--r-- | academic/antiprism/antiprism.SlackBuild | 2 | ||||
-rw-r--r-- | academic/cld2/cld2.SlackBuild | 4 | ||||
-rw-r--r-- | academic/gelemental/gcc.patch | 12 | ||||
-rw-r--r-- | academic/gelemental/gelemental.SlackBuild | 3 | ||||
-rw-r--r-- | academic/genometools/genometools.SlackBuild | 2 | ||||
-rw-r--r-- | academic/prank-msa/prank-msa.SlackBuild | 2 | ||||
-rw-r--r-- | academic/prank-msa/prank-msa.info | 6 | ||||
-rw-r--r-- | academic/primer3/primer3.SlackBuild | 4 | ||||
-rw-r--r-- | academic/root/root.SlackBuild | 9 | ||||
-rw-r--r-- | academic/root/root.info | 8 | ||||
-rw-r--r-- | academic/t_coffee/t_coffee.SlackBuild | 3 | ||||
-rw-r--r-- | academic/tophat/make_pair.patch | 24 | ||||
-rw-r--r-- | academic/tophat/tophat.SlackBuild | 3 | ||||
-rw-r--r-- | academic/ugene/ugene-1.22.0-dont_hardcode_includes.patch | 24 | ||||
-rw-r--r-- | academic/ugene/ugene.SlackBuild | 3 |
15 files changed, 88 insertions, 21 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/cld2/cld2.SlackBuild b/academic/cld2/cld2.SlackBuild index 0011d0d861..bd6f5526fe 100644 --- a/academic/cld2/cld2.SlackBuild +++ b/academic/cld2/cld2.SlackBuild @@ -68,7 +68,7 @@ cd $PRGNAM-$SRCREV chown -R root:root . ( cd internal - g++ -shared $SLKCFLAGS \ + g++ -shared $SLKCFLAGS -Wno-error=narrowing \ cldutil.cc cldutil_shared.cc compact_lang_det.cc compact_lang_det_hint_code.cc \ compact_lang_det_impl.cc debug.cc fixunicodevalue.cc \ generated_entities.cc generated_language.cc generated_ulscript.cc \ @@ -80,7 +80,7 @@ chown -R root:root . cld2_generated_distinctoctachrome.cc cld_generated_score_quad_octa_2.cc \ -o libcld2.so - g++ -shared $SLKCFLAGS \ + g++ -shared $SLKCFLAGS -Wno-error=narrowing \ cldutil.cc cldutil_shared.cc compact_lang_det.cc compact_lang_det_hint_code.cc \ compact_lang_det_impl.cc debug.cc fixunicodevalue.cc \ generated_entities.cc generated_language.cc generated_ulscript.cc \ 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 22beaf7d9c..f8a08e984d 100644 --- a/academic/gelemental/gelemental.SlackBuild +++ b/academic/gelemental/gelemental.SlackBuild @@ -84,6 +84,9 @@ sed -i "s:set_size_request (50, 50):set_size_request (64, 64):" src/buttons.cc # include glib.h instead of individual headers. patch -p1 -i $CWD/glib-single-include.patch +# Fix for the newer gcc +patch -p1 -i $CWD/gcc.patch + CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS -std=c++11" \ ./configure \ diff --git a/academic/genometools/genometools.SlackBuild b/academic/genometools/genometools.SlackBuild index e6ca3e09d0..a617ee7485 100644 --- a/academic/genometools/genometools.SlackBuild +++ b/academic/genometools/genometools.SlackBuild @@ -76,7 +76,7 @@ find -L . \ sed -i "s:lib/libgenometools:lib${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 $BUILDARCH \ prefix=/usr diff --git a/academic/prank-msa/prank-msa.SlackBuild b/academic/prank-msa/prank-msa.SlackBuild index e1180665b5..f9de0b7ec9 100644 --- a/academic/prank-msa/prank-msa.SlackBuild +++ b/academic/prank-msa/prank-msa.SlackBuild @@ -24,7 +24,7 @@ PRGNAM=prank-msa SRCNAM=prank.source -VERSION=${VERSION:-150803} +VERSION=${VERSION:-170427} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/prank-msa/prank-msa.info b/academic/prank-msa/prank-msa.info index 2d999b1d23..ab3041d52b 100644 --- a/academic/prank-msa/prank-msa.info +++ b/academic/prank-msa/prank-msa.info @@ -1,10 +1,10 @@ PRGNAM="prank-msa" -VERSION="150803" +VERSION="170427" HOMEPAGE="http://wasabiapp.org/software/prank/" DOWNLOAD="UNSUPPORTED" MD5SUM="" -DOWNLOAD_x86_64="http://wasabiapp.org/download/prank/prank.source.150803.tgz" -MD5SUM_x86_64="71ac2659e91c385c96473712c0a23e8a" +DOWNLOAD_x86_64="http://wasabiapp.org/download/prank/prank.source.170427.tgz" +MD5SUM_x86_64="a5cda14dc4e5efe1f14b84eb7a7caabd" REQUIRES="bppsuite mafft exonerate" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/primer3/primer3.SlackBuild b/academic/primer3/primer3.SlackBuild index 8e60d3fe02..78d8dbf3d5 100644 --- a/academic/primer3/primer3.SlackBuild +++ b/academic/primer3/primer3.SlackBuild @@ -72,13 +72,11 @@ find -L . \ cd ./src # Use our CFLAGS -sed -i "/^CFLAGS/s/=/+=/" Makefile +sed -i -e "s|-O2|$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="$SLKCFLAGS" \ make # This is recommended, but the tests take a really long time. diff --git a/academic/root/root.SlackBuild b/academic/root/root.SlackBuild index bb507f0536..e0ec409dca 100644 --- a/academic/root/root.SlackBuild +++ b/academic/root/root.SlackBuild @@ -18,7 +18,7 @@ # Modified by the slackbuilds.org project PRGNAM=root -VERSION=${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 $PKG | xargs file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneded 2> /dev/null || true diff --git a/academic/root/root.info b/academic/root/root.info index 450e1bde00..7df5c81738 100644 --- a/academic/root/root.info +++ b/academic/root/root.info @@ -1,10 +1,10 @@ PRGNAM="root" -VERSION="5.34.36" +VERSION="6.10.02" HOMEPAGE="http://root.cern.ch/drupal/" -DOWNLOAD="https://root.cern.ch/download/root_v5.34.36.source.tar.gz" -MD5SUM="6a1ad549b3b79b10bbb1f116b49067ee" +DOWNLOAD="https://root.cern.ch/download/root_v6.10.02.source.tar.gz" +MD5SUM="19f2285c845a48355db779938fb4db99" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="ftgl" +REQUIRES="ftgl unixODBC" MAINTAINER="Jože Zobec" EMAIL="jozze.zepl@gmail.com" diff --git a/academic/t_coffee/t_coffee.SlackBuild b/academic/t_coffee/t_coffee.SlackBuild index 7329c61e2f..b2b07568f2 100644 --- a/academic/t_coffee/t_coffee.SlackBuild +++ b/academic/t_coffee/t_coffee.SlackBuild @@ -73,7 +73,8 @@ find -L . \ cd t_coffee_source -CFLAGS="$SLKCFLAGS" \ +sed -i "s|-O3|$SLKCFLAGS -fpermissive|" makefile + CC="gcc" \ FCC="gfortran" \ make -i all 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 e579ff1e9a..bdddfa4182 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 < $CWD/make_pair.patch + CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ 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 87ba9524d7..617d64049e 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 |