diff options
Diffstat (limited to 'sci-biology')
628 files changed, 11032 insertions, 14343 deletions
diff --git a/sci-biology/ApE/ApE-2.0.7-r1.ebuild b/sci-biology/ApE/ApE-2.0.7-r1.ebuild deleted file mode 100644 index a56f50525205..000000000000 --- a/sci-biology/ApE/ApE-2.0.7-r1.ebuild +++ /dev/null @@ -1,53 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils - -DESCRIPTION="A Plasmid Editor" -HOMEPAGE="http://www.biology.utah.edu/jorgensen/wayned/ape/" -SRC_URI="http://www.biology.utah.edu/jorgensen/wayned/ape/Download/Linux/ApE_linux_current.zip -> ${P}.zip" - -LICENSE="ApE" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND="app-arch/unzip" -RDEPEND=" - dev-lang/tcl:0 - dev-lang/tk:0" - -RESTRICT="bindist mirror" - -S="${WORKDIR}/ApE Linux/" - -src_compile() { :; } - -src_install() { - cat >> "${T}/ApE" <<- "EOF" - #!/bin/bash - cmdArgs="" - - # AppMain.tcl searches files relative to the directory where it resides. - # Add absolute path to file here, if necessary. - for rfpath in "$@"; do - afpath="$PWD/${rfpath}" - if test -r "${afpath}"; then - cmdArgs="${cmdArgs} \"${afpath}\""; - else - cmdArgs="${cmdArgs} \"${rfpath}\""; - fi - done - - eval exec tclsh "\"/usr/share/ApE-2.0.7/AppMain.tcl\"" "${cmdArgs}" - EOF - - dobin "${T}/ApE" - insinto "/usr/share/${P}" - doins -r "${WORKDIR}"/ApE\ Linux/* - make_desktop_entry ${PN} ${PN} \ - "/usr/share/${P}/Accessory Files/Icons and images/monkey_icon.gif" \ - "Science" -} diff --git a/sci-biology/ApE/Manifest b/sci-biology/ApE/Manifest deleted file mode 100644 index 6e45b2ff5014..000000000000 --- a/sci-biology/ApE/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST ApE-2.0.7.zip 318454 BLAKE2B 420001d298b8c6b1bc26247446aafe8c3adcf6477ebabc689219c094d46fe5e836d216a493169bac0ccd9c3b669d9421edb3b023a1a39cf74d32a81df09e66d2 SHA512 073e3f96badf4888c10a7c7eb453a3775d5bb9136b0bd836d37d1be784847f887e0c68b37325f430eebfb90c2d94021f10d4e8ede92de89b1ab1ddc1ffdbc254 diff --git a/sci-biology/ApE/metadata.xml b/sci-biology/ApE/metadata.xml deleted file mode 100644 index 7a38bb900964..000000000000 --- a/sci-biology/ApE/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <!-- maintainer-needed --> -</pkgmetadata> diff --git a/sci-biology/GBrowse/GBrowse-2.48-r1.ebuild b/sci-biology/GBrowse/GBrowse-2.48-r1.ebuild deleted file mode 100644 index 739950568156..000000000000 --- a/sci-biology/GBrowse/GBrowse-2.48-r1.ebuild +++ /dev/null @@ -1,71 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -MODULE_AUTHOR=LDS -inherit perl-module webapp - -DESCRIPTION="Generic Model Organism Database Project - The Generic Genome Browser" -HOMEPAGE="http://gmod.org/wiki/GBrowse" -KEYWORDS="~amd64 ~x86" -IUSE="-minimal mysql postgres +sqlite" - -SLOT="0" -WEBAPP_MANUAL_SLOT="yes" - -CDEPEND="!<sci-biology/GBrowse-2.44-r1 - >=sci-biology/bioperl-1.6.9 - >=dev-perl/Bio-Graphics-2.09 - >=dev-perl/GD-2.07 - >=dev-perl/CGI-Session-4.02 - dev-perl/IO-String - dev-perl/JSON - dev-perl/libwww-perl - dev-perl/Statistics-Descriptive - !minimal? ( - dev-perl/Bio-Das - >=dev-perl/Bio-SamTools-1.20 - dev-perl/Crypt-SSLeay - dev-perl/DB_File-Lock - dev-perl/DBI - mysql? ( dev-perl/DBD-mysql ) - postgres? ( dev-perl/DBD-Pg ) - sqlite? ( dev-perl/DBD-SQLite ) - dev-perl/FCGI - dev-perl/File-NFSLock - dev-perl/GD-SVG - dev-perl/Net-OpenID-Consumer - dev-perl/Net-SMTP-SSL - )" -# >=dev-perl/Bio-DB-BigFile-1.00 - requires jklib to compile -DEPEND="dev-perl/Module-Build - dev-perl/Capture-Tiny - ${CDEPEND}" -RDEPEND="${CDEPEND}" - -PATCHES=( "${FILESDIR}"/GBrowseInstall.pm-2.39.patch ) - -src_configure() { - webapp_src_preinst - -# myconf="--install_base=${D}/usr" or "--install_base=/opt/gbrowse" - myconf="--conf=/etc/gbrowse2" - myconf="${myconf} --htdocs=${MY_HTDOCSDIR}" - myconf="${myconf} --cgibin=${MY_CGIBINDIR}" - myconf="${myconf} --tmp=/var/tmp/gbrowse2" - myconf="${myconf} --persistent=/var/db/gbrowse2" - myconf="${myconf} --databases=/var/db/gbrowse2/databases" - myconf="${myconf} --installconf=no" - myconf="${myconf} --installetc=no" - perl-module_src_configure -} - -src_install() { - dodir /var/tmp/gbrowse2 - dodir /var/db/gbrowse2/sessions - dodir /var/db/gbrowse2/userdata - webapp_serverowned -R /var/tmp/gbrowse2 /var/db/gbrowse2 - perl-module_src_install - webapp_src_install -} diff --git a/sci-biology/GBrowse/Manifest b/sci-biology/GBrowse/Manifest deleted file mode 100644 index 47384b63de9a..000000000000 --- a/sci-biology/GBrowse/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST GBrowse-2.48.tar.gz 11958127 BLAKE2B e9527eb47302775d62e37990c42154b677284fff0f0f9624e9173e30e46c5aebbc8a02ee8dec0a1e98761812ef2363e0183008087bce4d283528b7935b4d5f91 SHA512 d5a07caf1517fb15741e8e6056669763eb04678a42637a9e90788c91e74fb34515b5f86aac10a00f29d8848aceb19d6f5f7258d2dda0e281feee550e9e2fb3db diff --git a/sci-biology/GBrowse/files/GBrowseInstall.pm-2.39.patch b/sci-biology/GBrowse/files/GBrowseInstall.pm-2.39.patch deleted file mode 100644 index 5aa0be9df918..000000000000 --- a/sci-biology/GBrowse/files/GBrowseInstall.pm-2.39.patch +++ /dev/null @@ -1,72 +0,0 @@ -diff -durr GBrowse-2.39-orig/install_util/GBrowseInstall.pm GBrowse-2.39/install_util/GBrowseInstall.pm ---- GBrowse-2.39-orig/install_util/GBrowseInstall.pm 2011-07-19 20:14:52.434608020 +0000 -+++ GBrowse-2.39/install_util/GBrowseInstall.pm 2011-07-19 21:02:13.685107753 +0000 -@@ -454,33 +454,33 @@ - $gid =~ /^(\d+)$/; - $gid = $1; - -- unless (chown $uid,$gid,$tmp) { -- $self->ownership_warning($tmp,$user); -- } -+# unless (chown $uid,$gid,$tmp) { -+# $self->ownership_warning($tmp,$user); -+# } - - my $htdocs_i = File::Spec->catfile($self->install_path->{htdocs},'i'); - my $images = File::Spec->catfile($tmp,'images'); - my $htdocs = $self->install_path->{htdocs}; -- chown $uid,-1,$htdocs; -+# chown $uid,-1,$htdocs; - { - local $> = $uid; -- symlink($images,$htdocs_i); # so symlinkifowner match works! -+# symlink($images,$htdocs_i); # so symlinkifowner match works! - } -- chown $>,-1,$self->install_path->{htdocs}; -+# chown $>,-1,$self->install_path->{htdocs}; - - my $persistent = $self->install_path->{'persistent'}; - my $sessions = File::Spec->catfile($persistent,'sessions'); - my $userdata = File::Spec->catfile($persistent,'userdata'); -- mkpath([$sessions,$userdata],0711); -+# mkpath([$sessions,$userdata],0711); - - my $databases = $self->install_path->{'databases'}; - -- unless (chown $uid,$gid,glob(File::Spec->catfile($databases,'').'*')) { -- $self->ownership_warning($databases,$user); -- } -+# unless (chown $uid,$gid,glob(File::Spec->catfile($databases,'').'*')) { -+# $self->ownership_warning($databases,$user); -+# } - -- chmod 0755,File::Spec->catfile($self->install_path->{'etc'},'init.d','gbrowse-slave'); -- $self->fix_selinux; -+ # chmod 0755,File::Spec->catfile($self->install_path->{'etc'},'init.d','gbrowse-slave'); -+ # $self->fix_selinux; - - my $base = basename($self->install_path->{htdocs}); - -@@ -489,14 +489,14 @@ - my $metadb_script = File::Spec->catfile("bin", "gbrowse_metadb_config.pl"); - my $perl = $self->perl; - my @inc = map{"-I$_"} split ':',$self->added_to_INC; -- system $perl,@inc,$metadb_script; -- system 'sudo','chown','-R',"$uid.$gid",$sessions,$userdata; -+# system $perl,@inc,$metadb_script; -+# system 'sudo','chown','-R',"$uid.$gid",$sessions,$userdata; - -- if (Module::Build->y_n( -- "It is recommended that you restart Apache. Shall I try this for you?",'y' -- )) { -- system "sudo /etc/init.d/apache2 restart"; -- } -+# if (Module::Build->y_n( -+# "It is recommended that you restart Apache. Shall I try this for you?",'y' -+# )) { -+# system "sudo /etc/init.d/apache2 restart"; -+# } - - print STDERR "\n***INSTALLATION COMPLETE***\n"; - print STDERR "Load http://localhost/$base for demo and documentation.\n"; -Only in GBrowse-2.39/install_util: GBrowseInstall.pm~ diff --git a/sci-biology/GBrowse/metadata.xml b/sci-biology/GBrowse/metadata.xml deleted file mode 100644 index 1473cc001b3d..000000000000 --- a/sci-biology/GBrowse/metadata.xml +++ /dev/null @@ -1,11 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> -<maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> -</maintainer> -<upstream> - <remote-id type="cpan">GBrowse</remote-id> -</upstream> -</pkgmetadata> diff --git a/sci-biology/HTSeq/HTSeq-0.9.1.ebuild b/sci-biology/HTSeq/HTSeq-0.9.1.ebuild deleted file mode 100644 index 18a07a7b9f9f..000000000000 --- a/sci-biology/HTSeq/HTSeq-0.9.1.ebuild +++ /dev/null @@ -1,31 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python3_6 ) - -inherit distutils-r1 - -DESCRIPTION="Python support for SAM/BAM/Bowtie/FASTA/Q/GFF/GTF files" -HOMEPAGE="https://htseq.readthedocs.io/" - -if [[ ${PV} == *9999 ]]; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/simon-anders/htseq.git" -else - SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - KEYWORDS="~amd64" -fi - -LICENSE="GPL-3+" -SLOT="0" - -RDEPEND=" - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/matplotlib[${PYTHON_USEDEP}] - sci-biology/pysam[${PYTHON_USEDEP}]" -DEPEND=" - ${RDEPEND} - >=dev-lang/swig-3.0.8 - dev-python/cython[${PYTHON_USEDEP}]" diff --git a/sci-biology/HTSeq/HTSeq-9999.ebuild b/sci-biology/HTSeq/HTSeq-9999.ebuild deleted file mode 100644 index 18a07a7b9f9f..000000000000 --- a/sci-biology/HTSeq/HTSeq-9999.ebuild +++ /dev/null @@ -1,31 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python3_6 ) - -inherit distutils-r1 - -DESCRIPTION="Python support for SAM/BAM/Bowtie/FASTA/Q/GFF/GTF files" -HOMEPAGE="https://htseq.readthedocs.io/" - -if [[ ${PV} == *9999 ]]; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/simon-anders/htseq.git" -else - SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - KEYWORDS="~amd64" -fi - -LICENSE="GPL-3+" -SLOT="0" - -RDEPEND=" - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/matplotlib[${PYTHON_USEDEP}] - sci-biology/pysam[${PYTHON_USEDEP}]" -DEPEND=" - ${RDEPEND} - >=dev-lang/swig-3.0.8 - dev-python/cython[${PYTHON_USEDEP}]" diff --git a/sci-biology/HTSeq/Manifest b/sci-biology/HTSeq/Manifest deleted file mode 100644 index d521aef0c0b0..000000000000 --- a/sci-biology/HTSeq/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST HTSeq-0.9.1.tar.gz 596941 BLAKE2B 6865c36056bff2008ae8bf18d0ac81dbf721fb97cdcc8bbd9150356fc80ae99e0cb872033fac274b40df3d1c95e9bcfd83c4f7d033184725596ffc96081e26d1 SHA512 ec3e1ec9cf66918f2afacf7997ab5da02015896ddd97260f5abec8343a9013cf6e857872be38b2cd3bb5bde655abe602a3c22c32448190f32e1a8f1153a19344 diff --git a/sci-biology/HTSeq/metadata.xml b/sci-biology/HTSeq/metadata.xml deleted file mode 100644 index 8d3c9ccebe2a..000000000000 --- a/sci-biology/HTSeq/metadata.xml +++ /dev/null @@ -1,19 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@gmail.com</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>proxy-maint@gentoo.org</email> - <name>Proxy Maintainers</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="pypi">HTSeq</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/STAR/Manifest b/sci-biology/STAR/Manifest index 35d580101e14..d97c61cb21c0 100644 --- a/sci-biology/STAR/Manifest +++ b/sci-biology/STAR/Manifest @@ -1 +1 @@ -DIST STAR-2.5.3a.tar.gz 9857460 BLAKE2B 32cc633862e6e81f5a5bdfc59986dca74e8adc4970a11a06c501065c5ad9cb37fc788f8e67ab2353292e683c8c385778cd0ffee69c0b15803796dbc445013a43 SHA512 8bd86ad384f2c0331fd701873b02641301f4205a5ff0fceeb800d425da42c53b6c61a74500d37fee7fc13a5bff10e1fb44b9142811883b8f5cd012f51f1f9fdf +DIST STAR-2.7.10a.tar.gz 12270915 BLAKE2B 51a9cf2c838cfeb313df9e5024b53cd5a89088f08ac88c8dc57a9e08cd3ba394e46ffe86a8ff3b9484b25b681ecd960098c06d879e772d21afe8cc2d0d35175d SHA512 19a5f3c25d147bcd96cf68249d275dad7fd11425031a40c97c7ae15846f55839ced897d541ed60b426a6bf089d968ac86625af774db3950dc459035ac2b659c9 diff --git a/sci-biology/STAR/STAR-2.5.3a.ebuild b/sci-biology/STAR/STAR-2.7.10a.ebuild index 73743cbb4e59..c3deb5a94b0a 100644 --- a/sci-biology/STAR/STAR-2.5.3a.ebuild +++ b/sci-biology/STAR/STAR-2.7.10a.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit toolchain-funcs @@ -14,10 +14,13 @@ SLOT="0" KEYWORDS="~amd64" RDEPEND="sci-libs/htslib:=" -DEPEND="${RDEPEND} - virtual/pkgconfig" +DEPEND="${RDEPEND}" +BDEPEND="virtual/pkgconfig" -PATCHES=( "${FILESDIR}"/${PN}-2.5.3a-fix-build-system.patch ) +PATCHES=( + "${FILESDIR}"/${PN}-2.7.10a-fix-build-system.patch + "${FILESDIR}"/${PN}-2.7.10a-missing-include.patch +) DOCS=( README.md CHANGES.md RELEASEnotes.md doc/STARmanual.pdf ) pkg_pretend() { @@ -28,6 +31,13 @@ pkg_setup() { [[ ${MERGE_TYPE} != binary ]] && tc-check-openmp } +src_prepare() { + default + + # remove bundled htslib + rm -r source/htslib || die +} + src_configure() { tc-export CC CXX PKG_CONFIG } diff --git a/sci-biology/STAR/files/STAR-2.5.3a-fix-build-system.patch b/sci-biology/STAR/files/STAR-2.5.3a-fix-build-system.patch deleted file mode 100644 index 8e504fa429e0..000000000000 --- a/sci-biology/STAR/files/STAR-2.5.3a-fix-build-system.patch +++ /dev/null @@ -1,123 +0,0 @@ -* unbundle htslib -* honour all user flags -* use pkg-config for linking - ---- a/source/Makefile -+++ b/source/Makefile -@@ -8,24 +8,12 @@ - LDFLAGSextra ?= - CXXFLAGSextra ?= - --# user may define the compiler --CXX ?= g++ -- - # pre-defined flags --LDFLAGS_shared := -pthread -Lhtslib -Bstatic -lhts -Bdynamic -lz -lrt --LDFLAGS_static := -static -static-libgcc -pthread -Lhtslib -lhts -lz --LDFLAGS_Mac :=-pthread -lz htslib/libhts.a --LDFLAGS_Mac_static :=-pthread -lz -static-libgcc htslib/libhts.a --LDFLAGS_gdb := $(LDFLAGS_shared) -- - COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE="$(shell echo `date` $(HOSTNAME):`pwd`)"' - --CXXFLAGS_common := -pipe -std=c++11 -Wall -Wextra -fopenmp $(COMPTIMEPLACE) --CXXFLAGS_main := -O3 $(CXXFLAGS_common) --CXXFLAGS_gdb := -O0 -g $(CXXFLAGS_common) -- --CFLAGS := -O3 -pipe -Wall -Wextra $(CFLAGS) -- -+CFLAGS_common = -Wall -Wextra -pthread `$(PKG_CONFIG) --cflags htslib` `$(PKG_CONFIG) --cflags zlib` -+CXXFLAGS_common = $(CFLAGS_common) -std=c++11 -fopenmp $(COMPTIMEPLACE) -+LIBS_common = -pthread `$(PKG_CONFIG) --libs htslib` `$(PKG_CONFIG) --libs zlib` -lrt - - ########################################################################################################## - -@@ -54,10 +42,10 @@ - - - %.o : %.cpp -- $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $< -+ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_common) $< - - %.o : %.c -- $(CXX) -c $(CPPFLAGS) $(CFLAGS) $< -+ $(CXX) -c $(CPPFLAGS) $(CFLAGS) $(CFLAGS_common) $< - - all: STAR - -@@ -84,7 +72,7 @@ - ifneq ($(MAKECMDGOALS),CLEAN) - ifneq ($(MAKECMDGOALS),STARforMac) - ifneq ($(MAKECMDGOALS),STARforMacGDB) --Depend.list: $(SOURCES) parametersDefault.xxd htslib -+Depend.list: $(SOURCES) parametersDefault.xxd - echo $(SOURCES) - /bin/rm -f ./Depend.list - $(CXX) $(CXXFLAGS_common) -MM $^ >> Depend.list -@@ -95,57 +83,34 @@ - endif - endif - --htslib : htslib/libhts.a -- --htslib/libhts.a : -- $(MAKE) -C htslib lib-static -- - parametersDefault.xxd: parametersDefault - xxd -i parametersDefault > parametersDefault.xxd - --STAR : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) $(CXXFLAGS) --STAR : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS) - STAR : Depend.list parametersDefault.xxd $(OBJECTS) -- $(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS) -+ $(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STAR $(OBJECTS) $(LIBS) $(LIBS_common) - --POSIXSHARED : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -DPOSIX_SHARED_MEM $(CXXFLAGS) --POSIXSHARED : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS) - POSIXSHARED : Depend.list parametersDefault.xxd $(OBJECTS) -- $(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS) -+ $(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STAR $(OBJECTS) $(LIBS) $(LIBS_common) - --STARstatic : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) $(CXXFLAGS) --STARstatic : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_static) $(LDFLAGS) - STARstatic : Depend.list parametersDefault.xxd $(OBJECTS) -- $(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS) -+ $(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STAR $(OBJECTS) $(LIBS) $(LIBS_common) - --STARlong : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_LONG_READS' $(CXXFLAGS) --STARlong : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS) - STARlong : Depend.list parametersDefault.xxd $(OBJECTS) -- $(CXX) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LDFLAGS) -+ $(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STARlong $(OBJECTS) $(LIBS) $(LIBS_common) - --STARlongStatic : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_LONG_READS' $(CXXFLAGS) --STARlongStatic : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_static) $(LDFLAGS) - STARlongStatic : Depend.list parametersDefault.xxd $(OBJECTS) -- $(CXX) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LDFLAGS) -+ $(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STARlong $(OBJECTS) $(LIBS) $(LIBS_common) - --gdb : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_gdb) $(CXXFLAGS) --gdb : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_gdb) $(LDFLAGS) - gdb : Depend.list parametersDefault.xxd $(OBJECTS) -- $(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS) -+ $(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STAR $(OBJECTS) $(LIBS) $(LIBS_common) - --gdb-long : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_gdb) -D'COMPILE_FOR_LONG_READS' $(CXXFLAGS) --gdb-long : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_gdb) $(LDFLAGS) - gdb-long : Depend.list parametersDefault.xxd $(OBJECTS) -- $(CXX) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LDFLAGS) -+ $(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STARlong $(OBJECTS) $(LIBS) $(LIBS_common) - --STARforMacStatic : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_MAC' $(CXXFLAGS) --STARforMacStatic : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_Mac_static) $(LDFLAGS) - STARforMacStatic : Depend.list parametersDefault.xxd $(OBJECTS) -- $(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS) -+ $(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STAR $(OBJECTS) $(LIBS) $(LIBS_common) - --STARlongForMacStatic : CXXFLAGS := -D'COMPILE_FOR_LONG_READS' $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_MAC' $(CXXFLAGS) --STARlongForMacStatic : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_Mac_static) $(LDFLAGS) - STARlongForMacStatic : Depend.list parametersDefault.xxd $(OBJECTS) -- $(CXX) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LDFLAGS) -+ $(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STARlong $(OBJECTS) $(LIBS) $(LIBS_common) - - diff --git a/sci-biology/STAR/files/STAR-2.7.10a-fix-build-system.patch b/sci-biology/STAR/files/STAR-2.7.10a-fix-build-system.patch new file mode 100644 index 000000000000..0f06c94fb109 --- /dev/null +++ b/sci-biology/STAR/files/STAR-2.7.10a-fix-build-system.patch @@ -0,0 +1,195 @@ +--- a/source/bam_cat.c ++++ b/source/bam_cat.c +@@ -52,8 +52,8 @@ + #include <stdlib.h> + #include <unistd.h> + +-#include "htslib/htslib/bgzf.h" +-#include "htslib/htslib/sam.h" ++#include <htslib/bgzf.h> ++#include <htslib/sam.h> + #include <cstring> + + #define BUF_SIZE 0x10000 +--- a/source/bam_cat.h ++++ b/source/bam_cat.h +@@ -1,7 +1,7 @@ + #ifndef CODE_bam_cat + #define CODE_bam_cat + +-#include "htslib/htslib/sam.h" ++#include <htslib/sam.h> + + int bam_cat(int nfn, char * const *fn, const bam_hdr_t *h, const char* outbam); + +--- a/source/BAMfunctions.cpp ++++ b/source/BAMfunctions.cpp +@@ -1,5 +1,5 @@ + #include "BAMfunctions.h" +-#include "htslib/htslib/kstring.h" ++#include <htslib/kstring.h> + + + string bam_cigarString (bam1_t *b) {//output CIGAR string +--- a/source/bamRemoveDuplicates.cpp ++++ b/source/bamRemoveDuplicates.cpp +@@ -1,7 +1,7 @@ + #include <unordered_map> + #include "bamRemoveDuplicates.h" + #include <iostream> +-#include "htslib/htslib/sam.h" ++#include <htslib/sam.h> + #include "IncludeDefine.h" + #include SAMTOOLS_BGZF_H + #include "ErrorWarning.h" +--- a/source/IncludeDefine.h ++++ b/source/IncludeDefine.h +@@ -30,8 +30,8 @@ + #define ERROR_OUT string ( __FILE__ ) +":"+ to_string ( (uint) __LINE__ ) +":"+ string ( __FUNCTION__ ) + + //external libs +-#define SAMTOOLS_BGZF_H "htslib/htslib/bgzf.h" +-#define SAMTOOLS_SAM_H "htslib/htslib/sam.h" ++#define SAMTOOLS_BGZF_H <htslib/bgzf.h> ++#define SAMTOOLS_SAM_H <htslib/sam.h> + + using namespace std; + +--- a/source/Makefile ++++ b/source/Makefile +@@ -12,11 +12,7 @@ + CXX ?= g++ + + # pre-defined flags +-LDFLAGS_shared := -pthread -Lhtslib -Bstatic -lhts -Bdynamic -lz +-LDFLAGS_static := -static -static-libgcc -pthread -Lhtslib -lhts -lz +-LDFLAGS_Mac :=-pthread -lz htslib/libhts.a +-LDFLAGS_Mac_static :=-pthread -lz -static-libgcc htslib/libhts.a +-LDFLAGS_gdb := $(LDFLAGS_shared) ++LIBS := -pthread -lhts -lz + + DATE_FMT = --iso-8601=seconds + ifdef SOURCE_DATE_EPOCH +@@ -27,7 +23,7 @@ + + BUILD_PLACE ?= $(HOSTNAME):$(shell pwd) + +-COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE="$(BUILD_DATE) $(BUILD_PLACE)"' ++COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE=""' + + + GIT_CHECK := $(shell git status 1> /dev/null 2> /dev/null && echo 0) +@@ -41,13 +37,13 @@ + + # Defaults, can be overridden by make arguments or environment + CXXFLAGS ?= -pipe -Wall -Wextra +-CFLAGS ?= -pipe -Wall -Wextra -O3 ++CFLAGS ?= -pipe -Wall -Wextra + CXXFLAGS_SIMD ?= -mavx2 + + # Unconditionally set essential flags and optimization options + CXXFLAGS_common := -std=c++11 -fopenmp $(COMPTIMEPLACE) $(GIT_BRANCH_COMMIT_DIFF) +-CXXFLAGS_main := -O3 $(CXXFLAGS_common) +-CXXFLAGS_gdb := -O0 -g3 $(CXXFLAGS_common) ++CXXFLAGS_main := $(CXXFLAGS_common) ++CXXFLAGS_gdb := $(CXXFLAGS_common) + + ########################################################################################################## + OBJECTS = SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall_multiMappers.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o \ +@@ -130,7 +126,7 @@ + ifneq ($(MAKECMDGOALS),clean_solo) + ifneq ($(MAKECMDGOALS),STARforMac) + ifneq ($(MAKECMDGOALS),STARforMacGDB) +-Depend.list: $(SOURCES) parametersDefault.xxd htslib ++Depend.list: $(SOURCES) parametersDefault.xxd + echo $(SOURCES) + 'rm' -f ./Depend.list + $(CXX) $(CXXFLAGS_common) -MM $^ >> Depend.list +@@ -142,57 +138,43 @@ + endif + endif + +-htslib : htslib/libhts.a +- +-htslib/libhts.a : +- $(MAKE) -C htslib lib-static +- + parametersDefault.xxd: parametersDefault + xxd -i parametersDefault > parametersDefault.xxd + + STAR$(SFX) : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) $(CXXFLAGS) +-STAR$(SFX) : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS) + STAR$(SFX) : Depend.list parametersDefault.xxd $(OBJECTS) +- $(CXX) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LDFLAGS) ++ $(CXX) $(LDFLAGS) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LIBS) + + STARstatic$(SFX) : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) $(CXXFLAGS) +-STARstatic$(SFX) : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_static) $(LDFLAGS) + STARstatic$(SFX) : Depend.list parametersDefault.xxd $(OBJECTS) +- $(CXX) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LDFLAGS) ++ $(CXX) $(LDFLAGS) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LIBS) + + STARlong$(SFX) : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_LONG_READS' $(CXXFLAGS) +-STARlong$(SFX) : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS) + STARlong$(SFX) : Depend.list parametersDefault.xxd $(OBJECTS) +- $(CXX) -o STARlong$(SFX) $(CXXFLAGS) $(OBJECTS) $(LDFLAGS) ++ $(CXX) $(LDFLAGS) -o STARlong$(SFX) $(CXXFLAGS) $(OBJECTS) $(LIBS) + + STARlongStatic$(SFX) : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_LONG_READS' $(CXXFLAGS) +-STARlongStatic$(SFX) : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_static) $(LDFLAGS) + STARlongStatic$(SFX) : Depend.list parametersDefault.xxd $(OBJECTS) +- $(CXX) -o STARlong$(SFX) $(CXXFLAGS) $(OBJECTS) $(LDFLAGS) ++ $(CXX) $(LDFLAGS) -o STARlong$(SFX) $(CXXFLAGS) $(OBJECTS) $(LIBS) + + + + POSIXSHARED : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -DPOSIX_SHARED_MEM $(CXXFLAGS) +-POSIXSHARED : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS) + POSIXSHARED : Depend.list parametersDefault.xxd $(OBJECTS) +- $(CXX) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LDFLAGS) ++ $(CXX) $(LDFLAGS) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LIBS) + + gdb : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_gdb) $(CXXFLAGS) +-gdb : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_gdb) $(LDFLAGS) + gdb : Depend.list parametersDefault.xxd $(OBJECTS) +- $(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS) ++ $(CXX) $(LDFLAGS) -o STAR $(CXXFLAGS) $(OBJECTS) $(LIBS) + + gdb-long : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_gdb) -D'COMPILE_FOR_LONG_READS' $(CXXFLAGS) +-gdb-long : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_gdb) $(LDFLAGS) + gdb-long : Depend.list parametersDefault.xxd $(OBJECTS) +- $(CXX) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LDFLAGS) ++ $(CXX) $(LDFLAGS) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LIBS) + + STARforMacStatic : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_MAC' $(CXXFLAGS) +-STARforMacStatic : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_Mac_static) $(LDFLAGS) + STARforMacStatic : Depend.list parametersDefault.xxd $(OBJECTS) +- $(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS) ++ $(CXX) $(LDFLAGS) -o STAR $(CXXFLAGS) $(OBJECTS) $(LIBS) + + STARlongForMacStatic : CXXFLAGS := -D'COMPILE_FOR_LONG_READS' $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_MAC' $(CXXFLAGS) +-STARlongForMacStatic : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_Mac_static) $(LDFLAGS) + STARlongForMacStatic : Depend.list parametersDefault.xxd $(OBJECTS) +- $(CXX) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LDFLAGS) ++ $(CXX) $(LDFLAGS) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LIBS) +--- a/source/signalFromBAM.h ++++ b/source/signalFromBAM.h +@@ -1,6 +1,6 @@ + #ifndef CODE_signalFromBAM + #define CODE_signalFromBAM +-#include "htslib/htslib/sam.h" ++#include <htslib/sam.h> + #include <fstream> + #include <string> + #include "Stats.h" +--- a/source/STAR.cpp ++++ b/source/STAR.cpp +@@ -29,7 +29,7 @@ + + #include "twoPassRunPass1.h" + +-#include "htslib/htslib/sam.h" ++#include <htslib/sam.h> + #include "parametersDefault.xxd" + + void usage(int usageType) { diff --git a/sci-biology/STAR/files/STAR-2.7.10a-missing-include.patch b/sci-biology/STAR/files/STAR-2.7.10a-missing-include.patch new file mode 100644 index 000000000000..c056a8aad887 --- /dev/null +++ b/sci-biology/STAR/files/STAR-2.7.10a-missing-include.patch @@ -0,0 +1,22 @@ +From f5ad94329db4fd81fc6ae30684c298772002e30b Mon Sep 17 00:00:00 2001 +From: David Seifert <soap@gentoo.org> +Date: Sat, 7 May 2022 15:06:11 +0200 +Subject: [PATCH] Add missing `#include <array>` (GCC 12) + +Bug: https://bugs.gentoo.org/840586 +--- + source/SoloCommon.h | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/source/SoloCommon.h b/source/SoloCommon.h +index 2a1d5fcf..5adc5040 100644 +--- a/source/SoloCommon.h ++++ b/source/SoloCommon.h +@@ -1,6 +1,7 @@ + #ifndef H_SoloCommon + #define H_SoloCommon + ++#include <array> + #include <unordered_map> + + typedef struct{ diff --git a/sci-biology/STAR/metadata.xml b/sci-biology/STAR/metadata.xml index 10ecc35730e0..dd2e23471998 100644 --- a/sci-biology/STAR/metadata.xml +++ b/sci-biology/STAR/metadata.xml @@ -1,14 +1,6 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@gmail.com</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>proxy-maint@gentoo.org</email> - <name>Proxy Maintainers</name> - </maintainer> <maintainer type="project"> <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> diff --git a/sci-biology/aaindex/aaindex-9.1-r1.ebuild b/sci-biology/aaindex/aaindex-9.1-r2.ebuild index b51f64beaefc..76b95ddb1bcf 100644 --- a/sci-biology/aaindex/aaindex-9.1-r1.ebuild +++ b/sci-biology/aaindex/aaindex-9.1-r2.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2018 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 DESCRIPTION="Amino acid indices and similarity matrices" HOMEPAGE="https://www.genome.jp/aaindex/" @@ -14,14 +14,14 @@ SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" IUSE="emboss minimal" -DEPEND="emboss? ( sci-biology/emboss )" -RDEPEND="${DEPEND}" +BDEPEND="emboss? ( sci-biology/emboss )" +RDEPEND="${BDEPEND}" src_compile() { if use emboss; then mkdir AAINDEX || die einfo - einfo "Indexing AAindex for usage with EMBOSS." + einfo "Indexing AAindex for usage with EMBOSS" EMBOSS_DATA="." aaindexextract -auto -infile ${PN}1 || die "Indexing AAindex failed" einfo fi diff --git a/sci-biology/aaindex/metadata.xml b/sci-biology/aaindex/metadata.xml index ffe91c9020d6..44422e7c1cfd 100644 --- a/sci-biology/aaindex/metadata.xml +++ b/sci-biology/aaindex/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/abyss/Manifest b/sci-biology/abyss/Manifest index b18ccd652382..9c9041e2c936 100644 --- a/sci-biology/abyss/Manifest +++ b/sci-biology/abyss/Manifest @@ -1,2 +1 @@ -DIST abyss-2.0.2.tar.gz 1036135 BLAKE2B 6781a63203b5e6a1de70837a6dad7c79643d049b4c1e4b827471f2414cc821f82d98f9856518e3c24486e068c584520d0a1852d4e03d26247b896c776baaee41 SHA512 b19325b9d51e80378fc9818942c4005c94f470f0ad8ff6c1b8b593ad0216d35f9a99c0aa7c627082372690a6a7094ced8ca8efeb0bff6014ca46a67d7eb16a30 -DIST abyss-2.0.3.tar.gz 1049144 BLAKE2B 1a320cac735747225723f0d636af435ffcac9efb3273323150f258c0f4c27ed81bb104cb06a726aa664118cc9d2224b745d9deebfcac055face01dae3fc9de15 SHA512 15bc833e89839be89dfa35a23ae22ad0f9a19e8efd36211010c9f59e974de7c569576db36e26d6ab302543ff427604b5efb1b7badf62489a5e82a193ef155570 +DIST abyss-2.3.4.tar.gz 3511137 BLAKE2B 2b7449233055d22330f44951f9f6d5ff1a116fa3e19c09c17cd4fa517d2fc055c4f00ccb82c7e09b1b939ac6f7a1caf73cf73c33bd3c8aa9ff11879c227a2aaa SHA512 9d4e418399dd62883b53e831f51a0bd2ba228da73eda6c6459cd729c002eb0487f9613fca1c9bd0f4fbb076eed8a9b952505ee97143ab7dde537c23e4a246cd4 diff --git a/sci-biology/abyss/abyss-2.0.3.ebuild b/sci-biology/abyss/abyss-2.0.3.ebuild deleted file mode 100644 index ccce937c77ce..000000000000 --- a/sci-biology/abyss/abyss-2.0.3.ebuild +++ /dev/null @@ -1,54 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit autotools toolchain-funcs - -DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler" -HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/" -SRC_URI="https://github.com/bcgsc/abyss/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="abyss" -SLOT="0" -IUSE="+mpi openmp misc-haskell" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - dev-cpp/sparsehash - dev-libs/boost:= - misc-haskell? ( - dev-libs/gmp:0= - virtual/libffi:0= - ) - mpi? ( sys-cluster/openmpi )" -DEPEND="${RDEPEND} - misc-haskell? ( - dev-lang/ghc - )" - -# todo: --enable-maxk=N configure option -# todo: fix automagic mpi toggling - -pkg_pretend() { - [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp -} - -pkg_setup() { - [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp -} - -src_prepare() { - default - sed -i -e "s/-Werror//" configure.ac || die #365195 - sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die - eautoreconf -} - -src_configure() { - # disable building haskell tool Misc/samtobreak - # unless request by user: bug #534412 - use misc-haskell || export ac_cv_prog_ac_ct_GHC= - - econf $(use_enable openmp) -} diff --git a/sci-biology/abyss/abyss-2.0.2-r1.ebuild b/sci-biology/abyss/abyss-2.3.4.ebuild index 0d1c14ac265e..2c2c14d35bd5 100644 --- a/sci-biology/abyss/abyss-2.0.2-r1.ebuild +++ b/sci-biology/abyss/abyss-2.3.4.ebuild @@ -1,17 +1,17 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 -inherit autotools toolchain-funcs +inherit autotools flag-o-matic toolchain-funcs DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler" -HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/" +HOMEPAGE="https://www.bcgsc.ca/resources/software/abyss/" SRC_URI="https://github.com/bcgsc/abyss/archive/${PV}.tar.gz -> ${P}.tar.gz" -LICENSE="abyss" +LICENSE="GPL-3" SLOT="0" -IUSE="+mpi openmp misc-haskell" +IUSE="openmp misc-haskell" KEYWORDS="~amd64 ~x86" RDEPEND=" @@ -19,17 +19,19 @@ RDEPEND=" dev-libs/boost:= misc-haskell? ( dev-libs/gmp:0= - virtual/libffi:0= + dev-libs/libffi:0= ) - mpi? ( sys-cluster/openmpi )" + sys-cluster/openmpi + dev-db/sqlite:3 +" DEPEND="${RDEPEND} misc-haskell? ( dev-lang/ghc - dev-haskell/mmap - )" + ) +" # todo: --enable-maxk=N configure option -# todo: fix automagic mpi toggling +# todo: also allow build with mpich (--enable-mpich) pkg_pretend() { [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp @@ -42,14 +44,18 @@ pkg_setup() { src_prepare() { default sed -i -e "s/-Werror//" configure.ac || die #365195 - sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die eautoreconf } src_configure() { + # -Werror=lto-type-mismatch + # https://bugs.gentoo.org/862252 + # https://github.com/bcgsc/abyss/issues/474 + filter-lto + # disable building haskell tool Misc/samtobreak # unless request by user: bug #534412 use misc-haskell || export ac_cv_prog_ac_ct_GHC= - econf $(use_enable openmp) + econf $(use_enable openmp) --enable-maxk=256 } diff --git a/sci-biology/abyss/metadata.xml b/sci-biology/abyss/metadata.xml index 47116e507d89..04e203d593eb 100644 --- a/sci-biology/abyss/metadata.xml +++ b/sci-biology/abyss/metadata.xml @@ -1,18 +1,14 @@ -<?xml version='1.0' encoding='UTF-8'?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <maintainer type="project"> - <email>haskell@gentoo.org</email> - <name>Gentoo Haskell</name> - </maintainer> - <use> - <flag name="misc-haskell">build abyss-samtobreak tool, pull in haskell toolchain</flag> - </use> - <upstream> - <remote-id type="github">bcgsc/abyss</remote-id> - </upstream> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <use> + <flag name="misc-haskell">build abyss-samtobreak tool, pull in haskell toolchain</flag> + </use> + <upstream> + <remote-id type="github">bcgsc/abyss</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/amap/amap-2.2-r3.ebuild b/sci-biology/amap/amap-2.2-r5.ebuild index 7776e25bc56e..949749969c27 100644 --- a/sci-biology/amap/amap-2.2-r3.ebuild +++ b/sci-biology/amap/amap-2.2-r5.ebuild @@ -1,25 +1,24 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit java-pkg-opt-2 java-ant-2 toolchain-funcs MY_P=${PN}.${PV} DESCRIPTION="Protein multiple-alignment-based sequence annealing" -HOMEPAGE="http://bio.math.berkeley.edu/amap/" +HOMEPAGE="https://wiki.gentoo.org/wiki/No_homepage" SRC_URI="http://baboon.math.berkeley.edu/${PN}/download/${MY_P}.tar.gz" +S="${WORKDIR}/${PN}-align" LICENSE="GPL-2" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="java" -RDEPEND="java? ( >=virtual/jre-1.5 )" -DEPEND="java? ( >=virtual/jdk-1.5 )" - -S=${WORKDIR}/${PN}-align +RDEPEND="java? ( >=virtual/jre-1.8:* )" +BDEPEND="${RDEPEND}" PATCHES=( "${FILESDIR}"/${P}-makefile.patch @@ -31,8 +30,12 @@ src_prepare() { java-pkg-opt-2_src_prepare } +src_configure() { + tc-export CXX +} + src_compile() { - emake -C align CXX="$(tc-getCXX)" OPT_CXXFLAGS="${CXXFLAGS}" + emake -C align if use java; then pushd display >/dev/null || die @@ -46,8 +49,8 @@ src_install() { dodoc align/{README,PROBCONS.README} - insinto /usr/share/${PN}/examples - doins -r examples/. + insinto /usr/share/${PN} + doins -r examples if use java; then java-pkg_newjar display/AmapDisplay.jar amapdisplay.jar diff --git a/sci-biology/amap/files/amap-2.2-makefile.patch b/sci-biology/amap/files/amap-2.2-makefile.patch index 5a9841c98255..3749fa58682c 100644 --- a/sci-biology/amap/files/amap-2.2-makefile.patch +++ b/sci-biology/amap/files/amap-2.2-makefile.patch @@ -2,28 +2,25 @@ Respect {CXX,LD}FLAGS http://bugs.gentoo.org/332009 ---- amap-align/align/Makefile -+++ amap-align/align/Makefile -@@ -15,6 +15,8 @@ - # c) RELEASE mode +--- a/align/Makefile ++++ b/align/Makefile +@@ -6,7 +6,6 @@ + # 1) Choose C++ compiler. ################################################################################ -+OPT_CXXFLAGS = -O3 -W -Wall -pedantic -funroll-loops -+ - OTHERFLAGS = -DNumInsertStates=1 -DVERSION='"AMAP.2.2"' +-CXX = g++ - # debug mode -@@ -26,8 +28,7 @@ + ################################################################################ + # 2) Set C++ flags. +@@ -26,7 +25,7 @@ # release mode #CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -mmmx -msse -msse2 -mfpmath=sse -march=pentium4 -mcpu=pentium4 -funroll-loops -fomit-frame-pointer -CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -funroll-loops -- -+CXXFLAGS = $(OPT_CXXFLAGS) -DNDEBUG $(OTHERFLAGS) ++CXXFLAGS += -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) + ################################################################################ # 3) Dependencies - ################################################################################ - @@ -38,7 +37,7 @@ all : $(TARGETS) diff --git a/sci-biology/amap/metadata.xml b/sci-biology/amap/metadata.xml index e051c9b41035..b5b66eeee084 100644 --- a/sci-biology/amap/metadata.xml +++ b/sci-biology/amap/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/amos/Manifest b/sci-biology/amos/Manifest deleted file mode 100644 index 1dcaaed1bb97..000000000000 --- a/sci-biology/amos/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST amos-3.1.0-fix-c++14.patch.bz2 8033 BLAKE2B 942248f64906253205392df71010bf41105d2985fc8112e7443975d776cc484a4e2b6cf34284d4c384145bf32601892c06f156a0b0ccf0f2ce721de242e02e9b SHA512 76e26ca48a009cbf637d9462878223633e9b21cbd12d58a19e9a561f2cf4805791becc0b5f7aaf81975ca1e02b263cdd9d5ff310c4594670922ea65885ad9634 -DIST amos-3.1.0.tar.gz 2094268 BLAKE2B b9fb80d4e7b7e9e7769081c2680a3cba26591f00a4d9fdb17ad602e581dea5e8e2add4b0d9d3821a7f8a4ec1a45dfd867037baf35ecd401584f030c86b2b0f83 SHA512 7a416b9a0438b47425355383b709491a58f38c8d834df29e43c942170e710c6ea7e3bc8c509a58421b1340ad6eece9ea2da357ce5cd1d41ce08375676ee30491 diff --git a/sci-biology/amos/amos-3.1.0-r4.ebuild b/sci-biology/amos/amos-3.1.0-r4.ebuild deleted file mode 100644 index 0dbcaffd81da..000000000000 --- a/sci-biology/amos/amos-3.1.0-r4.ebuild +++ /dev/null @@ -1,52 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit autotools flag-o-matic python-single-r1 - -DESCRIPTION="A Modular, Open-Source whole genome assembler" -HOMEPAGE="http://amos.sourceforge.net/" -SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz - https://dev.gentoo.org/~soap/distfiles/${PN}-3.1.0-fix-c++14.patch.bz2" - -LICENSE="Artistic" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -DEPEND="" -RDEPEND="${DEPEND} - ${PYTHON_DEPS} - dev-perl/DBI - dev-perl/Statistics-Descriptive - sci-biology/mummer" - -PATCHES=( - "${FILESDIR}"/${P}-gcc-4.7.patch - "${FILESDIR}"/${P}-goBambus2.py-indent-and-cleanup.patch - "${WORKDIR}"/${P}-fix-c++14.patch - "${FILESDIR}"/${P}-qa-Wformat.patch - "${FILESDIR}"/${P}-fix-build-system.patch -) - -src_prepare() { - default - eautoreconf - - # prevent GCC 6 log pollution due - # to hash_map deprecation in C++11 - append-cxxflags -Wno-cpp -} - -src_configure() { - econf --with-qmake-qt4=no -} - -src_install() { - default - python_fix_shebang "${ED%/}"/usr/bin/goBambus2 -} diff --git a/sci-biology/amos/files/amos-3.1.0-fix-build-system.patch b/sci-biology/amos/files/amos-3.1.0-fix-build-system.patch deleted file mode 100644 index 9c824dd2f122..000000000000 --- a/sci-biology/amos/files/amos-3.1.0-fix-build-system.patch +++ /dev/null @@ -1,116 +0,0 @@ -* Use proper AR and not just 'ar' -* Fix build system to build in parallel - ---- a/configure.ac -+++ b/configure.ac -@@ -34,6 +34,7 @@ - AC_PROG_INSTALL - AC_PROG_LN_S - AC_PROG_RANLIB -+AM_PROG_AR - AC_PROG_CPP - AC_PATH_PROG(PERL, [perl], [:]) - AC_PATH_PROG(PYTHON, [python], [:]) ---- a/src/Align/Makefile.am -+++ b/src/Align/Makefile.am -@@ -133,7 +133,7 @@ - - ##-- hash-overlap - hash_overlap_LDADD = \ -- $(top_builddir)/src/Align/libAlign.a \ -+ libAlign.a \ - $(top_builddir)/src/CelMsg/libCelMsg.a \ - $(top_builddir)/src/Slice/libSlice.a \ - $(top_builddir)/src/Common/libCommon.a \ -@@ -172,7 +172,7 @@ - - ##-- make-consensus - make_consensus_LDADD = \ -- $(top_builddir)/src/Align/libAlign.a \ -+ libAlign.a \ - $(top_builddir)/src/CelMsg/libCelMsg.a \ - $(top_builddir)/src/Slice/libSlice.a \ - $(top_builddir)/src/Common/libCommon.a \ -@@ -182,7 +182,7 @@ - - ##-- make-consensus_poly - make_consensus_poly_LDADD = \ -- $(top_builddir)/src/Align/libAlign_poly.a \ -+ libAlign_poly.a \ - $(top_builddir)/src/CelMsg/libCelMsg.a \ - $(top_builddir)/src/Slice/libSlice.a \ - $(top_builddir)/src/Common/libCommon.a \ -@@ -192,7 +192,7 @@ - - ##-- maligntest - maligntest_LDADD = \ -- $(top_builddir)/src/Align/libAlign.a \ -+ libAlign.a \ - $(top_builddir)/src/CelMsg/libCelMsg.a \ - $(top_builddir)/src/Slice/libSlice.a \ - $(top_builddir)/src/Common/libCommon.a \ -@@ -202,7 +202,7 @@ - - ##-- merge-contigs - merge_contigs_LDADD = \ -- $(top_builddir)/src/Align/libAlign.a \ -+ libAlign.a \ - $(top_builddir)/src/CelMsg/libCelMsg.a \ - $(top_builddir)/src/Slice/libSlice.a \ - $(top_builddir)/src/Common/libCommon.a \ -@@ -235,7 +235,7 @@ - - ##-- show-ma-asm - show_ma_asm_LDADD = \ -- $(top_builddir)/src/Align/libAlign.a \ -+ libAlign.a \ - $(top_builddir)/src/Common/libCommon.a \ - $(top_builddir)/src/AMOS/libAMOS.a - show_ma_asm_SOURCES = \ -@@ -261,7 +261,7 @@ - - ##-- simple-overlap - simple_overlap_LDADD = \ -- $(top_builddir)/src/Align/libAlign.a \ -+ libAlign.a \ - $(top_builddir)/src/CelMsg/libCelMsg.a \ - $(top_builddir)/src/Slice/libSlice.a \ - $(top_builddir)/src/Common/libCommon.a \ -@@ -272,7 +272,7 @@ - - ##-- test-align - test_align_LDADD = \ -- $(top_builddir)/src/Align/libAlign.a \ -+ libAlign.a \ - $(top_builddir)/src/CelMsg/libCelMsg.a \ - $(top_builddir)/src/Slice/libSlice.a \ - $(top_builddir)/src/Common/libCommon.a \ ---- a/src/Bambus/Bundler/Makefile.am -+++ b/src/Bambus/Bundler/Makefile.am -@@ -47,7 +47,7 @@ - clk.cc - - MarkRepeats_LDADD = \ -- $(top_builddir)/src/Bambus/Bundler/libBundler.a \ -+ libBundler.a \ - $(top_builddir)/src/Common/libCommon.a \ - $(top_builddir)/src/AMOS/libAMOS.a \ - $(top_builddir)/src/GNU/libGNU.a -@@ -55,7 +55,7 @@ - MarkRepeats.cc - - OrientContigs_LDADD = \ -- $(top_builddir)/src/Bambus/Bundler/libBundler.a \ -+ libBundler.a \ - $(top_builddir)/src/Common/libCommon.a \ - $(top_builddir)/src/AMOS/libAMOS.a \ - $(top_builddir)/src/GNU/libGNU.a -@@ -63,7 +63,7 @@ - OrientContigs.cc - - FilterEdgesByCluster_LDADD = \ -- $(top_builddir)/src/Bambus/Bundler/libBundler.a \ -+ libBundler.a \ - $(top_builddir)/src/Common/libCommon.a \ - $(top_builddir)/src/AMOS/libAMOS.a \ - $(top_builddir)/src/GNU/libGNU.a diff --git a/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch b/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch deleted file mode 100644 index de2a41184c52..000000000000 --- a/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch +++ /dev/null @@ -1,15 +0,0 @@ - src/Align/find-tandem.cc | 1 + - 1 files changed, 1 insertions(+), 0 deletions(-) - -diff --git a/src/Align/find-tandem.cc b/src/Align/find-tandem.cc -index ddf1cab..a29e21e 100644 ---- a/src/Align/find-tandem.cc -+++ b/src/Align/find-tandem.cc -@@ -7,6 +7,7 @@ - #include <vector> - #include <ctime> - #include <sys/time.h> -+#include <unistd.h> - using namespace std; - - const int OFFSET_TABLE_SIZE = 100; diff --git a/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch b/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch deleted file mode 100644 index 97a8f59d0208..000000000000 --- a/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch +++ /dev/null @@ -1,25 +0,0 @@ ---- amos-3.1.0/src/Pipeline/goBambus2.py.orig 2013-09-11 01:05:29.850090457 +0200 -+++ amos-3.1.0/src/Pipeline/goBambus2.py 2013-09-11 01:07:03.250090701 +0200 -@@ -1,7 +1,7 @@ - #pipeline script for assembly + Bambus 2 - #contributed by Todd J Treangen - --import string, sys, os, subprocess#, spincursor -+import sys, os, subprocess#, spincursor - - RED = "\033[0;31m" - GREEN = "\033[0;32m" -@@ -360,7 +360,7 @@ - print "\t\t%s...failed%s"%(RED,NONE) - sys.exit(1) - -- p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile) -+ p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile) - - if xopt_dict["verbose"] == 1: - print "10) running OutputResults" -@@ -388,4 +388,3 @@ - else: - print "\t\t%s...failed%s"%(RED,NONE) - sys.exit(1) --) diff --git a/sci-biology/amos/files/amos-3.1.0-qa-Wformat.patch b/sci-biology/amos/files/amos-3.1.0-qa-Wformat.patch deleted file mode 100644 index 13f4eeb247a1..000000000000 --- a/sci-biology/amos/files/amos-3.1.0-qa-Wformat.patch +++ /dev/null @@ -1,136 +0,0 @@ -Fix QA warnings, due to using incorrect format specifiers in printf: -* contig-cmp.cc:237:50: warning: format ‘%u’ expects argument of type ‘unsigned int’, -* but argument 3 has type ‘std::vector<Contig_t>::size_type {aka long unsigned int}’ [-Wformat=] -* fprintf (stderr, "%u b contigs\n", b . size ()); - ---- a/src/Align/align.cc -+++ b/src/Align/align.cc -@@ -1936,7 +1936,7 @@ - n = align . size (); - con = consensus . c_str (); - -- fprintf (fp, "\nConsensus len = %d\n", consensus . length ()); -+ fprintf (fp, "\nConsensus len = %zu\n", consensus . length ()); - - for (i = 0; i < n; i ++) - { -@@ -3936,7 +3936,7 @@ - } - - // Array of sum of quality scores in the slice for A,C,G,T,- resp. -- for (j = 0; j < 6; j ++) -+ for (j = 0; j < 5; j ++) - qvsum [j] = 0; - - int nof_ambiguities = 0; ---- a/src/Align/align_poly.cc -+++ b/src/Align/align_poly.cc -@@ -1761,7 +1761,7 @@ - n = align . size (); - con = consensus . c_str (); - -- fprintf (fp, "\nConsensus len = %d\n", consensus . length ()); -+ fprintf (fp, "\nConsensus len = %zu\n", consensus . length ()); - for (i = 0; i < n; i ++) - { - fprintf (fp, "\nString #%d:\n", i); ---- a/src/Align/count-qmers.cc -+++ b/src/Align/count-qmers.cc -@@ -191,8 +191,8 @@ - - PrintMers(mer_table, min_count); - -- fprintf(stderr, "reporter:counter:asm,reads_total,%ld\n", COUNT); -- fprintf(stderr, "reporter:counter:asm,reads_bp,%ld\n", LEN); -+ fprintf(stderr, "reporter:counter:asm,reads_total,%lld\n", COUNT); -+ fprintf(stderr, "reporter:counter:asm,reads_bp,%lld\n", LEN); - } - catch (Exception_t & e) - { ---- a/src/Align/kmer-cov.cc -+++ b/src/Align/kmer-cov.cc -@@ -485,7 +485,7 @@ - Kmer_Len = s . length (); - else if (Kmer_Len != int (s . length ())) - { -- sprintf (Clean_Exit_Msg_Line, "New kmer \"%s\" length is %d instead of %d", -+ sprintf (Clean_Exit_Msg_Line, "New kmer \"%s\" length is %zu instead of %d", - s . c_str (), s . length (), Kmer_Len); - Clean_Exit (Clean_Exit_Msg_Line, __FILE__, __LINE__); - } ---- a/src/Align/kmer-cov-plot.cc -+++ b/src/Align/kmer-cov-plot.cc -@@ -316,7 +316,7 @@ - } - else if (Kmer_Len != int (s . length ())) - { -- sprintf (Clean_Exit_Msg_Line, "New kmer \"%s\" length is %d instead of %d", -+ sprintf (Clean_Exit_Msg_Line, "New kmer \"%s\" length is %zu instead of %d", - s . c_str (), s . length (), Kmer_Len); - Clean_Exit (Clean_Exit_Msg_Line, __FILE__, __LINE__); - } ---- a/src/Align/make-consensus.cc -+++ b/src/Align/make-consensus.cc -@@ -303,7 +303,7 @@ - break; - } - -- sprintf (sid, "%ld", ++layout_id); -+ sprintf (sid, "%u", ++layout_id); - cid = string (sid); - ID_t lid = layout.getIID (); - if (lid == 0) ---- a/src/Align/make-consensus_poly.cc -+++ b/src/Align/make-consensus_poly.cc -@@ -279,7 +279,7 @@ - break; - } - -- sprintf(sid, "%ld", ++layout_id); -+ sprintf(sid, "%u", ++layout_id); - cid = string(sid); - ID_t lid = layout.getIID(); - if (lid == 0) { ---- a/src/Align/simple-overlap.cc -+++ b/src/Align/simple-overlap.cc -@@ -422,7 +422,7 @@ - "Options:\n" - " -a Also show alignments of overlaps \n" - " -E <x> Maximum error rate for overlaps is <x>\n" -- " e.g., -E 0.06 for 6% error rate\n" -+ " e.g., -E 0.06 for 6%% error rate\n" - " -F Input is a fasta file\n" - " -h Print this usage message\n" - " -o <n> Set minimum overlap length to <n>\n" ---- a/src/Compare/contig-cmp.cc -+++ b/src/Compare/contig-cmp.cc -@@ -145,7 +145,7 @@ - - fclose (fp); - -- fprintf (stderr, "%u a contigs\n", a . size ()); -+ fprintf (stderr, "%zu a contigs\n", a . size ()); - vector <Unitig_t> a_contig (max_id + 1); - n = a . size (); - for (i = 0; i < n; i ++) -@@ -234,7 +234,7 @@ - - fclose (fp); - -- fprintf (stderr, "%u b contigs\n", b . size ()); -+ fprintf (stderr, "%zu b contigs\n", b . size ()); - vector <Unitig_t> b_contig (max_id + 1); - n = b . size (); - for (i = 0; i < n; i ++) ---- a/src/Staden/progs/trace_convert.c -+++ b/src/Staden/progs/trace_convert.c -@@ -6,6 +6,9 @@ - #include "traceType.h" - #include "seqIOABI.h" - -+#include <fcntl.h> -+#include <unistd.h> -+ - static char fileIdentifier[] = "$Id$"; - - struct opts { diff --git a/sci-biology/amos/metadata.xml b/sci-biology/amos/metadata.xml deleted file mode 100644 index 2668bce2ac8a..000000000000 --- a/sci-biology/amos/metadata.xml +++ /dev/null @@ -1,11 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">amos</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/augustus/Manifest b/sci-biology/augustus/Manifest index 7d0b1e3689b4..7ddb67b5c888 100644 --- a/sci-biology/augustus/Manifest +++ b/sci-biology/augustus/Manifest @@ -1 +1,2 @@ +DIST augustus-3.4.0.tar.gz 221652100 BLAKE2B dfc8c98107f5a955f688f3d2976ca936faf2ef7004095f6b9d7c1902a36ca5d3c9aef59cab1b82b56cd5c2abc7b67195c5030111ed68557d53128814b1bf6bab SHA512 ca1df1016589f55527a883429edd5024cbc32c1b32036c81f9df5e0967a7d194f5b7a82109e924f380627427d9731caa478e63cad8cd804c01521aed76d8c4a6 DIST augustus.2.5.5.tar.gz 70826249 BLAKE2B 3f3f1537c5c614f00298e1835eeb7bbe968987c3e0dee13299e1e26b4abf198d8635a93121b11722d2c90b63ff54cf153c72716d01c3ca033481bb54357b7bcf SHA512 33eb05d5c90200d2fc17026743d3a25e73aa3e217b8546f0bed4c94bcb460597d853377a67896e52e45ead5d736d13ed3b2c91b31fed8216da2920c825e8c20f diff --git a/sci-biology/augustus/augustus-2.5.5.ebuild b/sci-biology/augustus/augustus-2.5.5.ebuild index 5bf36e85cb9b..ed345330c4a7 100644 --- a/sci-biology/augustus/augustus-2.5.5.ebuild +++ b/sci-biology/augustus/augustus-2.5.5.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 @@ -11,7 +11,7 @@ SRC_URI="http://augustus.gobics.de/binaries/${PN}.${PV}.tar.gz" LICENSE="Artistic" SLOT="0" -KEYWORDS="amd64 x86" +KEYWORDS="amd64 ~x86" IUSE="examples" S="${WORKDIR}/${PN}.${PV}" diff --git a/sci-biology/augustus/augustus-3.4.0-r3.ebuild b/sci-biology/augustus/augustus-3.4.0-r3.ebuild new file mode 100644 index 000000000000..7c662aead62f --- /dev/null +++ b/sci-biology/augustus/augustus-3.4.0-r3.ebuild @@ -0,0 +1,51 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DOCS_BUILDER="doxygen" +DOCS_CONFIG_NAME="doxygen.conf" +inherit docs toolchain-funcs + +DESCRIPTION="Eukaryotic gene predictor" +HOMEPAGE="https://bioinf.uni-greifswald.de/augustus/" +SRC_URI="https://github.com/Gaius-Augustus/Augustus/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/${P^}" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + dev-db/sqlite:3 + dev-db/mysql++:= + dev-db/mysql-connector-c:= + dev-libs/boost:=[zlib] + sci-biology/bamtools:= + sci-biology/samtools:0 + sci-libs/gsl:= + sci-libs/htslib:= + sci-libs/suitesparse + sci-mathematics/lpsolve:= + sys-libs/zlib +" +DEPEND="${RDEPEND}" + +src_compile() { + tc-export CC CXX + + emake LINK.cc="$(tc-getCXX)" + + docs_compile +} + +src_install() { + einstalldocs + # from upstream Makefile install: + dodir "opt/${P}" + cp -a config bin scripts "${ED}/opt/${P}" || die + local file + for file in bin/*; do + dosym "../${P}/${file}" "/opt/${file}" + done +} diff --git a/sci-biology/augustus/metadata.xml b/sci-biology/augustus/metadata.xml index 959160fe46b1..a4352248acda 100644 --- a/sci-biology/augustus/metadata.xml +++ b/sci-biology/augustus/metadata.xml @@ -1,8 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">Gaius-Augustus/Augustus</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/bamtools/Manifest b/sci-biology/bamtools/Manifest index 424c08d51594..5076fcaf1834 100644 --- a/sci-biology/bamtools/Manifest +++ b/sci-biology/bamtools/Manifest @@ -1 +1 @@ -DIST bamtools-2.5.1.tar.gz 549750 BLAKE2B c00b42b10e074e2c6b06f8bc9277a57080b9e99cd10080b1ad9052d59a3db353b33ecf6c30642d1651897396ea65e1e19cb15db0d58a89d4375fe34a8ec38e55 SHA512 f2c761c5bf923cf2f3db3dc54e40b4781307106b9177784f930aab619bd11fae3b343f3cfd232524580d39f0526a2a2f18efcf820fe4d9c951406bdb6b953afb +DIST bamtools-2.5.2.tar.gz 245729 BLAKE2B 5034ea1ec16b205488e421461ed74d8a98eae87eb7fc061e5928ad15512497a5338c9dbacbde51009c940acd55c25fccc2f3be2840d2821a8755a2a0b0370944 SHA512 540a4664abfbd1304600c17d47424c312a46e4238b0f0868f4037ddcc54c4487424e3d7820153084b3b512be8a4603e3ec5377a73311a617061460de1bfe49ef diff --git a/sci-biology/bamtools/bamtools-2.5.1.ebuild b/sci-biology/bamtools/bamtools-2.5.2.ebuild index 78a0c3cd2553..a809a651df64 100644 --- a/sci-biology/bamtools/bamtools-2.5.1.ebuild +++ b/sci-biology/bamtools/bamtools-2.5.2.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 diff --git a/sci-biology/bamtools/metadata.xml b/sci-biology/bamtools/metadata.xml index f703e6a82899..aaba26efdc12 100644 --- a/sci-biology/bamtools/metadata.xml +++ b/sci-biology/bamtools/metadata.xml @@ -1,18 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@gmail.com</email> - <name>Martin Mokrejs</name> - </maintainer> <maintainer type="project"> <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> - <maintainer type="project"> - <email>proxy-maint@gentoo.org</email> - <name>Proxy Maintainers</name> - </maintainer> <longdescription>BAM (Binary Alignment/Map) format is useful for storing large DNA sequence alignments. It is closely related to the text-based SAM format, but optimized for random-access. BamTools provides a fast, flexible C++ API for reading and writing BAM files.</longdescription> <upstream> <remote-id type="github">pezmaster31/bamtools</remote-id> diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest index eef8daed7a75..9cbcbdd02db5 100644 --- a/sci-biology/bcftools/Manifest +++ b/sci-biology/bcftools/Manifest @@ -1,2 +1,2 @@ -DIST bcftools-1.5.tar.bz2 2975685 BLAKE2B 937b7db770dcaddafbd00b67c3b88501a3190564b2ca629b83e52b48b414a604dd203cd067e357e2b7d02c700387576fca458d1cab2982dafa3b2c215b528722 SHA512 66b8bc61b9fbb381679a6781f77a18f66e8105567992da011413bc573d99b619558a1cf58e9e1373ae347a8b81638dd91977802a07a4578ddc9c61fb53403233 -DIST bcftools-1.9.tar.bz2 3134355 BLAKE2B dd551b509b1ee554f70be9da28a6eaf81dfcec43fc0d1aa972d64ef846f9db47f39177345e8c1ca754d11defb9c0823976ae94d6b3e7cd99313eed4f381182ed SHA512 fd662fb0d214eb75ac04fc4494e8dbaca84d10698ca14801427341def6a5df4af99e7bd4cd873da5422ae921deb49b940cedb926da356b1eabfac525a38f806c +DIST bcftools-1.17.tar.bz2 7538043 BLAKE2B 82f65d53ebea0527ff000329f158ebdb1d603e04841a096cf8ca0434e7a5694ab43da7959ee10e9cb29328bf82301c03200e1203578a74e2e1118856b2641502 SHA512 39ae44a682e626a5261900e9412170a269e460b559d6607db697e6a12b1e512ffb3bdeb3486413e19b8adca26a8ccbb2bd4af24459decb74592c54473d2c6a68 +DIST bcftools-1.19.tar.bz2 7906216 BLAKE2B 43e7ac0fc6ffcf837607fb2fbbd58a72106a89b018d1fd4b24db0eb854a9bf0efd0c7762fae84bf7f51226346777be646d134159ea48e3eb3df71799e9353a3f SHA512 a203c65fa58fca8fb5276e73ed8fc23dfd841e9dc05881304a8b91327d60ac3b5fcf5a55a1f1bab5647037f037ff30f2881791052f6e29cf38c646cbc947a746 diff --git a/sci-biology/bcftools/bcftools-1.5.ebuild b/sci-biology/bcftools/bcftools-1.17.ebuild index 9b5df1130999..6adee705bb46 100644 --- a/sci-biology/bcftools/bcftools-1.5.ebuild +++ b/sci-biology/bcftools/bcftools-1.17.ebuild @@ -1,11 +1,11 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 -PYTHON_COMPAT=( python2_7 ) +PYTHON_COMPAT=( python3_{9..11} ) -inherit python-r1 +inherit python-single-r1 DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files" HOMEPAGE="http://www.htslib.org" @@ -14,24 +14,22 @@ SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2" LICENSE="MIT" SLOT="0" KEYWORDS="~amd64 ~x86" -IUSE="" REQUIRED_USE="${PYTHON_REQUIRED_USE}" RDEPEND=" dev-lang/perl - =sci-libs/htslib-${PV}*:= + $(python_gen_cond_dep 'dev-python/matplotlib[${PYTHON_USEDEP}]') + =sci-libs/htslib-$(ver_cut 1-2)*:= sys-libs/zlib ${PYTHON_DEPS}" DEPEND="${RDEPEND}" - -PATCHES=( - "${FILESDIR}"/${PN}-1.5-buildsystem.patch - "${FILESDIR}"/${PN}-1.5-fix-shebangs.patch -) +BDEPEND="${PYTHON_DEPS}" src_prepare() { default + python_fix_shebang misc/{gff2gff,guess-ploidy,plot-roh}.py + # remove bundled htslib rm -r htslib-* || die } @@ -40,6 +38,5 @@ src_configure() { econf \ --disable-bcftools-plugins \ --disable-libgsl \ - --disable-configure-htslib \ --with-htslib=system } diff --git a/sci-biology/bcftools/bcftools-1.9.ebuild b/sci-biology/bcftools/bcftools-1.19.ebuild index 53e47bc01a81..27d474fe35f9 100644 --- a/sci-biology/bcftools/bcftools-1.9.ebuild +++ b/sci-biology/bcftools/bcftools-1.19.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2018 Gentoo Authors +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python2_7 ) +PYTHON_COMPAT=( python3_{10..12} ) inherit python-single-r1 @@ -14,25 +14,21 @@ SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2" LICENSE="MIT" SLOT="0" KEYWORDS="~amd64 ~x86" -IUSE="" REQUIRED_USE="${PYTHON_REQUIRED_USE}" RDEPEND=" dev-lang/perl - =sci-libs/htslib-${PV}*:= - sys-libs/zlib:= + $(python_gen_cond_dep 'dev-python/matplotlib[${PYTHON_USEDEP}]') + =sci-libs/htslib-$(ver_cut 1-2)*:= + sys-libs/zlib ${PYTHON_DEPS}" DEPEND="${RDEPEND}" - -PATCHES=( - "${FILESDIR}"/${PN}-1.5-buildsystem.patch - "${FILESDIR}"/${PN}-1.9-fix-shebangs.patch -) +BDEPEND="${PYTHON_DEPS}" src_prepare() { default - python_fix_shebang misc/{guess-ploidy,plot-roh}.py + python_fix_shebang misc/{gff2gff,guess-ploidy,plot-roh}.py # remove bundled htslib rm -r htslib-* || die @@ -42,6 +38,5 @@ src_configure() { econf \ --disable-bcftools-plugins \ --disable-libgsl \ - --disable-configure-htslib \ --with-htslib=system } diff --git a/sci-biology/bcftools/files/bcftools-1.5-buildsystem.patch b/sci-biology/bcftools/files/bcftools-1.5-buildsystem.patch deleted file mode 100644 index 304fc03e7441..000000000000 --- a/sci-biology/bcftools/files/bcftools-1.5-buildsystem.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- a/Makefile -+++ b/Makefile -@@ -275,7 +275,6 @@ - $(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir) - $(INSTALL_SCRIPT) $(MISC_SCRIPTS) $(DESTDIR)$(misc_bindir) - $(INSTALL_MAN) doc/bcftools.1 $(DESTDIR)$(man1dir) -- $(INSTALL_PROGRAM) plugins/*.so $(DESTDIR)$(plugindir) - - clean: testclean clean-plugins - -rm -f gmon.out *.o *~ $(PROG) version.h plugins/*.so plugins/*.P diff --git a/sci-biology/bcftools/files/bcftools-1.5-fix-shebangs.patch b/sci-biology/bcftools/files/bcftools-1.5-fix-shebangs.patch deleted file mode 100644 index c6cfc8b991d3..000000000000 --- a/sci-biology/bcftools/files/bcftools-1.5-fix-shebangs.patch +++ /dev/null @@ -1,24 +0,0 @@ ---- a/misc/guess-ploidy.py -+++ b/misc/guess-ploidy.py -@@ -1,4 +1,4 @@ --#!/usr/bin/env python -+#!/usr/bin/env python2.7 - # - # Plot the output of "bcftools +guess-ploidy -v" - # ---- a/misc/plot-roh.py -+++ b/misc/plot-roh.py -@@ -1,4 +1,4 @@ --#!/usr/bin/python -+#!/usr/bin/env python2.7 - - import glob, gzip, csv, sys, os, copy, re - csv.register_dialect('tab', delimiter='\t', quoting=csv.QUOTE_NONE) ---- a/misc/vcfutils.pl -+++ b/misc/vcfutils.pl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - # - # Copyright (C) 2010 Broad Institute. - # Copyright (C) 2011, 2014 Genome Research Ltd. diff --git a/sci-biology/bcftools/files/bcftools-1.9-fix-shebangs.patch b/sci-biology/bcftools/files/bcftools-1.9-fix-shebangs.patch deleted file mode 100644 index 76610187c493..000000000000 --- a/sci-biology/bcftools/files/bcftools-1.9-fix-shebangs.patch +++ /dev/null @@ -1,8 +0,0 @@ ---- a/misc/vcfutils.pl -+++ b/misc/vcfutils.pl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - # - # Copyright (C) 2010 Broad Institute. - # Copyright (C) 2011, 2014 Genome Research Ltd. diff --git a/sci-biology/bcftools/metadata.xml b/sci-biology/bcftools/metadata.xml index a1fb64db6fe9..0ba86185e50d 100644 --- a/sci-biology/bcftools/metadata.xml +++ b/sci-biology/bcftools/metadata.xml @@ -1,14 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> - <maintainer type="person"> - <email>mmokrejs@gmail.com</email> - <name>Martin Mokrejs</name> - </maintainer> <upstream> <remote-id type="github">samtools/bcftools</remote-id> </upstream> diff --git a/sci-biology/bedtools/Manifest b/sci-biology/bedtools/Manifest index 642fe852658e..0b52182a52f6 100644 --- a/sci-biology/bedtools/Manifest +++ b/sci-biology/bedtools/Manifest @@ -1,2 +1,2 @@ -DIST bedtools-2.26.0-fix-buildsystem.patch.bz2 2584 BLAKE2B 550cd03a0c01217adb347587cb75bdc2ffa4e03ad6ad66535b22d423e6f030e237b0ccfd3d1bd3e434cb9cc2a007971517f03e9ceabc08b63c725bac786e23e8 SHA512 0a7835f560102ce6183736faea6a2be05609b69bb8efdaf98b9d7057e24aa1ebe9d6067118b95c76470ca341b151970db532094ee70ca333075aed7c47509ba3 -DIST bedtools-2.26.0.tar.gz 19939711 BLAKE2B 8f6ee6ed755c638dbdd0a4750a5348c28a865f36eaafef6160e90f62912cb0a6b719713935ba68dad74bc591e3f37db49eab54a06a316dc00e4ec82a5dca71dc SHA512 b224adcc09322e90ef389e8172e14572b68f164185fe1a8814db1c47bb4f15656ca8c0ff0061017eb54d76affbe0d0f5793d893b8ab489b56eaf0818616a5def +DIST bedtools-2.30.0.tar.gz 20648577 BLAKE2B 042bc31e846455cb1c20199f7a27a3850851f7c256a45b1e674c7aa48ecedc211b0fdfc5e25f915b588f21447e757ebff2bba16a65905bb10d3c88e4b17b1db1 SHA512 3993243cc3db12d194d6220aeae200e6af843d6d32d4e5a9a82d04c9d119f8ed47e618e87241edfa82cfac081bc9a40ada18f097d21b0cafc5f912ae012701c9 +DIST bedtools-2.31.1.tar.gz 19629373 BLAKE2B f09742ee74494c783cef4909c56abd7b8542344539fe006140716b0a6a1d972db4e3df4a03fb3996a71cb57709b0494be8686879cba15c0985236f3a1282c92d SHA512 fbdc23011566697b2fc44bf3e7b466949487d3f648e81957fa80e8ad4b192d0ef7e2e3944b9b18612774a7984ec99e3fc339c3fddb8889caa632b8ce8defa20d diff --git a/sci-biology/bedtools/bedtools-2.26.0.ebuild b/sci-biology/bedtools/bedtools-2.26.0.ebuild deleted file mode 100644 index 0ad6f3eb354d..000000000000 --- a/sci-biology/bedtools/bedtools-2.26.0.ebuild +++ /dev/null @@ -1,44 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python{2_7,3_6} ) - -inherit flag-o-matic python-any-r1 toolchain-funcs - -DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats" -HOMEPAGE="https://bedtools.readthedocs.io/" -SRC_URI="https://github.com/arq5x/${PN}2/releases/download/v${PV}/${P}.tar.gz - https://dev.gentoo.org/~mgorny/dist/${PN}-2.26.0-fix-buildsystem.patch.bz2" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="test" -RESTRICT="!test? ( test )" - -DEPEND="${PYTHON_DEPS} - test? ( - sci-libs/htslib - sci-biology/samtools:0 - )" -RDEPEND="sys-libs/zlib" - -S="${WORKDIR}/${PN}2" - -DOCS=( README.md RELEASE_HISTORY ) -PATCHES=( "${WORKDIR}/${PN}-2.26.0-fix-buildsystem.patch" ) - -src_configure() { - append-lfs-flags - export prefix="${EPREFIX}/usr" - tc-export AR CXX -} - -src_install() { - default - - insinto /usr/share/${PN} - doins -r genomes -} diff --git a/sci-biology/bedtools/bedtools-2.30.0.ebuild b/sci-biology/bedtools/bedtools-2.30.0.ebuild new file mode 100644 index 000000000000..b86b87e72dc4 --- /dev/null +++ b/sci-biology/bedtools/bedtools-2.30.0.ebuild @@ -0,0 +1,49 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{9..11} ) + +inherit python-any-r1 toolchain-funcs + +DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats" +HOMEPAGE="https://bedtools.readthedocs.io/" +SRC_URI="https://github.com/arq5x/${PN}2/releases/download/v${PV}/${P}.tar.gz" +S="${WORKDIR}/${PN}2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="test" +RESTRICT="!test? ( test )" + +RDEPEND=" + app-arch/bzip2 + app-arch/xz-utils + sys-libs/zlib" +DEPEND="${RDEPEND}" +BDEPEND=" + ${PYTHON_DEPS} + test? ( >=sci-biology/samtools-1.10:0 )" + +# bedtools2 has a *terrible* build system and development practices. +# Upstream has forked htslib 1.9 and extended it by adding clever callbacks +# that make unbundling it nigh impossible. There are no signs of upstream porting +# their fork to 1.10, which means we're stuck with the bundled version. +PATCHES=( + "${FILESDIR}"/${PN}-2.29.2-buildsystem.patch + "${FILESDIR}"/${PN}-2.29.2-python.patch + "${FILESDIR}"/${PN}-2.30.0-gcc13.patch +) + +src_configure() { + tc-export AR CC CXX RANLIB +} + +src_install() { + default + + insinto /usr/share/bedtools + doins -r genomes +} diff --git a/sci-biology/bedtools/bedtools-2.31.1.ebuild b/sci-biology/bedtools/bedtools-2.31.1.ebuild new file mode 100644 index 000000000000..57ee6c3fde3f --- /dev/null +++ b/sci-biology/bedtools/bedtools-2.31.1.ebuild @@ -0,0 +1,49 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) + +inherit python-any-r1 toolchain-funcs + +DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats" +HOMEPAGE="https://bedtools.readthedocs.io/" +SRC_URI="https://github.com/arq5x/${PN}2/releases/download/v${PV}/${P}.tar.gz" +S="${WORKDIR}/${PN}2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="test" +RESTRICT="!test? ( test )" + +RDEPEND=" + app-arch/bzip2 + app-arch/xz-utils + sys-libs/zlib" +DEPEND="${RDEPEND}" +BDEPEND=" + ${PYTHON_DEPS} + test? ( >=sci-biology/samtools-1.10:0 )" + +# bedtools2 has a *terrible* build system and development practices. +# Upstream has forked htslib 1.9 and extended it by adding clever callbacks +# that make unbundling it nigh impossible. There are no signs of upstream porting +# their fork to 1.10, which means we're stuck with the bundled version. +PATCHES=( + "${FILESDIR}"/${PN}-2.31.1-buildsystem.patch + "${FILESDIR}"/${PN}-2.31.1-python.patch + "${FILESDIR}"/${PN}-2.31.1-includes.patch +) + +src_configure() { + tc-export AR CC CXX RANLIB +} + +src_install() { + default + + insinto /usr/share/bedtools + doins -r genomes +} diff --git a/sci-biology/bedtools/files/bedtools-2.29.2-buildsystem.patch b/sci-biology/bedtools/files/bedtools-2.29.2-buildsystem.patch new file mode 100644 index 000000000000..573e88993bc9 --- /dev/null +++ b/sci-biology/bedtools/files/bedtools-2.29.2-buildsystem.patch @@ -0,0 +1,82 @@ +--- a/Makefile ++++ b/Makefile +@@ -4,44 +4,29 @@ + # (c) 2009 Aaron Quinlan + # ========================== + +-SHELL := /bin/bash -e ++SHELL := bash -e + + VERSION_FILE=./src/utils/version/version_git.h + RELEASED_VERSION_FILE=./src/utils/version/version_release.txt + + + # define our object and binary directories +-ifeq ($(VERBOSE),1) + CCPREFIX = +-else +-CCPREFIX = @ +-endif + + OBJ_DIR = obj + BIN_DIR = bin + SRC_DIR = src + +-CXX = g++ +- +-ifeq ($(DEBUG),1) +-BT_CPPFLAGS = -DDEBUG -D_DEBUG -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES) +-BT_CXXFLAGS = -Wconversion -Wall -Wextra -g -O0 +-else + BT_CPPFLAGS = -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES) +-BT_CXXFLAGS = -g -Wall -O2 +-endif ++BT_CXXFLAGS = -Wall + + # If the user has specified to do so, tell the compile to use rand() (instead of mt19937). +-ifeq ($(USE_RAND),1) +-BT_CXXFLAGS += -DUSE_RAND +-else + BT_CXXFLAGS += -std=c++11 +-endif + + BT_LDFLAGS = + BT_LIBS = -lz -lm -lbz2 -llzma -lpthread + +-prefix ?= /usr/local ++prefix = $(EPREFIX)/usr + + SUBDIRS = $(SRC_DIR)/annotateBed \ + $(SRC_DIR)/bamToBed \ +@@ -204,7 +189,7 @@ + + # make the "obj/" and "bin/" directories, if they don't exist + $(OBJ_DIR) $(BIN_DIR): +- @mkdir -p $@ ++ mkdir -p $@ + + + # Usually HTSlib's configure script has not been used (detected via config.mk +--- a/src/utils/htslib/Makefile ++++ b/src/utils/htslib/Makefile +@@ -22,20 +22,13 @@ + # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER + # DEALINGS IN THE SOFTWARE. + +-CC = gcc +-AR = ar +-RANLIB = ranlib +- + # Default libraries to link if configure is not used + htslib_default_libs = -lz -lm -lbz2 -llzma + +-CPPFLAGS = + # TODO: probably update cram code to make it compile cleanly with -Wc++-compat + # For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600 + #CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 -D__FUNCTION__=__func__ +-CFLAGS = -g -Wall -O2 + EXTRA_CFLAGS_PIC = -fpic +-LDFLAGS = + LIBS = $(htslib_default_libs) + + prefix = /usr/local diff --git a/sci-biology/bedtools/files/bedtools-2.29.2-python.patch b/sci-biology/bedtools/files/bedtools-2.29.2-python.patch new file mode 100644 index 000000000000..9576a78bd1dd --- /dev/null +++ b/sci-biology/bedtools/files/bedtools-2.29.2-python.patch @@ -0,0 +1,41 @@ +--- a/Makefile ++++ b/Makefile +@@ -183,7 +168,7 @@ + + $(BIN_DIR)/intersectBed: | $(BIN_DIR) + @echo "- Creating executables for old CLI." +- @python scripts/makeBashScripts.py ++ $(EPYTHON) scripts/makeBashScripts.py + @chmod +x bin/* + @echo "done." + +--- a/src/utils/BamTools/Makefile.frag ++++ b/src/utils/BamTools/Makefile.frag +@@ -1,4 +1,4 @@ + src/utils/BamTools/include/BamAlignment.mapping.hpp: src/utils/BamTools/mapping/BamAlignment.py src/utils/BamTools/mapping/BamAlignment.map + + src/utils/BamTools/include/%.mapping.hpp: src/utils/BamTools/mapping/%.py src/utils/BamTools/mapping/%.map +- python $^ > $@ ++ $(EPYTHON) $^ > $@ +--- a/test/bigchroms/test-bigchroms.sh ++++ b/test/bigchroms/test-bigchroms.sh +@@ -28,7 +28,7 @@ + rm obs + + if [[ "$BT_NO_BIG_FILES" != "" ]]; then +-python make-big-chrom.py ++${EPYTHON} make-big-chrom.py + + echo -e " bigchroms.t03...big get fasta \c" + $BT getfasta -fi bigx.fasta -bed bigx.bed | tail -1 > obs +--- a/test/fisher/cmp.sh ++++ b/test/fisher/cmp.sh +@@ -3,7 +3,7 @@ + echo "fisher,shuffled" + + for i in $(seq 1000); do +- fisher=$(python ./sim.py | tail -1 | cut -f 2) ++ fisher=$(${EPYTHON} ./sim.py | tail -1 | cut -f 2) + shuffle=$(bash shuf.sh) + echo "$fisher,$shuffle" + done diff --git a/sci-biology/bedtools/files/bedtools-2.30.0-gcc13.patch b/sci-biology/bedtools/files/bedtools-2.30.0-gcc13.patch new file mode 100644 index 000000000000..c63faf31c851 --- /dev/null +++ b/sci-biology/bedtools/files/bedtools-2.30.0-gcc13.patch @@ -0,0 +1,25 @@ +https://github.com/arq5x/bedtools2/pull/1045 + +From 7d7fb513b9b05b7a0512a83520e9f60036e5ff9a Mon Sep 17 00:00:00 2001 +From: David Seifert <soap@gentoo.org> +Date: Tue, 18 Apr 2023 11:59:58 +0200 +Subject: [PATCH] Add missing <cstdint> include + +* breaks build with GCC 13: + https://bugs.gentoo.org/895860 +--- + src/utils/general/ParseTools.h | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/src/utils/general/ParseTools.h b/src/utils/general/ParseTools.h +index e056c149..3418eff1 100644 +--- a/src/utils/general/ParseTools.h ++++ b/src/utils/general/ParseTools.h +@@ -16,6 +16,7 @@ + #include "string.h" + #include <cstdio> + #include <cstdlib> ++#include <cstdint> + + using namespace std; + diff --git a/sci-biology/bedtools/files/bedtools-2.31.1-buildsystem.patch b/sci-biology/bedtools/files/bedtools-2.31.1-buildsystem.patch new file mode 100644 index 000000000000..8bb2a096e917 --- /dev/null +++ b/sci-biology/bedtools/files/bedtools-2.31.1-buildsystem.patch @@ -0,0 +1,84 @@ +--- a/Makefile ++++ b/Makefile +@@ -4,46 +4,29 @@ + # (c) 2009 Aaron Quinlan + # ========================== + +-SHELL := /bin/bash -e ++SHELL := bash -e + + VERSION_FILE=./src/utils/version/version_git.h + RELEASED_VERSION_FILE=./src/utils/version/version_release.txt + + + # define our object and binary directories +-ifeq ($(VERBOSE),1) + CCPREFIX = +-else +-CCPREFIX = @ +-endif + + OBJ_DIR = obj + BIN_DIR = bin + SRC_DIR = src + +-CXX = g++ +- +-PYTHON ?= $(shell python --version >/dev/null 2>&1 && echo "python" || echo python3) +- +-ifeq ($(DEBUG),1) +-BT_CPPFLAGS = -DDEBUG -D_DEBUG -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES) +-BT_CXXFLAGS = -Wconversion -Wall -Wextra -g -O0 +-else + BT_CPPFLAGS = -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES) +-BT_CXXFLAGS = -g -Wall -O2 +-endif ++BT_CXXFLAGS = -Wall + + # If the user has specified to do so, tell the compile to use rand() (instead of mt19937). +-ifeq ($(USE_RAND),1) +-BT_CXXFLAGS += -DUSE_RAND +-else + BT_CXXFLAGS += -std=c++11 +-endif + + BT_LDFLAGS = + BT_LIBS = -lz -lm -lbz2 -llzma -lpthread + +-prefix ?= /usr/local ++prefix = $(EPREFIX)/usr + + SUBDIRS = $(SRC_DIR)/annotateBed \ + $(SRC_DIR)/bamToBed \ +@@ -213,7 +196,7 @@ + + # make the "obj/" and "bin/" directories, if they don't exist + $(OBJ_DIR) $(BIN_DIR): +- @mkdir -p $@ ++ mkdir -p $@ + + + # Usually HTSlib's configure script has not been used (detected via config.mk +--- a/src/utils/htslib/Makefile ++++ b/src/utils/htslib/Makefile +@@ -22,20 +22,13 @@ + # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER + # DEALINGS IN THE SOFTWARE. + +-CC = gcc +-AR = ar +-RANLIB = ranlib +- + # Default libraries to link if configure is not used + htslib_default_libs = -lz -lm -lbz2 -llzma + +-CPPFLAGS = + # TODO: probably update cram code to make it compile cleanly with -Wc++-compat + # For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600 + #CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 -D__FUNCTION__=__func__ +-CFLAGS = -g -Wall -O2 + EXTRA_CFLAGS_PIC = -fpic +-LDFLAGS = + LIBS = $(htslib_default_libs) + + prefix = /usr/local diff --git a/sci-biology/bedtools/files/bedtools-2.31.1-includes.patch b/sci-biology/bedtools/files/bedtools-2.31.1-includes.patch new file mode 100644 index 000000000000..927b1b944d6e --- /dev/null +++ b/sci-biology/bedtools/files/bedtools-2.31.1-includes.patch @@ -0,0 +1,180 @@ +https://github.com/arq5x/bedtools2/pull/1087 + +From 3fbf2ddc8ebf0fc1bd492d14a6046aadd59ecadb Mon Sep 17 00:00:00 2001 +From: David Seifert <soap@gentoo.org> +Date: Thu, 25 Apr 2024 11:18:48 +0200 +Subject: [PATCH] Add missing `stdint.h` includes + +* Musl is a lot stricter with transitive includes: + Bug: https://bugs.gentoo.org/907971 +--- a/src/bamToBed/bamToBed.cpp ++++ b/src/bamToBed/bamToBed.cpp +@@ -22,6 +22,7 @@ using namespace BamTools; + #include <sstream> + #include <fstream> + #include <stdlib.h> ++#include <stdint.h> + + using namespace std; + +--- a/src/clusterBed/clusterBed.cpp ++++ b/src/clusterBed/clusterBed.cpp +@@ -12,6 +12,8 @@ + #include "lineFileUtilities.h" + #include "clusterBed.h" + ++#include <stdint.h> ++ + // = Constructor = + BedCluster::BedCluster(string &bedFile, + int maxDistance, +--- a/src/pairToBed/pairToBed.h ++++ b/src/pairToBed/pairToBed.h +@@ -22,6 +22,7 @@ using namespace BamTools; + #include <vector> + #include <iostream> + #include <fstream> ++#include <stdint.h> + + using namespace std; + +--- a/src/randomBed/randomBed.h ++++ b/src/randomBed/randomBed.h +@@ -22,6 +22,7 @@ + #include <unistd.h> + #include <sys/types.h> + #include <algorithm> // for binary search ++#include <stdint.h> + using namespace std; + + const int MAX_TRIES = 1000000; +--- a/src/summaryFile/summaryFile.h ++++ b/src/summaryFile/summaryFile.h +@@ -12,6 +12,8 @@ + #include "ToolBase.h" + #include "ContextSummary.h" + ++#include <stdint.h> ++ + struct Interval { + CHRPOS start; + CHRPOS end; +--- a/src/utils/BamTools/include/BamAlignment.mapping.hpp ++++ b/src/utils/BamTools/include/BamAlignment.mapping.hpp +@@ -1,3 +1,4 @@ ++#include <stdint.h> + + struct _RefID_t { + operator int32_t() const {return (int32_t)(_ptr()->core.tid);} +--- a/src/utils/BamTools/include/api/BamAux.h ++++ b/src/utils/BamTools/include/api/BamAux.h +@@ -1,4 +1,5 @@ + #include <string> ++#include <stdint.h> + + #ifndef BAMAUX_H + #define BAMAUX_H +--- a/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h ++++ b/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h +@@ -9,6 +9,7 @@ + #define SINGLELINETEXTFILEREADER_H_ + + #include <algorithm> ++#include <stdint.h> + #include "FileReader.h" + #include "string.h" + #include "lineFileUtilities.h" +--- a/src/utils/FileRecordTools/Records/BamRecord.cpp ++++ b/src/utils/FileRecordTools/Records/BamRecord.cpp +@@ -10,6 +10,8 @@ + #include "BamFileReader.h" + #include "RecordKeyVector.h" + ++#include <stdint.h> ++ + BamRecord::BamRecord() + : _bamChromId(-1) + { +--- a/src/utils/GenomeFile/GenomeFile.h ++++ b/src/utils/GenomeFile/GenomeFile.h +@@ -19,6 +19,7 @@ + #include <fstream> + #include <cstring> + #include <cstdio> ++#include <stdint.h> + #include <algorithm> // for bsearch lower_bound() + #include "api/BamReader.h" + #include "api/BamAux.h" +--- a/src/utils/GenomeFile/NewGenomeFile.h ++++ b/src/utils/GenomeFile/NewGenomeFile.h +@@ -14,6 +14,7 @@ + #define NEW_GENOMEFILE_H + + #include <algorithm> // for bsearch lower_bound() ++#include <stdint.h> + + #include "BedtoolsTypes.h" + +--- a/src/utils/bedFilePE/bedFilePE.h ++++ b/src/utils/bedFilePE/bedFilePE.h +@@ -8,6 +8,7 @@ + #include <fstream> + #include <sstream> + #include <cstring> ++#include <stdint.h> + #include <algorithm> + #include "bedFile.h" + #include "lineFileUtilities.h" +--- a/src/utils/general/ParseTools.cpp ++++ b/src/utils/general/ParseTools.cpp +@@ -2,7 +2,7 @@ + #include <climits> + #include <cctype> + #include <cstring> +-#include <cstdint> ++#include <stdint.h> + #include <cstdio> + #include <cstdlib> + #include <sstream> +--- a/src/utils/lineFileUtilities/lineFileUtilities.h ++++ b/src/utils/lineFileUtilities/lineFileUtilities.h +@@ -4,6 +4,7 @@ + #include <vector> + #include <string> + #include <cstring> ++#include <stdint.h> + #include <cstdlib> + #include <sstream> + #include <iostream> +--- a/src/utils/sequenceUtilities/sequenceUtils.h ++++ b/src/utils/sequenceUtilities/sequenceUtils.h +@@ -4,6 +4,7 @@ + #include <string> + #include <algorithm> + #include <cctype> ++#include <stdint.h> + + using namespace std; + +--- a/src/windowMaker/windowMaker.h ++++ b/src/windowMaker/windowMaker.h +@@ -12,6 +12,8 @@ Licenced under the GNU General Public License 2.0 license. + #include "NewGenomeFile.h" + #include "bedFile.h" + ++#include <stdint.h> ++ + using namespace std; + + +--- a/src/windowMaker/windowMakerMain.cpp ++++ b/src/windowMaker/windowMakerMain.cpp +@@ -12,6 +12,8 @@ Licenced under the GNU General Public License 2.0 license. + #include "windowMaker.h" + #include "version.h" + ++#include <stdint.h> ++ + using namespace std; + + // define our program name diff --git a/sci-biology/bedtools/files/bedtools-2.31.1-python.patch b/sci-biology/bedtools/files/bedtools-2.31.1-python.patch new file mode 100644 index 000000000000..99fc1b1d480b --- /dev/null +++ b/sci-biology/bedtools/files/bedtools-2.31.1-python.patch @@ -0,0 +1,42 @@ +https://github.com/arq5x/bedtools2/pull/1087 + +From eabcd3dcb9caa1fcc17acd43df2ded4170ed1449 Mon Sep 17 00:00:00 2001 +From: David Seifert <soap@gentoo.org> +Date: Thu, 25 Apr 2024 11:18:47 +0200 +Subject: [PATCH] Allow PYTHON from environment + +* Distros need to be able to specify exactly which python + interpreter to run tests under. +--- a/test/bigchroms/test-bigchroms.sh ++++ b/test/bigchroms/test-bigchroms.sh +@@ -28,7 +28,7 @@ check obs abig.bed + rm obs + + if [[ "$BT_NO_BIG_FILES" != "" ]]; then +-python make-big-chrom.py ++${PYTHON:-python} make-big-chrom.py + + echo -e " bigchroms.t03...big get fasta \c" + $BT getfasta -fi bigx.fasta -bed bigx.bed | tail -1 > obs +--- a/test/fisher/cmp.sh ++++ b/test/fisher/cmp.sh +@@ -3,7 +3,7 @@ set -eo pipefail + echo "fisher,shuffled" + + for i in $(seq 1000); do +- fisher=$(python ./sim.py | tail -1 | cut -f 2) ++ fisher=$(${PYTHON:-python} ./sim.py | tail -1 | cut -f 2) + shuffle=$(bash shuf.sh) + echo "$fisher,$shuffle" + done +--- a/test/genomecov/test-genomecov.sh ++++ b/test/genomecov/test-genomecov.sh +@@ -288,7 +288,7 @@ CRAM_REFERENCE=test_ref.fa $BT genomecov -ibam empty.cram > obs + check obs exp + rm obs exp + +-python mk-deep.py > deep.sam ++${PYTHON:-python} mk-deep.py > deep.sam + echo -e " genomecov.t18...\c" + echo "c1 1 1000000" > exp + $BT genomecov -d -ibam deep.sam | head -1 > obs diff --git a/sci-biology/bedtools/metadata.xml b/sci-biology/bedtools/metadata.xml index 39869a9f2790..063085dad8ee 100644 --- a/sci-biology/bedtools/metadata.xml +++ b/sci-biology/bedtools/metadata.xml @@ -1,21 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@gmail.com</email> - <name>Martin Mokrejs</name> - </maintainer> <maintainer type="project"> <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> - <maintainer type="project"> - <email>proxy-maint@gentoo.org</email> - <name>Proxy Maintainers</name> - </maintainer> - <longdescription> - BEDTools: a flexible suite of utilities for comparing genomic features. - </longdescription> <upstream> <remote-id type="google-code">bedtools</remote-id> <remote-id type="github">arq5x/bedtools2</remote-id> diff --git a/sci-biology/bfast/bfast-0.7.0a.ebuild b/sci-biology/bfast/bfast-0.7.0a.ebuild index 97282d2244a4..dd4036c6030e 100644 --- a/sci-biology/bfast/bfast-0.7.0a.ebuild +++ b/sci-biology/bfast/bfast-0.7.0a.ebuild @@ -1,42 +1,29 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=7 -AUTOTOOLS_AUTORECONF=true - -inherit autotools-utils flag-o-matic +inherit autotools DESCRIPTION="Blat-like Fast Accurate Search Tool" HOMEPAGE="https://sourceforge.net/projects/bfast/" -SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" +SRC_URI="https://downloads.sourceforge.net/${PN}/${P}.tar.gz" LICENSE="GPL-2" SLOT="0" -IUSE="test" -RESTRICT="!test? ( test )" KEYWORDS="~amd64 ~x86" +IUSE="test" +RESTRICT="test" # tests broken, upstream unresponsive -DEPEND="" RDEPEND="dev-perl/XML-Simple" -src_prepare() { - sed \ - -e 's/-m64//' \ - -e 's/CFLAGS="${default_CFLAGS} ${extended_CFLAGS}"/CFLAGS="${CFLAGS} ${default_CFLAGS} ${extended_CFLAGS}"/' \ - -e 's:-g -O2::g' \ - -i configure.ac || die - sed \ - -e 's:. test.definitions.sh:. ./test.definitions.sh:g' \ - -i tests/*sh || die - - sed \ - -e '/docdir/d' \ - -i Makefile.am || die - - use test && AUTOTOOLS_IN_SOURCE_BUILD=1 +PATCHES=( + "${FILESDIR}"/${P}-autotools.patch + "${FILESDIR}"/${P}-test-sourcing.patch + "${FILESDIR}"/${P}-C99-inline.patch +) - append-flags -fgnu89-inline - - autotools-utils_src_prepare +src_prepare() { + default + eautoreconf } diff --git a/sci-biology/bfast/files/bfast-0.7.0a-C99-inline.patch b/sci-biology/bfast/files/bfast-0.7.0a-C99-inline.patch new file mode 100644 index 000000000000..86450c96048a --- /dev/null +++ b/sci-biology/bfast/files/bfast-0.7.0a-C99-inline.patch @@ -0,0 +1,74 @@ +--- a/bfast/AlignNTSpace.c ++++ b/bfast/AlignNTSpace.c +@@ -478,7 +478,7 @@ + } + } + +-inline void AlignNTSpaceFillInCell(char *read, ++void AlignNTSpaceFillInCell(char *read, + int32_t readLength, + char *reference, + int32_t referenceLength, +--- a/bfast/AlignNTSpace.h ++++ b/bfast/AlignNTSpace.h +@@ -10,5 +10,5 @@ + void AlignNTSpaceRecoverAlignmentFromMatrix(AlignedEntry*, AlignMatrix*, char*, int, char*, int, int32_t, int32_t, int, int32_t, char, int); + void AlignNTSpaceInitializeAtStart(AlignMatrix*, ScoringMatrix*, int32_t, int32_t); + void AlignNTSpaceInitializeToExtend(AlignMatrix*, ScoringMatrix*, int32_t, int32_t, int32_t, int32_t); +-inline void AlignNTSpaceFillInCell(char*, int32_t, char*, int32_t, ScoringMatrix*, AlignMatrix*, int32_t, int32_t, int32_t, int32_t); ++void AlignNTSpaceFillInCell(char*, int32_t, char*, int32_t, ScoringMatrix*, AlignMatrix*, int32_t, int32_t, int32_t, int32_t); + #endif +--- a/bfast/BLib.c ++++ b/bfast/BLib.c +@@ -90,7 +90,7 @@ + } + + /* TODO */ +-inline char ToUpper(char a) ++char ToUpper(char a) + { + if(97 <= a && a < 122) return (char)(a - 32); + return a; +--- a/bfast/BLib.h ++++ b/bfast/BLib.h +@@ -16,7 +16,7 @@ + int ParseFastaHeaderLine(char*); + char ToLower(char); + void ToLowerRead(char*, int); +-inline char ToUpper(char); ++char ToUpper(char); + void ToUpperRead(char*, int); + void ReverseRead(char*, char*, int); + void ReverseReadFourBit(int8_t*, int8_t*, int); +--- a/bfast/ScoringMatrix.c ++++ b/bfast/ScoringMatrix.c +@@ -98,14 +98,14 @@ + return 1; + } + +-inline int32_t ScoringMatrixGetNTScore(char a, ++int32_t ScoringMatrixGetNTScore(char a, + char b, + ScoringMatrix *sm) + { + return (ToUpper(a) == ToUpper(b)) ? sm->ntMatch : sm->ntMismatch; + } + +-inline int32_t ScoringMatrixGetColorScore(char a, ++int32_t ScoringMatrixGetColorScore(char a, + char b, + ScoringMatrix *sm) + { +--- a/bfast/ScoringMatrix.h ++++ b/bfast/ScoringMatrix.h +@@ -3,8 +3,8 @@ + + #include "BLibDefinitions.h" + +-inline int32_t ScoringMatrixGetNTScore(char, char, ScoringMatrix*); +-inline int32_t ScoringMatrixGetColorScore(char, char, ScoringMatrix*); ++int32_t ScoringMatrixGetNTScore(char, char, ScoringMatrix*); ++int32_t ScoringMatrixGetColorScore(char, char, ScoringMatrix*); + + int ScoringMatrixRead(char*, ScoringMatrix*, int); + void ScoringMatrixInitialize(ScoringMatrix*); diff --git a/sci-biology/bfast/files/bfast-0.7.0a-autotools.patch b/sci-biology/bfast/files/bfast-0.7.0a-autotools.patch new file mode 100644 index 000000000000..993f6a554662 --- /dev/null +++ b/sci-biology/bfast/files/bfast-0.7.0a-autotools.patch @@ -0,0 +1,41 @@ +--- a/configure.ac ++++ b/configure.ac +@@ -8,7 +8,7 @@ + AC_INIT([bfast],[0.7.0a],[bfast-help@lists.sourceforge.net],[bfast]) + AC_COPYRIGHT([See LICENSE for copyright information.]) + AC_CONFIG_AUX_DIR(config) +-AM_INIT_AUTOMAKE([dist-bzip2 subdir-objects]) ++AM_INIT_AUTOMAKE([dist-bzip2 subdir-objects serial-tests]) + AC_CONFIG_SRCDIR([config.h.in]) + AC_CONFIG_HEADERS([config.h]) + +@@ -21,10 +21,10 @@ + + AC_PROG_INSTALL + AC_GNU_SOURCE ++AC_SYS_LARGEFILE + + # set CFLAGS and CXXFLAGS +-default_CFLAGS="-Wall -g -O2 -pthread"; +-extended_CFLAGS="";# "-m64 -D_FILE_OFFSET_BITS=64"; ++default_CFLAGS="-Wall -pthread" + + # Define some variables + GITREV="Revision: undefined$"; +@@ -42,7 +42,7 @@ + AC_DEFINE(HAVE_LIBBZ2, 1, [Define to 1 if you have the <bzlib.h> header file.])], + AC_MSG_ERROR("could not find the bzlib library. Please use --disable-bzlib if you wish to disable bzlib support."))]) + +-CFLAGS="${default_CFLAGS} ${extended_CFLAGS}"; ++CFLAGS="${CFLAGS} ${default_CFLAGS} ${extended_CFLAGS}"; + + # Enable large file support; disable with --disable-largefile + AC_SYS_LARGEFILE +--- a/Makefile.am ++++ b/Makefile.am +@@ -16,5 +16,4 @@ + + SUBDIRS = bfast butil scripts tests + +-docdir = ${datadir}/doc/${PACKAGE} + dist_doc_DATA = LICENSE manual/bfast-book.pdf diff --git a/sci-biology/bfast/files/bfast-0.7.0a-test-sourcing.patch b/sci-biology/bfast/files/bfast-0.7.0a-test-sourcing.patch new file mode 100644 index 000000000000..f4dd64e75cac --- /dev/null +++ b/sci-biology/bfast/files/bfast-0.7.0a-test-sourcing.patch @@ -0,0 +1,79 @@ +--- a/tests/test.cleanup.sh ++++ b/tests/test.cleanup.sh +@@ -1,6 +1,6 @@ + #!/bin/sh + +-. test.definitions.sh ++. ./test.definitions.sh + + echo " Cleaning up files."; + +--- a/tests/test.diff.sh ++++ b/tests/test.diff.sh +@@ -1,6 +1,6 @@ + #!/bin/sh + +-. test.definitions.sh ++. ./test.definitions.sh + + #error() + #{ +--- a/tests/test.fasta2brg.sh ++++ b/tests/test.fasta2brg.sh +@@ -1,6 +1,6 @@ + #!/bin/sh + +-. test.definitions.sh ++. ./test.definitions.sh + TMP_DIR="tmp/"; + + echo " Building a reference genome."; +--- a/tests/test.index.sh ++++ b/tests/test.index.sh +@@ -1,5 +1,5 @@ + #!/bin/sh +-. test.definitions.sh ++. ./test.definitions.sh + + echo " Building an index."; + +--- a/tests/test.initialize.sh ++++ b/tests/test.initialize.sh +@@ -1,6 +1,6 @@ + #!/bin/sh + +-. test.definitions.sh ++. ./test.definitions.sh + + echo " Initializing data for tests."; + +--- a/tests/test.localalign.sh ++++ b/tests/test.localalign.sh +@@ -1,6 +1,6 @@ + #!/bin/sh + +-. test.definitions.sh ++. ./test.definitions.sh + + echo " Running local alignment."; + +--- a/tests/test.match.sh ++++ b/tests/test.match.sh +@@ -1,6 +1,6 @@ + #!/bin/sh + +-. test.definitions.sh ++. ./test.definitions.sh + + echo " Finding matches."; + +--- a/tests/test.postprocess.sh ++++ b/tests/test.postprocess.sh +@@ -1,6 +1,6 @@ + #!/bin/sh + +-. test.definitions.sh ++. ./test.definitions.sh + + echo " Running postprocessing."; + diff --git a/sci-biology/bfast/metadata.xml b/sci-biology/bfast/metadata.xml index 933dea84e1b3..5ec4a95ff146 100644 --- a/sci-biology/bfast/metadata.xml +++ b/sci-biology/bfast/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/biogrep/biogrep-1.0-r2.ebuild b/sci-biology/biogrep/biogrep-1.0-r3.ebuild index 55c780b9ddef..74019b09fb6b 100644 --- a/sci-biology/biogrep/biogrep-1.0-r2.ebuild +++ b/sci-biology/biogrep/biogrep-1.0-r3.ebuild @@ -1,13 +1,14 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit autotools DESCRIPTION="Multithreaded tool for matching large sets of patterns against biosequence DBs" HOMEPAGE="http://stephanopoulos.openwetware.org/BIOGREP.html" -SRC_URI="http://www.openwetware.org/images/3/3d/${P^}.tar.gz -> ${P}.tar.gz +SRC_URI=" + http://www.openwetware.org/images/3/3d/${P^}.tar.gz -> ${P}.tar.gz doc? ( http://www.openwetware.org/images/4/49/${PN^}.pdf -> ${P}.pdf )" LICENSE="GPL-2" @@ -17,19 +18,18 @@ IUSE="doc examples" src_prepare() { default - mv configure.{in,ac} || die eautoreconf } src_install() { - use doc && DOCS+=( "${DISTDIR}"/${P}.pdf ) + default + + use doc && dodoc "${DISTDIR}"/${P}.pdf if use examples; then # remove cruft before installing examples find examples/ \( -name 'CVS' -o -name '*~' \) -exec rm -rf '{}' + || die - DOCS+=( examples ) + dodoc -r examples docompress -x /usr/share/doc/${PF}/examples fi - - default } diff --git a/sci-biology/biogrep/metadata.xml b/sci-biology/biogrep/metadata.xml index 8417d1580d40..bdabd1d83788 100644 --- a/sci-biology/biogrep/metadata.xml +++ b/sci-biology/biogrep/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/biopandas/Manifest b/sci-biology/biopandas/Manifest deleted file mode 100644 index edc8d21dfb49..000000000000 --- a/sci-biology/biopandas/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST biopandas-0.2.1.tar.gz 209379 BLAKE2B 839a6f569f12b95c9b1c75dc755d009c77d7ef8224e517aed5026ffa6c33bd3826fe3862fec03469e967005a500600782fc372951d61358e2fe3bb56af734228 SHA512 0ea7aec84251d8d6ec4736c4968228133bd8622afb17d6916287168cb9f9757c5a97a4d5a52ac0e2f30027bf0edf9d76413db142f70d606f1359b8a4e06de7c8 diff --git a/sci-biology/biopandas/biopandas-0.2.1.ebuild b/sci-biology/biopandas/biopandas-0.2.1.ebuild deleted file mode 100644 index 8c892419b29c..000000000000 --- a/sci-biology/biopandas/biopandas-0.2.1.ebuild +++ /dev/null @@ -1,43 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python3_6 ) - -inherit distutils-r1 - -MY_PN="BioPandas" -MY_P="${MY_PN}-${PV}" - -DESCRIPTION="Molecular Structures in Pandas DataFrames" -HOMEPAGE=" - https://rasbt.github.io/biopandas/ - https://github.com/rasbt/biopandas - https://pypi.org/project/BioPandas/" -SRC_URI="mirror://pypi/${MY_P:0:1}/${MY_PN}/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="test" -RESTRICT="!test? ( test )" - -RDEPEND=" - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/pandas[${PYTHON_USEDEP}] - sci-libs/scipy[${PYTHON_USEDEP}] -" -DEPEND="${RDEPEND} - dev-python/setuptools[${PYTHON_USEDEP}] - test? ( - dev-python/nose[${PYTHON_USEDEP}] - )" - -python_test() { - "${EPYTHON}" --version - "${EPYTHON}" -c "import numpy; print('numpy %s' % numpy.__version__)" - "${EPYTHON}" -c "import scipy; print('scipy %s' % scipy.__version__)" - "${EPYTHON}" -c "import pandas; print('pandas %s' % pandas.__version__)" - nosetests -s --verbose ${PN} || die -} diff --git a/sci-biology/biopandas/metadata.xml b/sci-biology/biopandas/metadata.xml deleted file mode 100644 index f23da0b1ebe2..000000000000 --- a/sci-biology/biopandas/metadata.xml +++ /dev/null @@ -1,16 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="pypi">BioPandas</remote-id> - <maintainer status="unknown"> - <email>mail@sebastianraschka.com</email> - <name>Sebastian Raschka</name> - </maintainer> - <remote-id type="github">rasbt/biopandas</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/bioperl-db/bioperl-db-1.6.9-r1.ebuild b/sci-biology/bioperl-db/bioperl-db-1.6.9-r2.ebuild index facab7d5ffbe..435dc4a67173 100644 --- a/sci-biology/bioperl-db/bioperl-db-1.6.9-r1.ebuild +++ b/sci-biology/bioperl-db/bioperl-db-1.6.9-r2.ebuild @@ -1,54 +1,57 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 BIOPERL_RELEASE=1.6.9 DIST_NAME=BioPerl-DB DIST_AUTHOR=CJFIELDS DIST_VERSION=1.006900 +DIST_TEST="do" # Parallelism probably bad inherit perl-module DESCRIPTION="Perl tools for bioinformatics - Perl API that accesses the BioSQL schema" HOMEPAGE="http://www.bioperl.org/" SLOT="0" -KEYWORDS="~amd64 ~x86" -RESTRICT="test" +KEYWORDS="amd64 ~x86" IUSE="test" +RESTRICT="test" -DIST_TEST="do" # Parallelism probably bad -PATCHES=( "${FILESDIR}/${PN}-1.6.9-db.patch" ) RDEPEND=" >=sci-biology/bioperl-${PV} dev-perl/DBD-mysql dev-perl/DBI sci-biology/biosql" -DEPEND="${RDEPEND} - dev-perl/Module-Build +DEPEND=" + ${RDEPEND} test? ( dev-perl/Data-Stag dev-perl/Sub-Uplevel dev-perl/Test-Warn dev-perl/Test-Exception virtual/perl-Test-Simple - ) -" + )" +BDEPEND="dev-perl/Module-Build" + +PATCHES=( "${FILESDIR}"/${PN}-1.6.9-db.patch ) + src_prepare() { export GENTOO_DB_HOSTNAME=localhost perl-module_src_prepare } -src_install() { - mydoc="AUTHORS BUGS FAQ" - perl-module_src_install -} + src_test() { einfo "Removing bundled test libraries t/lib" rm -r "${S}/t/lib" || die "Cannot remove t/lib" ebegin "Setting up test database" + local mysql_install_db="${EPREFIX}/usr/share/mariadb/scripts/mysql_install_db" + [[ ! -x "${mysql_install_db}" ]] && mysql_install_db="${EPREFIX}/usr/bin/mysql_install_db" + [[ ! -x "${mysql_install_db}" ]] && die "mysql_install_db command not found!" + local mysqld="${EPREFIX}/usr/sbin/mysqld" local socket="${T}/mysql.sock" local pidfile="${T}/mysql.pid" @@ -58,27 +61,43 @@ src_test() { mkdir -p "${datadir}" || die "Can't make mysql database dir"; chmod 755 "${datadir}" || die "Can't fix mysql database dir perms"; - if $mysqld --help | grep -q MariaDB ; then - "${EPREFIX}"/usr/share/mysql/scripts/mysql_install_db \ - --basedir="${EPREFIX}/usr" \ - --datadir="${datadir}" \ - --user=$(whoami) || die "Can't initalize database" - fi - - ${mysqld} --no-defaults --user=$(whoami) --skip-networking \ - --socket="${socket}" \ - --pid-file="${pidfile}" \ - --datadir="${datadir}" & - maxtry=20 + "${mysql_install_db}" \ + --basedir="${EPREFIX}/usr" \ + --datadir="${datadir}" \ + --user=$(whoami) \ + || die "Failed to initalize test database" + + "${mysqld}" \ + --no-defaults \ + --user=$(whoami) \ + --skip-networking \ + --skip-grant \ + --socket="${socket}" \ + --pid-file="${pidfile}" \ + --datadir="${datadir}" & + + local maxtry=20 while ! [[ -S "${socket}" || "${maxtry}" -lt 1 ]] ; do maxtry=$((${maxtry}-1)) echo -n "." sleep 1 done - eend $? + + local rc=1 + [[ -S "${socket}" ]] && rc=0 + + eend ${rc} + + [[ ${rc} -ne 0 ]] && die "Failed to start mysqld test instance" + export MYSQL_UNIX_PORT="${socket}" perl-module_src_test ebegin "Shutting down mysql test database" pkill -F "${pidfile}" eend $? } + +src_install() { + mydoc="AUTHORS BUGS FAQ" + perl-module_src_install +} diff --git a/sci-biology/bioperl-db/bioperl-db-1.6.9.ebuild b/sci-biology/bioperl-db/bioperl-db-1.6.9.ebuild deleted file mode 100644 index e6f0c45958a9..000000000000 --- a/sci-biology/bioperl-db/bioperl-db-1.6.9.ebuild +++ /dev/null @@ -1,47 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI="5" - -BIOPERL_RELEASE=1.6.9 - -MY_PN=BioPerl-DB -MODULE_AUTHOR=CJFIELDS -MODULE_VERSION=1.006900 -inherit perl-module - -DESCRIPTION="Perl tools for bioinformatics - Perl API that accesses the BioSQL schema" -HOMEPAGE="http://www.bioperl.org/" - -SLOT="0" -KEYWORDS="amd64 x86" -IUSE="test" -RESTRICT="test" -SRC_TEST="do" - -CDEPEND=" - >=sci-biology/bioperl-${PV} - dev-perl/DBD-mysql - dev-perl/DBI - sci-biology/biosql" -DEPEND="${CDEPEND} - dev-perl/Module-Build - test? ( - dev-perl/Data-Stag - dev-perl/Sub-Uplevel - dev-perl/Test-Warn - dev-perl/Test-Exception - virtual/perl-Test-Simple - ) -" -RDEPEND="${CDEPEND}" - -src_install() { - mydoc="AUTHORS BUGS FAQ" - perl-module_src_install -} -src_test() { - einfo "Removing bundled test libraries t/lib" - rm -r "${S}/t/lib" || die "Cannot remove t/lib" - perl-module_src_test -} diff --git a/sci-biology/bioperl-db/metadata.xml b/sci-biology/bioperl-db/metadata.xml index 09e1cb381b7f..171d7d240b71 100644 --- a/sci-biology/bioperl-db/metadata.xml +++ b/sci-biology/bioperl-db/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/bioperl-network/bioperl-network-1.6.9-r1.ebuild b/sci-biology/bioperl-network/bioperl-network-1.6.9-r1.ebuild new file mode 100644 index 000000000000..fc51a12da036 --- /dev/null +++ b/sci-biology/bioperl-network/bioperl-network-1.6.9-r1.ebuild @@ -0,0 +1,26 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +BIOPERL_RELEASE=1.6.9 + +DIST_AUTHOR=CJFIELDS +DIST_NAME=BioPerl-Network +DIST_VERSION=1.006900 +inherit perl-module + +DESCRIPTION="Perl tools for bioinformatics - Analysis of protein-protein interaction networks" +HOMEPAGE="http://www.bioperl.org/" + +SLOT="0" +KEYWORDS="amd64 ~x86" +RESTRICT="test" # bug 298326 + +RDEPEND=" + >=sci-biology/bioperl-${PV} + >=dev-perl/Graph-0.86" +DEPEND="${RDEPEND}" +BDEPEND="dev-perl/Module-Build" + +mydoc="AUTHORS BUGS" diff --git a/sci-biology/bioperl-network/bioperl-network-1.6.9.ebuild b/sci-biology/bioperl-network/bioperl-network-1.6.9.ebuild deleted file mode 100644 index 65a72e06634f..000000000000 --- a/sci-biology/bioperl-network/bioperl-network-1.6.9.ebuild +++ /dev/null @@ -1,31 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI="5" - -BIOPERL_RELEASE=1.6.9 - -MY_PN=BioPerl-Network -MODULE_AUTHOR=CJFIELDS -MODULE_VERSION=1.006900 -inherit perl-module - -DESCRIPTION="Perl tools for bioinformatics - Analysis of protein-protein interaction networks" -HOMEPAGE="http://www.bioperl.org/" - -SLOT="0" -KEYWORDS="amd64 x86" -IUSE="test" -RESTRICT="!test? ( test )" -SRC_TEST="do" - -CDEPEND=">=sci-biology/bioperl-${PV} - >=dev-perl/Graph-0.86" -DEPEND="dev-perl/Module-Build - ${CDEPEND}" -RDEPEND="${CDEPEND}" - -src_install() { - mydoc="AUTHORS BUGS" - perl-module_src_install -} diff --git a/sci-biology/bioperl-network/metadata.xml b/sci-biology/bioperl-network/metadata.xml index 754b8d123313..868dd703d25b 100644 --- a/sci-biology/bioperl-network/metadata.xml +++ b/sci-biology/bioperl-network/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/bioperl-run/bioperl-run-1.6.9-r1.ebuild b/sci-biology/bioperl-run/bioperl-run-1.6.9-r1.ebuild new file mode 100644 index 000000000000..9c32c7eaa5f7 --- /dev/null +++ b/sci-biology/bioperl-run/bioperl-run-1.6.9-r1.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +BIOPERL_RELEASE=1.6.9 + +DIST_AUTHOR=CJFIELDS +DIST_NAME=BioPerl-Run +DIST_VERSION=1.006900 +inherit perl-module + +DESCRIPTION="Perl wrapper modules for key bioinformatics applications" +HOMEPAGE="http://www.bioperl.org/" + +SLOT="0" +KEYWORDS="amd64 ~x86" +IUSE="minimal test" +RESTRICT="test" + +RDEPEND=" + >=sci-biology/bioperl-${BIOPERL_RELEASE} + !minimal? ( + dev-perl/Algorithm-Diff + dev-perl/XML-Twig + dev-perl/IO-String + dev-perl/IPC-Run + dev-perl/File-Sort + )" +DEPEND="${RDEPEND}" +BDEPEND="dev-perl/Module-Build" + +mydoc="AUTHORS BUGS FAQ" diff --git a/sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild b/sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild deleted file mode 100644 index e5dc816bc78a..000000000000 --- a/sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild +++ /dev/null @@ -1,41 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI="5" - -BIOPERL_RELEASE=1.6.9 - -MY_PN=BioPerl-Run -MODULE_AUTHOR=CJFIELDS -MODULE_VERSION=1.006900 -inherit perl-module - -DESCRIPTION="Perl wrapper modules for key bioinformatics applications" -HOMEPAGE="http://www.bioperl.org/" - -SLOT="0" -KEYWORDS="amd64 x86" -IUSE="-minimal test" -#SRC_TEST="do" - -RESTRICT="test" - -CDEPEND=">=sci-biology/bioperl-${BIOPERL_RELEASE} - !minimal? ( - dev-perl/Algorithm-Diff - dev-perl/XML-Twig - dev-perl/IO-String - dev-perl/IPC-Run - dev-perl/File-Sort - )" -DEPEND="dev-perl/Module-Build - ${CDEPEND}" -RDEPEND="${CDEPEND}" - -src_install() { - mydoc="AUTHORS BUGS FAQ" - perl-module_src_install - # TODO: File collision in Bio/ConfigData.pm (a Module::Build internal file) - # with sci-biology/bioperl. Workaround: the "nuke it from orbit" solution :D - #find "${D}" -name '*ConfigData*' -print -delete -} diff --git a/sci-biology/bioperl-run/metadata.xml b/sci-biology/bioperl-run/metadata.xml index 5fccf50862ad..f3bb1f1db1d9 100644 --- a/sci-biology/bioperl-run/metadata.xml +++ b/sci-biology/bioperl-run/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/bioperl/bioperl-1.6.9.ebuild b/sci-biology/bioperl/bioperl-1.6.9-r1.ebuild index d2519a0d30b6..a692fe812401 100644 --- a/sci-biology/bioperl/bioperl-1.6.9.ebuild +++ b/sci-biology/bioperl/bioperl-1.6.9-r1.ebuild @@ -1,25 +1,25 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI="5" +EAPI=8 -MY_PN=BioPerl -MODULE_AUTHOR=CJFIELDS -MODULE_VERSION=1.6.901 +DIST_AUTHOR=CJFIELDS +DIST_NAME=BioPerl +DIST_VERSION=1.6.901 inherit perl-module SUBPROJECTS="+db +network +run" -MIN_PV=$PV +MIN_PV="${PV}" DESCRIPTION="Perl tools for bioinformatics - Core modules" HOMEPAGE="http://www.bioperl.org/" -SLOT="0" -KEYWORDS="amd64 x86" -IUSE="-minimal graphviz sqlite ${SUBPROJECTS}" +SLOT="0" +KEYWORDS="amd64 ~x86" +IUSE="minimal graphviz sqlite ${SUBPROJECTS}" REQUIRED_USE="minimal? ( !graphviz )" -CDEPEND=" +RDEPEND=" dev-perl/libwww-perl !minimal? ( dev-perl/Algorithm-Munkres @@ -54,14 +54,11 @@ CDEPEND=" ) graphviz? ( dev-perl/GraphViz ) sqlite? ( dev-perl/DBD-SQLite )" -DEPEND="dev-perl/Module-Build - ${CDEPEND}" -RDEPEND="${CDEPEND}" -PDEPEND="db? ( >=sci-biology/bioperl-db-${MIN_PV} ) +DEPEND="${RDEPEND}" +PDEPEND=" + db? ( >=sci-biology/bioperl-db-${MIN_PV} ) network? ( >=sci-biology/bioperl-network-${MIN_PV} ) run? ( >=sci-biology/bioperl-run-${MIN_PV} )" +BDEPEND="dev-perl/Module-Build" -src_install() { - mydoc="AUTHORS BUGS FAQ" - perl-module_src_install -} +mydoc="AUTHORS BUGS FAQ" diff --git a/sci-biology/bioperl/metadata.xml b/sci-biology/bioperl/metadata.xml index 1cd5db0e9619..20c00d4288ef 100644 --- a/sci-biology/bioperl/metadata.xml +++ b/sci-biology/bioperl/metadata.xml @@ -1,14 +1,14 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> <use> - <flag name="run">Install sci-biology/bioperl-run</flag> - <flag name="network">Install sci-biology/bioperl-run</flag> - <flag name="db">Install sci-biology/bioperl-run</flag> + <flag name="run">Install <pkg>sci-biology/bioperl-run</pkg></flag> + <flag name="network">Install <pkg>sci-biology/bioperl-run</pkg></flag> + <flag name="db">Install <pkg>sci-biology/bioperl-run</pkg></flag> </use> <upstream> <remote-id type="cpan">BioPerl</remote-id> diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest index ee3ffae9c3f3..0c16022dea2c 100644 --- a/sci-biology/biopython/Manifest +++ b/sci-biology/biopython/Manifest @@ -1 +1 @@ -DIST biopython-1.73.tar.gz 15715102 BLAKE2B b2c40f9ed02681f19607c88f91b469784985acefc6e81770a54e5c13c715915344bc7fd72e4a88ae50879a2463965ac6d0d04c6d263908887028d1e065620b95 SHA512 d067330ef8e25ca6881b56f4e5e89e16a816c89760473e2f32a6236ab202f805294650aa944f0b098987425bcb65727317da7a26deb4d4937f02b00123ea9a8f +DIST biopython-1.81.tar.gz 19324875 BLAKE2B be3a85f5b60638987d6186af498411b494f8d27389f24cd1b9e658bc6b1a29c799ec8b20a9ac0b955c6d4c239706f4dbb5b75f6d56908f63d731b1d56c9fd587 SHA512 1595fad6631bfb6cf4e1a92ed72e6093e2a0c24f3c0bd4182267ec9742fb03dff16099eedde139598aa6b5b8380bbac9e48246cb9ab8b44109333d60adfd00ed diff --git a/sci-biology/biopython/biopython-1.73.ebuild b/sci-biology/biopython/biopython-1.81-r1.ebuild index 94acdfc2a2cb..f4fd86ba3ffb 100644 --- a/sci-biology/biopython/biopython-1.73.ebuild +++ b/sci-biology/biopython/biopython-1.81-r1.ebuild @@ -1,19 +1,20 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{6,7} ) -inherit distutils-r1 eutils +PYTHON_COMPAT=( python3_{9..11} ) +DISTUTILS_USE_PEP517="setuptools" +DISTUTILS_EXT=1 + +inherit distutils-r1 optfeature pypi DESCRIPTION="Python modules for computational molecular biology" HOMEPAGE="https://www.biopython.org/ https://pypi.org/project/biopython/" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" LICENSE="HPND" SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="" RDEPEND=" dev-python/matplotlib[${PYTHON_USEDEP}] @@ -23,17 +24,18 @@ RDEPEND=" dev-python/pygraphviz[${PYTHON_USEDEP}] >=dev-python/reportlab-3.5.13-r1[${PYTHON_USEDEP}] dev-python/pydot[${PYTHON_USEDEP}]" -DEPEND="${RDEPEND} - dev-python/setuptools[${PYTHON_USEDEP}] - sys-devel/flex" +DEPEND="${RDEPEND}" +BDEPEND="app-alternatives/lex" DOCS=( {CONTRIB,DEPRECATED,NEWS,README}.rst Doc/. ) +PATCHES=( + "${FILESDIR}/${P}-reportlab4.patch" + "${FILESDIR}/${P}-python3.12.patch" +) + python_test() { - distutils_install_for_testing - cp -r "${S}"/{Doc,Tests} "${TEST_DIR}"/lib/ || die - cd "${TEST_DIR}"/lib/Tests || die - rm test_BioSQL_{psycopg2.py,MySQLdb.py,mysql_connector.py} || die + cd Tests || die "${EPYTHON}" run_tests.py --offline --verbose || die } @@ -48,10 +50,10 @@ python_install_all() { } pkg_postinst() { - elog "For database support you need to install:" - optfeature "MySQL" dev-python/mysql-python - optfeature "PostgreSQL" dev-python/psycopg + optfeature_header "For database support you need to install:" + optfeature "MySQL database support" dev-python/mysqlclient + optfeature "PostgreSQL database support" dev-python/psycopg:2 - elog "Some applications need extra packages:" + optfeature_header "Some applications need extra packages:" optfeature "EMBOSS (The European Molecular Biology Open Software Suite)" sci-biology/emboss } diff --git a/sci-biology/biopython/files/biopython-1.81-python3.12.patch b/sci-biology/biopython/files/biopython-1.81-python3.12.patch new file mode 100644 index 000000000000..8f903a4a39bd --- /dev/null +++ b/sci-biology/biopython/files/biopython-1.81-python3.12.patch @@ -0,0 +1,11 @@ +--- a/Tests/test_Entrez.orig.py 2023-02-13 04:07:42.000000000 +0100 ++++ b/Tests/test_Entrez.py 2023-06-30 14:42:58.177365639 +0200 +@@ -126,7 +126,7 @@ + :type params: dict + :param expected: Expected set of IDs, as colleciton of strings. + """ +- testcase.assertEquals(len(params["id"]), 1) ++ testcase.assertEqual(len(params["id"]), 1) + ids_str = params["id"][0] + # Compare up to ordering + testcase.assertCountEqual(ids_str.split(","), expected) diff --git a/sci-biology/biopython/files/biopython-1.81-reportlab4.patch b/sci-biology/biopython/files/biopython-1.81-reportlab4.patch new file mode 100644 index 000000000000..ef1994553614 --- /dev/null +++ b/sci-biology/biopython/files/biopython-1.81-reportlab4.patch @@ -0,0 +1,29 @@ +From 74fdf49ade95157c3c4b23a95831925be4899223 Mon Sep 17 00:00:00 2001 +From: Peter Cock <p.j.a.cock@googlemail.com> +Date: Mon, 5 Jun 2023 12:39:59 +0100 +Subject: [PATCH] Skip if ReportLab bitmap output module missing + +Would like to skip this earlier, but not so +easy in ReportLab v4 with a choice of backends +--- + Tests/test_GraphicsBitmaps.py | 5 ++++- + 1 file changed, 4 insertions(+), 1 deletion(-) + +diff --git a/Tests/test_GraphicsBitmaps.py b/Tests/test_GraphicsBitmaps.py +index 2ffdfb3dd71..76615a2fd1d 100644 +--- a/Tests/test_GraphicsBitmaps.py ++++ b/Tests/test_GraphicsBitmaps.py +@@ -111,9 +111,12 @@ def real_test(): + "Check the fonts needed by ReportLab if you want " + "bitmaps from Bio.Graphics\n" + str(err) + ) from None ++ elif str(err).startswith("cannot import desired renderPM backend rlPyCairo"): ++ raise MissingExternalDependencyError( ++ "Reportlab module rlPyCairo unavailable\n" + str(err) ++ ) from None + else: + raise +- + return True + + diff --git a/sci-biology/biopython/metadata.xml b/sci-biology/biopython/metadata.xml index 959160fe46b1..cd20d153fc2e 100644 --- a/sci-biology/biopython/metadata.xml +++ b/sci-biology/biopython/metadata.xml @@ -1,8 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="pypi">biopython</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/bioruby/Manifest b/sci-biology/bioruby/Manifest deleted file mode 100644 index 1acf988b81a4..000000000000 --- a/sci-biology/bioruby/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST bio-1.5.1.gem 1445376 BLAKE2B 4de704293ed1c4dee7edc9c86df4ddd35f66eb4433a339fadb58c3f877206e240a8b1dfe6aa8ccd92f0edf9d0f28825cc2b58e33f817fec6bab39e3162f179cf SHA512 822ac6c3d85847193fc1992087abc868e4d1a7cfca82da6ab1830af2927a2a582c3993bc681e129a6aac224ed1cb0b33056d8cc02d3e36d68c9d6a4153c321ca -DIST bio-1.5.2.gem 1447424 BLAKE2B 6377f7c546faef188d43b1e612f1924f5ab2db3a0017fac1f1b124b6cdf7caf4b66dde53d957d0a733601e3c928f0a84b18ae9da930f4a4908ab236f9365d385 SHA512 a0c4be950ef2983f07e8b9d0ac217310d80d91139ca0edb0263d8ae0a35e62fc07a21861ab26d8bace40003f0d9de4dce1be8f02c7d6d0f4afe3eb3debe3d5cd diff --git a/sci-biology/bioruby/bioruby-1.5.1.ebuild b/sci-biology/bioruby/bioruby-1.5.1.ebuild deleted file mode 100644 index 036b3be29b37..000000000000 --- a/sci-biology/bioruby/bioruby-1.5.1.ebuild +++ /dev/null @@ -1,22 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -USE_RUBY="ruby23 ruby24" - -RUBY_FAKEGEM_NAME="bio" - -RUBY_FAKEGEM_EXTRAINSTALL="etc" - -inherit ruby-fakegem - -DESCRIPTION="An integrated environment for bioinformatics using the Ruby language" -LICENSE="Ruby" -HOMEPAGE="http://bioruby.org/" - -SLOT="0" -IUSE="" -KEYWORDS="amd64 ~ppc x86" - -ruby_add_rdepend "dev-ruby/libxml" diff --git a/sci-biology/bioruby/bioruby-1.5.2.ebuild b/sci-biology/bioruby/bioruby-1.5.2.ebuild deleted file mode 100644 index 7977f4073da5..000000000000 --- a/sci-biology/bioruby/bioruby-1.5.2.ebuild +++ /dev/null @@ -1,22 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -USE_RUBY="ruby23 ruby24" - -RUBY_FAKEGEM_NAME="bio" - -RUBY_FAKEGEM_EXTRAINSTALL="etc" - -inherit ruby-fakegem - -DESCRIPTION="An integrated environment for bioinformatics using the Ruby language" -LICENSE="Ruby" -HOMEPAGE="http://bioruby.org/" - -SLOT="0" -IUSE="" -KEYWORDS="amd64 ~ppc x86" - -ruby_add_rdepend "dev-ruby/libxml" diff --git a/sci-biology/bioruby/metadata.xml b/sci-biology/bioruby/metadata.xml deleted file mode 100644 index 8417d1580d40..000000000000 --- a/sci-biology/bioruby/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/biosql/biosql-1.0.1-r1.ebuild b/sci-biology/biosql/biosql-1.0.1-r2.ebuild index 6508d6a3a2e8..838f3b443ed8 100644 --- a/sci-biology/biosql/biosql-1.0.1-r1.ebuild +++ b/sci-biology/biosql/biosql-1.0.1-r2.ebuild @@ -1,15 +1,15 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 DESCRIPTION="A generic bioinformatics relational database model" -HOMEPAGE="http://www.biosql.org/" -SRC_URI="http://biosql.org/DIST/${P}.tar.bz2" +HOMEPAGE="https://biosql.org/" +SRC_URI="https://biosql.org/DIST/${P}.tar.bz2" LICENSE="LGPL-3" SLOT="0" -KEYWORDS="amd64 x86" +KEYWORDS="amd64 ~x86" IUSE="mysql postgres" # WARNING: bioperl-db is claimed to be incompatible with >=postgresql-8.3 (see INSTALL) @@ -22,7 +22,7 @@ RDEPEND=" dev-lang/perl" src_install() { - insinto /usr/share/${PN} + insinto /usr/share/biosql doins -r sql scripts/. dodoc Changes README Release.txt doc/*.pdf @@ -38,6 +38,6 @@ src_install() { pkg_postinst() { elog elog "Please read the BioSQL schema installation instructions in" - elog "${EROOT%/}/usr/share/doc/${PF} to begin using the schema." + elog "${EROOT}/usr/share/doc/${PF} to begin using the schema." elog } diff --git a/sci-biology/biosql/metadata.xml b/sci-biology/biosql/metadata.xml index 959160fe46b1..ccdff086e20b 100644 --- a/sci-biology/biosql/metadata.xml +++ b/sci-biology/biosql/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/blat/blat-34-r2.ebuild b/sci-biology/blat/blat-34-r3.ebuild index e10bc367a311..18c4128ec578 100644 --- a/sci-biology/blat/blat-34-r2.ebuild +++ b/sci-biology/blat/blat-34-r3.ebuild @@ -1,33 +1,33 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit toolchain-funcs -MY_PN=${PN}Src +MY_PN="${PN}Src" DESCRIPTION="The BLAST-Like Alignment Tool, a fast genomic sequence aligner" HOMEPAGE="http://www.cse.ucsc.edu/~kent/" SRC_URI="http://www.soe.ucsc.edu/~kent/src/${MY_PN}${PV}.zip" +S="${WORKDIR}/${MY_PN}" LICENSE="blat" SLOT="0" KEYWORDS="~amd64 ~x86" -IUSE="" -RDEPEND="" -DEPEND="app-arch/unzip" +BDEPEND="app-arch/unzip" -S=${WORKDIR}/${MY_PN} - -PATCHES=( "${FILESDIR}"/${PN}-34-fix-build-system.patch ) +PATCHES=( + "${FILESDIR}"/${PN}-34-fix-build-system.patch + "${FILESDIR}"/${PN}-34-fno-common.patch +) src_compile() { tc-export AR CC export HOME="${S}" - export MACHTYPE=$(tc-arch) + export MACHTYPE="$(tc-arch)" [[ ${MACHTYPE} == "x86" ]] && MACHTYPE="i386" mkdir -p bin/${MACHTYPE} || die @@ -35,7 +35,7 @@ src_compile() { } src_install() { - export MACHTYPE=$(tc-arch) + export MACHTYPE="$(tc-arch)" [[ ${MACHTYPE} == "x86" ]] && MACHTYPE="i386" dobin bin/${MACHTYPE}/* diff --git a/sci-biology/blat/files/blat-34-fix-build-system.patch b/sci-biology/blat/files/blat-34-fix-build-system.patch index 361149cc1211..9aca3f841315 100644 --- a/sci-biology/blat/files/blat-34-fix-build-system.patch +++ b/sci-biology/blat/files/blat-34-fix-build-system.patch @@ -1,34 +1,36 @@ --- a/blat/makefile +++ b/blat/makefile -@@ -7,7 +7,7 @@ +@@ -7,8 +7,7 @@ O = blat.o blat: $O $(MYLIBS) - ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/blat $O $(MYLIBS) $L -+ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/blat $O $(MYLIBS) $L - ${STRIP} ${BINDIR}/blat${EXE} +- ${STRIP} ${BINDIR}/blat${EXE} ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/blat $O $(MYLIBS) $L all: + cd ../lib && ${MAKE} --- a/gfClient/makefile +++ b/gfClient/makefile -@@ -8,5 +8,5 @@ +@@ -8,5 +8,4 @@ X = gfClient gfClient: $O $(MYLIBS) - ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L -+ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L - ${STRIP} ${BINDIR}/$X${EXE} +- ${STRIP} ${BINDIR}/$X${EXE} ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L --- a/gfServer/makefile +++ b/gfServer/makefile -@@ -8,7 +8,7 @@ +@@ -8,8 +8,7 @@ X = gfServer gfServer: $O $(MYLIBS) - ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L -+ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L - ${STRIP} ${BINDIR}/$X${EXE} +- ${STRIP} ${BINDIR}/$X${EXE} ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L test: + ${MKDIR} tests/output --- a/hg/pslPretty/makefile +++ b/hg/pslPretty/makefile @@ -8,7 +8,7 @@ @@ -36,7 +38,7 @@ pslPretty: $O $(MYLIBS) - ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslPretty $O $(MYLIBS) $L -+ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/pslPretty $O $(MYLIBS) $L ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/pslPretty $O $(MYLIBS) $L test:: testRna testDnax @@ -47,7 +49,7 @@ pslReps: $O $(MYLIBS) - ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslReps${EXE} $O $(MYLIBS) $L -+ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/pslReps${EXE} $O $(MYLIBS) $L ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/pslReps${EXE} $O $(MYLIBS) $L lib: cd ../../lib && ${MAKE} @@ -58,10 +60,20 @@ pslSort: $O $(MYLIBS) - ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslSort $O $(MYLIBS) $L -+ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/pslSort $O $(MYLIBS) $L ++ ${CC} ${LDFLAGS} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/pslSort $O $(MYLIBS) $L lib: +--- a/inc/cgi_build_rules.mk ++++ b/inc/cgi_build_rules.mk +@@ -12,7 +12,6 @@ + mv $A${EXE} ${CGI_BIN}-beta/$A + + strip:: compile +- ${STRIP} $A${EXE} + chmod g+w $A${EXE} + chmod a+rx $A${EXE} + --- a/inc/common.mk +++ b/inc/common.mk @@ -1,20 +1,15 @@ @@ -87,15 +99,24 @@ endif endif # Apply the stronger checks to all code on our development machine: -@@ -37,7 +32,7 @@ +@@ -36,9 +31,6 @@ + BINDIR = ${HOME}/bin/${MACHTYPE} endif MKDIR=mkdir -p - ifeq (${STRIP},) +-ifeq (${STRIP},) - STRIP=strip -+ STRIP=true - endif +-endif CVS=cvs + # portable naming of compiled executables: add ".exe" if compiled on +@@ -55,6 +47,6 @@ + STRINGIFY = ${BINDIR}/stringify + + %.o: %.c +- ${CC} ${COPT} ${CFLAGS} ${HG_DEFS} ${HG_WARN} ${HG_INC} ${XINC} -o $@ -c $< ++ ${CC} ${CPPFLAGS} ${CFLAGS} ${HG_DEFS} ${HG_WARN} ${HG_INC} ${XINC} -o $@ -c $< + + --- a/jkOwnLib/makefile +++ b/jkOwnLib/makefile @@ -9,7 +9,7 @@ @@ -107,6 +128,15 @@ ../lib/$(MACHTYPE): mkdir ../lib/$(MACHTYPE) +--- a/jkOwnLib/tests/freen/makefile ++++ b/jkOwnLib/tests/freen/makefile +@@ -7,5 +7,5 @@ + O = freen.o + + hello: freen.o +- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/freen $O $(MYLIBS) $L ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/freen $O $(MYLIBS) $L + --- a/lib/makefile +++ b/lib/makefile @@ -32,7 +32,7 @@ @@ -118,6 +148,102 @@ $(MACHTYPE): mkdir $(MACHTYPE) +--- a/lib/tests/makefile ++++ b/lib/tests/makefile +@@ -14,22 +14,19 @@ + ${MKDIR} output ${BIN_DIR} + + errCatchTest: errCatchTest.o ${MYLIBS} mkdirs +- ${CC} ${COPT} -o ${BIN_DIR}/errCatchTest errCatchTest.o ${MYLIBS} $L +- ${STRIP} ${BIN_DIR}/errCatchTest${EXE} ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/errCatchTest errCatchTest.o ${MYLIBS} $L + ${BIN_DIR}/errCatchTest secret > output/errCatch.good + diff expected/errCatch.good output/errCatch.good + ${BIN_DIR}/errCatchTest bad > output/errCatch.bad + diff expected/errCatch.bad output/errCatch.bad + + htmlExpandUrlTest: htmlExpandUrlTest.o ${MYLIBS} mkdirs +- ${CC} ${COPT} -o ${BIN_DIR}/htmlExpandUrlTest htmlExpandUrlTest.o ${MYLIBS} $L +- ${STRIP} ${BIN_DIR}/htmlExpandUrlTest${EXE} ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/htmlExpandUrlTest htmlExpandUrlTest.o ${MYLIBS} $L + ${BIN_DIR}/htmlExpandUrlTest > output/htmlExpandUrlTest 2>&1 + diff expected/htmlExpandUrlTest output/htmlExpandUrlTest + + htmlPageTest: htmlPageTest.o ${MYLIBS} mkdirs +- ${CC} ${COPT} -o ${BIN_DIR}/htmlPageTest htmlPageTest.o ${MYLIBS} $L +- ${STRIP} ${BIN_DIR}/htmlPageTest${EXE} ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/htmlPageTest htmlPageTest.o ${MYLIBS} $L + ${BIN_DIR}/htmlPageTest input/google.html > output/google.out + diff expected/google.out output/google.out + +@@ -86,20 +83,20 @@ + diff -b expected/$@.err output/$@.err + + ${BIN_DIR}/pipelineTester: mkdirs pipelineTester.o ${MYLIBS} +- ${CC} ${COPT} -o ${BIN_DIR}/pipelineTester pipelineTester.o ${MYLIBS} $L ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/pipelineTester pipelineTester.o ${MYLIBS} $L + + + dyStringTest: ${BIN_DIR}/dyStringTester mkdirs + ${BIN_DIR}/dyStringTester + + ${BIN_DIR}/dyStringTester: mkdirs dyStringTester.o ${MYLIBS} +- ${CC} ${COPT} -o ${BIN_DIR}/dyStringTester dyStringTester.o ${MYLIBS} $L ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/dyStringTester dyStringTester.o ${MYLIBS} $L + + + mimeTests: mime1 mime2 mime3 mime4 mimeBin mime5 mimeAltHead mimeAutoBoundary mimeBlat + + ${BIN_DIR}/mimeTester: mkdirs mimeTester.o ${MYLIBS} +- ${CC} ${COPT} -o ${BIN_DIR}/mimeTester mimeTester.o ${MYLIBS} $L ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/mimeTester mimeTester.o ${MYLIBS} $L + + + mime1: ${BIN_DIR}/mimeTester mkdirs +@@ -142,7 +139,7 @@ + ${BIN_DIR}/mimeTester -sizeSeries=3000 + + ${BIN_DIR}/htmlMimeTest: mkdirs htmlMimeTest.o ${MYLIBS} +- ${CC} ${COPT} -o ${BIN_DIR}/htmlMimeTest htmlMimeTest.o ${MYLIBS} $L ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/htmlMimeTest htmlMimeTest.o ${MYLIBS} $L + + htmlMime1: ${BIN_DIR}/htmlMimeTest mkdirs + ${BIN_DIR}/htmlMimeTest http://hgwdev.cse.ucsc.edu/cgi-bin/hgBlat input/htmlMime.txt 3490 3502 > output/$@.out +@@ -152,7 +149,7 @@ + base64Tests: base64Encode base64Decode + + ${BIN_DIR}/testBase64: mkdirs testBase64.o ${MYLIBS} +- ${CC} ${COPT} -o ${BIN_DIR}/testBase64 testBase64.o ${MYLIBS} $L ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/testBase64 testBase64.o ${MYLIBS} $L + + base64Encode: ${BIN_DIR}/testBase64 mkdirs + ${BIN_DIR}/testBase64 'My Test String' > output/$@.out +@@ -167,7 +164,7 @@ + quotedPTests: quotedPEncode quotedPDecode + + ${BIN_DIR}/testQuotedP: mkdirs testQuotedP.o ${MYLIBS} +- ${CC} ${COPT} -o ${BIN_DIR}/testQuotedP testQuotedP.o ${MYLIBS} $L ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/testQuotedP testQuotedP.o ${MYLIBS} $L + + quotedPEncode: ${BIN_DIR}/testQuotedP mkdirs + ${BIN_DIR}/testQuotedP 'taxes are quite high ' > output/$@.out +@@ -178,14 +175,14 @@ + diff expected/$@.out output/$@.out + + ${BIN_DIR}/mimeDecodeTest: mkdirs mimeDecodeTest.o ${MYLIBS} +- ${CC} ${COPT} -o ${BIN_DIR}/mimeDecodeTest mimeDecodeTest.o ${MYLIBS} $L ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/mimeDecodeTest mimeDecodeTest.o ${MYLIBS} $L + + mimeDecodeTest: ${BIN_DIR}/mimeDecodeTest mkdirs + ${BIN_DIR}/mimeDecodeTest -cid -autoBoundary output < input/$@.txt + diff expected/noName1.html output/noName1.html + + ${BIN_DIR}/safeTester: mkdirs safeTester.o ${MYLIBS} +- ${CC} ${COPT} -o ${BIN_DIR}/safeTester safeTester.o ${MYLIBS} $L ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/safeTester safeTester.o ${MYLIBS} $L + + safeTest: ${BIN_DIR}/safeTester mkdirs + ${BIN_DIR}/safeTester --- a/makefile +++ b/makefile @@ -1,18 +1,18 @@ @@ -160,18 +286,19 @@ faToNib: $O $(MYLIBS) - ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/faToNib $O $(MYLIBS) $L -+ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/faToNib $O $(MYLIBS) $L ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/faToNib $O $(MYLIBS) $L --- a/utils/faToTwoBit/makefile +++ b/utils/faToTwoBit/makefile -@@ -7,7 +7,7 @@ +@@ -7,8 +7,7 @@ O = faToTwoBit.o faToTwoBit: $O ${MYLIBS} - ${CC} ${COPT} -o ${BINDIR}/faToTwoBit $O ${MYLIBS} $L -+ ${CC} ${COPT} ${LDFLAGS} -o ${BINDIR}/faToTwoBit $O ${MYLIBS} $L - ${STRIP} ${BINDIR}/faToTwoBit${EXE} +- ${STRIP} ${BINDIR}/faToTwoBit${EXE} ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/faToTwoBit $O ${MYLIBS} $L clean: + rm -f $O --- a/utils/nibFrag/makefile +++ b/utils/nibFrag/makefile @@ -4,7 +4,7 @@ @@ -179,29 +306,43 @@ nibFrag: $(O) - ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/nibFrag $O ../../lib/$(MACHTYPE)/jkweb.a -+ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/nibFrag $O ../../lib/$(MACHTYPE)/jkweb.a ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/nibFrag $O ../../lib/$(MACHTYPE)/jkweb.a --- a/utils/twoBitInfo/makefile +++ b/utils/twoBitInfo/makefile -@@ -7,7 +7,7 @@ +@@ -7,8 +7,7 @@ O = twoBitInfo.o twoBitInfo: $O ${MYLIBS} - ${CC} ${COPT} -o ${BINDIR}/twoBitInfo $O ${MYLIBS} $L -+ ${CC} ${COPT} ${LDFLAGS} -o ${BINDIR}/twoBitInfo $O ${MYLIBS} $L - ${STRIP} ${BINDIR}/twoBitInfo${EXE} +- ${STRIP} ${BINDIR}/twoBitInfo${EXE} ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/twoBitInfo $O ${MYLIBS} $L clean: + rm -f $O --- a/utils/twoBitToFa/makefile +++ b/utils/twoBitToFa/makefile -@@ -8,7 +8,7 @@ +@@ -8,8 +8,7 @@ O = twoBitToFa.o twoBitToFa: $O ${MYLIBS} - ${CC} ${COPT} -o ${BINDIR}/twoBitToFa $O ${MYLIBS} $L -+ ${CC} ${COPT} ${LDFLAGS} -o ${BINDIR}/twoBitToFa $O ${MYLIBS} $L - #${STRIP} ${BINDIR}/twoBitToFa${EXE} +- #${STRIP} ${BINDIR}/twoBitToFa${EXE} ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/twoBitToFa $O ${MYLIBS} $L clean: + rm -f $O +--- a/webBlat/makefile ++++ b/webBlat/makefile +@@ -7,8 +7,7 @@ + O = webBlat.o + + webBlat: $O ${MYLIBS} +- ${CC} ${COPT} -o webBlat $O ${MYLIBS} $L +- ${STRIP} webBlat${EXE} ++ ${CC} ${LDFLAGS} ${CFLAGS} -o webBlat $O ${MYLIBS} $L + + installOsX: webBlat + cp webBlat /Library/WebServer/CGI-Executables diff --git a/sci-biology/blat/files/blat-34-fno-common.patch b/sci-biology/blat/files/blat-34-fno-common.patch new file mode 100644 index 000000000000..63a49cf81299 --- /dev/null +++ b/sci-biology/blat/files/blat-34-fno-common.patch @@ -0,0 +1,11 @@ +--- a/inc/htmshell.h ++++ b/inc/htmshell.h +@@ -85,7 +85,7 @@ void htmlBadVar(char *varName); + void htmlImage(char *fileName, int width, int height); + /* Display centered image file. */ + +-jmp_buf htmlRecover; /* Error recovery jump. Exposed for cart's use. */ ++extern jmp_buf htmlRecover; /* Error recovery jump. Exposed for cart's use. */ + + void htmlVaWarn(char *format, va_list args); + /* Write an error message. (Generally you just call warn() or errAbort(). diff --git a/sci-biology/blat/metadata.xml b/sci-biology/blat/metadata.xml index 959160fe46b1..ccdff086e20b 100644 --- a/sci-biology/blat/metadata.xml +++ b/sci-biology/blat/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest index 824c7439adc1..274e5e7b9fb6 100644 --- a/sci-biology/bowtie/Manifest +++ b/sci-biology/bowtie/Manifest @@ -1,2 +1,2 @@ -DIST bowtie-1.1.2-src.zip 7713258 BLAKE2B ac10aca905099b5a70d3fab6f90e2dc4713bf7b460d027abf89a6ef6103979724e70b2915a86ffa571b59dcd9df768c80be1846cccd08f7f85dd402ce64c0cb0 SHA512 3d3d69bc3a865bb577b5a91440215d0d5b606c7a8751d565e606e36adbfbdef695b1718ae81cd3e2682a39ca7784c4d00976441e7618264ad99b04c7f53c36e8 -DIST bowtie2-2.2.9-source.zip 5734235 BLAKE2B ec48e09fe05403d1085bb4e0c6ef1325b8912da0a8c942061c34f3381c6dd7ccdcc64c4bcdbb18c1da84ac57e1e34cc866fe79809c33c2769a8d75ecde7d0846 SHA512 ead8f7641f3231638d986f9e500bc4ec7afe1e542048465bfcc2e93e2b2d2e499f0dd8aa5c1e3e21df285c9d195b187682eb7e12be4a408f6c50fb97c0e0a205 +DIST bowtie2-2.4.4-source.zip 10515984 BLAKE2B be4ceb9d3155d2a9a1f580e5032251b04b89ce0c8c9c89fc3551b34fe3bd71a683362488be7aad6daef24734c6f95c19223f20e67f198f745c4432381243039c SHA512 1b5dadd7e41b90bb9b05f50bfa171fe219cfd03aa8bb6f800de4baaffeb975eef6efc4fb8b49cb0d18833f74a1741cbe1556b87388f59188e04a55dcee6a02da +DIST bowtie2-2.5.1-source.zip 10528859 BLAKE2B 9dc22bfef4b3a1cfaa606cb235acd1d7688015678d82e8ca80d3d7cf269e1f45d6cb60bc29eb334fb6f0c25d5afd8202e83a83e53668c8965857b8885d2692c8 SHA512 31cc642e318ab50e7ef6035a9c2095024d46d92a317011ed0c3ac3ccb3d427a13bf724d0158d29a4f1e07115ddcb85229b95bcb2d4351164fcadd6568293565f diff --git a/sci-biology/bowtie/bowtie-1.1.2-r1.ebuild b/sci-biology/bowtie/bowtie-1.1.2-r1.ebuild deleted file mode 100644 index d8b607f870fc..000000000000 --- a/sci-biology/bowtie/bowtie-1.1.2-r1.ebuild +++ /dev/null @@ -1,74 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit flag-o-matic toolchain-funcs - -DESCRIPTION="Popular short read aligner for Next-generation sequencing data" -HOMEPAGE="http://bowtie-bio.sourceforge.net/" -SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip" - -LICENSE="Artistic" -SLOT="1" -KEYWORDS="~amd64 ~x86 ~x64-macos" - -IUSE="examples +tbb" - -RDEPEND="tbb? ( dev-cpp/tbb )" -DEPEND="${RDEPEND} - sci-biology/seqan:1.4 - app-arch/unzip" - -DOCS=( AUTHORS NEWS TUTORIAL doc/README ) -HTML_DOCS=( doc/{manual.html,style.css} ) - -PATCHES=( - "${FILESDIR}/${P}-_ContextLss-1.1-1.4.patch" - "${FILESDIR}/${P}-fix-setBegin-call.patch" - "${FILESDIR}/${P}-seqan-popcount.patch" - "${FILESDIR}/${P}-seqan-rename-ChunkPool.patch" - "${FILESDIR}/${P}-seqan-rename-fill-to-resize.patch" - "${FILESDIR}/${P}-spelling.patch" - "${FILESDIR}/${P}-tbb-tinythread-missing.patch" - "${FILESDIR}/${P}-unbundle-seqan.patch" -) - -src_prepare() { - default - - # remove bundled libraries, use system seqan 1.4 - rm -rf SeqAn-1.1/ third_party/ || die - - # innocuous non-security flags, prevent log pollution - append-cxxflags \ - -Wno-unused-local-typedefs \ - -Wno-unused-but-set-variable \ - -Wno-unused-variable -} - -src_compile() { - emake \ - CC="$(tc-getCC)" \ - CPP="$(tc-getCXX)" \ - CFLAGS="" \ - CXXFLAGS="" \ - EXTRA_FLAGS="${LDFLAGS}" \ - RELEASE_FLAGS="${CXXFLAGS}" \ - WITH_TBB="$(usex tbb 1 0)" -} - -src_install() { - dobin ${PN} ${PN}-* - - exeinto /usr/libexec/${PN} - doexe scripts/* - - newman MANUAL ${PN}.1 - einstalldocs - - if use examples; then - insinto /usr/share/${PN} - doins -r genomes indexes - fi -} diff --git a/sci-biology/bowtie/bowtie-2.2.9.ebuild b/sci-biology/bowtie/bowtie-2.2.9.ebuild deleted file mode 100644 index 0bacb8ca25d7..000000000000 --- a/sci-biology/bowtie/bowtie-2.2.9.ebuild +++ /dev/null @@ -1,61 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit toolchain-funcs - -DESCRIPTION="Popular short read aligner for Next-generation sequencing data" -HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/" -SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip" - -LICENSE="GPL-3" -SLOT="2" -KEYWORDS="~amd64 ~x86" - -IUSE="examples cpu_flags_x86_sse2 +tbb" - -RDEPEND="dev-lang/perl - tbb? ( dev-cpp/tbb )" -DEPEND="${RDEPEND} - app-arch/unzip" - -S="${WORKDIR}/${PN}2-${PV}" - -DOCS=( AUTHORS NEWS TUTORIAL ) -HTML_DOCS=( doc/{manual.html,style.css} ) -PATCHES=( "${FILESDIR}/${PN}-2.2.9-fix-c++14.patch" ) - -pkg_pretend() { - if ! use cpu_flags_x86_sse2 ; then - eerror "This package requires a CPU supporting the SSE2 instruction set." - die "SSE2 support missing" - fi -} - -src_compile() { - emake \ - CC="$(tc-getCC)" \ - CPP="$(tc-getCXX)" \ - CXX="$(tc-getCXX)" \ - CFLAGS="" \ - CXXFLAGS="" \ - EXTRA_FLAGS="${LDFLAGS}" \ - RELEASE_FLAGS="${CXXFLAGS} -msse2" \ - WITH_TBB="$(usex tbb 1 0)" -} - -src_install() { - dobin ${PN}2 ${PN}2-* - - exeinto /usr/libexec/${PN}2 - doexe scripts/* - - newman MANUAL ${PN}2.1 - einstalldocs - - if use examples; then - insinto /usr/share/${PN}2 - doins -r example - fi -} diff --git a/sci-biology/bowtie/bowtie-2.4.4.ebuild b/sci-biology/bowtie/bowtie-2.4.4.ebuild new file mode 100644 index 000000000000..de69bfadd825 --- /dev/null +++ b/sci-biology/bowtie/bowtie-2.4.4.ebuild @@ -0,0 +1,55 @@ +# Copyright 2021-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_10 ) + +inherit python-single-r1 toolchain-funcs + +DESCRIPTION="Popular short read aligner for Next-generation sequencing data" +HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/" +SRC_URI="https://downloads.sourceforge.net/project/${PN}-bio/bowtie2/${PV}/bowtie2-${PV}-source.zip" +S="${WORKDIR}/${PN}2-${PV}" + +LICENSE="GPL-3" +SLOT="2" +KEYWORDS="~amd64 ~x86" +IUSE="cpu_flags_x86_sse2 examples" +REQUIRED_USE="cpu_flags_x86_sse2 ${PYTHON_REQUIRED_USE}" + +RDEPEND=" + ${PYTHON_DEPS} + dev-lang/perl + sys-libs/zlib" +DEPEND="${RDEPEND}" +BDEPEND="app-arch/unzip" + +src_compile() { + emake \ + CXX="$(tc-getCXX)" \ + CXXFLAGS="" \ + CPPFLAGS="${CPPFLAGS}" \ + EXTRA_FLAGS="${LDFLAGS}" \ + RELEASE_FLAGS="${CXXFLAGS} -msse2" +} + +src_install() { + dobin bowtie2 bowtie2-* + + exeinto /usr/libexec/bowtie2 + doexe scripts/* + + HTML_DOCS=( doc/{manual.html,style.css} ) + einstalldocs + dodoc TUTORIAL + newman MANUAL bowtie2.1 + + python_fix_shebang "${ED}"/usr/bin/bowtie2-{build,inspect} + + if use examples; then + docinto examples + dodoc -r example/. + docompress -x /usr/share/doc/${PF}/examples + fi +} diff --git a/sci-biology/bowtie/bowtie-2.5.1.ebuild b/sci-biology/bowtie/bowtie-2.5.1.ebuild new file mode 100644 index 000000000000..b30a2b920f4e --- /dev/null +++ b/sci-biology/bowtie/bowtie-2.5.1.ebuild @@ -0,0 +1,73 @@ +# Copyright 2021-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) + +inherit python-single-r1 toolchain-funcs + +DESCRIPTION="Popular short read aligner for Next-generation sequencing data" +HOMEPAGE="https://bowtie-bio.sourceforge.net/bowtie2/" +SRC_URI="https://downloads.sourceforge.net/project/${PN}-bio/bowtie2/${PV}/bowtie2-${PV}-source.zip" +S="${WORKDIR}/${PN}2-${PV}" + +LICENSE="GPL-3" +SLOT="2" +KEYWORDS="~amd64 ~x86" + +IUSE="test cpu_flags_x86_sse2 examples" +# Test script missing from tarball +# ./scripts/sim/run.sh: No such file or directory +RESTRICT="test" +REQUIRED_USE="cpu_flags_x86_sse2 ${PYTHON_REQUIRED_USE}" + +RDEPEND=" + ${PYTHON_DEPS} + dev-lang/perl + sys-libs/zlib +" +DEPEND="${RDEPEND}" +BDEPEND=" + app-arch/unzip + test? ( + dev-perl/App-cpanminus + dev-perl/B-COW + dev-perl/Clone + dev-perl/Config-General + dev-perl/File-Which + dev-perl/local-lib + dev-perl/Math-Random + dev-perl/Test-Deep + dev-perl/Text-Template + ) +" + +src_compile() { + emake \ + CXX="$(tc-getCXX)" \ + CXXFLAGS="" \ + CPPFLAGS="${CPPFLAGS}" \ + EXTRA_FLAGS="${LDFLAGS}" \ + RELEASE_FLAGS="${CXXFLAGS} -msse2" +} + +src_install() { + dobin bowtie2 bowtie2-* + + exeinto /usr/libexec/bowtie2 + doexe scripts/* + + HTML_DOCS=( doc/{manual.html,style.css} ) + einstalldocs + dodoc TUTORIAL + newman MANUAL bowtie2.1 + + python_fix_shebang "${ED}"/usr/bin/bowtie2-{build,inspect} + + if use examples; then + docinto examples + dodoc -r example/. + docompress -x /usr/share/doc/${PF}/examples + fi +} diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-_ContextLss-1.1-1.4.patch b/sci-biology/bowtie/files/bowtie-1.1.2-_ContextLss-1.1-1.4.patch deleted file mode 100644 index 78b9c01a0462..000000000000 --- a/sci-biology/bowtie/files/bowtie-1.1.2-_ContextLss-1.1-1.4.patch +++ /dev/null @@ -1,17 +0,0 @@ -Description: Change class name of _Context_LSS - New version 1.4 of SeQan uses a different name of the class. -Forwarded: no -Author: Gert Wollny <gw.fossdev@gmail.com> -Last-Update: 2014-100-06 - ---- a/diff_sample.h -+++ b/diff_sample.h -@@ -856,7 +856,7 @@ void DifferenceCoverSample<TStr>::build( - { - Timer timer(cout, " Invoking Larsson-Sadakane on ranks time: ", this->verbose()); - VMSG_NL(" Invoking Larsson-Sadakane on ranks"); -- _Context_LSS<TIndexOff> c; -+ ContextLss_<TIndexOff> c; - c.suffixsort( - (TIndexOff*)begin(_isaPrime, Standard()), - (TIndexOff*)begin(sPrime, Standard()), diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-fix-setBegin-call.patch b/sci-biology/bowtie/files/bowtie-1.1.2-fix-setBegin-call.patch deleted file mode 100644 index af7f7f61cd5e..000000000000 --- a/sci-biology/bowtie/files/bowtie-1.1.2-fix-setBegin-call.patch +++ /dev/null @@ -1,42 +0,0 @@ -Description: Proper type-casting in using seqan::_setBegin(). - Required by newer versions of GCC. -Forwarded: no -Author: Ognyan Kulev <ogi@debian.org> -Last-Update: 2013-04-18 - ---- a/pat.h -+++ b/pat.h -@@ -82,20 +82,20 @@ struct ReadBuf { - ~ReadBuf() { - clearAll(); reset(); - // Prevent seqan from trying to free buffers -- _setBegin(patFw, NULL); -- _setBegin(patRc, NULL); -- _setBegin(qual, NULL); -- _setBegin(patFwRev, NULL); -- _setBegin(patRcRev, NULL); -- _setBegin(qualRev, NULL); -- _setBegin(name, NULL); -+ _setBegin(patFw, (Dna5*)NULL); -+ _setBegin(patRc, (Dna5*)NULL); -+ _setBegin(qual, (char*)NULL); -+ _setBegin(patFwRev, (Dna5*)NULL); -+ _setBegin(patRcRev, (Dna5*)NULL); -+ _setBegin(qualRev, (char*)NULL); -+ _setBegin(name, (char*)NULL); - for(int j = 0; j < 3; j++) { -- _setBegin(altPatFw[j], NULL); -- _setBegin(altPatFwRev[j], NULL); -- _setBegin(altPatRc[j], NULL); -- _setBegin(altPatRcRev[j], NULL); -- _setBegin(altQual[j], NULL); -- _setBegin(altQualRev[j], NULL); -+ _setBegin(altPatFw[j], (Dna5*)NULL); -+ _setBegin(altPatFwRev[j], (Dna5*)NULL); -+ _setBegin(altPatRc[j], (Dna5*)NULL); -+ _setBegin(altPatRcRev[j], (Dna5*)NULL); -+ _setBegin(altQual[j], (char*)NULL); -+ _setBegin(altQualRev[j], (char*)NULL); - } - } - diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-seqan-popcount.patch b/sci-biology/bowtie/files/bowtie-1.1.2-seqan-popcount.patch deleted file mode 100644 index 52cb4f496521..000000000000 --- a/sci-biology/bowtie/files/bowtie-1.1.2-seqan-popcount.patch +++ /dev/null @@ -1,24 +0,0 @@ -Description: Use SeqAn 1.4's seqan::popCount() function instead of own function -Author: Ognyan Kulev <ogi@debian.org> -Last-Update: 2014-03-08 ---- -This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ ---- a/diff_sample.h -+++ b/diff_sample.h -@@ -476,6 +476,8 @@ static String<T> getDeltaMap(T v, const - return amap; - } - -+// Debian: Use seqan::popCount -+#if 0 - /** - * Return population count (count of all bits set to 1) of i. - */ -@@ -488,6 +490,7 @@ static unsigned int popCount(T i) { - } - return cnt; - } -+#endif - - /** - * Calculate log-base-2 of i diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-ChunkPool.patch b/sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-ChunkPool.patch deleted file mode 100644 index 171f9bab8fae..000000000000 --- a/sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-ChunkPool.patch +++ /dev/null @@ -1,382 +0,0 @@ -Description: Renamed ChunkPool class to bowtieChunkPool. - SeqAn has a class with the same name and fatal name collision happens. -Forwarded: no -Author: Ognyan Kulev <ogi@debian.org> -Last-Update: 2013-04-18 - ---- a/aligner.h -+++ b/aligner.h -@@ -337,7 +337,7 @@ public: - bool verbose, - bool quiet, - int maxBts, -- ChunkPool *pool, -+ bowtieChunkPool *pool, - int *btCnt = NULL, - AlignerMetrics *metrics = NULL) : - Aligner(true, rangeMode), -@@ -544,7 +544,7 @@ protected: - bool quiet_; // don't print informational/warning info - - const int maxBts_; -- ChunkPool *pool_; -+ bowtieChunkPool *pool_; - int *btCnt_; - AlignerMetrics *metrics_; - }; -@@ -585,7 +585,7 @@ public: - bool verbose, - bool quiet, - int maxBts, -- ChunkPool *pool, -+ bowtieChunkPool *pool, - int *btCnt) : - Aligner(true, rangeMode), - refs_(refs), -@@ -1358,7 +1358,7 @@ protected: - bool quiet_; - - int maxBts_; -- ChunkPool *pool_; -+ bowtieChunkPool *pool_; - int *btCnt_; - - // Range-finding state for first mate -@@ -1482,7 +1482,7 @@ public: - bool verbose, - bool quiet, - int maxBts, -- ChunkPool *pool, -+ bowtieChunkPool *pool, - int *btCnt) : - Aligner(true, rangeMode), - refs_(refs), -@@ -2035,7 +2035,7 @@ protected: - TDriver* driver_; - - // Pool for distributing chunks of best-first path descriptor memory -- ChunkPool *pool_; -+ bowtieChunkPool *pool_; - - bool verbose_; - bool quiet_; ---- a/aligner_0mm.h -+++ b/aligner_0mm.h -@@ -32,7 +32,7 @@ public: - RangeCache* cacheFw, - RangeCache* cacheBw, - uint32_t cacheLimit, -- ChunkPool *pool, -+ bowtieChunkPool *pool, - BitPairReference* refs, - vector<String<Dna5> >& os, - bool maqPenalty, -@@ -124,7 +124,7 @@ private: - RangeCache *cacheFw_; - RangeCache *cacheBw_; - const uint32_t cacheLimit_; -- ChunkPool *pool_; -+ bowtieChunkPool *pool_; - BitPairReference* refs_; - vector<String<Dna5> >& os_; - bool maqPenalty_; -@@ -164,7 +164,7 @@ public: - RangeCache* cacheFw, - RangeCache* cacheBw, - uint32_t cacheLimit, -- ChunkPool *pool, -+ bowtieChunkPool *pool, - BitPairReference* refs, - vector<String<Dna5> >& os, - bool reportSe, -@@ -366,7 +366,7 @@ private: - RangeCache *cacheFw_; - RangeCache *cacheBw_; - const uint32_t cacheLimit_; -- ChunkPool *pool_; -+ bowtieChunkPool *pool_; - BitPairReference* refs_; - vector<String<Dna5> >& os_; - const bool reportSe_; ---- a/aligner_1mm.h -+++ b/aligner_1mm.h -@@ -32,7 +32,7 @@ public: - RangeCache *cacheFw, - RangeCache *cacheBw, - uint32_t cacheLimit, -- ChunkPool *pool, -+ bowtieChunkPool *pool, - BitPairReference* refs, - vector<String<Dna5> >& os, - bool maqPenalty, -@@ -161,7 +161,7 @@ private: - RangeCache *cacheFw_; - RangeCache *cacheBw_; - const uint32_t cacheLimit_; -- ChunkPool *pool_; -+ bowtieChunkPool *pool_; - BitPairReference* refs_; - vector<String<Dna5> >& os_; - const bool maqPenalty_; -@@ -201,7 +201,7 @@ public: - RangeCache *cacheFw, - RangeCache *cacheBw, - uint32_t cacheLimit, -- ChunkPool *pool, -+ bowtieChunkPool *pool, - BitPairReference* refs, - vector<String<Dna5> >& os, - bool reportSe, -@@ -478,7 +478,7 @@ private: - RangeCache *cacheFw_; - RangeCache *cacheBw_; - const uint32_t cacheLimit_; -- ChunkPool *pool_; -+ bowtieChunkPool *pool_; - BitPairReference* refs_; - vector<String<Dna5> >& os_; - const bool reportSe_; ---- a/aligner_23mm.h -+++ b/aligner_23mm.h -@@ -33,7 +33,7 @@ public: - RangeCache *cacheFw, - RangeCache *cacheBw, - uint32_t cacheLimit, -- ChunkPool *pool, -+ bowtieChunkPool *pool, - BitPairReference* refs, - vector<String<Dna5> >& os, - bool maqPenalty, -@@ -231,7 +231,7 @@ private: - RangeCache *cacheFw_; - RangeCache *cacheBw_; - const uint32_t cacheLimit_; -- ChunkPool *pool_; -+ bowtieChunkPool *pool_; - BitPairReference* refs_; - vector<String<Dna5> >& os_; - const bool maqPenalty_; -@@ -273,7 +273,7 @@ public: - RangeCache *cacheFw, - RangeCache *cacheBw, - uint32_t cacheLimit, -- ChunkPool *pool, -+ bowtieChunkPool *pool, - BitPairReference* refs, - vector<String<Dna5> >& os, - bool reportSe, -@@ -675,7 +675,7 @@ private: - RangeCache *cacheFw_; - RangeCache *cacheBw_; - const uint32_t cacheLimit_; -- ChunkPool *pool_; -+ bowtieChunkPool *pool_; - BitPairReference* refs_; - vector<String<Dna5> >& os_; - const bool reportSe_; ---- a/aligner_seed_mm.h -+++ b/aligner_seed_mm.h -@@ -37,7 +37,7 @@ public: - RangeCache* cacheFw, - RangeCache* cacheBw, - uint32_t cacheLimit, -- ChunkPool *pool, -+ bowtieChunkPool *pool, - BitPairReference* refs, - vector<String<Dna5> >& os, - bool maqPenalty, -@@ -554,7 +554,7 @@ private: - RangeCache *cacheFw_; - RangeCache *cacheBw_; - const uint32_t cacheLimit_; -- ChunkPool *pool_; -+ bowtieChunkPool *pool_; - BitPairReference* refs_; - vector<String<Dna5> >& os_; - bool strandFix_; -@@ -598,7 +598,7 @@ public: - RangeCache* cacheFw, - RangeCache* cacheBw, - uint32_t cacheLimit, -- ChunkPool *pool, -+ bowtieChunkPool *pool, - BitPairReference* refs, - vector<String<Dna5> >& os, - bool reportSe, -@@ -1375,7 +1375,7 @@ private: - RangeCache *cacheFw_; - RangeCache *cacheBw_; - const uint32_t cacheLimit_; -- ChunkPool *pool_; -+ bowtieChunkPool *pool_; - BitPairReference* refs_; - vector<String<Dna5> >& os_; - const bool reportSe_; ---- a/ebwt_search.cpp -+++ b/ebwt_search.cpp -@@ -111,7 +111,7 @@ static bool strandFix; // attempt to fi - static bool randomizeQuals; // randomize quality values - static bool stats; // print performance stats - static int chunkPoolMegabytes; // max MB to dedicate to best-first search frames per thread --static int chunkSz; // size of single chunk disbursed by ChunkPool -+static int chunkSz; // size of single chunk disbursed by bowtieChunkPool - static bool chunkVerbose; // have chunk allocator output status messages? - static bool recal; - static int recalMaxCycle; -@@ -223,7 +223,7 @@ static void resetOptions() { - randomizeQuals = false; // randomize quality values - stats = false; // print performance stats - chunkPoolMegabytes = 64; // max MB to dedicate to best-first search frames per thread -- chunkSz = 256; // size of single chunk disbursed by ChunkPool (in KB) -+ chunkSz = 256; // size of single chunk disbursed by bowtieChunkPool (in KB) - chunkVerbose = false; // have chunk allocator output status messages? - recal = false; - recalMaxCycle = 64; -@@ -1201,7 +1201,7 @@ static void exactSearchWorkerStateful(vo - PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid); - HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink); - -- ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose); -+ bowtieChunkPool *pool = new bowtieChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose); - UnpairedExactAlignerV1Factory alSEfact( - ebwt, - NULL, -@@ -1385,7 +1385,7 @@ static void mismatchSearchWorkerFullStat - // Global initialization - PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid); - HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink); -- ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose); -+ bowtieChunkPool *pool = new bowtieChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose); - - Unpaired1mmAlignerV1Factory alSEfact( - ebwtFw, -@@ -1687,7 +1687,7 @@ static void twoOrThreeMismatchSearchWork - PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid); - HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink); - -- ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose); -+ bowtieChunkPool *pool = new bowtieChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose); - Unpaired23mmAlignerV1Factory alSEfact( - ebwtFw, - &ebwtBw, -@@ -2156,7 +2156,7 @@ static void seededQualSearchWorkerFullSt - // Global initialization - PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid); - HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink); -- ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose); -+ bowtieChunkPool *pool = new bowtieChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose); - - AlignerMetrics *metrics = NULL; - if(stats) { ---- a/ebwt_search_backtrack.h -+++ b/ebwt_search_backtrack.h -@@ -2724,7 +2724,7 @@ public: - bool verbose, - bool quiet, - bool mate1, -- ChunkPool* pool, -+ bowtieChunkPool* pool, - int *btCnt) : - SingleRangeSourceDriver<EbwtRangeSource>( - params, rs, fw, sink, sinkPt, os, verbose, -@@ -2927,7 +2927,7 @@ public: - bool verbose, - bool quiet, - bool mate1, -- ChunkPool* pool, -+ bowtieChunkPool* pool, - int *btCnt = NULL) : - params_(params), - rs_(rs), -@@ -2986,7 +2986,7 @@ protected: - bool verbose_; - bool quiet_; - bool mate1_; -- ChunkPool* pool_; -+ bowtieChunkPool* pool_; - int *btCnt_; - }; - ---- a/pool.h -+++ b/pool.h -@@ -19,13 +19,13 @@ - * is set at construction time. Heap memory is only allocated at - * construction and deallocated at destruction. - */ --class ChunkPool { -+class bowtieChunkPool { - public: - /** - * Initialize a new pool with an initial size of about 'bytes' - * bytes. Exit with an error message if we can't allocate it. - */ -- ChunkPool(uint32_t chunkSz, uint32_t totSz, bool verbose_) : -+ bowtieChunkPool(uint32_t chunkSz, uint32_t totSz, bool verbose_) : - verbose(verbose_), patid(0), pool_(NULL), cur_(0), - chunkSz_(chunkSz), totSz_(totSz), lim_(totSz/chunkSz), - bits_(lim_), exhaustCrash_(false), -@@ -38,7 +38,7 @@ public: - } - } catch(std::bad_alloc& e) { - ThreadSafe _ts(&gLock); -- std::cerr << "Error: Could not allocate ChunkPool of " -+ std::cerr << "Error: Could not allocate bowtieChunkPool of " - << totSz << " bytes" << std::endl; - exhausted(); - throw 1; // Exit if we haven't already -@@ -48,7 +48,7 @@ public: - /** - * Delete all the pools. - */ -- ~ChunkPool() { -+ ~bowtieChunkPool() { - if(pool_ != NULL) delete[] pool_; - } - -@@ -189,7 +189,7 @@ public: - * Initialize a new pool with an initial size of about 'bytes' - * bytes. Exit with an error message if we can't allocate it. - */ -- AllocOnlyPool(ChunkPool* pool, const char *name) : -+ AllocOnlyPool(bowtieChunkPool* pool, const char *name) : - pool_(pool), name_(name), curPool_(0), cur_(0) - { - assert(pool != NULL); -@@ -388,7 +388,7 @@ protected: - lastCurInPool_.pop_back(); - } - -- ChunkPool* pool_; -+ bowtieChunkPool* pool_; - const char *name_; - std::vector<T*> pools_; /// the memory pools - uint32_t curPool_; /// pool we're current allocating from ---- a/range_source.h -+++ b/range_source.h -@@ -1388,7 +1388,7 @@ class PathManager { - - public: - -- PathManager(ChunkPool* cpool_, int *btCnt, bool verbose, bool quiet) : -+ PathManager(bowtieChunkPool* cpool_, int *btCnt, bool verbose, bool quiet) : - branchQ_(verbose, quiet), - cpool(cpool_), - bpool(cpool, "branch"), -@@ -1637,7 +1637,7 @@ protected: - - public: - -- ChunkPool *cpool; // pool for generic chunks of memory -+ bowtieChunkPool *cpool; // pool for generic chunks of memory - AllocOnlyPool<Branch> bpool; // pool for allocating Branches - AllocOnlyPool<RangeState> rpool; // pool for allocating RangeStates - AllocOnlyPool<Edit> epool; // pool for allocating Edits -@@ -1811,7 +1811,7 @@ public: - bool quiet, - bool mate1, - uint32_t minCostAdjustment, -- ChunkPool* pool, -+ bowtieChunkPool* pool, - int *btCnt) : - RangeSourceDriver<TRangeSource>(true, minCostAdjustment), - len_(0), mate1_(mate1), diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-fill-to-resize.patch b/sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-fill-to-resize.patch deleted file mode 100644 index 38664aeee989..000000000000 --- a/sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-fill-to-resize.patch +++ /dev/null @@ -1,85 +0,0 @@ -Description: Renamed seqan::fill function calls to use seqan::resize. - SeqAn 1.3 renamed seqan::fill() to seqan::resize(). - SeqAn ticket: http://trac.seqan.de/ticket/77 -Forwarded: no -Author: Ognyan Kulev <ogi@debian.org> -Last-Update: 2014-08-13 - ---- a/blockwise_sa.h -+++ b/blockwise_sa.h -@@ -456,8 +456,8 @@ void KarkkainenBlockwiseSA<TStr>::buildS - try { - // Allocate and initialize containers for holding bucket - // sizes and representatives. -- fill(bucketSzs, numBuckets, 0, Exact()); -- fill(bucketReps, numBuckets, OFF_MASK, Exact()); -+ resize(bucketSzs, numBuckets, 0, Exact()); -+ resize(bucketReps, numBuckets, OFF_MASK, Exact()); - } catch(bad_alloc &e) { - if(this->_passMemExc) { - throw e; // rethrow immediately -@@ -816,7 +816,7 @@ void KarkkainenBlockwiseSA<TStr>::nextBl - // Not the last bucket - assert_lt(_cur, length(_sampleSuffs)); - hi = _sampleSuffs[_cur]; -- fill(zHi, _dcV, 0, Exact()); -+ resize(zHi, _dcV, 0, Exact()); - assert_eq(zHi[0], 0); - calcZ(t, hi, zHi, this->verbose(), this->sanityCheck()); - } -@@ -825,7 +825,7 @@ void KarkkainenBlockwiseSA<TStr>::nextBl - assert_gt(_cur, 0); - assert_leq(_cur, length(_sampleSuffs)); - lo = _sampleSuffs[_cur-1]; -- fill(zLo, _dcV, 0, Exact()); -+ resize(zLo, _dcV, 0, Exact()); - assert_gt(_dcV, 3); - assert_eq(zLo[0], 0); - calcZ(t, lo, zLo, this->verbose(), this->sanityCheck()); ---- a/diff_sample.h -+++ b/diff_sample.h -@@ -452,7 +452,7 @@ static String<T> getDeltaMap(T v, const - // Declare anchor-map-related items - String<T> amap; - size_t amapEnts = 1; -- fill(amap, v, 0xffffffff, Exact()); -+ resize(amap, v, 0xffffffff, Exact()); - amap[0] = 0; - // Print out difference cover (and optionally calculate - // anchor map) -@@ -532,7 +532,7 @@ public: - assert_gt(_d, 0); - assert_eq(1, popCount(_v)); // must be power of 2 - // Build map from d's to idx's -- fill(_dInv, _v, 0xffffffff, Exact()); -+ resize(_dInv, _v, 0xffffffff, Exact()); - uint32_t lim = (uint32_t)length(_ds); - for(uint32_t i = 0; i < lim; i++) { - _dInv[_ds[i]] = i; -@@ -656,7 +656,7 @@ void DifferenceCoverSample<TStr>::doBuil - VMSG_NL(" Doing sanity check"); - TIndexOffU added = 0; - String<TIndexOffU> sorted; -- fill(sorted, length(_isaPrime), OFF_MASK, Exact()); -+ resize(sorted, length(_isaPrime), OFF_MASK, Exact()); - for(size_t di = 0; di < this->d(); di++) { - uint32_t d = _ds[di]; - size_t i = 0; -@@ -717,7 +717,7 @@ void DifferenceCoverSample<TStr>::buildS - assert_eq(length(_doffs), d+1); - // Size sPrime appropriately - reserve(sPrime, sPrimeSz+1, Exact()); // reserve extra slot for LS -- fill(sPrime, sPrimeSz, OFF_MASK, Exact()); -+ resize(sPrime, sPrimeSz, OFF_MASK, Exact()); - // Slot suffixes from text into sPrime according to the mu - // mapping; where the mapping would leave a blank, insert a 0 - TIndexOffU added = 0; -@@ -823,7 +823,7 @@ void DifferenceCoverSample<TStr>::build( - // arrays back into sPrime. - VMSG_NL(" Allocating rank array"); - reserve(_isaPrime, length(sPrime)+1, Exact()); -- fill(_isaPrime, length(sPrime), OFF_MASK, Exact()); -+ resize(_isaPrime, length(sPrime), OFF_MASK, Exact()); - assert_gt(length(_isaPrime), 0); - { - Timer timer(cout, " Ranking v-sort output time: ", this->verbose()); diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-spelling.patch b/sci-biology/bowtie/files/bowtie-1.1.2-spelling.patch deleted file mode 100644 index ff484dfa3ebb..000000000000 --- a/sci-biology/bowtie/files/bowtie-1.1.2-spelling.patch +++ /dev/null @@ -1,48 +0,0 @@ -Author: Andreas Tille <tille@debian.org> -Last-Update: Thu, 01 Oct 2015 09:47:23 +0200 -Description: Fix spelling - ---- a/MANUAL -+++ b/MANUAL -@@ -544,7 +544,7 @@ The `bowtie`, `bowtie-build` and `bowtie - actually wrapper scripts that call binary programs as appropriate. The - wrappers shield users from having to distinguish between "small" and - "large" index formats, discussed briefly in the following section. The --appropiate index type is selected based on the input size. -+appropriate index type is selected based on the input size. - - It is recommended that you always run the bowtie wrappers and not run - the binaries directly. ---- a/MANUAL.markdown -+++ b/MANUAL.markdown -@@ -559,7 +559,7 @@ The `bowtie`, `bowtie-build` and `bowtie - actually wrapper scripts that call binary programs as appropriate. The - wrappers shield users from having to distinguish between "small" and - "large" index formats, discussed briefly in the following section. The --appropiate index type is selected based on the input size. -+appropriate index type is selected based on the input size. - - It is recommended that you always run the bowtie wrappers and not run - the binaries directly. ---- a/doc/manual.html -+++ b/doc/manual.html -@@ -201,7 +201,7 @@ T2302111203131231130300111123220 - <p>Like other platforms, SOLiD supports generation of paired-end reads. When colorspace alignment is enabled, the default paired-end orientation setting is <a href="#bowtie-options-fr"><code>--ff</code></a>. This is because most SOLiD datasets have that orientation.</p> - <p>Note that SOLiD-generated read files can have "orphaned" mates; i.e. mates without a correpsondingly-named mate in the other file. To avoid problems due to orphaned mates, SOLiD paired-end output should first be converted to <code>.csfastq</code> files with unpaired mates omitted. This can be accomplished using, for example, [Galaxy]'s conversion tool (click "NGS: QC and manipulation", then "SOLiD-to-FASTQ" in the left-hand sidebar).</p> - <h2 id="wrapper-scripts">Wrapper scripts</h2> --<p>The <code>bowtie</code>, <code>bowtie-build</code> and <code>bowtie-inspect</code> executables are actually wrapper scripts that call binary programs as appropriate. The wrappers shield users from having to distinguish between "small" and "large" index formats, discussed briefly in the following section. The appropiate index type is selected based on the input size.</p> -+<p>The <code>bowtie</code>, <code>bowtie-build</code> and <code>bowtie-inspect</code> executables are actually wrapper scripts that call binary programs as appropriate. The wrappers shield users from having to distinguish between "small" and "large" index formats, discussed briefly in the following section. The appropriate index type is selected based on the input size.</p> - <p>It is recommended that you always run the bowtie wrappers and not run the binaries directly.</p> - <h2 id="small-and-large-indexes">Small and large indexes</h2> - <p><code>bowtie-build</code> can index reference genomes of any size. For genomes less than about 4 billion nucleotides in length, <code>bowtie-build</code> builds a "small" index using 32-bit numbers in various parts of the index. When the genome is longer, <code>bowtie-build</code> builds a "large" index using 64-bit numbers. Small indexes are stored in files with the <code>.ebwt</code> extension, and large indexes are stored in files with the <code>.ebwtl</code> extension. The user need not worry about whether a particular index is small or large; the wrapper scripts will automatically build and use the appropriate index.</p> ---- a/ref_read.cpp -+++ b/ref_read.cpp -@@ -263,7 +263,7 @@ fastaRefReadSizes(vector<FileBuf*>& in, - << "reference into smaller chunks and index each independently." << endl; - #else - cerr << "Error: Reference sequence has more than 2^32-1 characters! Please try to" << endl -- << "build a large index instead using the appropiate options." << endl; -+ << "build a large index instead using the appropriate options." << endl; - #endif - throw 1; - } diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch b/sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch deleted file mode 100644 index bc0f1d09557d..000000000000 --- a/sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch +++ /dev/null @@ -1,18 +0,0 @@ -Fixes missing tinythread.cpp when using TBB: - -ebwt_search.cpp:(.text+0x91bb): undefined reference to `tthread::thread::join()' - ---- bowtie-1.1.2/Makefile -+++ bowtie-1.1.2/Makefile -@@ -106,10 +106,7 @@ - endif - - OTHER_CPPS = ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp \ -- edit.cpp ebwt.cpp --ifneq (1,$(WITH_TBB)) -- OTHER_CPPS += tinythread.cpp --endif -+ edit.cpp ebwt.cpp tinythread.cpp - - SEARCH_CPPS = qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp \ - log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp \ diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-unbundle-seqan.patch b/sci-biology/bowtie/files/bowtie-1.1.2-unbundle-seqan.patch deleted file mode 100644 index 54391ae415a3..000000000000 --- a/sci-biology/bowtie/files/bowtie-1.1.2-unbundle-seqan.patch +++ /dev/null @@ -1,27 +0,0 @@ -Description: Use Debian packaged SeqAn library instead of copy in upstream source -Author: Andreas Tille <tille@debian.org> -Date: 2011-01-30 -Last-Update: 2013-04-18 -Reviewed-by: Ognyan Kulev <ogi@debian.org> - ---- a/Makefile -+++ b/Makefile -@@ -5,9 +5,7 @@ - prefix = /usr/local - bindir = $(prefix)/bin - --SEQAN_DIR = SeqAn-1.1 --SEQAN_INC = -I $(SEQAN_DIR) --INC = $(SEQAN_INC) -I third_party -+INC = `pkg-config --cflags seqan-1.4` - CPP = g++ - CXX = $(CPP) - CC = gcc -@@ -168,7 +166,6 @@ - $(wildcard genomes/NC_008253.fna) \ - $(wildcard reads/e_coli_1000.*) \ - $(wildcard reads/e_coli_1000_*) \ -- SeqAn-1.1 \ - bowtie \ - bowtie-build \ - bowtie-inspect \ diff --git a/sci-biology/bowtie/files/bowtie-2.2.9-fix-c++14.patch b/sci-biology/bowtie/files/bowtie-2.2.9-fix-c++14.patch deleted file mode 100644 index cd2a67b6a52b..000000000000 --- a/sci-biology/bowtie/files/bowtie-2.2.9-fix-c++14.patch +++ /dev/null @@ -1,29 +0,0 @@ -Fix building with C++14, which errors out due to differing semantics between C++98 -and C++14 with regards to allowing destructors to throw exceptions. -See also: https://bugs.gentoo.org/show_bug.cgi?id=593966 - ---- a/blockwise_sa.h -+++ b/blockwise_sa.h -@@ -87,7 +87,11 @@ - _logger(__logger) - { } - -- virtual ~BlockwiseSA() { } -+ virtual ~BlockwiseSA() -+#if __cplusplus >= 201103L -+ noexcept(false) -+#endif -+ { } - - /** - * Get the next suffix; compute the next bucket if necessary. -@@ -216,6 +220,9 @@ - { _randomSrc.init(__seed); reset(); } - - ~KarkkainenBlockwiseSA() -+#if __cplusplus >= 201103L -+ noexcept(false) -+#endif - { - #ifdef WITH_TBB - tbb_grp.wait(); diff --git a/sci-biology/bowtie/metadata.xml b/sci-biology/bowtie/metadata.xml index 71e8d3bb8e0f..c48ae535cfaf 100644 --- a/sci-biology/bowtie/metadata.xml +++ b/sci-biology/bowtie/metadata.xml @@ -1,16 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">bowtie-bio</remote-id> - </upstream> - <use> - <flag name="tbb">Enables building bowtie with the Intel - Threading Building Blocks from <pkg>dev-cpp/tbb</pkg>. This - flag is recommended.</flag> - </use> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">bowtie-bio</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/bwa/Manifest b/sci-biology/bwa/Manifest index 9da3adbeb40a..5f912dc43cf0 100644 --- a/sci-biology/bwa/Manifest +++ b/sci-biology/bwa/Manifest @@ -1 +1 @@ -DIST bwa-0.7.16a.tar.bz2 190773 BLAKE2B e1064381b6b1aa4c9b78d12222c7b783a55676a163b94ad8596a2af64c9b0d60bbebd8e840aaa13b25e1ca4f10466c2c39c99830f1ca58e558d724d1ad583944 SHA512 8bbe223f79efd328d66adb88baf995e894f5944aad912ac1b464dc84dc9b4e22ddf77b60dcbe468e0eedc344ee58d08dc498777f0d2794a2c1e0ddd33dad606d +DIST bwa-0.7.17.tar.gz 232593 BLAKE2B fa48aad72a47547d66c767e2e2a5aadfcfc7c77c517410812230f51a2222ee66bb04383b068036b696af0a57b04b35e97bed11e3c44793aa899a8c0807f3df5e SHA512 114e61b7cc5edcb67172d1eca7be1fa670ea33dd48b5c02c98318e254871363775c0dab327fd7ee7023200a5fedc745fa01cbe0fd9550d783f091d4df6926f48 diff --git a/sci-biology/bwa/bwa-0.7.16a.ebuild b/sci-biology/bwa/bwa-0.7.16a.ebuild deleted file mode 100644 index b29bf210169a..000000000000 --- a/sci-biology/bwa/bwa-0.7.16a.ebuild +++ /dev/null @@ -1,36 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit toolchain-funcs - -DESCRIPTION="Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner" -HOMEPAGE="https://bio-bwa.sourceforge.net/" -SRC_URI="mirror://sourceforge/bio-bwa/${P}.tar.bz2" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~x64-macos" - -RDEPEND="dev-lang/perl" - -PATCHES=( - "${FILESDIR}"/${PN}-0.7.15-Makefile.patch - "${FILESDIR}"/${PN}-0.7.16a-gcc-10.patch -) -DOCS=( NEWS.md README-alt.md README.md ) - -src_configure() { - tc-export CC AR -} - -src_install() { - dobin bwa - - exeinto /usr/libexec/${PN} - doexe qualfa2fq.pl xa2multi.pl - - einstalldocs - doman bwa.1 -} diff --git a/sci-biology/bwa/bwa-0.7.17.ebuild b/sci-biology/bwa/bwa-0.7.17.ebuild new file mode 100644 index 000000000000..e1b6dbb6184e --- /dev/null +++ b/sci-biology/bwa/bwa-0.7.17.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +inherit flag-o-matic toolchain-funcs + +DESCRIPTION="Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner" +HOMEPAGE="https://github.com/lh3/bwa/" +SRC_URI="https://github.com/lh3/bwa/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~x64-macos" + +DEPEND="sys-libs/zlib" +RDEPEND=" + ${DEPEND} + dev-lang/perl" + +PATCHES=( + "${FILESDIR}"/${PN}-0.7.17-Makefile.patch + "${FILESDIR}"/${PN}-0.7.17-gcc-10.patch +) +DOCS=( NEWS.md README-alt.md README.md ) + +src_configure() { + # -Werror=lto-type-mismatch + # https://bugs.gentoo.org/862255 + # https://github.com/lh3/bwa/issues/411 + filter-lto + + tc-export CC AR +} + +src_install() { + dobin bwa + + exeinto /usr/libexec/${PN} + doexe qualfa2fq.pl xa2multi.pl + + einstalldocs + doman bwa.1 +} diff --git a/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch b/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch deleted file mode 100644 index 39b437a02897..000000000000 --- a/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch +++ /dev/null @@ -1,27 +0,0 @@ ---- bwa-0.7.13/Makefile -+++ bwa-0.7.13/Makefile -@@ -1,8 +1,8 @@ --CC= gcc -+CC?= gcc - #CC= clang --analyze --CFLAGS= -g -Wall -Wno-unused-function -O2 -+CFLAGS?= -g -Wall -Wno-unused-function -O2 - WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS --AR= ar -+AR?= ar - DFLAGS= -DHAVE_PTHREAD $(WRAP_MALLOC) - LOBJS= utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o - AOBJS= QSufSort.o bwt_gen.o bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \ -@@ -26,10 +26,10 @@ - all:$(PROG) - - bwa:libbwa.a $(AOBJS) main.o -- $(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS) -+ $(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS) - - bwamem-lite:libbwa.a example.o -- $(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS) -+ $(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS) - - libbwa.a:$(LOBJS) - $(AR) -csru $@ $(LOBJS) diff --git a/sci-biology/bwa/files/bwa-0.7.16a-gcc-10.patch b/sci-biology/bwa/files/bwa-0.7.16a-gcc-10.patch deleted file mode 100644 index 40056ffeaaa9..000000000000 --- a/sci-biology/bwa/files/bwa-0.7.16a-gcc-10.patch +++ /dev/null @@ -1,7 +0,0 @@ ---- a/rle.h -+++ b/rle.h -@@ -32,3 +32,3 @@ extern "C" { - --const uint8_t rle_auxtab[8]; -+extern const uint8_t rle_auxtab[8]; - diff --git a/sci-biology/bwa/files/bwa-0.7.17-Makefile.patch b/sci-biology/bwa/files/bwa-0.7.17-Makefile.patch new file mode 100644 index 000000000000..944369cb75e2 --- /dev/null +++ b/sci-biology/bwa/files/bwa-0.7.17-Makefile.patch @@ -0,0 +1,42 @@ +--- a/Makefile ++++ b/Makefile +@@ -1,9 +1,7 @@ +-CC= gcc + #CC= clang --analyze +-CFLAGS= -g -Wall -Wno-unused-function -O2 ++CFLAGS+= -Wall -Wno-unused-function + WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS +-AR= ar +-DFLAGS= -DHAVE_PTHREAD $(WRAP_MALLOC) ++CPPFLAGS+= -DHAVE_PTHREAD $(WRAP_MALLOC) + LOBJS= utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o \ + QSufSort.o bwt_gen.o rope.o rle.o is.o bwtindex.o + AOBJS= bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \ +@@ -21,16 +19,13 @@ + + .SUFFIXES:.c .o .cc + +-.c.o: +- $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@ +- + all:$(PROG) + + bwa:libbwa.a $(AOBJS) main.o +- $(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS) ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS) + + bwamem-lite:libbwa.a example.o +- $(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS) ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) example.o -o $@ -L. -lbwa $(LIBS) + + libbwa.a:$(LOBJS) + $(AR) -csru $@ $(LOBJS) +@@ -39,7 +34,7 @@ + rm -f gmon.out *.o a.out $(PROG) *~ *.a + + depend: +- ( LC_ALL=C ; export LC_ALL; makedepend -Y -- $(CFLAGS) $(DFLAGS) -- *.c ) ++ ( LC_ALL=C ; export LC_ALL; makedepend -Y -- $(CFLAGS) $(CPPFLAGS) -- *.c ) + + # DO NOT DELETE THIS LINE -- make depend depends on it. + diff --git a/sci-biology/bwa/files/bwa-0.7.17-gcc-10.patch b/sci-biology/bwa/files/bwa-0.7.17-gcc-10.patch new file mode 100644 index 000000000000..1babb8356c4a --- /dev/null +++ b/sci-biology/bwa/files/bwa-0.7.17-gcc-10.patch @@ -0,0 +1,11 @@ +--- a/rle.h ++++ b/rle.h +@@ -30,7 +30,7 @@ + *** 43+3 codec *** + ******************/ + +-const uint8_t rle_auxtab[8]; ++extern const uint8_t rle_auxtab[8]; + + #define RLE_MIN_SPACE 18 + #define rle_nptr(block) ((uint16_t*)(block)) diff --git a/sci-biology/bwa/metadata.xml b/sci-biology/bwa/metadata.xml index ceb43ead2a3f..21fbf032d0bf 100644 --- a/sci-biology/bwa/metadata.xml +++ b/sci-biology/bwa/metadata.xml @@ -1,11 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">bio-bwa</remote-id> - </upstream> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="github">lh3/bwa</remote-id> + <remote-id type="sourceforge">bio-bwa</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/cd-hit/cd-hit-4.6.6.ebuild b/sci-biology/cd-hit/cd-hit-4.6.6-r1.ebuild index ebe345f15245..20e7e2d784fe 100644 --- a/sci-biology/cd-hit/cd-hit-4.6.6.ebuild +++ b/sci-biology/cd-hit/cd-hit-4.6.6-r1.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 -inherit flag-o-matic toolchain-funcs +inherit toolchain-funcs RELDATE="2016-0711" RELEASE="${PN}-v${PV}-${RELDATE}" @@ -11,6 +11,7 @@ RELEASE="${PN}-v${PV}-${RELDATE}" DESCRIPTION="Clustering Database at High Identity with Tolerance" HOMEPAGE="http://weizhong-lab.ucsd.edu/cd-hit/" SRC_URI="https://github.com/weizhongli/cdhit/releases/download/V${PV}/${RELEASE}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}"/${RELEASE} LICENSE="GPL-2" SLOT="0" @@ -19,8 +20,6 @@ IUSE="openmp" RDEPEND="dev-lang/perl" -S="${WORKDIR}"/${RELEASE} - PATCHES=( "${FILESDIR}"/${PN}-4.6.6-fix-perl-shebangs.patch "${FILESDIR}"/${PN}-4.6.6-fix-build-system.patch diff --git a/sci-biology/cd-hit/metadata.xml b/sci-biology/cd-hit/metadata.xml index 1f3b075216dd..3bb799e0ba9e 100644 --- a/sci-biology/cd-hit/metadata.xml +++ b/sci-biology/cd-hit/metadata.xml @@ -1,5 +1,5 @@ -<?xml version='1.0' encoding='UTF-8'?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/clustal-omega/clustal-omega-1.2.4.ebuild b/sci-biology/clustal-omega/clustal-omega-1.2.4-r1.ebuild index 1e7e1f8b166d..4d5b2a779bf9 100644 --- a/sci-biology/clustal-omega/clustal-omega-1.2.4.ebuild +++ b/sci-biology/clustal-omega/clustal-omega-1.2.4-r1.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit autotools @@ -11,8 +11,7 @@ SRC_URI="http://www.clustal.org/omega/${P}.tar.gz" LICENSE="GPL-2" SLOT="0" -KEYWORDS="amd64 x86" -IUSE="static-libs" +KEYWORDS="amd64 ~x86" DEPEND="dev-libs/argtable" RDEPEND="${DEPEND}" @@ -25,13 +24,7 @@ src_prepare() { eautoreconf } -src_configure() { - econf \ - --enable-shared \ - $(use_enable static-libs static) -} - src_install() { default - find "${D}" -name '*.la' -delete || die + find "${ED}" -name '*.la' -delete || die } diff --git a/sci-biology/clustal-omega/metadata.xml b/sci-biology/clustal-omega/metadata.xml index 959160fe46b1..ccdff086e20b 100644 --- a/sci-biology/clustal-omega/metadata.xml +++ b/sci-biology/clustal-omega/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r2.ebuild b/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r3.ebuild index 76d3b80cde32..334c34e78ce6 100644 --- a/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r2.ebuild +++ b/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r3.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 inherit toolchain-funcs @@ -12,28 +12,31 @@ SRC_URI="http://web.bii.a-star.edu.sg/~kuobin/${PN}/${P}.tar.gz" LICENSE="public-domain" SLOT="0" KEYWORDS="~amd64 ~x86" -IUSE="mpi_njtree static_pairalign" +IUSE="mpi-njtree static-pairalign" DEPEND="virtual/mpi" RDEPEND="${DEPEND}" -PATCHES=( "${FILESDIR}"/${PV}-gentoo.patch ) +PATCHES=( + "${FILESDIR}"/${P}-makefile.patch + "${FILESDIR}"/${P}-fno-common.patch +) src_prepare() { default - if use mpi_njtree; then + if use mpi-njtree; then sed -e "s/TREES_FLAG/#TREES_FLAG/" -i Makefile || \ die "Failed to configure MPI code for NJ trees" fi - if use static_pairalign; then + if use static-pairalign; then sed -e "s/DDYNAMIC_SCHEDULING/DSTATIC_SCHEDULING/" -i Makefile || \ die "Failed to configure static scheduling for pair alignments" fi } src_install() { - dobin ${PN} - newdoc README.${PN} README + dobin clustalw-mpi + newdoc README.clustalw-mpi README } diff --git a/sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-fno-common.patch b/sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-fno-common.patch new file mode 100644 index 000000000000..da74f0ba172d --- /dev/null +++ b/sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-fno-common.patch @@ -0,0 +1,13 @@ +--- a/parallel_compare.c ++++ b/parallel_compare.c +@@ -74,8 +74,8 @@ + static sint **accum; + static sint *diag_index; + static char *slopes; +-sint ktup,window,wind_gap,signif; +-sint *zza, *zzb, *zzc, *zzd; ++extern sint ktup,window,wind_gap,signif; ++extern sint *zza, *zzb, *zzc, *zzd; + extern Boolean percent; + static void make_p_ptrs(sint *tptr, sint *pl, sint naseq, sint l); + static void make_n_ptrs(sint *tptr, sint *pl, sint naseq, sint len); diff --git a/sci-biology/clustalw-mpi/files/0.13-gentoo.patch b/sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-makefile.patch index 6e36061cbb39..6e36061cbb39 100644 --- a/sci-biology/clustalw-mpi/files/0.13-gentoo.patch +++ b/sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-makefile.patch diff --git a/sci-biology/clustalw-mpi/metadata.xml b/sci-biology/clustalw-mpi/metadata.xml index 8ab4494152c8..bda43acf10c1 100644 --- a/sci-biology/clustalw-mpi/metadata.xml +++ b/sci-biology/clustalw-mpi/metadata.xml @@ -1,14 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> -</maintainer> -<use> - <flag name="mpi_njtree">Use MPI (as opposed to serial) code for computing - neighbor-joining trees</flag> - <flag name="static_pairalign">Use static (as opposed to dynamic) scheduling - for pair alignments</flag> -</use> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <use> + <flag name="mpi-njtree">Use MPI (as opposed to serial) code for computing neighbor-joining trees</flag> + <flag name="static-pairalign">Use static (as opposed to dynamic) scheduling for pair alignments</flag> + </use> </pkgmetadata> diff --git a/sci-biology/clustalw/clustalw-1.83-r4.ebuild b/sci-biology/clustalw/clustalw-1.83-r4.ebuild index 7f6accd6b4c8..23c4ba9a3229 100644 --- a/sci-biology/clustalw/clustalw-1.83-r4.ebuild +++ b/sci-biology/clustalw/clustalw-1.83-r4.ebuild @@ -1,34 +1,35 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit toolchain-funcs DESCRIPTION="General purpose multiple alignment program for DNA and proteins" HOMEPAGE="http://www.embl-heidelberg.de/~seqanal/" SRC_URI="ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/${PN}${PV}.UNIX.tar.gz" +S="${WORKDIR}/${PN}${PV}" LICENSE="clustalw" SLOT="1" -KEYWORDS="~alpha amd64 ppc ppc64 sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" -IUSE="" +KEYWORDS="amd64 ~ppc ppc64 sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" -S="${WORKDIR}"/${PN}${PV} - -PATCHES=( "${FILESDIR}"/${PV}-as-needed.patch ) +PATCHES=( + "${FILESDIR}"/${PV}-as-needed.patch + "${FILESDIR}"/${PV}-clang.patch +) src_prepare() { default - - sed \ - -e "/^CC/s:cc:$(tc-getCC):g" \ - -i makefile || die sed \ - -e "s%clustalw_help%/usr/share/doc/${PF}/clustalw_help%" \ + -e "s|clustalw_help|${EPREFIX}/usr/share/doc/${PF}/clustalw_help|" \ -i clustalw.c || die } +src_configure() { + tc-export CC +} + src_install() { dobin clustalw dodoc README clustalv.doc clustalw{.doc,.ms,_help} diff --git a/sci-biology/clustalw/clustalw-2.1-r1.ebuild b/sci-biology/clustalw/clustalw-2.1-r2.ebuild index 0b46aeb5bfd4..16a957f6c636 100644 --- a/sci-biology/clustalw/clustalw-2.1-r1.ebuild +++ b/sci-biology/clustalw/clustalw-2.1-r2.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 DESCRIPTION="General purpose multiple alignment program for DNA and proteins" HOMEPAGE="http://www.clustal.org/" @@ -9,10 +9,9 @@ SRC_URI="http://www.clustal.org/download/current/${P}.tar.gz" LICENSE="GPL-3 LGPL-3" SLOT="2" -KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" -IUSE="" +KEYWORDS="amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" src_install() { default - rmdir "${ED%/}"/usr/share/aclocal || die + rmdir "${ED}"/usr/share/aclocal || die } diff --git a/sci-biology/clustalw/files/1.83-as-needed.patch b/sci-biology/clustalw/files/1.83-as-needed.patch index 9bb35b43f24a..54b78b0811e0 100644 --- a/sci-biology/clustalw/files/1.83-as-needed.patch +++ b/sci-biology/clustalw/files/1.83-as-needed.patch @@ -1,17 +1,36 @@ --- a/makefile +++ b/makefile -@@ -11,11 +11,11 @@ +@@ -10,25 +10,22 @@ + HEADERS = general.h clustalw.h - CC = cc +-CC = cc -CFLAGS = -c -O -LFLAGS = -O -lm -+CFLAGS += -c -+LIBS = -lm ++# C99 for gets() ++CFLAGS += -std=gnu99 ++LIBS += -lm clustalw : $(OBJECTS) amenu.o clustalw.o - $(CC) -o $@ $(OBJECTS) amenu.o clustalw.o $(LFLAGS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJECTS) amenu.o clustalw.o $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(OBJECTS) amenu.o clustalw.o $(LIBS) interface.o : interface.c $(HEADERS) param.h - $(CC) $(CFLAGS) $*.c +- $(CC) $(CFLAGS) $*.c ++ $(CC) $(CFLAGS) $(CPPFLAGS) -c $< + + amenu.o : amenu.c $(HEADERS) param.h +- $(CC) $(CFLAGS) $*.c ++ $(CC) $(CFLAGS) $(CPPFLAGS) -c $< + + readmat.o : readmat.c $(HEADERS) matrices.h +- $(CC) $(CFLAGS) $*.c ++ $(CC) $(CFLAGS) $(CPPFLAGS) -c $< + + trees.o : trees.c $(HEADERS) dayhoff.h +- $(CC) $(CFLAGS) $*.c +- +-.c.o : +- $(CC) $(CFLAGS) $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) -c $< + diff --git a/sci-biology/clustalw/files/1.83-clang.patch b/sci-biology/clustalw/files/1.83-clang.patch new file mode 100644 index 000000000000..ea1202079d9e --- /dev/null +++ b/sci-biology/clustalw/files/1.83-clang.patch @@ -0,0 +1,11 @@ +--- a/interface.c ++++ b/interface.c +@@ -210,7 +210,7 @@ + Boolean name1 = FALSE; + sint ajb; + +- if(args[0]==NULL) return; ++ if(args[0]==NULL) return 0; + + + diff --git a/sci-biology/clustalw/metadata.xml b/sci-biology/clustalw/metadata.xml index 959160fe46b1..ccdff086e20b 100644 --- a/sci-biology/clustalw/metadata.xml +++ b/sci-biology/clustalw/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/clustalx/clustalx-2.1-r3.ebuild b/sci-biology/clustalx/clustalx-2.1-r3.ebuild index 4a3199f352c9..fa956bd186e8 100644 --- a/sci-biology/clustalx/clustalx-2.1-r3.ebuild +++ b/sci-biology/clustalx/clustalx-2.1-r3.ebuild @@ -1,19 +1,19 @@ -# Copyright 1999-2018 Gentoo Foundation +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 inherit desktop qmake-utils DESCRIPTION="Graphical interface for the ClustalW multiple alignment program" -HOMEPAGE="http://www.ebi.ac.uk/tools/clustalw2/" +HOMEPAGE="https://www.ebi.ac.uk/Tools/msa/clustalw2/" SRC_URI=" http://www.clustal.org/download/current/${P}.tar.gz https://dev.gentoo.org/~jlec/distfiles/${PN}.png.xz" LICENSE="GPL-3 LGPL-3" SLOT="0" -KEYWORDS="amd64 x86" +KEYWORDS="amd64 ~x86" IUSE="" DEPEND=" @@ -40,7 +40,7 @@ src_prepare() { -e "s|clustalx.hlp|${EPREFIX}/usr/share/${PN}/clustalx.hlp|" \ -i HelpDisplayWidget.cpp || \ die "Failed to patch help file location." - rm -rf usr || die + rm -r usr || die } src_configure() { diff --git a/sci-biology/clustalx/metadata.xml b/sci-biology/clustalx/metadata.xml index 959160fe46b1..ccdff086e20b 100644 --- a/sci-biology/clustalx/metadata.xml +++ b/sci-biology/clustalx/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/consed/Manifest b/sci-biology/consed/Manifest deleted file mode 100644 index eb7d7f06c3ee..000000000000 --- a/sci-biology/consed/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST consed-29-linux.tar.gz 36172715 BLAKE2B 6706576b404c0bccb7ed28ab6fe2dec86fdac6f7651406d3f30e35caac3e49a66b4762edace2133d2dfb776bbeb730b74797c7323deb950f2648a46c4594fe98 SHA512 63a95d84cb58009045a9d898c8b1a94f98516bed9189f624a5930338cc8f51562504257f309d945fafcc07e0811ffeea122b640789f75fbd6c94535178dab4dd -DIST consed-29-sources.tar.gz 3258845 BLAKE2B 508763ff2a240047cff0a43ba4b9b9a7f9302c0a023478c6b08f86bb77fb2c12a62a9b16165fe6257fe6c86af853dabe279bd9e05632c3e112e3fb7fad2c6bd3 SHA512 fd711a65a02ef1238cca12b90fe7fa9b67da6c37d43cd105f38c7b6475fbc073c1f4d7f99703dec9d3a0a7a2a9317cb14999a114bb6f52589cb9b6e34700eb93 diff --git a/sci-biology/consed/consed-29.ebuild b/sci-biology/consed/consed-29.ebuild deleted file mode 100644 index 32eba4cb16d0..000000000000 --- a/sci-biology/consed/consed-29.ebuild +++ /dev/null @@ -1,110 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit flag-o-matic toolchain-funcs - -DESCRIPTION="A genome sequence finishing program" -HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html" -SRC_URI=" - ${P}-sources.tar.gz - ${P}-linux.tar.gz" - -LICENSE="phrap" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="examples" - -COMMON_DEPEND=" - x11-libs/libX11 - x11-libs/motif:0 - sci-biology/samtools:0.1-legacy -" -DEPEND=" - ${COMMON_DEPEND} - virtual/pkgconfig -" -RDEPEND=" - ${COMMON_DEPEND} - dev-lang/perl - >=sci-biology/phred-071220-r1 - >=sci-biology/phrap-1.080812-r2 -" - -S="${WORKDIR}" - -RESTRICT="fetch" -PATCHES=( - "${FILESDIR}/${PN}-29-fix-build-system.patch" - "${FILESDIR}/${PN}-29-fix-c++14.patch" - "${FILESDIR}/${PN}-29-fix-qa.patch" - "${FILESDIR}/${PN}-29-fix-perl-shebang.patch" -) - -pkg_nofetch() { - einfo "Please visit ${HOMEPAGE} and obtain the file" - einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\"" - einfo "and place it into your DISTDIR directory," - einfo "obtain the file" - einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\"" - einfo "and place it into your DISTDIR directory." -} - -src_prepare() { - default - - sed \ - -e "s!\$szPhredParameterFile = .*!\$szPhredParameterFile = \$ENV{'PHRED_PARAMETER_FILE'} || \'"${EPREFIX}"/usr/share/phred/phredpar.dat\';!" \ - -e "s:/usr/local/genome:${EPREFIX}/usr:" \ - -e "s:niceExe = \"/bin/nice\":niceExe = \"${EPREFIX}/usr/bin/nice\":" \ - -e "s:/wt1/gordon/genome:${EPREFIX}/usr/bin:" \ - -i scripts/* contributions/* || die -} - -src_configure() { - append-cflags -std=gnu99 - append-lfs-flags -} - -src_compile() { - emake \ - CC="$(tc-getCC)" \ - CXX="$(tc-getCXX)" \ - CFLAGS="${CFLAGS}" \ - CXXFLAGS="${CXXFLAGS}" \ - CPPFLAGS="${CPPFLAGS}" \ - LDFLAGS="${LDFLAGS}" \ - SAMTOOLS_CPPFLAGS="-I${EPREFIX}/usr/include/bam-0.1-legacy" \ - LIBS="-L${EPREFIX}/usr/$(get_libdir)" \ - X11_LIBS="$($(tc-getPKG_CONFIG) --libs x11)" \ - SAMTOOLS_LIBS="-lbam-0.1-legacy" -} - -src_install() { - dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} scripts/* contributions/* - - insinto /usr/lib/screenLibs - doins misc/*.{fa*,seq} - - if use examples; then - insinto /usr/share/${PN}/examples - doins -r \ - standard polyphred autofinish assembly_view 454_newbler \ - align454reads align454reads_answer solexa_example \ - solexa_example_answer selectRegions selectRegionsAnswer - fi - - cat > 99consed <<-_EOF_ || die - CONSED_HOME=${EPREFIX}/usr - CONSED_PARAMETERS=${EPREFIX}/etc/consedrc - _EOF_ - doenvd 99consed - - dodoc README.txt *_announcement.txt -} - -pkg_postinst() { - einfo "Package documentation is available at" - einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt" -} diff --git a/sci-biology/consed/files/consed-29-fix-build-system.patch b/sci-biology/consed/files/consed-29-fix-build-system.patch deleted file mode 100644 index 30819f93ac80..000000000000 --- a/sci-biology/consed/files/consed-29-fix-build-system.patch +++ /dev/null @@ -1,197 +0,0 @@ -Make build system semi-sane: -* Respect CC, CXX, CFLAGS, CXXFLAGS, CPPFLAGS, LDFLAGS and LIBS -* Remove default optimisation flags -* Remove -fpermissive from DEFS (as source builds fine now) -* Add large file support (LFS) via CPPFLAGS and not in Makefile - ---- a/makefile -+++ b/makefile -@@ -47,23 +47,20 @@ - # - # compilation - # --CXX= g++ --KRCC= gcc --CC=gcc -+CXX ?= g++ -+CC ?= gcc - - # - # --CFLGS= -w -DINLINE_RWTPTRORDEREDVECTOR -DINLINE_RWTVALORDEREDVECTOR -DINLINE_MBTVALVECTOR -DLINUX_COMPILE -DSOCKLEN_T_DEFINED -D__BOOL_DEFINED -DANSI_C -DOFSTREAM_OPEN_WITHOUT_PERMISSIONS -fpermissive -DNO_POUND_POUND_MACROS -DUSE_USING_IN_PUBLIC_TEMPLATE_CLASSES -DINT_CHAR_OPERATOR -D_FILE_OFFSET_BITS=64 -DSAMTOOLS_AVAILABLE -+DEFS = -DINLINE_RWTPTRORDEREDVECTOR -DINLINE_RWTVALORDEREDVECTOR -DINLINE_MBTVALVECTOR -DLINUX_COMPILE -DSOCKLEN_T_DEFINED -D__BOOL_DEFINED -DANSI_C -DOFSTREAM_OPEN_WITHOUT_PERMISSIONS -DNO_POUND_POUND_MACROS -DUSE_USING_IN_PUBLIC_TEMPLATE_CLASSES -DINT_CHAR_OPERATOR -DSAMTOOLS_AVAILABLE - --OPT= -O - # - # Include directory for template classes must be included - # in both compilation & link lines, even if .h file is - # found in default path. C front, gotta love it. - # --INC= -I/usr/X11R6/include -I/me1/gordon/samtools/samtools-0.1.18 -+INCLUDES = $(SAMTOOLS_CPPFLAGS) - --DEPENDENCIES= - # - # - # Linking -@@ -80,12 +77,9 @@ - # /lib/ld-linux.so.2 (0x003ee000) - # - # To fix cut/paste bug, I've made X11 always dynamic. --CLIBS= -lX11 --LPATH= -L/usr/X11R6/lib --ARCHIVES= /usr/X11R6/lib/libXm.a \ --/usr/X11R6/lib/libXt.a /usr/X11R6/lib/libSM.a \ --/usr/X11R6/lib/libICE.a /usr/X11R6/lib/libXext.a /usr/X11R6/lib/libXmu.a \ --/usr/X11R6/lib/libXp.a /usr/lib/libm.a /me1/gordon/samtools/samtools-0.1.18/libbam.a /me1/gordon/samtools/samtools-0.1.18/bcftools/libbcf.a /me1/gordon/zlib/zlib-1.2.5/libz.a -+ -+MOTIF_LIBS ?= -lXm -lXt -+ALL_LIBS = $(LIBS) $(MOTIF_LIBS) $(X11_LIBS) $(SAMTOOLS_LIBS) - - - -@@ -94,7 +88,6 @@ - # - #LDFLGS= -g - # static linking --LDFLGS= -g -rdynamic - - # - # the subdirectory used by cfront compilers gets cleaned -@@ -112,10 +105,10 @@ - # general compilation rules for .cpp, .cxx, .c files - # - .cpp.o: -- $(CXX) $(CFLGS) $(OPT) $(INC) -c $< -+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) $(DEFS) -c $< - - .c.o: -- $(CXX) $(CFLGS) $(OPT) $(INC) -c $< -+ $(CC) $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $(DEFS) -c $< - - # - # targets file included in generated makefile -@@ -593,17 +586,23 @@ - writeToRewriteReferenceFile.o \ - xsynchronize.o - -+SUBDIRS := misc/454 misc/mktrace misc/phd2fasta -+ -+all: consed $(SUBDIRS) -+ -+$(SUBDIRS): -+ $(MAKE) -C $@ -+ -+.PHONY: all $(SUBDIRS) -+ - consed: $(CONSED_OBJS) makefile checkLicenseKeyStub.o -- $(CXX) $(INC) $(LDFLGS) -o consed $(CONSED_OBJS) checkLicenseKeyStub.o \ -- $(ARCHIVES) $(LPATH) $(WARNINGS) $(CLIBS) $(XLIBS) -+ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o consed $(CONSED_OBJS) checkLicenseKeyStub.o $(ALL_LIBS) - - trial_consed: $(CONSED_OBJS) makefile checkLicenseKey.o -- $(CXX) $(INC) $(LDFLGS) -o trial_consed $(CONSED_OBJS) checkLicenseKey.o \ -- $(ARCHIVES) $(LPATH) $(WARNINGS) $(CLIBS) $(XLIBS) -+ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o trial_consed $(CONSED_OBJS) checkLicenseKey.o $(ALL_LIBS) - - pure: $(CONSED_OBJS) makefile checkLicenseKeyStub.o -- $(PURIFY) $(CXX) $(INC) $(LDFLGS) -o consed $(CONSED_OBJS) checkLicenseKeyStub.o \ -- $(ARCHIVES) $(LPATH) $(WARNINGS) $(CLIBS) $(XLIBS) -+ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o consed $(CONSED_OBJS) checkLicenseKeyStub.o $(ALL_LIBS) - - clean: - rm -rf *.o core $(TEMPLATE_DIR) -@@ -613,15 +612,15 @@ - # the Solaris 5.x compiler cannot optimize the following - - consedResources.o: -- $(CXX) $(WARNINGS) $(CFLGS) $(INC) $(DEPENDENCIES) -c consedResources.cpp -+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) $(DEFS) -c consedResources.cpp - - consedResources2.o: -- $(CXX) $(WARNINGS) $(CFLGS) $(INC) $(DEPENDENCIES) -c consedResources2.cpp -+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) $(DEFS) -c consedResources2.cpp - - # tlingit cannot optimize the following: - - guiEditResources.o: -- $(CXX) $(WARNINGS) $(CFLGS) $(INC) $(DEPENDENCIES) -c guiEditResources.cpp -+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) $(DEFS) -c guiEditResources.cpp - - guiEditResources.o : \ - assemblyViewTagTypeAndLine.h assert.h bIsNumericDouble.h \ ---- a/misc/454/Makefile -+++ b/misc/454/Makefile -@@ -0,0 +1,16 @@ -+CC ?= cc -+LIBM = -lm -+ -+DEFS = -DANSI_C -+ -+OBJS= sff2scf.c -+ -+sff2scf: $(OBJS) -+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $^ $(LIBM) -+ -+.c.o: -+ $(CC) $(CFLAGS) $(CPPFLAGS) $(DEFS) -c $< -+ -+clean: -+ rm -f $(OBJS) sff2scf -+ ---- a/misc/mktrace/Makefile -+++ b/misc/mktrace/Makefile -@@ -1,13 +1,17 @@ --CC= cc --CFLAGS= -g --CLIB= -lm -+CC ?= cc -+LIBM = -lm -+ -+DEFS = -DANSI_C - - OBJS= mktrace.o readFASTA.o writeSCF.o synTrace.o \ - freeTrace.o rwUtil.o writePhd.o getTime.o \ - readQUAL.o - - mktrace: $(OBJS) -- $(CC) $(CFLAGS) -o mktrace $(OBJS) $(CLIB) -+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $^ $(LIBM) -+ -+.c.o: -+ $(CC) $(CFLAGS) $(CPPFLAGS) $(DEFS) -c $< - - clean: - rm -f $(OBJS) mktrace ---- a/misc/phd2fasta/Makefile -+++ b/misc/phd2fasta/Makefile -@@ -1,8 +1,9 @@ --CC=cc --CFLAGS=-O -w --CLIB=-lm -+CC ?= cc -+LIBM = -lm - --OBJ= phd2fasta.o \ -+DEFS = -DANSI_C -+ -+OBJS= phd2fasta.o \ - readParam.o initParam.o checkParam.o \ - freeParam.o helpParam.o \ - readFOF.o readDIR.o readFOX.o \ -@@ -15,10 +16,11 @@ - - INC= phd2fasta.h - --SRC = $(OBJ:.o=.c) -- --phd2fasta: $(OBJ) -- $(CC) $(CFLAGS) -o phd2fasta $(OBJ) $(CLIB) -+phd2fasta: $(OBJS) -+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $^ $(LIBM) -+ -+.c.o: -+ $(CC) $(CFLAGS) $(CPPFLAGS) $(DEFS) -c $< - - clean: - rm -f $(OBJ) phd2fasta diff --git a/sci-biology/consed/files/consed-29-fix-c++14.patch b/sci-biology/consed/files/consed-29-fix-c++14.patch deleted file mode 100644 index 212b8d63d1e3..000000000000 --- a/sci-biology/consed/files/consed-29-fix-c++14.patch +++ /dev/null @@ -1,376 +0,0 @@ -Fix building with C++14: -* Add 'noexcept(false)' to throwing destructors in C++11 mode -* Properly guard C declarations with extern "C" scopes -* Avoid erroneous overloaded suffix operator errors, due to missing spaces -* Add explicit casts to avoid -Wnarrowing errors -* Add 'this->' for dependent identifiers in derived class templates, - previously required -fpermissive - ---- a/bvAlignedReads.cpp -+++ b/bvAlignedReads.cpp -@@ -126,7 +126,11 @@ - } - - --bvAlignedReads :: ~bvAlignedReads() { -+bvAlignedReads :: ~bvAlignedReads() -+#if __cplusplus >= 201103L -+ noexcept(false) -+#endif -+{ - - - assert( pBamView_->aBVAlignedReads_.remove( this ) ); ---- a/bvAlignedReads.h -+++ b/bvAlignedReads.h -@@ -81,7 +81,11 @@ - const FileName& filReferenceSequenceFile, - bamView* pBamView ); - -- ~bvAlignedReads(); -+ ~bvAlignedReads() -+#if __cplusplus >= 201103L -+ noexcept(false) -+#endif -+ ; - - bool operator==( const bvAlignedReads& myBVAlignedReads ) const { - return( this == &myBVAlignedReads ); ---- a/chromatData.h -+++ b/chromatData.h -@@ -58,6 +58,9 @@ - #ifndef CHROMATDATA_DEFINED - #define CHROMATDATA_DEFINED - -+#ifdef __cplusplus -+extern "C" { -+#endif - - #ifndef FLOAT - #define FLOAT double -@@ -131,4 +134,8 @@ - int freeChromatData(); - #endif - -+#ifdef __cplusplus -+} -+#endif -+ - #endif ---- a/compareContigs.cpp -+++ b/compareContigs.cpp -@@ -126,6 +126,9 @@ - - - compareContigs :: ~compareContigs() -+#if __cplusplus >= 201103L -+ noexcept(false) -+#endif - { - - if ( !bCalledFromMakeJoins_ ) { ---- a/compareContigs.h -+++ b/compareContigs.h -@@ -137,7 +137,11 @@ - compareContigs( ContigWin* pContigWin, const int nConsPos1); - compareContigs(); // for assemblyView - -- ~compareContigs(); -+ ~compareContigs() -+#if __cplusplus >= 201103L -+ noexcept(false) -+#endif -+ ; - - // this makes RWTPtrOrderedVector in ConsEd happy - bool operator==( const compareContigs& compC ) const { - ---- a/filePopupAndGetAceFilename.cpp -+++ b/filePopupAndGetAceFilename.cpp -@@ -317,7 +317,7 @@ - struct tm* pTM = localtime( &( pAceFile->stat_.st_mtime ) ); - - strftime( szDateTime, nDateTimeSize, -- quote(%H)":"quote(%M)":"quote(%S)" %e-%h-%Y", -+ quote(%H) ":" quote(%M) ":" quote(%S) " %e-%h-%Y", - pTM ); - - RWCString soDescription = RWCString( szDateTime ) + " " + (*pAceFile); -@@ -620,7 +620,7 @@ - struct tm* pTM = localtime( &( pAceFile->stat_.st_mtime ) ); - - strftime( szDateTime, nDateTimeSize, -- quote(%H)":"quote(%M)":"quote(%S)" %e-%h-%Y", -+ quote(%H) ":" quote(%M) ":" quote(%S) " %e-%h-%Y", - pTM ); - - RWCString soDescription = RWCString( szDateTime ) + " " + (*pAceFile); ---- a/findTraceExtrema.h -+++ b/findTraceExtrema.h -@@ -44,8 +44,15 @@ - - #include "chromatData.h" - -+#ifdef __cplusplus -+extern "C" { -+#endif -+ - int findTraceExtrema( ChromatData *chromatData ); - -+#ifdef __cplusplus -+} -+#endif - - #endif - ---- a/makeUpper.h -+++ b/makeUpper.h -@@ -42,6 +42,14 @@ - #ifndef MAKEUPPER_INCLUDED - #define MAKEUPPER_INCLUDED - -+#ifdef __cplusplus -+extern "C" { -+#endif -+ - void makeUpper( char* szStringOfMixedCase ); - -+#ifdef __cplusplus -+} -+#endif -+ - #endif ---- a/nextPhredPipeline.cpp -+++ b/nextPhredPipeline.cpp -@@ -476,7 +476,7 @@ - void nextPhredPipeline :: openAndLockControlFile() { - - -- nFDControlFile_ = open( filControlFile_.data(), O_CREAT |O_RDWR ); -+ nFDControlFile_ = open( filControlFile_.data(), O_CREAT |O_RDWR, 0600); - if ( nFDControlFile_ == -1 ) { - THROW_FILE_ERROR( filControlFile_ ); - } ---- a/readABI.h -+++ b/readABI.h -@@ -56,10 +56,18 @@ - - #include "chromatData.h" - -+#ifdef __cplusplus -+extern "C" { -+#endif -+ - #ifdef ANSI_C - ChromatData *readABI( char *fn, int *status ); - #else - ChromatData *readABI(); - #endif - -+#ifdef __cplusplus -+} -+#endif -+ - #endif ---- a/readData.h -+++ b/readData.h -@@ -44,6 +44,14 @@ - - #include "chromatData.h" - -+#ifdef __cplusplus -+extern "C" { -+#endif -+ - ChromatData *readData( char *filename, int* status ); - -+#ifdef __cplusplus -+} -+#endif -+ - #endif ---- a/readESD.h -+++ b/readESD.h -@@ -53,6 +53,10 @@ - - #include "chromatData.h" - -+#ifdef __cplusplus -+extern "C" { -+#endif -+ - typedef unsigned int4 DWORD; - typedef unsigned char TCHAR; - typedef char BYTE; -@@ -187,5 +191,7 @@ - ChromatData *readESD(); - #endif - -- -+#ifdef __cplusplus -+} -+#endif - ---- a/readSCF.h -+++ b/readSCF.h -@@ -56,6 +56,10 @@ - - #include "chromatData.h" - -+#ifdef __cplusplus -+extern "C" { -+#endif -+ - /* ---- Constants ---- */ - #define SCF_MAGIC (((((int4)'.'<<8)+(int4)'s'<<8)+(int4)'c'<<8)+(int4)'f') - #define scale(V,OLDMAX,NEWMAX) (int2)( (FLOAT) V * (FLOAT) NEWMAX / (FLOAT) OLDMAX ) -@@ -144,4 +148,8 @@ - int readSCF3(); - #endif - -+#ifdef __cplusplus -+} -+#endif -+ - #endif ---- a/readsense_bitmaps.h -+++ b/readsense_bitmaps.h -@@ -56,10 +56,10 @@ - static const int forward_bitmap_height = 19; - static char forward_bitmap_bits[] = { - 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, -- 0x00, 0x00, 0x00, 0x00, 0x38, 0x00, 0x00, 0x00, 0xf8, 0x07, 0x00, 0x00, -- 0xf8, 0xff, 0x00, 0x00, 0xf8, 0xff, 0x3f, 0x00, 0xf8, 0xff, 0xff, 0x07, -- 0xf8, 0xff, 0xff, 0x0f, 0xf8, 0xff, 0xff, 0x07, 0xf8, 0xff, 0x1f, 0x00, -- 0xf8, 0xff, 0x00, 0x00, 0xf8, 0x07, 0x00, 0x00, 0x38, 0x00, 0x00, 0x00, -+ 0x00, 0x00, 0x00, 0x00, 0x38, 0x00, 0x00, 0x00, (char)0xf8, 0x07, 0x00, 0x00, -+ (char)0xf8, (char)0xff, 0x00, 0x00, (char)0xf8, (char)0xff, 0x3f, 0x00, (char)0xf8, (char)0xff, (char)0xff, 0x07, -+ (char)0xf8, (char)0xff, (char)0xff, 0x0f, (char)0xf8, (char)0xff, (char)0xff, 0x07, (char)0xf8, (char)0xff, 0x1f, 0x00, -+ (char)0xf8, (char)0xff, 0x00, 0x00, (char)0xf8, 0x07, 0x00, 0x00, 0x38, 0x00, 0x00, 0x00, - 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, - 0x00, 0x00, 0x00, 0x00}; - -@@ -67,10 +67,10 @@ - static const int reverse_bitmap_height = 19; - static char reverse_bitmap_bits[] = { - 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, -- 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x07, 0x00, 0x00, 0xf8, 0x07, -- 0x00, 0xc0, 0xff, 0x07, 0x00, 0xff, 0xff, 0x07, 0xf8, 0xff, 0xff, 0x07, -- 0xfc, 0xff, 0xff, 0x07, 0xf8, 0xff, 0xff, 0x07, 0x00, 0xfe, 0xff, 0x07, -- 0x00, 0xc0, 0xff, 0x07, 0x00, 0x00, 0xf8, 0x07, 0x00, 0x00, 0x00, 0x07, -+ 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x07, 0x00, 0x00, (char)0xf8, 0x07, -+ 0x00, (char)0xc0, (char)0xff, 0x07, 0x00, (char)0xff, (char)0xff, 0x07, (char)0xf8, (char)0xff, (char)0xff, 0x07, -+ (char)0xfc, (char)0xff, (char)0xff, 0x07, (char)0xf8, (char)0xff, (char)0xff, 0x07, 0x00, (char)0xfe, (char)0xff, 0x07, -+ 0x00, (char)0xc0, (char)0xff, 0x07, 0x00, 0x00, (char)0xf8, 0x07, 0x00, 0x00, 0x00, 0x07, - 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, - 0x00, 0x00, 0x00, 0x00}; - ---- a/readType.h -+++ b/readType.h -@@ -56,11 +56,19 @@ - - #include "chromatData.h" - -+#ifdef __cplusplus -+extern "C" { -+#endif -+ - #ifdef ANSI_C - int readType( char *filename ); - #else - int readType(); - #endif - -+#ifdef __cplusplus -+} -+#endif -+ - #endif - ---- a/rwtptrsortedvector.h -+++ b/rwtptrsortedvector.h -@@ -57,7 +57,6 @@ - #ifdef USE_USING_IN_PUBLIC_TEMPLATE_CLASSES - using RWTPtrOrderedVector<TP>::nCurrentLength_; - using RWTPtrOrderedVector<TP>::isEmpty; -- using RWTPtrOrderedVector<TP>::nCurrentLength_; - using RWTPtrOrderedVector<TP>::length; - using RWTPtrOrderedVector<TP>::ppArray_; - using RWTPtrOrderedVector<TP>::data; -@@ -84,7 +83,7 @@ - if ( nInsertBeforeIndex == RW_NPOS ) - nInsertBeforeIndex = nCurrentLength_; - -- insertAt( nInsertBeforeIndex, pVal ); -+ this->insertAt( nInsertBeforeIndex, pVal ); - } - - // don't copy this. copy mbtValOrderedVectorOfRWCString's method instead ---- a/rwtvalsortedvector.h -+++ b/rwtvalsortedvector.h -@@ -74,7 +74,7 @@ - if ( nPos == RW_NPOS ) - nPos = nCurrentLength_; - -- insertAt( nPos, val ); -+ this->insertAt( nPos, val ); - } - - ---- a/rwUtil.h -+++ b/rwUtil.h -@@ -51,6 +51,10 @@ - *|***************************************************************************|* - */ - -+#ifdef __cplusplus -+extern "C" { -+#endif -+ - #ifdef ANSI_C - int2 inSwpSint2( char *ptr ); - int4 inSwpSint4( char *ptr ); -@@ -97,3 +101,6 @@ - int writeUint4(); - #endif - -+#ifdef __cplusplus -+} -+#endif ---- a/soGetDateTime.cpp -+++ b/soGetDateTime.cpp -@@ -62,13 +62,13 @@ - else if ( nFormat == nDotInMiddle ) { - strftime( szDateTime, - nDateTimeSize, -- "%y%m%d."quote(%H)quote(%M)quote(%S), -+ "%y%m%d." quote(%H)quote(%M)quote(%S), - localtime( &timee ) ); - } - else { - strftime( szDateTime, - nDateTimeSize, -- "%y%m%d:"quote(%H)quote(%M)quote(%S), -+ "%y%m%d:" quote(%H)quote(%M)quote(%S), - localtime( &timee ) ); - } - ---- a/szGetTime.h -+++ b/szGetTime.h -@@ -42,9 +42,15 @@ - #ifndef szGetTime_included - #define szGetTime_included - --char *szGetTime(); -+#ifdef __cplusplus -+extern "C" { -+#endif - -+char *szGetTime(); - -+#ifdef __cplusplus -+} -+#endif - - #endif - diff --git a/sci-biology/consed/files/consed-29-fix-perl-shebang.patch b/sci-biology/consed/files/consed-29-fix-perl-shebang.patch deleted file mode 100644 index a27a3537a8d1..000000000000 --- a/sci-biology/consed/files/consed-29-fix-perl-shebang.patch +++ /dev/null @@ -1,701 +0,0 @@ -Make perl shebangs portable, such that the scripts can also be used on Gentoo Prefix. -Rationale: https://blogs.gentoo.org/mgorny/2016/02/08/a-quick-note-on-portable-shebangs/ - ---- a/contributions/ace2fof -+++ b/contributions/ace2fof -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - - # .-----------------------------------------------------------------------------------. - # | | -@@ -107,6 +107,7 @@ - # | | - # `-----------------------------------------------------------------------------------' - #Fixed this file for taking Aracne's Ace file by syang 05152002 -+use warnings; - use strict; - use POSIX qw(fmod); - ---- a/contributions/ace2OligosWithComments.perl -+++ b/contributions/ace2OligosWithComments.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - # - # ace2Oligos.perl - # -@@ -18,6 +18,8 @@ - # Rev: 020528 to print comments in oligo tags upon request (Peter Kos) - # - -+use warnings; -+ - $szUsage = "\nUsage: $0 (name of ace file) (name of oligo file) [Print|Comment|PrintComment]\n"; - - die "$szUsage" if (( $#ARGV != 1 ) && ( $#ARGV != 2 )); ---- a/contributions/aceContigs2Phds.perl -+++ b/contributions/aceContigs2Phds.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - # - # aceContigs2Phd.perl - # -@@ -13,6 +13,8 @@ - # Acknowledgements: Borrowed as much as I could from determineReadTypes.Perl - # and fasta2Phd.perl - -+use warnings; -+ - $szUsage = "Usage: aceContigs2Phds.perl [-s minimum-contig-size] <name of ace file>"; - $nContigLimit = 2000; - ---- a/contributions/acestatus.pl -+++ b/contributions/acestatus.pl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - - # acestatus.pl - # author: Cliff Wollam -@@ -14,6 +14,7 @@ - # USAGE FROM THE COMMAND LINE: - # acestatus.pl ace_filename - -+use warnings; - use strict; - - if($#ARGV >= 0) { ---- a/contributions/cons.perl -+++ b/contributions/cons.perl -@@ -1,5 +1,6 @@ --#!/usr/bin/perl -+#!/usr/bin/env perl - -+use warnings; - use strict; - use Cwd; - ---- a/contributions/mergeAces.perl -+++ b/contributions/mergeAces.perl -@@ -1,4 +1,4 @@ --#! /usr/local/bin/perl -w -+#!/usr/bin/env perl - - # Bugs and complaints to Bill Gilliland, billg@ucdavis.edu. - # mergeAces.perl v. 0.2 5/22/01 -@@ -9,6 +9,7 @@ - # project directory (if it doesn't already exist) with all the cgrams - # and phd files of the original projects. - -+use warnings; - use Getopt::Long; - use File::Copy; - $pathRoot = $ENV{"PWD"}; ---- a/contributions/phredPhrapWithPhdBalls -+++ b/contributions/phredPhrapWithPhdBalls -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - # - # phredPhrapWithPhdBalls - # modified from phredPhrap by Ben Allen at LANL -@@ -73,6 +73,7 @@ - # Rev: 120312 to not duplicate consensus tags during miniassembly - # Rev: 120717 Ben Allen (LANL) to use reads from phdballs as well as phd_dir - -+use warnings; - - $szVersion = "120312"; - ---- a/contributions/recover_consensus_tags -+++ b/contributions/recover_consensus_tags -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - - # Purpose: Transfers all consensus tags from a set of old assemblies to - # a new assembly. -@@ -14,6 +14,7 @@ - # rct ace_filename <only ace file to be transfer (optional)> - # You must be in the edit_dir where the ace file is located - -+use warnings; - use strict; - - ---- a/contributions/revert_fof -+++ b/contributions/revert_fof -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - - # PURPOSE: If the user really screws up a read, to back out all changes. - # You must reassemble after using this. -@@ -19,6 +19,8 @@ - # phd extensions. - # revert_fof use file of files to give reads to revert 3/14/01 SL - -+use warnings; -+ - $szUsage = "Enter a file of files name, please!"; - - die $szUsage if ( $#ARGV != 0 ); ---- a/contributions/sff2phd.perl -+++ b/contributions/sff2phd.perl -@@ -1,4 +1,5 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl -+use warnings; - use strict; - # SFF to PHD files converter, with 454 paired reads and MID support - # Version 0.15 - 111229 ---- a/contributions/sff2phd_Samborskyy -+++ b/contributions/sff2phd_Samborskyy -@@ -1,4 +1,5 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl -+use warnings; - use strict; - # SFF to PHD files converter, with 454 paired reads and MID support - # Version 0.10 - 101110 ---- a/scripts/ace2Fasta.perl -+++ b/scripts/ace2Fasta.perl -@@ -1,7 +1,9 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - # - # Purpose: makes a contigs file out of an ace file - -+use warnings; -+ - $szUsage = "Usage: ace2Contigs.perl (ace file)"; - - ---- a/scripts/ace2Oligos.perl -+++ b/scripts/ace2Oligos.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - # - # ace2Oligos.perl - # -@@ -16,6 +16,8 @@ - # Rev: 000330 to handle comments in oligo tags - # - -+use warnings; -+ - $szUsage = "Usage: ace2Oligos.perl (name of ace file) (name of oligo file)"; - - if ( $ARGV[0] eq "-V" || $ARGV[0] eq "-v" ) { ---- a/scripts/add454Reads.perl -+++ b/scripts/add454Reads.perl -@@ -1,11 +1,11 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - - # add454Reads.perl - # part of Consed package - # - # DG with help from Hao Wang to screen vector - -- -+use warnings; - use File::Basename; - - ---- a/scripts/addReads2Consed.perl -+++ b/scripts/addReads2Consed.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - # - # Purpose: called by consed in order to add new reads to an - # existing assembly without reassemblying -@@ -29,6 +29,7 @@ - # Rev: 080320 (David Gordon) to use discrep_lists instead of alignments - # Rev: 130828 (David Gordon) to handle slashes (/) in read names - -+use warnings; - - $szVersion = "130828"; - if ( $#ARGV >= 0 ) { ---- a/scripts/addSangerReads.perl -+++ b/scripts/addSangerReads.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - - # addSangerReads.perl - -@@ -32,7 +32,7 @@ - # added is printed in a report ending with ".log". The name of this - # file is listed in auto.fof - -- -+use warnings; - - - $szVersion = "120717"; ---- a/scripts/addSolexaReads.perl -+++ b/scripts/addSolexaReads.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - - # addSolexaReads.perl - -@@ -54,7 +54,7 @@ - - $szUsage = "addSolexaReads.perl -ace (ace file) -fastqfof (solexa files) -fasta (fasta file) -readsList (file of list of desired reads) where -readsList is optional"; - -- -+use warnings; - use Getopt::Long; - - GetOptions( "ace=s" => \$szAceFile, ---- a/scripts/alignRNA2Genomic.perl -+++ b/scripts/alignRNA2Genomic.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - - # alignRNA2Genomic.perl - -@@ -6,6 +6,8 @@ - # consed-ready ace and phd ball with the RNA aligned against the - # genomic with introns being represented by large gaps - -+use warnings; -+ - $szVersion = "120717"; - - if ( $#ARGV == 0 ) { ---- a/scripts/alignSolexaReads2Refs.perl -+++ b/scripts/alignSolexaReads2Refs.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - - # Input: a file where each line looks like this: - # (solexa seq file) (read prefix) -@@ -10,6 +10,7 @@ - - # Output: a list of alignment files - -+use warnings; - - defined( $szConsedHome = $ENV{'CONSED_HOME'} ) || - ( $szConsedHome = "/usr/local/genome" ); ---- a/scripts/amplifyTranscripts.perl -+++ b/scripts/amplifyTranscripts.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - - # PURPOSE: runs consed -autoPCRAmplify in order to pick pcr primers - # for a large group of regions -@@ -40,7 +40,7 @@ - # That is, the left primers are given in top strand orientation, and - # the right primers are given in bottom strand orientation. - -- -+use warnings; - - defined( $szConsedHome = $ENV{'CONSED_HOME'} ) || - ( $szConsedHome = "/usr/local/genome" ); ---- a/scripts/autoPrimers.perl -+++ b/scripts/autoPrimers.perl -@@ -1,5 +1,6 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - -+use warnings; - - $szUsage = "autoPrimers.perl (fasta file of targets)"; - $szVersion = "141226"; ---- a/scripts/bam2Ace.perl -+++ b/scripts/bam2Ace.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - - - # Purpose: runs: -@@ -6,6 +6,7 @@ - # 2) consed -renameDuplicates - # 3) consed -removeColumnsOfPads - -+use warnings; - - $szUsage = "usage: bam2Ace.perl -bamFile (bam file) -regionsFile (regions file) (see README.txt for format of the regions file) -exec (consed executable name) -newAceFile (new ace file name) where the -exec (exec) is optional"; - ---- a/scripts/convertBedToBamScape.perl -+++ b/scripts/convertBedToBamScape.perl -@@ -1,4 +1,6 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl -+ -+use warnings; - - $szUsage = "usage: convertBedToBamScape.perl (Bed file) (BamScape file) (fasta file of all sequences) (conversion of reference names--optional)"; - ---- a/scripts/countEditedBases.perl -+++ b/scripts/countEditedBases.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - # - # countEditedBases.perl - # -@@ -11,6 +11,8 @@ - # - # - -+use warnings; -+ - while(<>) { - if ( /^CO / ) { - @aWords = split; ---- a/scripts/determineReadTypes.perl -+++ b/scripts/determineReadTypes.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - # determineReadTypes.perl - # - # Purpose: to write into the phd file information about the template -@@ -173,6 +173,7 @@ - # - ############################################################### - -+use warnings; - - # you can remove or comment out this line when you are satisfied with - # your customized version of this file. ---- a/scripts/fasta2Ace.perl -+++ b/scripts/fasta2Ace.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - # - # manyFasta2Ace.perl - # -@@ -13,6 +13,7 @@ - # - # NOTE: you must run this in edit_dir - -+use warnings; - use Getopt::Long; - - $szRevision = "141212"; ---- a/scripts/fasta2PhdBall.perl -+++ b/scripts/fasta2PhdBall.perl -@@ -1,4 +1,6 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl -+ -+use warnings; - - $nQuality = 20; - ---- a/scripts/fasta2Phd.perl -+++ b/scripts/fasta2Phd.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - # - # fasta2Phd.perl - # -@@ -20,6 +20,7 @@ - # June 2002, Bill Gilliland to allow the user to specify - # the quality value - -+use warnings; - use Getopt::Long; - GetOptions( "quality=i" => \$qualityValue); - ---- a/scripts/fastq2Phrap.perl -+++ b/scripts/fastq2Phrap.perl -@@ -1,4 +1,6 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl -+ -+use warnings; - - $szUsage = "fastq2Phrap.perl (fastq) or for paired reads fastq2Phrap.perl (fastq1) (fastq2) where fastq1 and fastq2 have corresponding mate pairs--e.g., the 5th read in fastq1 is the mate of the 5th read in fastq2--these fastq files are assumed to be in ../solexa_dir--not the current directory\n"; - ---- a/scripts/filter454Reads.perl -+++ b/scripts/filter454Reads.perl -@@ -1,6 +1,6 @@ --#!/usr/bin/perl -w -- -+#!/usr/bin/env perl - -+use warnings; - use File::Basename; - - ---- a/scripts/findSequenceMatchesForConsed.perl -+++ b/scripts/findSequenceMatchesForConsed.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - - # findSequenceMatchesForConsed.perl - -@@ -16,6 +16,8 @@ - # REVISIONS: 021127 (DG) to write (project).(date).(time).fasta instead of - # (project).fasta.screen.ace.1.(date).(time).fasta - -+use warnings; -+ - $szVersion = "021127"; - - $szUsage = "Usage: findSequenceMatchesForConsed.perl (ace file) (crossmatch parameters, if any)"; ---- a/scripts/fixContigEnd.perl -+++ b/scripts/fixContigEnd.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - - # fixContigEnd.perl - -@@ -7,6 +7,7 @@ - # consed -ace (acefile) -fixContigEnds - # - -+use warnings; - - $szUsage = "fixContigEnd.perl (fasta file of reads for input) (fof for ace file, output)"; - ---- a/scripts/lib2Phd.perl -+++ b/scripts/lib2Phd.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - # - # lib2Phd.perl - # -@@ -23,6 +23,8 @@ - # accept fasta library files as input. The output file is named - # according to the first, non-space block of text on each fasta defline. - -+use warnings; -+ - $nQuality = 20; - - $szUsage = "Usage: lib2Phd.perl <name of file with fasta library>"; ---- a/scripts/makePhdBall.perl -+++ b/scripts/makePhdBall.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - - # PURPOSE: concatenate all phd file into a single phd.ball - # for the purpose of fast startup of consed -@@ -9,6 +9,7 @@ - # - # February 2008, David Gordon - -+use warnings; - - if ( $#ARGV >= 0 ) { - if ( $ARGV[0] eq "-v" || $ARGV[0] eq "-V" ) { ---- a/scripts/makeRegionsFile.perl -+++ b/scripts/makeRegionsFile.perl -@@ -1,10 +1,12 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - - # makeRegionsFile.perl - # To be used with consed -bam2Ace - # Takes a fasta file of sequences and makes a regions file that - # specifies the entire length of each sequence. - -+use warnings; -+ - $szUsage = "makeRegionsFile.perl (name of fasta file)"; - - $szVersion = "110914"; ---- a/scripts/orderPrimerPairs.perl -+++ b/scripts/orderPrimerPairs.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - - # PURPOSE: puts the primers in 96 well format for ordering. - # creates a file that can be emailed to -@@ -13,6 +13,8 @@ - # 2) a file of primer pairs, sorted by product size - # 3) a fasta file of the primers, for your convenience for analysis - -+use warnings; -+ - $| = 1; - - $szUsage = "orderPrimerPairs.perl"; ---- a/scripts/phd2Ace.perl -+++ b/scripts/phd2Ace.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - # - # phd2Ace.perl - # -@@ -13,6 +13,8 @@ - # REV: 981002 (David Gordon) for new ace format - # 981210 (DG) to eliminate warning message - -+use warnings; -+ - $szPhdDirPath = "../phd_dir"; - - $szUsage = "Usage: phd2Ace.perl <filename (without directory) of phd file>\nThe phd file is assumed to reside in $szPhdDirPath"; ---- a/scripts/phredPhrap -+++ b/scripts/phredPhrap -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - # - # phredPhrap - # -@@ -70,6 +70,8 @@ - # Rev: 110609 to allow masking of vector sequence when doing miniassemblies - # Rev: 120312 to not duplicate consensus tags during miniassembly - -+use warnings; -+ - $szVersion = "120312"; - - ---- a/scripts/picard2Regions.perl -+++ b/scripts/picard2Regions.perl -@@ -1,10 +1,12 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - - # PURPOSE: takes a file of locations in the format for bamScape custom - # navigation (Picard IntervalList format), adds 2000 bases of context - # to each side of each location, and prints a region file in format to - # be used by bam2Ace - -+use warnings; -+ - $szRevision = "140903"; # David Gordon - - if ( defined( $ARGV[0] ) && ---- a/scripts/removeReads -+++ b/scripts/removeReads -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - # - # PURPOSE: removes a list of chromats from an assembly. After running this, - # you must reassemble to create an ace file without the given phd files. -@@ -16,6 +16,8 @@ - # removeReads (name of fof's) - # - -+use warnings; -+ - $szUsage = "Usage: removeReads listOfReads.fof"; - - die "$szUsage" if ( $#ARGV != 0 ); ---- a/scripts/revertToUneditedRead -+++ b/scripts/revertToUneditedRead -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - # - # PURPOSE: If the user really screws up a read, to back out all changes. - # You must reassemble after using this. -@@ -16,6 +16,7 @@ - # REV: 7/24/98 (DG) - # REV: 8/28/2013 (DG) to handle readnames with slashes (/) - -+use warnings; - - $szUsage = "Usage: revertToUneditedRead (read name without any .phd.# extension)"; - ---- a/scripts/selectOneRegion.perl -+++ b/scripts/selectOneRegion.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - - # selectOneRegion.perl - # -@@ -11,6 +11,7 @@ - # and you will create an ace file chr15_51000000.ace or chr15_51000000.ace.1 - # (or higher extension) - -+use warnings; - use Getopt::Long; - - ---- a/scripts/selectRegions.perl -+++ b/scripts/selectRegions.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - - # selectRegions.perl - # -@@ -43,7 +43,7 @@ - # my_new_ace.ace says what the ace file should be called (the - # extension may not start at 1 if there is already a .1 - -- -+use warnings; - - $SIG{__WARN__} = dieWhenGetWarning; - sub dieWhenGetWarning { ---- a/scripts/tagRepeats.perl -+++ b/scripts/tagRepeats.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - # - # PROGRAM: tagRepeats.perl - # PURPOSE: to put consensus tags on any found ALU or any other -@@ -10,6 +10,7 @@ - # INPUTS: The ace file. You must also provide a fasta file of the - # ALU or any other sequence you want to tag - -+use warnings; - - $szVersion = "090209"; - if ( $#ARGV >= 0 ) { ---- a/scripts/testSocket.perl -+++ b/scripts/testSocket.perl -@@ -1,7 +1,8 @@ --#! /usr/local/bin/perl -w -+#!/usr/bin/env perl - - # open a socket to consed -- -+ -+use warnings; - use IO::Socket; - - # Consed makes a file which has nothing but the port number. ---- a/scripts/transferConsensusTags.perl -+++ b/scripts/transferConsensusTags.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - # - # Purpose: Transfers consensus tags from an old assembly to - # a new assembly. -@@ -44,6 +44,8 @@ - # Nov 2001, DG to handle cloneEnd tags which have orientation - # Mar 2012, DG to prevent duplicating tags after miniassembly - -+use warnings; -+ - $szUsage = "Usage: transferConsensusTags.perl (old ace file) (new ace file) (file of list of old contigs with consensus tags to be transferred)"; - - if ( $ARGV[0] eq "-V" || $ARGV[0] eq "-v" ) { diff --git a/sci-biology/consed/files/consed-29-fix-qa.patch b/sci-biology/consed/files/consed-29-fix-qa.patch deleted file mode 100644 index 90e180da0174..000000000000 --- a/sci-biology/consed/files/consed-29-fix-qa.patch +++ /dev/null @@ -1,294 +0,0 @@ -Fix various QA violations, due to -* implicit declarations -* incorrect printf() format specifiers -* incorrect function prototypes -* remove unsafe gets() fucntion - ---- a/misc/454/sff2scf.c -+++ b/misc/454/sff2scf.c -@@ -39,6 +39,7 @@ - void writeScfFile(char *filearg, char *outfile); - void writeScfCommand(char *filearg, char *outfile); - -+int sffinfo(int argc, char *argv[], FILE* pTempFile ); - - int main(int argc, char *argv[]) - { ---- a/misc/mktrace/mktrace.c -+++ b/misc/mktrace/mktrace.c -@@ -70,9 +70,9 @@ - else - { - printf( "enter FASTA filename: " ); -- gets( ifnm ); -+ fgets( ifnm, sizeof(ifnm), stdin ); - printf( "enter output filename: " ); -- gets( ofnm ); -+ fgets( ofnm, sizeof(ofnm), stdin ); - } - - /* -@@ -192,7 +192,7 @@ - /* - ** Write phd file. - */ -- if( writePhd( ofnm, numBase, seq, qual, pos, numPoint, trace ) == ERROR ) -+ if( writePhd( ofnm, numBase, seq, qual, pos, numPoint ) == ERROR ) - { - fprintf( stderr, "mktrace: error: bad status: writePhd\n" ); - free( seq ); ---- a/misc/mktrace/mktrace.h -+++ b/misc/mktrace/mktrace.h -@@ -37,8 +37,8 @@ - int writeSCF( char *filename, int numBase, char *seq, int numPoint, float **trace ); - int freeTrace( float **trace ); - char *readFASTA( char *filename, char *entryName, char *comments, int *len ); --int writePhd( char *ofnm, int numBase, char *seq, int *pos, int numPoint ); - int *readQUAL( char *filename, char *entryName, char *comments, int *len ); -+char *getTime( void ); - #else - int writePhd(); - float **synTrace(); ---- a/misc/phd2fasta/phd2fasta.h -+++ b/misc/phd2fasta/phd2fasta.h -@@ -276,6 +276,10 @@ - Comments *comments, Seq *seq, TagList *tagList, char *emsg ); - int checkIntString( char *string ); - int delimiterTest( char *string, unsigned int mask ); -+int checkParam( Option *option ); -+char* getVersion( void ); -+int showDoc( void ); -+char* getTime( void ); - #else - Option *getOption(); - struct Tag *allocTag(); ---- a/misc/phd2fasta/readStdTag.c -+++ b/misc/phd2fasta/readStdTag.c -@@ -699,11 +699,11 @@ - if( fstat ) - { - fprintf( stderr, -- "readStdTag: %s: line: %d: unexpected delimiter %s\n", -+ "readStdTag: %s: line: %p: unexpected delimiter %s\n", - filename, - nline, - line ); -- sprintf( emsg, "%s: line: %d: unexpected delimiter %s\n", -+ sprintf( emsg, "%s: line: %p: unexpected delimiter %s\n", - filename, - nline, - line ); ---- a/misc/phd2fasta/readWholeReadTag.c -+++ b/misc/phd2fasta/readWholeReadTag.c -@@ -393,11 +393,11 @@ - if( fstat ) - { - fprintf( stderr, -- "readWholeReadTag: %s: line: %d: unexpected delimiter %s\n", -+ "readWholeReadTag: %s: line: %p: unexpected delimiter %s\n", - filename, - nline, - line ); -- sprintf( emsg, "%s: line: %d: unexpected delimiter %s\n", -+ sprintf( emsg, "%s: line: %p: unexpected delimiter %s\n", - filename, - nline, - line ); ---- a/misc/phd2fasta/writeFasta.c -+++ b/misc/phd2fasta/writeFasta.c -@@ -39,7 +39,7 @@ - #include "phd2fasta.h" - - #ifdef ANSI_C --writeFasta( FILE *sfp, FILE *qfp, FILE *bfp, -+int writeFasta( FILE *sfp, FILE *qfp, FILE *bfp, - int outBasePosOption, - Comments *comments, Seq *seq, TagList *tagList, char *emsg ) - #else ---- a/motifutils.cpp -+++ b/motifutils.cpp -@@ -202,13 +202,13 @@ - void printButtonEvent( XButtonEvent* pEvent ) { - - printf( "type = %d\n", pEvent->type ); -- printf( "serial = %d\n", pEvent->serial ); -+ printf( "serial = %lu\n", pEvent->serial ); - printf( "send_event = %s\n", szPrintBool( pEvent->send_event ) ); -- printf( "*display = %x\n", pEvent->display ); -- printf( "window = %x\n", pEvent->window ); -- printf( "root = %x\n", pEvent->root ); -- printf( "subwindow = %x\n", pEvent->subwindow ); -- printf( "time = %d\n", pEvent->time ); -+ printf( "*display = %p\n", pEvent->display ); -+ printf( "window = %lu\n", pEvent->window ); -+ printf( "root = %lu\n", pEvent->root ); -+ printf( "subwindow = %lu\n", pEvent->subwindow ); -+ printf( "time = %lu\n", pEvent->time ); - printf( "x = %d\n", pEvent->x ); - printf( "y = %d\n", pEvent->y ); - printf( "x_root = %d\n", pEvent->x_root ); ---- a/parseAceFile.cpp -+++ b/parseAceFile.cpp -@@ -45,6 +45,7 @@ - using namespace std; - #include "basesegment.h" - #include <stdio.h> -+#include <stddef.h> - #include <string.h> - #include <sstream> - #include "mbt_errors.h" -@@ -292,7 +293,7 @@ - char* szPossibleComp = szReadName + nLength - nCOMP; - - if (memcmp( szPossibleComp, szCOMP, nCOMP ) == 0 ) { -- szPossibleComp = '\0'; -+ szPossibleComp = NULL; - return( true ); - } - else ---- a/phaster2PhdBall.cpp -+++ b/phaster2PhdBall.cpp -@@ -547,7 +547,7 @@ - - int nTokens = - sscanf( soLine_.data(), -- "%s %*s %d %d %lld %s %s %*s %d %d %lld %s %s\n", -+ "%s %*s %d %d %ld %s %s %*s %d %d %ld %s %s\n", - soReadName_.data(), - &nRead1Left_, - &nRead1Right_, ---- a/printAutoFinishMiscInfo.cpp -+++ b/printAutoFinishMiscInfo.cpp -@@ -80,7 +80,7 @@ - int nError = stat( (char*) soAceFileFullPathname.data(), &statBuffer ); - - if (nError == 0 ) { -- fprintf( pAO,"size: %d date: %s\n", -+ fprintf( pAO,"size: %ld date: %s\n", - (long) statBuffer.st_size, - ctime( &( statBuffer.st_mtime )) ); - ---- a/printAutoFinishParameters.cpp -+++ b/printAutoFinishParameters.cpp -@@ -206,7 +206,7 @@ - pCP->nInexactSearchForStringMaxPerCentMismatch_ ); - - fprintf( pAO, "! when using the inexact search for string, allow up to this\n"); -- fprintf( pAO, "! % mismatch: the sum of the insertion, deletion, and substitution\n"); -+ fprintf( pAO, "! %% mismatch: the sum of the insertion, deletion, and substitution\n"); - fprintf( pAO, "! differences divided by the length of the query string\n"); - fprintf( pAO, "! (YES)\n"); - fprintf( pAO, "consed.onlyAllowOneReadWriteConsedAtATime: %s\n", -@@ -825,7 +825,7 @@ - fprintf( pAO, "! template will be 1500 bases from the forward read. But if this template\n"); - fprintf( pAO, "! has an insert that is shorter than average, the walk may walk into vector.\n"); - fprintf( pAO, "! To be conservative, we may want to assume that the insert is somewhat \n"); -- fprintf( pAO, "! shorter than average. By default, we assume that it is 90% as large as \n"); -+ fprintf( pAO, "! shorter than average. By default, we assume that it is 90%% as large as \n"); - fprintf( pAO, "! the average. This parameter gives that percentage. This parameter\n"); - fprintf( pAO, "! is used both by Consed and Autofinish.\n"); - fprintf( pAO, "! (OK)\n"); -@@ -1249,9 +1249,9 @@ - pCP->nAutoFinishConfidenceThatReadWillCoverSingleSubcloneRegion_ ); - - fprintf( pAO, "! Autofinish computes the per cent of existing reads are aligned at\n"); -- fprintf( pAO, "! each base position. Typically, this number starts at around 0% at\n"); -- fprintf( pAO, "! base position 1, rises to close to 100% at around base position 300,\n"); -- fprintf( pAO, "! and then drops again to 0% at base position 800 or so. This number\n"); -+ fprintf( pAO, "! each base position. Typically, this number starts at around 0%% at\n"); -+ fprintf( pAO, "! base position 1, rises to close to 100%% at around base position 300,\n"); -+ fprintf( pAO, "! and then drops again to 0%% at base position 800 or so. This number\n"); - fprintf( pAO, "! specifies how high the number must be for Autofinish to consider an\n"); - fprintf( pAO, "! Autofinish read to cover a single subclone region.\n"); - fprintf( pAO, "! (OK)\n"); -@@ -1295,7 +1295,7 @@ - ( ( pCP->bCheckIfTooManyWalks_ ) ? "true" : "false" ) ); - - fprintf( pAO, "! this just checks if the number of walks, pcr ends, and unknown reads\n"); -- fprintf( pAO, "! exceeds 20% of the total number of reads. If this is exceeded, then \n"); -+ fprintf( pAO, "! exceeds 20%% of the total number of reads. If this is exceeded, then \n"); - fprintf( pAO, "! a warning message is given. Typically, such a warning indicates\n"); - fprintf( pAO, "! that you have incorrectly customized determineReadTypes.perl\n"); - fprintf( pAO, "! (OK)\n"); -@@ -1446,7 +1446,7 @@ - ( ( pCP->bProcessMatePairsAtStartup_ ) ? "true" : "false" ) ); - - fprintf( pAO, "! This is necessary to show the mate pair flags, but it does add\n"); -- fprintf( pAO, "! around 15% to startup time.\n"); -+ fprintf( pAO, "! around 15%% to startup time.\n"); - fprintf( pAO, "! (OK)\n"); - fprintf( pAO, "consed.maximumNumberOfTracesShown: %d\n", - pCP->nMaximumNumberOfTracesShown_ ); -@@ -1796,7 +1796,7 @@ - (char*)pCP->soStoreTracePeakPositions_.data() ); - - fprintf( pAO, "! never, always or whenChromatAvailable\n"); -- fprintf( pAO, "! changing this to \"always\" increases memory usage by close to 100%,\n"); -+ fprintf( pAO, "! changing this to \"always\" increases memory usage by close to 100%%,\n"); - fprintf( pAO, "! especially if the assembler is Newbler. always means it will store\n"); - fprintf( pAO, "! the positions if they are present in the phd file/ball.\n"); - fprintf( pAO, "! \"whenChromatAvailable\" means it will store trace peak positions for\n"); ---- a/readPrimerScreenSequences.cpp -+++ b/readPrimerScreenSequences.cpp -@@ -167,7 +167,7 @@ - ++nSequenceNumber ) { - if ( pnLengthOfSequence[ nSequenceNumber ] != - strlen( pszSequence[ nSequenceNumber ] ) ) { -- sprintf( szErrorMessage, "inconsistency between pnLengthOfSequence %d and pszSequence %d for sequence number %d", -+ sprintf( szErrorMessage, "inconsistency between pnLengthOfSequence %d and pszSequence %zu for sequence number %d", - pnLengthOfSequence[ nSequenceNumber ], - strlen( pszSequence[ nSequenceNumber ] ), - nSequenceNumber ); ---- a/rwcstring.cpp -+++ b/rwcstring.cpp -@@ -235,7 +235,7 @@ - - nMaxLength_ = nDefaultLengthForConversions; - -- nCurrentLength_ = sprintf( sz_, "%d", lNumberToConvert ); -+ nCurrentLength_ = sprintf( sz_, "%ld", lNumberToConvert ); - - if ( nCurrentLength_ > nMaxLength_ ) { - // big trouble--might not even make it here--might segmentation fault ---- a/someOtherProgramSentACommandToConsed.cpp -+++ b/someOtherProgramSentACommandToConsed.cpp -@@ -89,7 +89,7 @@ - - char szLine2[ nMaxLine ]; - -- sprintf( szLine2, "# of chars = %d %s", strlen( szLine ), szLine ); -+ sprintf( szLine2, "# of chars = %zu %s", strlen( szLine ), szLine ); - - cout << szLine2 << endl; - ---- a/tag.cpp -+++ b/tag.cpp -@@ -466,7 +466,7 @@ - fprintf( pPhdFile, "DATE: %s\n", soDate_.data() ); - - if ( lID_ != nUndefinedTagID ) { -- fprintf( pPhdFile, "ID: %d\n", lID_ ); -+ fprintf( pPhdFile, "ID: %ld\n", lID_ ); - } - - ---- a/userDefinedTagField.cpp -+++ b/userDefinedTagField.cpp -@@ -64,7 +64,7 @@ - - void userDefinedIntegerTagField :: writeThyselfToAceFileOrPhdBall( FILE* pFile ) { - -- fprintf( pFile, "%s %d\n", -+ fprintf( pFile, "%s %ld\n", - pUserDefinedTagFieldType_->soFieldName_.data(), - l_ ); - } -@@ -119,7 +119,7 @@ - - void userDefinedPointerTagField :: writeThyselfToAceFileOrPhdBall( FILE* pFile ) { - -- fprintf( pFile, "%s %d\n", -+ fprintf( pFile, "%s %ld\n", - pUserDefinedTagFieldType_->soFieldName_.data(), - lID_ ); - diff --git a/sci-biology/consed/metadata.xml b/sci-biology/consed/metadata.xml deleted file mode 100644 index 959160fe46b1..000000000000 --- a/sci-biology/consed/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/cutg/cutg-160-r1.ebuild b/sci-biology/cutg/cutg-160-r1.ebuild index 9a8130969019..417248e5890c 100644 --- a/sci-biology/cutg/cutg-160-r1.ebuild +++ b/sci-biology/cutg/cutg-160-r1.ebuild @@ -1,49 +1,42 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=7 DESCRIPTION="Codon usage tables calculated from GenBank" HOMEPAGE="http://www.kazusa.or.jp/codon/" SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz" -SLOT="0" LICENSE="public-domain" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" # Minimal build keeps only the indexed files (if applicable) and the # documentation. The non-indexed database is not installed. IUSE="emboss minimal" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" - -DEPEND="emboss? ( sci-biology/emboss )" -RDEPEND="${DEPEND}" - RESTRICT="binchecks strip" +RDEPEND="emboss? ( sci-biology/emboss )" +BDEPEND="${RDEPEND}" + src_compile() { if use emboss; then mkdir CODONS || die ebegin "Indexing CUTG for usage with EMBOSS." - EMBOSS_DATA="." cutgextract -auto -directory "${S}" || die \ - "Indexing CUTG failed." - eend + EMBOSS_DATA="." cutgextract -auto -directory "${S}" + eend $? "Indexing CUTG failed" || die fi } src_install() { - local file dodoc README CODON_LABEL SPSUM_LABEL + if ! use minimal; then - dodir /usr/share/${PN} - mv *.codon *.spsum "${ED}"/usr/share/${PN} || die \ - "Installing raw CUTG database failed." + insinto /usr/share/cutg + doins *.codon *.spsum fi if use emboss; then - dodir /usr/share/EMBOSS/data/CODONS - cd CODONS || die - for file in *; do - mv ${file} "${ED}"/usr/share/EMBOSS/data/CODONS/ || die \ - "Installing the EMBOSS-indexed database failed." - done + insinto /usr/share/EMBOSS/data + doins -r CODONS fi } diff --git a/sci-biology/cutg/metadata.xml b/sci-biology/cutg/metadata.xml index 0f8a9b77b269..aa55dcc37fe9 100644 --- a/sci-biology/cutg/metadata.xml +++ b/sci-biology/cutg/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/dialign-tx/dialign-tx-1.0.2-r2.ebuild b/sci-biology/dialign-tx/dialign-tx-1.0.2-r2.ebuild index 123977916f06..78681265a0b7 100644 --- a/sci-biology/dialign-tx/dialign-tx-1.0.2-r2.ebuild +++ b/sci-biology/dialign-tx/dialign-tx-1.0.2-r2.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 inherit toolchain-funcs @@ -15,12 +15,13 @@ LICENSE="LGPL-2.1" SLOT="0" KEYWORDS="~amd64 ~x86" -S=${WORKDIR}/${MY_P} +S="${WORKDIR}/${MY_P}" PATCHES=( "${FILESDIR}"/${P}-fix-build-system.patch "${FILESDIR}"/${P}-implicits.patch "${FILESDIR}"/${P}-modernize.patch "${FILESDIR}"/${P}-gnu89-inline.patch + "${FILESDIR}"/${P}-fno-common.patch ) src_configure() { @@ -34,12 +35,12 @@ src_compile() { src_install() { dobin source/dialign-tx - insinto /usr/$(get_libdir)/${PN}/conf + insinto /usr/$(get_libdir)/dialign-tx/conf doins -r conf/. } pkg_postinst() { einfo "The configuration directory is" - einfo "${EROOT%/}/usr/$(get_libdir)/${PN}/conf" - einfo "You will need to pass this to ${PN} on every run." + einfo "${EROOT}/usr/$(get_libdir)/dialign-tx/conf" + einfo "You will need to pass this to dialign-tx on every run." } diff --git a/sci-biology/dialign-tx/files/dialign-tx-1.0.2-fno-common.patch b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-fno-common.patch new file mode 100644 index 000000000000..de3104fa0ebb --- /dev/null +++ b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-fno-common.patch @@ -0,0 +1,22 @@ +--- a/source/parameters.c ++++ b/source/parameters.c +@@ -26,6 +26,8 @@ + + extern char *optarg; + extern int optind, opterr, optopt; ++ ++struct parameters* para; + /**************************** + * PROTEIN DEFAULT VALUES! * + ****************************/ +--- a/source/parameters.h ++++ b/source/parameters.h +@@ -138,7 +138,7 @@ + /* global variable */ + /* */ + /************************************************/ +-struct parameters* para; ++extern struct parameters* para; + + + diff --git a/sci-biology/dialign-tx/files/dialign-tx-1.0.2-gnu89-inline.patch b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-gnu89-inline.patch index 21f576f07052..fc8d0284e6ab 100644 --- a/sci-biology/dialign-tx/files/dialign-tx-1.0.2-gnu89-inline.patch +++ b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-gnu89-inline.patch @@ -1,5 +1,25 @@ +--- a/source/assemble.c ++++ b/source/assemble.c +@@ -574,7 +574,7 @@ + * returns a value <0 if there is an non-conflicting overlap + * returns 0 in all other non-conflicting cases + */ +-inline char confl_diag(struct alignment *algn, char *layer, struct diag *dg1, struct diag *dg2) { ++static inline char confl_diag(struct alignment *algn, char *layer, struct diag *dg1, struct diag *dg2) { + // if(dg1->multi_dg || dg2->multi_dg) error(" confl_diag(): cannot accept multi dgs!"); + int s1_1 = dg1->seq_p1.num; + int s1_2 = dg1->seq_p2.num; --- a/source/diag.c +++ b/source/diag.c +@@ -312,7 +312,7 @@ + /** + * calculates the overlap weight for the given diag + */ +-inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, ++void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, + struct prob_dist *pdist) { + int sn1 = dg->seq_p1.num; + int sn2 = dg->seq_p2.num; @@ -958,7 +958,7 @@ * The pointer returned (and the ones included in the struct) * has to be deallocted explicitely from memory. diff --git a/sci-biology/dialign-tx/metadata.xml b/sci-biology/dialign-tx/metadata.xml index 959160fe46b1..ccdff086e20b 100644 --- a/sci-biology/dialign-tx/metadata.xml +++ b/sci-biology/dialign-tx/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/dialign2/dialign2-2.2.1.ebuild b/sci-biology/dialign2/dialign2-2.2.1-r1.ebuild index db310e3fe8d3..13b56b66c37b 100644 --- a/sci-biology/dialign2/dialign2-2.2.1.ebuild +++ b/sci-biology/dialign2/dialign2-2.2.1-r1.ebuild @@ -1,24 +1,26 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 -inherit flag-o-matic toolchain-funcs +inherit toolchain-funcs DESCRIPTION="Multiple sequence alignment" HOMEPAGE="http://bibiserv.techfak.uni-bielefeld.de/dialign" SRC_URI="http://bibiserv.techfak.uni-bielefeld.de/applications/dialign/resources/downloads/dialign-${PV}-src.tar.gz" +S="${WORKDIR}/dialign_package" LICENSE="LGPL-2.1" SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -S=${WORKDIR}/dialign_package -PATCHES=( "${FILESDIR}"/${PN}-2.2.1-fix-build-system.patch ) +PATCHES=( + "${FILESDIR}"/${PN}-2.2.1-fix-build-system.patch + "${FILESDIR}"/${PN}-2.2.1-Wimplicit.patch +) src_configure() { tc-export CC - append-cppflags -I. -DCONS } src_compile() { @@ -26,12 +28,12 @@ src_compile() { } src_install() { - dobin src/${PN}-2 - insinto /usr/share/${PN} + dobin src/dialign2-2 + + insinto /usr/share/dialign2 doins -r dialign2_dir/. - cat >> "${T}"/80${PN} <<- EOF || die - DIALIGN2_DIR="${EPREFIX}/usr/share/${PN}" + newenvd - 80dialign2 <<- EOF + DIALIGN2_DIR="${EPREFIX}/usr/share/dialign2" EOF - doenvd "${T}"/80${PN} } diff --git a/sci-biology/dialign2/files/dialign2-2.2.1-Wimplicit.patch b/sci-biology/dialign2/files/dialign2-2.2.1-Wimplicit.patch new file mode 100644 index 000000000000..3f886171b070 --- /dev/null +++ b/sci-biology/dialign2/files/dialign2-2.2.1-Wimplicit.patch @@ -0,0 +1,205 @@ +--- a/src/alig_graph_closure.c ++++ b/src/alig_graph_closure.c +@@ -27,7 +27,7 @@ + void init_seq(CLOSURE *clos, int nbreseq, int *longseq); + void desinit_seq(CLOSURE *clos); + +-int print_aligSets(CLOSURE *clos, int nseq, int i); ++void print_aligSets(CLOSURE *clos, int nseq, int i); + + char DEBUG=0; + +@@ -309,7 +309,7 @@ + } + + +-int print_aligSets(CLOSURE *clos, int nseq, int i) ++void print_aligSets(CLOSURE *clos, int nseq, int i) + { + char nouveau_, terminer; + int n, ng, nd, nn, k; +@@ -395,7 +395,7 @@ + liberer(clos); + } + +-int addAlignedPositions(CLOSURE *clos, int seq1, int i, int seq2, int j) ++void addAlignedPositions(CLOSURE *clos, int seq1, int i, int seq2, int j) + { + char nouveau_, terminer; + int n, n1, n2, ng1, ng2, nd1, nd2, nn, k; +@@ -623,7 +623,7 @@ + return(!path(clos, y, j, x, i)); + } + +-int addAlignedSegments(CLOSURE *clos, int x, int i, int y, int j, int l) ++void addAlignedSegments(CLOSURE *clos, int x, int i, int y, int j, int l) + { + int k; + +--- a/src/alig_graph_closure.h ++++ b/src/alig_graph_closure.h +@@ -43,13 +43,13 @@ + + void freeAligGraphClosure(CLOSURE *clos); + +-int addAlignedPositions(CLOSURE *clos, int x, int i, int y, int j); ++void addAlignedPositions(CLOSURE *clos, int x, int i, int y, int j); + + int alignablePositions(CLOSURE *clos, int x, int i, int y, int j); + + int alignedPositions(CLOSURE *clos, int x, int i, int y, int j); + +-int addAlignedSegments(CLOSURE *clos, int x, int i, int y, int j, int l); ++void addAlignedSegments(CLOSURE *clos, int x, int i, int y, int j, int l); + + int alignableSegments(CLOSURE *clos, int x, int i, int y, int j, int l); + +--- a/src/anchor.c ++++ b/src/anchor.c +@@ -17,6 +17,7 @@ + #include "define.h" + #include "dialign.h" + #include "alig_graph_closure.h" ++#include "pratique.h" + + + extern int anc_num, *seqlen ; +@@ -24,6 +25,8 @@ + extern char *seq[MAX_SEQNUM]; + extern struct multi_frag *anchor_frg ; + ++extern int word_count( char *seq ); ++ + void anchor_check( int s1, int s2, int b1, int b2, int l , float scr ) { + + if( +@@ -101,7 +104,7 @@ + } + + +-int multi_anc_read( char *file_name ) { ++void multi_anc_read( char *file_name ) { + + char anc_file_name[ NAME_LEN ] ; + FILE *fp; +--- a/src/dialign.c ++++ b/src/dialign.c +@@ -218,7 +218,7 @@ + extern void subst_mat(char *file_name, int fragno , struct multi_frag *smp ); + extern int seq_read( char *in_file , char *sq[MAX_SEQNUM] , char **sqn , char **fsqn) ; + extern int anc_read( char *file_name ) ; +- extern int multi_anc_read( char *file_name ) ; ++ extern void multi_anc_read( char *file_name ) ; + extern void randomize( int r_numb , FILE *fp1 ); + extern int mini2(int a, int b); + extern int maxi2(int a, int b); +@@ -250,6 +250,9 @@ + extern void av_tree_print(); + extern void matrix_read( FILE *fp_mat ) ; + extern void mem_alloc( ) ; ++ extern void regex_parse( char *mot_regex ) ; ++ extern void seq_parse( char *mot_regex ) ; ++ extern void exclude_frg_read( char *file_name , int ***exclude_list) ; + + + /******************************/ +@@ -258,7 +261,7 @@ + + + +-main(int argc, char **argv) ++int main(int argc, char **argv) + { + int k, anc1, dia_counter, tmpi1, tmpi2 ; + +--- a/src/functions.c ++++ b/src/functions.c +@@ -853,7 +853,7 @@ + } + } + +-wgt_type_count( int num , int e_len, int *plus_cnt, int *minus_cnt, ++void wgt_type_count( int num , int e_len, int *plus_cnt, int *minus_cnt, + int *nuc_cnt , int *frg_inv, struct multi_frag *dia ) { + + int i, dc, pc, s1, pos; +@@ -882,7 +882,7 @@ + + + +-plot_calc( int num , int e_len, float *w_count, float *pl, ++void plot_calc( int num , int e_len, float *w_count, float *pl, + struct multi_frag *dia , FILE *fp_csc ) + { + int i, dc, pc, s1, pos; +--- a/src/input.c ++++ b/src/input.c +@@ -17,6 +17,7 @@ + #include "define.h" + #include "dialign.h" + #include "alig_graph_closure.h" ++#include "pratique.h" + + extern int max_dia , self_comparison ; + extern int sim_score[21][21]; +@@ -370,8 +371,11 @@ + } + + +- if ( fgets( line , MLINE , fp ) == NULL ) +- erreur("\n\n problem with file %s \n\n", file_name ); ++ if ( fgets( line , MLINE , fp ) == NULL ) { ++ char buffer [500]; ++ snprintf ( buffer, 500, "\n\n problem with file %s \n\n", file_name ); ++ erreur( buffer ); ++ } + else + if( w_type % 2 ) + av_sim_score_nuc = atof( line ); +--- a/src/output.c ++++ b/src/output.c +@@ -61,9 +61,9 @@ + extern void mini(int *a, int b); + extern void maxi(int *a, int b); + extern int int_test(float f); +- extern plot_calc( int num , int e_len, float *w_count, float *pl, ++ extern void plot_calc( int num , int e_len, float *w_count, float *pl, + struct multi_frag *dia , FILE *fp_csc ) ; +- extern wgt_type_count( int num , int e_len, int *plus_cnt, int *minus_cnt, ++ extern void wgt_type_count( int num , int e_len, int *plus_cnt, int *minus_cnt, + int *nuc_cnt , int *frg_inv, struct multi_frag *dia ) ; + + +--- a/src/pratique.c ++++ b/src/pratique.c +@@ -4,7 +4,7 @@ + + /* ------------------------------------------------------------*/ + +-void erreur(char *message) ++_Noreturn void erreur(char *message) + { + printf("%s\n", message); + exit(1); +--- a/src/pratique.h ++++ b/src/pratique.h +@@ -12,7 +12,7 @@ + + #define TAILLE_MAX_LIGNE_FICHIER 10000 + +-void erreur(char *message); ++_Noreturn void erreur(char *message); + + void *allouer(size_t taille); + void *reallouer(void *pointeur, size_t taille); +--- a/src/regex.c ++++ b/src/regex.c +@@ -151,7 +151,7 @@ + + } + +-seq_parse( char *mot_regex ) { ++void seq_parse( char *mot_regex ) { + int sn, ok , i ; + int sp, ap, rp, hv, match; + max_mot_offset = sqrt ( - log ( 0.1 ) * 10 / mot_factor ) * mot_offset_factor; diff --git a/sci-biology/dialign2/files/dialign2-2.2.1-fix-build-system.patch b/sci-biology/dialign2/files/dialign2-2.2.1-fix-build-system.patch index 45365c56e3a4..a4940ee867ee 100644 --- a/sci-biology/dialign2/files/dialign2-2.2.1-fix-build-system.patch +++ b/sci-biology/dialign2/files/dialign2-2.2.1-fix-build-system.patch @@ -1,14 +1,16 @@ --- a/src/makefile +++ b/src/makefile -@@ -10,8 +10,6 @@ +@@ -10,9 +10,7 @@ ############################### -CC = gcc -CFLAGS = -c -O -I$ -DCONS - #CFLAGS = -g -c -I$ -DCONS +-#CFLAGS = -g -c -I$ -DCONS ++CPPFLAGS += -I. -DCONS LIBS = -lm # + @@ -23,33 +21,4 @@ # diff --git a/sci-biology/dialign2/metadata.xml b/sci-biology/dialign2/metadata.xml index 959160fe46b1..ccdff086e20b 100644 --- a/sci-biology/dialign2/metadata.xml +++ b/sci-biology/dialign2/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/diya/Manifest b/sci-biology/diya/Manifest deleted file mode 100644 index 7a98449a5c8d..000000000000 --- a/sci-biology/diya/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST diya-1.0-rc4.tar.gz 386706 BLAKE2B 9d000892c3da9ec307a8e089056611bc9cd566ac2dea046601506215c1a5c5fb67621324d2d9e1de94ee4e00129325448e3a1a8aa417e5d8c07f564a77e287d6 SHA512 64a00cb7f07200882d0b97f58e6b7f26d08ab0eab43834c3d19ab08f61080f8edb4a63833095e876c72c087324d39b2c4334ed1d3aa0280b7efb6a7ab3e08007 diff --git a/sci-biology/diya/diya-1.0_rc4.ebuild b/sci-biology/diya/diya-1.0_rc4.ebuild deleted file mode 100644 index ae923b60da8d..000000000000 --- a/sci-biology/diya/diya-1.0_rc4.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI="5" - -inherit perl-module - -DESCRIPTION="Do It Yourself Annotation, tools & libraries for sequence assembly & annotation" -HOMEPAGE="http://gmod.org/wiki/Diya" -SRC_URI="mirror://sourceforge/diyg/files/diya/diya-1.0/diya-${PV/_/-}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -IUSE="-minimal" -KEYWORDS="~amd64 ~x86" - -DEPEND="sci-biology/bioperl - dev-perl/Data-Utilities - dev-perl/XML-Simple" -RDEPEND="${DEPEND} - !minimal? ( - sci-biology/mummer - sci-biology/glimmer - sci-biology/trnascan-se - sci-biology/infernal )" - -# see ftp://ftp.ncbi.nih.gov/blast/ to check if blast and blast+ are different from ncbi-tools and ncbi-tools++ -# * rfamscan.pl v0.1 (http://www.sanger.ac.uk/Users/sgj/code/) -# * UniRef50 (http://www.ebi.ac.uk/uniref/) -# * Protein Clusters (ftp://ftp.ncbi.nih.gov/genomes/Bacteria/CLUSTERS/) -# The file cddid_all.tbl can be found at ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/. - -S="${WORKDIR}/diya-${PV/_/-}" - -SRC_TEST=do - -src_install() { - mydoc="INSTALL README docs/diya.html" - perl-module_src_install - insinto /usr/share/${PN} - doins -r diya.conf docs examples scripts -} diff --git a/sci-biology/diya/metadata.xml b/sci-biology/diya/metadata.xml deleted file mode 100644 index 37bde911b940..000000000000 --- a/sci-biology/diya/metadata.xml +++ /dev/null @@ -1,11 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">diyg</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/elph/elph-1.0.1-r1.ebuild b/sci-biology/elph/elph-1.0.1-r3.ebuild index c166dd93e41d..6cfc05845358 100644 --- a/sci-biology/elph/elph-1.0.1-r1.ebuild +++ b/sci-biology/elph/elph-1.0.1-r3.ebuild @@ -1,22 +1,23 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit toolchain-funcs DESCRIPTION="Estimated Locations of Pattern Hits - Motif finder program" -LICENSE="Artistic" HOMEPAGE="http://cbcb.umd.edu/software/ELPH/" SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/elph/ELPH-${PV}.tar.gz" +S="${WORKDIR}/${PN^^}/sources" +LICENSE="Artistic" SLOT="0" -IUSE="" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos" -S=${WORKDIR}/${PN^^}/sources - -PATCHES=( "${FILESDIR}/${PN}-1.0.1-fix-build-system.patch" ) +PATCHES=( + "${FILESDIR}"/${PN}-1.0.1-fix-build-system.patch + "${FILESDIR}"/${PN}-1.0.1-drop-register-keyword.patch +) src_configure() { tc-export CC CXX diff --git a/sci-biology/elph/files/elph-1.0.1-drop-register-keyword.patch b/sci-biology/elph/files/elph-1.0.1-drop-register-keyword.patch new file mode 100644 index 000000000000..c05a280d4679 --- /dev/null +++ b/sci-biology/elph/files/elph-1.0.1-drop-register-keyword.patch @@ -0,0 +1,102 @@ +Bug: https://bugs.gentoo.org/898116 + +--- a/GBase.cpp ++++ b/GBase.cpp +@@ -208,8 +208,8 @@ char* rstrstr(char* rstart, char *lend, char* substr) { /*like strstr, but star + + //hash function used for strings in GHash + int strhash(const char* str){ +- register int h=0; +- register int g; ++ int h=0; ++ int g; + while (*str) { + h=(h<<4)+*str++; + g=h&0xF0000000; +--- a/GString.cpp ++++ b/GString.cpp +@@ -364,8 +364,8 @@ GString& GString::appendfmt(const char *fmt,...) { + } + + GString& GString::trim(char c) { +- register int istart; +- register int iend; ++ int istart; ++ int iend; + for (istart=0; istart<length() && chars()[istart]==c;istart++); + if (istart==length()) { + make_unique(); //edit operation ahead +@@ -384,8 +384,8 @@ GString& GString::trim(char c) { + } + + GString& GString::trim(char* c) { +- register int istart; +- register int iend; ++ int istart; ++ int iend; + for (istart=0; istart<length() && strchr(c, chars()[istart])!=NULL ;istart++); + if (istart==length()) { + replace_data(0); //string was entirely trimmed +@@ -405,7 +405,7 @@ GString& GString::trim(char* c) { + GString& GString::trimR(char c) { + //only trim the right end + //register int istart; +- register int iend; ++ int iend; + for (iend=length()-1; iend>=0 && chars()[iend]==c;iend--); + if (iend==-1) { + replace_data(0); //string was entirely trimmed +@@ -423,7 +423,7 @@ GString& GString::trimR(char c) { + } + + GString& GString::trimR(char* c) { +- register int iend; ++ int iend; + for (iend=length()-1; iend>=0 && strchr(c,chars()[iend])!=NULL;iend--); + if (iend==-1) { + replace_data(0); //string was entirely trimmed +@@ -440,7 +440,7 @@ GString& GString::trimR(char* c) { + } + + GString& GString::trimL(char c) { +- register int istart; ++ int istart; + for (istart=0; istart<length() && chars()[istart]==c;istart++); + if (istart==length()) { + replace_data(0); //string was entirely trimmed +@@ -457,7 +457,7 @@ GString& GString::trimL(char c) { + } + + GString& GString::trimL(char* c) { +- register int istart; ++ int istart; + for (istart=0; istart<length() && strchr(c,chars()[istart])!=NULL;istart++); + if (istart==length()) { + replace_data(0); //string was entirely trimmed +@@ -598,7 +598,7 @@ bool GString::is_space() const { + if (my_data == &null_data) + return false; + +- for (register const char *p = chars(); *p; p++) ++ for (const char *p = chars(); *p; p++) + if (!isspace(*p)) + return false; + +@@ -889,7 +889,7 @@ GString& GString::append(const GString& s) { + + GString& GString::upper() { + make_unique(); //edit operation ahead +- for (register char *p = chrs(); *p; p++) ++ for (char *p = chrs(); *p; p++) + *p = (char) toupper(*p); + + return *this; +@@ -900,7 +900,7 @@ GString& GString::upper() { + GString& GString::lower() { + make_unique(); + +- for (register char *p = chrs(); *p; p++) ++ for (char *p = chrs(); *p; p++) + *p = (char) tolower(*p); + + return *this; diff --git a/sci-biology/elph/metadata.xml b/sci-biology/elph/metadata.xml index 979dde87e15d..3be54ddaef3c 100644 --- a/sci-biology/elph/metadata.xml +++ b/sci-biology/elph/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.660.ebuild b/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.660-r1.ebuild index 6104a470f3f7..40dafb6bb62c 100644 --- a/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.660.ebuild +++ b/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.660-r1.ebuild @@ -1,15 +1,18 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 EBO_DESCRIPTION="Applications from the CBS group" -EBO_EAUTORECONF=1 - -inherit emboss-r2 +inherit autotools emboss-r3 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" S="${WORKDIR}/CBSTOOLS-1.0.0.650" PATCHES=( "${FILESDIR}"/${PN}-1.0.0.650_fix-build-system.patch ) + +src_prepare() { + default + eautoreconf +} diff --git a/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch b/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch index d29310efcb47..7ed96e5ff23b 100644 --- a/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch +++ b/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch @@ -1,13 +1,6 @@ - configure.ac | 49 +++++++------------------------------------------ - emboss_acd/Makefile.am | 2 +- - src/Makefile.am | 6 ++---- - 3 files changed, 10 insertions(+), 47 deletions(-) - -diff --git a/configure.ac b/configure.ac -index a70d4d2..b8f5e79 100644 ---- a/configure.ac -+++ b/configure.ac -@@ -635,33 +635,6 @@ AS_CASE([${host_os}], +--- a/configure.in ++++ b/configure.in +@@ -635,33 +635,6 @@ @@ -41,7 +34,7 @@ index a70d4d2..b8f5e79 100644 dnl FIXME: This does no longer seem required with Autoconf 2.67? dnl Intel MacOSX 10.6 puts X11 in a non-standard place dnl AS_IF([test "x${with_x}" != "xno"], -@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL +@@ -737,21 +710,6 @@ @@ -63,7 +56,7 @@ index a70d4d2..b8f5e79 100644 dnl Test if --enable-localforce given locallink="no" embprefix="/usr/local" -@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], +@@ -874,6 +832,13 @@ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) @@ -77,8 +70,6 @@ index a70d4d2..b8f5e79 100644 # Enable the purify tool: --enable-purify, sets CC and LIBTOOL -diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am -index e1c1878..e253c95 100644 --- a/emboss_acd/Makefile.am +++ b/emboss_acd/Makefile.am @@ -1,3 +1,3 @@ @@ -86,11 +77,9 @@ index e1c1878..e253c95 100644 -pkgdata_DATA = *.acd +pkgdata_DATA = $(srcdir)/*.acd pkgdatadir=$(prefix)/share/EMBOSS/acd -diff --git a/src/Makefile.am b/src/Makefile.am -index 824a03c..9db171d 100644 --- a/src/Makefile.am +++ b/src/Makefile.am -@@ -19,9 +19,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ +@@ -19,9 +19,7 @@ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ -I../../../ajax/acd -I../../../plplot else @@ -101,10 +90,21 @@ index 824a03c..9db171d 100644 endif if ISSHARED -@@ -65,5 +63,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ +@@ -36,7 +34,7 @@ + -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre \ + $(NLAIXLIBS) -leplplot + else +-AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \ ++AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \ + -lajaxdb -lensembl -lajaxg -lajax -lepcre $(NLAIXLIBS) -leplplot + endif + endif +@@ -64,6 +62,6 @@ + ../../../plplot/libeplplot.la \ $(XLIB) else - LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +-LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ - -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++LDADD = -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ + -lajax $(NLADD) $(XLIB) endif diff --git a/sci-biology/embassy-cbstools/metadata.xml b/sci-biology/embassy-cbstools/metadata.xml index d1b9a7602ec2..55784cd1ea18 100644 --- a/sci-biology/embassy-cbstools/metadata.xml +++ b/sci-biology/embassy-cbstools/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.660.ebuild b/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.660-r1.ebuild index 2d2a2c62632c..600b75769e5f 100644 --- a/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.660.ebuild +++ b/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.660-r1.ebuild @@ -1,13 +1,11 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 EBO_DESCRIPTION="Clustal Omega - Multiple Sequence Alignment" -EBO_EAUTORECONF=1 - -inherit emboss-r2 +inherit autotools emboss-r3 KEYWORDS="~amd64 ~x86 ~x86-linux" @@ -15,3 +13,8 @@ RDEPEND="sci-biology/clustal-omega" S="${WORKDIR}/CLUSTALOMEGA-1.1.0" PATCHES=( "${FILESDIR}"/${PN}-1.1.0_fix-build-system.patch ) + +src_prepare() { + default + eautoreconf +} diff --git a/sci-biology/embassy-clustalomega/files/embassy-clustalomega-1.1.0_fix-build-system.patch b/sci-biology/embassy-clustalomega/files/embassy-clustalomega-1.1.0_fix-build-system.patch index 5525d79b525f..024f8bfc3a09 100644 --- a/sci-biology/embassy-clustalomega/files/embassy-clustalomega-1.1.0_fix-build-system.patch +++ b/sci-biology/embassy-clustalomega/files/embassy-clustalomega-1.1.0_fix-build-system.patch @@ -1,12 +1,6 @@ - configure.ac | 49 +++++++------------------------------------------ - src/Makefile.am | 6 ++---- - 2 files changed, 9 insertions(+), 46 deletions(-) - -diff --git a/configure.ac b/configure.ac -index f12ed19..b143922 100644 ---- a/configure.ac -+++ b/configure.ac -@@ -635,33 +635,6 @@ AS_CASE([${host_os}], +--- a/configure.in ++++ b/configure.in +@@ -635,33 +635,6 @@ @@ -40,7 +34,7 @@ index f12ed19..b143922 100644 dnl FIXME: This does no longer seem required with Autoconf 2.67? dnl Intel MacOSX 10.6 puts X11 in a non-standard place dnl AS_IF([test "x${with_x}" != "xno"], -@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL +@@ -737,21 +710,6 @@ @@ -62,7 +56,7 @@ index f12ed19..b143922 100644 dnl Test if --enable-localforce given locallink="no" embprefix="/usr/local" -@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], +@@ -874,6 +832,13 @@ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) @@ -76,11 +70,9 @@ index f12ed19..b143922 100644 # Enable the purify tool: --enable-purify, sets CC and LIBTOOL -diff --git a/src/Makefile.am b/src/Makefile.am -index 9135679..c201149 100644 --- a/src/Makefile.am +++ b/src/Makefile.am -@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ +@@ -17,9 +17,7 @@ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ -I../../../ajax/acd -I../../../plplot else @@ -91,10 +83,21 @@ index 9135679..c201149 100644 endif if ISSHARED -@@ -62,5 +60,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ +@@ -34,7 +32,7 @@ + -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre \ + $(NLAIXLIBS) -leplplot + else +-AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \ ++AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \ + -lajaxdb -lensembl -lajaxg -lajax -lepcre $(NLAIXLIBS) -leplplot + endif + endif +@@ -61,6 +59,6 @@ + ../../../plplot/libeplplot.la \ $(XLIB) else - LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +-LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ - -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++LDADD = -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ + -lajax $(NLADD) $(XLIB) endif diff --git a/sci-biology/embassy-clustalomega/metadata.xml b/sci-biology/embassy-clustalomega/metadata.xml index d1b9a7602ec2..55784cd1ea18 100644 --- a/sci-biology/embassy-clustalomega/metadata.xml +++ b/sci-biology/embassy-clustalomega/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.660.ebuild b/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.660-r1.ebuild index 4607d87fdc17..affd53e8a3b4 100644 --- a/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.660.ebuild +++ b/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.660-r1.ebuild @@ -1,15 +1,18 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 EBO_DESCRIPTION="Protein domain analysis add-on package" -EBO_EAUTORECONF=1 - -inherit emboss-r2 +inherit autotools emboss-r3 KEYWORDS="~amd64 ~x86 ~x86-linux" S="${WORKDIR}/DOMAINATRIX-0.1.650" PATCHES=( "${FILESDIR}"/${PN}-0.1.650_fix-build-system.patch ) + +src_prepare() { + default + eautoreconf +} diff --git a/sci-biology/embassy-domainatrix/files/embassy-domainatrix-0.1.650_fix-build-system.patch b/sci-biology/embassy-domainatrix/files/embassy-domainatrix-0.1.650_fix-build-system.patch index a932e1ebe21e..849da318d245 100644 --- a/sci-biology/embassy-domainatrix/files/embassy-domainatrix-0.1.650_fix-build-system.patch +++ b/sci-biology/embassy-domainatrix/files/embassy-domainatrix-0.1.650_fix-build-system.patch @@ -1,12 +1,6 @@ - configure.ac | 49 +++++++------------------------------------------ - src/Makefile.am | 6 ++---- - 2 files changed, 9 insertions(+), 46 deletions(-) - -diff --git a/configure.ac b/configure.ac -index d16cc02..d327a0d 100644 ---- a/configure.ac -+++ b/configure.ac -@@ -635,33 +635,6 @@ AS_CASE([${host_os}], +--- a/configure.in ++++ b/configure.in +@@ -635,33 +635,6 @@ @@ -40,7 +34,7 @@ index d16cc02..d327a0d 100644 dnl FIXME: This does no longer seem required with Autoconf 2.67? dnl Intel MacOSX 10.6 puts X11 in a non-standard place dnl AS_IF([test "x${with_x}" != "xno"], -@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL +@@ -737,21 +710,6 @@ @@ -62,7 +56,7 @@ index d16cc02..d327a0d 100644 dnl Test if --enable-localforce given locallink="no" embprefix="/usr/local" -@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], +@@ -874,6 +832,13 @@ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) @@ -76,11 +70,9 @@ index d16cc02..d327a0d 100644 # Enable the purify tool: --enable-purify, sets CC and LIBTOOL -diff --git a/src/Makefile.am b/src/Makefile.am -index d405d00..54be7ca 100644 --- a/src/Makefile.am +++ b/src/Makefile.am -@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ +@@ -17,9 +17,7 @@ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ -I../../../ajax/acd -I../../../plplot else @@ -91,10 +83,21 @@ index d405d00..54be7ca 100644 endif if ISSHARED -@@ -64,5 +62,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ +@@ -34,7 +32,7 @@ + -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre \ + $(NLAIXLIBS) -leplplot + else +-AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \ ++AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \ + -lajaxdb -lensembl -lajaxg -lajax -lepcre $(NLAIXLIBS) -leplplot + endif + endif +@@ -63,6 +61,6 @@ + ../../../plplot/libeplplot.la \ $(XLIB) else - LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +-LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ - -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++LDADD = -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ + -lajax $(NLADD) $(XLIB) endif diff --git a/sci-biology/embassy-domainatrix/metadata.xml b/sci-biology/embassy-domainatrix/metadata.xml index d1b9a7602ec2..55784cd1ea18 100644 --- a/sci-biology/embassy-domainatrix/metadata.xml +++ b/sci-biology/embassy-domainatrix/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/embassy-domalign/embassy-domalign-0.1.660.ebuild b/sci-biology/embassy-domalign/embassy-domalign-0.1.660-r1.ebuild index a897dba4b060..106fbd13912b 100644 --- a/sci-biology/embassy-domalign/embassy-domalign-0.1.660.ebuild +++ b/sci-biology/embassy-domalign/embassy-domalign-0.1.660-r1.ebuild @@ -1,15 +1,18 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 EBO_DESCRIPTION="Protein domain alignment add-on package" -EBO_EAUTORECONF=1 - -inherit emboss-r2 +inherit autotools emboss-r3 KEYWORDS="~amd64 ~x86 ~x86-linux" S="${WORKDIR}/DOMALIGN-0.1.650" PATCHES=( "${FILESDIR}"/${PN}-0.1.650_fix-build-system.patch ) + +src_prepare() { + default + eautoreconf +} diff --git a/sci-biology/embassy-domalign/files/embassy-domalign-0.1.650_fix-build-system.patch b/sci-biology/embassy-domalign/files/embassy-domalign-0.1.650_fix-build-system.patch index 033ddf7b6535..873deaa645ab 100644 --- a/sci-biology/embassy-domalign/files/embassy-domalign-0.1.650_fix-build-system.patch +++ b/sci-biology/embassy-domalign/files/embassy-domalign-0.1.650_fix-build-system.patch @@ -1,12 +1,6 @@ - configure.ac | 49 +++++++------------------------------------------ - src/Makefile.am | 7 ++----- - 2 files changed, 9 insertions(+), 47 deletions(-) - -diff --git a/configure.ac b/configure.ac -index 693eb4d..dc0fda9 100644 ---- a/configure.ac -+++ b/configure.ac -@@ -635,33 +635,6 @@ AS_CASE([${host_os}], +--- a/configure.in ++++ b/configure.in +@@ -635,33 +635,6 @@ @@ -40,7 +34,7 @@ index 693eb4d..dc0fda9 100644 dnl FIXME: This does no longer seem required with Autoconf 2.67? dnl Intel MacOSX 10.6 puts X11 in a non-standard place dnl AS_IF([test "x${with_x}" != "xno"], -@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL +@@ -737,21 +710,6 @@ @@ -62,7 +56,7 @@ index 693eb4d..dc0fda9 100644 dnl Test if --enable-localforce given locallink="no" embprefix="/usr/local" -@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], +@@ -874,6 +832,13 @@ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) @@ -76,11 +70,9 @@ index 693eb4d..dc0fda9 100644 # Enable the purify tool: --enable-purify, sets CC and LIBTOOL -diff --git a/src/Makefile.am b/src/Makefile.am -index 8785446..fe85f11 100644 --- a/src/Makefile.am +++ b/src/Makefile.am -@@ -17,10 +17,7 @@ AM_CPPFLAGS = -I../include -I../../../nucleus -I../../../ajax/pcre \ +@@ -17,10 +17,7 @@ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ -I../../../ajax/acd -I../../../plplot else @@ -92,10 +84,21 @@ index 8785446..fe85f11 100644 endif if ISSHARED -@@ -63,5 +60,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ +@@ -35,7 +32,7 @@ + -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre \ + $(NLAIXLIBS) -leplplot + else +-AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \ ++AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \ + -lajaxdb -lensembl -lajaxg -lajax -lepcre $(NLAIXLIBS) -leplplot + endif + endif +@@ -62,6 +59,6 @@ + ../../../ajax/zlib/libezlib.la \ ../../../plplot/libeplplot.la $(XLIB) else - LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +-LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ - -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++LDADD = -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ + -lajax $(NLADD) $(XLIB) endif diff --git a/sci-biology/embassy-domalign/metadata.xml b/sci-biology/embassy-domalign/metadata.xml index d1b9a7602ec2..55784cd1ea18 100644 --- a/sci-biology/embassy-domalign/metadata.xml +++ b/sci-biology/embassy-domalign/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/embassy-domsearch/embassy-domsearch-0.1.660.ebuild b/sci-biology/embassy-domsearch/embassy-domsearch-0.1.660-r1.ebuild index a47adcfb8457..07a16e7e2272 100644 --- a/sci-biology/embassy-domsearch/embassy-domsearch-0.1.660.ebuild +++ b/sci-biology/embassy-domsearch/embassy-domsearch-0.1.660-r1.ebuild @@ -1,15 +1,18 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 EBO_DESCRIPTION="Protein domain search add-on package" -EBO_EAUTORECONF=1 - -inherit emboss-r2 +inherit autotools emboss-r3 KEYWORDS="~amd64 ~x86 ~x86-linux" S="${WORKDIR}/DOMSEARCH-0.1.650" PATCHES=( "${FILESDIR}"/${PN}-0.1.650_fix-build-system.patch ) + +src_prepare() { + default + eautoreconf +} diff --git a/sci-biology/embassy-domsearch/files/embassy-domsearch-0.1.650_fix-build-system.patch b/sci-biology/embassy-domsearch/files/embassy-domsearch-0.1.650_fix-build-system.patch index d24857c8386d..2fe1803f8452 100644 --- a/sci-biology/embassy-domsearch/files/embassy-domsearch-0.1.650_fix-build-system.patch +++ b/sci-biology/embassy-domsearch/files/embassy-domsearch-0.1.650_fix-build-system.patch @@ -1,12 +1,6 @@ - configure.ac | 49 +++++++------------------------------------------ - src/Makefile.am | 6 ++---- - 2 files changed, 9 insertions(+), 46 deletions(-) - -diff --git a/configure.ac b/configure.ac -index f0f97fa..d419d7d 100644 ---- a/configure.ac -+++ b/configure.ac -@@ -635,33 +635,6 @@ AS_CASE([${host_os}], +--- a/configure.in ++++ b/configure.in +@@ -635,33 +635,6 @@ @@ -40,7 +34,7 @@ index f0f97fa..d419d7d 100644 dnl FIXME: This does no longer seem required with Autoconf 2.67? dnl Intel MacOSX 10.6 puts X11 in a non-standard place dnl AS_IF([test "x${with_x}" != "xno"], -@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL +@@ -737,21 +710,6 @@ @@ -62,7 +56,7 @@ index f0f97fa..d419d7d 100644 dnl Test if --enable-localforce given locallink="no" embprefix="/usr/local" -@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], +@@ -874,6 +832,13 @@ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) @@ -76,11 +70,9 @@ index f0f97fa..d419d7d 100644 # Enable the purify tool: --enable-purify, sets CC and LIBTOOL -diff --git a/src/Makefile.am b/src/Makefile.am -index 9829ebd..433a5c5 100644 --- a/src/Makefile.am +++ b/src/Makefile.am -@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ +@@ -17,9 +17,7 @@ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ -I../../../ajax/acd -I../../../plplot else @@ -91,10 +83,21 @@ index 9829ebd..433a5c5 100644 endif if ISSHARED -@@ -62,5 +60,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ +@@ -34,7 +32,7 @@ + -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre \ + $(NLAIXLIBS) -leplplot + else +-AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \ ++AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \ + -lajaxdb -lensembl -lajaxg -lajax -lepcre $(NLAIXLIBS) -leplplot + endif + endif +@@ -61,6 +59,6 @@ + ../../../ajax/pcre/libepcre.la \ ../../../plplot/libeplplot.la $(XLIB) else - LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +-LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ - -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++LDADD = -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ + -lajax $(NLADD) $(XLIB) endif diff --git a/sci-biology/embassy-domsearch/metadata.xml b/sci-biology/embassy-domsearch/metadata.xml index d1b9a7602ec2..55784cd1ea18 100644 --- a/sci-biology/embassy-domsearch/metadata.xml +++ b/sci-biology/embassy-domsearch/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/embassy-emnu/embassy-emnu-1.05.660-r1.ebuild b/sci-biology/embassy-emnu/embassy-emnu-1.05.660-r1.ebuild new file mode 100644 index 000000000000..8f26aee861c1 --- /dev/null +++ b/sci-biology/embassy-emnu/embassy-emnu-1.05.660-r1.ebuild @@ -0,0 +1,27 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +EBO_DESCRIPTION="Simple menu of EMBOSS applications" + +inherit autotools emboss-r3 + +KEYWORDS="~amd64 ~x86 ~x86-linux" + +RDEPEND="sys-libs/ncurses:0=" +DEPEND="${RDEPEND}" + +S="${WORKDIR}/EMNU-1.05.650" +PATCHES=( "${FILESDIR}"/${PN}-1.05.650_fix-build-system.patch ) + +src_prepare() { + default + eautoreconf +} + +src_configure() { + # --disable-curses is not a thing, + # EMNU hard depends on ncurses really, #752216 + emboss-r3_src_configure --enable-curses +} diff --git a/sci-biology/embassy-emnu/embassy-emnu-1.05.660.ebuild b/sci-biology/embassy-emnu/embassy-emnu-1.05.660.ebuild deleted file mode 100644 index fd6b02d8d235..000000000000 --- a/sci-biology/embassy-emnu/embassy-emnu-1.05.660.ebuild +++ /dev/null @@ -1,22 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -EBO_DESCRIPTION="Simple menu of EMBOSS applications" - -EBO_EAUTORECONF=1 - -inherit emboss-r2 - -KEYWORDS="~amd64 ~x86 ~x86-linux" -IUSE="ncurses" - -RDEPEND="ncurses? ( sys-libs/ncurses:0= )" - -S="${WORKDIR}/EMNU-1.05.650" -PATCHES=( "${FILESDIR}"/${PN}-1.05.650_fix-build-system.patch ) - -src_configure() { - emboss-r2_src_configure $(use_enable ncurses curses) -} diff --git a/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch b/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch index 4e14bac1704a..3039ac9c83f0 100644 --- a/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch +++ b/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch @@ -1,13 +1,6 @@ - configure.ac | 67 +++++++++++--------------------------------------- - emboss_acd/Makefile.am | 2 +- - src/Makefile.am | 7 +++--- - 3 files changed, 18 insertions(+), 58 deletions(-) - -diff --git a/configure.ac b/configure.ac -index 7482ade..b815bdb 100644 ---- a/configure.ac -+++ b/configure.ac -@@ -635,33 +635,6 @@ AS_CASE([${host_os}], +--- a/configure.in ++++ b/configure.in +@@ -635,33 +635,6 @@ @@ -41,7 +34,7 @@ index 7482ade..b815bdb 100644 dnl FIXME: This does no longer seem required with Autoconf 2.67? dnl Intel MacOSX 10.6 puts X11 in a non-standard place dnl AS_IF([test "x${with_x}" != "xno"], -@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL +@@ -737,21 +710,6 @@ @@ -63,7 +56,7 @@ index 7482ade..b815bdb 100644 dnl Test if --enable-localforce given locallink="no" embprefix="/usr/local" -@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], +@@ -874,6 +832,13 @@ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) @@ -77,23 +70,24 @@ index 7482ade..b815bdb 100644 # Enable the purify tool: --enable-purify, sets CC and LIBTOOL -@@ -899,20 +864,16 @@ dnl fi +@@ -899,20 +864,16 @@ dnl emnu and mse only: uses curses -dnl Test if --with-curses is given -AC_ARG_WITH([curses], -[AS_HELP_STRING([--with-curses], [curses (or ncurses)])]) -+dnl Test if --enable-curses is given -+AC_ARG_ENABLE([curses], -+[AS_HELP_STRING([--enable-curses], [curses])]) - +- -AC_MSG_CHECKING([for curses]) - -AS_IF([test "${with_curses}"], -[ - CPPFLAGS="$CPPFLAGS -I${with_curses}/include -I${with_curses}/include/ncurses" - LDFLAGS="$LDFLAGS -L${with_curses}/lib" ++dnl Test if --enable-curses is given ++AC_ARG_ENABLE([curses], ++[AS_HELP_STRING([--enable-curses], [curses])]) ++ +AS_IF([test "x$enable_curses" = "xyes"], [ + PKG_CHECK_MODULES([NCURSES], [ncurses]) + PKG_CHECK_MODULES([FORM], [form]) @@ -105,8 +99,6 @@ index 7482ade..b815bdb 100644 -diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am -index e1c1878..e253c95 100644 --- a/emboss_acd/Makefile.am +++ b/emboss_acd/Makefile.am @@ -1,3 +1,3 @@ @@ -114,11 +106,9 @@ index e1c1878..e253c95 100644 -pkgdata_DATA = *.acd +pkgdata_DATA = $(srcdir)/*.acd pkgdatadir=$(prefix)/share/EMBOSS/acd -diff --git a/src/Makefile.am b/src/Makefile.am -index b295079..330c76f 100644 --- a/src/Makefile.am +++ b/src/Makefile.am -@@ -17,9 +17,8 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ +@@ -17,9 +17,8 @@ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ -I../../../ajax/acd -I../../../plplot else @@ -130,10 +120,21 @@ index b295079..330c76f 100644 endif if ISSHARED -@@ -57,5 +56,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ +@@ -34,7 +33,7 @@ + -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre \ + $(NLAIXLIBS) -leplplot + else +-AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \ ++AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \ + -lajaxdb -lensembl -lajaxg -lajax -lepcre $(NLAIXLIBS) -leplplot + endif + endif +@@ -56,6 +55,6 @@ + ../../../ajax/pcre/libepcre.la \ ../../../plplot/libeplplot.la -lmenu -lform $(XLIB) else - LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +-LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ - -lajax -lepcre $(NLADD) -leplplot -lmenu -lform $(XLIB) ++LDADD = -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ + -lajax $(NLADD) $(NCURSES_LIBS) $(FORM_LIBS) $(MENU_LIBS) $(XLIB) endif diff --git a/sci-biology/embassy-emnu/metadata.xml b/sci-biology/embassy-emnu/metadata.xml index d1b9a7602ec2..55784cd1ea18 100644 --- a/sci-biology/embassy-emnu/metadata.xml +++ b/sci-biology/embassy-emnu/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/embassy-esim4/embassy-esim4-1.0.0.660.ebuild b/sci-biology/embassy-esim4/embassy-esim4-1.0.0.660-r1.ebuild index 16b6d29ebdaf..ab0fee10dc58 100644 --- a/sci-biology/embassy-esim4/embassy-esim4-1.0.0.660.ebuild +++ b/sci-biology/embassy-esim4/embassy-esim4-1.0.0.660-r1.ebuild @@ -1,15 +1,18 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 EBO_DESCRIPTION="sim4 - Alignment of cDNA and genomic DNA" -EBO_EAUTORECONF=1 - -inherit emboss-r2 +inherit autotools emboss-r3 KEYWORDS="~amd64 ~x86 ~x86-linux" S="${WORKDIR}/ESIM4-1.0.0.650" PATCHES=( "${FILESDIR}"/${PN}-1.0.0.650_fix-build-system.patch ) + +src_prepare() { + default + eautoreconf +} diff --git a/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch b/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch index ead54c91b5f3..7ffa00c52f75 100644 --- a/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch +++ b/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch @@ -1,13 +1,6 @@ - configure.ac | 49 +++++++------------------------------------------ - emboss_acd/Makefile.am | 2 +- - src/Makefile.am | 6 ++---- - 3 files changed, 10 insertions(+), 47 deletions(-) - -diff --git a/configure.ac b/configure.ac -index 924220a..2c45f46 100644 ---- a/configure.ac -+++ b/configure.ac -@@ -635,33 +635,6 @@ AS_CASE([${host_os}], +--- a/configure.in ++++ b/configure.in +@@ -635,33 +635,6 @@ @@ -41,7 +34,7 @@ index 924220a..2c45f46 100644 dnl FIXME: This does no longer seem required with Autoconf 2.67? dnl Intel MacOSX 10.6 puts X11 in a non-standard place dnl AS_IF([test "x${with_x}" != "xno"], -@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL +@@ -737,21 +710,6 @@ @@ -63,7 +56,7 @@ index 924220a..2c45f46 100644 dnl Test if --enable-localforce given locallink="no" embprefix="/usr/local" -@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], +@@ -874,6 +832,13 @@ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) @@ -77,8 +70,6 @@ index 924220a..2c45f46 100644 # Enable the purify tool: --enable-purify, sets CC and LIBTOOL -diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am -index e1c1878..e253c95 100644 --- a/emboss_acd/Makefile.am +++ b/emboss_acd/Makefile.am @@ -1,3 +1,3 @@ @@ -86,11 +77,9 @@ index e1c1878..e253c95 100644 -pkgdata_DATA = *.acd +pkgdata_DATA = $(srcdir)/*.acd pkgdatadir=$(prefix)/share/EMBOSS/acd -diff --git a/src/Makefile.am b/src/Makefile.am -index 0620938..0304bb8 100644 --- a/src/Makefile.am +++ b/src/Makefile.am -@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ +@@ -17,9 +17,7 @@ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ -I../../../ajax/acd -I../../../plplot else @@ -101,10 +90,21 @@ index 0620938..0304bb8 100644 endif if ISSHARED -@@ -63,5 +61,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ +@@ -34,7 +32,7 @@ + -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre \ + $(NLAIXLIBS) -leplplot + else +-AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \ ++AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \ + -lajaxdb -lensembl -lajaxg -lajax -lepcre $(NLAIXLIBS) -leplplot + endif + endif +@@ -62,6 +60,6 @@ + ../../../plplot/libeplplot.la \ $(XLIB) else - LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +-LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ - -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++LDADD = -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ + -lajax $(NLADD) $(XLIB) endif diff --git a/sci-biology/embassy-esim4/metadata.xml b/sci-biology/embassy-esim4/metadata.xml index d1b9a7602ec2..55784cd1ea18 100644 --- a/sci-biology/embassy-esim4/metadata.xml +++ b/sci-biology/embassy-esim4/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.660.ebuild b/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.660-r1.ebuild index 4fa2defa1f7d..964e637d657c 100644 --- a/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.660.ebuild +++ b/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.660-r1.ebuild @@ -1,13 +1,11 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 EBO_DESCRIPTION="HMMER wrapper - sequence analysis with profile HMMs" -EBO_EAUTORECONF=1 - -inherit emboss-r2 +inherit autotools emboss-r3 KEYWORDS="~amd64 ~x86 ~x86-linux" @@ -19,3 +17,8 @@ PATCHES=( # sci-biology/hmmer:2 has renamed commandline program names "${FILESDIR}"/${PN}-2.3.2.660-slotted-hmmer2.patch ) + +src_prepare() { + default + eautoreconf +} diff --git a/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch b/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch index 90c45632eada..dd1660dfbd5b 100644 --- a/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch +++ b/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch @@ -1,12 +1,6 @@ - configure.ac | 49 +++++++------------------------------------------ - src/Makefile.am | 6 ++---- - 2 files changed, 9 insertions(+), 46 deletions(-) - -diff --git a/configure.ac b/configure.ac -index 037ca00..f539ab6 100644 ---- a/configure.ac -+++ b/configure.ac -@@ -635,33 +635,6 @@ AS_CASE([${host_os}], +--- a/configure.in ++++ b/configure.in +@@ -635,33 +635,6 @@ @@ -40,7 +34,7 @@ index 037ca00..f539ab6 100644 dnl FIXME: This does no longer seem required with Autoconf 2.67? dnl Intel MacOSX 10.6 puts X11 in a non-standard place dnl AS_IF([test "x${with_x}" != "xno"], -@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL +@@ -737,21 +710,6 @@ @@ -62,7 +56,7 @@ index 037ca00..f539ab6 100644 dnl Test if --enable-localforce given locallink="no" embprefix="/usr/local" -@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], +@@ -874,6 +832,13 @@ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) @@ -76,11 +70,9 @@ index 037ca00..f539ab6 100644 # Enable the purify tool: --enable-purify, sets CC and LIBTOOL -diff --git a/src/Makefile.am b/src/Makefile.am -index dc789bc..5a8c38e 100644 --- a/src/Makefile.am +++ b/src/Makefile.am -@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ +@@ -17,9 +17,7 @@ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ -I../../../ajax/acd -I../../../plplot else @@ -91,10 +83,21 @@ index dc789bc..5a8c38e 100644 endif if ISSHARED -@@ -67,5 +65,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ +@@ -34,7 +32,7 @@ + -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre \ + $(NLAIXLIBS) -leplplot + else +-AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \ ++AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \ + -lajaxdb -lensembl -lajaxg -lajax -lepcre $(NLAIXLIBS) -leplplot + endif + endif +@@ -66,6 +64,6 @@ + ../../../plplot/libeplplot.la \ $(XLIB) else - LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +-LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ - -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++LDADD = -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ + -lajax $(NLADD) $(XLIB) endif diff --git a/sci-biology/embassy-hmmer/metadata.xml b/sci-biology/embassy-hmmer/metadata.xml index d1b9a7602ec2..55784cd1ea18 100644 --- a/sci-biology/embassy-hmmer/metadata.xml +++ b/sci-biology/embassy-hmmer/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.660.ebuild b/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.660-r1.ebuild index 3279ed3bc8e8..4dd5c3cb354e 100644 --- a/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.660.ebuild +++ b/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.660-r1.ebuild @@ -1,15 +1,18 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 EBO_DESCRIPTION="InterProScan motif detection add-on package" -EBO_EAUTORECONF=1 - -inherit emboss-r2 +inherit autotools emboss-r3 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" S="${WORKDIR}/IPRSCAN-4.3.1.650" PATCHES=( "${FILESDIR}"/${PN}-4.3.1.650_fix-build-system.patch ) + +src_prepare() { + default + eautoreconf +} diff --git a/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch b/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch index 8c8a1060e30f..7af8ae2f9ca5 100644 --- a/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch +++ b/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch @@ -1,13 +1,6 @@ - configure.ac | 49 +++++++------------------------------------------ - emboss_acd/Makefile.am | 2 +- - src/Makefile.am | 6 ++---- - 3 files changed, 10 insertions(+), 47 deletions(-) - -diff --git a/configure.ac b/configure.ac -index 9052ca5..c12c268 100644 ---- a/configure.ac -+++ b/configure.ac -@@ -635,33 +635,6 @@ AS_CASE([${host_os}], +--- a/configure.in ++++ b/configure.in +@@ -635,33 +635,6 @@ @@ -41,7 +34,7 @@ index 9052ca5..c12c268 100644 dnl FIXME: This does no longer seem required with Autoconf 2.67? dnl Intel MacOSX 10.6 puts X11 in a non-standard place dnl AS_IF([test "x${with_x}" != "xno"], -@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL +@@ -737,21 +710,6 @@ @@ -63,7 +56,7 @@ index 9052ca5..c12c268 100644 dnl Test if --enable-localforce given locallink="no" embprefix="/usr/local" -@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], +@@ -874,6 +832,13 @@ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) @@ -77,8 +70,6 @@ index 9052ca5..c12c268 100644 # Enable the purify tool: --enable-purify, sets CC and LIBTOOL -diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am -index e1c1878..e253c95 100644 --- a/emboss_acd/Makefile.am +++ b/emboss_acd/Makefile.am @@ -1,3 +1,3 @@ @@ -86,11 +77,9 @@ index e1c1878..e253c95 100644 -pkgdata_DATA = *.acd +pkgdata_DATA = $(srcdir)/*.acd pkgdatadir=$(prefix)/share/EMBOSS/acd -diff --git a/src/Makefile.am b/src/Makefile.am -index 0afc96a..904b41a 100644 --- a/src/Makefile.am +++ b/src/Makefile.am -@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ +@@ -17,9 +17,7 @@ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ -I../../../ajax/acd -I../../../plplot else @@ -101,10 +90,21 @@ index 0afc96a..904b41a 100644 endif if ISSHARED -@@ -58,5 +56,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ +@@ -34,7 +32,7 @@ + -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre \ + $(NLAIXLIBS) -leplplot + else +-AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \ ++AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \ + -lajaxdb -lensembl -lajaxg -lajax -lepcre $(NLAIXLIBS) -leplplot + endif + endif +@@ -57,6 +55,6 @@ + ../../../plplot/libeplplot.la \ $(XLIB) else - LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +-LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ - -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++LDADD = -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ + -lajax $(NLADD) $(XLIB) endif diff --git a/sci-biology/embassy-iprscan/metadata.xml b/sci-biology/embassy-iprscan/metadata.xml index d1b9a7602ec2..55784cd1ea18 100644 --- a/sci-biology/embassy-iprscan/metadata.xml +++ b/sci-biology/embassy-iprscan/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/embassy-meme/Manifest b/sci-biology/embassy-meme/Manifest deleted file mode 100644 index 551af7aef93e..000000000000 --- a/sci-biology/embassy-meme/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST embassy-meme-4.7.660.tar.gz 622448 BLAKE2B 93bbbe3de085aa2cd843349f8397b2d1f547be62afdb7deb30eec90a891f7825c847b92754bd956388b1bfe0250cabcbc7ad68f7d0378748a7949001016d344c SHA512 0536531b198aac09a9fe6c17cf1c60c766789c94a7f83f743a90aaa65061c95534bf398c53611a34549b7ec1a4928fdc45fe0d2553f25f85eeda41f90c2e8c6f diff --git a/sci-biology/embassy-meme/embassy-meme-4.7.660.ebuild b/sci-biology/embassy-meme/embassy-meme-4.7.660.ebuild deleted file mode 100644 index 8752e78d8fc9..000000000000 --- a/sci-biology/embassy-meme/embassy-meme-4.7.660.ebuild +++ /dev/null @@ -1,17 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -EBO_DESCRIPTION="MEME - Multiple Em for Motif Elicitation" - -EBO_EAUTORECONF=1 - -inherit emboss-r2 - -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" - -RDEPEND="sci-biology/meme" - -S="${WORKDIR}/MEME-4.7.650" -PATCHES=( "${FILESDIR}"/${PN}-4.7.650_fix-build-system.patch ) diff --git a/sci-biology/embassy-meme/files/embassy-meme-4.7.650_fix-build-system.patch b/sci-biology/embassy-meme/files/embassy-meme-4.7.650_fix-build-system.patch deleted file mode 100644 index 56f5814e1efa..000000000000 --- a/sci-biology/embassy-meme/files/embassy-meme-4.7.650_fix-build-system.patch +++ /dev/null @@ -1,100 +0,0 @@ - configure.ac | 49 +++++++------------------------------------------ - src/Makefile.am | 6 ++---- - 2 files changed, 9 insertions(+), 46 deletions(-) - -diff --git a/configure.ac b/configure.ac -index 391989f..d921f25 100644 ---- a/configure.ac -+++ b/configure.ac -@@ -635,33 +635,6 @@ AS_CASE([${host_os}], - - - --dnl PCRE library definitions - see the MAJOR and MINOR values --dnl to see which version's configure.in these lines come from -- --dnl Provide the current PCRE version information. Do not use numbers --dnl with leading zeros for the minor version, as they end up in a C --dnl macro, and may be treated as octal constants. Stick to single --dnl digits for minor numbers less than 10. There are unlikely to be --dnl that many releases anyway. -- --PCRE_MAJOR="7" --PCRE_MINOR="9" --PCRE_DATE="11-Apr-2009" --PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" -- --dnl Default values for miscellaneous macros -- --POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" -- --dnl Provide versioning information for libtool shared libraries that --dnl are built by default on Unix systems. -- --PCRE_LIB_VERSION="0:1:0" --PCRE_POSIXLIB_VERSION="0:0:0" -- -- -- -- - dnl FIXME: This does no longer seem required with Autoconf 2.67? - dnl Intel MacOSX 10.6 puts X11 in a non-standard place - dnl AS_IF([test "x${with_x}" != "xno"], -@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL - - - --dnl "Export" these variables for PCRE -- --AC_SUBST([HAVE_MEMMOVE]) --AC_SUBST([HAVE_STRERROR]) --AC_SUBST([PCRE_MAJOR]) --AC_SUBST([PCRE_MINOR]) --AC_SUBST([PCRE_DATE]) --AC_SUBST([PCRE_VERSION]) --AC_SUBST([PCRE_LIB_VERSION]) --AC_SUBST([PCRE_POSIXLIB_VERSION]) --AC_SUBST([POSIX_MALLOC_THRESHOLD]) -- -- -- -- - dnl Test if --enable-localforce given - locallink="no" - embprefix="/usr/local" -@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], - AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) - - -+AS_IF([test "x${enable_systemlibs}" = "xyes"], -+[ -+dnl using system libraries -+ PKG_CHECK_MODULES([PLPLOT], [plplotd], -+ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] -+ ) -+]) - - - # Enable the purify tool: --enable-purify, sets CC and LIBTOOL -diff --git a/src/Makefile.am b/src/Makefile.am -index 1600399..9f28162 100644 ---- a/src/Makefile.am -+++ b/src/Makefile.am -@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ - -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ - -I../../../ajax/acd -I../../../plplot - else --AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ -- $(NLINCLUDES) \ -- -I${embprefix}/include/epcre -+AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) - endif - - if ISSHARED -@@ -60,5 +58,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ - $(XLIB) - else - LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ -- -lajax -lepcre $(NLADD) -leplplot $(XLIB) -+ -lajax $(NLADD) $(XLIB) - endif diff --git a/sci-biology/embassy-meme/metadata.xml b/sci-biology/embassy-meme/metadata.xml deleted file mode 100644 index d1b9a7602ec2..000000000000 --- a/sci-biology/embassy-meme/metadata.xml +++ /dev/null @@ -1,11 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">emboss</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/embassy-mse/embassy-mse-3.0.0.660.ebuild b/sci-biology/embassy-mse/embassy-mse-3.0.0.660-r1.ebuild index c22970155918..a806410e6366 100644 --- a/sci-biology/embassy-mse/embassy-mse-3.0.0.660.ebuild +++ b/sci-biology/embassy-mse/embassy-mse-3.0.0.660-r1.ebuild @@ -1,28 +1,31 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 EBO_DESCRIPTION="MSE - Multiple Sequence Screen Editor" -EBO_EAUTORECONF=1 - -inherit emboss-r2 +inherit autotools emboss-r3 KEYWORDS="~amd64 ~x86 ~x86-linux" -IUSE="ncurses" -RDEPEND="ncurses? ( sys-libs/ncurses:0= )" +RDEPEND="sys-libs/ncurses:=" +DEPEND="${RDEPEND}" S="${WORKDIR}/MSE-3.0.0.650" PATCHES=( "${FILESDIR}"/${PN}-3.0.0.650_fix-build-system.patch ) +src_prepare() { + default + eautoreconf +} + src_configure() { - emboss-r2_src_configure $(use_enable ncurses curses) + emboss-r3_src_configure --enable-curses } src_install() { - emboss-r2_src_install + emboss-r3_src_install insinto /usr/include/emboss/mse doins h/*.h diff --git a/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch b/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch index c1095b266d60..72d7932a188d 100644 --- a/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch +++ b/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch @@ -1,11 +1,3 @@ - ckit/Makefile.am | 2 +- - configure.ac | 67 +++++++++++--------------------------------------- - emboss_acd/Makefile.am | 2 +- - src/Makefile.am | 6 ++--- - 4 files changed, 18 insertions(+), 59 deletions(-) - -diff --git a/ckit/Makefile.am b/ckit/Makefile.am -index f87b131..a670d2b 100644 --- a/ckit/Makefile.am +++ b/ckit/Makefile.am @@ -2,7 +2,7 @@ @@ -17,11 +9,9 @@ index f87b131..a670d2b 100644 CKITSRC = datafiles.c next.c seqentry.c strings.c gcg.c pir.c \ seqspec.c ttyinterface.c nextseqentry.c \ -diff --git a/configure.ac b/configure.ac -index a20d488..eb208bf 100644 ---- a/configure.ac -+++ b/configure.ac -@@ -635,33 +635,6 @@ AS_CASE([${host_os}], +--- a/configure.in ++++ b/configure.in +@@ -635,33 +635,6 @@ @@ -55,7 +45,7 @@ index a20d488..eb208bf 100644 dnl FIXME: This does no longer seem required with Autoconf 2.67? dnl Intel MacOSX 10.6 puts X11 in a non-standard place dnl AS_IF([test "x${with_x}" != "xno"], -@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL +@@ -737,21 +710,6 @@ @@ -77,7 +67,7 @@ index a20d488..eb208bf 100644 dnl Test if --enable-localforce given locallink="no" embprefix="/usr/local" -@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], +@@ -874,6 +832,13 @@ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) @@ -91,7 +81,7 @@ index a20d488..eb208bf 100644 # Enable the purify tool: --enable-purify, sets CC and LIBTOOL -@@ -1000,17 +965,13 @@ AS_IF([test "x${enable_savestats}" = "xyes"], +@@ -1000,17 +965,13 @@ @@ -116,8 +106,6 @@ index a20d488..eb208bf 100644 -diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am -index e1c1878..e253c95 100644 --- a/emboss_acd/Makefile.am +++ b/emboss_acd/Makefile.am @@ -1,3 +1,3 @@ @@ -125,11 +113,9 @@ index e1c1878..e253c95 100644 -pkgdata_DATA = *.acd +pkgdata_DATA = $(srcdir)/*.acd pkgdatadir=$(prefix)/share/EMBOSS/acd -diff --git a/src/Makefile.am b/src/Makefile.am -index b44632a..84e89b5 100644 --- a/src/Makefile.am +++ b/src/Makefile.am -@@ -18,9 +18,7 @@ AM_CPPFLAGS = -I../h \ +@@ -18,9 +18,7 @@ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ -I../../../ajax/acd -I../../../plplot else @@ -140,10 +126,21 @@ index b44632a..84e89b5 100644 endif if ISSHARED -@@ -60,5 +58,5 @@ LDADD = ../ckit/libckit.la \ +@@ -35,7 +33,7 @@ + -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre \ + $(NLAIXLIBS) -leplplot + else +-AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \ ++AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \ + -lajaxdb -lensembl -lajaxg -lajax -lepcre $(NLAIXLIBS) -leplplot + endif + endif +@@ -59,6 +57,6 @@ + ../../../plplot/libeplplot.la \ $(XLIB) else - LDADD = ../ckit/libckit.la -L${embprefix}/lib -lnucleus -lacd -lajaxdb \ +-LDADD = ../ckit/libckit.la -L${embprefix}/lib -lnucleus -lacd -lajaxdb \ - -lensembl -lajaxg -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++LDADD = ../ckit/libckit.la -lnucleus -lacd -lajaxdb \ + -lensembl -lajaxg -lajax $(NLADD) $(NCURSES_LIBS) $(XLIB) endif diff --git a/sci-biology/embassy-mse/metadata.xml b/sci-biology/embassy-mse/metadata.xml index d1b9a7602ec2..a956caede067 100644 --- a/sci-biology/embassy-mse/metadata.xml +++ b/sci-biology/embassy-mse/metadata.xml @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">emboss</remote-id> - </upstream> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">emboss</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660-r1.ebuild b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660-r1.ebuild new file mode 100644 index 000000000000..d7dc57a64fc8 --- /dev/null +++ b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660-r1.ebuild @@ -0,0 +1,23 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +EBO_DESCRIPTION="The Phylogeny Inference Package" + +inherit autotools emboss-r3 + +LICENSE+=" free-noncomm" + +KEYWORDS="~amd64 ~x86 ~x86-linux" + +S="${WORKDIR}/PHYLIPNEW-3.69.650" +PATCHES=( + "${FILESDIR}"/${PN}-3.69.650_fix-build-system.patch + "${FILESDIR}"/${PN}-3.69.650-fno-common.patch +) + +src_prepare() { + default + eautoreconf +} diff --git a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660.ebuild b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660.ebuild deleted file mode 100644 index 3ac088ed6ef9..000000000000 --- a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660.ebuild +++ /dev/null @@ -1,17 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -EBO_DESCRIPTION="The Phylogeny Inference Package" - -EBO_EAUTORECONF=1 - -inherit emboss-r2 - -LICENSE+=" free-noncomm" - -KEYWORDS="~amd64 ~x86 ~x86-linux" - -S="${WORKDIR}/PHYLIPNEW-3.69.650" -PATCHES=( "${FILESDIR}"/${PN}-3.69.650_fix-build-system.patch ) diff --git a/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650-fno-common.patch b/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650-fno-common.patch new file mode 100644 index 000000000000..448000547471 --- /dev/null +++ b/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650-fno-common.patch @@ -0,0 +1,627 @@ +--- a/include/draw.h ++++ b/include/draw.h +@@ -116,19 +116,19 @@ + + + #ifndef X_DISPLAY_MISSING +-Display *display; /* the X display */ ++extern Display *display; /* the X display */ + extern Window mainwin; /* the main display window */ +-int x, y; /* the corner of the window */ +-unsigned int width, height; /* the width and height of the window */ ++extern int x, y; /* the corner of the window */ ++extern unsigned int width, height; /* the width and height of the window */ + #define FONT "-*-new century schoolbook-medium-r-*-*-14-*" +-char *fontrsc; /* the font resource */ +-XFontStruct *fontst; /* the font strcture for the font */ +-XGCValues gcv; /* graphics context values */ +-GC gc1; /* a graphics context */ +-XtAppContext appcontext; +-Widget toplevel; +-int nargc; +-char** nargv; ++extern char *fontrsc; /* the font resource */ ++extern XFontStruct *fontst; /* the font strcture for the font */ ++extern XGCValues gcv; /* graphics context values */ ++extern GC gc1; /* a graphics context */ ++extern XtAppContext appcontext; ++extern Widget toplevel; ++extern int nargc; ++extern char** nargv; + extern String res[16]; + + #define DEFGEOMETRY "600x400+20+50" +--- a/include/phylip.h ++++ b/include/phylip.h +@@ -349,7 +349,8 @@ + extern AjPFile embossancfile; + extern AjPFile embossmixfile; + extern AjPFile embossfactfile; +-extern long spp, words, bits; ++extern AjPPhyloState* phylostates; ++extern long spp, words, bits, outgrno; + extern boolean ibmpc, ansi, tranvsp; + extern naym *nayme; /* names of species */ + +--- a/src/clique.c ++++ b/src/clique.c +@@ -9,7 +9,6 @@ + + #define FormWide 80 /* width of outfile page */ + +-AjPPhyloState* phylostates; + AjPPhyloProp phyloanc = NULL; + AjPPhyloProp phylofact = NULL; + AjPPhyloProp phyloweights = NULL; +@@ -72,10 +71,8 @@ + Char infilename[FNMLNGTH], ancfilename[FNMLNGTH], factfilename[FNMLNGTH], weightfilename[FNMLNGTH]; + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + +-long ActualChars, Cliqmin, outgrno, ++long ActualChars, Cliqmin, + col, ith, msets, setsz; + boolean ancvar, Clmin, Factors, outgropt, trout, weights, noroot, justwts, + printcomp, progress, treeprint, mulsets, firstset; +--- a/src/cons.c ++++ b/src/cons.c +@@ -6,7 +6,7 @@ + Char intreename[FNMLNGTH], intree2name[FNMLNGTH]; + node *root; + +-long numopts, outgrno, col, setsz; ++long numopts, col, setsz; + long maxgrp; /* max. no. of groups in all trees found */ + + boolean trout, firsttree, noroot, outgropt, didreroot, prntsets, +--- a/src/consense.c ++++ b/src/consense.c +@@ -19,8 +19,6 @@ + + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + + long trees_in; + +--- a/src/contml.c ++++ b/src/contml.c +@@ -69,10 +69,8 @@ + + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + +-long nonodes2, loci, totalleles, df, outgrno, col, ++long nonodes2, loci, totalleles, df, col, + datasets, ith, njumble, jumb=0; + long inseed, inseed0; + long *alleles, *locus, *weight; +--- a/src/contrast.c ++++ b/src/contrast.c +@@ -40,7 +40,6 @@ + + + const char* outfilename; +-AjPFile embossoutfile; + + + +--- a/src/discboot.c ++++ b/src/discboot.c +@@ -56,7 +56,6 @@ + + + const char* outfilename; +-AjPFile embossoutfile; + + const char* outweightfilename; + AjPFile embossoutweightfile; +--- a/src/disc.c ++++ b/src/disc.c +@@ -1,7 +1,6 @@ + #include "phylip.h" + #include "disc.h" + +-AjPPhyloState* phylostates; + + /* version 3.6. (c) Copyright 1993-2002 by the University of Washington. + Written by Joseph Felsenstein, Akiko Fuseki, Sean Lamont, and Andrew Keeffe. +--- a/src/discrete.c ++++ b/src/discrete.c +@@ -6,7 +6,7 @@ + Permission is granted to copy and use this program provided no fee is + charged for it and provided that this copyright notice is not removed. */ + +-long nonodes, endsite, outgrno, nextree, which; ++long nonodes, endsite, nextree, which; + boolean interleaved, printdata, outgropt, treeprint, dotdiff; + steptr weight, category, alias, location, ally; + sequence y, convtab; +--- a/src/dnacomp.c ++++ b/src/dnacomp.c +@@ -53,8 +53,6 @@ + + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + + node *root, *p; + long chars, col, ith, njumble, jumb, msets, numtrees; +--- a/src/dnadist.c ++++ b/src/dnadist.c +@@ -27,7 +27,6 @@ + + Char infilename[FNMLNGTH], catfilename[FNMLNGTH], weightfilename[FNMLNGTH]; + const char* outfilename; +-AjPFile embossoutfile; + + long sites, categs, weightsum, datasets, ith, rcategs; + boolean freqsfrom, jukes, kimura, logdet, gama, invar, similarity, lower, f84, +--- a/src/dnainvar.c ++++ b/src/dnainvar.c +@@ -51,7 +51,6 @@ + Char infilename[FNMLNGTH], weightfilename[FNMLNGTH]; + + const char* outfilename; +-AjPFile embossoutfile; + + long sites, msets, ith; + boolean weights, progress, prntpat, printinv, mulsets, firstset, justwts; +--- a/src/dnaml.c ++++ b/src/dnaml.c +@@ -93,12 +93,10 @@ + + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + + double *rate, *rrate, *probcat; + long nonodes2, sites, weightsum, categs, datasets, ith, njumble, jumb; +-long parens, outgrno; ++long parens; + boolean freqsfrom, global, jumble, weights, trout, usertree, + ctgry, rctgry, auto_, hypstate, ttr, progress, mulsets, justwts, + firstset, improve, smoothit, polishing, lngths, gama, invar,inserting=false; +--- a/src/dnamlk.c ++++ b/src/dnamlk.c +@@ -119,8 +119,6 @@ + + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + double *rrate; + long sites, weightsum, categs, datasets, ith, njumble, jumb, numtrees, shimotrees; + /* sites = number of sites in actual sequences +--- a/src/dnamove.c ++++ b/src/dnamove.c +@@ -127,7 +127,6 @@ + node *root; + + const char* outtreename; +-AjPFile embossouttree; + + long chars, screenlines, col, treelines, leftedge, topedge, vmargin, + hscroll, vscroll, scrollinc, screenwidth, farthest, whichtree, othertree; +--- a/src/dnapenny.c ++++ b/src/dnapenny.c +@@ -47,8 +47,6 @@ + + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + node *root, *p; + long *zeros=NULL; + long chars, howmany, howoften, col, msets, ith; +--- a/src/dollop.c ++++ b/src/dollop.c +@@ -10,7 +10,6 @@ + + #define maxtrees 100 /* maximum number of tied trees stored */ + +-AjPPhyloState* phylostates = NULL; + AjPPhyloProp phyloanc = NULL; + AjPPhyloProp phyloweights = NULL; + AjPPhyloTree* phylotrees = NULL; +@@ -47,8 +46,6 @@ + + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + + + node *root; +--- a/src/dolmove.c ++++ b/src/dolmove.c +@@ -11,7 +11,6 @@ + #define overr 4 + #define which 1 + +-AjPPhyloState* phylostates = NULL; + AjPPhyloProp phyloanc = NULL; + AjPPhyloProp phylofact = NULL; + AjPPhyloProp phyloweights = NULL; +@@ -73,10 +72,9 @@ + Char infilename[FNMLNGTH],intreename[FNMLNGTH], ancfilename[FNMLNGTH], factfilename[FNMLNGTH], weightfilename[FNMLNGTH]; + + const char* outtreename; +-AjPFile embossouttree; + + node *root; +-long outgrno, col, screenlines, screenwidth, scrollinc,treelines, ++long col, screenlines, screenwidth, scrollinc,treelines, + leftedge,topedge,vmargin,hscroll,vscroll,farthest; + /* outgrno indicates outgroup */ + boolean weights, thresh, ancvar, questions, dollo, factors, +--- a/src/dolpenny.c ++++ b/src/dolpenny.c +@@ -15,7 +15,6 @@ + typedef double *valptr; + typedef long *placeptr; + +-AjPPhyloState* phylostates = NULL; + AjPPhyloProp phyloanc = NULL; + AjPPhyloProp phyloweights = NULL; + +@@ -40,8 +39,6 @@ + Char infilename[FNMLNGTH], weightfilename[FNMLNGTH], ancfilename[FNMLNGTH]; + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + + node *root; + long howmany, howoften, col, msets, ith; +--- a/src/draw.c ++++ b/src/draw.c +@@ -10,6 +10,20 @@ + #include "phylip.h" + #include "draw.h" + ++#ifndef X_DISPLAY_MISSING ++Display *display; ++int x, y; ++unsigned int width, height; ++char *fontrsc; ++XFontStruct *fontst; ++XGCValues gcv; ++GC gc1; ++XtAppContext appcontext; ++Widget toplevel; ++int nargc; ++char** nargv; ++#endif ++ + #ifdef QUICKC + struct videoconfig myscreen; + void setupgraphics(); +--- a/src/factor.c ++++ b/src/factor.c +@@ -54,7 +54,6 @@ + const char* outfactname; + const char* outancname; + AjPFile inputfile; +-AjPFile embossoutfile; + AjPFile embossoutfact; + AjPFile embossoutanc; + +--- a/src/fitch.c ++++ b/src/fitch.c +@@ -60,11 +60,9 @@ + + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + + Char infilename[FNMLNGTH], intreename[FNMLNGTH]; +-long nonodes2, outgrno, nums, col, datasets, ith, njumble, jumb=0, numtrees; ++long nonodes2, nums, col, datasets, ith, njumble, jumb=0, numtrees; + long inseed; + vector *x; + intvector *reps; +--- a/src/freqboot.c ++++ b/src/freqboot.c +@@ -52,7 +52,6 @@ + + + const char* outfilename; +-AjPFile embossoutfile; + + const char* outweightfilename; + AjPFile embossoutweightfile; +--- a/src/gendist.c ++++ b/src/gendist.c +@@ -24,7 +24,6 @@ + #endif + + const char* outfilename; +-AjPFile embossoutfile; + + long loci, totalleles, df, datasets, ith; + long nonodes; +--- a/src/kitsch.c ++++ b/src/kitsch.c +@@ -51,8 +51,6 @@ + + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + + + Char infilename[FNMLNGTH], intreename[FNMLNGTH]; +--- a/src/mix.c ++++ b/src/mix.c +@@ -13,7 +13,6 @@ + + typedef long *placeptr; + +-AjPPhyloState* phylostates = NULL; + AjPPhyloProp phyloweights = NULL; + AjPPhyloProp phyloanc = NULL; + AjPPhyloProp phylomix = NULL; +@@ -52,11 +51,9 @@ + Char infilename[FNMLNGTH], intreename[FNMLNGTH], weightfilename[FNMLNGTH], ancfilename[FNMLNGTH], mixfilename[FNMLNGTH]; + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + + node2 *root; +-long outgrno, msets, ith, njumble, jumb, numtrees; ++long msets, ith, njumble, jumb, numtrees; + /* outgrno indicates outgroup */ + long inseed, inseed0; + boolean jumble, usertree, weights, ancvar, questions, allsokal, +--- a/src/move.c ++++ b/src/move.c +@@ -13,7 +13,6 @@ + #define which 1 + + +-AjPPhyloState* phylostates = NULL; + AjPPhyloProp phyloweights = NULL; + AjPPhyloProp phyloanc = NULL; + AjPPhyloProp phylomix = NULL; +@@ -77,10 +76,9 @@ + + char infilename[FNMLNGTH],intreename[FNMLNGTH], weightfilename[FNMLNGTH], ancfilename[FNMLNGTH], mixfilename[FNMLNGTH], factfilename[FNMLNGTH]; + const char* outtreename; +-AjPFile embossouttree; + + node *root; +-long outgrno, screenlines, col, treelines, leftedge, topedge, ++long screenlines, col, treelines, leftedge, topedge, + vmargin, hscroll, vscroll, scrollinc, screenwidth, farthest; + /* outgrno indicates outgroup */ + boolean weights, outgropt, ancvar, questions, allsokal, +--- a/src/neighbor.c ++++ b/src/neighbor.c +@@ -32,11 +32,9 @@ + + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + + Char infilename[FNMLNGTH]; +-long nonodes2, outgrno, col, datasets, ith; ++long nonodes2, col, datasets, ith; + long inseed; + vector *x; + intvector *reps; +--- a/src/pars.c ++++ b/src/pars.c +@@ -9,7 +9,6 @@ + + #define MAXNUMTREES 1000000 /* bigger than number of user trees can be */ + +-AjPPhyloState* phylostates = NULL; + AjPPhyloProp phyloweights = NULL; + AjPPhyloTree* phylotrees = NULL; + +--- a/src/penny.c ++++ b/src/penny.c +@@ -12,7 +12,6 @@ + #define often 100 /* how often to notify how many trees examined */ + #define many 1000 /* how many multiples of howoften before stop */ + +-AjPPhyloState* phylostates = NULL; + AjPPhyloProp phyloweights = NULL; + AjPPhyloProp phyloanc = NULL; + AjPPhyloProp phylomix = NULL; +@@ -44,11 +43,9 @@ + Char infilename[FNMLNGTH], weightfilename[FNMLNGTH], ancfilename[FNMLNGTH], mixfilename[FNMLNGTH]; + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + + node2 *root; +-long outgrno, rno, howmany, howoften, col, msets, ith; ++long rno, howmany, howoften, col, msets, ith; + /* outgrno indicates outgroup */ + + boolean weights, ancvar, questions, allsokal, allwagner, +--- a/src/phylip.c ++++ b/src/phylip.c +@@ -46,7 +46,8 @@ + AjPFile embossancfile; + AjPFile embossmixfile; + AjPFile embossfactfile; +-long spp, words, bits; ++AjPPhyloState* phylostates = NULL; ++long spp, words, bits, outgrno; + boolean ibmpc, ansi, tranvsp; + naym *nayme; /* names of species */ + +--- a/src/proml.c ++++ b/src/proml.c +@@ -89,8 +89,6 @@ + Char infilename[100], intreename[100], catfilename[100], weightfilename[100]; + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + + double *rate, *rrate, *probcat; + long nonodes2, sites, weightsum, categs, +--- a/src/promlk.c ++++ b/src/promlk.c +@@ -88,8 +88,6 @@ + + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + + Char infilename[FNMLNGTH], intreename[FNMLNGTH], + catfilename[FNMLNGTH], weightfilename[FNMLNGTH]; +--- a/src/protdist.c ++++ b/src/protdist.c +@@ -79,7 +79,6 @@ + char infilename[100], catfilename[100], weightfilename[100]; + + const char* outfilename; +-AjPFile embossoutfile; + + + /* Local variables for makedists, propagated globally for c version: */ +--- a/src/protpars.c ++++ b/src/protpars.c +@@ -76,8 +76,6 @@ + + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + + node *root; + long chars, col, msets, ith, njumble, jumb, numtrees; +--- a/src/restboot.c ++++ b/src/restboot.c +@@ -54,7 +54,6 @@ + + + const char* outfilename; +-AjPFile embossoutfile; + + const char* outweightfilename; + AjPFile embossoutweightfile; +--- a/src/restdist.c ++++ b/src/restdist.c +@@ -13,7 +13,6 @@ + + extern sequence y; + +-AjPPhyloState* phylostates = NULL; + + + #ifndef OLDC +@@ -40,7 +39,6 @@ + Char infilename[FNMLNGTH]; + + const char* outfilename; +-AjPFile embossoutfile; + + long sites, weightsum, datasets, ith; + boolean restsites, neili, gama, weights, lower, +--- a/src/restml.c ++++ b/src/restml.c +@@ -17,7 +17,6 @@ + + AjPPhyloProp phyloweights = NULL; + AjPPhyloTree* phylotrees; +-AjPPhyloState* phylostates = NULL; + + #ifndef OLDC + /* function prototypes */ +@@ -101,8 +100,6 @@ + + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + + + ajint numwts; +--- a/src/retree.c ++++ b/src/retree.c +@@ -123,7 +123,7 @@ + + node *root, *garbage; + +-long nonodes, outgrno, screenwidth, vscreenwidth, ++long nonodes, screenwidth, vscreenwidth, + screenlines, col, treenumber, leftedge, topedge, treelines, + hscroll, vscroll, scrollinc, whichtree, othertree, + numtrees, treesread; +@@ -145,7 +145,6 @@ + char intreename[FNMLNGTH]; + + const char* outtreename; +-AjPFile embossouttree; + + boolean subtree, written, readnext; + node *nuroot; +--- a/src/seqbootall.c ++++ b/src/seqbootall.c +@@ -109,7 +109,6 @@ + + + const char* outfilename; +-AjPFile embossoutfile; + + const char* outweightfilename; + AjPFile embossoutweightfile; +--- a/src/seqboot.c ++++ b/src/seqboot.c +@@ -92,7 +92,6 @@ + + + const char* outfilename; +-AjPFile embossoutfile; + + const char* outweightfilename; + AjPFile embossoutweightfile; +--- a/src/seq.c ++++ b/src/seq.c +@@ -7,7 +7,7 @@ + Permission is granted to copy and use this program provided no fee is + charged for it and provided that this copyright notice is not removed. */ + +-long nonodes, endsite, outgrno, nextree, which; ++long nonodes, endsite, nextree, which; + boolean interleaved, printdata, outgropt, treeprint, dotdiff, transvp; + steptr weight, category, alias, location, ally; + sequence y; +--- a/src/treedist.c ++++ b/src/treedist.c +@@ -16,7 +16,6 @@ + extern node *root; + + const char* outfilename; +-AjPFile embossoutfile; + + long trees_in_1, trees_in_2; + +--- a/src/treedistpair.c ++++ b/src/treedistpair.c +@@ -16,7 +16,6 @@ + extern node *root; + + const char* outfilename; +-AjPFile embossoutfile; + + long trees_in_1, trees_in_2; + diff --git a/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch b/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch index 1cba944094a2..589408ed4a9e 100644 --- a/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch +++ b/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch @@ -1,13 +1,6 @@ - configure.ac | 49 +++++++------------------------------------------ - emboss_acd/Makefile.am | 2 +- - src/Makefile.am | 7 ++----- - 3 files changed, 10 insertions(+), 48 deletions(-) - -diff --git a/configure.ac b/configure.ac -index e5bfaf1..09ed517 100644 ---- a/configure.ac -+++ b/configure.ac -@@ -635,33 +635,6 @@ AS_CASE([${host_os}], +--- a/configure.in ++++ b/configure.in +@@ -635,33 +635,6 @@ @@ -41,7 +34,7 @@ index e5bfaf1..09ed517 100644 dnl FIXME: This does no longer seem required with Autoconf 2.67? dnl Intel MacOSX 10.6 puts X11 in a non-standard place dnl AS_IF([test "x${with_x}" != "xno"], -@@ -781,21 +754,6 @@ AX_LIB_POSTGRESQL +@@ -781,21 +754,6 @@ @@ -63,7 +56,7 @@ index e5bfaf1..09ed517 100644 dnl Test if --enable-localforce given locallink="no" embprefix="/usr/local" -@@ -918,6 +876,13 @@ AC_ARG_ENABLE([systemlibs], +@@ -918,6 +876,13 @@ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) @@ -77,8 +70,6 @@ index e5bfaf1..09ed517 100644 # Enable the purify tool: --enable-purify, sets CC and LIBTOOL -diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am -index e1c1878..e253c95 100644 --- a/emboss_acd/Makefile.am +++ b/emboss_acd/Makefile.am @@ -1,3 +1,3 @@ @@ -86,11 +77,9 @@ index e1c1878..e253c95 100644 -pkgdata_DATA = *.acd +pkgdata_DATA = $(srcdir)/*.acd pkgdatadir=$(prefix)/share/EMBOSS/acd -diff --git a/src/Makefile.am b/src/Makefile.am -index 1883ce9..fb1787f 100644 --- a/src/Makefile.am +++ b/src/Makefile.am -@@ -16,10 +16,7 @@ AM_CPPFLAGS = -I../include -I../../../nucleus -I../../../ajax/pcre \ +@@ -16,10 +16,7 @@ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ -I../../../ajax/acd -I../../../plplot else @@ -102,10 +91,21 @@ index 1883ce9..fb1787f 100644 endif if ISSHARED -@@ -120,5 +117,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ +@@ -34,7 +31,7 @@ + -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre \ + $(NLAIXLIBS) -leplplot + else +-AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \ ++AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \ + -lajaxdb -lensembl -lajaxg -lajax -lepcre $(NLAIXLIBS) -leplplot + endif + endif +@@ -119,6 +116,6 @@ + ../../../ajax/pcre/libepcre.la \ ../../../plplot/libeplplot.la $(XLIB) else - LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +-LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ - -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++LDADD = -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ + -lajax $(NLADD) $(XLIB) endif diff --git a/sci-biology/embassy-phylipnew/metadata.xml b/sci-biology/embassy-phylipnew/metadata.xml index d1b9a7602ec2..55784cd1ea18 100644 --- a/sci-biology/embassy-phylipnew/metadata.xml +++ b/sci-biology/embassy-phylipnew/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/embassy-signature/embassy-signature-0.1.660.ebuild b/sci-biology/embassy-signature/embassy-signature-0.1.660-r1.ebuild index c0ea3e302504..6f04a1432d9b 100644 --- a/sci-biology/embassy-signature/embassy-signature-0.1.660.ebuild +++ b/sci-biology/embassy-signature/embassy-signature-0.1.660-r1.ebuild @@ -1,15 +1,18 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 EBO_DESCRIPTION="Protein signature add-on package" -EBO_EAUTORECONF=1 - -inherit emboss-r2 +inherit autotools emboss-r3 KEYWORDS="~amd64 ~x86 ~x86-linux" S="${WORKDIR}/SIGNATURE-0.1.650" PATCHES=( "${FILESDIR}"/${PN}-0.1.650_fix-build-system.patch ) + +src_prepare() { + default + eautoreconf +} diff --git a/sci-biology/embassy-signature/files/embassy-signature-0.1.650_fix-build-system.patch b/sci-biology/embassy-signature/files/embassy-signature-0.1.650_fix-build-system.patch index 32e4d684cbb3..a453b25bde66 100644 --- a/sci-biology/embassy-signature/files/embassy-signature-0.1.650_fix-build-system.patch +++ b/sci-biology/embassy-signature/files/embassy-signature-0.1.650_fix-build-system.patch @@ -1,12 +1,6 @@ - configure.ac | 49 +++++++------------------------------------------ - src/Makefile.am | 6 ++---- - 2 files changed, 9 insertions(+), 46 deletions(-) - -diff --git a/configure.ac b/configure.ac -index 2f5ddd0..827543f 100644 ---- a/configure.ac -+++ b/configure.ac -@@ -635,33 +635,6 @@ AS_CASE([${host_os}], +--- a/configure.in ++++ b/configure.in +@@ -635,33 +635,6 @@ @@ -40,7 +34,7 @@ index 2f5ddd0..827543f 100644 dnl FIXME: This does no longer seem required with Autoconf 2.67? dnl Intel MacOSX 10.6 puts X11 in a non-standard place dnl AS_IF([test "x${with_x}" != "xno"], -@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL +@@ -737,21 +710,6 @@ @@ -62,7 +56,7 @@ index 2f5ddd0..827543f 100644 dnl Test if --enable-localforce given locallink="no" embprefix="/usr/local" -@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], +@@ -874,6 +832,13 @@ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) @@ -76,11 +70,9 @@ index 2f5ddd0..827543f 100644 # Enable the purify tool: --enable-purify, sets CC and LIBTOOL -diff --git a/src/Makefile.am b/src/Makefile.am -index d77e43c..849f17a 100644 --- a/src/Makefile.am +++ b/src/Makefile.am -@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ +@@ -17,9 +17,7 @@ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ -I../../../ajax/acd -I../../../plplot else @@ -91,10 +83,21 @@ index d77e43c..849f17a 100644 endif if ISSHARED -@@ -68,5 +66,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ +@@ -34,7 +32,7 @@ + -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre \ + $(NLAIXLIBS) -leplplot + else +-AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \ ++AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \ + -lajaxdb -lensembl -lajaxg -lajax -lepcre $(NLAIXLIBS) -leplplot + endif + endif +@@ -67,6 +65,6 @@ + ../../../plplot/libeplplot.la \ $(XLIB) else - LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +-LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ - -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++LDADD = -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ + -lajax $(NLADD) $(XLIB) endif diff --git a/sci-biology/embassy-signature/metadata.xml b/sci-biology/embassy-signature/metadata.xml index d1b9a7602ec2..55784cd1ea18 100644 --- a/sci-biology/embassy-signature/metadata.xml +++ b/sci-biology/embassy-signature/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/embassy-structure/embassy-structure-0.1.660.ebuild b/sci-biology/embassy-structure/embassy-structure-0.1.660-r1.ebuild index eaf74b5ea841..ba0b94964d2f 100644 --- a/sci-biology/embassy-structure/embassy-structure-0.1.660.ebuild +++ b/sci-biology/embassy-structure/embassy-structure-0.1.660-r1.ebuild @@ -1,15 +1,18 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 EBO_DESCRIPTION="Protein structure add-on package" -EBO_EAUTORECONF=1 - -inherit emboss-r2 +inherit autotools emboss-r3 KEYWORDS="~amd64 ~x86 ~x86-linux" S="${WORKDIR}/STRUCTURE-0.1.650" PATCHES=( "${FILESDIR}"/${PN}-0.1.650_fix-build-system.patch ) + +src_prepare() { + default + eautoreconf +} diff --git a/sci-biology/embassy-structure/files/embassy-structure-0.1.650_fix-build-system.patch b/sci-biology/embassy-structure/files/embassy-structure-0.1.650_fix-build-system.patch index bdd9e37714e4..32826f8ebbbe 100644 --- a/sci-biology/embassy-structure/files/embassy-structure-0.1.650_fix-build-system.patch +++ b/sci-biology/embassy-structure/files/embassy-structure-0.1.650_fix-build-system.patch @@ -1,12 +1,6 @@ - configure.ac | 49 +++++++------------------------------------------ - src/Makefile.am | 6 ++---- - 2 files changed, 9 insertions(+), 46 deletions(-) - -diff --git a/configure.ac b/configure.ac -index ee482ef..e4af4b1 100644 ---- a/configure.ac -+++ b/configure.ac -@@ -635,33 +635,6 @@ AS_CASE([${host_os}], +--- a/configure.in ++++ b/configure.in +@@ -635,33 +635,6 @@ @@ -40,7 +34,7 @@ index ee482ef..e4af4b1 100644 dnl FIXME: This does no longer seem required with Autoconf 2.67? dnl Intel MacOSX 10.6 puts X11 in a non-standard place dnl AS_IF([test "x${with_x}" != "xno"], -@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL +@@ -737,21 +710,6 @@ @@ -62,7 +56,7 @@ index ee482ef..e4af4b1 100644 dnl Test if --enable-localforce given locallink="no" embprefix="/usr/local" -@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], +@@ -874,6 +832,13 @@ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) @@ -76,11 +70,9 @@ index ee482ef..e4af4b1 100644 # Enable the purify tool: --enable-purify, sets CC and LIBTOOL -diff --git a/src/Makefile.am b/src/Makefile.am -index 81ade5d..2ed0d14 100644 --- a/src/Makefile.am +++ b/src/Makefile.am -@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ +@@ -17,9 +17,7 @@ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ -I../../../ajax/acd -I../../../plplot else @@ -91,10 +83,21 @@ index 81ade5d..2ed0d14 100644 endif if ISSHARED -@@ -66,5 +64,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ +@@ -34,7 +32,7 @@ + -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre \ + $(NLAIXLIBS) -leplplot + else +-AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \ ++AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \ + -lajaxdb -lensembl -lajaxg -lajax -lepcre $(NLAIXLIBS) -leplplot + endif + endif +@@ -65,6 +63,6 @@ + ../../../plplot/libeplplot.la \ $(XLIB) else - LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +-LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ - -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++LDADD = -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ + -lajax $(NLADD) $(XLIB) endif diff --git a/sci-biology/embassy-structure/metadata.xml b/sci-biology/embassy-structure/metadata.xml index d1b9a7602ec2..55784cd1ea18 100644 --- a/sci-biology/embassy-structure/metadata.xml +++ b/sci-biology/embassy-structure/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/embassy-topo/embassy-topo-2.0.660.ebuild b/sci-biology/embassy-topo/embassy-topo-2.0.660-r1.ebuild index 009adfe73914..583d93297669 100644 --- a/sci-biology/embassy-topo/embassy-topo-2.0.660.ebuild +++ b/sci-biology/embassy-topo/embassy-topo-2.0.660-r1.ebuild @@ -1,15 +1,18 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 EBO_DESCRIPTION="Transmembrane protein display" -EBO_EAUTORECONF=1 - -inherit emboss-r2 +inherit autotools emboss-r3 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" S="${WORKDIR}/TOPO-2.0.650" PATCHES=( "${FILESDIR}"/${PN}-2.0.650_fix-build-system.patch ) + +src_prepare() { + default + eautoreconf +} diff --git a/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch b/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch index 3c37879de8c8..e1a2439b713b 100644 --- a/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch +++ b/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch @@ -1,13 +1,6 @@ - configure.ac | 49 +++++++------------------------------------------ - emboss_acd/Makefile.am | 2 +- - src/Makefile.am | 6 ++---- - 3 files changed, 10 insertions(+), 47 deletions(-) - -diff --git a/configure.ac b/configure.ac -index 8eeb8ca..4fd28ac 100644 ---- a/configure.ac -+++ b/configure.ac -@@ -635,33 +635,6 @@ AS_CASE([${host_os}], +--- a/configure.in ++++ b/configure.in +@@ -635,33 +635,6 @@ @@ -41,7 +34,7 @@ index 8eeb8ca..4fd28ac 100644 dnl FIXME: This does no longer seem required with Autoconf 2.67? dnl Intel MacOSX 10.6 puts X11 in a non-standard place dnl AS_IF([test "x${with_x}" != "xno"], -@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL +@@ -737,21 +710,6 @@ @@ -63,7 +56,7 @@ index 8eeb8ca..4fd28ac 100644 dnl Test if --enable-localforce given locallink="no" embprefix="/usr/local" -@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], +@@ -874,6 +832,13 @@ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) @@ -77,8 +70,6 @@ index 8eeb8ca..4fd28ac 100644 # Enable the purify tool: --enable-purify, sets CC and LIBTOOL -diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am -index e1c1878..e253c95 100644 --- a/emboss_acd/Makefile.am +++ b/emboss_acd/Makefile.am @@ -1,3 +1,3 @@ @@ -86,11 +77,9 @@ index e1c1878..e253c95 100644 -pkgdata_DATA = *.acd +pkgdata_DATA = $(srcdir)/*.acd pkgdatadir=$(prefix)/share/EMBOSS/acd -diff --git a/src/Makefile.am b/src/Makefile.am -index 1cdb0b1..0e86a4b 100644 --- a/src/Makefile.am +++ b/src/Makefile.am -@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ +@@ -17,9 +17,7 @@ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ -I../../../ajax/acd -I../../../plplot else @@ -101,10 +90,21 @@ index 1cdb0b1..0e86a4b 100644 endif if ISSHARED -@@ -60,5 +58,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ +@@ -34,7 +32,7 @@ + -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre \ + $(NLAIXLIBS) -leplplot + else +-AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \ ++AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \ + -lajaxdb -lensembl -lajaxg -lajax -lepcre $(NLAIXLIBS) -leplplot + endif + endif +@@ -59,6 +57,6 @@ + ../../../plplot/libeplplot.la \ $(XLIB) else - LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +-LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ - -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++LDADD = -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ + -lajax $(NLADD) $(XLIB) endif diff --git a/sci-biology/embassy-topo/metadata.xml b/sci-biology/embassy-topo/metadata.xml index d1b9a7602ec2..55784cd1ea18 100644 --- a/sci-biology/embassy-topo/metadata.xml +++ b/sci-biology/embassy-topo/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/embassy-vienna/embassy-vienna-1.7.2.660-r1.ebuild b/sci-biology/embassy-vienna/embassy-vienna-1.7.2.660-r1.ebuild new file mode 100644 index 000000000000..241194af375e --- /dev/null +++ b/sci-biology/embassy-vienna/embassy-vienna-1.7.2.660-r1.ebuild @@ -0,0 +1,21 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +EBO_DESCRIPTION="Vienna RNA package - RNA folding" + +inherit autotools emboss-r3 + +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + +S="${WORKDIR}/VIENNA-1.7.2.650" +PATCHES=( + "${FILESDIR}"/${PN}-1.7.2.650_fix-build-system.patch + "${FILESDIR}"/${PN}-1.7.2.650-C99-inline.patch +) + +src_prepare() { + default + eautoreconf +} diff --git a/sci-biology/embassy-vienna/embassy-vienna-1.7.2.660.ebuild b/sci-biology/embassy-vienna/embassy-vienna-1.7.2.660.ebuild deleted file mode 100644 index d82532a4f623..000000000000 --- a/sci-biology/embassy-vienna/embassy-vienna-1.7.2.660.ebuild +++ /dev/null @@ -1,20 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -EBO_DESCRIPTION="Vienna RNA package - RNA folding" - -EBO_EAUTORECONF=1 - -inherit emboss-r2 flag-o-matic - -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" - -S="${WORKDIR}/VIENNA-1.7.2.650" -PATCHES=( "${FILESDIR}"/${PN}-1.7.2.650_fix-build-system.patch ) - -src_configure() { - append-cflags -std=gnu89 - emboss-r2_src_configure -} diff --git a/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650-C99-inline.patch b/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650-C99-inline.patch new file mode 100644 index 000000000000..1eda10172dc5 --- /dev/null +++ b/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650-C99-inline.patch @@ -0,0 +1,32 @@ +--- a/src/fold.c ++++ b/src/fold.c +@@ -65,9 +65,9 @@ + PRIVATE int fill_arrays(const char *sequence); + /*@unused@*/ + INLINE PRIVATE int oldLoopEnergy(int i, int j, int p, int q, int type, int type_2); +-INLINE int LoopEnergy(int n1, int n2, int type, int type_2, ++int LoopEnergy(int n1, int n2, int type, int type_2, + int si1, int sj1, int sp1, int sq1); +-INLINE int HairpinE(int size, int type, int si1, int sj1, const char *string); ++int HairpinE(int size, int type, int si1, int sj1, const char *string); + int loop_energy(short * ptable, short *s, short *s1, int i); + char *backtrack_fold_from_pair(char *sequence, int i, int j); + void export_circfold_arrays(int *Fc_p, int *FcH_p, int *FcI_p, int *FcM_p, int **fM2_p, +@@ -831,7 +831,7 @@ + } + /*---------------------------------------------------------------------------*/ + +-INLINE int HairpinE(int size, int type, int si1, int sj1, const char *string) { ++int HairpinE(int size, int type, int si1, int sj1, const char *string) { + int energy; + energy = (size <= 30) ? P->hairpin[size] : + P->hairpin[30]+(int)(P->lxc*log((size)/30.)); +@@ -901,7 +901,7 @@ + + /*--------------------------------------------------------------------------*/ + +-INLINE int LoopEnergy(int n1, int n2, int type, int type_2, ++int LoopEnergy(int n1, int n2, int type, int type_2, + int si1, int sj1, int sp1, int sq1) { + /* compute energy of degree 2 loop (stack bulge or interior) */ + int nl, ns, energy; diff --git a/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch b/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch index 5ce365ed5497..ea96e9d47fa9 100644 --- a/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch +++ b/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch @@ -1,12 +1,6 @@ - configure.ac | 49 +++++++------------------------------------------ - src/Makefile.am | 7 +++---- - 2 files changed, 10 insertions(+), 46 deletions(-) - -diff --git a/configure.ac b/configure.ac -index f5a4ecf..bbe0743 100644 ---- a/configure.ac -+++ b/configure.ac -@@ -649,33 +649,6 @@ AS_CASE([${host_os}], +--- a/configure.in ++++ b/configure.in +@@ -649,33 +649,6 @@ @@ -40,7 +34,7 @@ index f5a4ecf..bbe0743 100644 dnl FIXME: This does no longer seem required with Autoconf 2.67? dnl Intel MacOSX 10.6 puts X11 in a non-standard place dnl AS_IF([test "x${with_x}" != "xno"], -@@ -751,21 +724,6 @@ AX_LIB_POSTGRESQL +@@ -751,21 +724,6 @@ @@ -62,7 +56,7 @@ index f5a4ecf..bbe0743 100644 dnl Test if --enable-localforce given locallink="no" embprefix="/usr/local" -@@ -888,6 +846,13 @@ AC_ARG_ENABLE([systemlibs], +@@ -888,6 +846,13 @@ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) @@ -76,11 +70,18 @@ index f5a4ecf..bbe0743 100644 # Enable the purify tool: --enable-purify, sets CC and LIBTOOL -diff --git a/src/Makefile.am b/src/Makefile.am -index 1f5b756..e178914 100644 --- a/src/Makefile.am +++ b/src/Makefile.am -@@ -32,9 +32,7 @@ AM_CPPFLAGS = -I../H -I../../../nucleus -I../../../ajax/pcre \ +@@ -10,7 +10,7 @@ + -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -leplplot -leexpat \ + -lezlib -lepcre + else +-CYGWIN_LDVIENNA = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl \ ++CYGWIN_LDVIENNA = -lnucleus -lacd -lajaxdb -lensembl \ + -lajaxg -lajax -leplplot -leexpat -lezlib -lepcre + endif + endif +@@ -32,9 +32,7 @@ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ -I../../../ajax/acd -I../../../plplot else @@ -91,7 +92,16 @@ index 1f5b756..e178914 100644 endif if ISSHARED -@@ -87,6 +85,7 @@ LINKFLAGS = $(VERS_INF) +@@ -49,7 +47,7 @@ + -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -leexpat -lepcre \ + $(NLAIXLIBS) -leplplot + else +-AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \ ++AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \ + -lajaxdb -lensembl -lajaxg -lajax -leexpat -lepcre $(NLAIXLIBS) -leplplot + endif + endif +@@ -87,6 +85,7 @@ endif liboviennarna_la_LDFLAGS = $(LINKFLAGS) @@ -99,10 +109,12 @@ index 1f5b756..e178914 100644 ovrnaalifold_SOURCES = vrnaalifold.c ovrnaalifoldpf_SOURCES = vrnaalifoldpf.c -@@ -119,5 +118,5 @@ LDADD = liboviennarna.la \ +@@ -118,6 +117,6 @@ + ../../../plplot/libeplplot.la \ $(XLIB) else - LDADD = liboviennarna.la -L${embprefix}/lib -lnucleus -lacd -lajaxdb \ +-LDADD = liboviennarna.la -L${embprefix}/lib -lnucleus -lacd -lajaxdb \ - -lensembl -lajaxg -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++LDADD = liboviennarna.la -lnucleus -lacd -lajaxdb \ + -lensembl -lajaxg -lajax $(NLADD) $(XLIB) endif diff --git a/sci-biology/embassy-vienna/metadata.xml b/sci-biology/embassy-vienna/metadata.xml index d1b9a7602ec2..55784cd1ea18 100644 --- a/sci-biology/embassy-vienna/metadata.xml +++ b/sci-biology/embassy-vienna/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/embassy/embassy-6.6.0-r1.ebuild b/sci-biology/embassy/embassy-6.6.0-r3.ebuild index b30223eda805..63feacc58663 100644 --- a/sci-biology/embassy/embassy-6.6.0-r1.ebuild +++ b/sci-biology/embassy/embassy-6.6.0-r3.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 DESCRIPTION="A meta-package for installing all EMBASSY packages (EMBOSS add-ons)" HOMEPAGE="http://emboss.sourceforge.net/embassy/" @@ -20,7 +20,6 @@ RDEPEND=" >=sci-biology/embassy-esim4-1.0.0.660 >=sci-biology/embassy-hmmer-2.3.2.660 >=sci-biology/embassy-iprscan-4.3.1.660 - >=sci-biology/embassy-meme-4.7.660 >=sci-biology/embassy-mse-3.0.0.660 >=sci-biology/embassy-phylipnew-3.69.660 >=sci-biology/embassy-signature-0.1.660 diff --git a/sci-biology/embassy/metadata.xml b/sci-biology/embassy/metadata.xml index d1b9a7602ec2..55784cd1ea18 100644 --- a/sci-biology/embassy/metadata.xml +++ b/sci-biology/embassy/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/emboss/Manifest b/sci-biology/emboss/Manifest index e4650c04fb9a..fa61d72a1db4 100644 --- a/sci-biology/emboss/Manifest +++ b/sci-biology/emboss/Manifest @@ -1 +1,2 @@ DIST EMBOSS-6.6.0.tar.gz 117962028 BLAKE2B 91bf3c680290bd975d2ddb5251089d7f75f8a44a26e1247e93d2c9cf2f23e6b89c4218022ba1af0c940136ff56782f40d2c4604dc756b400ae23f223da7f3cca SHA512 2d28a03381f7dc98d205aa50202fbbac02ad218fc775d86579d310296be124403623484b1907154d915f15cd32a9f8cf16ecfaa6c4a28b362e24dc8e6380b75a +DIST emboss-6.6.0-patches-r1.tar.xz 5384 BLAKE2B 7899141862880d000e1624e9df914b1918cd02645c0d14128bcffd41d76e3669404a718f25471795268e4a00d610377186b7cb73a126e30f74df80d04d22faf9 SHA512 95825a3bcaa6340d26fde65f3b77574e42fd424440ee48f2fad94b6e696346fe4f6e4ab48c7dcfe1e9c3311a8a7750defc004c2db40cc36f42e980a19e6bd0bd diff --git a/sci-biology/emboss/emboss-6.6.0-r1.ebuild b/sci-biology/emboss/emboss-6.6.0-r3.ebuild index 2aa5aa9bc5c9..5a43c0ff89ef 100644 --- a/sci-biology/emboss/emboss-6.6.0-r1.ebuild +++ b/sci-biology/emboss/emboss-6.6.0-r3.ebuild @@ -1,22 +1,24 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 -EBO_EAUTORECONF=1 - -inherit emboss-r2 readme.gentoo-r1 +inherit autotools emboss-r3 readme.gentoo-r1 DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package" -SRC_URI="ftp://emboss.open-bio.org/pub/${PN^^}/${P^^}.tar.gz" +SRC_URI=" + ftp://emboss.open-bio.org/pub/${PN^^}/${P^^}.tar.gz + https://dev.gentoo.org/~soap/distfiles/${P}-patches-r1.tar.xz" +S="${WORKDIR}/${P^^}" +LICENSE+=" Apache-2.0 GPL-3+ CC-BY-3.0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" IUSE="minimal" -LICENSE+=" Apache-2.0 GPL-3+ CC-BY-3.0" RDEPEND=" + !dev-build/cons !games-action/xbomber - !sys-devel/cons" +" PDEPEND=" !minimal? ( sci-biology/aaindex @@ -27,36 +29,44 @@ PDEPEND=" sci-biology/rebase )" -S="${WORKDIR}/${P^^}" - PATCHES=( - "${FILESDIR}"/${P}_fix-build-system.patch - "${FILESDIR}"/${P}_FORTIFY_SOURCE-fix.patch - "${FILESDIR}"/${P}_plplot-declarations.patch - "${FILESDIR}"/${P}_qa-implicit-declarations.patch + "${WORKDIR}"/patches/${P}-fix-build-system.patch + "${WORKDIR}"/patches/${P}-FORTIFY_SOURCE-fix.patch + "${WORKDIR}"/patches/${P}-plplot-declarations.patch + "${WORKDIR}"/patches/${P}-qa-implicit-declarations.patch + "${WORKDIR}"/patches/${P}-C99-bool.patch + "${WORKDIR}"/patches/${P}-Wimplicit-function-declaration.patch ) +src_prepare() { + default + eautoreconf +} + src_install() { - emboss-r2_src_install + emboss-r3_src_install readme.gentoo_create_doc # Install env file for setting libplplot and acd files path. - cat > 22emboss <<- EOF || die + newenvd - 22emboss <<- EOF # ACD files location EMBOSS_ACDROOT="${EPREFIX}/usr/share/EMBOSS/acd" EMBOSS_DATA="${EPREFIX}/usr/share/EMBOSS/data" EOF - doenvd 22emboss # Remove useless dummy files - find "${ED%/}"/usr/share/EMBOSS -name dummyfile -delete || die "Failed to remove dummy files" + find "${ED}"/usr/share/EMBOSS -name dummyfile -delete \ + || die "Failed to remove dummy files" # Move the provided codon files to a different directory. This will avoid # user confusion and file collisions on case-insensitive file systems (see # bug #115446). This change is documented in "README.gentoo". - mv "${ED%/}"/usr/share/EMBOSS/data/CODONS{,.orig} \ + mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} \ || die "Failed to move CODON directory" + + # collision with dev-texlive/texlive-latexextra, bug #927976 + mv "${ED}"/usr/bin/{,emboss-}wordcount || die } pkg_postinst() { diff --git a/sci-biology/emboss/files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch b/sci-biology/emboss/files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch deleted file mode 100644 index 7704873e9d26..000000000000 --- a/sci-biology/emboss/files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- EMBOSS-6.6.0/emboss/embossversion.c -+++ EMBOSS-6.6.0/emboss/embossversion.c -@@ -415,7 +415,7 @@ - ajFmtPrintF(outfile, "X_DISPLAY_MISSING %d\n", X_DISPLAY_MISSING); - #endif - #ifdef _FORTIFY_SOURCE -- ajFmtPrintF(outfile, "_FORTIFY_SOURCE %d\n", _FORTIFY_SOURCE); -+ ajFmtPrintF(outfile, "_FORTIFY_SOURCE %d\n", __USE_FORTIFY_LEVEL); - #endif - ajFmtPrintF(outfile, "\n"); - ajFmtPrintF(outfile, "Sizes (bytes):\n"); diff --git a/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch b/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch deleted file mode 100644 index 266bddd95a37..000000000000 --- a/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch +++ /dev/null @@ -1,411 +0,0 @@ - Makefile.am | 9 +++--- - ajax/Makefile.am | 4 +-- - ajax/acd/Makefile.am | 8 +++-- - ajax/ajaxdb/Makefile.am | 6 ++-- - ajax/core/Makefile.am | 6 ++-- - ajax/core/ajreg.h | 7 ++-- - ajax/ensembl/Makefile.am | 6 ++-- - ajax/graphics/Makefile.am | 8 +++-- - configure.ac | 82 ++++++++++++++++++++++++++--------------------- - emboss/Makefile.am | 13 +++++--- - jemboss/lib/Makefile.am | 2 +- - m4/idxdbs.m4 | 17 +++------- - nucleus/Makefile.am | 8 +++-- - 13 files changed, 100 insertions(+), 76 deletions(-) - -diff --git a/Makefile.am b/Makefile.am -index 177dec5..18dd99a 100644 ---- a/Makefile.am -+++ b/Makefile.am -@@ -12,8 +12,11 @@ LICENSE \ - ONEWS \ - PROBLEMS - --SUBDIRS = \ --plplot \ -+SUBDIRS = -+if !ESYSTEMLIBS -+SUBDIRS += plplot -+endif -+SUBDIRS += \ - ajax \ - nucleus \ - emboss \ -@@ -33,5 +36,3 @@ dist-hook: - tar cBf - doc | ( cd $(distdir); tar xBf - ; find doc -name CVS | xargs rm -rf; ) - tar cBf - jemboss | ( cd $(distdir); tar xBf - ; find jemboss -name CVS | xargs rm -rf; find jemboss -name Makefile | xargs rm -rf; find jemboss -name .cvsignore | xargs rm -rf ) - --install-exec-hook: -- $(bindir)/embossupdate -diff --git a/ajax/Makefile.am b/ajax/Makefile.am -index f27472c..de34e17 100644 ---- a/ajax/Makefile.am -+++ b/ajax/Makefile.am -@@ -1,7 +1,7 @@ - ## Process this file with automake to produce Makefile.in - --SUBDIRS = pcre -+SUBDIRS = - if !ESYSTEMLIBS --SUBDIRS += expat zlib -+SUBDIRS += pcre expat zlib - endif - SUBDIRS += core graphics ensembl ajaxdb acd -diff --git a/ajax/acd/Makefile.am b/ajax/acd/Makefile.am -index 9f0f700..3295a1d 100644 ---- a/ajax/acd/Makefile.am -+++ b/ajax/acd/Makefile.am -@@ -3,16 +3,20 @@ - lib_LTLIBRARIES = libacd.la - - libacd_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) -+libacd_la_LIBADD = ../core/libajax.la ../graphics/libajaxg.la - - libacd_la_CPPFLAGS = -I$(top_srcdir)/ajax/ajaxdb -+libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/core - libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl - libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/graphics --libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre - if !ESYSTEMLIBS -+libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre - libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat - libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib --endif - libacd_la_CPPFLAGS += -I$(top_srcdir)/plplot -+else -+libacd_la_CFLAGS += $(PLPLOT_CFLAGS) -+endif - libacd_la_CPPFLAGS += $(JAVA_CPPFLAGS) - - libacd_la_LDFLAGS = -version-info 6:5:0 -diff --git a/ajax/ajaxdb/Makefile.am b/ajax/ajaxdb/Makefile.am -index c2b0c00..9de14fe 100644 ---- a/ajax/ajaxdb/Makefile.am -+++ b/ajax/ajaxdb/Makefile.am -@@ -3,14 +3,16 @@ - lib_LTLIBRARIES = libajaxdb.la - - libajaxdb_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) -+libajaxdb_la_LIBADD = ../core/libajax.la ../ensembl/libensembl.la - - libajaxdb_la_CPPFLAGS = -I$(top_srcdir)/ajax/ensembl --libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre -+libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/core - if !ESYSTEMLIBS -+libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre - libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat - libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib --endif - libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/plplot -+endif - libajaxdb_la_CPPFLAGS += $(AXIS2C_CPPFLAGS) - libajaxdb_la_CPPFLAGS += $(JAVA_CPPFLAGS) - -diff --git a/ajax/core/Makefile.am b/ajax/core/Makefile.am -index 2906837..3189c34 100644 ---- a/ajax/core/Makefile.am -+++ b/ajax/core/Makefile.am -@@ -3,13 +3,15 @@ - lib_LTLIBRARIES = libajax.la - - libajax_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) -+libajax_la_LIBADD = $(EXPAT_LIBS) $(PCRE_LIBS) $(ZLIB_LIBS) - --libajax_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre -+libajax_la_CPPFLAGS = - if !ESYSTEMLIBS -+libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre - libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat - libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib --endif - libajax_la_CPPFLAGS += -I$(top_srcdir)/plplot -+endif - libajax_la_CPPFLAGS += $(JAVA_CPPFLAGS) - libajax_la_CPPFLAGS += $(MYSQL_CPPFLAGS) - libajax_la_CPPFLAGS += $(POSTGRESQL_CPPFLAGS) -diff --git a/ajax/core/ajreg.h b/ajax/core/ajreg.h -index 1623c82..5d928cf 100644 ---- a/ajax/core/ajreg.h -+++ b/ajax/core/ajreg.h -@@ -39,9 +39,8 @@ - #include "ajdefine.h" - #include "ajstr.h" - --#include "pcre_config.h" --#include "pcre_internal.h" --#include "pcreposix.h" -+#include <pcre.h> -+#include <pcreposix.h> - - AJ_BEGIN_DECLS - -@@ -84,7 +83,7 @@ AJ_BEGIN_DECLS - - typedef struct AjSRegexp - { -- real_pcre *pcre; -+ struct real_pcre *pcre; - pcre_extra *extra; - int *ovector; - const char* orig; -diff --git a/ajax/ensembl/Makefile.am b/ajax/ensembl/Makefile.am -index 0d1250b..5484c02 100644 ---- a/ajax/ensembl/Makefile.am -+++ b/ajax/ensembl/Makefile.am -@@ -3,13 +3,15 @@ - lib_LTLIBRARIES = libensembl.la - - libensembl_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) -+libensembl_la_LIBADD = ../core/libajax.la - --libensembl_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre -+libensembl_la_CPPFLAGS = -I$(top_srcdir)/ajax/core - if !ESYSTEMLIBS -+libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre - libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat - libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib --endif - libensembl_la_CPPFLAGS += -I$(top_srcdir)/plplot -+endif - libensembl_la_CPPFLAGS += $(JAVA_CPPFLAGS) - - libensembl_la_LDFLAGS = -version-info 6:5:0 -diff --git a/ajax/graphics/Makefile.am b/ajax/graphics/Makefile.am -index a4f202b..1114c2c 100644 ---- a/ajax/graphics/Makefile.am -+++ b/ajax/graphics/Makefile.am -@@ -3,12 +3,16 @@ - lib_LTLIBRARIES = libajaxg.la - - libajaxg_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) -+libajaxg_la_LIBADD = ../core/libajax.la $(PLPLOT_LIBS) - --libajaxg_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre -+libajaxg_la_CPPFLAGS = -I$(top_srcdir)/ajax/core - if !ESYSTEMLIBS -+libajaxg_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre - libajaxg_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat --endif - libajaxg_la_CPPFLAGS += -I$(top_srcdir)/plplot -+else -+libajaxg_la_CFLAGS += $(PLPLOT_CFLAGS) -+endif - libajaxg_la_CPPFLAGS += $(JAVA_CPPFLAGS) - - libajaxg_la_LDFLAGS = -version-info 6:5:0 -diff --git a/configure.ac b/configure.ac -index a7bd9c6..9ba3121 100644 ---- a/configure.ac -+++ b/configure.ac -@@ -629,32 +629,6 @@ AS_CASE([${host_os}], - - - -- --dnl PCRE library definitions - see the MAJOR and MINOR values --dnl to see which version's configure.in these lines come from -- --dnl Provide the current PCRE version information. Do not use numbers --dnl with leading zeros for the minor version, as they end up in a C --dnl macro, and may be treated as octal constants. Stick to single --dnl digits for minor numbers less than 10. There are unlikely to be --dnl that many releases anyway. -- --PCRE_MAJOR="7" --PCRE_MINOR="9" --PCRE_DATE="11-Apr-2009" --PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" -- --dnl Default values for miscellaneous macros -- --POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" -- --dnl Provide versioning information for libtool shared libraries that --dnl are built by default on Unix systems. -- --PCRE_LIB_VERSION="0:1:0" --PCRE_POSIXLIB_VERSION="0:0:0" -- -- - dnl Define where the EMBOSS package is located - AC_SUBST([AJAX_FIXED_ROOT]) - AJAX_FIXED_ROOT="\\\"`pwd`/emboss\\\"" -@@ -743,17 +717,7 @@ AX_LIB_POSTGRESQL - - - --dnl "Export" these variables for PCRE - --AC_SUBST([HAVE_MEMMOVE]) --AC_SUBST([HAVE_STRERROR]) --AC_SUBST([PCRE_MAJOR]) --AC_SUBST([PCRE_MINOR]) --AC_SUBST([PCRE_DATE]) --AC_SUBST([PCRE_VERSION]) --AC_SUBST([PCRE_LIB_VERSION]) --AC_SUBST([PCRE_POSIXLIB_VERSION]) --AC_SUBST([POSIX_MALLOC_THRESHOLD]) - - - -@@ -849,7 +813,53 @@ AC_ARG_ENABLE([systemlibs], - - AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) - -+AS_IF([test "x${enable_systemlibs}" = "xyes"], -+[ -+dnl using system libraries -+ PKG_CHECK_MODULES([PCRE], [libpcre]) -+ PKG_CHECK_MODULES([EXPAT], [expat]) -+ PKG_CHECK_MODULES([ZLIB], [zlib]) -+ PKG_CHECK_MODULES([PLPLOT], [plplotd], -+ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] -+ ) -+], -+[ -+dnl using bundled libraries -+ dnl PCRE library definitions - see the MAJOR and MINOR values -+ dnl to see which version's configure.ac these lines come from - -+ dnl Provide the current PCRE version information. Do not use numbers -+ dnl with leading zeros for the minor version, as they end up in a C -+ dnl macro, and may be treated as octal constants. Stick to single -+ dnl digits for minor numbers less than 10. There are unlikely to be -+ dnl that many releases anyway. -+ -+ PCRE_MAJOR="7" -+ PCRE_MINOR="9" -+ PCRE_DATE="11-Apr-2009" -+ PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" -+ -+ dnl Default values for miscellaneous macros -+ -+ POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" -+ -+ dnl Provide versioning information for libtool shared libraries that -+ dnl are built by default on Unix systems. -+ -+ PCRE_LIB_VERSION="0:1:0" -+ PCRE_POSIXLIB_VERSION="0:0:0" -+ -+ dnl "Export" these variables for PCRE -+ AC_SUBST([HAVE_MEMMOVE]) -+ AC_SUBST([HAVE_STRERROR]) -+ AC_SUBST([PCRE_MAJOR]) -+ AC_SUBST([PCRE_MINOR]) -+ AC_SUBST([PCRE_DATE]) -+ AC_SUBST([PCRE_VERSION]) -+ AC_SUBST([PCRE_LIB_VERSION]) -+ AC_SUBST([PCRE_POSIXLIB_VERSION]) -+ AC_SUBST([POSIX_MALLOC_THRESHOLD]) -+]) - - - # Enable the purify tool: --enable-purify, sets CC and LIBTOOL -diff --git a/emboss/Makefile.am b/emboss/Makefile.am -index 89ada78..f987d40 100644 ---- a/emboss/Makefile.am -+++ b/emboss/Makefile.am -@@ -28,15 +28,18 @@ endif - - AM_CPPFLAGS = -I$(top_srcdir)/ajax/acd - AM_CPPFLAGS += -I$(top_srcdir)/ajax/ajaxdb -+AM_CPPFLAGS += -I$(top_srcdir)/ajax/core - AM_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl - AM_CPPFLAGS += -I$(top_srcdir)/ajax/graphics -+if !ESYSTEMLIBS - AM_CPPFLAGS += -I$(top_srcdir)/ajax/pcre --if !ESYSTEMLIBS - AM_CPPFLAGS += -I$(top_srcdir)/ajax/expat - AM_CPPFLAGS += -I$(top_srcdir)/ajax/zlib --endif --AM_CPPFLAGS += -I$(top_srcdir)/nucleus - AM_CPPFLAGS += -I$(top_srcdir)/plplot -+else -+AM_CFLAGS += $(PLPLOT_CFLAGS) -+endif -+AM_CPPFLAGS += -I$(top_srcdir)/nucleus - AM_CPPFLAGS += $(AXIS2C_CPPFLAGS) - AM_CPPFLAGS += $(JAVA_CPPFLAGS) - -@@ -49,9 +52,11 @@ LDADD += ../ajax/core/libajax.la - if !ESYSTEMLIBS - LDADD += ../ajax/zlib/libezlib.la - LDADD += ../ajax/expat/libeexpat.la --endif - LDADD += ../ajax/pcre/libepcre.la - LDADD += ../plplot/libeplplot.la -+else -+LDADD += $(EXPAT_LIBS) $(PCRE_LIBS) $(ZLIB_LIBS) $(PLPLOT_LIBS) -+endif - LDADD += $(XLIB) - - #if PURIFY -diff --git a/jemboss/lib/Makefile.am b/jemboss/lib/Makefile.am -index 5f7e21e..8b45ce2 100644 ---- a/jemboss/lib/Makefile.am -+++ b/jemboss/lib/Makefile.am -@@ -12,7 +12,7 @@ mail.jar \ - jalviewApplet.jar \ - jemboss.jar - --jemboss.jar:../org/emboss/jemboss/server/JembossFile*Server.java -+jemboss.jar:$(srcdir)/../org/emboss/jemboss/server/JembossFile*Server.java - if JAVA_BUILD - $(ANT) -f ../build.xml package -Demboss.data=../emboss/data -Dname=jemboss -Djar.dir=lib -Dnotformemboss=yes; - endif -diff --git a/m4/idxdbs.m4 b/m4/idxdbs.m4 -index 0ca7ea9..9b54f2a 100644 ---- a/m4/idxdbs.m4 -+++ b/m4/idxdbs.m4 -@@ -1,17 +1,8 @@ - AC_DEFUN([CHECK_IDXDBS], - [ --AC_MSG_CHECKING(for EMBOSS pre-indexed databases) -+AC_MSG_NOTICE(checking for EMBOSS pre-indexed databases) - -- --if test -f ./emboss/index/edam.xac; then --AC_MSG_RESULT(yes) --else --AC_MSG_RESULT(no) --echo "" --echo "Pre-indexed edam, taxon + drcat databases not found." --echo "Please download them from within this directory using:" --echo " rsync -av rsync://emboss.open-bio.org/EMBOSS/ ." --echo "and then repeat the configure step." --exit 1 --fi -+AC_CHECK_FILE([$srcdir/emboss/index/edam.xac], -+ [], -+ [AC_MSG_ERROR([cannot find pre-indexed edam, taxon + drcat databases])]) - ]) -diff --git a/nucleus/Makefile.am b/nucleus/Makefile.am -index 37b8543..5819c89 100644 ---- a/nucleus/Makefile.am -+++ b/nucleus/Makefile.am -@@ -3,6 +3,7 @@ - lib_LTLIBRARIES = libnucleus.la - - libnucleus_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) -+libnucleus_la_LIBADD = ../ajax/core/libajax.la ../ajax/ajaxdb/libajaxdb.la ../ajax/acd/libacd.la - - if ISSHARED - if ISAIXIA64 -@@ -10,11 +11,14 @@ libnucleus_la_CFLAGS += -Wl,-G -lm - endif - endif - --libnucleus_la_CPPFLAGS = -I$(top_srcdir)/plplot --libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre -+libnucleus_la_CPPFLAGS = -I$(top_srcdir)/ajax/core - if !ESYSTEMLIBS -+libnucleus_la_CPPFLAGS += -I$(top_srcdir)/plplot -+libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre - libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat - libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib -+else -+libnucleus_la_CFLAGS += $(PLPLOT_CFLAGS) - endif - libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/graphics - libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl diff --git a/sci-biology/emboss/files/emboss-6.6.0_plplot-declarations.patch b/sci-biology/emboss/files/emboss-6.6.0_plplot-declarations.patch deleted file mode 100644 index 15f5f967a07d..000000000000 --- a/sci-biology/emboss/files/emboss-6.6.0_plplot-declarations.patch +++ /dev/null @@ -1,61 +0,0 @@ ---- EMBOSS-6.6.0/ajax/graphics/ajgraph.c -+++ EMBOSS-6.6.0/ajax/graphics/ajgraph.c -@@ -49,7 +49,7 @@ - - #define GRAPH_DEBUG 1 - --#include "plplotP.h" -+#include <plplotP.h> - - - static void GraphArray(ajuint numofpoints, -@@ -964,10 +964,10 @@ - if(!thys->ready) - { - #if GRAPH_DEBUG -- ajDebug("=g= plxsfnam ('%S', '%s')\n", txt, ext); -+ ajDebug("=g= plsfnam ('%S')\n", txt); - #endif - -- plxsfnam(ajStrGetPtr(txt), ext); -+ plsfnam(ajStrGetPtr(txt)); - ajStrAssignS(&graphBasename, txt); - ajStrAssignC(&graphExtension, ext); - if(ajStrGetCharFirst(graphExtension) == '.') -@@ -1213,10 +1213,10 @@ - void ajGraphicsSetPenwidth(float penwidth) - { - #if GRAPH_DEBUG -- ajDebug("=g= plwid(%.2f) [width]\n", penwidth); -+ ajDebug("=g= c_plwidth(%.2f) [width]\n", penwidth); - #endif - -- plwid((PLINT)penwidth); -+ c_plwidth((PLINT)penwidth); - - return; - } -@@ -1538,10 +1538,10 @@ - static void GraphSetPen(ajint colour) - { - #if GRAPH_DEBUG -- ajDebug("=g= plcol(%d '%s') [colour]\n", colour, graphColourName[colour]); -+ ajDebug("=g= plcol0(%d '%s') [colour]\n", colour, graphColourName[colour]); - #endif - -- plcol((PLINT)colour); -+ plcol0((PLINT)colour); - - return; - } ---- EMBOSS-6.6.0/ajax/graphics/ajgraph.h -+++ EMBOSS-6.6.0/ajax/graphics/ajgraph.h -@@ -32,7 +32,7 @@ - /* ========================================================================= */ - - #include "ajdefine.h" --#include "plplot.h" -+#include <plplot.h> - #include "ajgraphstruct.h" - #include "ajdefine.h" - #include "ajstr.h" diff --git a/sci-biology/emboss/files/emboss-6.6.0_qa-implicit-declarations.patch b/sci-biology/emboss/files/emboss-6.6.0_qa-implicit-declarations.patch deleted file mode 100644 index eff10b2e6700..000000000000 --- a/sci-biology/emboss/files/emboss-6.6.0_qa-implicit-declarations.patch +++ /dev/null @@ -1,74 +0,0 @@ ---- EMBOSS-6.6.0/ajax/core/ajfeatread.c -+++ EMBOSS-6.6.0/ajax/core/ajfeatread.c -@@ -45,6 +45,7 @@ - - #include <limits.h> - #include <math.h> -+#include <string.h> - #include <errno.h> - - #ifdef WIN32 ---- EMBOSS-6.6.0/ajax/core/ajfeatwrite.c -+++ EMBOSS-6.6.0/ajax/core/ajfeatwrite.c -@@ -43,7 +43,7 @@ - - #include <limits.h> - #include <math.h> -- -+#include <string.h> - - static AjPRegexp featoutRegUfoFmt = NULL; - static AjPRegexp featoutRegUfoFile = NULL; ---- EMBOSS-6.6.0/ajax/core/ajpdbio.c -+++ EMBOSS-6.6.0/ajax/core/ajpdbio.c -@@ -37,7 +37,7 @@ - - #include <limits.h> - #include <math.h> -- -+#include <string.h> - - - ---- EMBOSS-6.6.0/ajax/core/ajreg.c -+++ EMBOSS-6.6.0/ajax/core/ajreg.c -@@ -32,6 +32,7 @@ - #include "ajlib.h" - - #include "ajreg.h" -+#include <string.h> - - - ---- EMBOSS-6.6.0/ajax/core/ajseqtype.c -+++ EMBOSS-6.6.0/ajax/core/ajseqtype.c -@@ -32,7 +32,7 @@ - #include "ajfeat.h" - #include "ajfile.h" - #include "ajreg.h" -- -+#include <string.h> - - - ---- EMBOSS-6.6.0/nucleus/embindex.c -+++ EMBOSS-6.6.0/nucleus/embindex.c -@@ -35,6 +35,7 @@ - #include "ajnam.h" - - #include <errno.h> -+#include <string.h> - - #define BTENTRYFILE ".ent" - #define KWLIMIT 12 ---- EMBOSS-6.6.0/nucleus/embword.c -+++ EMBOSS-6.6.0/nucleus/embword.c -@@ -36,7 +36,7 @@ - #include "ajutil.h" - - #include <math.h> -- -+#include <string.h> - - - diff --git a/sci-biology/emboss/metadata.xml b/sci-biology/emboss/metadata.xml index 7443e66b770f..e08634d4ff12 100644 --- a/sci-biology/emboss/metadata.xml +++ b/sci-biology/emboss/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/eugene/eugene-4.1d.ebuild b/sci-biology/eugene/eugene-4.1d-r1.ebuild index dbf8139e9e20..3800d7a2bdc3 100644 --- a/sci-biology/eugene/eugene-4.1d.ebuild +++ b/sci-biology/eugene/eugene-4.1d-r1.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit autotools @@ -11,17 +11,14 @@ SRC_URI="https://mulcyber.toulouse.inra.fr/frs/download.php/1359/${P}.tar.gz" LICENSE="Artistic" SLOT="0" -KEYWORDS="amd64 x86" -IUSE="" +KEYWORDS="amd64 ~x86" +RESTRICT="test" DEPEND=" media-libs/gd[png] - media-libs/libpng:0= - " + media-libs/libpng:=" RDEPEND="${DEPEND}" -RESTRICT="test" - PATCHES=( # https://mulcyber.toulouse.inra.fr/tracker/index.php?func=detail&aid=1170 "${FILESDIR}"/${PN}-3.6-overflow.patch @@ -29,6 +26,8 @@ PATCHES=( "${FILESDIR}"/${PN}-4.1-format-security.patch "${FILESDIR}"/${PN}-4.1d-fix-c++14.patch "${FILESDIR}"/${PN}-4.1d-Wformat.patch + "${FILESDIR}"/${PN}-4.1d-portable-getopt.patch + "${FILESDIR}"/${PN}-4.1d-clang16.patch ) src_prepare() { @@ -37,5 +36,6 @@ src_prepare() { -e '/SUBDIRS/ s/doc//' \ -e '/INSTALL.*doc/ s/\(.*\)//' \ -i Makefile.am || die + rm src/getopt.h || die eautoreconf } diff --git a/sci-biology/eugene/files/eugene-3.6-plugins.patch b/sci-biology/eugene/files/eugene-3.6-plugins.patch index 1e910a13d5b1..e7424f73fc63 100644 --- a/sci-biology/eugene/files/eugene-3.6-plugins.patch +++ b/sci-biology/eugene/files/eugene-3.6-plugins.patch @@ -1,7 +1,36 @@ -http://bugs.gentoo.org/show_bug.cgi?id=297536 +https://bugs.gentoo.org/297536 ---- eugene-3.6/src/Makefile.am -+++ eugene-3.6/src/Makefile.am +--- a/configure.ac ++++ b/configure.ac +@@ -28,6 +28,7 @@ + AC_PROG_CC + AC_PROG_AWK + AC_PROG_LN_S ++AM_PROG_AR + AC_PROG_RANLIB + + +--- a/Makefile.am ++++ b/Makefile.am +@@ -137,7 +137,7 @@ + $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/web/Style + $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/web/Javascripts + $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/web/Images +- $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/plugins ++ $(INSTALL) -d $(DESTDIR)/$(libdir)/eugene/plugins + $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/cfg + $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/models + $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/models/WAM +@@ -160,6 +160,6 @@ + $(INSTALL) -m 644 $(srcdir)/web/Images/*jpg $(DESTDIR)/$(pkgdatadir)/web/Images + $(INSTALL) -m 644 $(srcdir)/cfg/*.obo $(DESTDIR)/$(pkgdatadir)/cfg + $(INSTALL) -m 644 $(srcdir)/cfg/*.par $(DESTDIR)/$(pkgdatadir)/cfg +- $(INSTALL) src/SensorPlugins/*/*.so $(DESTDIR)/$(pkgdatadir)/plugins ++ $(INSTALL) src/SensorPlugins/*/*.so $(DESTDIR)/$(libdir)/eugene/plugins + $(INSTALL) $(srcdir)/Procedures/Eval/egn_* $(DESTDIR)/$(pkgdatadir)/Procedures/Eval + $(INSTALL) $(srcdir)/Procedures/Get/egn_* $(DESTDIR)/$(pkgdatadir)/Procedures/Get +--- a/src/Makefile.am ++++ b/src/Makefile.am @@ -20,7 +20,7 @@ SUBDIRS = Parametrization GDIF . SensorPlugins @@ -11,8 +40,8 @@ http://bugs.gentoo.org/show_bug.cgi?id=297536 AM_CFLAGS = bin_PROGRAMS = eugene ---- eugene-3.6/src/MSensor.cc -+++ eugene-3.6/src/MSensor.cc +--- a/src/MSensor.cc ++++ b/src/MSensor.cc @@ -97,7 +97,7 @@ std::string use_name; @@ -22,22 +51,3 @@ http://bugs.gentoo.org/show_bug.cgi?id=297536 // On récupère les couples nom de sensor/priorité du .par PAR.ResetIter(); ---- eugene-3.6/Makefile.am -+++ eugene-3.6/Makefile.am -@@ -125,7 +125,7 @@ - $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/web/Style - $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/web/Javascripts - $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/web/Images -- $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/plugins -+ $(INSTALL) -d $(DESTDIR)/$(libdir)/eugene/plugins - $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/cfg - $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/models - $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/models/WAM -@@ -144,6 +144,6 @@ - $(INSTALL) -m 644 $(srcdir)/web/Images/*jpg $(DESTDIR)/$(pkgdatadir)/web/Images - $(INSTALL) -m 644 $(srcdir)/cfg/*.obo $(DESTDIR)/$(pkgdatadir)/cfg - $(INSTALL) -m 644 $(srcdir)/cfg/*.par $(DESTDIR)/$(pkgdatadir)/cfg -- $(INSTALL) src/SensorPlugins/*/*.so $(DESTDIR)/$(pkgdatadir)/plugins -+ $(INSTALL) src/SensorPlugins/*/*.so $(DESTDIR)/$(libdir)/eugene/plugins - $(INSTALL) $(srcdir)/Procedures/Eval/egn_* $(DESTDIR)/$(pkgdatadir)/Procedures/Eval - $(INSTALL) $(srcdir)/Procedures/Get/egn_* $(DESTDIR)/$(pkgdatadir)/Procedures/Get diff --git a/sci-biology/eugene/files/eugene-4.1d-clang16.patch b/sci-biology/eugene/files/eugene-4.1d-clang16.patch new file mode 100644 index 000000000000..21a3ec0a8b62 --- /dev/null +++ b/sci-biology/eugene/files/eugene-4.1d-clang16.patch @@ -0,0 +1,22 @@ +--- a/src/GDIF/gdIF.c ++++ b/src/GDIF/gdIF.c +@@ -228,7 +228,7 @@ + ToY(phase, pos), (unsigned char *)st, Col[col]); + } + +-void ClosePNG() ++void ClosePNG(void) + { + int i; + +--- a/src/SensorPlugins/0_SensorTk/markov.cc ++++ b/src/SensorPlugins/0_SensorTk/markov.cc +@@ -790,7 +790,7 @@ + // cumule les valeurs des cases des codons synonymes et renvoie le total. + template<class CHAINE, typename T> T TabChaine<CHAINE,T> :: cumuleVAL (int indice) const + { +- char* codegenetique=CODEGENETIQUE; ++ const char* codegenetique=CODEGENETIQUE; + T cumul=0; + for (int i=0 ; i<64 ; i++) { + if ( codegenetique[i] == codegenetique[indice] ) diff --git a/sci-biology/eugene/files/eugene-4.1d-portable-getopt.patch b/sci-biology/eugene/files/eugene-4.1d-portable-getopt.patch new file mode 100644 index 000000000000..156cb4bbdfac --- /dev/null +++ b/sci-biology/eugene/files/eugene-4.1d-portable-getopt.patch @@ -0,0 +1,74 @@ +--- a/src/Param.h ++++ b/src/Param.h +@@ -28,26 +28,14 @@ + #include <vector> + #include <string> + #include <string.h> ++#include <unistd.h> + #ifdef HAVE_STRINGS_H + #include <strings.h> + #endif +-// MacOS-X has getopt() defined is stdlib and the library in the libSystem +-#ifndef __APPLE__ +-#ifdef HAVE_GETOPT_H +-#include <getopt.h> +-#else +-#ifndef HAVE_GETOPT +-#include "getopt.h" +-#endif +-#endif +-#endif + + #include "Const.h" + #include "System.h" + +-extern char *optarg; +-extern int optind; +- + + class ltstr + { +--- a/src/SensorPlugins/MarkovIMM/GetData/CEM.cc ++++ b/src/SensorPlugins/MarkovIMM/GetData/CEM.cc +@@ -22,18 +22,11 @@ + #include "../../../../config.h" + #endif + +-#ifdef HAVE_GETOPT_H +-#include <getopt.h> +-#else +-#ifndef HAVE_GETOPT +-#include "../../../getopt.h" +-#endif +-#endif +- + #include "../../../System.cc" + #include "../../../Const.h" + #include "../../0_SensorTk/EndianConv.h" + #include "strarray.h" ++#include "unistd.h" + #include <vector> + + // Constantes +--- a/src/SensorPlugins/MarkovIMM/GetData/TrainIMM.cc ++++ b/src/SensorPlugins/MarkovIMM/GetData/TrainIMM.cc +@@ -22,18 +22,11 @@ + #include "../../../../config.h" + #endif + +-#ifdef HAVE_GETOPT_H +-#include <getopt.h> +-#else +-#ifndef HAVE_GETOPT +-#include "../../../getopt.h" +-#endif +-#endif +- + #include "../../../System.cc" + #include "../../../Const.h" + #include "../../0_SensorTk/EndianConv.h" + #include "strarray.h" ++#include "unistd.h" + + + // Constantes diff --git a/sci-biology/eugene/metadata.xml b/sci-biology/eugene/metadata.xml index 959160fe46b1..ccdff086e20b 100644 --- a/sci-biology/eugene/metadata.xml +++ b/sci-biology/eugene/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/exonerate/exonerate-2.2.0-r2.ebuild b/sci-biology/exonerate/exonerate-2.2.0-r2.ebuild deleted file mode 100644 index 53ae5a97c6ae..000000000000 --- a/sci-biology/exonerate/exonerate-2.2.0-r2.ebuild +++ /dev/null @@ -1,48 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit autotools toolchain-funcs - -DESCRIPTION="Generic tool for pairwise sequence comparison" -HOMEPAGE="https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate" -SRC_URI="http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~ppc-macos ~x64-macos" -IUSE="test threads utils" -RESTRICT="!test? ( test )" -REQUIRED_USE="test? ( utils )" - -DEPEND="dev-libs/glib:2" -RDEPEND="${DEPEND}" - -PATCHES=( "${FILESDIR}"/${P}-asneeded.patch ) - -src_prepare() { - default - sed \ - -e 's: -O3 -finline-functions::g' \ - -i configure.in || die - mv configure.{in,ac} || die - - eautoreconf -} - -src_configure() { - tc-export CC - - econf \ - --enable-glib2 \ - --enable-largefile \ - $(use_enable utils utilities) \ - $(use_enable threads pthreads) -} - -src_install() { - default - - doman doc/man/man1/*.1 -} diff --git a/sci-biology/exonerate/exonerate-2.2.0-r3.ebuild b/sci-biology/exonerate/exonerate-2.2.0-r3.ebuild new file mode 100644 index 000000000000..9d7683b6dc4d --- /dev/null +++ b/sci-biology/exonerate/exonerate-2.2.0-r3.ebuild @@ -0,0 +1,50 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit autotools flag-o-matic toolchain-funcs + +DESCRIPTION="Generic tool for pairwise sequence comparison" +HOMEPAGE="https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate" +SRC_URI="https://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~ppc-macos ~x64-macos" +IUSE="test utils" +REQUIRED_USE="test? ( utils )" +RESTRICT="!test? ( test )" + +DEPEND="dev-libs/glib:2" +RDEPEND="${DEPEND}" + +PATCHES=( "${FILESDIR}"/${P}-autotools.patch ) + +src_prepare() { + default + eautoreconf +} + +src_configure() { + # -Werror=lto-type-mismatch + # https://bugs.gentoo.org/862264 + # Upstream doesn't use a bug tracker, so I fired them an email about it. -- Eli + filter-lto + + # the bootstrapping code loads AR and CC from the environment + tc-export CC RANLIB + export C4_AR="$(tc-getAR)" + + econf \ + --enable-glib2 \ + --enable-largefile \ + --enable-pthreads \ + $(use_enable utils utilities) +} + +src_install() { + default + + doman doc/man/man1/*.1 +} diff --git a/sci-biology/exonerate/files/exonerate-2.2.0-asneeded.patch b/sci-biology/exonerate/files/exonerate-2.2.0-asneeded.patch deleted file mode 100644 index 5c428979a1af..000000000000 --- a/sci-biology/exonerate/files/exonerate-2.2.0-asneeded.patch +++ /dev/null @@ -1,15 +0,0 @@ -Fix build with --as-needed - -https://bugs.gentoo.org/268094 - ---- a/configure.in -+++ b/configure.in -@@ -289,7 +289,7 @@ - if test "$enable_pthreads" = yes; then - echo "Using PTHREADS" - CFLAGS="$CFLAGS -DUSE_PTHREADS" -- LDFLAGS="$LDFLAGS -lpthread" -+ LIBS="$LIBS -lpthread" - elif test "$enable_pthreads" = no; then - echo "Not using pthreads" - else diff --git a/sci-biology/exonerate/files/exonerate-2.2.0-autotools.patch b/sci-biology/exonerate/files/exonerate-2.2.0-autotools.patch new file mode 100644 index 000000000000..af95b5c8f77a --- /dev/null +++ b/sci-biology/exonerate/files/exonerate-2.2.0-autotools.patch @@ -0,0 +1,43 @@ +Fix build with --as-needed + +https://bugs.gentoo.org/268094 + +--- a/configure.in ++++ b/configure.in +@@ -144,11 +145,6 @@ + elif test "$enable_assert" = no; then + CFLAGS="$CFLAGS -DG_DISABLE_ASSERT" + echo "Turning assertions off" +- if test "$GCC" = "yes"; then +- # Not currently using -fomit-frame-pointer as clashes with -pg +- # CFLAGS="$CFLAGS -O3 -fomit-frame-pointer -finline-functions" +- CFLAGS="$CFLAGS -O3 -finline-functions" +- fi + else + echo "error: must be yes or no: --enable-assert:[$enable_assert]" + exit 1 +@@ -289,7 +285,7 @@ + if test "$enable_pthreads" = yes; then + echo "Using PTHREADS" + CFLAGS="$CFLAGS -DUSE_PTHREADS" +- LDFLAGS="$LDFLAGS -lpthread" ++ LIBS="$LIBS -lpthread" + elif test "$enable_pthreads" = no; then + echo "Not using pthreads" + else +--- a/src/model/bootstrapper.c ++++ b/src/model/bootstrapper.c +@@ -146,8 +146,12 @@ + + static void Bootstrapper_index_archive(Bootstrapper *bs){ + register gchar *command; ++ register gchar *ranlib = "ranlib"; ++ register gchar *tmp = (gchar*)g_getenv("RANLIB"); ++ if(tmp) ++ ranlib = tmp; + register gint ret_val; +- command = g_strdup_printf("ranlib %s", bs->archive_path); ++ command = g_strdup_printf("%s %s", ranlib, bs->archive_path); + g_message("Indexing archive [%s]", bs->archive_path); + g_print("%s\n", command); + ret_val = system(command); diff --git a/sci-biology/exonerate/metadata.xml b/sci-biology/exonerate/metadata.xml index 7851377e083e..421b8ef55beb 100644 --- a/sci-biology/exonerate/metadata.xml +++ b/sci-biology/exonerate/metadata.xml @@ -1,14 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> - <longdescription lang="en"> - exonerate is a generic tool for pairwise sequence comparison - </longdescription> <use> - <flag name="utils">Install all utilities</flag> + <flag name="utils">Install the follow binaries: esd2esi, fasta2esd, fastaannotatecdna, fastachecksum, fastaclean, fastaclip, fastacomposition, fastadiff, fastaexplode, fastafetch, fastahardmask, fastaindex, fastalength, fastanrdb, fastaoverlap, fastareformat, fastaremove, fastarevcomp, fastasoftmask, fastasort, fastasplit, fastasubseq, fastatranslate, fastavalidcds</flag> </use> </pkgmetadata> diff --git a/sci-biology/express/Manifest b/sci-biology/express/Manifest deleted file mode 100644 index 9c2cc4ebf499..000000000000 --- a/sci-biology/express/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST express-1.5.1-src.tgz 931166 BLAKE2B 5eb185e4b001f26f0dd32885b256b9fa48c89f546d67d7f8472cade69dde25375a5fc8efed5f01b615d63b641b674f7034a13f9483eb7967a6fd784a55c8878e SHA512 59cf6511a879311247c65334285ea056d571d4fd950aa6243041fa10075ff0d1ddd2afbcfe12e5f7f3e7cdd22fe37fd7f6b43ed4a8eb28d7a33d72366dc549ee diff --git a/sci-biology/express/express-1.5.1.ebuild b/sci-biology/express/express-1.5.1.ebuild deleted file mode 100644 index 148df8a8ce14..000000000000 --- a/sci-biology/express/express-1.5.1.ebuild +++ /dev/null @@ -1,38 +0,0 @@ -# Copyright 1999-2018 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit cmake-utils - -DESCRIPTION="Streaming RNA-Seq Analysis" -HOMEPAGE="http://bio.math.berkeley.edu/eXpress/" -SRC_URI="http://bio.math.berkeley.edu/eXpress/downloads/${P}/${P}-src.tgz" - -LICENSE="Artistic" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND=" - >=dev-libs/boost-1.52.0:= - dev-libs/protobuf - dev-util/google-perftools - sci-biology/bamtools - sys-libs/zlib -" -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${P}-src" - -PATCHES=( - "${FILESDIR}"/${P}-buildsystem.patch - "${FILESDIR}"/${P}-gcc6.patch -) - -src_configure() { - local mycmakeargs=( - -DBAMTOOLS_INCLUDE="${EPREFIX}/usr/include/bamtools" - ) - cmake-utils_src_configure -} diff --git a/sci-biology/express/files/express-1.5.1-buildsystem.patch b/sci-biology/express/files/express-1.5.1-buildsystem.patch deleted file mode 100644 index fca5feadd111..000000000000 --- a/sci-biology/express/files/express-1.5.1-buildsystem.patch +++ /dev/null @@ -1,55 +0,0 @@ - CMakeLists.txt | 8 +++----- - src/CMakeLists.txt | 4 ++-- - 2 files changed, 5 insertions(+), 7 deletions(-) - -diff --git a/CMakeLists.txt b/CMakeLists.txt -index c768e28..65d5633 100644 ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -6,14 +6,12 @@ set(${PROJECT_NAME}_VERSION_MAJOR 1) - set(${PROJECT_NAME}_VERSION_MINOR 5) - set(${PROJECT_NAME}_VERSION_PATCH 1) - --set(CMAKE_CXX_FLAGS "-Wall") -- - set(CMAKE_CXX_FLAGS_DEBUG "-g ${CMAKE_CXX_FLAGS}") - set(CMAKE_CXX_FLAGS_RHDEBINFO "-O3 -g ${CMAKE_CXX_FLAGS}") - set(CMAKE_CXX_FLAGS_MINSIZEREL "-Os ${CMAKE_CXX_FLAGS}") - - set(CMAKE_BUILD_TYPE Release) --set(Boost_USE_STATIC_LIBS ON) -+set(Boost_USE_STATIC_LIBS OFF) - - find_package(Boost 1.39 - COMPONENTS -@@ -33,10 +31,10 @@ endif(GPERFTOOLS_TCMALLOC_LIB) - - find_package(Protobuf) - if (PROTOBUF_FOUND) -- include_directories(${Boost_INCLUDE_DIRS} ${PROTOBUF_INCLUDE_DIR} "${CMAKE_CURRENT_SOURCE_DIR}/bamtools/include") -+ include_directories(${Boost_INCLUDE_DIRS} ${PROTOBUF_INCLUDE_DIR} ${BAMTOOLS_INCLUDE}) - set(PROTO_INT 1) - else (PROTOBUF_FOUND) -- include_directories(${Boost_INCLUDE_DIRS} "${CMAKE_CURRENT_SOURCE_DIR}/bamtools/include") -+ include_directories(${Boost_INCLUDE_DIRS} ${BAMTOOLS_INCLUDE}) - set(PROTO_INT 0) - endif(PROTOBUF_FOUND) - -diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt -index 1cc0c01..8929d1f 100644 ---- a/src/CMakeLists.txt -+++ b/src/CMakeLists.txt -@@ -16,11 +16,11 @@ endif (GPERFTOOLS_TCMALLOC) - if(WIN32) - set(LIBRARIES ${LIBRARIES} "${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/libbamtools.lib" "${CMAKE_CURRENT_SOURCE_DIR}/../win_build/zlibd.lib") - else(WIN32) -- set(LIBRARIES ${LIBRARIES} "${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/libbamtools.a" "pthread") -+ set(LIBRARIES ${LIBRARIES} "bamtools" "pthread") - endif(WIN32) - - if (PROTOBUF_FOUND) -- set(LIBRARIES ${LIBRARIES} "libprotobuf.a") -+ set(LIBRARIES ${LIBRARIES} "protobuf") - endif(PROTOBUF_FOUND) - - target_link_libraries(express ${LIBRARIES}) diff --git a/sci-biology/express/files/express-1.5.1-gcc6.patch b/sci-biology/express/files/express-1.5.1-gcc6.patch deleted file mode 100644 index 8a608b97b056..000000000000 --- a/sci-biology/express/files/express-1.5.1-gcc6.patch +++ /dev/null @@ -1,19 +0,0 @@ -Bug: https://bugs.gentoo.org/610692 - ---- a/src/targets.cpp -+++ b/src/targets.cpp -@@ -113,12 +113,12 @@ - - double ll = LOG_1; - double tot_mass = mass(with_pseudo); -- double tot_eff_len = cached_effective_length(lib.bias_table); -+ double tot_eff_len = cached_effective_length(static_cast<bool>(lib.bias_table)); - if (neighbors) { - foreach (const Target* neighbor, *neighbors) { - tot_mass = log_add(tot_mass, neighbor->mass(with_pseudo)); - tot_eff_len = log_add(tot_eff_len, -- neighbor->cached_effective_length(lib.bias_table)); -+ neighbor->cached_effective_length(static_cast<bool>(lib.bias_table))); - } - } - ll += tot_mass - tot_eff_len; diff --git a/sci-biology/express/metadata.xml b/sci-biology/express/metadata.xml deleted file mode 100644 index 959160fe46b1..000000000000 --- a/sci-biology/express/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/fasta/Manifest b/sci-biology/fasta/Manifest index 800c5b2628b4..c0bd97106d3a 100644 --- a/sci-biology/fasta/Manifest +++ b/sci-biology/fasta/Manifest @@ -1 +1 @@ -DIST fasta-36.3.5e.tar.gz 943763 BLAKE2B 6234d0aee76af6614e6d25ebcfbdfae080db5bc5adf611aeb6edc53ed7c6cb6cef257bf852ed39bc286527cec4175c251765ce23ea5ff39d12ff8947dba97ac6 SHA512 ddfcae36dadd7e2ed5c8c8c0bda2eed077e9f6cd55e4ebf507690671af156358e9da4e7cb1406d2b8713c326c54a9d829fc25e668b16dfa6df48d18e3a009812 +DIST fasta-36.3.8h.tar.gz 1257682 BLAKE2B e6bd9087563150355fed6edf52a24a0b31ef0658b1e95c3df6d5b5711fc4d137ddd773fb8b3b2fa82fe3f5c310689b2f89668f5b51654eed41ed71f9ef140f99 SHA512 30d160ad083a605397c6c35d2b28f6064cd96f51f99b3664b424ec1dbbbd09772c72e89731a7257306ab58c4ad4b877e229873abd0e09407c64fae643bc04391 diff --git a/sci-biology/fasta/fasta-36.3.5e.ebuild b/sci-biology/fasta/fasta-36.3.8h-r1.ebuild index 392ee4c76410..1cd7ca60dcde 100644 --- a/sci-biology/fasta/fasta-36.3.5e.ebuild +++ b/sci-biology/fasta/fasta-36.3.8h-r1.ebuild @@ -1,22 +1,24 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=8 -inherit eutils flag-o-matic toolchain-funcs +inherit flag-o-matic toolchain-funcs + +MY_PV="${PV}_04-May-2020" DESCRIPTION="FASTA is a DNA and Protein sequence alignment software package" HOMEPAGE="https://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml" -SRC_URI="http://faculty.virginia.edu/wrpearson/${PN}/${PN}36/${P}.tar.gz" +SRC_URI="https://github.com/wrpearson/fasta36/archive/refs/tags/v${MY_PV}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/${PN}36-${MY_PV}" LICENSE="fasta" SLOT="0" -KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos" IUSE="debug cpu_flags_x86_sse2 test" RESTRICT="!test? ( test )" -DEPEND="test? ( app-shells/tcsh )" -RDEPEND="" +BDEPEND="test? ( app-shells/tcsh )" src_prepare() { CC_ALT= @@ -25,11 +27,11 @@ src_prepare() { use debug && append-flags -DDEBUG - if [[ $(tc-getCC) == *icc* ]]; then + if [[ "$(tc-getCC)" == *icc* ]]; then CC_ALT=icc ALT="${ALT}_icc" else - CC_ALT=$(tc-getCC) + CC_ALT="$(tc-getCC)" use x86 && ALT="32" use amd64 && ALT="64" fi @@ -37,23 +39,23 @@ src_prepare() { if use cpu_flags_x86_sse2 ; then ALT="${ALT}_sse2" append-flags -msse2 - [[ $(tc-getCC) == *icc* ]] || append-flags -ffast-math + [[ "$(tc-getCC)" == *icc* ]] || append-flags -ffast-math fi export CC_ALT="${CC_ALT}" export ALT="${ALT}" - epatch "${FILESDIR}"/${P}-ldflags.patch + eapply "${FILESDIR}"/${P}-ldflags.patch sed \ -e 's:-ffast-math::g' \ -i make/Makefile* || die + eapply_user } src_compile() { - cd src || die - emake -f ../make/Makefile.linux${ALT} CC="${CC_ALT} ${CFLAGS}" HFLAGS="${LDFLAGS} -o" all + emake -C src -f ../make/Makefile.linux${ALT} CC="${CC_ALT} ${CFLAGS}" HFLAGS="${LDFLAGS} -o" all } src_test() { @@ -62,18 +64,18 @@ src_test() { } src_install() { - local bin dobin bin/* - pushd bin > /dev/null || die - for bin in *36; do - dosym ${bin} /usr/bin/${bin%36} - done - popd + pushd bin >/dev/null || die + local i + for i in *36; do + dosym ${i} /usr/bin/${i%36} + done + popd >/dev/null || die insinto /usr/share/${PN} - doins -r conf/* data seq + doins -r conf/. data seq doman doc/{prss3.1,fasta36.1,fasts3.1,fastf3.1,ps_lav.1,map_db.1} - dodoc FASTA_LIST README doc/{README.versions,readme*,fasta*,changes*} + dodoc FASTA_LIST README* doc/{README*,readme*,fasta*,changes*} } diff --git a/sci-biology/fasta/files/fasta-36.3.5e-ldflags.patch b/sci-biology/fasta/files/fasta-36.3.8h-ldflags.patch index a6eeabfdf46c..40070d50fe76 100644 --- a/sci-biology/fasta/files/fasta-36.3.5e-ldflags.patch +++ b/sci-biology/fasta/files/fasta-36.3.8h-ldflags.patch @@ -1,14 +1,7 @@ - make/Makefile.pcom | 8 ++++---- - make/Makefile.pcom_s | 8 ++++---- - make/Makefile.pcom_t | 8 ++++---- - 3 files changed, 12 insertions(+), 12 deletions(-) - -diff --git a/make/Makefile.pcom b/make/Makefile.pcom -index 9c5f801..33fc001 100644 --- a/make/Makefile.pcom +++ b/make/Makefile.pcom -@@ -209,14 +209,14 @@ print_pssm : print_pssm.c getseq.c karlin.c apam.c - $(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c $(LIB_M) +@@ -216,14 +216,14 @@ + $(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c pssm_asn_subs.c $(LIB_M) $(LIB_DB) map_db : map_db.c uascii.h ncbl2_head.h - $(CC) $(CFLAGS) -o $(BIN)/map_db map_db.c @@ -26,12 +19,10 @@ index 9c5f801..33fc001 100644 lav2svg : lav2plt.o lavplt_svg.o - $(CC) -DUNIX -o $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm + $(CC) -DUNIX $(HFLAGS) $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm -diff --git a/make/Makefile.pcom_s b/make/Makefile.pcom_s -index dc53001..8a45044 100644 --- a/make/Makefile.pcom_s +++ b/make/Makefile.pcom_s -@@ -143,14 +143,14 @@ print_pssm : print_pssm.c getseq.c karlin.c apam.c - $(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c $(LIB_M) +@@ -149,14 +149,14 @@ + $(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c pssm_asn_subs.c $(LIB_M) $(LIB_DB) map_db : map_db.c uascii.h ncbl2_head.h - $(CC) $(CFLAGS) -o $(BIN)/map_db map_db.c @@ -49,12 +40,10 @@ index dc53001..8a45044 100644 lav2svg : lav2plt.o lavplt_svg.o - $(CC) -DUNIX -o $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm + $(CC) -DUNIX $(HFLAGS) $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm -diff --git a/make/Makefile.pcom_t b/make/Makefile.pcom_t -index 8a71438..5b08a50 100644 --- a/make/Makefile.pcom_t +++ b/make/Makefile.pcom_t -@@ -164,14 +164,14 @@ print_pssm : print_pssm.c getseq.c karlin.c apam.c - $(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c $(LIB_M) +@@ -171,14 +171,14 @@ + $(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c pssm_asn_subs.c $(LIB_M) $(LIB_DB) map_db : map_db.c uascii.h ncbl2_head.h - $(CC) $(CFLAGS) -o $(BIN)/map_db map_db.c diff --git a/sci-biology/fasta/metadata.xml b/sci-biology/fasta/metadata.xml index 959160fe46b1..be62121d4e2d 100644 --- a/sci-biology/fasta/metadata.xml +++ b/sci-biology/fasta/metadata.xml @@ -1,8 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="github">wrpearson/fasta36</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/fasttree/Manifest b/sci-biology/fasttree/Manifest index 1aedce930c6c..cf6d3bc20337 100644 --- a/sci-biology/fasttree/Manifest +++ b/sci-biology/fasttree/Manifest @@ -1,3 +1,3 @@ -DIST FastTree-2.1.8.c 385231 BLAKE2B 6f42025ef69b990e051263ccfa23f95d0cde326798c54d8f702c50127338711898c380d1dbd82ab775667eada047048ba8d68288b030af4984019a5f2c23729f SHA512 39a7d284412a602208c2a5df3d0a9a30fe3a584f7f7788d741fb1463b698692017f47bb23f70046d0873e9c8fd27c84ec23f6ca48adb0594193765ac732e6559 -DIST FastTreeUPGMA-2.1.8.c 95271 BLAKE2B 1de328881f6452b9c7423c9ed381ab2eb31c4f3ee6426481a6b1089c1359627d4cbbfbea868ebeab9538f82e17f45f1bff8ec07c7370e6432bef6bae449798a8 SHA512 4d6a8e2cb28b8ee201091172a3baa59d432420839c6d2244b5fb8230ed9daa626b6bed22cb692393ca3d78b8f2d071fe18fbb4f9bdcdc47ef149c31e3f45546c -DIST MOTreeComparison-2.1.8.tar.gz 13523 BLAKE2B 97638edd945412ff00e3dfcfc89ec6ea52ae8c43531d5cb680d97e9c62fcad80e861f58ec987abcd2282166dd7886101edba4875531bd9d6ac23df242e0dbd5b SHA512 24d2247650d7728942bd1d987b548cefd65a16b433a3810876613e9fd1cff223d4349ee720b3d8d10a73af220c2c9f59a24d77ad34ff009325fe9f22aa35c72b +DIST FastTree-2.1.11.c 395543 BLAKE2B 5bea3fba66ddf077ce42c3e1791505a9fa909bb619e30e0c0370631996d932c63ca172fffc1721ac9f081a16bed3b1c99a9c7f6e4a3bb269b82545e2978904d3 SHA512 2bbb1cc078b04125a55b8c02f65c9fbfb6db894c2fbfdaac8f86cc0084f2579723cdc4f6aa63bf4338b767d0fdaffa8dd503e4126c3f5f700d4f3da9fc085ee5 +DIST FastTreeUPGMA-2.1.11.c 95271 BLAKE2B 1de328881f6452b9c7423c9ed381ab2eb31c4f3ee6426481a6b1089c1359627d4cbbfbea868ebeab9538f82e17f45f1bff8ec07c7370e6432bef6bae449798a8 SHA512 4d6a8e2cb28b8ee201091172a3baa59d432420839c6d2244b5fb8230ed9daa626b6bed22cb692393ca3d78b8f2d071fe18fbb4f9bdcdc47ef149c31e3f45546c +DIST MOTreeComparison-2.1.11.tar.gz 13523 BLAKE2B 97638edd945412ff00e3dfcfc89ec6ea52ae8c43531d5cb680d97e9c62fcad80e861f58ec987abcd2282166dd7886101edba4875531bd9d6ac23df242e0dbd5b SHA512 24d2247650d7728942bd1d987b548cefd65a16b433a3810876613e9fd1cff223d4349ee720b3d8d10a73af220c2c9f59a24d77ad34ff009325fe9f22aa35c72b diff --git a/sci-biology/fasttree/fasttree-2.1.8.ebuild b/sci-biology/fasttree/fasttree-2.1.11.ebuild index 3f9e4ad5f759..cb2d16791ee3 100644 --- a/sci-biology/fasttree/fasttree-2.1.8.ebuild +++ b/sci-biology/fasttree/fasttree-2.1.11.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2018 Gentoo Authors +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 -inherit cmake-utils +inherit cmake DESCRIPTION="Fast inference of approximately-maximum-likelihood phylogenetic trees" HOMEPAGE="http://www.microbesonline.org/fasttree/" @@ -29,11 +29,7 @@ src_unpack() { cd "${S}" || die unpack ${A} cp "${DISTDIR}"/{FastTreeUPGMA-${PV}.c,FastTree-${PV}.c} . || die -} - -src_prepare() { cp "${FILESDIR}"/CMakeLists.txt . || die - cmake-utils_src_prepare } src_configure() { @@ -43,5 +39,5 @@ src_configure() { -DUSE_OPENMP=$(usex openmp) -DUSE_DOUBLE=$(usex double-precision) ) - cmake-utils_src_configure + cmake_src_configure } diff --git a/sci-biology/fasttree/files/CMakeLists.txt b/sci-biology/fasttree/files/CMakeLists.txt index e7c53afdaf36..c52b90cc7be2 100644 --- a/sci-biology/fasttree/files/CMakeLists.txt +++ b/sci-biology/fasttree/files/CMakeLists.txt @@ -1,23 +1,24 @@ -cmake_minimum_required (VERSION 2.6) +cmake_minimum_required (VERSION 2.8.12) project(fasttree C) +include(GNUInstallDirs) + option(USE_OPENMP "Use OpenMP to parallelize many of the steps in computing a tree" ON) -option(USE_DOUBLE "Use double precission" OFF) +option(USE_DOUBLE "Use double precision" OFF) option(HAS_SSE3 "Use SSE2/SSE3 instructions to speed up some inner loops" ON) if(USE_OPENMP) - SET( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DOPENMP -fopenmp" ) - SET( CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -DOPENMP -fopenmp" ) -endif(USE_OPENMP) + set( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DOPENMP -fopenmp" ) + set( CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -DOPENMP -fopenmp" ) +endif() if(USE_DOUBLE) - SET( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DUSE_DOUBLE" ) -endif(USE_DOUBLE) + set( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DUSE_DOUBLE" ) +endif() if(NOT HAS_SSE3) - SET( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DNO_SSE" ) -endif(NOT HAS_SSE3) - + set( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DNO_SSE" ) +endif() add_executable(FastTree FastTree-${VERSION}.c) add_executable(FastTreeUPGMA FastTreeUPGMA-${VERSION}.c) @@ -25,6 +26,6 @@ add_executable(FastTreeUPGMA FastTreeUPGMA-${VERSION}.c) target_link_libraries(FastTree m) target_link_libraries(FastTreeUPGMA m) -install (TARGETS FastTree FastTreeUPGMA DESTINATION bin) +install (TARGETS FastTree FastTreeUPGMA DESTINATION ${CMAKE_INSTALL_BINDIR}) -install(FILES MOTree.pm CompareTree.pl CompareToBootstrap.pl DESTINATION share/fasttree) +install(FILES MOTree.pm CompareTree.pl CompareToBootstrap.pl DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/fasttree) diff --git a/sci-biology/fasttree/files/fasttree-2.1.8-format-security.patch b/sci-biology/fasttree/files/fasttree-2.1.11-format-security.patch index 15f5c174ec40..45023e4215f6 100644 --- a/sci-biology/fasttree/files/fasttree-2.1.8-format-security.patch +++ b/sci-biology/fasttree/files/fasttree-2.1.11-format-security.patch @@ -1,10 +1,10 @@ - FastTreeUPGMA-2.1.8.c | 4 ++-- + FastTreeUPGMA-2.1.11.c | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) -diff --git a/FastTreeUPGMA-2.1.8.c b/FastTreeUPGMA-2.1.8.c +diff --git a/FastTreeUPGMA-2.1.11.c b/FastTreeUPGMA-2.1.11.c index af76cb1..4065f42 100644 ---- a/FastTreeUPGMA-2.1.8.c -+++ b/FastTreeUPGMA-2.1.8.c +--- a/FastTreeUPGMA-2.1.11.c ++++ b/FastTreeUPGMA-2.1.11.c @@ -535,7 +535,7 @@ int main(int argc, char **argv) { break; } diff --git a/sci-biology/fasttree/metadata.xml b/sci-biology/fasttree/metadata.xml index 674816fe4822..23e67193e363 100644 --- a/sci-biology/fasttree/metadata.xml +++ b/sci-biology/fasttree/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/fastx_toolkit/fastx_toolkit-0.0.14.ebuild b/sci-biology/fastx_toolkit/fastx_toolkit-0.0.14-r1.ebuild index d9012a54e166..24c67f24c536 100644 --- a/sci-biology/fastx_toolkit/fastx_toolkit-0.0.14.ebuild +++ b/sci-biology/fastx_toolkit/fastx_toolkit-0.0.14-r1.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2018 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit autotools @@ -12,16 +12,14 @@ SRC_URI="https://github.com/agordon/fastx_toolkit/releases/download/${PV}/${P}.t LICENSE="AGPL-3" SLOT="0" KEYWORDS="~amd64 ~x86" -IUSE="" -DEPEND=" - sci-biology/libgtextutils - virtual/pkgconfig" +DEPEND="sci-biology/libgtextutils:=" RDEPEND=" + ${DEPEND} dev-perl/PerlIO-gzip dev-perl/GDGraph - sci-biology/libgtextutils:= sci-visualization/gnuplot" +BDEPEND="virtual/pkgconfig" PATCHES=( "${FILESDIR}"/${P}-fix-build-system.patch diff --git a/sci-biology/fastx_toolkit/metadata.xml b/sci-biology/fastx_toolkit/metadata.xml index 880cea0165ff..85393fae8f0d 100644 --- a/sci-biology/fastx_toolkit/metadata.xml +++ b/sci-biology/fastx_toolkit/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci@gentoo.org</email> diff --git a/sci-biology/finchtv/finchtv-1.3.1-r2.ebuild b/sci-biology/finchtv/finchtv-1.3.1-r2.ebuild deleted file mode 100644 index a08312d9033e..000000000000 --- a/sci-biology/finchtv/finchtv-1.3.1-r2.ebuild +++ /dev/null @@ -1,29 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -MY_PV="${PV//./_}" -MY_P=${PN}_${MY_PV} - -DESCRIPTION="Graphical viewer for chromatogram files" -HOMEPAGE="http://www.geospiza.com/finchtv/" -SRC_URI="http://www.geospiza.com/finchtv/download/programs/linux/${MY_P}.tar.gz" - -LICENSE="finchtv" -SLOT="0" -KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" -IUSE="" - -S="${WORKDIR}/${MY_P}" - -QA_PREBUILT="opt/bin/*" - -src_install() { - exeinto /opt/bin - doexe finchtv - dodoc ReleaseNotes.txt - dohtml -r Help/* - insinto /usr/share/doc/${PN} - doins -r SampleData -} diff --git a/sci-biology/finchtv/finchtv-1.3.1-r3.ebuild b/sci-biology/finchtv/finchtv-1.3.1-r3.ebuild index 09ab304a7a3d..d3634ac607b1 100644 --- a/sci-biology/finchtv/finchtv-1.3.1-r3.ebuild +++ b/sci-biology/finchtv/finchtv-1.3.1-r3.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 -inherit eutils +inherit desktop MY_PV="${PV//./_}" MY_P=${PN}_${MY_PV} @@ -14,8 +14,7 @@ SRC_URI="http://www.geospiza.com/finchtv/download/programs/linux/${MY_P}.tar.gz" LICENSE="finchtv" SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="" +KEYWORDS="amd64 ~x86 ~amd64-linux ~x86-linux" S="${WORKDIR}/${MY_P}" @@ -26,11 +25,13 @@ src_install() { doexe finchtv dodoc ReleaseNotes.txt - docinto html - dodoc -r Help/* - insinto /usr/share/doc/${PN} - doins -r SampleData + docinto examples + dodoc -r SampleData/. + docompress -x /usr/share/doc/${PF}/examples + + docinto html + dodoc -r Help/. newicon Help/media/FinchTV_Mac_App.png ${PN}.png } diff --git a/sci-biology/finchtv/metadata.xml b/sci-biology/finchtv/metadata.xml index a46ebf47e871..ccdff086e20b 100644 --- a/sci-biology/finchtv/metadata.xml +++ b/sci-biology/finchtv/metadata.xml @@ -1,11 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> - <longdescription lang="en"> -A cross-platform graphical viewer for chromatogram files. -</longdescription> </pkgmetadata> diff --git a/sci-biology/foldingathome/Manifest b/sci-biology/foldingathome/Manifest index e611180008f8..cfd020a01a88 100644 --- a/sci-biology/foldingathome/Manifest +++ b/sci-biology/foldingathome/Manifest @@ -1 +1,2 @@ -DIST fahclient_7.5.1-64bit-release.tar.bz2 3438239 BLAKE2B 69fb60cdd5356fe4f5ad1f106b67d078baf0394c5d3c474dff2f1ac840bcb31bfd9ca9a9c6112b9ee9497dcdc223732627a21c50b455e46c096a52587d5d229b SHA512 5f6f2f882d57fe53ad0a55b48f09fc3803af6aebbbf0e92be39477d4c4da92237d6edabec61dd8183678bdcfe3923ff9b0938647a77edc2c69ce8958defcfdf1 +DIST fahclient_7.6.13-64bit-release.tar.bz2 3951134 BLAKE2B 2748b7c1987d166bdda08caf5ff2f331523ff519e24768cd7e111c6d3a93f54c10c88d8adbf733230b6c51547360135dbcb272e5d43fd06d01918481601382a1 SHA512 f39f2990d78d075e1061ceaff9453b703a000770a3422965b7b8a91d1814f8804837628d8a34be5afd914228ef787f699f2488523baad295a8d9c1e3bb4f35cf +DIST fahclient_7.6.21-64bit-release.tar.bz2 4081015 BLAKE2B b47f99bb2c568ee78dfb8998f6faa6c19aa78492a7882d128917596fa51ca7fb9f02dc0a822b6859ee4b333812f961cbcba504b9b188a3a16e7c5c9489cbfbdb SHA512 b52d97c0169eea8686ac3e52a713bb8513ae2b33a853fbf88a0311569aee22681e9ac87bcc01acdaf31d5af5c3641bd5611d34fcbdbb6c1f0ebbb3fc1efeabdb diff --git a/sci-biology/foldingathome/foldingathome-7.5.1.ebuild b/sci-biology/foldingathome/foldingathome-7.6.13-r1.ebuild index 08e9c15149d7..c45300719bff 100644 --- a/sci-biology/foldingathome/foldingathome-7.5.1.ebuild +++ b/sci-biology/foldingathome/foldingathome-7.6.13-r1.ebuild @@ -1,33 +1,36 @@ -# Copyright 1999-2018 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 -inherit versionator user systemd +inherit systemd DESCRIPTION="Folding@Home is a distributed computing project for protein folding" HOMEPAGE="https://foldingathome.org/" -SRC_URI="https://download.foldingathome.org/releases/public/release/fahclient/centos-6.7-64bit/v$(get_version_component_range 1-2)/fahclient_${PV}-64bit-release.tar.bz2" - -RESTRICT="mirror bindist strip" +SRC_URI="https://download.foldingathome.org/releases/public/release/fahclient/centos-6.7-64bit/v$(ver_cut 1-2)/fahclient_${PV}-64bit-release.tar.bz2" +S="${WORKDIR}/fahclient_${PV}-64bit-release" LICENSE="FAH-EULA-2014 FAH-special-permission" SLOT="0" KEYWORDS="~amd64" -IUSE="" +RESTRICT="mirror bindist strip" + # Expressly listing all deps, as this is a binpkg and it is doubtful whether # i.e. uclibc or clang can provide what is necessary at runtime DEPEND="dev-util/patchelf" -RDEPEND="app-arch/bzip2 +RDEPEND=" + acct-group/foldingathome + acct-group/video + acct-user/foldingathome + app-arch/bzip2 || ( dev-libs/openssl-compat:1.0.0 =dev-libs/openssl-1.0*:* ) sys-devel/gcc sys-libs/glibc - sys-libs/zlib" - -S="${WORKDIR}/fahclient_${PV}-64bit-release" + sys-libs/zlib +" QA_PREBUILT="opt/foldingathome/*" @@ -42,8 +45,6 @@ pkg_setup() { elog "" elog "(ref: http://foldingforum.org/viewtopic.php?f=16&t=22524&p=241992#p241992 )" elog "" - - enewuser foldingathome -1 -1 "${EPREFIX}"/opt/foldingathome } src_install() { @@ -62,7 +63,7 @@ src_install() { newconfd "${FILESDIR}"/7.3/folding-conf.d foldingathome cat <<EOF >"${T}"/fah-init #!/sbin/openrc-run -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 start_stop_daemon_args="--chdir \"${EPREFIX}/opt/foldingathome\"" @@ -82,12 +83,16 @@ Documentation=https://foldingathome.org [Service] Type=simple User=foldingathome +Group=foldingathome +Nice=19 WorkingDirectory=${EPREFIX}/opt/foldingathome -PIDFile=/run/fahclient.pid -ExecStart=${EPREFIX}/opt/foldingathome/FAHClient -v start -ExecReload=${EPREFIX}/opt/foldingathome/FAHClient -v restart -ExecStop=${EPREFIX}/opt/foldingathome/FAHClient -v stop -KillMode=process +ExecStart=${EPREFIX}/opt/foldingathome/FAHClient --fork=false --pid=false --respawn=false --service=false +NoNewPrivileges=yes +PrivateTmp=yes +ProtectControlGroups=yes +ProtectSystem=full +RestrictRealtime=true +ProtectControlGroups=yes [Install] WantedBy=multi-user.target diff --git a/sci-biology/foldingathome/foldingathome-7.6.21.ebuild b/sci-biology/foldingathome/foldingathome-7.6.21.ebuild new file mode 100644 index 000000000000..04b1ff468a1e --- /dev/null +++ b/sci-biology/foldingathome/foldingathome-7.6.21.ebuild @@ -0,0 +1,138 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit systemd + +DESCRIPTION="Folding@Home is a distributed computing project for protein folding" +HOMEPAGE="https://foldingathome.org/" +SRC_URI="https://download.foldingathome.org/releases/public/release/fahclient/centos-6.7-64bit/v$(ver_cut 1-2)/fahclient_${PV}-64bit-release.tar.bz2" +S="${WORKDIR}/fahclient_${PV}-64bit-release" + +LICENSE="FAH-EULA-2014 FAH-special-permission" +SLOT="0" +KEYWORDS="~amd64" +RESTRICT="mirror bindist strip" + +# Expressly listing all deps, as this is a binpkg and it is doubtful whether +# i.e. uclibc or clang can provide what is necessary at runtime +DEPEND="dev-util/patchelf" +RDEPEND=" + acct-group/foldingathome + acct-group/video + acct-user/foldingathome + app-arch/bzip2 + || ( + dev-libs/openssl-compat:1.0.0 + =dev-libs/openssl-1.0*:* + ) + sys-devel/gcc + sys-libs/glibc + sys-libs/zlib +" + +QA_PREBUILT="opt/foldingathome/*" + +pkg_setup() { + elog "" + elog "Special permission is hereby granted to the Gentoo project to provide an" + elog "automated installer package which downloads and installs the Folding@home client" + elog "software. Permission is also granted for future Gentoo installer packages on the" + elog "condition that they continue to adhere to all of the terms of the accompanying" + elog "Folding@home license agreements and display this notice." + elog "-- Vijay S. Pande, Stanford University, 07 May 2013" + elog "" + elog "(ref: http://foldingforum.org/viewtopic.php?f=16&t=22524&p=241992#p241992 )" + elog "" +} + +src_install() { + patchelf --set-rpath "${EPREFIX}/opt/foldingathome" FAHClient || die + patchelf --set-rpath "${EPREFIX}/opt/foldingathome" FAHCoreWrapper || die + + dosym "../../usr/$(get_libdir)/libssl.so.1.0.0" /opt/foldingathome/libssl.so.10 + dosym "../../usr/$(get_libdir)/libcrypto.so.1.0.0" /opt/foldingathome/libcrypto.so.10 + + exeinto /opt/foldingathome + doexe {FAHClient,FAHCoreWrapper} + + insinto /opt/foldingathome + doins sample-config.xml + + newconfd "${FILESDIR}"/7.3/folding-conf.d foldingathome + cat <<EOF >"${T}"/fah-init || die +#!/sbin/openrc-run +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +start_stop_daemon_args="--chdir \"${EPREFIX}/opt/foldingathome\"" +command="${EPREFIX}/opt/foldingathome/FAHClient" +command_args="\${FOLD_OPTS}" +command_user=foldingathome +command_background=1 +pidfile="\${PIDFILE}" +EOF + newinitd "${T}"/fah-init foldingathome + + cat <<EOF >"${T}"/fah-init.service || die +[Unit] +Description=Folding@Home V7 Client +Documentation=https://foldingathome.org + +[Service] +Type=simple +User=foldingathome +Group=foldingathome +Nice=19 +WorkingDirectory=${EPREFIX}/opt/foldingathome +ExecStart=${EPREFIX}/opt/foldingathome/FAHClient --fork=false --pid=false --respawn=false --service=false +NoNewPrivileges=yes +PrivateTmp=yes +ProtectControlGroups=yes +ProtectSystem=full +RestrictRealtime=true +ProtectControlGroups=yes + +[Install] +WantedBy=multi-user.target +EOF + systemd_newunit "${T}"/fah-init.service foldingathome.service + + fowners -R foldingathome:foldingathome /opt/foldingathome +} + +pkg_postinst() { + elog "To run Folding@home in the background at boot:" + elog "(openrc)\trc-update add foldingathome default" + elog "(systemd)\tsystemctl enable foldingathome" + elog "" + if [ ! -e "${EPREFIX}"/opt/foldingathome/config.xml ]; then + elog "No config.xml file found -- please run" + elog "emerge --config ${P} to configure your client, or specify" + elog "all necessary runtime options in FOLD_OPTS within" + elog "${EPREFIX}/etc/conf.d/foldingathome" + elog "" + fi + if [[ -n ${REPLACING_VERSIONS} ]]; then + elog "NOTE, the 'initfolding' helper script has been dropped, please" + elog "use emerge --config ${P} or run FAHClient --configure directly" + elog "and adjust file permissions and ownership yourself" + elog "" + fi + elog "Please see ${EPREFIX}/opt/foldingathome/FAHClient --help for more details." + einfo "" + einfo "The original package maintainer encourages you to acquire a username and join team 36480." + einfo "http://folding.stanford.edu/English/Download#ntoc2" + einfo "" +} + +pkg_postrm() { + elog "Folding@home data files were not removed." + elog "Remove them manually from ${EPREFIX}/opt/foldingathome" +} + +pkg_config() { + cd "${EPREFIX}"/opt/foldingathome || die + su foldingathome -s /bin/sh -c "./FAHClient --configure" || die +} diff --git a/sci-biology/foldingathome/metadata.xml b/sci-biology/foldingathome/metadata.xml index 2a9179e910a9..b5b66eeee084 100644 --- a/sci-biology/foldingathome/metadata.xml +++ b/sci-biology/foldingathome/metadata.xml @@ -1,10 +1,6 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<maintainer type="person"> - <email>axs@gentoo.org</email> - <name>Ian Stakenvicius</name> -</maintainer> <maintainer type="project"> <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> diff --git a/sci-biology/gatk/Manifest b/sci-biology/gatk/Manifest deleted file mode 100644 index 58798a939a0f..000000000000 --- a/sci-biology/gatk/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST gatk-2.4.tar.gz 9106774 BLAKE2B a9ac1602091a2f0902c2841942f8dd739562ef6ebbd35894fa445e6a28d748f3c645936914acbdafc8fa59330149ee5ef0738657d8e78d5cf4af5bd26e37ab6b SHA512 9050fc2024d0b3c9a6b5617787831c0496276bcd7318a872f6c1128c31fc31c6f59429a1b189e5c2cc740909b42d846b5e041f8626b03af3a80442294db34ace diff --git a/sci-biology/gatk/gatk-2.4.ebuild b/sci-biology/gatk/gatk-2.4.ebuild deleted file mode 100644 index 1a885b922b87..000000000000 --- a/sci-biology/gatk/gatk-2.4.ebuild +++ /dev/null @@ -1,38 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -EANT_BUILD_TARGET="dist" -EANT_NEEDS_TOOLS="true" -JAVA_ANT_REWRITE_CLASSPATH="true" - -inherit java-pkg-2 java-ant-2 vcs-snapshot - -DESCRIPTION="The Genome Analysis Toolkit" -HOMEPAGE="http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit" -SRC_URI="https://github.com/broadgsa/gatk/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -IUSE="" -KEYWORDS="~amd64" - -COMMON_DEPS="" -DEPEND=" - >=virtual/jdk-1.6 - ${COMMON_DEPS}" -RDEPEND=" - >=virtual/jre-1.6 - ${COMMON_DEPS}" - -src_prepare() { - sed -i '/property name="ivy.home"/ s|${user.home}|'${WORKDIR}'|' build.xml || die - java-pkg-2_src_prepare -} - -src_install() { - java-pkg_dojar dist/*.jar - java-pkg_dolauncher GenomeAnalysisTK --jar GenomeAnalysisTK.jar - java-pkg_dolauncher AnalyzeCovariates --jar AnalyzeCovariates.jar -} diff --git a/sci-biology/gatk/metadata.xml b/sci-biology/gatk/metadata.xml deleted file mode 100644 index 8c1bb65774cc..000000000000 --- a/sci-biology/gatk/metadata.xml +++ /dev/null @@ -1,11 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="github">broadgsa/gatk</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/gibbs/Manifest b/sci-biology/gibbs/Manifest deleted file mode 100644 index 24b52453c962..000000000000 --- a/sci-biology/gibbs/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST gibbs-3.1.tar.gz 563300 BLAKE2B 74b97407ccdac49d19dd2fa5fe3a5384b52a3ae871f197c1212e818fb7ce2307f2d04a91cf8a1d14c82d57b6f7266bbae849091bec9e580b8d473b595a836212 SHA512 b1ffc0d0c7debaced3c3d850eb7d2c42e13358d1e7c6ff5e6be0273446edc50bd655c52c5ae904a9054d47d7a48abd54a7684534ba7681375b657ad77fb8cb52 diff --git a/sci-biology/gibbs/files/gibbs-3.1-fix-CFLAGS.patch b/sci-biology/gibbs/files/gibbs-3.1-fix-CFLAGS.patch deleted file mode 100644 index 6eaad637cfc8..000000000000 --- a/sci-biology/gibbs/files/gibbs-3.1-fix-CFLAGS.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- a/configure.in -+++ b/configure.in -@@ -51,7 +51,7 @@ - fi
- ])
-
--CFLAGS="$OPTFLAGS $MPIFLAGS -Wall -Werror $MACFLAG"
-+CFLAGS="$CFLAGS $OPTFLAGS $MPIFLAGS -Wall $MACFLAG"
-
- AC_PROG_CC([$COMP_LIST])
-
diff --git a/sci-biology/gibbs/gibbs-3.1.ebuild b/sci-biology/gibbs/gibbs-3.1.ebuild deleted file mode 100644 index a06d0880ee4d..000000000000 --- a/sci-biology/gibbs/gibbs-3.1.ebuild +++ /dev/null @@ -1,47 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit autotools - -DESCRIPTION="Identify motifs, conserved regions, in DNA or protein sequences" -HOMEPAGE="http://bayesweb.wadsworth.org/gibbs/gibbs.html" -SRC_URI="mirror://gentoo/gibbs-${PV}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="amd64 x86" -IUSE="mpi" - -DEPEND=" - mpi? ( - virtual/mpi - sys-cluster/mpe2 - )" -RDEPEND="${DEPEND}" - -PATCHES=( "${FILESDIR}"/${PN}-3.1-fix-CFLAGS.patch ) - -src_prepare() { - default - mv configure.{in,ac} || die - eautoreconf -} - -src_configure() { - use mpi && export CC=mpicc - econf $(use_enable mpi) -} - -src_install() { - default - - exeinto /usr/$(get_libdir)/${PN} - doexe *.pl -} - -pkg_postinst() { - einfo "Supplementary Perl scripts for Gibbs have been installed into ${EROOT}/usr/$(get_libdir)/${PN}." - einfo "These scripts require installation of sci-biology/bioperl." -} diff --git a/sci-biology/gibbs/metadata.xml b/sci-biology/gibbs/metadata.xml deleted file mode 100644 index fc9e1d2b4594..000000000000 --- a/sci-biology/gibbs/metadata.xml +++ /dev/null @@ -1,13 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <longdescription> - The Gibbs motif sampler stochastically examines candidate alignments - in an effort to find the best alignment as measured by the maximum - a posteriori (MAP) log-likelihood ratio. - </longdescription> -</pkgmetadata> diff --git a/sci-biology/glimmer/Manifest b/sci-biology/glimmer/Manifest index fc38be4881f5..aa2a22056a4f 100644 --- a/sci-biology/glimmer/Manifest +++ b/sci-biology/glimmer/Manifest @@ -1,2 +1 @@ -DIST glimmer302.tar.gz 5637075 BLAKE2B 07fc22a9192644c42291bd305a24bd7c40881cf5e8b668885ffdd5695100a2370b9cdbb275956e36df9007b1cb7bbfba84ab84863f26b70e68638fdf35e608d0 SHA512 c28e5902bffab00566560fa0bcf61909921932935f8298f098361aeb58eb67a40403c23709cf5075fb47dc87bcf54e25572840f110bb15cd21325a072050407c DIST glimmer302b.tar.gz 5637975 BLAKE2B 76c0b19fe08e9ece3e930fe3e53444a2b620e565ac3c83db484294627403e34c3ab77165e4b82176282df340fe47672bf28e5694edbcea9e17a57b61a502ae11 SHA512 00d44a02a8099ceac4b4d2a1cd5d69cc2b787942bb87f612cd63edacf7e502bc9a65cdf9b9270ad789981a84c940cc01e187882d21d2c9de4dcc12b492b041a6 diff --git a/sci-biology/glimmer/files/glimmer-3.02-glibc210.patch b/sci-biology/glimmer/files/glimmer-3.02-glibc210.patch deleted file mode 100644 index f6051ec82054..000000000000 --- a/sci-biology/glimmer/files/glimmer-3.02-glibc210.patch +++ /dev/null @@ -1,24 +0,0 @@ -diff -durr glimmer3.02-orig/src/Common/gene.cc glimmer3.02/src/Common/gene.cc ---- glimmer3.02-orig/src/Common/gene.cc 2009-12-28 13:34:21.577437056 +0000 -+++ glimmer3.02/src/Common/gene.cc 2009-12-28 13:36:06.914974685 +0000 -@@ -443,7 +443,7 @@ - // Return a subscript corresponding to character ch . - - { -- char * p; -+ const char * p; - - p = strchr (CONVERSION_STRING, tolower (ch)); - if (p == NULL) -diff -durr glimmer3.02-orig/src/ICM/icm.cc glimmer3.02/src/ICM/icm.cc ---- glimmer3.02-orig/src/ICM/icm.cc 2009-12-28 13:34:21.577437056 +0000 -+++ glimmer3.02/src/ICM/icm.cc 2009-12-28 13:36:44.649451803 +0000 -@@ -1981,7 +1981,7 @@ - // model) for character ch . - - { -- char * p; -+ const char * p; - - p = strchr (ALPHA_STRING, tolower (Filter (ch))); - if (p == NULL) diff --git a/sci-biology/glimmer/files/glimmer-3.02-jobserver-fix.patch b/sci-biology/glimmer/files/glimmer-3.02-jobserver-fix.patch deleted file mode 100644 index 91498b116d12..000000000000 --- a/sci-biology/glimmer/files/glimmer-3.02-jobserver-fix.patch +++ /dev/null @@ -1,22 +0,0 @@ -diff -ru glimmer3.02-orig/src/Makefile glimmer3.02/src/Makefile ---- glimmer3.02-orig/src/Makefile 2006-06-12 21:40:14.000000000 +0200 -+++ glimmer3.02/src/Makefile 2010-03-18 14:30:15.000000000 +0100 -@@ -2,12 +2,12 @@ - - - all: -- @ TGT=objs -- @ $(dosubdirs) -- @ TGT=libs -- @ $(dosubdirs) -- @ TGT=progs -- @ $(dosubdirs) -+ @+ TGT=objs -+ @+ $(dosubdirs) -+ @+ TGT=libs -+ @+ $(dosubdirs) -+ @+ TGT=progs -+ @+ $(dosubdirs) - - - install: all diff --git a/sci-biology/glimmer/files/glimmer-3.02-ldflags.patch b/sci-biology/glimmer/files/glimmer-3.02-ldflags.patch deleted file mode 100644 index 0a04fbef1dcc..000000000000 --- a/sci-biology/glimmer/files/glimmer-3.02-ldflags.patch +++ /dev/null @@ -1,88 +0,0 @@ -diff --git a/src/c_make.gen b/src/c_make.gen -index 414dead..84c3030 100644 ---- a/src/c_make.gen -+++ b/src/c_make.gen -@@ -200,45 +200,12 @@ LOCAL_SYS_INC=$(SEP_PATH)/../SYS/inc - #### Do not redefine if (a) passed in on command line, or (b) - #### defined in an environment variable. - --ifneq "$(origin CC)" "environment" --CC = cc --endif -- --ifneq "$(origin CPPFLAGS)" "environment" --CPPFLAGS= --endif -- --ifneq "$(origin CFLAGS)" "environment" --CFLAGS = --endif -- --ifneq "$(origin CDEFS)" "environment" --CDEFS = --endif -- --ifneq "$(origin CXX)" "environment" --CXX = g++ --endif -- --ifneq "$(origin CXXFLAGS)" "environment" --CXXFLAGS= --endif -- --ifneq "$(origin CXXDEFS)" "environment" --CXXDEFS= -D__cplusplus --endif -- --ifneq "$(origin AR)" "environment" --AR = ar --endif -- --ifneq "$(origin ARFLAGS)" "environment" --ARFLAGS = rvs --endif -- --ifneq "$(origin LDFLAGS)" "environment" --LDFLAGS = --endif -+CC ?= cc -+CXX ?= g++ -+CXXFLAGS ?= -+CXXDEFS = -D__cplusplus -+AR ?= ar -+ARFLAGS ?= rvs - - #### Delete default suffix rules - .SUFFIXES: -@@ -359,13 +326,13 @@ $(PROGS): - cd $(LOCAL_OBJ); \ - if $(CC) -o $(LOCAL_BIN)/$(notdir $@) $(LDFLAGS) \ - $(LD_DIRS) $(filter-out lib%.a, $+) \ -- $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) ; then \ -+ $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LIBS) ; then \ - true; else rm -f $(LOCAL_BIN)/$(notdir $@); fi; \ - else \ - cd $(LOCAL_OBJ); \ - if $(CXX) -o $(LOCAL_BIN)/$(notdir $@) $(LDFLAGS) \ - $(LD_DIRS) $(filter-out lib%.a, $+) \ -- $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) ; then \ -+ $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LIBS) ; then \ - true; else rm -f $(LOCAL_BIN)/$(notdir $@); fi; \ - fi ; - -diff --git a/src/c_make.glm b/src/c_make.glm -index 0decc17..b82131c 100644 ---- a/src/c_make.glm -+++ b/src/c_make.glm -@@ -8,10 +8,7 @@ include $(LOCAL_WORK)/src/c_make.gen - - SUBDIRS = Common ICM Glimmer Util - --CFLAGS = -g -Wall --CXXFLAGS = -g -Wall -- --LDFLAGS = -g -lm -+LIBS = -lm - - - #AS_BUILD_DIR =$(LOCAL_WORK) diff --git a/sci-biology/glimmer/files/glimmer-3.02b-ldflags.patch b/sci-biology/glimmer/files/glimmer-3.02b-ldflags.patch index 0a04fbef1dcc..dc41ef00de7e 100644 --- a/sci-biology/glimmer/files/glimmer-3.02b-ldflags.patch +++ b/sci-biology/glimmer/files/glimmer-3.02b-ldflags.patch @@ -1,8 +1,6 @@ -diff --git a/src/c_make.gen b/src/c_make.gen -index 414dead..84c3030 100644 --- a/src/c_make.gen +++ b/src/c_make.gen -@@ -200,45 +200,12 @@ LOCAL_SYS_INC=$(SEP_PATH)/../SYS/inc +@@ -200,45 +200,11 @@ #### Do not redefine if (a) passed in on command line, or (b) #### defined in an environment variable. @@ -48,13 +46,12 @@ index 414dead..84c3030 100644 +CC ?= cc +CXX ?= g++ +CXXFLAGS ?= -+CXXDEFS = -D__cplusplus +AR ?= ar +ARFLAGS ?= rvs #### Delete default suffix rules .SUFFIXES: -@@ -359,13 +326,13 @@ $(PROGS): +@@ -359,13 +325,13 @@ cd $(LOCAL_OBJ); \ if $(CC) -o $(LOCAL_BIN)/$(notdir $@) $(LDFLAGS) \ $(LD_DIRS) $(filter-out lib%.a, $+) \ @@ -70,11 +67,9 @@ index 414dead..84c3030 100644 true; else rm -f $(LOCAL_BIN)/$(notdir $@); fi; \ fi ; -diff --git a/src/c_make.glm b/src/c_make.glm -index 0decc17..b82131c 100644 --- a/src/c_make.glm +++ b/src/c_make.glm -@@ -8,10 +8,7 @@ include $(LOCAL_WORK)/src/c_make.gen +@@ -8,18 +8,14 @@ SUBDIRS = Common ICM Glimmer Util @@ -86,3 +81,12 @@ index 0decc17..b82131c 100644 #AS_BUILD_DIR =$(LOCAL_WORK) + INC_IMPORT_DIRS += \ + $(patsubst %, $(LOCAL_WORK)/src/%, $(strip $(SUBDIRS))) \ + $(LOCAL_WORK)/inc +-LIB_IMPORT_DIRS += $(LOCAL_WORK)/lib /usr/lib /usr/shlib /usr/X11R6/lib \ +- $(SYBASE)/lib ++LIB_IMPORT_DIRS += $(LOCAL_WORK)/lib + + OBJ_SEARCH_PATH = $(LOCAL_WORK)/obj + diff --git a/sci-biology/glimmer/glimmer-3.02-r3.ebuild b/sci-biology/glimmer/glimmer-3.02-r3.ebuild deleted file mode 100644 index 9a32e3dbf895..000000000000 --- a/sci-biology/glimmer/glimmer-3.02-r3.ebuild +++ /dev/null @@ -1,60 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI="5" - -inherit eutils toolchain-funcs - -MY_PV=${PV//./} - -DESCRIPTION="An HMM-based microbial gene finding system from TIGR" -HOMEPAGE="https://ccb.jhu.edu/software/glimmer/index.shtml" -SRC_URI="http://www.cbcb.umd.edu/software/${PN}/${PN}${MY_PV}.tar.gz" - -LICENSE="Artistic" -SLOT="0" -IUSE="" -KEYWORDS="amd64 x86" - -DEPEND="" -RDEPEND="app-shells/tcsh" - -S="${WORKDIR}/${PN}${PV}" - -PATCHES=( - "${FILESDIR}"/${P}-glibc210.patch - "${FILESDIR}"/${P}-jobserver-fix.patch - "${FILESDIR}"/${P}-ldflags.patch - "${FILESDIR}"/${PN}-3.02b-rename_extract.patch -) - -src_prepare() { - sed -i -e 's|\(set awkpath =\).*|\1 /usr/share/'${PN}'/scripts|' \ - -e 's|\(set glimmerpath =\).*|\1 /usr/bin|' scripts/* || die "failed to rewrite paths" - # Fix Makefile to die on failure - sed -i 's/$(MAKE) $(TGT)/$(MAKE) $(TGT) || exit 1/' src/c_make.gen || die - # GCC 4.3 include fix - sed -i 's/include <string>/include <string.h>/' src/Common/delcher.hh || die - epatch "${PATCHES[@]}" -} - -src_compile() { - emake \ - -C src \ - CC=$(tc-getCC) \ - CXX=$(tc-getCXX) \ - AR=$(tc-getAR) \ - CXXFLAGS="${CXXFLAGS}" \ - CFLAGS="${CFLAGS}" \ - LDFLAGS="${LDFLAGS}" -} - -src_install() { - rm bin/test || die - dobin bin/* - - insinto /usr/share/${PN} - doins -r scripts - - dodoc glim302notes.pdf -} diff --git a/sci-biology/glimmer/glimmer-3.02b.ebuild b/sci-biology/glimmer/glimmer-3.02b.ebuild index 4318b60ff949..35bea17dd8ab 100644 --- a/sci-biology/glimmer/glimmer-3.02b.ebuild +++ b/sci-biology/glimmer/glimmer-3.02b.ebuild @@ -1,28 +1,25 @@ -# Copyright 1999-2018 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI="5" +EAPI=7 -inherit eutils toolchain-funcs +inherit toolchain-funcs MY_PV=${PV//./} DESCRIPTION="An HMM-based microbial gene finding system from TIGR" HOMEPAGE="https://ccb.jhu.edu/software/glimmer/index.shtml" SRC_URI="https://ccb.jhu.edu/software/${PN}/${PN}${MY_PV}.tar.gz" +S="${WORKDIR}/${PN}3.02" LICENSE="Artistic" SLOT="0" -IUSE="" KEYWORDS="~amd64 ~x86" -DEPEND="" -RDEPEND="app-shells/tcsh +RDEPEND=" + app-shells/tcsh sci-biology/elph" -#S="${WORKDIR}/${PN}${PV}" -S="${WORKDIR}/${PN}3.02" - PATCHES=( "${FILESDIR}"/${P}-jobserver-fix.patch "${FILESDIR}"/${P}-ldflags.patch @@ -37,20 +34,21 @@ src_prepare() { # GCC 4.3 include fix sed -i 's/include <string>/include <string.h>/' src/Common/delcher.hh || die # - sed -i "s+/fs/szgenefinding/Glimmer3/bin+%${D}/bin/glimmer3+" scripts/g3-* || die - sed -i "s+/fs/szgenefinding/Glimmer3/scripts+%${D}/share/glimmer/scripts+" scripts/g3-* || die - sed -i "s+/nfshomes/adelcher/bin/elph+%${D}/bin/elph+" scripts/g3-* || die + sed -i "s:/fs/szgenefinding/Glimmer3/bin:%${EPREFIX}/usr/bin/glimmer3:" scripts/g3-* || die + sed -i "s:/fs/szgenefinding/Glimmer3/scripts:%${EPREFIX}/usr/share/glimmer/scripts:" scripts/g3-* || die + sed -i "s:/nfshomes/adelcher/bin/elph:%${EPREFIX}/usr/bin/elph:" scripts/g3-* || die sed -i "s/@ if/if/" src/c_make.gen || die + # avoid file collision on /usr/bin/extract #247394 - epatch "${PATCHES[@]}" + default } src_compile() { emake \ -C src \ - CC=$(tc-getCC) \ - CXX=$(tc-getCXX) \ - AR=$(tc-getAR) \ + CC="$(tc-getCC)" \ + CXX="$(tc-getCXX)" \ + AR="$(tc-getAR)" \ CXXFLAGS="${CXXFLAGS}" \ CFLAGS="${CFLAGS}" \ LDFLAGS="${LDFLAGS}" @@ -60,7 +58,7 @@ src_install() { rm bin/test || die dobin bin/* - insinto /usr/share/${PN} + insinto /usr/share/glimmer doins -r scripts dodoc glim302notes.pdf diff --git a/sci-biology/glimmer/metadata.xml b/sci-biology/glimmer/metadata.xml index 959160fe46b1..ccdff086e20b 100644 --- a/sci-biology/glimmer/metadata.xml +++ b/sci-biology/glimmer/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/glimmerhmm/Manifest b/sci-biology/glimmerhmm/Manifest index 4b994830e4b9..20a57a2ca4b6 100644 --- a/sci-biology/glimmerhmm/Manifest +++ b/sci-biology/glimmerhmm/Manifest @@ -1 +1,2 @@ DIST GlimmerHMM-3.0.1.tar.gz 45475952 BLAKE2B 355f4e9f26c31167e0935de8012fa99a243838d0dd47e0e46ae4cb1df4eaf188a13fb365025bc4be82805c89f36f534a9907030515f96b9422340e9e966f4ea6 SHA512 15307d1982527bd83433882552cd3e12c76a65a2a119b6911a748dc801f80b1fc5732cb769a52e5c6281bdd48cf619a02edbd1b96ee40319fc620a3a7cdd82b7 +DIST GlimmerHMM-3.0.4.tar.gz 45692137 BLAKE2B e271ea506e77d0038e343030be1875de0c92265ac2808cf35b7ba872a2d2f9416d645cd373f2ba6816f8352b4367a3a7c878c4dea772fcadf8954aabd91fca64 SHA512 e10d89550c938faf4b1e2a259213ad88a7443b7597cf753c7041698ac78d468f4ed93e0f7736640cd2fe97abe227d54eb7feca1fe7450d72f83896a94ef7a70b diff --git a/sci-biology/glimmerhmm/files/0001-fix-ridiculous-ODR-violation.patch b/sci-biology/glimmerhmm/files/0001-fix-ridiculous-ODR-violation.patch new file mode 100644 index 000000000000..58fa92819b59 --- /dev/null +++ b/sci-biology/glimmerhmm/files/0001-fix-ridiculous-ODR-violation.patch @@ -0,0 +1,27 @@ +From 282b1a113e002d8b90dedb6a5b6a6dc35e7310d1 Mon Sep 17 00:00:00 2001 +From: Eli Schwartz <eschwartz93@gmail.com> +Date: Tue, 12 Mar 2024 01:45:16 -0400 +Subject: [PATCH] fix ridiculous ODR violation + +The return value of a function defined in another file is whatever that +file defines, not "void because we didn't assign it to anything". +--- + sources/oc1.h | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/sources/oc1.h b/sources/oc1.h +index 7b068c8..e28017d 100644 +--- a/sources/oc1.h ++++ b/sources/oc1.h +@@ -49,7 +49,7 @@ struct tree_node + EDGE edge; /* used only in the display module. */ + }; + +-void error(char *); ++int error(char *); + void free_ivector(int *,int,int); + void free_vector(float *,int,int); + void free_dvector(double*,int,float); +-- +2.43.2 + diff --git a/sci-biology/glimmerhmm/files/3.0.4-gentoo.patch b/sci-biology/glimmerhmm/files/3.0.4-gentoo.patch new file mode 100644 index 000000000000..d3838b1dc9bc --- /dev/null +++ b/sci-biology/glimmerhmm/files/3.0.4-gentoo.patch @@ -0,0 +1,153 @@ +diff --git a/sources/makefile b/sources/makefile +index f287d71..c560f48 100644 +--- a/sources/makefile ++++ b/sources/makefile +@@ -2,25 +2,22 @@ + + + +-CC=g++ +-CFLAGS=-g +- + all: glimmerhmm + + glimmerhmm: glimmerhmm.o graph.o sites.o tree_util_prob.o util.o +- $(CC) $(CFLAGS) -o glimmerhmm glimmerhmm.o graph.o sites.o tree_util_prob.o util.o -lm ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o glimmerhmm glimmerhmm.o graph.o sites.o tree_util_prob.o util.o -lm + + glimmerhmm.o: glimmerhmm.c +- $(CC) $(CFLAGS) -c glimmerhmm.c ++ $(CXX) $(CXXFLAGS) -c glimmerhmm.c + + graph.o: graph.c +- $(CC) $(CFLAGS) -c graph.c ++ $(CXX) $(CXXFLAGS) -c graph.c + + sites.o: sites.c +- $(CC) $(CFLAGS) -c sites.c ++ $(CXX) $(CXXFLAGS) -c sites.c + + tree_util_prob.o: tree_util_prob.c +- $(CC) $(CFLAGS) -c tree_util_prob.c ++ $(CXX) $(CXXFLAGS) -c tree_util_prob.c + + util.o: util.c +- $(CC) $(CFLAGS) -c util.c ++ $(CXX) $(CXXFLAGS) -c util.c +diff --git a/train/makefile b/train/makefile +index 56eaa13..d660cf1 100644 +--- a/train/makefile ++++ b/train/makefile +@@ -2,11 +2,8 @@ + + # C compiler + +-C = gcc +-CC = g++ + #CFLAGS = -O1 ${SEARCHDIRS} + #CFLAGS = -O3 -g -Wall +-CFLAGS = -Wall -g + LIBS = -lm + + MAKEFILE= makefile +@@ -16,67 +13,79 @@ all: build-icm build-icm-noframe build1 build2 falsecomp findsites karlin sco + + + misc.o: misc.c +- ${C} ${CFLAGS} -c misc.c ++ $(CC) $(CFLAGS) -c misc.c + + build-icm.o: build-icm.c +- ${C} ${CFLAGS} -c build-icm.c ++ $(CC) $(CFLAGS) -c build-icm.c + + build-icm: build-icm.o misc.o +- $(C) ${CFLAGS} -o $@ build-icm.o misc.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ build-icm.o misc.o $(LIBS) + + build-icm-noframe.o: build-icm-noframe.c +- ${C} ${CFLAGS} -c build-icm-noframe.c ++ $(CC) $(CFLAGS) -c build-icm-noframe.c + + build-icm-noframe: build-icm-noframe.o misc.o +- $(C) ${CFLAGS} -o $@ build-icm-noframe.o misc.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ build-icm-noframe.o misc.o $(LIBS) + + build1: build1.o +- ${CC} ${CFLAGS} build1.c -o build1 $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) build1.o -o build1 $(LIBS) + + build2: build2.o +- ${CC} ${CFLAGS} build2.c -o build2 $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) build2.o -o build2 $(LIBS) + + falsecomp: falsecomp.o +- ${CC} ${CFLAGS} falsecomp.c -o falsecomp $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) falsecomp.o -o falsecomp $(LIBS) + + findsites: findsites.o +- ${CC} ${CFLAGS} findsites.c -o findsites $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) findsites.o -o findsites $(LIBS) + + karlin: karlin.o +- ${CC} ${CFLAGS} karlin.c -o karlin $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) karlin.o -o karlin $(LIBS) + + score: score.o +- ${CC} ${CFLAGS} score.c -o score $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) score.o -o score $(LIBS) + + score2: score2.o +- ${CC} ${CFLAGS} score2.c -o score2 $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) score2.o -o score2 $(LIBS) + + scoreATG: scoreATG.o +- ${CC} ${CFLAGS} scoreATG.c -o scoreATG $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) scoreATG.o -o scoreATG $(LIBS) + + scoreATG2: scoreATG2.o +- ${CC} ${CFLAGS} scoreATG2.c -o scoreATG2 $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) scoreATG2.o -o scoreATG2 $(LIBS) + + scoreSTOP: scoreSTOP.o +- ${CC} ${CFLAGS} scoreSTOP.c -o scoreSTOP $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) scoreSTOP.o -o scoreSTOP $(LIBS) + + escoreSTOP2: scoreSTOP2.o +- ${CC} ${CFLAGS} scoreSTOP2.c -o scoreSTOP2 $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) scoreSTOP2.o -o scoreSTOP2 $(LIBS) + + rfapp: erfapp.o +- ${CC} ${CFLAGS} erfapp.c -o erfapp $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) erfapp.c -o erfapp $(LIBS) + + sites.o: sites.c +- ${CC} ${CFLAGS} -c sites.c ++ $(CXX) $(CXXFLAGS) -c sites.c ++ ++scoreATG.o: scoreATG.c ++ $(CXX) $(CXXFLAGS) -c scoreATG.c ++ ++scoreSTOP.o: scoreSTOP.c ++ $(CXX) $(CXXFLAGS) -c scoreSTOP.c ++ ++scoreSTOP2.o: scoreSTOP2.c ++ $(CXX) $(CXXFLAGS) -c scoreSTOP2.c ++ ++scoreATG2.o: scoreATG2.c ++ $(CXX) $(CXXFLAGS) -c scoreATG2.c + + utils.o: utils.c +- ${CC} ${CFLAGS} -c utils.c ++ $(CXX) $(CXXFLAGS) -c utils.c + + splicescore.o: splicescore.c +- ${CC} ${CFLAGS} -c splicescore.c ++ $(CXX) $(CXXFLAGS) -c splicescore.c + + splicescore: splicescore.o sites.o utils.o +- ${CC} splicescore.o sites.o utils.o -o splicescore $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) splicescore.o sites.o utils.o -o splicescore $(LIBS) + .PHONY : clean + clean:: + /bin/rm -f core* splicescore *.o score build? build-icm \ diff --git a/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild b/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild index 5424e942a7f7..d118ce0996da 100644 --- a/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild +++ b/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 @@ -13,13 +13,14 @@ SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/glimmerhmm/${MY_P}-${PV}.tar.gz" LICENSE="Artistic" SLOT="0" -KEYWORDS="amd64 x86" +KEYWORDS="amd64 ~x86" S="${WORKDIR}/${MY_P}" PATCHES=( "${FILESDIR}"/${PV}-gentoo.patch "${FILESDIR}"/${PN}-3.0.1-fix-data-path.patch + "${FILESDIR}"/0001-fix-ridiculous-ODR-violation.patch ) src_configure() { diff --git a/sci-biology/glimmerhmm/glimmerhmm-3.0.4.ebuild b/sci-biology/glimmerhmm/glimmerhmm-3.0.4.ebuild new file mode 100644 index 000000000000..829e79d4db85 --- /dev/null +++ b/sci-biology/glimmerhmm/glimmerhmm-3.0.4.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit toolchain-funcs + +MY_P=GlimmerHMM + +DESCRIPTION="A eukaryotic gene finding system from TIGR" +HOMEPAGE="http://www.cbcb.umd.edu/software/GlimmerHMM/" +SRC_URI="https://ccb.jhu.edu/software/glimmerhmm/dl/${MY_P}-${PV}.tar.gz" +S="${WORKDIR}/${MY_P}" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +PATCHES=( + "${FILESDIR}"/${PV}-gentoo.patch + "${FILESDIR}"/${PN}-3.0.1-fix-data-path.patch + "${FILESDIR}"/0001-fix-ridiculous-ODR-violation.patch +) + +src_configure() { + tc-export CC CXX +} + +src_compile() { + emake -C sources + emake -C train +} + +src_install() { + dobin sources/glimmerhmm train/trainGlimmerHMM + + insinto /usr/share/${PN}/lib + doins train/*.pm + + insinto /usr/share/${PN}/models + doins -r trained_dir/. + + exeinto /usr/libexec/${PN}/training_utils + doexe train/{build{1,2,-icm,-icm-noframe},erfapp,falsecomp,findsites,karlin,score,score{2,ATG,ATG2,STOP,STOP2},splicescore} + + dodoc README.first train/readme.train +} diff --git a/sci-biology/glimmerhmm/metadata.xml b/sci-biology/glimmerhmm/metadata.xml index 959160fe46b1..ccdff086e20b 100644 --- a/sci-biology/glimmerhmm/metadata.xml +++ b/sci-biology/glimmerhmm/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/gmap/Manifest b/sci-biology/gmap/Manifest index a43611ecf589..6f045f9bf37f 100644 --- a/sci-biology/gmap/Manifest +++ b/sci-biology/gmap/Manifest @@ -1 +1 @@ -DIST gmap-gsnap-2015-12-31.v5.tar.gz 4169874 BLAKE2B bbbf53b72b5b7f97ba0eb05db7daa3d1f8a9330f32b96c2460a904a9f9f22078093f6fa585a12d4275e0943145ee78ef99348de4f19349dfa4e81d5f65572e1c SHA512 d42623c60c298d9d3009893432f3eef8cb764bf7cf26b42e6a95b27a468fffab20c8307597c4c8e1afdd61f35652246568c3162137ce59fc4850aaab1062bb48 +DIST gmap-gsnap-2020-10-27.tar.gz 4480720 BLAKE2B 9f8e8bfab19c079111d42ec466dd145385d35e3fde0a809e46776ed1b62b599664f12618803ea4475b6961a053423a8794d0b77eb0b308bdfa927b5bcaa7d49c SHA512 22e59adf404f5ef524b3cd472fb3124d03c8c55aa7946b9dc3901f5070339dc765f8f1ecc7e394b69a14bf80923f7a9db8d545e45328a346996b3288115a535b diff --git a/sci-biology/gmap/files/gmap-2020.10.27-fno-common.patch b/sci-biology/gmap/files/gmap-2020.10.27-fno-common.patch new file mode 100644 index 000000000000..cc225a78c26e --- /dev/null +++ b/sci-biology/gmap/files/gmap-2020.10.27-fno-common.patch @@ -0,0 +1,22 @@ +--- a/src/dynprog_end.c ++++ b/src/dynprog_end.c +@@ -109,7 +109,7 @@ + static Trieoffset_T *trieoffsets_max; + static Triecontent_T *triecontents_max; + +-bool homopolymerp; ++static bool homopolymerp; + + void + Dynprog_end_setup (Univcoord_T *splicesites_in, Splicetype_T *splicetypes_in, +--- a/src/dynprog_single.c ++++ b/src/dynprog_single.c +@@ -91,7 +91,7 @@ + + #define T Dynprog_T + +-bool homopolymerp; ++static bool homopolymerp; + + void + Dynprog_single_setup (bool homopolymerp_in) { diff --git a/sci-biology/gmap/gmap-2015.12.31.5.ebuild b/sci-biology/gmap/gmap-2020.10.27.ebuild index 82ae6f3f2748..a90f0f631068 100644 --- a/sci-biology/gmap/gmap-2015.12.31.5.ebuild +++ b/sci-biology/gmap/gmap-2020.10.27.ebuild @@ -1,12 +1,9 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 -inherit versionator - -MY_BASE_PV="$(replace_all_version_separators '-' $(get_version_component_range 1-3))" -MY_PV="${MY_BASE_PV}.v$(get_version_component_range 4)" +MY_PV="$(ver_rs 1- '-')" DESCRIPTION="A Genomic Mapping and Alignment Program for mRNA and EST Sequences" HOMEPAGE="http://research-pub.gene.com/gmap/" @@ -14,7 +11,7 @@ SRC_URI="http://research-pub.gene.com/gmap/src/gmap-gsnap-${MY_PV}.tar.gz" LICENSE="gmap" SLOT="0" -IUSE="" KEYWORDS="~amd64 ~x86" -S="${WORKDIR}/gmap-${MY_BASE_PV}" +S="${WORKDIR}/gmap-${MY_PV}" +PATCHES=( "${FILESDIR}"/${PN}-2020.10.27-fno-common.patch ) diff --git a/sci-biology/gmap/metadata.xml b/sci-biology/gmap/metadata.xml index 959160fe46b1..ccdff086e20b 100644 --- a/sci-biology/gmap/metadata.xml +++ b/sci-biology/gmap/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/hmmer/files/hmmer-2.3.2-fix-missing-include-in-configure.patch b/sci-biology/hmmer/files/hmmer-2.3.2-fix-missing-include-in-configure.patch new file mode 100644 index 000000000000..37683d425edb --- /dev/null +++ b/sci-biology/hmmer/files/hmmer-2.3.2-fix-missing-include-in-configure.patch @@ -0,0 +1,18 @@ +--- a/squid/configure 2024-05-08 09:21:15.751063495 -0000 ++++ b/squid/configure 2024-05-08 09:22:50.491502934 -0000 +@@ -2493,6 +2493,7 @@ + cat confdefs.h >>conftest.$ac_ext + cat >>conftest.$ac_ext <<_ACEOF + /* end confdefs.h. */ ++#include <stdlib.h> + int + main () + { +@@ -3500,6 +3501,7 @@ + cat >>conftest.$ac_ext <<_ACEOF + /* end confdefs.h. */ + #include <ctype.h> ++#include <stdlib.h> + #if ((' ' & 0x0FF) == 0x020) + # define ISLOWER(c) ('a' <= (c) && (c) <= 'z') + # define TOUPPER(c) (ISLOWER(c) ? 'A' + ((c) - 'a') : (c)) diff --git a/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-header-install-path.patch b/sci-biology/hmmer/files/hmmer-3.1_beta2-makefile.patch index b9ff5b92b8f9..1c08d67e7bdd 100644 --- a/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-header-install-path.patch +++ b/sci-biology/hmmer/files/hmmer-3.1_beta2-makefile.patch @@ -1,4 +1,5 @@ -Install headers into 'hmmer3' subdir and not into global includedir. +* Install headers into 'hmmer3' subdir and not into global includedir +* Respect AR --- a/easel/Makefile.in +++ b/easel/Makefile.in @@ -17,6 +18,26 @@ Install headers into 'hmmer3' subdir and not into global includedir. ${QUIET_SUBDIR0}miniapps ${QUIET_SUBDIR1} install # "make uninstall" reverses the steps of "make install" +--- a/libdivsufsort/Makefile.in ++++ b/libdivsufsort/Makefile.in +@@ -16,7 +16,7 @@ + CFLAGS = @CFLAGS@ @PTHREAD_CFLAGS@ @PIC_FLAGS@ + CPPFLAGS = @CPPFLAGS@ + MPILIBS = @MPILIBS@ +-AR = @AR@ rc ++AR = @AR@ + RANLIB = @RANLIB@ + INSTALL = @INSTALL@ + +@@ -43,7 +43,7 @@ + + + libdivsufsort.a: $(OBJS) +- ${QUIET_AR}${AR} libdivsufsort.a $(OBJS) ++ ${QUIET_AR}${AR} rc libdivsufsort.a $(OBJS) + @${RANLIB} libdivsufsort.a + @chmod 644 libdivsufsort.a + --- a/Makefile.in +++ b/Makefile.in @@ -143,6 +143,7 @@ diff --git a/sci-biology/hmmer/hmmer-2.3.2-r4.ebuild b/sci-biology/hmmer/hmmer-2.3.2-r6.ebuild index a58b60f93288..74a8a151b0c4 100644 --- a/sci-biology/hmmer/hmmer-2.3.2-r4.ebuild +++ b/sci-biology/hmmer/hmmer-2.3.2-r6.ebuild @@ -1,35 +1,44 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 + +inherit flag-o-matic toolchain-funcs DESCRIPTION="Sequence analysis using profile hidden Markov models" -LICENSE="GPL-2" HOMEPAGE="http://hmmer.org/" SRC_URI="http://eddylab.org/software/${PN}/${PV}/${P}.tar.gz" +LICENSE="GPL-2" SLOT="2" -IUSE="altivec test threads" -RESTRICT="!test? ( test )" KEYWORDS="~amd64 ~x86" +IUSE="cpu_flags_ppc_altivec test" +RESTRICT="!test? ( test )" -DEPEND="test? ( dev-lang/perl )" -RDEPEND="" +BDEPEND="test? ( dev-lang/perl )" PATCHES=( "${FILESDIR}/${P}-fix-perl-shebangs.patch" "${FILESDIR}/${P}-fix-build-system-destdir.patch" + "${FILESDIR}/${P}-fix-missing-include-in-configure.patch" ) src_configure() { + # required to expose pthread_setconcurrency(), #882279 + append-cppflags -D_XOPEN_SOURCE=500 + # prevent stray environmental variable # from causing issues in the test phase unset TMPDIR econf \ --enable-lfs \ - $(use_enable altivec) \ - $(use_enable threads) + --enable-threads \ + $(use_enable cpu_flags_ppc_altivec altivec) +} + +src_compile() { + emake AR="$(tc-getAR) rcs" } src_install() { @@ -52,14 +61,14 @@ src_install() { local i # first rename man pages... - pushd "${ED%/}"/usr/share/man/man1/ >/dev/null || die + pushd "${ED}"/usr/share/man/man1/ >/dev/null || die for i in hmm*.1; do mv ${i%.1}{,2}.1 || die done popd >/dev/null || die # ... then rename binaries - pushd "${ED%/}"/usr/bin/ >/dev/null || die + pushd "${ED}"/usr/bin/ >/dev/null || die for i in hmm*; do mv ${i}{,2} || die done diff --git a/sci-biology/hmmer/hmmer-3.1_beta2.ebuild b/sci-biology/hmmer/hmmer-3.1_beta2-r1.ebuild index b65fa0824f9b..666d21cd5532 100644 --- a/sci-biology/hmmer/hmmer-3.1_beta2.ebuild +++ b/sci-biology/hmmer/hmmer-3.1_beta2-r1.ebuild @@ -1,49 +1,55 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 + +inherit toolchain-funcs MY_PV="${PV/_beta/b}" DESCRIPTION="Sequence analysis using profile hidden Markov models" HOMEPAGE="http://hmmer.org/" SRC_URI="http://eddylab.org/software/${PN}3/${MY_PV}/hmmer-${MY_PV}.tar.gz" +S="${WORKDIR}/${PN}-${MY_PV}" LICENSE="GPL-3" SLOT="0" -IUSE="altivec cpu_flags_x86_sse gsl mpi test +threads" -RESTRICT="!test? ( test )" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos" +IUSE="cpu_flags_ppc_altivec cpu_flags_x86_sse gsl mpi test" +RESTRICT="!test? ( test )" RDEPEND=" mpi? ( virtual/mpi ) gsl? ( sci-libs/gsl:= )" -DEPEND="${RDEPEND} - test? ( dev-lang/perl )" +DEPEND="${RDEPEND}" +BDEPEND="test? ( dev-lang/perl )" -S="${WORKDIR}/${PN}-${MY_PV}" PATCHES=( - "${FILESDIR}/${PN}-3.1_beta2-fix-perl-shebangs.patch" - "${FILESDIR}/${PN}-3.1_beta2-fix-header-install-path.patch" + "${FILESDIR}"/${PN}-3.1_beta2-fix-perl-shebangs.patch + "${FILESDIR}"/${PN}-3.1_beta2-makefile.patch ) src_configure() { - # make build verbose, bug 429308 + # make build verbose, bug #429308 export V=1 econf \ --disable-pic \ - $(use_enable altivec vmx) \ + --enable-threads \ + $(use_enable cpu_flags_ppc_altivec vmx) \ $(use_enable cpu_flags_x86_sse sse) \ $(use_enable mpi) \ - $(use_enable threads) \ $(use_with gsl) } +src_compile() { + emake AR="$(tc-getAR)" +} + src_install() { default dodoc Userguide.pdf - insinto /usr/share/${PN} + insinto /usr/share/hmmer doins -r tutorial } diff --git a/sci-biology/hmmer/metadata.xml b/sci-biology/hmmer/metadata.xml index 8417d1580d40..bdabd1d83788 100644 --- a/sci-biology/hmmer/metadata.xml +++ b/sci-biology/hmmer/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/iedera/files/iedera-1.05-fix-buildsystem.patch b/sci-biology/iedera/files/iedera-1.05-fix-buildsystem.patch index f232d7de162b..8803ab64b4e1 100644 --- a/sci-biology/iedera/files/iedera-1.05-fix-buildsystem.patch +++ b/sci-biology/iedera/files/iedera-1.05-fix-buildsystem.patch @@ -1,7 +1,7 @@ iedera sets default flags that override user {C,CXX,LD}FLAGS ---- iedera-1.05/configure.ac -+++ iedera-1.05/configure.ac +--- iedera-1.05/configure.in ++++ iedera-1.05/configure.in @@ -4,11 +4,5 @@ AC_PROG_INSTALL AC_PROG_CXX diff --git a/sci-biology/iedera/iedera-1.05-r1.ebuild b/sci-biology/iedera/iedera-1.05-r1.ebuild deleted file mode 100644 index 115b5495f617..000000000000 --- a/sci-biology/iedera/iedera-1.05-r1.ebuild +++ /dev/null @@ -1,25 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit autotools - -DESCRIPTION="A subset seed design tool for DNA sequence alignment" -HOMEPAGE="http://bioinfo.lifl.fr/yass/iedera.php" -SRC_URI="http://bioinfo.lifl.fr/yass/files/${P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -IUSE="" -KEYWORDS="~amd64 ~x86" - -PATCHES=( - "${FILESDIR}/${P}-fix-buildsystem.patch" -) - -src_prepare() { - mv configure.{in,ac} || die - default - eautoreconf -} diff --git a/sci-biology/iedera/iedera-1.05-r2.ebuild b/sci-biology/iedera/iedera-1.05-r2.ebuild new file mode 100644 index 000000000000..22a4bd9225f2 --- /dev/null +++ b/sci-biology/iedera/iedera-1.05-r2.ebuild @@ -0,0 +1,21 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit autotools + +DESCRIPTION="Subset seed design tool for DNA sequence alignment" +HOMEPAGE="https://bioinfo.lifl.fr/yass/iedera.php" +SRC_URI="https://bioinfo.lifl.fr/yass/files/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +PATCHES=( "${FILESDIR}"/${P}-fix-buildsystem.patch ) + +src_prepare() { + default + eautoreconf +} diff --git a/sci-biology/iedera/metadata.xml b/sci-biology/iedera/metadata.xml index 959160fe46b1..ccdff086e20b 100644 --- a/sci-biology/iedera/metadata.xml +++ b/sci-biology/iedera/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/infernal/files/infernal-1.0.2-fix-build-system.patch b/sci-biology/infernal/files/infernal-1.0.2-fix-build-system.patch new file mode 100644 index 000000000000..41ab3103594b --- /dev/null +++ b/sci-biology/infernal/files/infernal-1.0.2-fix-build-system.patch @@ -0,0 +1,135 @@ +* Fix parallel build +* Respect AR +* Respect DESTDIR +* Respect LDFLAGS + +--- a/easel/Makefile.in ++++ b/easel/Makefile.in +@@ -17,7 +17,6 @@ + # + CC = @CC@ + CFLAGS = @CFLAGS@ +-AR = @AR@ rcv + LN = ln + RANLIB = @RANLIB@ + LDFLAGS = -static @LDFLAGS@ +@@ -132,13 +131,13 @@ + esl_wuss.o + + all: libeasel.a +- (cd miniapps; make) ++ $(MAKE) -C miniapps + + .c.o: + ${CC} -I. ${CFLAGS} ${SIMDFLAGS} ${DEFS} -c $< + + libeasel.a: $(OBJS) +- $(AR) libeasel.a $(OBJS) ++ $(AR) rcv libeasel.a $(OBJS) + $(RANLIB) libeasel.a + chmod 644 libeasel.a + +--- a/easel/testsuite/Makefile.in ++++ b/easel/testsuite/Makefile.in +@@ -15,7 +15,6 @@ + LIBS = @LIBGSL@ @LIBS@ -lm + MPILIBS = @MPILIBS@ + +-AR = @AR@ rcv + RANLIB = @RANLIB@ + + ESLDIR = .. +--- a/iinfernal-1/Makefile.in ++++ b/iinfernal-1/Makefile.in +@@ -20,7 +20,6 @@ + # only used for building the testsuite anyway... e.g. we + # make a "libhmmer.a" library for building the testsuite. + # +-AR = @AR@ rcv + RANLIB = @RANLIB@ + + MPILIBS = @MPILIBS@ +@@ -63,7 +62,7 @@ + module: libinfernal.a + + libinfernal.a: $(OBJS) +- $(AR) libinfernal.a $(OBJS) ++ $(AR) rcv libinfernal.a $(OBJS) + $(RANLIB) libinfernal.a + chmod 644 libinfernal.a + +--- a/Makefile.in ++++ b/Makefile.in +@@ -82,9 +82,10 @@ + all: core + + core: +- (cd easel; make CC="$(CC)" CFLAGS="$(CFLAGS)"; make) +- (cd src; make CC="$(CC)" CFLAGS="$(CFLAGS)"; make module) +- (cd testsuite; make CC="$(CC)" CFLAGS="$(CFLAGS)") ++ $(MAKE) -C easel ++ $(MAKE) -C src ++ $(MAKE) -C src module ++ $(MAKE) -C testsuite + + #.PHONY: $(RIGFILTERS) + #$(RIGFILTERS): core +@@ -202,9 +203,9 @@ + # "make install" installs the programs in BINDIR + # + install: +- mkdir -p ${BINDIR} ++ mkdir -p $(DESTDIR)${BINDIR} + for file in $(PROGS); do\ +- cp src/$$file $(BINDIR)/;\ ++ cp src/$$file $(DESTDIR)$(BINDIR)/;\ + done + # if test -d $(RIGFILTERS); then\ + # for file in $(RFPROGS); do\ +--- a/rigfilters/cfsqp/Makefile.in ++++ b/rigfilters/cfsqp/Makefile.in +@@ -24,7 +24,6 @@ + ## archiving command, and ranlib command. + # these are used to create the libcfsqp.a library, necessary for cm2hmm + # +-AR = @AR@ rcv + RANLIB = @RANLIB@ + + OBJS = cfsqp.o\ +@@ -41,7 +40,7 @@ + all: libcfsqp.a + + libcfsqp.a: $(OBJS) ${HDRS} +- $(AR) libcfsqp.a $(OBJS) ++ $(AR) rcv libcfsqp.a $(OBJS) + $(RANLIB) libcfsqp.a + chmod 644 libcfsqp.a + +--- a/src/Makefile.in ++++ b/src/Makefile.in +@@ -27,7 +27,6 @@ + # only used for building the testsuite anyway... e.g. we + # make a "libinfernal.a" library for building the testsuite. + # +-AR = @AR@ rcv + RANLIB = @RANLIB@ + + # configuration for optional MPI functionality +@@ -86,7 +85,7 @@ + all: $(PROGS) + + $(PROGS): @EXEC_DEPENDENCY@ $(OBJS) ${HDRS} +- $(CC) $(CFLAGS) $(DEFS) $(MYLIBDIR) -o $@ $@.o $(OBJS) $(MYLIBS) $(LIBS) $(MPILIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(DEFS) $(MYLIBDIR) -o $@ $@.o $(OBJS) $(MYLIBS) $(LIBS) $(MPILIBS) + + + ################################################################# +@@ -95,7 +94,7 @@ + module: libinfernal.a + + libinfernal.a: $(OBJS) ${HDRS} +- $(AR) libinfernal.a $(OBJS) ++ $(AR) rcv libinfernal.a $(OBJS) + $(RANLIB) libinfernal.a + chmod 644 libinfernal.a + diff --git a/sci-biology/infernal/files/infernal-1.0.2-ldflags.patch b/sci-biology/infernal/files/infernal-1.0.2-ldflags.patch deleted file mode 100644 index f688dce152ed..000000000000 --- a/sci-biology/infernal/files/infernal-1.0.2-ldflags.patch +++ /dev/null @@ -1,15 +0,0 @@ -Respect LDFLAGS - -http://bugs.gentoo.org/show_bug.cgi?id=338177 - ---- a/src/Makefile.in -+++ b/src/Makefile.in -@@ -86,7 +86,7 @@ - all: $(PROGS) - - $(PROGS): @EXEC_DEPENDENCY@ $(OBJS) ${HDRS} -- $(CC) $(CFLAGS) $(DEFS) $(MYLIBDIR) -o $@ $@.o $(OBJS) $(MYLIBS) $(LIBS) $(MPILIBS) -+ $(CC) $(LDFLAGS) $(CFLAGS) $(DEFS) $(MYLIBDIR) -o $@ $@.o $(OBJS) $(MYLIBS) $(LIBS) $(MPILIBS) - - - ################################################################# diff --git a/sci-biology/infernal/files/infernal-1.0.2-parallel-build.patch b/sci-biology/infernal/files/infernal-1.0.2-parallel-build.patch deleted file mode 100644 index 67ffa6fda7f6..000000000000 --- a/sci-biology/infernal/files/infernal-1.0.2-parallel-build.patch +++ /dev/null @@ -1,31 +0,0 @@ -Fix parallel build - -http://bugs.gentoo.org/show_bug.cgi?id=311919 - ---- a/Makefile.in -+++ b/Makefile.in -@@ -82,9 +82,10 @@ - all: core - - core: -- (cd easel; make CC="$(CC)" CFLAGS="$(CFLAGS)"; make) -- (cd src; make CC="$(CC)" CFLAGS="$(CFLAGS)"; make module) -- (cd testsuite; make CC="$(CC)" CFLAGS="$(CFLAGS)") -+ $(MAKE) -C easel -+ $(MAKE) -C src -+ $(MAKE) -C src module -+ $(MAKE) -C testsuite - - #.PHONY: $(RIGFILTERS) - #$(RIGFILTERS): core ---- a/easel/Makefile.in -+++ b/easel/Makefile.in -@@ -132,7 +132,7 @@ - esl_wuss.o - - all: libeasel.a -- (cd miniapps; make) -+ $(MAKE) -C miniapps - - .c.o: - ${CC} -I. ${CFLAGS} ${SIMDFLAGS} ${DEFS} -c $< diff --git a/sci-biology/infernal/files/infernal-1.0.2-respect-DESTDIR.patch b/sci-biology/infernal/files/infernal-1.0.2-respect-DESTDIR.patch deleted file mode 100644 index ea465e592ffa..000000000000 --- a/sci-biology/infernal/files/infernal-1.0.2-respect-DESTDIR.patch +++ /dev/null @@ -1,16 +0,0 @@ -Build system does not respect DESTDIR by default. - ---- a/Makefile.in -+++ b/Makefile.in -@@ -203,9 +203,9 @@ - # "make install" installs the programs in BINDIR - # - install: -- mkdir -p ${BINDIR} -+ mkdir -p $(DESTDIR)${BINDIR} - for file in $(PROGS); do\ -- cp src/$$file $(BINDIR)/;\ -+ cp src/$$file $(DESTDIR)$(BINDIR)/;\ - done - # if test -d $(RIGFILTERS); then\ - # for file in $(RFPROGS); do\ diff --git a/sci-biology/infernal/infernal-1.0.2-r1.ebuild b/sci-biology/infernal/infernal-1.0.2-r1.ebuild index e906c23024ff..9aa5fd13f4db 100644 --- a/sci-biology/infernal/infernal-1.0.2-r1.ebuild +++ b/sci-biology/infernal/infernal-1.0.2-r1.ebuild @@ -1,7 +1,9 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 + +inherit toolchain-funcs DESCRIPTION="Inference of RNA alignments" HOMEPAGE="http://infernal.janelia.org/" @@ -9,21 +11,20 @@ SRC_URI="ftp://selab.janelia.org/pub/software/${PN}/${P}.tar.gz" LICENSE="GPL-3" SLOT="0" +KEYWORDS="amd64 ~x86" IUSE="mpi" -KEYWORDS="amd64 x86" RDEPEND="mpi? ( virtual/mpi )" DEPEND="${RDEPEND}" PATCHES=( - "${FILESDIR}"/${P}-parallel-build.patch + "${FILESDIR}"/${P}-fix-build-system.patch "${FILESDIR}"/${P}-overflows.patch "${FILESDIR}"/${P}-perl-5.16-2.patch - "${FILESDIR}"/${P}-ldflags.patch - "${FILESDIR}"/${P}-respect-DESTDIR.patch ) src_configure() { + tc-export AR econf $(use_enable mpi) } diff --git a/sci-biology/infernal/metadata.xml b/sci-biology/infernal/metadata.xml index 959160fe46b1..ccdff086e20b 100644 --- a/sci-biology/infernal/metadata.xml +++ b/sci-biology/infernal/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/iqpnni/iqpnni-3.3.2-r1.ebuild b/sci-biology/iqpnni/iqpnni-3.3.2-r2.ebuild index 1edeeada187b..4175330026a1 100644 --- a/sci-biology/iqpnni/iqpnni-3.3.2-r1.ebuild +++ b/sci-biology/iqpnni/iqpnni-3.3.2-r2.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 DESCRIPTION="Important Quartet Puzzling and NNI Operation" HOMEPAGE="http://www.cibiv.at/software/iqpnni/" @@ -12,18 +12,15 @@ SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="doc" -DEPEND="" -RDEPEND="${DEPEND}" - PATCHES=( - "${FILESDIR}/${P}-cpp14.patch" # bug #594332 + "${FILESDIR}"/${P}-cpp14.patch # bug #594332 ) src_install() { dobin src/iqpnni if use doc ; then - HTML_DOCS+=( manual/iqpnni-manual.html ) + HTML_DOCS=( manual/iqpnni-manual.html ) dodoc manual/iqpnni-manual.pdf fi einstalldocs diff --git a/sci-biology/iqpnni/metadata.xml b/sci-biology/iqpnni/metadata.xml index 959160fe46b1..ccdff086e20b 100644 --- a/sci-biology/iqpnni/metadata.xml +++ b/sci-biology/iqpnni/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/kalign/files/kalign-2.03-makefile.patch b/sci-biology/kalign/files/kalign-2.03-makefile.patch new file mode 100644 index 000000000000..61e65c0b73ce --- /dev/null +++ b/sci-biology/kalign/files/kalign-2.03-makefile.patch @@ -0,0 +1,39 @@ +--- a/Makefile.in ++++ b/Makefile.in +@@ -1,7 +1,11 @@ +-PREFIX = /usr/local/bin ++prefix = @prefix@ ++exec_prefix = @exec_prefix@ ++bindir = @bindir@ + TEST = test/ +-CC = gcc +-CFLAGS = -O9 -Wall ++CC = @CC@ ++CFLAGS = @CFLAGS@ ++CPPFLAGS = @CPPFLAGS@ ++LDFLAGS = @LDFLAGS@ + DEBUGFLAGS = -ggdb -Wall + + SOURCES = kalign2_distance_calculation.c kalign2_dp.c kalign2_input.c kalign2_main.c kalign2_mem.c kalign2_inferface.c kalign2_misc.c kalign2_tree.c kalign2_profile.c kalign2_alignment_types.c kalign2_feature.c kalign2_hirschberg.c kalign2_advanced_gaps.c kalign2_hirschberg_dna.c kalign2_output.c kalign2_string_matching.c kalign2_profile_alignment.c +@@ -16,10 +20,7 @@ + .PHONY: clean + + all: $(OBJECTS) +- $(CC) $(CFLAGS) $(OBJECTS) -o $(PROGS) +- +-%.o: %.c +- $(CC) $(CFLAGS) -c $< ++ $(CC) $(LDFLAGS) $(CFLAGS) $(OBJECTS) -o $(PROGS) + + debug: $(DEBUGOBJECTS) + $(CC) $(DEBUGFLAGS) $(DEBUGOBJECTS) -o $(DEBUGPROGS) +@@ -29,7 +30,8 @@ + + + install: +- cp $(PROGS) /usr/local/bin/ ++ mkdir -p $(DESTDIR)$(bindir) ++ cp $(PROGS) $(DESTDIR)$(bindir) + + clean: + rm -f $(PROGS) $(OBJECTS) diff --git a/sci-biology/kalign/kalign-2.03-r2.ebuild b/sci-biology/kalign/kalign-2.03-r2.ebuild deleted file mode 100644 index 53b4490bef71..000000000000 --- a/sci-biology/kalign/kalign-2.03-r2.ebuild +++ /dev/null @@ -1,33 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit toolchain-funcs - -DESCRIPTION="Global and progressive multiple sequence alignment" -HOMEPAGE="http://msa.cgb.ki.se/" -SRC_URI="mirror://debian/pool/main/k/kalign/${PN}_${PV}.orig.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -IUSE="" -KEYWORDS="~amd64 ~x86" - -S=${WORKDIR}/${PN} - -src_prepare() { - default - sed \ - -e "s/\$(CFLAGS) \$(OBJECTS)/\$(LDFLAGS) &/" \ - -i Makefile.in || die -} - -src_compile() { - emake CC="$(tc-getCC)" CFLAGS="${CFLAGS}" -} - -src_install() { - dobin ${PN} - einstalldocs -} diff --git a/sci-biology/kalign/kalign-2.03-r3.ebuild b/sci-biology/kalign/kalign-2.03-r3.ebuild new file mode 100644 index 000000000000..22d92963a0ea --- /dev/null +++ b/sci-biology/kalign/kalign-2.03-r3.ebuild @@ -0,0 +1,15 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DESCRIPTION="Global and progressive multiple sequence alignment" +HOMEPAGE="http://msa.cgb.ki.se/" +SRC_URI="mirror://debian/pool/main/k/kalign/${PN}_${PV}.orig.tar.gz" +S="${WORKDIR}/${PN}" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +PATCHES=( "${FILESDIR}"/${P}-makefile.patch ) diff --git a/sci-biology/kalign/metadata.xml b/sci-biology/kalign/metadata.xml index 959160fe46b1..ccdff086e20b 100644 --- a/sci-biology/kalign/metadata.xml +++ b/sci-biology/kalign/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/kallisto/Manifest b/sci-biology/kallisto/Manifest index 720b078417b1..a880b853ffd7 100644 --- a/sci-biology/kallisto/Manifest +++ b/sci-biology/kallisto/Manifest @@ -1 +1 @@ -DIST kallisto-0.43.1.tar.gz 1067076 BLAKE2B 15a2fc65f0c9db431d9be6b2c8434b582ff7bf95fb659a9838d287feb3486744bca6201563d0f318be47c0f8532b805148a2eabfda633075d6b55bad1c3a406a SHA512 c7725a2d649cf96fcd24a20d542b409777cfd9fe97c09f0f459a5ec2981e0a4f5f0ea03d76d3ec3edf0e498c799fc7d074d442d5e35ddb4043d1f7634619dda8 +DIST kallisto-0.46.2.tar.gz 2693869 BLAKE2B 73d725e74133d64b9f7910f69a5fff85eac05b93ad6891807a6fd4e16a1fa16a55306058db3fcb4e0fbfeb0719d3a9d3c8da7d2b76b64dde5a2fea51b0254b99 SHA512 6aca29afa0abe1c6896d27745fd2436c9b9aaf298d70276baf877dbf0aaaba94df54b9a42829c8f8f7c02e7262ecd1837b8a021625c3066a10c0cc0551179093 diff --git a/sci-biology/kallisto/files/kallisto-0.46.2-catch2.patch b/sci-biology/kallisto/files/kallisto-0.46.2-catch2.patch new file mode 100644 index 000000000000..3ff6a0c33be0 --- /dev/null +++ b/sci-biology/kallisto/files/kallisto-0.46.2-catch2.patch @@ -0,0 +1,38 @@ +--- a/unit_tests/main.cpp ++++ b/unit_tests/main.cpp +@@ -1,2 +1,2 @@ + #define CATCH_CONFIG_MAIN +-#include "catch.hpp" ++#include <catch2/catch_all.hpp> +--- a/unit_tests/test_index.cpp ++++ b/unit_tests/test_index.cpp +@@ -1,4 +1,4 @@ +-#include "catch.hpp" ++#include <catch2/catch_all.hpp> + + #include "common.h" + #include "KmerIndex.h" +--- a/unit_tests/test_kmerhashtable.cpp ++++ b/unit_tests/test_kmerhashtable.cpp +@@ -1,4 +1,4 @@ +-#include "catch.hpp" ++#include <catch2/catch_all.hpp> + + #include <random> + #include <string> +--- a/unit_tests/test_multinomial.cpp ++++ b/unit_tests/test_multinomial.cpp +@@ -1,4 +1,4 @@ +-#include "catch.hpp" ++#include <catch2/catch_all.hpp> + + #include <iostream> + #include <vector> +--- a/unit_tests/test_weights.cpp ++++ b/unit_tests/test_weights.cpp +@@ -1,4 +1,4 @@ +-#include "catch.hpp" ++#include <catch2/catch_all.hpp> + + #include <vector> + diff --git a/sci-biology/kallisto/files/kallisto-0.46.2-cmake.patch b/sci-biology/kallisto/files/kallisto-0.46.2-cmake.patch new file mode 100644 index 000000000000..6516f162e906 --- /dev/null +++ b/sci-biology/kallisto/files/kallisto-0.46.2-cmake.patch @@ -0,0 +1,149 @@ +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -11,9 +11,6 @@ + add_compile_definitions("USE_HDF5=ON") + endif(USE_HDF5) + +-set(EXT_PROJECTS_DIR ${PROJECT_SOURCE_DIR}/ext) +-set(CMAKE_CXX_FLAGS_PROFILE "-g") +- + # Set Release type for builds where CMAKE_BUILD_TYPE is unset + # This is usually a good default as this implictly enables + # +@@ -33,44 +30,12 @@ + set(CMAKE_CXX_EXTENSIONS OFF) + endif() + +-#add_compile_options(-Wall -Wno-unused-function) +- +-if(LINK MATCHES static) +- message("static build") +-ELSE(LINK MATCHES shared) +- message("shared build") +-ENDIF(LINK MATCHES static) +- +- +-include(ExternalProject) +-ExternalProject_Add(htslib +- PREFIX ${PROJECT_SOURCE_DIR}/ext/htslib +- SOURCE_DIR ${PROJECT_SOURCE_DIR}/ext/htslib +- BUILD_IN_SOURCE 1 +- CONFIGURE_COMMAND autoheader && autoconf && ${PROJECT_SOURCE_DIR}/ext/htslib/configure +- --prefix=${PREFIX} --disable-bz2 --disable-lzma --disable-libcurl +- BUILD_COMMAND make lib-static +- INSTALL_COMMAND "" +-) +- +-include_directories(${htslib_PREFIX}/src/htslib) +- +- +- +-# add_compile_options(-Wdeprecated-register) +- + add_subdirectory(src) +-include_directories(${EXT_PROJECTS_DIR}) + + option(BUILD_TESTING "Build unit tests." OFF) + include(CTest) + + if (BUILD_TESTING) +- add_subdirectory(${EXT_PROJECTS_DIR}/catch) +- +- # Includes Catch in the project: +- include_directories(${CATCH_INCLUDE_DIR} ${COMMON_INCLUDES}) +- + add_subdirectory(unit_tests) + endif(BUILD_TESTING) + +--- a/src/CMakeLists.txt ++++ b/src/CMakeLists.txt +@@ -3,30 +3,17 @@ + + list(REMOVE_ITEM sources main.cpp) + +-include_directories(../ext/htslib) +- + add_library(kallisto_core ${sources} ${headers}) + target_include_directories(kallisto_core PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}) + + add_executable(kallisto main.cpp) + +-find_package( Threads REQUIRED ) +-target_link_libraries(kallisto kallisto_core pthread ${CMAKE_CURRENT_SOURCE_DIR}/../ext/htslib/libhts.a) +- +-if(LINK MATCHES static) +- set(BUILD_SHARED_LIBS OFF) +- set(HDF5_USE_STATIC_LIBRARIES 1) +- +- if (UNIX AND NOT APPLE) +- #set(CMAKE_EXE_LINKER_FLAGS "-static -static-libgcc -static-libstdc++") +- set(CMAKE_EXE_LINKER_FLAGS "-static -static-libstdc++") +- SET(CMAKE_FIND_LIBRARY_SUFFIXES ".a") +- set(CMAKE_EXE_LINKER_FLAGS "-static -static-libgcc -static-libstdc++") +- endif(UNIX AND NOT APPLE) +- +- SET_TARGET_PROPERTIES(kallisto kallisto_core PROPERTIES LINK_SEARCH_END_STATIC 1) +-endif(LINK MATCHES static) ++find_package( PkgConfig REQUIRED ) ++pkg_check_modules( HTSLIB REQUIRED htslib ) + ++find_package( Threads REQUIRED ) ++target_include_directories(kallisto PRIVATE ${HTSLIB_CFLAGS}) ++target_link_libraries(kallisto PRIVATE kallisto_core Threads::Threads ${HTSLIB_LDFLAGS}) + + if(USE_HDF5) + find_package( HDF5 REQUIRED ) +@@ -36,7 +23,7 @@ + + if ( ZLIB_FOUND ) + include_directories( ${ZLIB_INCLUDE_DIRS} ) +- target_link_libraries(kallisto kallisto_core ${ZLIB_LIBRARIES}) ++ target_link_libraries(kallisto PRIVATE kallisto_core ${ZLIB_LIBRARIES}) + else() + message(FATAL_ERROR "zlib not found. Required for to output files" ) + endif( ZLIB_FOUND ) +@@ -44,22 +31,17 @@ + if(USE_HDF5) + if(HDF5_FOUND) + include_directories( ${HDF5_INCLUDE_DIRS} ) +- target_link_libraries( kallisto_core ${HDF5_LIBRARIES} ) +- target_link_libraries( kallisto ${HDF5_LIBRARIES} ) ++ target_link_libraries( kallisto_core PRIVATE ${HDF5_LIBRARIES} ) ++ target_link_libraries( kallisto PRIVATE ${HDF5_LIBRARIES} ) + else() + message(FATAL_ERROR "HDF5 not found. Required to output files") + endif() + endif(USE_HDF5) + +-if(LINK MATCHES static) +- if (UNIX AND NOT APPLE) +- target_link_libraries(kallisto librt.a) +- endif() +-else() +- if (UNIX AND NOT APPLE) +- target_link_libraries(kallisto rt) +- endif() +-endif(LINK MATCHES static) +- ++target_compile_options( kallisto_core PRIVATE ${HTSLIB_CFLAGS} ) ++target_link_libraries( kallisto_core PRIVATE ${HTSLIB_LDFLAGS} ) + +-install(TARGETS kallisto DESTINATION "${CMAKE_INSTALL_BINDIR}") +\ No newline at end of file ++install(TARGETS kallisto DESTINATION "${CMAKE_INSTALL_BINDIR}") ++if ( BUILD_SHARED_LIBS ) ++ install(TARGETS kallisto_core DESTINATION "${CMAKE_INSTALL_LIBDIR}") ++endif() +--- a/unit_tests/CMakeLists.txt ++++ b/unit_tests/CMakeLists.txt +@@ -8,6 +8,10 @@ + add_executable(tests ${sources}) + add_test(unittest tests) + ++find_package( Catch2 REQUIRED ) ++include_directories( ${Catch2_INCLUDE_DIRS} ) ++target_link_libraries( tests Catch2::Catch2WithMain ) ++ + find_package( ZLIB REQUIRED ) + if ( ZLIB_FOUND ) + include_directories( ${ZLIB_INCLUDE_DIRS} ) diff --git a/sci-biology/kallisto/files/kallisto-0.46.2-gcc11.patch b/sci-biology/kallisto/files/kallisto-0.46.2-gcc11.patch new file mode 100644 index 000000000000..19594f067776 --- /dev/null +++ b/sci-biology/kallisto/files/kallisto-0.46.2-gcc11.patch @@ -0,0 +1,21 @@ +From 1d63e9d731bada64f6038818e27f06da63007d73 Mon Sep 17 00:00:00 2001 +From: Nilesh Patra <npatra974@gmail.com> +Date: Thu, 4 Mar 2021 23:38:30 +0530 +Subject: [PATCH] Fix GCC-11 Build Failure: include limits lib + +--- + src/MinCollector.h | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/src/MinCollector.h b/src/MinCollector.h +index a905f1f..c4460fb 100644 +--- a/src/MinCollector.h ++++ b/src/MinCollector.h +@@ -7,6 +7,7 @@ + #include <sstream> + #include <vector> + #include <unordered_map> ++#include <limits> + + #include "KmerIndex.h" + #include "weights.h" diff --git a/sci-biology/kallisto/files/kallisto-0.46.2-htslib.patch b/sci-biology/kallisto/files/kallisto-0.46.2-htslib.patch new file mode 100644 index 000000000000..0e926136261c --- /dev/null +++ b/sci-biology/kallisto/files/kallisto-0.46.2-htslib.patch @@ -0,0 +1,52 @@ +--- a/src/KmerIndex.cpp ++++ b/src/KmerIndex.cpp +@@ -4,7 +4,7 @@ + #include <ctype.h> + #include <zlib.h> + #include <unordered_set> +-#include "kseq.h" ++#include <htslib/kseq.h> + + #ifndef KSEQ_INIT_READY + #define KSEQ_INIT_READY +--- a/src/ProcessReads.cpp ++++ b/src/ProcessReads.cpp +@@ -1,6 +1,6 @@ + /* + #include <zlib.h> +-#include "kseq.h" ++#include <htslib/kseq.h> + #include <string> + #include <vector> + #include <unordered_map> +@@ -20,7 +20,7 @@ + #include <iomanip> + + #include "ProcessReads.h" +-#include "kseq.h" ++#include <htslib/kseq.h> + #include "PseudoBam.h" + #include "Fusion.hpp" + #include "BUSData.h" +--- a/src/ProcessReads.h ++++ b/src/ProcessReads.h +@@ -2,7 +2,7 @@ + #define KALLISTO_PROCESSREADS_H + + #include <zlib.h> +-#include "kseq.h" ++#include <htslib/kseq.h> + #include <string> + #include <vector> + #include <unordered_map> +--- a/unit_tests/test_kmerhashtable.cpp ++++ b/unit_tests/test_kmerhashtable.cpp +@@ -13,7 +13,7 @@ + #include "KmerHashTable.h" + + #include <zlib.h> +-#include "kseq.h" ++#include <htslib/kseq.h> + + #ifndef KSEQ_INIT_READY + #define KSEQ_INIT_READY diff --git a/sci-biology/kallisto/kallisto-0.43.1.ebuild b/sci-biology/kallisto/kallisto-0.43.1.ebuild deleted file mode 100644 index 0020e891a032..000000000000 --- a/sci-biology/kallisto/kallisto-0.43.1.ebuild +++ /dev/null @@ -1,25 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit cmake-utils - -DESCRIPTION="Near-optimal RNA-Seq quantification" -HOMEPAGE="http://pachterlab.github.io/kallisto/" - -if [[ ${PV} == *9999 ]]; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/pachterlab/kallisto.git" -else - SRC_URI="https://github.com/pachterlab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" - KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -fi - -LICENSE="BSD" -SLOT="0" - -RDEPEND=" - sci-libs/hdf5:= - sys-libs/zlib:=" -DEPEND="${RDEPEND}" diff --git a/sci-biology/kallisto/kallisto-0.46.2-r1.ebuild b/sci-biology/kallisto/kallisto-0.46.2-r1.ebuild new file mode 100644 index 000000000000..68640687cf9d --- /dev/null +++ b/sci-biology/kallisto/kallisto-0.46.2-r1.ebuild @@ -0,0 +1,68 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit cmake flag-o-matic + +DESCRIPTION="Near-optimal RNA-Seq quantification" +HOMEPAGE="http://pachterlab.github.io/kallisto/" + +if [[ ${PV} == *9999 ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/pachterlab/kallisto.git" +else + SRC_URI="https://github.com/pachterlab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +fi + +LICENSE="BSD" +SLOT="0" +IUSE="hdf5 test" +RESTRICT="!test? ( test )" + +RDEPEND=" + sci-libs/htslib:= + sys-libs/zlib:= + hdf5? ( sci-libs/hdf5:= )" +DEPEND=" + ${RDEPEND} + test? ( + >=dev-cpp/catch-3:0 + sci-libs/hdf5 + )" +BDEPEND="virtual/pkgconfig" + +PATCHES=( + "${FILESDIR}"/${P}-cmake.patch + "${FILESDIR}"/${P}-htslib.patch + "${FILESDIR}"/${P}-catch2.patch + "${FILESDIR}"/${P}-gcc11.patch +) + +src_prepare() { + cmake_src_prepare + # bundled catch2 + rm -r ext || die + # bundled htslib structs + rm src/kseq.h || die + + # the test suite is cheesy and relies on a + # specific builddir nesting structure. + sed -e "s|../test/input/short_reads.fastq|$(readlink -f unit_tests/input/short_reads.fastq)|g" \ + -i unit_tests/test_kmerhashtable.cpp || die + + # This randomly hardcodes a particular std, which unfortunately is too old for catch2. + sed -i '/CMAKE_CXX_STANDARD/d' CMakeLists.txt || die + append-cxxflags -std=c++14 +} + +src_configure() { + local mycmakeargs=( + -DUSE_HDF5=$(usex hdf5) + -DBUILD_TESTING=$(usex test) + # convenience library only + -DBUILD_SHARED_LIBS=OFF + ) + cmake_src_configure +} diff --git a/sci-biology/kallisto/kallisto-9999.ebuild b/sci-biology/kallisto/kallisto-9999.ebuild deleted file mode 100644 index 0020e891a032..000000000000 --- a/sci-biology/kallisto/kallisto-9999.ebuild +++ /dev/null @@ -1,25 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit cmake-utils - -DESCRIPTION="Near-optimal RNA-Seq quantification" -HOMEPAGE="http://pachterlab.github.io/kallisto/" - -if [[ ${PV} == *9999 ]]; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/pachterlab/kallisto.git" -else - SRC_URI="https://github.com/pachterlab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" - KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -fi - -LICENSE="BSD" -SLOT="0" - -RDEPEND=" - sci-libs/hdf5:= - sys-libs/zlib:=" -DEPEND="${RDEPEND}" diff --git a/sci-biology/kallisto/metadata.xml b/sci-biology/kallisto/metadata.xml index aba0d0ebf330..5d84bfa5c986 100644 --- a/sci-biology/kallisto/metadata.xml +++ b/sci-biology/kallisto/metadata.xml @@ -1,14 +1,6 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="person"> - <email>mschu.dev@gmail.com</email> - <name>Michael Schubert</name> - </maintainer> - <maintainer type="project"> - <email>proxy-maint@gentoo.org</email> - <name>Proxy Maintainers</name> - </maintainer> <maintainer type="project"> <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> diff --git a/sci-biology/lagan/files/lagan-2.0-C99-static-inline.patch b/sci-biology/lagan/files/lagan-2.0-C99-static-inline.patch new file mode 100644 index 000000000000..2c9d88111aee --- /dev/null +++ b/sci-biology/lagan/files/lagan-2.0-C99-static-inline.patch @@ -0,0 +1,258 @@ +--- a/src/fchaos.c ++++ b/src/fchaos.c +@@ -985,7 +985,7 @@ + SLremove(mylist, tbf->mysles[i]); + } + +-inline int CHmatchscore(unsigned char a, unsigned char b) { ++static inline int CHmatchscore(unsigned char a, unsigned char b) { + return substmatrix[a][b]; + /* + if (translated) +--- a/src/multial.c ++++ b/src/multial.c +@@ -59,16 +59,16 @@ + int normf; + int normprev; + +-inline int ismatch(char a, char b) { ++static inline int ismatch(char a, char b) { + return (a == b); + } + +-inline int isGap(align* ali, int seqn, int loc) { ++static inline int isGap(align* ali, int seqn, int loc) { + int i = !((ali->algn[loc] >> seqn) & 1); + return i; + } + +-inline int scoreLocal(int which, align* ali, int loc) { ++static inline int scoreLocal(int which, align* ali, int loc) { + int i, lets = 0; + for (i=0; i < 4; i++) + lets += ali->cnts[i][loc]; +@@ -83,7 +83,7 @@ + return lets+ali->cnts[CNTS_GS][loc] * gapcont; + } + +-inline hll* reverseHLL(hll* tbr) { ++static inline hll* reverseHLL(hll* tbr) { + hll *nn, *prev=0; + while (tbr) { + nn = tbr->next; +@@ -171,7 +171,7 @@ + return res; + } + +-inline void reverse (long long int* a, int length) { ++static inline void reverse (long long int* a, int length) { + long long int lft; + int i; + for (i=0; i < length/2; i++) { +@@ -409,7 +409,7 @@ + */ + } + +-inline int scoreGap(int numgs, int numgc, int numge, int numseq) { ++static inline int scoreGap(int numgs, int numgc, int numge, int numseq) { + return (MIN2(numgc, numseq-numgc) * gapcont) + + (MIN2(numgs, numseq-numgs) * gapstart) + + (MIN2(numge, numseq-numge) * gapend); +@@ -493,7 +493,7 @@ + fclose (file); + } + +-inline int chmatchscore (unsigned char a, unsigned char b, int substmatrix[256][256]) { ++static inline int chmatchscore (unsigned char a, unsigned char b, int substmatrix[256][256]) { + return substmatrix[a][b]; + } + +@@ -539,14 +539,14 @@ + // printcache(); + } + +-inline int v (int y){ ++static inline int v (int y){ + if (y >= 0 && y <= MAX_SEQ) return y; + fprintf(stderr, "Got %d in v\n", y); + assert (0); + return 0; + } + +-inline int matchscore (align*a, int ai, align *b, int bi){ ++static inline int matchscore (align*a, int ai, align *b, int bi){ + + return + matchcache[v(a->cnts[0][ai] + b->cnts[0][bi]) | +@@ -559,30 +559,30 @@ + (v(a->numseq + b->numseq - (a->cnts[CNTS_CB][ai] + b->cnts[CNTS_CB][bi])) << 18)]; + } + +-inline int scoreOpp (align *other, int ow, int oppnum){ ++static inline int scoreOpp (align *other, int ow, int oppnum){ + return matchcache[v(other->cnts[0][ow]) | + (v(other->cnts[1][ow]) << 6) | + (v(other->cnts[2][ow]) << 12) | + (v(other->cnts[3][ow]) << 18)]; + } + +-inline int endGap0 (align* a, int ai, align* b, int bi){ ++static inline int endGap0 (align* a, int ai, align* b, int bi){ + return gapcache[(v(a->cnts[CNTS_GE][ai]+b->cnts[CNTS_GE][bi])<<12) | + (v(a->numseq + b->numseq-(b->cnts[CNTS_CB][bi]+a->cnts[CNTS_CB][ai])) << 18)]; + } + +-inline int endGap1 (align* a, int ai, align* b, int bi){ ++static inline int endGap1 (align* a, int ai, align* b, int bi){ + + return gapcache[(v((b->numseq - b->cnts[CNTS_GS][bi] - b->cnts[CNTS_GC][bi]) + a->cnts[CNTS_GE][ai]) << 12) | + (v(a->numseq + b->numseq - (b->cnts[CNTS_CB][bi]+a->cnts[CNTS_CB][ai])) << 18)]; + } + +-inline int endGap2 (align* a, int ai, align* b, int bi){ ++static inline int endGap2 (align* a, int ai, align* b, int bi){ + return gapcache[(v((a->numseq - a->cnts[CNTS_GS][ai] - a->cnts[CNTS_GC][ai]) + b->cnts[CNTS_GE][bi])<<12) | + (v(a->numseq + b->numseq - (b->cnts[CNTS_CB][bi]+a->cnts[CNTS_CB][ai])) << 18)]; + } + +-inline int contGap(align* ali, int myw, align* other, int ow, int *sopp) { ++static inline int contGap(align* ali, int myw, align* other, int ow, int *sopp) { + return gapcache[(v(other->cnts[CNTS_GS][ow])) | + (v(ali->numseq + other->cnts[CNTS_GC][ow]) << 6) | + (v(other->cnts[CNTS_GE][ow]) << 12) | +@@ -590,7 +590,7 @@ + sopp[ow]; + } + +-inline int openGap(align* ali, int w, align* other, int ow, int *sopp, char *desc) { ++static inline int openGap(align* ali, int w, align* other, int ow, int *sopp, char *desc) { + int alopen, pen, sav, i; + + alopen = ali->cnts[CNTS_GC][w] + ali->cnts[CNTS_GE][w]; +--- a/src/order.c ++++ b/src/order.c +@@ -454,11 +454,11 @@ + } + + +-inline int ismatch(char a, char b) { ++static inline int ismatch(char a, char b) { + return a == b; + } + +-inline int matchscore (unsigned char a, unsigned char b) { ++static inline int matchscore (unsigned char a, unsigned char b) { + return substmatrix[a][b]; + /* + +--- a/src/utils/cstat.c ++++ b/src/utils/cstat.c +@@ -121,7 +121,7 @@ + return res; + } + +-inline int getScore (align* a, int i){ ++static inline int getScore (align* a, int i){ + return + ((a->cnts[0][i] * (a->cnts[0][i] - 1)) + + (a->cnts[1][i] * (a->cnts[1][i] - 1)) + +--- a/src/utils/getbounds.c ++++ b/src/utils/getbounds.c +@@ -6,8 +6,8 @@ + + #define EXPAND 2 + +-inline int max (int a, int b){ if (a > b) return a; return b; } +-inline int min (int a, int b){ if (a < b) return a; return b; } ++static inline int max (int a, int b){ if (a > b) return a; return b; } ++static inline int min (int a, int b){ if (a < b) return a; return b; } + + int getLength (char *filename){ + FILE *file; +--- a/src/utils/scorealign.c ++++ b/src/utils/scorealign.c +@@ -18,17 +18,17 @@ + int matchscore[256][256]; + int gapopen = -1500, gapcont = -50; + +-inline int min (int a, int b){ ++static inline int min (int a, int b){ + if (a < b) return a; + return b; + } + +-inline int max (int a, int b){ ++static inline int max (int a, int b){ + if (a > b) return a; + return b; + } + +-inline int scoreMatch (char c, char d){ ++static inline int scoreMatch (char c, char d){ + if (c == '-' && d == '-') return 0; + if (c == '-' || d == '-') return gapcont; + return matchscore[(unsigned char) c][(unsigned char) d]; +@@ -235,7 +235,7 @@ + } + } + +-inline int issymbol (char ch){ ++static inline int issymbol (char ch){ + return ch == 'A' || ch == 'C' || ch == 'G' || ch == 'T' || ch == 'N' || ch == '.' || ch == '-'; + } + +--- a/src/utils/scorecontigs.c ++++ b/src/utils/scorecontigs.c +@@ -133,7 +133,7 @@ + return res; + } + +-inline int getstate (char c, char d){ ++static inline int getstate (char c, char d){ + if (c == '-' || d == '-') return 2; + if (c == 'N' || d == 'N') return 3; + return c == d; +@@ -235,7 +235,7 @@ + return r; + } + +-inline int getdata (rangelist **ranges, int *offs, int j, int i){ ++static inline int getdata (rangelist **ranges, int *offs, int j, int i){ + i -= offs[j]; + if (i >= 0 && i < ranges[j]->seqlen) + return ranges[j]->score[i]; +@@ -243,14 +243,14 @@ + } + + +-inline int match (rangelist **ranges, int numContigs, int i, int j, int *offs){ ++static inline int match (rangelist **ranges, int numContigs, int i, int j, int *offs){ + int k; + for (k = 0; k < numContigs; k++) + if ((getdata (ranges, offs, k, i) != 0) != (getdata (ranges, offs, k, j) != 0)) return 0; + return 1; + } + +-inline int allzeroes (rangelist **ranges, int numContigs, int pos, int *offs){ ++static inline int allzeroes (rangelist **ranges, int numContigs, int pos, int *offs){ + int i; + + for (i = 0; i < numContigs; i++) +@@ -258,7 +258,7 @@ + return 1; + } + +-inline void print (int start, int end, int *score, int numContigs){ ++static inline void print (int start, int end, int *score, int numContigs){ + int j; + + printf ("(%7d %7d)", start, end); +@@ -303,7 +303,7 @@ + free (pattern); + } + +-inline double scoregap (int gaplen){ ++static inline double scoregap (int gaplen){ + if (gaplen == 0) return 0; + //return (gaplen - 1) * -1 - 50; + return (log (gaplen) / log (10) + 1) * scoreGapOpen; diff --git a/sci-biology/lagan/files/lagan-2.0-ambiguous-end.patch b/sci-biology/lagan/files/lagan-2.0-ambiguous-end.patch new file mode 100644 index 000000000000..945120b1fc47 --- /dev/null +++ b/sci-biology/lagan/files/lagan-2.0-ambiguous-end.patch @@ -0,0 +1,49 @@ +Author: Steffen Moeller +Last-Update: 2018-09-07 15:08:19 +0200 +Description: Fix build issue + +Index: lagan/src/glocal/rightinfluence.cpp +=================================================================== +--- lagan.orig/src/glocal/rightinfluence.cpp ++++ lagan/src/glocal/rightinfluence.cpp +@@ -1,6 +1,6 @@ + #include <rightinfluence.h> + +-Fragment origin, end; ++static Fragment originFrag, endFrag; + + // Sets the first default owner of the whole region + void initRI(RI *RightInfluence, long long int scoreIndex) { +@@ -13,22 +13,22 @@ void initRI(RI *RightInfluence, long lon + } + + // will lose to anyone +- origin.seq1End = 0; origin.seq2End = 0; +- origin.seq1Start = 0; origin.seq2Start = 0; ++ originFrag.seq1End = 0; originFrag.seq2End = 0; ++ originFrag.seq1Start = 0; originFrag.seq2Start = 0; + + // hack to aid winner selection +- origin.score = -1; +- end.score = -2; +- origin.totalScore = end.totalScore = 0; ++ originFrag.score = -1; ++ endFrag.score = -2; ++ originFrag.totalScore = endFrag.totalScore = 0; + + // will win against anyone +- end.seq1End = 0; end.seq2End = 0; +- end.seq1Start = 0; end.seq2Start = 0; ++ endFrag.seq1End = 0; endFrag.seq2End = 0; ++ endFrag.seq1Start = 0; endFrag.seq2Start = 0; + +- origin.back = NULL; ++ originFrag.back = NULL; + +- RightInfluence->act[-INF] = &origin; +- RightInfluence->act[+INF] = &end; ++ RightInfluence->act[-INF] = &originFrag; ++ RightInfluence->act[+INF] = &endFrag; + } + + diff --git a/sci-biology/lagan/files/lagan-2.0-conflicting-getline.patch b/sci-biology/lagan/files/lagan-2.0-conflicting-getline.patch new file mode 100644 index 000000000000..075753a924c9 --- /dev/null +++ b/sci-biology/lagan/files/lagan-2.0-conflicting-getline.patch @@ -0,0 +1,24 @@ +Author: Andreas Tille <tille@debian.org> +LastChanged: Fri, 15 Nov 2013 10:31:20 +0100 +Description: Prevent conflicting getline by simply renaming it + +--- a/src/anchors.c ++++ b/src/anchors.c +@@ -225,7 +225,7 @@ char* rolltonum(char* str) { + return &str[i]; + } + +-int getline(FILE* infile, hll* tt) { ++int anchors_getline(FILE* infile, hll* tt) { + char temp[1024]; + char* help; + int z, h; +@@ -248,7 +248,7 @@ hll* parseCHAOS(FILE* infile, int* totnu + *totnum = 0; + while(!feof(infile)) { + tt = (hll*) malloc(sizeof(hll)); +- while (!feof(infile) && !getline(infile, tt)) ++ while (!feof(infile) && !anchors_getline(infile, tt)) + ; + if (feof(infile)) break; + if (gapfreechunks) { diff --git a/sci-biology/lagan/files/lagan-2.0-fix-c++14.patch b/sci-biology/lagan/files/lagan-2.0-fix-c++14.patch deleted file mode 100644 index 9865f2756c5a..000000000000 --- a/sci-biology/lagan/files/lagan-2.0-fix-c++14.patch +++ /dev/null @@ -1,473 +0,0 @@ -Fix building with C++14, which errors out due to namespace collisions with std::end -in C++14 mode, due to crappy 'using namespace std' declared everywhere. -See also: https://bugs.gentoo.org/show_bug.cgi?id=594148 - ---- a/src/ancseq.cpp -+++ b/src/ancseq.cpp -@@ -30,7 +30,6 @@ - #include <stdlib.h> - #include <stdio.h> - --using namespace std; - - #include "util.cpp" - #include "faindex.cpp" ---- a/src/ancseqrest.cpp -+++ b/src/ancseqrest.cpp -@@ -31,7 +31,6 @@ - #include <stdlib.h> - #include <stdio.h> - --using namespace std; - - #define fastaRowLength 50 - typedef char* pchar; ---- a/src/cutmfa.cpp -+++ b/src/cutmfa.cpp -@@ -45,7 +45,6 @@ - #include <stdlib.h> - #include <stdio.h> - --using namespace std; - - // TODO refactor in classes and normal make project - ---- a/src/glocal/glocal.cpp -+++ b/src/glocal/glocal.cpp -@@ -7,9 +7,9 @@ - } - - //vectors that would be needed globally --vector<Fragment> fragments; --vector<Point>startPoints; --vector<Point>endPoints; -+std::vector<Fragment> fragments; -+std::vector<Point>startPoints; -+std::vector<Point>endPoints; - long long int numFragments; - InterPoint inter; - -@@ -19,7 +19,7 @@ - RI RI_regions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)]; - LI LI_regions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)]; - --vector<class Score*> scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)]; -+std::vector<class Score*> scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)]; - - Name allNames; - ---- a/src/glocal/io.cpp -+++ b/src/glocal/io.cpp -@@ -3,9 +3,9 @@ - #include<io.h> - #include<algorithm> - --extern vector <Fragment> fragments; --extern vector <Point> startPoints; --extern vector <Point> endPoints; -+extern std::vector <Fragment> fragments; -+extern std::vector <Point> startPoints; -+extern std::vector <Point> endPoints; - extern Name allNames; - - bool PointCompare(const Point &f1, const Point &f2) { -@@ -223,8 +223,8 @@ - startPoints.push_back(startPoint); - endPoints.push_back(endPoint); - } -- sort(startPoints.begin(), startPoints.end(), PointCompare); -- sort(endPoints.begin(), endPoints.end(), PointCompare); -+ std::sort(startPoints.begin(), startPoints.end(), PointCompare); -+ std::sort(endPoints.begin(), endPoints.end(), PointCompare); - } - - ---- a/src/glocal/leftinfluence.cpp -+++ b/src/glocal/leftinfluence.cpp -@@ -154,8 +154,8 @@ - - if (second->score == -1) { return TRUE; } - -- dummy.seq1Start = max(first->seq1End, second->seq1End) + 2; -- dummy.seq2Start = max(first->getSeq2End(LeftInfluence->reflectFlag), second->getSeq2End(LeftInfluence->reflectFlag)) + 1; -+ dummy.seq1Start = std::max(first->seq1End, second->seq1End) + 2; -+ dummy.seq2Start = std::max(first->getSeq2End(LeftInfluence->reflectFlag), second->getSeq2End(LeftInfluence->reflectFlag)) + 1; - - if (first->getSeq2End(LeftInfluence->reflectFlag) > second->getSeq2End(LeftInfluence->reflectFlag)) { - dummy.nameIter = first->nameIter; -@@ -444,7 +444,7 @@ - temp.seq1 = col - diag; - temp.seq2 = col; - -- pair<Point,LI*> pairp(temp, LeftInfluence); -+ std::pair<Point,LI*> pairp(temp, LeftInfluence); - tempinter = inter.insert(pairp); - - colInter->second = tempinter; ---- a/src/glocal/leftinfluence.h -+++ b/src/glocal/leftinfluence.h -@@ -39,15 +39,15 @@ - - - --typedef list<Fragment*> Owner; --typedef map <long long int ,Owner::iterator,longlongCompare2> CBound; -+typedef std::list<Fragment*> Owner; -+typedef std::map <long long int ,Owner::iterator,longlongCompare2> CBound; - --typedef multimap <Point ,struct LI *,paircomp> InterPoint; -+typedef std::multimap <Point ,struct LI *,paircomp> InterPoint; - --typedef map <long long int ,InterPoint::iterator,longlongCompare2> CInter; --typedef map <long long int,Owner::iterator,longlongCompare2> DBound; -+typedef std::map <long long int ,InterPoint::iterator,longlongCompare2> CInter; -+typedef std::map <long long int,Owner::iterator,longlongCompare2> DBound; - --typedef map <long long int,InterPoint::iterator,longlongCompare2> DInter; -+typedef std::map <long long int,InterPoint::iterator,longlongCompare2> DInter; - - - ---- a/src/glocal/rightinfluence.h -+++ b/src/glocal/rightinfluence.h -@@ -17,7 +17,7 @@ - }; - - --typedef map<const long long int , Fragment*,longlongCompare> Active; -+typedef std::map<const long long int , Fragment*,longlongCompare> Active; - - typedef struct RI { - //List of active regions ---- a/src/glocal/score.cpp -+++ b/src/glocal/score.cpp -@@ -4,7 +4,7 @@ - #include<rightinfluence.h> - #include<fstream> - --extern vector<class Score*> scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)]; -+extern std::vector<class Score*> scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)]; - - - float Score::getScore(Fragment *up, Fragment * down) { -@@ -36,7 +36,7 @@ - - - void initScoreFunctionPointers(char * scoreFileName) { -- ifstream SFP; -+ std::ifstream SFP; - char line[255]; - - SFP.open(scoreFileName); ---- a/src/glocal/structs.h -+++ b/src/glocal/structs.h -@@ -12,7 +12,6 @@ - #include <list> - #include <string.h> - --using namespace std; - - #define RIGHT 0 - #define LEFT 1 -@@ -49,7 +48,7 @@ - }; - - --typedef map<const char*,long long int ,ltstr> Name; -+typedef std::map<const char*,long long int ,ltstr> Name; - - - typedef struct Fragment { ---- a/src/lagan2mfa.cpp -+++ b/src/lagan2mfa.cpp -@@ -6,7 +6,6 @@ - #include <stdlib.h> - #include <stdio.h> - --using namespace std; - - // TODO refactor in classes and normal make project - ---- a/src/makecons.cpp -+++ b/src/makecons.cpp -@@ -18,7 +18,6 @@ - #include <ctype.h> - #include <time.h> - --using namespace std; - - #define fastaRowLength 50 - #define bufSize 2000 ---- a/src/utils/Glue.cpp -+++ b/src/utils/Glue.cpp -@@ -170,7 +170,7 @@ - } - - void printCoordinates (int seq, int begin, int end){ -- cout << seqs[seq].getID() << ":" << getSeqCoord(seq, begin) << "-" << getSeqCoord(seq, end) << " "; -+ std::cout << seqs[seq].getID() << ":" << getSeqCoord(seq, begin) << "-" << getSeqCoord(seq, end) << " "; - } - - int printRegion (int begin, int end){ -@@ -183,7 +183,7 @@ - score += rescoreRegion (seqs[i], seqs[j], begin, end); - } - } -- cout << score << endl; -+ std::cout << score << std::endl; - return score; - } - -@@ -223,7 +223,7 @@ - } - } - -- cout << "= score=" << score << endl; -+ std::cout << "= score=" << score << std::endl; - } - - int countLets (SafeVector<char> &data){ -@@ -355,7 +355,7 @@ - FILE* outfile; - - if (argc < 2 || argc > 3){ -- cerr << "Usage: Glue align.mfa \n" << endl; -+ std::cerr << "Usage: Glue align.mfa \n" << std::endl; - exit (1); - } - -@@ -375,7 +375,7 @@ - SafeVector<int> merged1label, merged2label; - int begin1 = 1, end1 = 1; - -- ifstream data (argv[1]); -+ std::ifstream data (argv[1]); - int alignNum = 0; - strand.push_back ('?'); // nothing for alignNum 0 - -@@ -452,7 +452,7 @@ - SafeVector<char> temp1 (begin1 - 1, 'N'); - SafeVector<char> temp2 (begin1 - 1, '-'); - -- for (int i = 0; i < min ((int) temp2.size(), CNTG_BRK_N); i++) -+ for (int i = 0; i < std::min ((int) temp2.size(), CNTG_BRK_N); i++) - temp2[i] = 'N'; - - merged1 = merge (temp1, merged1); -@@ -471,12 +471,12 @@ - if (isalpha(merged2[j])) pos2++; - - if (merged1label[j] == i){ -- min1 = min (min1, pos1); -- max1 = max (max1, pos1); -+ min1 = std::min (min1, pos1); -+ max1 = std::max (max1, pos1); - } - if (merged2label[j] == i){ -- min2 = min (min2, pos2); -- max2 = max (max2, pos2); -+ min2 = std::min (min2, pos2); -+ max2 = std::max (max2, pos2); - } - } - -@@ -489,6 +489,6 @@ - fprintf (outfile, "%d %d %d 0 0 0 0 %c 0 %d %d\n", i, min1, max1, strand[i], min2, max2); - } - -- printMFA (cout, merged1, string ("first"), 60); -- printMFA (cout, merged2, string ("second"), 60); -+ printMFA (std::cout, merged1, std::string ("first"), 60); -+ printMFA (std::cout, merged2, std::string ("second"), 60); - } ---- a/src/utils/MultiSequence.h -+++ b/src/utils/MultiSequence.h -@@ -12,7 +12,6 @@ - #include "Sequence.h" - #include "SafeVector.h" - --using namespace std; - - class MultiSequence { - private: -@@ -54,10 +53,10 @@ - - // Read in all of the Sequences in an MFA file and append them to the - // existing MultiSequence object. -- void addRawFromMFA (const string& filename){ -+ void addRawFromMFA (const std::string& filename){ - - // open up file for reading -- ifstream infile (filename.c_str()); -+ std::ifstream infile (filename.c_str()); - - // check for error - assert (!infile.fail()); -@@ -75,7 +74,7 @@ - - // Read in all of the Sequences in an MFA file and append them to the - // existing MultiSequence object. -- void addRawFromMFA (ifstream &infile){ -+ void addRawFromMFA (std::ifstream &infile){ - - // check for error - assert (!infile.fail()); -@@ -89,7 +88,7 @@ - } - - // Writes sequences to outfile in XMFA format. -- void writeToXMFA (ostream &outfile, int numColumns) const { -+ void writeToXMFA (std::ostream &outfile, int numColumns) const { - for (int i = 0; i < (int) sequences.size(); ++i){ - sequences[i].writeToXMFA (outfile, numColumns); - } ---- a/src/utils/Output.h -+++ b/src/utils/Output.h -@@ -2,18 +2,18 @@ - #define OUTPUT_H - - // print reversed string in MFA format --void printMFA (ostream &outfile, SafeVector<char> &data, string comment, int numColumns){ -+void printMFA (std::ostream &outfile, SafeVector<char> &data, std::string comment, int numColumns){ - - int charsWritten = 0; - -- outfile << ">" << comment << endl; -+ outfile << ">" << comment << std::endl; - for (int i = 0; i < (int) data.size(); i++){ - outfile << data[i]; - charsWritten++; -- if (charsWritten % numColumns == 0) outfile << endl; -+ if (charsWritten % numColumns == 0) outfile << std::endl; - } - -- if (charsWritten % numColumns != 0) outfile << endl; -+ if (charsWritten % numColumns != 0) outfile << std::endl; - } - - ---- a/src/utils/SafeVector.h -+++ b/src/utils/SafeVector.h -@@ -10,7 +10,6 @@ - #include <assert.h> - #include <vector> - --using namespace std; - - // class derived from the STL std::vector - template<class TYPE> -@@ -19,9 +18,9 @@ - - // miscellaneous constructors - SafeVector () {} -- SafeVector (size_t size) : vector<TYPE>(size) {} -- SafeVector (size_t size, const TYPE &value) : vector<TYPE>(size, value) {} -- SafeVector (const SafeVector &source) : vector<TYPE>(source) {} -+ SafeVector (size_t size) : std::vector<TYPE>(size) {} -+ SafeVector (size_t size, const TYPE &value) : std::vector<TYPE>(size, value) {} -+ SafeVector (const SafeVector &source) : std::vector<TYPE>(source) {} - - #ifdef ENABLE_CHECKS - ---- a/src/utils/Sequence.h -+++ b/src/utils/Sequence.h -@@ -8,15 +8,14 @@ - #include <string> - #include "SafeVector.h" - --using namespace std; - - class Sequence { - - private: - - // Read header of MFA/XMFA file. -- bool readHeader (ifstream &infile, bool &isXMFA){ -- string header; -+ bool readHeader (std::ifstream &infile, bool &isXMFA){ -+ std::string header; - - while (true){ - -@@ -24,7 +23,7 @@ - if (infile.fail() || infile.eof()) return false; - - // get new header line -- getline (infile, header); -+ std::getline (infile, header); - - // check that header line is not empty - if (header.length() != 0) break; -@@ -64,7 +63,7 @@ - int startCoord; // sequence position of first character - int endCoord; // sequence position of last character - char direction; // + or - -- string comment; // comments -+ std::string comment; // comments - - public: - -@@ -77,7 +76,7 @@ - } - - // Constructor. Reads in a sequence from the input file. -- Sequence (ifstream &infile){ -+ Sequence (std::ifstream &infile){ - - bool isXMFA = true; - -@@ -147,7 +146,7 @@ - } - - // Constructor. Gets sequence from array data. -- Sequence (SafeVector<char> data, string comment) : data(data), comment(comment) { -+ Sequence (SafeVector<char> data, std::string comment) : data(data), comment(comment) { - length = data.size() - 1; - id = 0; - startCoord = 1; -@@ -165,7 +164,7 @@ - return temp; - } - -- const string getComment () const { -+ const std::string getComment () const { - return comment; - } - -@@ -197,9 +196,9 @@ - const int getEndCoord () const { assert (isValid); return endCoord; } - - // Print XMFA header only. -- void writeXMFAHeader (ostream &outfile) const { -+ void writeXMFAHeader (std::ostream &outfile) const { - assert (isValid); -- outfile << '>' << id << ':' << startCoord << '-' << endCoord << ' ' << direction << ' ' << comment << endl; -+ outfile << '>' << id << ':' << startCoord << '-' << endCoord << ' ' << direction << ' ' << comment << std::endl; - } - - // Return sequence ID. -@@ -209,20 +208,20 @@ - void setID (int id) { assert (isValid); this->id = id; } - - // Writes sequence to XMFA format. -- void writeToXMFA (ostream &outfile, int numColumns) const { -+ void writeToXMFA (std::ostream &outfile, int numColumns) const { - - assert (isValid); - - // print XMFA header -- outfile << ">" << comment << endl; -+ outfile << ">" << comment << std::endl; - // outfile << '>' << id << ':' << startCoord << '-' << endCoord << ' ' << direction << ' ' << comment << endl; - - // print character data - for (int i = 1; i <= length; ++i){ - outfile << data[i]; -- if (i % numColumns == 0) outfile << endl; -+ if (i % numColumns == 0) outfile << std::endl; - } -- if (length % numColumns != 0) outfile << endl; -+ if (length % numColumns != 0) outfile << std::endl; - } - }; - diff --git a/sci-biology/lagan/files/lagan-2.0-gcc-10.patch b/sci-biology/lagan/files/lagan-2.0-gcc-10.patch new file mode 100644 index 000000000000..bd9824cf2ed0 --- /dev/null +++ b/sci-biology/lagan/files/lagan-2.0-gcc-10.patch @@ -0,0 +1,27 @@ +Description: Add patch to build with GCC-10 +Bug-Debian: https://bugs.debian.org/957415 +Author: Nilesh Patra <npatra974@gmail.com> +Date: Fri Apr 17 21:13:21 2020 +0530 + +--- a/src/fchaos.c ++++ b/src/fchaos.c +@@ -29,7 +29,7 @@ + int offset; + } match; + +-extern int indeces[256]; ++int indeces[256]; + + + void remElem(LList* tbf, int i); +--- a/src/thrtrie.h ++++ b/src/thrtrie.h +@@ -2,7 +2,7 @@ + #define MAX_DEGEN 2 + + +-int indeces[256]; ++extern int indeces[256]; + + typedef struct PrevHits { + int* inds1; diff --git a/sci-biology/lagan/files/lagan-2.0-gcc-4.8.patch b/sci-biology/lagan/files/lagan-2.0-gcc-4.8.patch new file mode 100644 index 000000000000..3d7ed780445f --- /dev/null +++ b/sci-biology/lagan/files/lagan-2.0-gcc-4.8.patch @@ -0,0 +1,25 @@ +Author: Andreas Tille <tille@debian.org> +LastChanged: Fri, 15 Nov 2013 10:31:20 +0100 +Description: Fix some includes to build using gcc-4.8 + +--- a/src/utils/Glue.cpp ++++ b/src/utils/Glue.cpp +@@ -6,6 +6,7 @@ + #include <fstream> + #include <iostream> + #include <algorithm> ++#include <string.h> + + #define NUCLEOTIDE_MATRIX_FILE "nucmatrix.txt" + #define MAX_LINE_LENGTH 1024 +--- a/src/glocal/score.cpp ++++ b/src/glocal/score.cpp +@@ -2,7 +2,7 @@ + #include<score.h> + #include<leftinfluence.h> + #include<rightinfluence.h> +-#include<fstream.h> ++#include<fstream> + + extern vector<class Score*> scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)]; + diff --git a/sci-biology/lagan/files/lagan-2.0-gcc-9.patch b/sci-biology/lagan/files/lagan-2.0-gcc-9.patch new file mode 100644 index 000000000000..6ea30e57a854 --- /dev/null +++ b/sci-biology/lagan/files/lagan-2.0-gcc-9.patch @@ -0,0 +1,25 @@ +# Two patches to bring lagan up to speed with gcc-9 +Index: lagan/src/fchaos.c +=================================================================== +--- lagan.orig/src/fchaos.c ++++ lagan/src/fchaos.c +@@ -430,7 +430,7 @@ int chain(LList* second, int off2, LList + int tc =0; + int wc = 0; + +-inline void findPrev(LList* curr, int position, int offset, float baseval) { ++void findPrev(LList* curr, int position, int offset, float baseval) { + int j,k; + LList* temp; + sle* iterator; +Index: lagan/src/filebuffer.c +=================================================================== +--- lagan.orig/src/filebuffer.c ++++ lagan/src/filebuffer.c +@@ -1,5 +1,6 @@ + #include "filebuffer.h" + #include <stdlib.h> ++#include <ctype.h> + #include <string.h> + #include <stdio.h> + #include <assert.h> diff --git a/sci-biology/lagan/files/lagan-2.0-gcc4.3.patch b/sci-biology/lagan/files/lagan-2.0-gcc4.3.patch deleted file mode 100644 index a4b1d6808e2f..000000000000 --- a/sci-biology/lagan/files/lagan-2.0-gcc4.3.patch +++ /dev/null @@ -1,23 +0,0 @@ -diff -durr lagan20-orig/src/glocal/score.cpp lagan20/src/glocal/score.cpp ---- lagan20-orig/src/glocal/score.cpp 2009-02-04 15:25:57.698333297 +0000 -+++ lagan20/src/glocal/score.cpp 2009-02-04 15:27:23.894092890 +0000 -@@ -2,7 +2,7 @@ - #include<score.h> - #include<leftinfluence.h> - #include<rightinfluence.h> --#include<fstream.h> -+#include<fstream> - - extern vector<class Score*> scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)]; - -diff -durr lagan20-orig/src/utils/Glue.cpp lagan20/src/utils/Glue.cpp ---- lagan20-orig/src/utils/Glue.cpp 2009-02-04 15:25:57.702333182 +0000 -+++ lagan20/src/utils/Glue.cpp 2009-02-04 15:27:04.190822654 +0000 -@@ -1,6 +1,7 @@ - #include "MultiSequence.h" - #include "SafeVector.h" - #include "Output.h" -+#include <string.h> - #include <math.h> - #include <assert.h> - #include <fstream> diff --git a/sci-biology/lagan/files/lagan-2.0-flags.patch b/sci-biology/lagan/files/lagan-2.0-makefile.patch index e324ef64c4c6..1bef6721ab9b 100644 --- a/sci-biology/lagan/files/lagan-2.0-flags.patch +++ b/sci-biology/lagan/files/lagan-2.0-makefile.patch @@ -1,107 +1,120 @@ -diff --git a/Makefile b/Makefile -index fbbbe79..a1d449b 100644 --- a/Makefile +++ b/Makefile -@@ -1,5 +1,5 @@ +@@ -1,5 +1,8 @@ all: - (cd src; $(MAKE)) + $(MAKE) -C src clean: rm -f chaos anchors order glocal utils/bin2bl mlagan utils/cstat utils/bin2mf utils/rc *~ utils/contigorder utils/getbounds utils/cextract utils/seqmerge utils/getlength utils/getoverlap utils/*~ utils/scorealign utils/scorecontigs mlagan.purify utils/getcontigpos utils/fa2xfa utils/Glue utils/dotplot utils/overlay - (cd src; $(MAKE) clean) -diff --git a/src/Makefile b/src/Makefile -index 7f6b6fd..dd6309b 100644 +- (cd src; $(MAKE) clean) ++ $(MAKE) -C src clean ++ ++check: all ++ (LAGAN_DIR="." ./mlagan -h || true) | grep -q version && echo "[ok]" || echo "[fail]" +--- a/src/glocal/Makefile ++++ b/src/glocal/Makefile +@@ -1,19 +1,13 @@ +-CC = g++ +-OPTFLAGS = +-CFLAGS = $(OPTFLAGS) -O3 +-CLINKER = g++ +-# LIBDIR = -L/usr/local/lib ++CXXFLAGS += -Wno-deprecated ++CPPFLAGS += -I./ ++ + MLIB = -lm +-INCDIR = -I./ + TRGT_DIR = ../.. + TRGT = glocal + OBJECTS = glocal.o io.o rightinfluence.o leftinfluence.o score.o + +-.cpp.o: +- $(CC) -Wno-deprecated $(CFLAGS) $(INCDIR) -c $*.cpp +- + $(TRGT): $(OBJECTS) +- $(CLINKER) $(OPTFLAGS) $(OBJECTS) -o $(TRGT_DIR)/$(TRGT) $(MLIB) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) $(OBJECTS) -o $(TRGT_DIR)/$(TRGT) $(MLIB) + + clean : + rm -f *.o ./*~ *~ core --- a/src/Makefile +++ b/src/Makefile -@@ -4,51 +4,51 @@ CFLAGS = -O3 # -Wall -W +@@ -1,54 +1,51 @@ +-CC = gcc $(CFLAGS) +-CPP = g++ $(CFLAGS) +-CFLAGS = -O3 # -Wall -W TRGT_DIR = .. all: ../anchors ../chaos ../order ../mlagan ../prolagan ../utils/bin2mf ../utils/bin2bl ../utils/cextract ../utils/cstat ../utils/contigorder ../utils/getbounds ../utils/getlength ../utils/getoverlap ../utils/rc ../utils/seqmerge ../utils/scorealign ../utils/scorecontigs ../utils/getcontigpos ../utils/fa2xfa ../utils/Glue ../utils/dotplot ../utils/overlay - (cd glocal; $(MAKE)) -+ $(MAKE) -C glocal ++ (cd glocal && $(MAKE)) clean: rm -f *.o *~ utils/*~ mlagan.purify core - (cd glocal; $(MAKE) clean) +- (cd glocal; $(MAKE) clean) ++ (cd glocal && $(MAKE) clean) ../anchors: anchors.c skiplist.c - $(CC) -o $(TRGT_DIR)/anchors anchors.c skiplist.c -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/anchors anchors.c skiplist.c ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/anchors anchors.c skiplist.c ../chaos: fchaos.c thrtrie.c skiplist.c global.c translate.c mempage.c filebuffer.c - $(CC) -o $(TRGT_DIR)/chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG ../order: order.c diagmatrix.c filebuffer.c - $(CC) -o $(TRGT_DIR)/order order.c diagmatrix.c filebuffer.c -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/order order.c diagmatrix.c filebuffer.c ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/order order.c diagmatrix.c filebuffer.c ../mlagan: mlagan.c diagmatrix.c multial.c skiplist.c filebuffer.c - $(CC) -o $(TRGT_DIR)/mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG ../prolagan: prolagan.c diagmatrix.c multial.c skiplist.c filebuffer.c - $(CC) -o $(TRGT_DIR)/prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG ../utils/bin2mf: utils/bin2mf.c - $(CC) -o $(TRGT_DIR)/utils/bin2mf utils/bin2mf.c -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/bin2mf utils/bin2mf.c ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/bin2mf utils/bin2mf.c ../utils/bin2bl: utils/bin2bl.c - $(CC) -o $(TRGT_DIR)/utils/bin2bl utils/bin2bl.c -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/bin2bl utils/bin2bl.c ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/bin2bl utils/bin2bl.c ../utils/cextract: utils/cextract.c - $(CC) -o $(TRGT_DIR)/utils/cextract utils/cextract.c -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/cextract utils/cextract.c ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/cextract utils/cextract.c ../utils/cstat: utils/cstat.c - $(CC) -o $(TRGT_DIR)/utils/cstat utils/cstat.c -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/cstat utils/cstat.c ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/cstat utils/cstat.c ../utils/contigorder: utils/contigorder.c - $(CC) -o $(TRGT_DIR)/utils/contigorder utils/contigorder.c -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/contigorder utils/contigorder.c ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/contigorder utils/contigorder.c ../utils/getbounds: utils/getbounds.c - $(CC) -o $(TRGT_DIR)/utils/getbounds utils/getbounds.c -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getbounds utils/getbounds.c ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getbounds utils/getbounds.c ../utils/getcontigpos: utils/getcontigpos.c - $(CC) -o $(TRGT_DIR)/utils/getcontigpos utils/getcontigpos.c -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getcontigpos utils/getcontigpos.c ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getcontigpos utils/getcontigpos.c ../utils/getlength: utils/getlength.c - $(CC) -o $(TRGT_DIR)/utils/getlength utils/getlength.c -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getlength utils/getlength.c ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getlength utils/getlength.c ../utils/getoverlap: utils/getoverlap.c - $(CC) -o $(TRGT_DIR)/utils/getoverlap utils/getoverlap.c -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getoverlap utils/getoverlap.c ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getoverlap utils/getoverlap.c ../utils/rc: utils/rc.c - $(CC) -o $(TRGT_DIR)/utils/rc utils/rc.c -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/rc utils/rc.c ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/rc utils/rc.c ../utils/seqmerge: utils/seqmerge.c - $(CC) -o $(TRGT_DIR)/utils/seqmerge utils/seqmerge.c -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/seqmerge utils/seqmerge.c ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/seqmerge utils/seqmerge.c ../utils/scorealign: utils/scorealign.c - $(CC) -o $(TRGT_DIR)/utils/scorealign utils/scorealign.c -lm -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/scorealign utils/scorealign.c -lm ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/scorealign utils/scorealign.c -lm ../utils/scorecontigs: utils/scorecontigs.c - $(CC) -o $(TRGT_DIR)/utils/scorecontigs utils/scorecontigs.c -lm -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/scorecontigs utils/scorecontigs.c -lm ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/scorecontigs utils/scorecontigs.c -lm ../utils/fa2xfa: utils/fa2xfa.c - $(CC) -o $(TRGT_DIR)/utils/fa2xfa utils/fa2xfa.c -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/fa2xfa utils/fa2xfa.c ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/fa2xfa utils/fa2xfa.c ../utils/overlay: utils/overlay.c - $(CC) -o $(TRGT_DIR)/utils/overlay utils/overlay.c -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/overlay utils/overlay.c ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/overlay utils/overlay.c ../utils/Glue: utils/Glue.cpp - $(CPP) -o $(TRGT_DIR)/utils/Glue utils/Glue.cpp -+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/Glue utils/Glue.cpp ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/Glue utils/Glue.cpp ../utils/dotplot: utils/dotplot.cpp - $(CPP) -o $(TRGT_DIR)/utils/dotplot utils/dotplot.cpp -+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/dotplot utils/dotplot.cpp -diff --git a/src/glocal/Makefile b/src/glocal/Makefile -index ce1421a..b82507f 100755 ---- a/src/glocal/Makefile -+++ b/src/glocal/Makefile -@@ -10,10 +10,10 @@ TRGT = glocal - OBJECTS = glocal.o io.o rightinfluence.o leftinfluence.o score.o - - .cpp.o: -- $(CC) -Wno-deprecated $(CFLAGS) $(INCDIR) -c $*.cpp -+ $(CXX) $(CXXFLAGS) $(INCDIR) -c $*.cpp - - $(TRGT): $(OBJECTS) -- $(CLINKER) $(OPTFLAGS) $(OBJECTS) -o $(TRGT_DIR)/$(TRGT) $(MLIB) -+ $(CXX) $(LDFLAGS) $(OBJECTS) -o $(TRGT_DIR)/$(TRGT) $(MLIB) - - clean : - rm -f *.o ./*~ *~ core ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/dotplot utils/dotplot.cpp diff --git a/sci-biology/lagan/files/lagan-2.0-qa-implicit-declarations.patch b/sci-biology/lagan/files/lagan-2.0-qa-implicit-declarations.patch index 4ba4ce49d770..29db043d5f34 100644 --- a/sci-biology/lagan/files/lagan-2.0-qa-implicit-declarations.patch +++ b/sci-biology/lagan/files/lagan-2.0-qa-implicit-declarations.patch @@ -1,69 +1,34 @@ -Fix QA warnings due to implicit declarations: -* filebuffer.c:123:34: warning: implicit declaration of function ‘toupper’ [-Wimplicit-function-declaration] -* temp[i] = (strchr (alphabet, toupper ((char) i)) != 0) ? - ---- a/src/filebuffer.c -+++ b/src/filebuffer.c -@@ -3,6 +3,7 @@ - #include <string.h> - #include <stdio.h> - #include <assert.h> -+#include <ctype.h> - - #ifdef CHAOS__FLAG - char* alphabet = "ATCGNPCMHDEKRQSILVFYWX*"; --- a/src/mlagan.c +++ b/src/mlagan.c -@@ -934,6 +934,7 @@ - return k; +@@ -46,6 +46,7 @@ + return 1; } +int printXMFAAlign(FILE* outfile, align* myalign); - int main(int argc, char** argv) { - FileBuffer seqfile; + void usage(void) { + printf("mlagan seqfile_1 seqfile_2 [... seqfile_%d] [-parameters]\n\n", --- a/src/order.c +++ b/src/order.c -@@ -398,6 +398,9 @@ - free(ends); - } +@@ -28,6 +28,8 @@ + + align* makeAlign(dmat* mydm, char* seq1, char* seq2); +int printMFAAlign(char* seq1, char* seq2, align* myalign, char* n1, char* n2); +int printXMFAAlign(char* seq1, char* seq2, align* myalign, char* n1, char* n2); -+ - void doAlign(dmat* mydm, seq* seq1, seq* seq2) { - align *a = (align*) makeAlign(mydm, seq1->lets, seq2->lets); - // printf("into printing\n"); + + char* alpha = "ATCGN."; + --- a/src/prolagan.c +++ b/src/prolagan.c -@@ -949,6 +949,7 @@ - return k; +@@ -49,6 +49,7 @@ + return 1; } +int printXMFAAlign(FILE* outfile, align* myalign); - int main(int argc, char** argv) { - FileBuffer seqfile; ---- a/src/utils/contigorder.c -+++ b/src/utils/contigorder.c -@@ -12,7 +12,7 @@ - int dummy, i; - - if (!(file = fopen (filename, "r"))){ -- fprintf (stderr, "contigorder: Error opening file: %s\n"); -+ fprintf (stderr, "contigorder: Error opening file: %s\n", filename); - exit (1); - } - -@@ -49,7 +49,7 @@ - } - - if (!(file = fopen (filename, "r"))){ -- fprintf (stderr, "contigorder: Error opening file: %s\n"); -+ fprintf (stderr, "contigorder: Error opening file: %s\n", filename); - exit (1); - } - + void usage(void) { + printf("mlagan seqfile_1 seqfile_2 [... seqfile_%d] [-parameters]\n\n", --- a/src/utils/cstat.c +++ b/src/utils/cstat.c @@ -3,6 +3,7 @@ diff --git a/sci-biology/lagan/lagan-2.0-r3.ebuild b/sci-biology/lagan/lagan-2.0-r3.ebuild deleted file mode 100644 index e326331e09fb..000000000000 --- a/sci-biology/lagan/lagan-2.0-r3.ebuild +++ /dev/null @@ -1,71 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit toolchain-funcs - -MY_P="lagan20" - -DESCRIPTION="The LAGAN suite of tools for whole-genome multiple alignment of genomic DNA" -HOMEPAGE="http://lagan.stanford.edu/lagan_web/index.shtml" -SRC_URI="http://lagan.stanford.edu/lagan_web/${MY_P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -IUSE="" -KEYWORDS="~amd64 ~x86" - -RDEPEND="dev-lang/perl" - -S="${WORKDIR}/${MY_P}" - -PATCHES=( - "${FILESDIR}/${PN}-2.0-flags.patch" - "${FILESDIR}/${PN}-2.0-gcc4.3.patch" - "${FILESDIR}/${PN}-2.0-fix-c++14.patch" - "${FILESDIR}/${PN}-2.0-qa-implicit-declarations.patch" -) - -src_prepare() { - sed -i "/use Getopt::Long;/ i use lib \"/usr/$(get_libdir)/${PN}/lib\";" "${S}/supermap.pl" || die - # NB: Testing with glibc-2.10 has uncovered a bug in src/utils/Sequence.h - # where libc getline is erroneously used instead of own getline - sed -i 's/getline/my_getline/' "${S}"/src/{anchors.c,glocal/io.cpp} || die - - default -} - -src_compile() { - emake \ - CC=$(tc-getCC) \ - CXX=$(tc-getCXX) \ - CXXFLAGS="${CXXFLAGS}" \ - CFLAGS="${CFLAGS}" -} - -src_install() { - newbin lagan.pl lagan - newbin slagan.pl slagan - dobin mlagan - rm -f lagan.pl slagan.pl utils/Utils.pm || die - - insinto /usr/$(get_libdir)/${PN}/lib - doins Utils.pm - - exeinto /usr/$(get_libdir)/${PN}/utils - doexe utils/* - - exeinto /usr/$(get_libdir)/${PN} - doexe *.pl anchors chaos glocal order prolagan - - insinto /usr/$(get_libdir)/${PN} - doins *.txt - - dosym /usr/$(get_libdir)/${PN}/supermap.pl /usr/bin/supermap - - echo "LAGAN_DIR=\"/usr/$(get_libdir)/${PN}\"" > 99${PN} || die - doenvd 99${PN} - - dodoc Readmes/README.* -} diff --git a/sci-biology/lagan/lagan-2.0-r4.ebuild b/sci-biology/lagan/lagan-2.0-r4.ebuild new file mode 100644 index 000000000000..4582d8f1078e --- /dev/null +++ b/sci-biology/lagan/lagan-2.0-r4.ebuild @@ -0,0 +1,67 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +inherit toolchain-funcs + +MY_P="lagan20" + +DESCRIPTION="The LAGAN suite of tools for whole-genome multiple alignment of genomic DNA" +HOMEPAGE="http://lagan.stanford.edu/lagan_web/index.shtml" +SRC_URI="http://lagan.stanford.edu/lagan_web/${MY_P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND="dev-lang/perl" + +S="${WORKDIR}/${MY_P}" +PATCHES=( + "${FILESDIR}"/${P}-makefile.patch + "${FILESDIR}"/${P}-conflicting-getline.patch + "${FILESDIR}"/${P}-gcc-4.8.patch + "${FILESDIR}"/${P}-ambiguous-end.patch + "${FILESDIR}"/${P}-gcc-9.patch + "${FILESDIR}"/${P}-gcc-10.patch + "${FILESDIR}"/${P}-C99-static-inline.patch + "${FILESDIR}"/${P}-qa-implicit-declarations.patch +) + +src_prepare() { + default + sed -i "/use Getopt::Long;/ i use lib \"/usr/$(get_libdir)/lagan/lib\";" \ + supermap.pl || die +} + +src_configure() { + tc-export CC CXX +} + +src_install() { + newbin lagan.pl lagan + newbin slagan.pl slagan + dobin mlagan + rm lagan.pl slagan.pl utils/Utils.pm || die + + insinto /usr/$(get_libdir)/lagan/lib + doins Utils.pm + + exeinto /usr/$(get_libdir)/lagan/utils + doexe utils/* + + exeinto /usr/$(get_libdir)/lagan + doexe *.pl anchors chaos glocal order prolagan + + insinto /usr/$(get_libdir)/lagan + doins *.txt + + dosym ../$(get_libdir)/lagan/supermap.pl /usr/bin/supermap + + newenvd - 99lagan <<- _EOF_ + LAGAN_DIR="${EPREFIX}/usr/$(get_libdir)/lagan" + _EOF_ + + dodoc Readmes/README.* +} diff --git a/sci-biology/lagan/metadata.xml b/sci-biology/lagan/metadata.xml index 959160fe46b1..ccdff086e20b 100644 --- a/sci-biology/lagan/metadata.xml +++ b/sci-biology/lagan/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/last/Manifest b/sci-biology/last/Manifest deleted file mode 100644 index 22e3590e9d28..000000000000 --- a/sci-biology/last/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST last-299.zip 453159 BLAKE2B 3f8ddc24a2eba189880f2547f458ebbc2b349f0517c25165257f4cf3a90f68d8df313f7eece3930c33376aa0e16185c54b586b6f411975a1fb15e6426c535ca0 SHA512 74e89129cc17482ec1a99e2d940ca62374c130fea2fa53ea7d2c3703b6ca5751f348110909d61562c4839d8fb1793619c2f41c25c8968b3ab53f0c7191f4a00b diff --git a/sci-biology/last/files/last-299-fix-build-system.patch b/sci-biology/last/files/last-299-fix-build-system.patch deleted file mode 100644 index 0a89cea60278..000000000000 --- a/sci-biology/last/files/last-299-fix-build-system.patch +++ /dev/null @@ -1,74 +0,0 @@ -Make build system respect user flags - ---- a/makefile -+++ b/makefile -@@ -1,6 +1,5 @@ --CXXFLAGS = -O3 - all: -- @cd src && $(MAKE) CXXFLAGS="$(CXXFLAGS)" -+ $(MAKE) -C src - - prefix = /usr/local - exec_prefix = $(prefix) -@@ -10,15 +9,15 @@ - cp src/last?? scripts/*.?? $(bindir) - - clean: -- @cd src && $(MAKE) clean -+ $(MAKE) -C src clean - - html: -- @cd doc && $(MAKE) -+ $(MAKE) -C doc - - distdir = last-`hg id -n` - - dist: log html -- @cd src && $(MAKE) version.hh -+ $(MAKE) -C src version.hh - rsync -rC --exclude 'last??' doc examples makefile s* *.txt $(distdir) - zip -qrm $(distdir) $(distdir) - ---- a/src/makefile -+++ b/src/makefile -@@ -1,12 +1,9 @@ --CXX = g++ --CC = gcc -- --CXXFLAGS = -O3 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef \ ---Wcast-align -Wno-long-long -ansi -pedantic -+last_CXXFLAGS = -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef \ -+-Wcast-align -Wno-long-long -pedantic - # -Wconversion - # -fomit-frame-pointer ? - --CFLAGS = -Wall -+last_CFLAGS = -Wall - - DBSRC = Alphabet.cc MultiSequence.cc CyclicSubsetSeed.cc \ - SubsetSuffixArray.cc LastdbArguments.cc io.cc fileMap.cc \ -@@ -49,17 +46,20 @@ - - all: lastdb lastal lastex - -+.cpp.o: -+ $(CXX) $(CPPFLAGS) $(last_CXXFLAGS) $(CXXFLAGS) -c -o $@ $< -+ - lastdb: $(DBSRC) $(DBINC) makefile -- $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(DBSRC) -+ $(CXX) $(CPPFLAGS) $(last_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(DBSRC) - - lastal: $(ALSRC) $(ALINC) makefile $(OBJ) -- $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(ALSRC) $(OBJ) -+ $(CXX) $(CPPFLAGS) $(last_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(ALSRC) $(OBJ) - - lastex: $(EXSRC) $(EXINC) makefile -- $(CXX) -Igumbel_params $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(EXSRC) -+ $(CXX) $(CPPFLAGS) -Igumbel_params $(last_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(EXSRC) - - $(OBJ): CA_code/*.c CA_code/*.h makefile -- $(CC) $(CPPFLAGS) $(CFLAGS) -c CA_code/lambda_calculator.c -+ $(CC) $(CPPFLAGS) $(last_CFLAGS) $(CFLAGS) -c -o $@ CA_code/lambda_calculator.c - - clean: - rm -f lastdb lastal lastex $(OBJ) diff --git a/sci-biology/last/files/last-299-portable-shebangs.patch b/sci-biology/last/files/last-299-portable-shebangs.patch deleted file mode 100644 index 03ecbdcbde20..000000000000 --- a/sci-biology/last/files/last-299-portable-shebangs.patch +++ /dev/null @@ -1,99 +0,0 @@ -Make shebangs portable and prefix friendly -See also: https://blogs.gentoo.org/mgorny/2016/02/08/a-quick-note-on-portable-shebangs/ - ---- a/scripts/last-dotplot.py -+++ b/scripts/last-dotplot.py -@@ -1,4 +1,4 @@ --#! /usr/bin/env python -+#!/usr/bin/env python2 - - # Read pair-wise alignments in MAF or LAST tabular format: write an - # "Oxford grid", a.k.a. dotplot. ---- a/scripts/last-map-probs.py -+++ b/scripts/last-map-probs.py -@@ -1,4 +1,4 @@ --#! /usr/bin/env python -+#!/usr/bin/env python2 - - # Copyright 2010, 2011, 2012 Martin C. Frith - ---- a/scripts/last-merge-batches.py -+++ b/scripts/last-merge-batches.py -@@ -1,4 +1,4 @@ --#! /usr/bin/env python -+#!/usr/bin/env python2 - - # Copyright 2010, 2011 Martin C. Frith - ---- a/scripts/last-pair-probs.py -+++ b/scripts/last-pair-probs.py -@@ -1,4 +1,4 @@ --#! /usr/bin/env python -+#!/usr/bin/env python2 - - # Copyright 2011, 2012, 2013 Martin C. Frith - ---- a/scripts/last-reduce-alignments.sh -+++ b/scripts/last-reduce-alignments.sh -@@ -1,4 +1,4 @@ --#! /bin/sh -+#!/usr/bin/env sh - - # This script reads MAF-format alignments with lastal header - # information, removes "uninteresting" alignments, and writes the ---- a/scripts/last-remove-dominated.py -+++ b/scripts/last-remove-dominated.py -@@ -1,4 +1,4 @@ --#! /usr/bin/env python -+#!/usr/bin/env python2 - - # Read MAF-format alignments, and write those are not "dominated" by - # any other one. X dominates Y if they overlap on the top sequence, ---- a/scripts/last-split-probs.py -+++ b/scripts/last-split-probs.py -@@ -1,4 +1,4 @@ --#! /usr/bin/env python -+#!/usr/bin/env python2 - - # Copyright 2012 Martin C. Frith - ---- a/scripts/maf-convert.py -+++ b/scripts/maf-convert.py -@@ -1,4 +1,4 @@ --#! /usr/bin/env python -+#!/usr/bin/env python2 - # Copyright 2010, 2011 Martin C. Frith - # Read MAF-format alignments: write them in other formats. - # Seems to work with Python 2.x, x>=4 ---- a/scripts/maf-cull.py -+++ b/scripts/maf-cull.py -@@ -1,4 +1,4 @@ --#! /usr/bin/env python -+#!/usr/bin/env python2 - - # Read MAF-format alignments. Write them, omitting alignments whose - # coordinates in the top-most sequence are contained in those of >= ---- a/scripts/maf-join.py -+++ b/scripts/maf-join.py -@@ -1,4 +1,4 @@ --#! /usr/bin/env python -+#!/usr/bin/env python2 - - # Copyright 2009, 2010, 2011 Martin C. Frith - ---- a/scripts/maf-sort.sh -+++ b/scripts/maf-sort.sh -@@ -1,4 +1,4 @@ --#! /bin/sh -+#!/usr/bin/env sh - - # Sort MAF-format alignments by sequence name, then strand, then start - # position, then end position, of the top sequence. Also, merge ---- a/scripts/maf-swap.py -+++ b/scripts/maf-swap.py -@@ -1,4 +1,4 @@ --#! /usr/bin/env python -+#!/usr/bin/env python2 - - # Read MAF-format alignments, and write them, after moving the Nth - # sequence to the top in each alignment. diff --git a/sci-biology/last/last-299-r1.ebuild b/sci-biology/last/last-299-r1.ebuild deleted file mode 100644 index b6adee215970..000000000000 --- a/sci-biology/last/last-299-r1.ebuild +++ /dev/null @@ -1,45 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit toolchain-funcs python-single-r1 - -DESCRIPTION="Genome-scale comparison of biological sequences" -HOMEPAGE="http://last.cbrc.jp/" -SRC_URI="http://last.cbrc.jp/${P}.zip" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND="${PYTHON_DEPS}" -DEPEND="app-arch/unzip" - -PATCHES=( - "${FILESDIR}"/${PN}-299-fix-build-system.patch - "${FILESDIR}"/${PN}-299-portable-shebangs.patch -) - -src_configure() { - tc-export CC CXX -} - -src_install() { - local DOCS=( doc/*.txt ChangeLog.txt README.txt ) - local HTML_DOCS=( doc/*html ) - einstalldocs - - dobin src/last{al,db,ex} - - cd scripts || die - local i - for i in *py; do - newbin ${i} ${i%.py} - done - dobin *sh -} diff --git a/sci-biology/last/metadata.xml b/sci-biology/last/metadata.xml deleted file mode 100644 index 959160fe46b1..000000000000 --- a/sci-biology/last/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/libgtextutils/libgtextutils-0.6.1.ebuild b/sci-biology/libgtextutils/libgtextutils-0.6.1-r1.ebuild index 8f0455e5322c..2ffb1c3338b8 100644 --- a/sci-biology/libgtextutils/libgtextutils-0.6.1.ebuild +++ b/sci-biology/libgtextutils/libgtextutils-0.6.1-r1.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2018 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit autotools @@ -12,7 +12,6 @@ SRC_URI="http://hannonlab.cshl.edu/fastx_toolkit/${P}.tar.bz2" LICENSE="AGPL-3" SLOT="0/0" KEYWORDS="~amd64 ~x86" -IUSE="" PATCHES=( "${FILESDIR}"/${P}-fix-build-system.patch @@ -24,13 +23,8 @@ src_prepare() { eautoreconf } -src_configure() { - econf --disable-static -} - src_install() { default - # package installs .pc files - find "${D}" -name '*.la' -delete || die + find "${ED}" -name '*.la' -delete || die } diff --git a/sci-biology/libgtextutils/metadata.xml b/sci-biology/libgtextutils/metadata.xml index 138cb7705c0a..2de5d595743e 100644 --- a/sci-biology/libgtextutils/metadata.xml +++ b/sci-biology/libgtextutils/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> + <maintainer type="person" proxied="yes"> + <email>mmokrejs@gmail.com</email> <name>Martin Mokrejs</name> </maintainer> <maintainer type="project"> diff --git a/sci-biology/mafft/Manifest b/sci-biology/mafft/Manifest index 0cf407adadf0..1c8c429c954d 100644 --- a/sci-biology/mafft/Manifest +++ b/sci-biology/mafft/Manifest @@ -1,3 +1 @@ -DIST mafft-7.050-without-extensions-src.tgz 380375 BLAKE2B 86b5813c3cc9897a4f52e4dd3d7317d96b78e5f39530d1d5a34c3493965ba12f80e95fbecbc61a58738913132541a2b7265cd928327019dfdbeafcb10c060351 SHA512 ffddedcd03f37241b1493a62bf843eb23caa04089bd0182006aa7669f74de27204d324817e22fec1cb4ae11c4c226db5b725d03ba9f73b30a71ca3d38368d73e -DIST mafft-7.215-without-extensions-src.tgz 393239 BLAKE2B a8aad83a004d468c5723a15c20b30745f6edb47157d545622b0cb1904d8663d1ce64a1a4d067ce96a150e58bfacb90db933967ad4dda61f14f29b68bc1c4d4a4 SHA512 1a44b968e2f9ac9db5d17487163a38a7138dc784e63b3aa4082ff6a16c8e168edd09948e2cf182bc7a466802d4a07bdd7ab23386e251df13520acdfb69ebdada -DIST mafft-7.305-without-extensions-src.tgz 458448 BLAKE2B 5d5fa86e6faa472182c5c48f42056d81bbf545db56426969ff44a24146d4189a7650e85ea6e9fa8b40bb613392bf53bc5dea26012a86eb873c18bee91e6fdc41 SHA512 2aa351dd9b329024f183642cd98287239d12a00a2a65937e072560cba54925bed1fab19fafc734d9a5048ff85151560193ddb0796e0d7510d921fafc4553ebb9 +DIST mafft-7.490-without-extensions-src.tgz 605510 BLAKE2B f432ea3001f1d9c18cecea50d19f48570ffe7edf56e64088f8854acc1ee17fd7c1696244133f90ae0bf916f4499becfbfa8a770ca51a370219191f2a29f73db4 SHA512 dd87b731fdee48828da93c715ef480de474870de2fa42727e8d34b62bc136fb486dd9079ca2acdf1745f0a621fe4f413e25c05f7534f1673b6f9c1199ce70b8e diff --git a/sci-biology/mafft/files/mafft-7.037-respect.patch b/sci-biology/mafft/files/mafft-7.037-respect.patch deleted file mode 100644 index 6fba7153622d..000000000000 --- a/sci-biology/mafft/files/mafft-7.037-respect.patch +++ /dev/null @@ -1,217 +0,0 @@ - core/Makefile | 100 +++++++++++++++++++++++++++++----------------------------- - 1 file changed, 50 insertions(+), 50 deletions(-) - -diff --git a/core/Makefile b/core/Makefile -index 9acebb3..3838a45 100644 ---- a/core/Makefile -+++ b/core/Makefile -@@ -145,151 +145,151 @@ mltaln.h : functions.h - touch mltaln.h - - version : version.c mltaln.h -- $(CC) -o $@ version.c $(MYCFLAGS) -+ $(CC) $(LDFLAGS) -o $@ version.c $(MYCFLAGS) - - tbfast : $(OBJTBFAST) -- $(CC) -o $@ $(OBJTBFAST) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJTBFAST) $(MYCFLAGS) $(LIBS) - - addsingle : $(OBJADDSINGLE) -- $(CC) -o $@ $(OBJADDSINGLE) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJADDSINGLE) $(MYCFLAGS) $(LIBS) - - tbfast2 : $(OBJTBFAST2) -- $(CC) -o $@ $(OBJTBFAST2) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJTBFAST2) $(MYCFLAGS) $(LIBS) - - disttbfast : $(OBJDISTTBFAST) -- $(CC) -o $@ $(OBJDISTTBFAST) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJDISTTBFAST) $(MYCFLAGS) $(LIBS) - - makedirectionlist : $(OBJMAKEDIRECTIONLIST) -- $(CC) -o $@ $(OBJMAKEDIRECTIONLIST) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJMAKEDIRECTIONLIST) $(MYCFLAGS) $(LIBS) - - splittbfast : $(OBJSPLITTBFAST) -- $(CC) -o $@ $(OBJSPLITTBFAST) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJSPLITTBFAST) $(MYCFLAGS) $(LIBS) - - splitfromaln : $(OBJSPLITFROMALN) -- $(CC) -o $@ $(OBJSPLITFROMALN) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJSPLITFROMALN) $(MYCFLAGS) $(LIBS) - - splittbfast2 : $(OBJSPLITTBFAST2) -- $(CC) -o $@ $(OBJSPLITTBFAST2) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJSPLITTBFAST2) $(MYCFLAGS) $(LIBS) - - dummy : $(OBJDUMMY) -- $(CC) -o $@ $(OBJDUMMY) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJDUMMY) $(MYCFLAGS) $(LIBS) - - setcore : $(OBJSETCORE) -- $(CC) -o $@ $(OBJSETCORE) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJSETCORE) $(MYCFLAGS) $(LIBS) - - countlen : $(OBJCOUNTLEN) -- $(CC) -o $@ $(OBJCOUNTLEN) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJCOUNTLEN) $(MYCFLAGS) $(LIBS) - - seq2regtable : $(OBJSEQ2REGTABLE) -- $(CC) -o $@ $(OBJSEQ2REGTABLE) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJSEQ2REGTABLE) $(MYCFLAGS) $(LIBS) - - regtable2seq : $(OBJREGTABLE2SEQ) -- $(CC) -o $@ $(OBJREGTABLE2SEQ) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJREGTABLE2SEQ) $(MYCFLAGS) $(LIBS) - - setdirection : $(OBJSETDIRECTION) -- $(CC) -o $@ $(OBJSETDIRECTION) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJSETDIRECTION) $(MYCFLAGS) $(LIBS) - - replaceu : $(OBJREPLACEU) -- $(CC) -o $@ $(OBJREPLACEU) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJREPLACEU) $(MYCFLAGS) $(LIBS) - - restoreu : $(OBJRESTOREU) -- $(CC) -o $@ $(OBJRESTOREU) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJRESTOREU) $(MYCFLAGS) $(LIBS) - - f2cl : $(OBJF2CL) -- $(CC) -o $@ $(OBJF2CL) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJF2CL) $(MYCFLAGS) $(LIBS) - - mccaskillwrap : $(OBJMCCASKILLWRAP) -- $(CC) -o $@ $(OBJMCCASKILLWRAP) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJMCCASKILLWRAP) $(MYCFLAGS) $(LIBS) - - contrafoldwrap : $(OBJCONTRAFOLDWRAP) -- $(CC) -o $@ $(OBJCONTRAFOLDWRAP) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJCONTRAFOLDWRAP) $(MYCFLAGS) $(LIBS) - - pairlocalalign : $(OBJPAIRLOCALALIGN) -- $(CC) -o $@ $(OBJPAIRLOCALALIGN) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJPAIRLOCALALIGN) $(MYCFLAGS) $(LIBS) - - pairash : $(OBJPAIRASH) -- $(CC) -o $@ $(OBJPAIRASH) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJPAIRASH) $(MYCFLAGS) $(LIBS) - - rnatest : $(OBJRNATEST) -- $(CC) -o $@ $(OBJRNATEST) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJRNATEST) $(MYCFLAGS) $(LIBS) - - pair2hat3s : $(OBJPAIR2HAT3S) -- $(CC) -o $@ $(OBJPAIR2HAT3S) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJPAIR2HAT3S) $(MYCFLAGS) $(LIBS) - - multi2hat3s : $(OBJMULTI2HAT3S) -- $(CC) -o $@ $(OBJMULTI2HAT3S) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJMULTI2HAT3S) $(MYCFLAGS) $(LIBS) - - getlag : $(OBJGETLAG) -- $(CC) -o $@ $(OBJGETLAG) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJGETLAG) $(MYCFLAGS) $(LIBS) - - tditr : $(OBJTDITR) -- $(CC) -o $@ $(OBJTDITR) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJTDITR) $(MYCFLAGS) $(LIBS) - - dvtditr : $(OBJDVTDITR) -- $(CC) -o $@ $(OBJDVTDITR) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJDVTDITR) $(MYCFLAGS) $(LIBS) - - mafft-profile : $(OBJGALN) -- $(CC) -o $@ $(OBJGALN) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJGALN) $(MYCFLAGS) $(LIBS) - - gapfill : $(OBJGAPFILL) -- $(CC) -o $@ $(OBJGAPFILL) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJGAPFILL) $(MYCFLAGS) $(LIBS) - - dndfast4 : $(OBJDNDFAST4) -- $(CC) -o $@ $(OBJDNDFAST4) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST4) $(MYCFLAGS) $(LIBS) - - dndfast5 : $(OBJDNDFAST5) -- $(CC) -o $@ $(OBJDNDFAST5) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST5) $(MYCFLAGS) $(LIBS) - - dndfast6 : $(OBJDNDFAST6) -- $(CC) -o $@ $(OBJDNDFAST6) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST6) $(MYCFLAGS) $(LIBS) - - dndfast7 : $(OBJDNDFAST7) -- $(CC) -o $@ $(OBJDNDFAST7) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST7) $(MYCFLAGS) $(LIBS) - - dndblast : $(OBJDNDBLAST) -- $(CC) -o $@ $(OBJDNDBLAST) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJDNDBLAST) $(MYCFLAGS) $(LIBS) - - dndfast3 : $(OBJDNDFAST3) -- $(CC) -o $@ $(OBJDNDFAST3) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST3) $(MYCFLAGS) $(LIBS) - - triplet : $(OBJTRIPLET) -- $(CC) -o $@ $(OBJTRIPLET) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET) $(MYCFLAGS) $(LIBS) - - triplet3 : $(OBJTRIPLET3) -- $(CC) -o $@ $(OBJTRIPLET3) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET3) $(MYCFLAGS) $(LIBS) - - sextet3 : $(OBJSEXTET3) -- $(CC) -o $@ $(OBJSEXTET3) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJSEXTET3) $(MYCFLAGS) $(LIBS) - - sextet4 : $(OBJSEXTET4) -- $(CC) -o $@ $(OBJSEXTET4) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJSEXTET4) $(MYCFLAGS) $(LIBS) - - sextet5 : $(OBJSEXTET5) -- $(CC) -o $@ $(OBJSEXTET5) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJSEXTET5) $(MYCFLAGS) $(LIBS) - - mafft-distance : $(OBJDISTANCE) -- $(CC) -o $@ $(OBJDISTANCE) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJDISTANCE) $(MYCFLAGS) $(LIBS) - - triplet5 : $(OBJTRIPLET5) -- $(CC) -o $@ $(OBJTRIPLET5) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET5) $(MYCFLAGS) $(LIBS) - - triplet6 : $(OBJTRIPLET6) -- $(CC) -o $@ $(OBJTRIPLET6) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET6) $(MYCFLAGS) $(LIBS) - - octet4 : $(OBJOCTET4) -- $(CC) -o $@ $(OBJOCTET4) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJOCTET4) $(MYCFLAGS) $(LIBS) - - dndpre : $(OBJDNDPRE) -- $(CC) -o $@ $(OBJDNDPRE) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJDNDPRE) $(MYCFLAGS) $(LIBS) - - dndpre2 : $(OBJDNDPRESCORE) -- $(CC) -o $@ $(OBJDNDPRESCORE) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJDNDPRESCORE) $(MYCFLAGS) $(LIBS) - - score : $(OBJSCORE) -- $(CC) -o $@ $(OBJSCORE) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJSCORE) $(MYCFLAGS) $(LIBS) - - genMtx : $(OBJGENMTX) -- $(CC) -o $@ $(OBJGENMTX) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJGENMTX) $(MYCFLAGS) $(LIBS) - - gapfill.o : gapfill.c $(HEADER) - $(CC) $(MYCFLAGS) -c gapfill.c -@@ -525,7 +525,7 @@ install : all - chmod 755 $(SCRIPTS) - $(INSTALL) $(SCRIPTS) $(BINDIR) - chmod 755 $(PROGS) -- $(INSTALL) -s $(PROGS) $(LIBDIR) -+ $(INSTALL) $(PROGS) $(LIBDIR) - $(INSTALL) -m 644 $(MANPAGES) $(LIBDIR) - - ( cd $(BINDIR); \ diff --git a/sci-biology/mafft/mafft-7.050.ebuild b/sci-biology/mafft/mafft-7.050.ebuild deleted file mode 100644 index 5da5d12d1b31..000000000000 --- a/sci-biology/mafft/mafft-7.050.ebuild +++ /dev/null @@ -1,60 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils flag-o-matic multilib toolchain-funcs - -EXTENSIONS="-without-extensions" - -DESCRIPTION="Multiple sequence alignments using a variety of algorithms" -HOMEPAGE="https://mafft.cbrc.jp/alignment/software/index.html" -SRC_URI="https://mafft.cbrc.jp/alignment/software/${P}${EXTENSIONS}-src.tgz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" -IUSE="threads" - -S="${WORKDIR}"/${P}${EXTENSIONS} - -src_prepare() { - epatch "${FILESDIR}"/${PN}-7.037-respect.patch - use threads && append-cppflags -Denablemultithread - sed "s:GENTOOLIBDIR:$(get_libdir):g" -i core/Makefile || die - sed -i -e "s/(PREFIX)\/man/(PREFIX)\/share\/man/" "${S}"/core/Makefile || die "sed failed" -} - -src_compile() { - pushd core > /dev/null || die - emake \ - $(usex threads ENABLE_MULTITHREAD="-Denablemultithread" ENABLE_MULTITHREAD="") \ - PREFIX="${EPREFIX}"/usr \ - CC="$(tc-getCC)" \ - CFLAGS="${CFLAGS}" - popd > /dev/null || die -} - -src_test() { - export MAFFT_BINARIES="${S}"/core - cd test || die - bash ../core/mafft sample > test.fftns2 || die - bash ../core/mafft --maxiterate 100 sample > test.fftnsi || die - bash ../core/mafft --globalpair sample > test.gins1 || die - bash ../core/mafft --globalpair --maxiterate 100 sample > test.ginsi || die - bash ../core/mafft --localpair sample > test.lins1 || die - bash ../core/mafft --localpair --maxiterate 100 sample > test.linsi || die - - diff test.fftns2 sample.fftns2 || die - diff test.fftnsi sample.fftnsi || die - diff test.gins1 sample.gins1 || die - diff test.ginsi sample.ginsi || die - diff test.lins1 sample.lins1 || die -} - -src_install() { - pushd core - emake PREFIX="${ED}usr" install - popd - dodoc readme -} diff --git a/sci-biology/mafft/mafft-7.215.ebuild b/sci-biology/mafft/mafft-7.215.ebuild deleted file mode 100644 index 05c3d8d52399..000000000000 --- a/sci-biology/mafft/mafft-7.215.ebuild +++ /dev/null @@ -1,64 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils flag-o-matic multilib toolchain-funcs - -EXTENSIONS="-without-extensions" - -DESCRIPTION="Multiple sequence alignments using a variety of algorithms" -HOMEPAGE="https://mafft.cbrc.jp/alignment/software/index.html" -SRC_URI="https://mafft.cbrc.jp/alignment/software/${P}${EXTENSIONS}-src.tgz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" -IUSE="threads" - -S="${WORKDIR}"/${P}${EXTENSIONS} - -src_prepare() { -# epatch "${FILESDIR}"/${PN}-7.037-respect.patch - use threads && append-cppflags -Denablemultithread -# sed "s:GENTOOLIBDIR:$(get_libdir):g" -i core/Makefile || die - sed -i -e "s/(PREFIX)\/man/(PREFIX)\/share\/man/" "${S}"/core/Makefile || die "sed failed" - sed \ - -e 's:$(LDFLAGS)::g' \ - -e 's:$(CC) -o $@:$(CC) $(LDFLAGS) -o $@:g' \ - -e 's:$(CC) -shared -o $@:$(CC) $(LDFLAGS) -shared -o $@:g' \ - -e '/INSTALL/s: -s : :g' \ - -i core/Makefile || die -} - -src_compile() { - cd core || die - emake \ - $(usex threads ENABLE_MULTITHREAD="-Denablemultithread" ENABLE_MULTITHREAD="") \ - PREFIX="${EPREFIX}"/usr \ - CC="$(tc-getCC)" \ - CFLAGS="${CFLAGS} -Wno-unused-result" -} - -src_test() { - export MAFFT_BINARIES="${S}"/core - cd test || die - bash ../core/mafft sample > test.fftns2 || die - bash ../core/mafft --maxiterate 100 sample > test.fftnsi || die - bash ../core/mafft --globalpair sample > test.gins1 || die - bash ../core/mafft --globalpair --maxiterate 100 sample > test.ginsi || die - bash ../core/mafft --localpair sample > test.lins1 || die - bash ../core/mafft --localpair --maxiterate 100 sample > test.linsi || die - - diff test.fftns2 sample.fftns2 || die - diff test.fftnsi sample.fftnsi || die - diff test.gins1 sample.gins1 || die - diff test.ginsi sample.ginsi || die - diff test.lins1 sample.lins1 || die -} - -src_install() { - dodoc readme - cd core || die - emake PREFIX="${ED}usr" install -} diff --git a/sci-biology/mafft/mafft-7.305.ebuild b/sci-biology/mafft/mafft-7.490.ebuild index 9f9f631416b2..a5ff0a5764d6 100644 --- a/sci-biology/mafft/mafft-7.305.ebuild +++ b/sci-biology/mafft/mafft-7.490.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2018 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit flag-o-matic toolchain-funcs @@ -10,20 +10,15 @@ EXTENSIONS="-without-extensions" DESCRIPTION="Multiple sequence alignments using a variety of algorithms" HOMEPAGE="https://mafft.cbrc.jp/alignment/software/index.html" SRC_URI="https://mafft.cbrc.jp/alignment/software/${P}${EXTENSIONS}-src.tgz" +S="${WORKDIR}/${P}${EXTENSIONS}" LICENSE="BSD" SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" -IUSE="threads" - -S="${WORKDIR}/${P}${EXTENSIONS}" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" src_prepare() { default - append-cflags -Wno-unused-result - use threads && append-cppflags -Denablemultithread - sed \ -e 's/(PREFIX)\/man/(PREFIX)\/share\/man/' \ -e 's:$(LDFLAGS)::g' \ @@ -33,10 +28,12 @@ src_prepare() { -i core/Makefile || die } +src_configure() { + append-cflags -Wno-unused-result +} + src_compile() { - cd core || die - emake \ - $(usex threads ENABLE_MULTITHREAD="-Denablemultithread" ENABLE_MULTITHREAD="") \ + emake -C core \ PREFIX="${EPREFIX}"/usr \ CC="$(tc-getCC)" \ CFLAGS="${CFLAGS}" @@ -60,9 +57,6 @@ src_test() { } src_install() { - DOCS=( readme ) - einstalldocs - - cd core || die - emake PREFIX="${ED%/}/usr" install + emake -C core DESTDIR="${D}" STRIP=":" PREFIX="${EPREFIX}"/usr install + dodoc readme } diff --git a/sci-biology/mafft/metadata.xml b/sci-biology/mafft/metadata.xml index 959160fe46b1..ccdff086e20b 100644 --- a/sci-biology/mafft/metadata.xml +++ b/sci-biology/mafft/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/maq/files/maq-0.7.1-gcc14-build-fix.patch b/sci-biology/maq/files/maq-0.7.1-gcc14-build-fix.patch new file mode 100644 index 000000000000..b92b7711bfe0 --- /dev/null +++ b/sci-biology/maq/files/maq-0.7.1-gcc14-build-fix.patch @@ -0,0 +1,23 @@ +Bug: https://bugs.gentoo.org/921137 +--- a/fastq2bfq.c ++++ b/fastq2bfq.c +@@ -15,7 +15,7 @@ int64_t fastq2bfq(FILE *fp_fq, const char *fn_bfq, int n_reads) + char name[256], str[1024]; + int l, is_new = 0, l_prefix = 0; + bit64_t n; +- gzFile *fp = 0; ++ gzFile fp = 0; + INIT_SEQ(seq); INIT_SEQ(qual); + seq_set_block_size(256); + n = 0; +--- a/simulate.c ++++ b/simulate.c +@@ -74,7 +74,7 @@ int maq_simutrain(int argc, char *argv[]) + { + fqc_t *fqc; + FILE *fp; +- gzFile *fpout; ++ gzFile fpout; + if (argc < 3) { + fprintf(stderr, "Usage: maq simutrain <simupars.dat> <known_reads.fastq>\n"); + return 1; diff --git a/sci-biology/maq/maq-0.7.1-r2.ebuild b/sci-biology/maq/maq-0.7.1-r4.ebuild index 14b0284b7f58..75a84d87b16c 100644 --- a/sci-biology/maq/maq-0.7.1-r2.ebuild +++ b/sci-biology/maq/maq-0.7.1-r4.ebuild @@ -1,19 +1,18 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit autotools DESCRIPTION="Mapping and Assembly with Qualities, mapping NGS reads to reference genomes" -HOMEPAGE="http://maq.sourceforge.net/" +HOMEPAGE="https://maq.sourceforge.net/" SRC_URI=" - mirror://sourceforge/${PN}/${P}.tar.bz2 - mirror://sourceforge/${PN}/calib-36.dat.gz" + https://downloads.sourceforge.net/${PN}/${P}.tar.bz2 + https://downloads.sourceforge.net/${PN}/calib-36.dat.gz" LICENSE="GPL-3" SLOT="0" -IUSE="" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" RDEPEND="sys-libs/zlib" @@ -24,6 +23,7 @@ PATCHES=( "${FILESDIR}"/${P}-bfr-overfl.patch "${FILESDIR}"/${P}-gcc-4.7.patch "${FILESDIR}"/${P}-remove-64bit-flag.patch + "${FILESDIR}"/${P}-gcc14-build-fix.patch ) src_prepare() { @@ -34,9 +34,9 @@ src_prepare() { src_install() { default - insinto /usr/share/${PN} + insinto /usr/share/maq doins "${WORKDIR}"/*.dat doman maq.1 - dodoc ${PN}.pdf + dodoc maq.pdf } diff --git a/sci-biology/maq/metadata.xml b/sci-biology/maq/metadata.xml index 0b39d2a8530d..c555decd8d6f 100644 --- a/sci-biology/maq/metadata.xml +++ b/sci-biology/maq/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/maqview/files/maqview-0.2.5-gcc14-build-fix.patch b/sci-biology/maqview/files/maqview-0.2.5-gcc14-build-fix.patch new file mode 100644 index 000000000000..8f973f38a272 --- /dev/null +++ b/sci-biology/maqview/files/maqview-0.2.5-gcc14-build-fix.patch @@ -0,0 +1,12 @@ +Bug: https://bugs.gentoo.org/930767 +--- a/socket_view.c ++++ b/socket_view.c +@@ -267,7 +267,7 @@ int service_core(ViewServer *server, int sock){ + + int runViewServer(ViewServer *server){ + int i, sock, state; +- size_t size; ++ socklen_t size; + fd_set active_fd_set, read_fd_set; + struct timeval timeout; + struct sockaddr_in clientname; diff --git a/sci-biology/maqview/maqview-0.2.5-r3.ebuild b/sci-biology/maqview/maqview-0.2.5-r5.ebuild index 2d6574217029..2ffe5fa8ecf6 100644 --- a/sci-biology/maqview/maqview-0.2.5-r3.ebuild +++ b/sci-biology/maqview/maqview-0.2.5-r5.ebuild @@ -1,17 +1,17 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit autotools DESCRIPTION="GUI for sci-biology/maq, a short read mapping assembler" -HOMEPAGE="http://maq.sourceforge.net/" -SRC_URI="mirror://sourceforge/maq/${P}.tar.gz" +HOMEPAGE="https://maq.sourceforge.net/" +SRC_URI="https://downloads.sourceforge.net/maq/${P}.tar.gz" +S="${WORKDIR}/${PN}" LICENSE="GPL-3" SLOT="0" -IUSE="" KEYWORDS="~amd64 ~x86" DEPEND=" @@ -20,12 +20,11 @@ DEPEND=" RDEPEND="${DEPEND} sci-biology/maq" -S="${WORKDIR}/${PN}" - PATCHES=( "${FILESDIR}"/${PV}-ldflags.patch "${FILESDIR}"/${PV}-zlib.patch "${FILESDIR}"/${P}-gcc4.7.patch + "${FILESDIR}"/${P}-gcc14-build-fix.patch ) src_prepare() { diff --git a/sci-biology/maqview/metadata.xml b/sci-biology/maqview/metadata.xml index 0b39d2a8530d..c555decd8d6f 100644 --- a/sci-biology/maqview/metadata.xml +++ b/sci-biology/maqview/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/mcl/files/mcl-14.137-fix-autotools.patch b/sci-biology/mcl/files/mcl-14.137-fix-autotools.patch new file mode 100644 index 000000000000..0d2c052a91b0 --- /dev/null +++ b/sci-biology/mcl/files/mcl-14.137-fix-autotools.patch @@ -0,0 +1,52 @@ +--- a/configure.ac ++++ b/configure.ac +@@ -144,6 +144,7 @@ + AC_PROG_INSTALL + AC_PROG_LN_S + AC_PROG_RANLIB ++AM_PROG_AR + + # Checks for libraries. + # FIXME: Replace `main' with a function in `-lm': +--- a/doc/Makefile.am ++++ b/doc/Makefile.am +@@ -9,7 +9,6 @@ + ## http://www.w3.org/People/Raggett/tidy/ , by Dave Raggett <dsr@w3.org> + TIDY = tidy + +-docdir = $(datadir)/doc/$(PACKAGE) + + # mclfamily.html mclfamily.ps + +--- a/graphs/Makefile.am ++++ b/graphs/Makefile.am +@@ -1,7 +1,7 @@ + ## Process this file with automake to produce Makefile.in + ## $Id: Makefile.am,v 1.7 2007-01-29 11:35:37 flux Exp $ + +-exampledir = $(datadir)/doc/$(PACKAGE)/examples ++exampledir = $(docdir)/examples + + example_DATA = falkner.mci falkner2.mci falkner.coords make-falkner.pl \ + proteins.mci matula.mci lattice.mci honey.mci seven.mci infinity.mci \ +--- a/img/Makefile.am ++++ b/img/Makefile.am +@@ -1,7 +1,7 @@ + ## Process this file with automake to produce Makefile.in + ## $Id: Makefile.am,v 1.7 2007-01-29 11:35:37 flux Exp $ + +-exampledir = $(datadir)/doc/$(PACKAGE)/examples ++exampledir = $(docdir)/examples + + example_DATA = fa_1024.png fa_400.png fa_600.png fa_large.png fa.ps falkner-bidi.ps falkner.ps small.ps small.png + +--- a/src/alien/oxygen/doc/Makefile.am ++++ b/src/alien/oxygen/doc/Makefile.am +@@ -17,7 +17,6 @@ + ## http://www.w3.org/People/Raggett/tidy/ , by Dave Raggett <dsr@w3.org> + TIDY = tidy + +-docdir = $(datadir)/doc/$(PACKAGE) + + ## zoemtut.html is "on hold": do not install; zoem is not yet ready + ## for prime time diff --git a/sci-biology/mcl/files/mcl-14.137-qa-implicit-declarations.patch b/sci-biology/mcl/files/mcl-14.137-fix-declarations.patch index df4309874d48..4974d352bf7b 100644 --- a/sci-biology/mcl/files/mcl-14.137-qa-implicit-declarations.patch +++ b/sci-biology/mcl/files/mcl-14.137-fix-declarations.patch @@ -5,8 +5,34 @@ Fix QA issues related to implicit declarations. * clmadjust.c:184:10: warning: implicit declaration of function ‘mcxFree’ [-Wimplicit-function-declaration] * mcxi.c:42:16: warning: implicit declaration of function ‘isatty’ [-Wimplicit-function-declaration] ---- mcl-14-137/src/shcl/clmadjust.c -+++ mcl-14-137/src/shcl/clmadjust.c +--- a/src/impala/iface.h ++++ b/src/impala/iface.h +@@ -16,15 +16,15 @@ + + /* This file currently provides nothing */ + +-dim nu_meet_can ; +-dim nu_meet_sl ; +-dim nu_meet_zip ; +-dim nu_diff_can ; +-dim nu_diff_sl ; +-dim nu_diff_zip ; +-double nu_magic ; ++extern dim nu_meet_can ; ++extern dim nu_meet_sl ; ++extern dim nu_meet_zip ; ++extern dim nu_diff_can ; ++extern dim nu_diff_sl ; ++extern dim nu_diff_zip ; ++extern double nu_magic ; + +-dim mclx_n_thread_g ; ++extern dim mclx_n_thread_g ; + + #endif + +--- a/src/shcl/clmadjust.c ++++ b/src/shcl/clmadjust.c @@ -14,6 +14,7 @@ #include "report.h" #include "clmadjust.h" @@ -15,8 +41,8 @@ Fix QA issues related to implicit declarations. #include "util/io.h" #include "util/types.h" #include "util/err.h" ---- mcl-14-137/src/shmcx/mcxi.c -+++ mcl-14-137/src/shmcx/mcxi.c +--- a/src/shmcx/mcxi.c ++++ b/src/shmcx/mcxi.c @@ -8,6 +8,7 @@ */ diff --git a/sci-biology/mcl/mcl-14.137.ebuild b/sci-biology/mcl/mcl-14.137.ebuild index e48198deca29..e7924bccec30 100644 --- a/sci-biology/mcl/mcl-14.137.ebuild +++ b/sci-biology/mcl/mcl-14.137.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 inherit autotools @@ -16,16 +16,14 @@ SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="+blast" -PATCHES=("${FILESDIR}/${P}-qa-implicit-declarations.patch") S="${WORKDIR}/${MY_P}" +PATCHES=( + "${FILESDIR}"/${P}-fix-declarations.patch + "${FILESDIR}"/${P}-fix-autotools.patch +) + src_prepare() { - find \ - -name Makefile.am \ - -exec sed \ - -e '/docdir/d' \ - -e '/exampledir/s:doc::g' \ - -i '{}' + || die default eautoreconf } diff --git a/sci-biology/mcl/metadata.xml b/sci-biology/mcl/metadata.xml index 25048faf1643..ddda352c113d 100644 --- a/sci-biology/mcl/metadata.xml +++ b/sci-biology/mcl/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/meme/Manifest b/sci-biology/meme/Manifest deleted file mode 100644 index fd161837618b..000000000000 --- a/sci-biology/meme/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST meme_4.11.2.tar.gz 18004930 BLAKE2B accacc7d2422ff6ea3411ff43ea664c94f5d6ba320e1cfec642a88cb6ea5303b2fe8c99a6c35d865c377560118402ab11f869930fd108f02eeaa06321db21655 SHA512 c97c3815e71e2fb5491548152f00688cdfbf4365f6027657e0ffc68e5d96cdd10a4708e0882ab7a5a61d78d93113c925cf5bb300fbe93fa4b2961becef497894 diff --git a/sci-biology/meme/files/meme-4.11.2_p2-fix-build-system.patch b/sci-biology/meme/files/meme-4.11.2_p2-fix-build-system.patch deleted file mode 100644 index b548de5a39a5..000000000000 --- a/sci-biology/meme/files/meme-4.11.2_p2-fix-build-system.patch +++ /dev/null @@ -1,346 +0,0 @@ -Fix and modernise build system -* Remove all *FLAGS setting, just append to the user-supplied ones -* Add --enable-doc and --enable-examples configure flags -* Install documentation and examples in correct directories -* Discover libxml2 and libxslt dependencies using PKG_CHECK_MODULES -* Install python and perl modules correctly - ---- a/configure.ac -+++ b/configure.ac -@@ -76,61 +76,10 @@ - AM_CONDITIONAL(WANT_STRLCPY, test ["$have_strlcpy" = no]) - - # Check for compiler-specific settings --LARGE_FILE_SUPPORT=`getconf LFS_CFLAGS` --if test "${GCC}" = "yes"; then -- ac_cc_opt="-O3" -- ac_cc_debug_opt="-O0" -- ac_cc_warn="-Wall -Wno-unused" -- ac_cc_debug="-ggdb" -- # Check for OS X llvm (clang) compiler -- if `gcc --version |grep llvm >/dev/null`; then -- ac_cc_debug="-g" -- fi -- CFLAGS="-std="gnu89" $ac_cc_warn -DUNIX -D__USE_FIXED_PROTOTYPES__ $LARGE_FILE_SUPPORT" --else -- ac_cc_opt="-O" -- ac_cc_debug_opt="" -- ac_cc_warn="" -- ac_cc_debug="-g" -- CFLAGS="$ac_cc_warn -DUNIX -D__USE_FIXED_PROTOTYPES__ $LARGE_FILE_SUPPORT" --fi -- --# Set up default libxml2 settings --# check for installed copy of libxml2 --build_libxml2="yes" --if test -n "$XML2_CONFIG"; then -- # Require at least version 2.6 -- required_libxml2_version="2006000" -- LIBXML2_VERSION="`$XML2_CONFIG --version | \ -- awk 'BEGIN { FS = "."; } { printf "%d", ($1 * 1000 + $2) * 1000 + $3;}'`" -- if test -n "$LIBXML2_VERSION" && \ -- test "$LIBXML2_VERSION" -ge "$required_libxml2_version"; then -- build_libxml2="no" -- LIBXML2_LIBS="`$XML2_CONFIG --libs`" -- LIBXML2_CFLAGS="`$XML2_CONFIG --cflags`" -- fi --fi --if test -z "$LIBXML2_LIBS"; then -- AC_MSG_WARN([libxml2 library not found]) -- LIBXML2_LIBS="\${top_builddir}/src/libxml2/libxml2.la" -- LIBXML2_CFLAGS="-I\${top_srcdir}/src/libxml2/include" --fi -- --# Set up default libxslt settings --# check for installed copy of libxslt --build_libxslt="yes" --if test -n "$XSLT_CONFIG"; then -- build_libxslt="no" -- LIBXSLT_LIBS="`$XSLT_CONFIG --libs` -lexslt" -- LIBXSLT_CFLAGS="`$XSLT_CONFIG --cflags`" --fi --if test -z "$LIBXSLT_LIBS"; then -- AC_MSG_WARN([libxslt library not found]) -- LIBEXSLT_LIBS="\${top_builddir}/src/libexslt/libexslt.la" -- LIBXSLT_LIBS="\${top_builddir}/src/libxslt/libxslt.la" -- LIBEXSLT_CFLAGS="-I\${top_srcdir}/src/libexslt" -- LIBXSLT_CFLAGS="-I\${top_srcdir}/src/" --fi -+AC_PROG_MKDIR_P -+AC_SYS_LARGEFILE -+CFLAGS="-std=gnu89 -Wall -Wno-unused ${CFLAGS}" -+CPPFLAGS="-DUNIX -D__USE_FIXED_PROTOTYPES__ ${CPPFLAGS}" - - # who is installing - USER=`whoami` -@@ -279,6 +227,16 @@ - AM_CONDITIONAL(PARALLEL, test ["$parallel" != no]) - AM_CONDITIONAL(PARALLEL_IS_LAM, test -n ["$lammpi"]) - -+dnl Documentation -+AC_ARG_ENABLE([doc], -+ AS_HELP_STRING([--enable-doc], [Enable installation of documentation])) -+AM_CONDITIONAL([ENABLE_DOC], [test "x$enable_doc" = "xyes"]) -+ -+dnl Examples -+AC_ARG_ENABLE([examples], -+ AS_HELP_STRING([--enable-examples], [Enable installation of examples])) -+AM_CONDITIONAL([ENABLE_EXAMPLES], [test "x$enable_examples" = "xyes"]) -+ - AC_ARG_ENABLE( - webservice, - [ --enable-webservice=deploy_dir Deploy the MEME service on an existing Opal 2.5+ installation], -@@ -309,24 +267,35 @@ - AM_CONDITIONAL(WEBEITHER, test ["x$OPAL_DEPLOY" != "x" -o "x$OPAL_URL" != "xno"]) - - # enable building of included libxml2 --AC_ARG_ENABLE( -- build_libxml2, -- [ --enable-build-libxml2 Build included version of libxml2. Default is to use pre-existing locally installed copy.], -- build_libxml2=$enableval; \ -- LIBXML2_LIBS="\${top_builddir}/src/libxml2/libxml2.la"; \ -- LIBXML2_CFLAGS="-I\${top_srcdir}/src/libxml2/include" , ) --AM_CONDITIONAL(BUILD_LIBXML2, test ["$build_libxml2" = yes]) -+AC_ARG_ENABLE([build-libxml2], -+ AS_HELP_STRING([--enable-build-libxml2], [Build included version of libxml2. Default is to use pre-existing locally installed copy.])) -+AS_IF([test "x$enable_build_libxml2" = "xyes"], [ -+ dnl Enable building of bundled libs -+ LIBXML2_CFLAGS="-I\${top_srcdir}/src/libxml2/include" -+ LIBXML2_LIBS="\${top_builddir}/src/libxml2/libxml2.la" -+ ],[ -+ dnl Use system libraries -+ PKG_CHECK_MODULES([LIBXML2], [libxml-2.0 >= 2.6]) -+]) -+AM_CONDITIONAL([BUILD_LIBXML2], [test "x$enable_build_libxml2" = "xyes"]) -+ - - # enable building of included libxslt --AC_ARG_ENABLE( -- build_libxslt, -- [ --enable-build-libxslt Build included version of libxslt. Default is to use pre-existing locally installed copy.], -- build_libxslt=$enableval; \ -- LIBEXSLT_LIBS="\${top_builddir}/src/libexslt/libexslt.la"; \ -- LIBXSLT_LIBS="\${top_builddir}/src/libxslt/libxslt.la"; \ -- LIBEXSLT_CFLAGS="-I\${top_srcdir}/src/libexslt"; \ -- LIBXSLT_CFLAGS="-I\${top_srcdir}/src/" , ) --AM_CONDITIONAL(BUILD_LIBXSLT, test ["$build_libxslt" = yes]) -+AC_ARG_ENABLE([build-libxslt], -+ AS_HELP_STRING([--enable-build-libxslt], [Build included version of libxslt. Default is to use pre-existing locally installed copy.])) -+AS_IF([test "x$enable_build_libxslt" = "xyes"], [ -+ dnl Enable building of bundled libs -+ LIBXSLT_CFLAGS="-I\${top_srcdir}/src/" -+ LIBXSLT_LIBS="\${top_builddir}/src/libxslt/libxslt.la" -+ -+ LIBEXSLT_CFLAGS="-I\${top_srcdir}/src/libexslt" -+ LIBEXSLT_LIBS="\${top_builddir}/src/libexslt/libexslt.la" -+ ],[ -+ dnl Use system libraries -+ PKG_CHECK_MODULES([LIBXSLT], [libxslt]) -+ PKG_CHECK_MODULES([LIBEXSLT], [libexslt]) -+]) -+AM_CONDITIONAL([BUILD_LIBXSLT], [test "x$enable_build_libxslt" = "xyes"]) - - # set website url - AC_ARG_WITH( -@@ -427,13 +396,13 @@ - [AC_PATH_PROG(PERL, perl)]) - AC_DEFINE_UNQUOTED(PERL, "$PERL", [Path to Perl] ) - -+AC_ARG_WITH([perl-dir], -+ AS_HELP_STRING([--with-perl-dir], [Perl modules directory]), [perlmoddir="$with_perl_dir"], [perlmoddir="lib/perl"]) -+AC_SUBST([perlmoddir]) -+ -+ - # set path to Python --AC_ARG_WITH( -- python, -- [ --with-python=NAME Set path to Python. Default is to take from user's PATH.], -- [PYTHON=$withval], -- [AC_PATH_PROG(PYTHON, python)]) --AC_DEFINE_UNQUOTED(PYTHON, "$PYTHON", [Path to Python] ) -+AM_PATH_PYTHON - - # set path to convert utility - AC_ARG_WITH( -@@ -586,13 +555,15 @@ - Configuration parameters - ======================== - -- Install path: ${prefix} -+ Install path (prefix): ${prefix} - Install UID: ${MEME_USER} - Version: ${VERSION} -- C compiler: ${CC} -- C compiler flags: ${CFLAGS} -- Linker: ${LD} -- Special Libs: ${LIBS} -+ C compiler (CC): ${CC} -+ C compiler flags (CFLAGS): ${CFLAGS} -+ C preproc flags (CPPFLAGS): ${CPPFLAGS} -+ Linker (LD): ${LD} -+ Linker flags (LDFLAGS): ${LDFLAGS} -+ Special Libs (LIBS): ${LIBS} - MPICC ${MPICC} - MPIRUN ${MPIRUN} - MPI_CMD ${MPI_CMD} ---- a/doc/css/Makefile.am -+++ b/doc/css/Makefile.am -@@ -5,7 +5,7 @@ - - EXTRA_DIST = $(NORMAL_FILES) - --if ! WEBSITE --doccssdir = $(prefix)/doc/css -+if ENABLE_DOC -+doccssdir = $(htmldir)/css - doccss_DATA = $(NORMAL_FILES) - endif ---- a/doc/examples/compute_prior_dist_example_output_files/Makefile.am -+++ b/doc/examples/compute_prior_dist_example_output_files/Makefile.am -@@ -7,8 +7,8 @@ - EXAMPLES = \ - prior.dist.txt - --if ! WEBSITE --exdir = $(prefix)/doc/examples/compute_prior_dist_example_output_files -+if ENABLE_EXAMPLES -+exdir = $(docdir)/examples/compute_prior_dist_example_output_files - ex_DATA = $(EXAMPLES) - endif - ---- a/doc/examples/Makefile.am -+++ b/doc/examples/Makefile.am -@@ -22,8 +22,8 @@ - # load the EXAMPLE_OUTPUT_FILES variable - include examples.mk - --if ! WEBSITE --exdir = $(prefix)/doc/examples -+if ENABLE_EXAMPLES -+exdir = $(docdir)/examples - nobase_dist_ex_DATA = $(EXAMPLES) $(EXAMPLE_OUTPUT_FILES) - endif - ---- a/doc/examples/sample_opal_scripts/Makefile.am -+++ b/doc/examples/sample_opal_scripts/Makefile.am -@@ -15,8 +15,8 @@ - MemeClient.pl \ - MemeClient.py - --if ! WEBSITE --exdir = $(prefix)/doc/examples/sample_opal_scripts -+if ENABLE_EXAMPLES -+exdir = $(docdir)/examples/sample_opal_scripts - ex_DATA = $(EXAMPLES) - endif - ---- a/doc/images/Makefile.am -+++ b/doc/images/Makefile.am -@@ -30,8 +30,8 @@ - - MEME_IMAGES = $(PROGRAM_ICONS) $(OTHER_IMAGES) - --if ! WEBSITE --memeimgdir = $(prefix)/doc/images -+if ENABLE_DOC -+memeimgdir = $(htmldir)/images - memeimg_DATA = $(MEME_IMAGES) - endif - ---- a/doc/js/Makefile.am -+++ b/doc/js/Makefile.am -@@ -41,8 +41,8 @@ - - BUILT_SOURCES = $(BUILT_FILES) - --if ! WEBSITE --docjsdir = $(prefix)/doc/js -+if ENABLE_DOC -+docjsdir = $(htmldir)/js - docjs_DATA = $(NORMAL_FILES) $(BUILT_FILES) $(SYMLINK_FILES) - endif - ---- a/doc/Makefile.am -+++ b/doc/Makefile.am -@@ -129,8 +129,8 @@ - update-sequence-db.html \ - ismb94.pdf - --if ! WEBSITE --memedocdir = $(prefix)/doc -+if ENABLE_DOC -+memedocdir = $(htmldir) - memedoc_DATA = $(NORMAL_FILES) - endif - ---- a/Makefile.am -+++ b/Makefile.am -@@ -52,7 +52,7 @@ - endif - - dbdir: -- mkdir -p $(MEME_DB) -+ $(MKDIR_P) $(DESTDIR)/$(MEME_DB) - - all-local: - if WEBSITE -@@ -64,8 +64,8 @@ - endif - - install-data-local: -- mkdir -p $(MEME_LOGS) -- chmod a+w $(MEME_LOGS) -+ $(MKDIR_P) $(DESTDIR)/$(MEME_LOGS) -+ chmod a+w $(DESTDIR)/$(MEME_LOGS) - - distdir = $(PACKAGE)_$(VERSION) - ---- a/scripts/Makefile.am -+++ b/scripts/Makefile.am -@@ -22,8 +22,8 @@ - -e 's%@WHICHJAVA@%$(JAVA)%' \ - -e 's%@WHICHCONVERT@%$(CONVERT)%' \ - -e 's%@WHICHGHOSTSCRIPT@%$(GHOSTSCRIPT)%' \ -- -e 's%@PERLLIBDIR@%$(libdir)/perl%' \ -- -e 's%@PYTHONLIBDIR@%$(libdir)/python%' \ -+ -e 's%@PERLLIBDIR@%$(perlmoddir)%' \ -+ -e 's%@PYTHONLIBDIR@%$(pythondir)%' \ - -e 's%@JAVALIBDIR@%$(libdir)/java%' \ - -e 's%@LAM_BIN@%$(LAMBIN)%' \ - -e 's%@APPCONFIGDIR@%$(sysconfdir)%' \ -@@ -62,7 +62,7 @@ - DiffXML.pm \ - HypergeometricDynProg.pm - --perlmoddir=$(libdir)/perl -+perlmoddir = $(exec_prefix)/@perlmoddir@ - perlmod_SCRIPTS = \ - $(BUILT_PERL_MOD) \ - $(NORMAL_PERL_MOD) -@@ -76,8 +76,7 @@ - hypergeometric.py \ - sequence.py - --pythonlibdir=$(libdir)/python --pythonlib_SCRIPTS = \ -+python_PYTHON = \ - $(BUILT_PYTHON_LIB) \ - $(NORMAL_PYTHON_LIB) - ---- a/src/Makefile.am -+++ b/src/Makefile.am -@@ -19,7 +19,13 @@ - ARCHIVE_REVISION = $(shell cat ../ARCHIVE_REVISION) - ARCHIVE_DATE = $(shell cat ../ARCHIVE_DATE) - --SUBDIRS = filters libxml2 libxslt libexslt . parallel -+SUBDIRS = filters . parallel -+if BUILD_LIBXML2 -+SUBDIRS += libxml2 -+endif -+if BUILD_LIBXSLT -+SUBDIRS += libxslt libexslt -+endif - - BUILT_SOURCES = dir.h projrel.h - diff --git a/sci-biology/meme/files/meme-4.11.2_p2-patch1.patch b/sci-biology/meme/files/meme-4.11.2_p2-patch1.patch deleted file mode 100644 index 30a182f8f43a..000000000000 --- a/sci-biology/meme/files/meme-4.11.2_p2-patch1.patch +++ /dev/null @@ -1,383 +0,0 @@ ---- a/doc/alphabet-format.html -+++ b/doc/alphabet-format.html -@@ -233,7 +233,7 @@ - providing a reference on the meaning of the symbols used. If present, the - symbol name must be the second field.</p> - <p>The "<span class="pdat">name</span>" follows the rules of -- <a href="qstr">quoted text</a>.</p> -+ <a href="#qstr">quoted text</a>.</p> - </div> - <h5>color</h5> - <div class="indent"> ---- a/doc/release-notes.html -+++ b/doc/release-notes.html -@@ -14,8 +14,26 @@ - <h2>Motif-based sequence analysis tools</h2> - </div> - <h2>MEME Suite Release Notes</h2> -+ <hr> -+ <b>MEME version 4.11.2 patch 1 -- June 16, 2016</b> -+ <ul> -+ <li> -+ <b>Bug fixes</b> -+ <ul> -+ <li> -+ Fixed bug in MCAST 4.11.2 that caused it to prematurely truncate -+ reading the sequence file. -+ </li> -+ <li> -+ Modified MEME to fall back to a simple Dirichlet prior when -+ using DNA or a custom alphabet with a prior that requires -+ a prior library, but no prior libray is specified. -+ </li> -+ </ul -+ </li> -+ </ul> -+ <p> - <hr> -- <p> - <b>MEME version 4.11.2 -- May 5 2016</b> - </p> - <ul> ---- a/src/fasta-io.c -+++ b/src/fasta-io.c -@@ -14,6 +14,7 @@ - #include "alphabet.h" - #include "fasta-io.h" - #include "io.h" -+#include "seq-reader-from-fasta.h" - #include "prior-reader-from-psp.h" - #include "seq.h" - -@@ -159,61 +160,6 @@ - } - - /**************************************************************************** -- * Read raw sequence until a new sequence is encountered or too many letters -- * are read. The new sequence is appended to the end of the given -- * sequence. -- * -- * Return: Was the sequence read completely? -- ****************************************************************************/ --static BOOLEAN_T read_raw_sequence_from_reader( -- DATA_BLOCK_READER_T *fasta_reader, // Sequence source -- char* name, // Sequence ID (used in error messages). -- ALPH_T* alph, // Alphabet in use -- unsigned int offset, // Current position in raw_sequence. -- unsigned int max_chars, // Maximum chars in raw_sequence. -- char* raw_sequence // Pre-allocated sequence. --) { -- // tlb; change a_char to integer so it will compile on SGI -- int a_char; -- int start_update; -- BOOLEAN_T return_value = TRUE; -- -- // Start at the end of the given sequence. -- assert(offset < max_chars); -- -- DATA_BLOCK_T *seq_block = new_sequence_block(max_chars - offset); -- return_value = !fasta_reader->get_next_block(fasta_reader, seq_block); -- -- char *seq_buffer = get_sequence_from_data_block(seq_block); -- size_t seq_buffer_size = get_num_read_into_data_block(seq_block); -- int i; -- for (i = 0; i < seq_buffer_size; ++i) { -- a_char = seq_buffer[i]; -- // Skip non-alphabetic characters. -- if (!isalnum(a_char) && a_char != '-' && a_char != '*' && a_char != '.') { -- if ((a_char != ' ') && (a_char != '\t') && (a_char != '\n') && (a_char != '\r')) { -- fprintf(stderr, "Warning: Skipping character %c in sequence %s.\n", -- a_char, name); -- } -- } else { -- // skip check if unknown alph -- if (alph != NULL && !alph_is_known(alph, a_char)) { -- fprintf(stderr, "Warning: Converting illegal character %c to %c ", -- a_char, alph_wildcard(alph)); -- fprintf(stderr, "in sequence %s.\n", name); -- a_char = alph_wildcard(alph); -- } -- raw_sequence[offset] = (char) a_char; -- ++offset; -- } -- } -- -- raw_sequence[offset] = '\0'; -- free_data_block(seq_block); -- return(return_value); --} -- --/**************************************************************************** - * Read one sequence from a file in Fasta format. - * - * Return: Was a sequence successfully read? -@@ -320,44 +266,6 @@ - } - - /**************************************************************************** -- * Read up to max_chars letters of one sequence from a DATA_BLOCK_T readder -- * and copy them in to the raw sequence in the SEQ_T object starting at the -- * given buffer offset. -- ****************************************************************************/ --void read_one_fasta_segment_from_reader( -- DATA_BLOCK_READER_T *fasta_reader, -- size_t max_size, -- size_t buffer_offset, -- SEQ_T *sequence --) { -- -- assert(sequence != NULL); -- assert(get_seq_length(sequence) <= max_size); -- -- // Get the raw sequence buffer from the SEQ_T -- char *raw_sequence = get_raw_sequence(sequence); -- if (raw_sequence == NULL) { -- // Allocate space for raw sequence if not done yet. -- raw_sequence = mm_malloc(sizeof(char) * max_size + 1); -- raw_sequence[0] = 0; -- } -- -- // Read a block of sequence charaters into the -- // raw sequence buffer for the SEQ_T. -- char *name = get_seq_name(sequence); -- BOOLEAN_T is_complete = read_raw_sequence_from_reader( -- fasta_reader, -- name, -- NULL, //FIXME this is dodgy, need a proper way of getting the alphabet. The fasta_reader has it but it is not accessable! -- buffer_offset, -- max_size, -- raw_sequence -- ); -- set_raw_sequence(raw_sequence, is_complete, sequence); -- --} -- --/**************************************************************************** - * Read all the sequences from a FASTA file at once. - Multiple files can be appended by calling this more than once. - ****************************************************************************/ ---- a/src/fasta-io.h -+++ b/src/fasta-io.h -@@ -43,19 +43,6 @@ - ); - - /**************************************************************************** -- * Read up to max_chars letters of one sequence from a DATA_BLOCK_T readder -- * and copy them in to the raw sequence in the SEQ_T object starting at the -- * given buffer offset. -- ****************************************************************************/ --void read_one_fasta_segment_from_reader( -- DATA_BLOCK_READER_T *fasta_reader, -- size_t max_size, -- size_t buffer_offset, -- SEQ_T* sequence --); -- -- --/**************************************************************************** - * Read all the sequences from a file in Fasta format. - ****************************************************************************/ - void read_many_fastas ---- a/src/init.c -+++ b/src/init.c -@@ -767,10 +767,16 @@ - if (alph_is_builtin_protein(alph)) { // default mixture prior for proteins - plib_name = make_path_to_file(get_meme_etc_dir(), PROTEIN_PLIB); - } else { -- fprintf(stderr, "The prior library must be specified for DNA or custom " -- "alphabets when specifiying a prior type of 'dmix', 'mega' " -- "or 'megap'."); -- exit(1); -+ fprintf( -+ stderr, -+ "WARNING: When using DNA or a custom alphabet, " -+ "and specifiying a prior type of\n" -+ "'dmix', 'mega' or 'megap', a prior library must be provided.\n" -+ "No prior library was provided, so a simple Dirichlet prior will be used.\n" -+ ); -+ prior = "dirichlet"; -+ ptype = Dirichlet; -+ if (beta <= 0) beta = 0.01; // default b = 0.01 for simple Dirichlet - } - } - } ---- a/src/seq-reader-from-fasta.c -+++ b/src/seq-reader-from-fasta.c -@@ -639,11 +639,140 @@ - return fasta_reader->current_position; - } - -+ -+/**************************************************************************** -+ * Read up to max_chars letters of one sequence from a DATA_BLOCK_T readder -+ * and copy them in to the raw sequence in the SEQ_T object starting at the -+ * given buffer offset. -+ ****************************************************************************/ -+void read_one_fasta_segment_from_reader( -+ DATA_BLOCK_READER_T *fasta_reader, -+ size_t max_size, -+ size_t offset, -+ SEQ_T *sequence -+) { -+ -+ -+ assert(sequence != NULL); -+ assert(offset < max_size); -+ -+ // Get the raw sequence buffer from the SEQ_T -+ char *raw_sequence = get_raw_sequence(sequence); -+ if (raw_sequence == NULL) { -+ // Allocate space for raw sequence if not done yet. -+ raw_sequence = mm_malloc(sizeof(char) * max_size + 1); -+ raw_sequence[0] = 0; -+ } -+ -+ // Read a block of sequence charaters into the -+ // raw sequence buffer for the SEQ_T, starting at offset. -+ BOOLEAN_T is_complete = read_raw_sequence_from_reader( -+ fasta_reader, -+ max_size - offset, -+ raw_sequence + offset -+ ); -+ set_raw_sequence(raw_sequence, is_complete, sequence); -+} -+ -+/**************************************************************************** -+ * Read raw sequence until a new sequence is encountered or too many letters -+ * are read. -+ * -+ * Return: Was the sequence read completely? -+ ****************************************************************************/ -+BOOLEAN_T read_raw_sequence_from_reader( -+ DATA_BLOCK_READER_T *reader, // Sequence source -+ unsigned int max_chars, // Maximum chars in raw_sequence. -+ char* raw_sequence // Pre-allocated sequence buffer. -+) { -+ -+ SEQ_READER_FROM_FASTA_T *fasta_reader -+ = (SEQ_READER_FROM_FASTA_T *) get_data_block_reader_data(reader); -+ -+ // Read sequence into temp. buffer from the sequence file. -+ char buffer[max_chars]; -+ long start_file_pos = ftell(fasta_reader->fasta_file); -+ size_t seq_index = 0; -+ size_t total_read = 0; -+ while (seq_index < max_chars) { -+ -+ size_t num_char_read = fread( -+ buffer, -+ sizeof(char), -+ max_chars - seq_index, -+ fasta_reader->fasta_file -+ ); -+ fasta_reader->current_position += num_char_read; -+ total_read += num_char_read; -+ -+ if (feof(fasta_reader->fasta_file)) { -+ fasta_reader->at_end_of_file = TRUE; -+ } -+ else if (num_char_read < (max_chars - seq_index)) { -+ die( -+ "Error while reading sequence from file:%s.\nError message: %s\n", -+ fasta_reader->filename, -+ strerror(ferror(fasta_reader->fasta_file)) -+ ); -+ } -+ -+ size_t i; -+ for(i = 0; i < num_char_read; ++i) { -+ char c = buffer[i]; -+ assert(c != 0); -+ if (isspace(c)) { -+ // Skip over white space -+ fasta_reader->at_start_of_line = (c == '\n'); -+ } -+ else if (c == '>' && fasta_reader->at_start_of_line == TRUE) { -+ // We found the start of a new sequence while trying -+ // to fill the buffer. Leave the buffer incomplete. -+ // and wind back the file -+ fseek(fasta_reader->fasta_file, start_file_pos + i - 1, SEEK_SET); -+ fasta_reader->current_position = start_file_pos + i - 1; -+ fasta_reader->at_end_of_seq = TRUE; -+ fasta_reader->at_start_of_line = FALSE; -+ fasta_reader->at_end_of_file = FALSE; -+ break; -+ } -+ else { -+ fasta_reader->at_start_of_line = FALSE; -+ // Check that character is legal in alphabet. -+ // If not, replace with wild card character. -+ if (alph_is_known(fasta_reader->alphabet, c)) { -+ raw_sequence[seq_index] = c; -+ } -+ else { -+ raw_sequence[seq_index] = alph_wildcard(fasta_reader->alphabet); -+ fprintf( -+ stderr, -+ "Warning: %c is not a valid character in %s alphabet.\n" -+ " Converting %c to %c.\n", -+ c, -+ alph_name(fasta_reader->alphabet), -+ c, -+ raw_sequence[i] -+ ); -+ } -+ ++seq_index; -+ } -+ } -+ if (fasta_reader->at_end_of_seq | fasta_reader->at_end_of_file) { -+ break; -+ } -+ } -+ -+ raw_sequence[seq_index] = '\0'; -+ return(fasta_reader->at_end_of_seq | fasta_reader->at_end_of_file); -+} -+ - /****************************************************************************** -- * Fills in the next data block for the sequence. -- * During the first call for the sequence it fills in the full data block. -- * On successive calls, shifts the sequence in the block down one position -- * and reads one more character. -+ * Populates the data block for the with the next block of sequence. -+ * -+ * During the first call for the sequence it fills in a buffer from a file, -+ * The sequence pointer in the data block is set to point at the start of the buffer. -+ * On successive calls, the sequence pointer in the block is shifted down one position -+ * in the buffer. When the end of the buffer is reached, it is filled again from the file. - * - * Returns TRUE if it was able to completely fill the block, FALSE if - * the next sequence or EOF was reached before the block was filled. ---- a/src/seq-reader-from-fasta.h -+++ b/src/seq-reader-from-fasta.h -@@ -37,5 +37,30 @@ - int * end_ptr // end position of sequence (chr:\d+-(\d+)) - ); - -+/**************************************************************************** -+ * Read raw sequence until a new sequence is encountered or too many letters -+ * are read. -+ * -+ * Return: Was the sequence read completely? -+ ****************************************************************************/ -+BOOLEAN_T read_raw_sequence_from_reader( -+ DATA_BLOCK_READER_T *fasta_reader, // Sequence source -+ unsigned int max_chars, // Maximum chars in raw_sequence. -+ char* raw_sequence // Pre-allocated sequence. -+); -+ -+/**************************************************************************** -+ * Read up to max_chars letters of one sequence from a DATA_BLOCK_T readder -+ * and copy them in to the raw sequence in the SEQ_T object starting at the -+ * given buffer offset. -+ ****************************************************************************/ -+void read_one_fasta_segment_from_reader( -+ DATA_BLOCK_READER_T *reader, -+ size_t max_size, -+ size_t offset, -+ SEQ_T *sequence -+); -+ -+ - size_t get_current_pos_from_seq_reader_from_fasta(DATA_BLOCK_READER_T *reader); - #endif diff --git a/sci-biology/meme/files/meme-4.11.2_p2-patch2.patch b/sci-biology/meme/files/meme-4.11.2_p2-patch2.patch deleted file mode 100644 index 498d1df7b664..000000000000 --- a/sci-biology/meme/files/meme-4.11.2_p2-patch2.patch +++ /dev/null @@ -1,54 +0,0 @@ ---- a/doc/release-notes.html -+++ b/doc/release-notes.html -@@ -15,6 +15,21 @@ - </div> - <h2>MEME Suite Release Notes</h2> - <hr> -+ <b>MEME version 4.11.2 patch 2 -- October 24, 2016</b> -+ <ul> -+ <li> -+ <b>Bug fixes</b> -+ <ul> -+ <li> -+ Fixed bug in handling of RNA-like custom alphabets. -+ </li> -+ <li> -+ Fixed bug in MAST -comp option. -+ </li> -+ </ul -+ </li> -+ </ul> -+ <hr> - <b>MEME version 4.11.2 patch 1 -- June 16, 2016</b> - <ul> - <li> ---- a/src/alph-in.c -+++ b/src/alph-in.c -@@ -1044,7 +1044,7 @@ - lookup[0] = sym->complement; - comp2 = (ALPH_SYM_T*)rbtree_get(reader->merged, lookup); - } -- if (comp1 != comp2) { -+ if (comp1 && (comp1 != comp2)) { - add_msg(reader, parmsg_create(SEVERITY_ERROR, -1, -1, -1, - "not like %s alphabet as %c complement rules are incorrect", - ext_name, req_syms[i])); ---- a/src/mast-util.c -+++ b/src/mast-util.c -@@ -740,14 +740,14 @@ - - // create the frequency array - alph = xlate ? xlate_dest_alph(xlate) : alph; -- freq = allocate_array(alph_size_core(alph)); -+ freq = allocate_array(alph_size_full(alph)); - init_array(0, freq); - - // count the number of letters of each type - if (xlate) { - for (n=0; sequence[n]; n++) { - i = xlate_index(xlate, false, sequence+n); -- if (i > 0 && i < alph_size_core(alph)) incr_array_item(i, 1, freq); -+ if (i > 0 && i < alph_size_full(alph)) incr_array_item(i, 1, freq); - } - } else { - for (n=0; sequence[n]; n++) { diff --git a/sci-biology/meme/meme-4.11.2_p2.ebuild b/sci-biology/meme/meme-4.11.2_p2.ebuild deleted file mode 100644 index 0f7d25b43368..000000000000 --- a/sci-biology/meme/meme-4.11.2_p2.ebuild +++ /dev/null @@ -1,109 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit autotools perl-functions python-single-r1 versionator - -MY_PV=$(get_version_component_range 1-3) -MY_P=${PN}_${MY_PV} - -DESCRIPTION="The MEME/MAST system - Motif discovery and search" -HOMEPAGE="http://meme-suite.org/tools/meme" -SRC_URI="http://meme-suite.org/meme-software/${MY_PV}/${MY_P}.tar.gz" - -LICENSE="meme" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="debug doc examples mpi" - -RDEPEND=" - ${PYTHON_DEPS} - app-shells/tcsh - dev-libs/libxml2:2 - dev-libs/libxslt - sys-libs/zlib - app-text/ghostscript-gpl - media-gfx/imagemagick - dev-lang/perl:= - dev-perl/HTML-Parser - dev-perl/HTML-Template - dev-perl/Log-Log4perl - dev-perl/Math-CDF - dev-perl/XML-Compile-SOAP - dev-perl/XML-Compile-WSDL11 - dev-perl/XML-Parser - dev-perl/XML-Simple - virtual/perl-Data-Dumper - virtual/perl-Exporter - virtual/perl-File-Path - virtual/perl-File-Spec - virtual/perl-File-Temp - virtual/perl-Getopt-Long - virtual/perl-Scalar-List-Utils - virtual/perl-Time-HiRes - mpi? ( virtual/mpi )" -DEPEND="${RDEPEND}" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -S="${WORKDIR}/${MY_P}" -PATCHES=( - "${FILESDIR}"/${PN}-4.11.2_p2-patch1.patch - "${FILESDIR}"/${PN}-4.11.2_p2-patch2.patch - "${FILESDIR}"/${PN}-4.11.2_p2-fix-build-system.patch -) - -pkg_setup() { - python-single-r1_pkg_setup - perl_set_version -} - -src_prepare() { - default - eautoreconf -} - -src_configure() { - econf \ - --sysconfdir="${EPREFIX}"/etc/${PN} \ - --with-logs="${EPREFIX}"/var/log/${PN} \ - --with-perl=perl \ - --with-convert=convert \ - --with-gs=gs \ - --disable-build-libxml2 \ - --disable-build-libxslt \ - $(use_enable debug) \ - $(use_enable doc) \ - $(use_enable examples) \ - $(use_enable !mpi serial) \ - --with-perl-dir="${VENDOR_LIB#${EPREFIX}/usr}" \ - PYTHON="${EPYTHON}" - - # delete bundled libs, just to be sure. These need - # to be removed after econf, else AC_OUTPUT will fail - rm -r src/{libxml2,lib{,e}xslt} || die -} - -src_test() { - # bug #297070 - emake -j1 test -} - -src_install() { - default - docompress -x /usr/share/doc/${PF}/examples - - # prefix all binaries with 'meme-', in order - # to prevent collisions, bug 455010 - cd "${ED%/}"/usr/bin/ || die - local i - for i in *; do - if [[ $i != meme-* ]]; then - mv {,meme-}"${i}" || die - fi - done - - keepdir /var/log/meme -} diff --git a/sci-biology/meme/metadata.xml b/sci-biology/meme/metadata.xml deleted file mode 100644 index 959160fe46b1..000000000000 --- a/sci-biology/meme/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/metadata.xml b/sci-biology/metadata.xml index 7a808874b6e6..6b9dcbff3e29 100644 --- a/sci-biology/metadata.xml +++ b/sci-biology/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE catmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE catmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <catmetadata> <longdescription lang="en"> The sci-biology category contains software that can be used @@ -43,4 +43,3 @@ Kategoria sci-biology zawiera programy naukowe związane z biologią. </longdescription> </catmetadata> - diff --git a/sci-biology/mira/Manifest b/sci-biology/mira/Manifest deleted file mode 100644 index 48fa9af279dd..000000000000 --- a/sci-biology/mira/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST mira-4.0.2.tar.bz2 10368046 BLAKE2B cc84c6c13c8024409634ccafd103be8a4f2a9e27fa7f19d2ef401393db9e8063a6fac2f21cd25dfe58e90aee8cf38983369d928241f9bc65e78da0e95fa41d3b SHA512 a7f9845de207cefb87ffa652f4f6b9b85735ef22eeb29b456e4d946ba1675e7dd2c78abb2da56f11fddcb699f5c0700a08ce298196ce1a8e586a758a8d3bdc7e -DIST mira_3rdparty_06-07-2012.tar.bz2 31656 BLAKE2B 7e952d96e9073acd8ab1d1fc7c51c37f6526287d31698c5090500d421147285b535e8cab7e49f4e51a5634c901d1cd969206b1727e683d3fcebdc195399e3589 SHA512 4d4dbdf7ab5126f9d47160bee8bc127b6a225de8087f6b9914c754324a74d966333207c86a3f38cf0ea9f91408707e2a24086dbe1318fdfa2870b0c39bc5033b diff --git a/sci-biology/mira/files/mira-4.0.2-boost-1.50.patch b/sci-biology/mira/files/mira-4.0.2-boost-1.50.patch deleted file mode 100644 index 50f83c9021dc..000000000000 --- a/sci-biology/mira/files/mira-4.0.2-boost-1.50.patch +++ /dev/null @@ -1,22 +0,0 @@ -ax_boost_regex.m4 | 4 ++-- -1 file changed, 2 insertions(+), 2 deletions(-) - ---- mira-4.0.2/m4/ax_boost_regex.m4 -+++ mira-4.0.2/m4/ax_boost_regex.m4 -@@ -78,14 +78,14 @@ - for libextension in `ls $BOOSTLIBDIR/libboost_regex*.so* $BOOSTLIBDIR/libboost_regex*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_regex.*\)\.so.*$;\1;' -e 's;^lib\(boost_regex.*\)\.a*$;\1;'` ; do - ax_lib=${libextension} - AC_CHECK_LIB($ax_lib, exit, -- [BOOST_REGEX_LIB="-l$ax_lib"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break], -+ [BOOST_REGEX_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break], - [link_regex="no"]) - done - if test "x$link_regex" != "xyes"; then - for libextension in `ls $BOOSTLIBDIR/boost_regex*.{dll,a}* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_regex.*\)\.dll.*$;\1;' -e 's;^\(boost_regex.*\)\.a*$;\1;'` ; do - ax_lib=${libextension} - AC_CHECK_LIB($ax_lib, exit, -- [BOOST_REGEX_LIB="-l$ax_lib"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break], -+ [BOOST_REGEX_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break], - [link_regex="no"]) - done - fi diff --git a/sci-biology/mira/files/mira-4.0.2-cmath.patch b/sci-biology/mira/files/mira-4.0.2-cmath.patch deleted file mode 100644 index a4a020177af7..000000000000 --- a/sci-biology/mira/files/mira-4.0.2-cmath.patch +++ /dev/null @@ -1,14 +0,0 @@ ---- mira-4.0.2/src/mira/ads.C -+++ mira-4.0.2/src/mira/ads.C -@@ -31,10 +31,11 @@ - * Routines for computing scores and some other classification number are - * provided, too. - * - */ - -+#include <cmath> - - #include "ads.H" - - #include "errorhandling/errorhandling.H" - #include "util/dptools.H" diff --git a/sci-biology/mira/files/mira-4.0.2-cout.patch b/sci-biology/mira/files/mira-4.0.2-cout.patch deleted file mode 100644 index 78e7168cb49d..000000000000 --- a/sci-biology/mira/files/mira-4.0.2-cout.patch +++ /dev/null @@ -1,27 +0,0 @@ - src/progs/quirks.C | 2 ++ - 1 file changed, 2 insertions(+) - -diff --git a/src/progs/quirks.C b/src/progs/quirks.C -index 47e5ee8..060b6f3 100644 ---- a/src/progs/quirks.C -+++ b/src/progs/quirks.C -@@ -25,6 +25,8 @@ - - #include <boost/filesystem.hpp> - -+#include <iostream> -+ - // make the "tcmalloc: large alloc" messages from TCMallom disappear - // by setting the reporting environment variable to a very large value - // see: http://groups.google.com/group/google-perftools/browse_thread/thread/24a003fc35f3d470?pli=1 ---- a/src/mira/parameters.C -+++ b/src/mira/parameters.C -@@ -2222,7 +2222,7 @@ - MIRANOTIFY(Notify::FATAL, "File not found: " << pfile); - } - -- parse(fin, Pv, nullptr); -+ parse(fin, Pv, false); - - fin.close(); - diff --git a/sci-biology/mira/metadata.xml b/sci-biology/mira/metadata.xml deleted file mode 100644 index 0704cef4806d..000000000000 --- a/sci-biology/mira/metadata.xml +++ /dev/null @@ -1,11 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">mira-assembler</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/mira/mira-4.0.2.ebuild b/sci-biology/mira/mira-4.0.2.ebuild deleted file mode 100644 index f5ac6cfe70f5..000000000000 --- a/sci-biology/mira/mira-4.0.2.ebuild +++ /dev/null @@ -1,97 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -MIRA_3RDPARTY_PV="06-07-2012" -MY_PV="${PV/_}" # convert from mira-4.0_rc2 (Gentoo ebuild filename derived) to mira-4.0rc2 (upstream fromat) - -inherit autotools eutils multilib - -DESCRIPTION="Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Illumina" -HOMEPAGE="http://www.chevreux.org/projects_mira.html" -SRC_URI=" - https://sourceforge.net/projects/mira-assembler/files/MIRA/stable/"${PN}"-"${MY_PV}".tar.bz2 - mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2" -# https://sourceforge.net/projects/mira-assembler/files/MIRA/development/${P}.tar.bz2 -# mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2" - -S="${WORKDIR}"/"${PN}"-"${MY_PV}" - -SLOT="0" -LICENSE="GPL-2" -KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~x86-macos" -IUSE="doc" - -CDEPEND=" - dev-libs/boost[threads] - dev-util/google-perftools" -DEPEND="${CDEPEND} - sys-devel/flex - app-editors/vim-core - dev-libs/expat" -RDEPEND="${CDEPEND}" - -#DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED -# THANKS doc/3rdparty/scaffolding_MIRA_BAMBUS.pdf ) -DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED THANKS ) - -PATCHES=( - "${FILESDIR}/${PN}-4.0.2-boost-1.50.patch" - "${FILESDIR}/${PN}-4.0.2-cout.patch" - "${FILESDIR}/${PN}-4.0.2-cmath.patch" -) - -src_prepare() { - find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die - - default - - sed \ - -e "s:-O[23]::g" \ - -e "s:-funroll-loops::g" \ - -i configure.ac || die - - eautoreconf - - # Remove C++ source files that upstream built with flex. - local f - local PREBUILT_CXX_LEXER_FILES=( - "${S}"/src/caf/caf_flexer.cc - "${S}"/src/io/exp_flexer.cc - "${S}"/src/mira/parameters_flexer.cc - ) - - for f in "${PREBUILT_CXX_LEXER_FILES[@]}"; do - if [[ -f ${f} ]] ; then - rm "${f}" || die "Failed to remove ${f}" - else - die "${f} not found" - fi - done -} - -src_configure() { - econf \ - --with-boost="${EPREFIX}/usr/$(get_libdir)" \ - --with-boost-libdir="${EPREFIX}/usr/$(get_libdir)" \ - --with-boost-thread=boost_thread-mt -} - -#src_compile() { -# base_src_compile -# # TODO: resolve docbook incompatibility for building docs -# use doc && emake -C doc clean docs -#} - -src_install() { - default - - dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl} - dodoc "${WORKDIR}"/3rdparty/{README.txt,midi_screen.fasta} -} - -pkg_postinst() { - einfo "Documentation is no longer built, you can find it at:" - einfo "http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html" -} diff --git a/sci-biology/mosaik/files/mosaik-2.2.30-gcc11.patch b/sci-biology/mosaik/files/mosaik-2.2.30-gcc11.patch new file mode 100644 index 000000000000..918d882983a3 --- /dev/null +++ b/sci-biology/mosaik/files/mosaik-2.2.30-gcc11.patch @@ -0,0 +1,60 @@ +--- a/CommonSource/DataStructures/UnorderedMap.h ++++ b/CommonSource/DataStructures/UnorderedMap.h +@@ -42,13 +42,9 @@ + + #else // all decent C++ compilers + +-#ifdef WIN32 + #include <unordered_map> +-#else // Linux +-#include <tr1/unordered_map> +-#endif + +-using namespace std::tr1; ++using namespace std; + + #endif + +--- a/CommonSource/DataStructures/UnorderedSet.h ++++ b/CommonSource/DataStructures/UnorderedSet.h +@@ -42,13 +42,9 @@ + + #else // all decent C++ compilers + +-#ifdef WIN32 + #include <unordered_set> +-#else // Linux +-#include <tr1/unordered_set> +-#endif + +-using namespace std::tr1; ++using namespace std; + + #endif + +--- a/CommonSource/Utilities/RegexUtilities.h ++++ b/CommonSource/Utilities/RegexUtilities.h +@@ -12,10 +12,7 @@ + #define REGEXUTILITIES_H_ + + #include <iostream> +-#ifdef WIN32 + #include <regex> +-using namespace std::tr1; +-#endif + #include <string> + #include <vector> + #include <cstdlib> +--- a/MosaikBuild/MosaikBuild.h ++++ b/MosaikBuild/MosaikBuild.h +@@ -15,10 +15,7 @@ + #include <iostream> + #include <fstream> + #include <map> +-#ifdef WIN32 + #include <regex> +-using namespace std::tr1; +-#endif + #include <set> + #include <sstream> + #include "ColorspaceUtilities.h" diff --git a/sci-biology/mosaik/files/mosaik-2.2.30-gcc12-time.patch b/sci-biology/mosaik/files/mosaik-2.2.30-gcc12-time.patch new file mode 100644 index 000000000000..1bc63bfd4776 --- /dev/null +++ b/sci-biology/mosaik/files/mosaik-2.2.30-gcc12-time.patch @@ -0,0 +1,11 @@ +https://bugs.gentoo.org/851669 +--- a/CommonSource/Utilities/SafeFunctions.h ++++ b/CommonSource/Utilities/SafeFunctions.h +@@ -17,6 +17,7 @@ + #include <cstdio> + #include <cstdarg> + #include <cstring> ++#include <ctime> + #include <stdio.h> + #include <stdlib.h> + #include <errno.h> diff --git a/sci-biology/mosaik/metadata.xml b/sci-biology/mosaik/metadata.xml index a3eca9b62b1c..cbe93c59213f 100644 --- a/sci-biology/mosaik/metadata.xml +++ b/sci-biology/mosaik/metadata.xml @@ -1,5 +1,5 @@ -<?xml version='1.0' encoding='UTF-8'?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/mosaik/mosaik-2.2.30.ebuild b/sci-biology/mosaik/mosaik-2.2.30.ebuild index 874edba4504d..a929f1160f67 100644 --- a/sci-biology/mosaik/mosaik-2.2.30.ebuild +++ b/sci-biology/mosaik/mosaik-2.2.30.ebuild @@ -1,25 +1,26 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 inherit flag-o-matic toolchain-funcs vcs-snapshot DESCRIPTION="A reference-guided aligner for next-generation sequencing technologies" HOMEPAGE="https://github.com/wanpinglee/MOSAIK" SRC_URI="https://github.com/wanpinglee/MOSAIK/archive/5c25216d3522d6a33e53875cd76a6d65001e4e67.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/${P}/src" LICENSE="GPL-2" SLOT="0" KEYWORDS="~amd64 ~x86" -S="${WORKDIR}/${P}/src" - PATCHES=( "${FILESDIR}"/${P}-remove-platform-code.patch "${FILESDIR}"/${P}-fix-build-system.patch "${FILESDIR}"/${P}-Wformat-security.patch "${FILESDIR}"/${P}-gcc7.patch + "${FILESDIR}"/${P}-gcc11.patch + "${FILESDIR}"/${P}-gcc12-time.patch ) src_configure() { @@ -31,8 +32,8 @@ src_configure() { src_compile() { emake \ - CC=$(tc-getCC) \ - CXX=$(tc-getCXX) \ + CC="$(tc-getCC)" \ + CXX="$(tc-getCXX)" \ CFLAGS="${CFLAGS}" \ CXXFLAGS="${CXXFLAGS}" \ CPPFLAGS="${CPPFLAGS}" \ diff --git a/sci-biology/mothur/Manifest b/sci-biology/mothur/Manifest index 9d78212016cd..ada6350ceeef 100644 --- a/sci-biology/mothur/Manifest +++ b/sci-biology/mothur/Manifest @@ -1 +1,2 @@ DIST mothur-1.27.0.zip 7095054 BLAKE2B 96a6410d36f64ff50591955aa22bfddf6217c7568022c8c7f70ab70c65d57af2217477de56b6f9ceaf11237cdc5380bd354cf6564002357546539585d0f58221 SHA512 81821ca95d4ce3f0d1e6aa920c4fe3fddd70f716157312ed0590c1c4ad728e6786bfe79f6badddcfb060ed5d1996cc1b5062c320a59209fef35f68e687ba3dd5 +DIST mothur-1.48.0.tar.gz 1652711 BLAKE2B 39e1d2a32a63d441267b4e0e739505bdcb3ab392c169c96d60e816dbd9fab6b92745e8a9eaae31062711f2de0130dae540bba34c6bd97e76a921711f58c11f65 SHA512 a43ef6a223238d40e51c15043360ba9cae86347affea2f1a4e365635fb0949981ad32001b88d4061a033b2a002e944df16923a0622a40bf061791f06143467e1 diff --git a/sci-biology/mothur/files/mothur-1.48.0-build.patch b/sci-biology/mothur/files/mothur-1.48.0-build.patch new file mode 100644 index 000000000000..da9784e20dd8 --- /dev/null +++ b/sci-biology/mothur/files/mothur-1.48.0-build.patch @@ -0,0 +1,79 @@ +Fix building and don't use bundled uchime. +--- a/Makefile ++++ b/Makefile +@@ -104,12 +104,19 @@ endif + # INCLUDE directories for mothur + # + # +- VPATH=source/calculators:source/chimera:source/classifier:source/clearcut:source/commands:source/communitytype:source/datastructures:source/engines:source/metastats:source/read:source/svm:source/ ++ VPATH=source:source/calculators:source/chimera:source/classifier:source/clearcut:source/commands:source/communitytype:source/datastructures:source/engines:source/metastats:source/read:source/svm:source/ ++ source := source + skipUchime := source/uchime_src/ ++ skipTestMothur := source/TestMothur/ ++ skipSeqnoise := seqnoise.cpp + subdirs := $(sort $(dir $(filter-out $(skipUchime), $(wildcard source/*/)))) ++ subdirs := $(filter-out $(skipTestMothur), $(subdirs)) + subDirIncludes = $(patsubst %, -I %, $(subdirs)) ++ subDirIncludes += $(patsubst %, -I %, $(source)) + subDirLinking = $(patsubst %, -L%, $(subdirs)) +- CXXFLAGS += -I. $(subDirIncludes) ++ subDirLinking += $(patsubst %, -L%, $(source)) ++ subdirs := $(dir source) $(sort $(dir $(filter-out $(skipUchime), $(wildcard source/*/)))) ++ CXXFLAGS += -Isource -I. $(subDirIncludes) + LDFLAGS += $(subDirLinking) + + +@@ -118,15 +125,14 @@ endif + # + OBJECTS=$(patsubst %.cpp,%.o,$(wildcard $(addsuffix *.cpp,$(subdirs)))) + OBJECTS+=$(patsubst %.c,%.o,$(wildcard $(addsuffix *.c,$(subdirs)))) ++ OBJECTS+=$(patsubst %.cpp,%.o,$(filter-out $(skipSeqnoise), $(wildcard source/*.cpp))) ++ OBJECTS+=$(patsubst %.cpp,%.o,$(filter-out $(skipSeqnoise), $(wildcard source/*.c))) + OBJECTS+=$(patsubst %.cpp,%.o,$(wildcard *.cpp)) + OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c)) + +-mothur : $(OBJECTS) uchime ++mothur : $(OBJECTS) + $(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS) + +-uchime : +- cd source/uchime_src && export CXX=$(CXX) && make clean && make && mv uchime ../../ && cd .. +- + install : mothur + + ifeq ($(strip $(INSTALL_DIR)),"\"Enter_your_mothur_install_path_here\"") +--- a/makefile-internal ++++ b/makefile-internal +@@ -115,7 +115,6 @@ endif + + mothur : $(OBJECTS) + $(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS) +- strip mothur + + %.o : %.c %.h + $(COMPILE.c) $(OUTPUT_OPTION) $< +--- a/source/uchime_src/makefile ++++ b/source/uchime_src/makefile +@@ -1,4 +1,4 @@ +-CXXFLAGS = -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 ++CXXFLAGS = -std=c++11 -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 + LDFLAGS = -g + + # +@@ -26,4 +26,4 @@ install : uchime + + clean : + @rm -f $(OBJECTS) +- +\ No newline at end of file ++ +--- a/source/writer.h ++++ b/source/writer.h +@@ -9,6 +9,7 @@ + #ifndef writer_h + #define writer_h + ++#include <memory> + #include "sharedwriter.hpp" + + /***********************************************************************/ diff --git a/sci-biology/mothur/metadata.xml b/sci-biology/mothur/metadata.xml index 959160fe46b1..15fc0072ba17 100644 --- a/sci-biology/mothur/metadata.xml +++ b/sci-biology/mothur/metadata.xml @@ -1,8 +1,16 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <use> + <flag name="boost">Depend on <pkg>dev-libs/boost</pkg> for make.contigs to read .gz compressed files.</flag> + <flag name="gsl">Use <pkg>sci-libs/gsl</pkg> to support diversity estimates for estimiator.single.</flag> + <flag name="hdf5">Support Biom format 2.0 for the biom.info command via <pkg>sci-libs/hdf5</pkg>.</flag> + </use> + <upstream> + <remote-id type="github">mothur/mothur</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/mothur/mothur-1.27.0-r1.ebuild b/sci-biology/mothur/mothur-1.27.0-r1.ebuild index 9e9bf2160310..3f5603e9ecb5 100644 --- a/sci-biology/mothur/mothur-1.27.0-r1.ebuild +++ b/sci-biology/mothur/mothur-1.27.0-r1.ebuild @@ -1,43 +1,42 @@ -# Copyright 1999-2018 Gentoo Foundation +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=7 -inherit eutils flag-o-matic fortran-2 toolchain-funcs +inherit flag-o-matic fortran-2 toolchain-funcs DESCRIPTION="A suite of algorithms for ecological bioinformatics" HOMEPAGE="https://www.mothur.org/" SRC_URI="https://www.mothur.org/w/images/c/cb/Mothur.${PV}.zip -> ${P}.zip" +S="${WORKDIR}/${PN^}.source" LICENSE="GPL-3" SLOT="0" +KEYWORDS="amd64 ~x86" IUSE="mpi +readline" -KEYWORDS="amd64 x86" RDEPEND=" sci-biology/uchime mpi? ( virtual/mpi )" -DEPEND="${RDEPEND} - app-arch/unzip" +DEPEND="${RDEPEND}" +BDEPEND="app-arch/unzip" -S=${WORKDIR}/Mothur.source +PATCHES=( + "${FILESDIR}"/${P}-makefile.patch + "${FILESDIR}"/${P}-overflows.patch +) -pkg_setup() { - fortran-2_pkg_setup - use mpi && export CXX=mpicxx || export CXX=$(tc-getCXX) +src_configure() { + use mpi && export CXX=mpicxx || tc-export CXX use amd64 && append-cppflags -DBIT_VERSION } -src_prepare() { - epatch \ - "${FILESDIR}"/${P}-makefile.patch \ - "${FILESDIR}"/${P}-overflows.patch -} - src_compile() { - emake USEMPI=$(usex mpi) USEREADLINE=$(usex readline) + emake \ + USEMPI=$(usex mpi) \ + USEREADLINE=$(usex readline) } src_install() { - dobin ${PN} + dobin mothur } diff --git a/sci-biology/mothur/mothur-1.48.0.ebuild b/sci-biology/mothur/mothur-1.48.0.ebuild new file mode 100644 index 000000000000..7d54bf273ac0 --- /dev/null +++ b/sci-biology/mothur/mothur-1.48.0.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit flag-o-matic toolchain-funcs + +DESCRIPTION="A suite of algorithms for ecological bioinformatics" +HOMEPAGE="https://mothur.org/" +SRC_URI="https://github.com/mothur/mothur/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="boost gsl hdf5 mpi +readline" + +RDEPEND=" + sci-biology/uchime + boost? ( dev-libs/boost:=[zlib] ) + gsl? ( sci-libs/gsl:= ) + hdf5? ( sci-libs/hdf5:=[cxx] ) + mpi? ( virtual/mpi ) +" +DEPEND="${RDEPEND}" + +PATCHES=( + "${FILESDIR}"/${PN}-1.48.0-build.patch +) + +src_configure() { + use mpi && export CXX=mpicxx || tc-export CXX + use amd64 && append-cppflags -DBIT_VERSION +} + +src_compile() { + # bug #862273 + append-flags -fno-strict-aliasing + filter-lto + + # USEBOOST - link with boost libraries. Must install boost. Allows the make.contigs command to read .gz files. + # USEHDF5 - link with HDF5cpp libraries. Must install HDF5. Allows the biom.info command to read Biom format 2.0. + # USEGSL - link with GNU Scientific libraries. Must install GSL. Allows the estimiator.single command to find diversity estimates. + emake \ + USEBOOST=$(usex boost) \ + USEHDF5=$(usex hdf5) \ + USEGSL=$(usex gsl) \ + USEMPI=$(usex mpi) \ + USEREADLINE=$(usex readline) \ + OPTIMIZE=no +} + +src_install() { + dobin mothur +} diff --git a/sci-biology/mrbayes/Manifest b/sci-biology/mrbayes/Manifest index 799aafc484a4..3d68a52ee87a 100644 --- a/sci-biology/mrbayes/Manifest +++ b/sci-biology/mrbayes/Manifest @@ -1 +1,2 @@ DIST mrbayes-3.1.2.tar.gz 545968 BLAKE2B f4c5bbdde765fb9e596c17d5fd890b168c22cefb0d24b67c1c68623e1dcfa4df716a896fe120f7a1cac4234125b6ed524973506e47492ba3ec26e389783d618a SHA512 2fb0ee7224cbb69c1acf2ffb0c6c8974f63002cda4f39a626eadf80fad9cfc23861f8c03f5545970f3a81e02093d62b6a0549ab7d7f7080557e91e21b2c3ee14 +DIST mrbayes-3.2.7.tar.gz 9787214 BLAKE2B 2d0ebbc376712e15fc1ed146053d977ad1af96f44c31b8fd0fdbd47ef9bafc41cbb8904db94bc8d30c753c0267a1dcce0d08c73d8b35c20e0f15206bc8fef6ff SHA512 4dc869cd07cf384b3a3945ac8d91a7cc2982e8c5cd8d1f097b46a479a071cb71e71c60e152aa4fc01b0bb296295c5fa9f5a48aa8e913b920c33e30cbb3a6ed37 diff --git a/sci-biology/mrbayes/files/mb_readline_312.patch b/sci-biology/mrbayes/files/mb_readline_312.patch index 2f8bab1e7665..d41986704708 100644 --- a/sci-biology/mrbayes/files/mb_readline_312.patch +++ b/sci-biology/mrbayes/files/mb_readline_312.patch @@ -1,25 +1,13 @@ -Index: Makefile -=================================================================== -RCS file: /cvsroot/mrbayes/mrbayes/Makefile,v -retrieving revision 3.23 -retrieving revision 3.24 -diff -U2 -r3.23 -r3.24 ---- Makefile 22 Dec 2005 16:13:06 -0000 3.23 -+++ Makefile 3 Jan 2006 16:43:13 -0000 3.24 +--- a/Makefile ++++ b/Makefile @@ -50,4 +50,5 @@ ifeq ($(strip $(USEREADLINE)),yes) CFLAGS += -DUSE_READLINE +# CFLAGS += -DCOMPLETIONMATCHES LIBS += -lncurses -lreadline endif -Index: bayes.c -=================================================================== -RCS file: /cvsroot/mrbayes/mrbayes/bayes.c,v -retrieving revision 3.39 -retrieving revision 3.40 -diff -U2 -r3.39 -r3.40 ---- bayes.c 23 Dec 2005 16:26:28 -0000 3.39 -+++ bayes.c 3 Jan 2006 16:43:13 -0000 3.40 +--- a/bayes.c ++++ b/bayes.c @@ -382,9 +382,11 @@ char **readline_completion(const char *text, int start, int stop) { char **matches = (char **) NULL; diff --git a/sci-biology/mrbayes/metadata.xml b/sci-biology/mrbayes/metadata.xml index ca6afd95a12e..2fbcd4fa4f98 100644 --- a/sci-biology/mrbayes/metadata.xml +++ b/sci-biology/mrbayes/metadata.xml @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <longdescription> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> MrBayes is a program for the Bayesian estimation of phylogeny. Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a @@ -14,8 +14,9 @@ Bayes's theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees. -</longdescription> - <upstream> - <remote-id type="sourceforge">mrbayes</remote-id> - </upstream> + </longdescription> + <upstream> + <remote-id type="sourceforge">mrbayes</remote-id> + <remote-id type="github">NBISweden/MrBayes</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild b/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild index ebe9926212c9..3d9f683d4666 100644 --- a/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild +++ b/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild @@ -1,26 +1,29 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=8 -inherit eutils toolchain-funcs +inherit toolchain-funcs DESCRIPTION="Bayesian Inference of Phylogeny" HOMEPAGE="http://mrbayes.csit.fsu.edu/" -SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" +SRC_URI="https://downloads.sourceforge.net/${PN}/${P}.tar.gz" -SLOT="0" LICENSE="GPL-2" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos" IUSE="debug mpi readline" DEPEND=" - sys-libs/ncurses:0= + sys-libs/ncurses:= mpi? ( virtual/mpi ) - readline? ( sys-libs/readline:0= )" + readline? ( sys-libs/readline:= ) +" RDEPEND="${DEPEND}" src_prepare() { + default + if use mpi; then sed -e "s:MPI ?= no:MPI=yes:" -i Makefile || die "Patching MPI support." fi @@ -30,7 +33,7 @@ src_prepare() { else # Only needed for OSX with an old (4.x) version of # libreadline, but it doesn't hurt for other distributions. - epatch "${FILESDIR}"/mb_readline_312.patch + eapply "${FILESDIR}"/mb_readline_312.patch fi sed -e 's:-ggdb::g' -i Makefile || die } @@ -41,7 +44,7 @@ src_compile() { if use mpi; then mycc=mpicc else - mycc=$(tc-getCC) + mycc="$(tc-getCC)" fi use mpi && myconf="MPI=yes" diff --git a/sci-biology/mrbayes/mrbayes-3.2.7.ebuild b/sci-biology/mrbayes/mrbayes-3.2.7.ebuild new file mode 100644 index 000000000000..4fbad2f65473 --- /dev/null +++ b/sci-biology/mrbayes/mrbayes-3.2.7.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DESCRIPTION="Bayesian Inference of Phylogeny" +HOMEPAGE="https://nbisweden.github.io/MrBayes/" +SRC_URI="https://github.com/NBISweden/MrBayes/releases/download/v${PV}/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos" +IUSE="debug mpi readline" +# --with-readline was given, but MPI support requires readline to be disabled. +REQUIRED_USE="mpi? ( !readline )" + +DEPEND=" + sys-libs/ncurses:= + mpi? ( virtual/mpi ) + readline? ( sys-libs/readline:= ) +" +RDEPEND="${DEPEND}" + +src_configure() { + econf \ + "$(use_with mpi)" \ + "$(use_with readline)" \ + "$(use_enable debug )" \ + # configure checks cpuid and enables fma{3,4}, sse{1..4} if detected. + # Configure options only allow disabling the auto-detection, but do not + # actually allow toggling the individual cpu instruction sets. The only + # way to guarantee that cross-compiling and binpkgs will work on machines + # other than the host is to unconditionally disable sse/fma/avx. + #"$(use_enable cpu_flags_x86_sse sse )" \ + #"$(use_enable cpu_flags_x86_avx avx )" \ + #"$(use_enable cpu_flags_x86_fma3 fma )" \ + # Has optional support for sci-biology/beagle::science + # "$(use_with beagle)" +} + +src_compile() { + # The --disable options for the cpu instruction sets don't actually work so + # we override it here and also set the user specified CFLAGS. + emake SIMD_FLAGS= CPUEXT_FLAGS= CFLAGS="${CFLAGS}" +} diff --git a/sci-biology/mummer/metadata.xml b/sci-biology/mummer/metadata.xml index 4a3fe8e7bd15..16d1e87a1b24 100644 --- a/sci-biology/mummer/metadata.xml +++ b/sci-biology/mummer/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/mummer/mummer-3.23.ebuild b/sci-biology/mummer/mummer-3.23-r1.ebuild index 4839053f4191..1359833dc21d 100644 --- a/sci-biology/mummer/mummer-3.23.ebuild +++ b/sci-biology/mummer/mummer-3.23-r1.ebuild @@ -1,26 +1,24 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit flag-o-matic toolchain-funcs DESCRIPTION="A rapid whole genome aligner" HOMEPAGE="http://mummer.sourceforge.net/" -SRC_URI="mirror://sourceforge/mummer/MUMmer${PV}.tar.gz" +SRC_URI="https://downloads.sourceforge.net/mummer/MUMmer${PV}.tar.gz" +S="${WORKDIR}/MUMmer${PV}" LICENSE="Artistic" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="doc" -DEPEND="" RDEPEND=" app-shells/tcsh dev-lang/perl" -S=${WORKDIR}/MUMmer${PV} - PATCHES=( "${FILESDIR}"/${PN}-3.23-fix-build-system.patch "${FILESDIR}"/${PN}-3.23-fix-c++-qa.patch @@ -38,7 +36,7 @@ src_install() { dobin scripts/{exact-tandems,mapview,mummerplot,dnadiff,nucmer,promer,run-mummer1,run-mummer3,nucmer2xfig} newbin src/tigr/annotate mummer-annotate - insinto /usr/share/${PN}/lib + insinto /usr/share/mummer/lib doins scripts/Foundation.pm einstalldocs diff --git a/sci-biology/muscle/Manifest b/sci-biology/muscle/Manifest index f1ec094f5a69..0741cc695e2f 100644 --- a/sci-biology/muscle/Manifest +++ b/sci-biology/muscle/Manifest @@ -1 +1,2 @@ +DIST muscle-5.1.0.tar.gz 185437 BLAKE2B b3742c37179fc8c36fb6160be4c3a8b4afa2f686bc018ec8e97a10834c1f1901b54b489faa9c365aa65c8514f378b7b5518d91a4e2fb067492e32202a06c4f64 SHA512 0cafc7ce07e5d0c261811e085e0fec8e44318a3d2604ad530ad95b370d6386143a4eeb59012e17cfc703f54bde5ee0752c3ce7fc8bb489748dbe89b2229dd6eb DIST muscle3.8.31_src.tar.gz 515267 BLAKE2B 79a8517f7a14d8ee907104e9035e1284fcabec556544508fd9b712789759448969ce39ecbefcedac62c435dc91e109b3b5b7027120691310ffebda80ca80dd9e SHA512 2baf2aae354ae1e3f529e627be2ace86e89dd15567e1f642a625b63f08ebe3d4bd7315080c7d786d95e3eda8703545ec74af9fe83ad1523d55d00137fb7274ce diff --git a/sci-biology/muscle/files/0001-Makefile-fix-horribleness-so-that-it-respects-build-.patch b/sci-biology/muscle/files/0001-Makefile-fix-horribleness-so-that-it-respects-build-.patch new file mode 100644 index 000000000000..a8604239105b --- /dev/null +++ b/sci-biology/muscle/files/0001-Makefile-fix-horribleness-so-that-it-respects-build-.patch @@ -0,0 +1,49 @@ +From 9ef231e4612263524a4c41ecb841cdcf0e17d011 Mon Sep 17 00:00:00 2001 +From: Eli Schwartz <eschwartz93@gmail.com> +Date: Tue, 19 Mar 2024 23:44:43 -0400 +Subject: [PATCH] Makefile: fix horribleness so that it respects build system + environment + +Do not strip, that is portage's job. Respect $CXX, don't override use +-O. +--- + Makefile | 15 ++++----------- + 1 file changed, 4 insertions(+), 11 deletions(-) + +diff --git a/Makefile b/Makefile +index df16673..086aba3 100644 +--- a/Makefile ++++ b/Makefile +@@ -19,14 +19,10 @@ OS := $(shell uname) + + CPPFLAGS := $(CPPFLAGS) -DNDEBUG -pthread + +-CXX := g++ +-ifeq ($(OS),Darwin) +- CXX := g++-11 +-endif ++CXX ?= g++ ++CXXFLAGS := $(CXXFLAGS) -fopenmp -ffast-math + +-CXXFLAGS := $(CXXFLAGS) -O3 -fopenmp -ffast-math +- +-LDFLAGS := $(LDFLAGS) -O3 -fopenmp -pthread -lpthread ${LDFLAGS2} ++LDFLAGS := $(LDFLAGS) -fopenmp -pthread -lpthread ${LDFLAGS2} + + HDRS := $(shell echo *.h) + OBJS := $(shell echo *.cpp | sed "-es/^/$(OS)\//" | sed "-es/ / $(OS)\//g" | sed "-es/\.cpp/.o/g") +@@ -35,10 +31,7 @@ SRCS := $(shell ls *.cpp *.h) + .PHONY: clean + + $(OS)/muscle : gitver.txt $(OS)/ $(OBJS) +- $(CXX) $(LDFLAGS) $(OBJS) -o $@ +- +- # Warning: do not add -d option to strip, this is not portable +- strip $(OS)/muscle ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) $(OBJS) -o $@ + + gitver.txt : $(SRCS) + bash ./gitver.bash +-- +2.43.2 + diff --git a/sci-biology/muscle/files/3.8.31-make.patch b/sci-biology/muscle/files/3.8.31-make.patch index 7c0e7308df54..fa3f5c3a014b 100644 --- a/sci-biology/muscle/files/3.8.31-make.patch +++ b/sci-biology/muscle/files/3.8.31-make.patch @@ -1,7 +1,5 @@ -diff --git a/src/mk b/src/mk -index 475d25a..d4b7e83 100755 ---- a/src/mk -+++ b/src/mk +--- a/mk ++++ b/mk @@ -5,17 +5,14 @@ ObjNames='aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o aln rm -f *.o muscle.make.stdout.txt muscle.make.stderr.txt for CPPName in $CPPNames diff --git a/sci-biology/muscle/metadata.xml b/sci-biology/muscle/metadata.xml index 959160fe46b1..adacdd12bcf1 100644 --- a/sci-biology/muscle/metadata.xml +++ b/sci-biology/muscle/metadata.xml @@ -1,8 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="github">rcedgar/muscle</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/muscle/muscle-3.8.31.ebuild b/sci-biology/muscle/muscle-3.8.31.ebuild index 1e62a9d28eee..faefc5b1a280 100644 --- a/sci-biology/muscle/muscle-3.8.31.ebuild +++ b/sci-biology/muscle/muscle-3.8.31.ebuild @@ -1,32 +1,39 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=7 -inherit eutils toolchain-funcs +inherit flag-o-matic toolchain-funcs MY_P="${PN}${PV}_src" DESCRIPTION="Multiple sequence comparison by log-expectation" -HOMEPAGE="http://www.drive5.com/muscle/" -SRC_URI="http://www.drive5.com/muscle/downloads${PV}/${MY_P}.tar.gz" +HOMEPAGE="https://www.drive5.com/muscle/" +SRC_URI="https://www.drive5.com/muscle/downloads${PV}/${MY_P}.tar.gz" LICENSE="public-domain" SLOT="0" -KEYWORDS="amd64 ppc x86" -IUSE="" +KEYWORDS="amd64 ~ppc ~x86" RDEPEND="!sci-libs/libmuscle" -DEPEND="" S="${WORKDIR}"/${PN}${PV}/src -src_prepare() { - epatch "${FILESDIR}"/${PV}-make.patch +PATCHES=( "${FILESDIR}"/${PV}-make.patch ) + +src_configure() { + # -Werror=strict-aliasing + # https://bugs.gentoo.org/862276 + # Fixed upstream in later releases + # + # Do not trust with LTO either. + append-flags -fno-strict-aliasing + filter-lto + tc-export CXX } src_install() { - dobin "${PN}" + dobin muscle dodoc *.txt } diff --git a/sci-biology/muscle/muscle-5.1.0.ebuild b/sci-biology/muscle/muscle-5.1.0.ebuild new file mode 100644 index 000000000000..84c0c2266804 --- /dev/null +++ b/sci-biology/muscle/muscle-5.1.0.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit toolchain-funcs + +DESCRIPTION="Multiple sequence comparison by log-expectation" +HOMEPAGE="https://www.drive5.com/muscle/" +SRC_URI="https://github.com/rcedgar/muscle/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}"/${P}/src + +LICENSE="public-domain" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86" + +RDEPEND="!sci-libs/libmuscle" + +PATCHES=( + "${FILESDIR}"/0001-Makefile-fix-horribleness-so-that-it-respects-build-.patch +) + +src_configure() { + tc-export CXX + printf '"%s"\n' "${PV}" > gitver.txt +} + +src_install() { + local OS=$(uname) || die + dobin ${OS}/muscle + dodoc *.txt +} diff --git a/sci-biology/ncbi-tools/Manifest b/sci-biology/ncbi-tools/Manifest deleted file mode 100644 index 3513d8ffc44f..000000000000 --- a/sci-biology/ncbi-tools/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST ncbi-tools-2.2.26.tar.gz 68691452 BLAKE2B 21444227c6896c387f46a5490db1e4cf3ac437f94029c68f11ee3c5438bf2c34584d4b1b0ab18d3996f9c4e423a7e17fece510a96a1aa8be5dea6c5a2688f24c SHA512 da167216b56386b8c91a660e8ea0f3ac39b991d4519af9e02fc26aa16ed602eb3d9d874446f69a8f6840ae31a4d5a29da170e04e8a72b56f8c3ca038d1437014 diff --git a/sci-biology/ncbi-tools/files/21ncbi-r1 b/sci-biology/ncbi-tools/files/21ncbi-r1 deleted file mode 100644 index d4de68e6081a..000000000000 --- a/sci-biology/ncbi-tools/files/21ncbi-r1 +++ /dev/null @@ -1,6 +0,0 @@ -# Location of the formatdb data sets -BLASTDB="/usr/share/ncbi/formatdb" -# Location of the BLAST matrixes. -BLASTMAT="/usr/share/ncbi/data" -# Location of the ".ncbi.rc" file which sets the default path for shared data. -NCBI=/etc/ncbi diff --git a/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch b/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch deleted file mode 100644 index bbc4623609c8..000000000000 --- a/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch +++ /dev/null @@ -1,81 +0,0 @@ - corelib/ncbilcl.beos | 2 +- - corelib/ncbilcl.hlx | 2 +- - corelib/ncbilcl.lnx | 4 ++-- - corelib/ncbilcl.plx | 2 +- - corelib/ncbilcl.qnx | 2 +- - 5 files changed, 6 insertions(+), 6 deletions(-) - -diff --git a/corelib/ncbilcl.beos b/corelib/ncbilcl.beos -index f720567..fe6346f 100644 ---- a/corelib/ncbilcl.beos -+++ b/corelib/ncbilcl.beos -@@ -77,7 +77,7 @@ - #endif - - /* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */ --#define _SVID_SOURCE 1 -+#define _DEFAULT_SOURCE 1 - - - /*----------------------------------------------------------------------*/ -diff --git a/corelib/ncbilcl.hlx b/corelib/ncbilcl.hlx -index 1492f93..0e98fb6 100644 ---- a/corelib/ncbilcl.hlx -+++ b/corelib/ncbilcl.hlx -@@ -67,7 +67,7 @@ - #endif - - /* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */ --/*#define _SVID_SOURCE 1 */ -+/*#define _DEFAULT_SOURCE 1 */ - - - /*----------------------------------------------------------------------*/ -diff --git a/corelib/ncbilcl.lnx b/corelib/ncbilcl.lnx -index 46e2978..b3256b3 100644 ---- a/corelib/ncbilcl.lnx -+++ b/corelib/ncbilcl.lnx -@@ -65,7 +65,7 @@ - * fixes for new RedHat6.2 - * - * Revision 6.3 2000/02/10 16:36:32 vakatov --* Added _SVID_SOURCE -+* Added _DEFAULT_SOURCE - * - * Revision 6.2 1999/07/12 05:50:49 vakatov - * Avoid redefinition of #_REENTRANT -@@ -141,7 +141,7 @@ - #endif - - /* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */ --#define _SVID_SOURCE 1 -+#define _DEFAULT_SOURCE 1 - #define _GNU_SOURCE 1 - - /*----------------------------------------------------------------------*/ -diff --git a/corelib/ncbilcl.plx b/corelib/ncbilcl.plx -index bf5824c..f2b53e1 100644 ---- a/corelib/ncbilcl.plx -+++ b/corelib/ncbilcl.plx -@@ -68,7 +68,7 @@ - #endif - - /* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */ --/*#define _SVID_SOURCE 1 */ -+/*#define _DEFAULT_SOURCE 1 */ - - - /*----------------------------------------------------------------------*/ -diff --git a/corelib/ncbilcl.qnx b/corelib/ncbilcl.qnx -index c3d1f0a..4b27bd1 100644 ---- a/corelib/ncbilcl.qnx -+++ b/corelib/ncbilcl.qnx -@@ -72,7 +72,7 @@ - #endif - - /* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */ --#define _SVID_SOURCE 1 -+#define _DEFAULT_SOURCE 1 - - - diff --git a/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-bfr-overflow.patch b/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-bfr-overflow.patch deleted file mode 100644 index e6763214a6e5..000000000000 --- a/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-bfr-overflow.patch +++ /dev/null @@ -1,103 +0,0 @@ - cdromlib/cdnewlib.c | 6 +++--- - corelib/ncbierr.c | 2 +- - corelib/ncbisgml.c | 8 ++++---- - demo/errhdr.c | 2 +- - 4 files changed, 9 insertions(+), 9 deletions(-) - -diff --git a/cdromlib/cdnewlib.c b/cdromlib/cdnewlib.c -index 461292c..be4a2d6 100644 ---- a/cdromlib/cdnewlib.c -+++ b/cdromlib/cdnewlib.c -@@ -2676,7 +2676,7 @@ static int CdDevice_FileBuildPath (CdDevice *cddev, char *fpath, const char *fdi - char volname[16]; - volname[0] = '\0'; - if (cddev->volume != NULL) -- strncat(volname,cddev->volume->volume_name,sizeof volname); -+ strncat(volname,cddev->volume->volume_name,sizeof volname - 1); - else - sprintf(volname,"entrez%d",cddev->hint); - if (!FileBuildPath(fpath,volname,NULL)) -@@ -2748,7 +2748,7 @@ static int CdDevice_Init (CdDevice *cddev) - memset((void*)&info,0,sizeof info); - fpath[0] = '\0'; - if (cddev->inf.root !=NULL) -- strncat(fpath,cddev->inf.root,sizeof fpath); -+ strncat(fpath,cddev->inf.root,sizeof fpath - 1); - - if (cddev->ins_volname) - { -@@ -2766,7 +2766,7 @@ static int CdDevice_Init (CdDevice *cddev) - { - fpath[0] = '\0'; - if (cddev->inf.root !=NULL) -- strncat(fpath,cddev->inf.root,sizeof fpath); -+ strncat(fpath,cddev->inf.root,sizeof fpath - 1); - sprintf(volname,"entrez%d",j+1); - FileBuildPath(fpath,volname,NULL); - if (CdTestPath(fpath,&info)) -diff --git a/corelib/ncbierr.c b/corelib/ncbierr.c -index 0429d86..7b96a2e 100644 ---- a/corelib/ncbierr.c -+++ b/corelib/ncbierr.c -@@ -952,7 +952,7 @@ static FILE * ErrMsgRoot_fopen (ErrMsgRoot *ctx) - if (FileLength(file)==0 || (fd = FileOpen(file,s_msg_mode)) == NULL) - { - strcpy(path,info->msgpath); -- strncat(path,file,sizeof(path)); -+ strncat(path,file,sizeof(path) - 1); - fd = FileOpen(path,s_msg_mode); - } - -diff --git a/corelib/ncbisgml.c b/corelib/ncbisgml.c -index 99412be..a653aef 100644 ---- a/corelib/ncbisgml.c -+++ b/corelib/ncbisgml.c -@@ -260,7 +260,7 @@ NLM_EXTERN char * LIBCALL Nlm_Sgml2Ascii (const char *sgml, char *ascii, size_t - } - if (i >= num_sgml_entity) - { -- char bad[SGML_ERROR_MSG_LIM]; -+ char bad[SGML_ERROR_MSG_LIM + 2]; - bad[0] = '\0'; - strncat(bad,sgml,SGML_ERROR_MSG_LIM); - ErrPostEx(SEV_ERROR,E_SGML,3,"Unrecognized SGML entity &%s in [%s]",tbuf,bad); -@@ -279,7 +279,7 @@ NLM_EXTERN char * LIBCALL Nlm_Sgml2Ascii (const char *sgml, char *ascii, size_t - from++; - if (*from == '\0') - { -- char bad[SGML_ERROR_MSG_LIM]; -+ char bad[SGML_ERROR_MSG_LIM + 2]; - bad[0] = '\0'; - strncat(bad,sgml,SGML_ERROR_MSG_LIM); - ErrPostEx(SEV_ERROR,E_SGML,2, "Unbalanced <> in SGML [%s]",bad); -@@ -335,7 +335,7 @@ NLM_EXTERN size_t LIBCALL Nlm_Sgml2AsciiLen (const char *sgml) - } - if (i >= num_sgml_entity) - { -- char bad[SGML_ERROR_MSG_LIM]; -+ char bad[SGML_ERROR_MSG_LIM + 2]; - bad[0] = '\0'; - strncat(bad,sgml,SGML_ERROR_MSG_LIM); - ErrPostEx(SEV_ERROR,E_SGML,3,"Unrecognized SGML entity &%s in [%s]",tbuf,bad); -@@ -349,7 +349,7 @@ NLM_EXTERN size_t LIBCALL Nlm_Sgml2AsciiLen (const char *sgml) - from++; - if (*from == '\0') - { -- char bad[SGML_ERROR_MSG_LIM]; -+ char bad[SGML_ERROR_MSG_LIM + 2]; - bad[0] = '\0'; - strncat(bad,sgml,SGML_ERROR_MSG_LIM); - ErrPostEx(SEV_ERROR,E_SGML,2,"Unbalanced <> in SGML [%s]",bad); -diff --git a/demo/errhdr.c b/demo/errhdr.c -index 01cd955..5081489 100644 ---- a/demo/errhdr.c -+++ b/demo/errhdr.c -@@ -41,7 +41,7 @@ int main (int argc, char **argv) - else if (mod[0] == '\0') - { - char *p; -- strncat(mod,argv[i],sizeof mod); -+ strncat(mod,argv[i],sizeof mod - 1); - if ((p = strstr(argv[i],".msg")) != NULL) - *p = '\0'; - } diff --git a/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-format-security.patch b/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-format-security.patch deleted file mode 100644 index c12feff51af1..000000000000 --- a/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-format-security.patch +++ /dev/null @@ -1,124 +0,0 @@ - api/alignmgr2.c | 2 +- - api/pgppop.c | 2 +- - api/txalign.c | 10 +++++----- - desktop/seqpanel.c | 4 ++-- - tools/spidey.c | 4 ++-- - 5 files changed, 11 insertions(+), 11 deletions(-) - -diff --git a/api/alignmgr2.c b/api/alignmgr2.c -index 5b43ef3..4b9007e 100644 ---- a/api/alignmgr2.c -+++ b/api/alignmgr2.c -@@ -5616,7 +5616,7 @@ NLM_EXTERN void AlnMgr2PrintSeqAlign(SeqAlignPtr sap, Int4 linesize, Boolean isn - spp = SeqPortNew(bsp, amp->from_row, amp->to_row, amp->strand, seqcode); - ctr = SeqPortRead(spp, (Uint1Ptr)buf, amp->to_row-amp->from_row+1); - buf[ctr] = '\0'; -- fprintf(ofp, buf); -+ fprintf(ofp, "%s", buf); - SeqPortFree(spp); - } - } -diff --git a/api/pgppop.c b/api/pgppop.c -index d16d79d..b359378 100644 ---- a/api/pgppop.c -+++ b/api/pgppop.c -@@ -2994,7 +2994,7 @@ Char DefLine[255]; - if (szSeq){ - if (!DDV_GetSequenceFromParaG(pgp,&szSeq,bspLength,IsAA,NULL, - NULL,NULL)) continue; -- fprintf(fp,szSeq); -+ fprintf(fp, "%s", szSeq); - fprintf(fp,"\n"); - MemFree(szSeq); - } -diff --git a/api/txalign.c b/api/txalign.c -index 5877f9c..cb35fbc 100644 ---- a/api/txalign.c -+++ b/api/txalign.c -@@ -1767,13 +1767,13 @@ static CharPtr DrawTextToBuffer(ValNodePtr tdp_list, CharPtr PNTR m_buf, Boolean - if(options&TXALIGN_HTML&&options&TXALIGN_MASTER&&DbHasGi&&(options&TXALIGN_GET_SEQUENCE)){ - Char checkboxBuf[200]; - sprintf(checkboxBuf, "<input type=\"checkbox\" name=\"getSeqGi\" value=\"%ld\" onClick=\"synchronizeCheck(this.value, 'getSeqAlignment%ld', 'getSeqGi', this.checked)\">", sip->data.intvalue, query_number_glb); -- sprintf(docbuf+pos,checkboxBuf); -+ sprintf(docbuf+pos,"%s", checkboxBuf); - - pos += StringLen(checkboxBuf); - } - - html_len = StringLen(HTML_buffer); -- sprintf(docbuf+pos, HTML_buffer); -+ sprintf(docbuf+pos, "%s", HTML_buffer); - pos += html_len; - - pos += print_label_to_buffer_all_ex(docbuf+pos, tdp->label, tdp->pos, -@@ -1790,7 +1790,7 @@ static CharPtr DrawTextToBuffer(ValNodePtr tdp_list, CharPtr PNTR m_buf, Boolean - sprintf(HTML_buffer, "<a name = THC%ld></a><a href=\"http://www.tigr.org/docs/tigr-scripts/hgi_scripts/thc_report.spl?est=THC%ld&report_type=n\">", (long) oip->id, (long) oip->id); - - html_len = StringLen(HTML_buffer); -- sprintf(docbuf+pos, HTML_buffer); -+ sprintf(docbuf+pos, "%s", HTML_buffer); - pos += html_len; - pos += print_label_to_buffer_all_ex(docbuf+pos, tdp->label, tdp->pos, - tdp->strand, FALSE, TRUE, label_size, num_size, show_strand, strip_semicolon); -@@ -1799,7 +1799,7 @@ static CharPtr DrawTextToBuffer(ValNodePtr tdp_list, CharPtr PNTR m_buf, Boolean - sprintf(HTML_buffer, "<a name = TI%ld></a><a href=\"http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=retrieve&dopt=fasta&val=%ld\">", (long) oip->id, (long) oip->id); - - html_len = StringLen(HTML_buffer); -- sprintf(docbuf+pos, HTML_buffer); -+ sprintf(docbuf+pos, "%s", HTML_buffer); - pos += html_len; - pos += print_label_to_buffer_all_ex(docbuf+pos, tdp->label, tdp->pos, - tdp->strand, FALSE, TRUE, label_size, num_size, show_strand, strip_semicolon); -@@ -1816,7 +1816,7 @@ static CharPtr DrawTextToBuffer(ValNodePtr tdp_list, CharPtr PNTR m_buf, Boolean - if(options&TXALIGN_HTML&&options&TXALIGN_MASTER&&DbHasGi&&(options&TXALIGN_GET_SEQUENCE)){ - Char checkboxBuf[200]; - sprintf(checkboxBuf, "<input type=\"checkbox\" name=\"getSeqMaster\" value=\"\" onClick=\"uncheckable('getSeqAlignment%ld', 'getSeqMaster')\">", query_number_glb); -- sprintf(docbuf+pos,checkboxBuf); -+ sprintf(docbuf+pos,"%s",checkboxBuf); - - pos += StringLen(checkboxBuf); - } -diff --git a/desktop/seqpanel.c b/desktop/seqpanel.c -index 2e78e13..c7538aa 100644 ---- a/desktop/seqpanel.c -+++ b/desktop/seqpanel.c -@@ -8661,7 +8661,7 @@ WriteAlignmentInterleaveToFileEx - seqbuf, alnbuf, &alnbuf_len, - show_substitutions); - MemCpy (printed_line + label_len + 1 + coord_len, alnbuf, alnbuf_len); -- fprintf (fp, printed_line); -+ fprintf (fp, "%s", printed_line); - } - fprintf (fp, "\n"); - start = stop + 1; -@@ -8757,7 +8757,7 @@ extern void WriteAlignmentContiguousToFile - seqbuf, alnbuf, &alnbuf_len, - show_substitutions); - MemCpy (printed_line, alnbuf, alnbuf_len); -- fprintf (fp, printed_line); -+ fprintf (fp, "%s", printed_line); - start = stop + 1; - stop += seq_chars_per_row; - } -diff --git a/tools/spidey.c b/tools/spidey.c -index d6ce62d..ac9f59a 100644 ---- a/tools/spidey.c -+++ b/tools/spidey.c -@@ -2088,7 +2088,7 @@ static void SPI_PrintResult(FILE *ofp, FILE *ofp2, SPI_RegionInfoPtr srip, Biose - fprintf(ofp2, " "); - ctr++; - } -- fprintf(ofp2, buf); -+ fprintf(ofp2, "%s", buf); - if (spp){ - SeqPortFree(spp); - } -@@ -2417,7 +2417,7 @@ static void SPI_PrintHerdResult(FILE *ofp, FILE *ofp2, SPI_mRNAToHerdPtr herd, S - ctr = SeqPortRead(spp, (Uint1Ptr)buf, 10); - if (ctr > 0) - buf[ctr] = '\0'; -- fprintf(ofp2, buf); -+ fprintf(ofp2, "%s", buf); - SeqPortFree(spp); - } - done = TRUE; diff --git a/sci-biology/ncbi-tools/files/ncbi-tools-extra_vib.patch b/sci-biology/ncbi-tools/files/ncbi-tools-extra_vib.patch deleted file mode 100644 index cb7d1adf9208..000000000000 --- a/sci-biology/ncbi-tools/files/ncbi-tools-extra_vib.patch +++ /dev/null @@ -1,37 +0,0 @@ ---- ncbi-20061015/make/makedis.csh 2006-09-14 17:37:03.000000000 +0200 -+++ ncbi/make/makedis.csh 2007-03-07 21:00:36.090836460 +0100 -@@ -485,6 +485,34 @@ - - set net_stat = $status - -+if ( $net_stat == 0 ) then -+ # Compile additional tools, usually hidden -+ if ( ! $?EXTRA_VIB ) then -+ set EXTRA_VIB = ( asn2all ) -+ endif -+ -+ if ("$?NCBI_MT_OTHERLIBS" == "1") then -+ set CMD='make $MFLG -f makenet.unx \ -+ CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE\" \ -+ LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \ -+ AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" RAN=\"$NCBI_RANLIB\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \ -+ THREAD_OBJ=$NCBI_THREAD_OBJ \ -+ THREAD_OTHERLIBS=\"$NCBI_MT_OTHERLIBS\" \ -+ NETENTREZVERSION=\"$NETENTREZVERSION\" $NET_VIB $EXTRA_VIB' -+ else -+ set CMD='make $MFLG -f makenet.unx \ -+ CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE\" \ -+ LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \ -+ AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" RAN=\"$NCBI_RANLIB\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \ -+ NETENTREZVERSION=\"$NETENTREZVERSION\" $NET_VIB $EXTRA_VIB' -+ endif -+ eval echo $CMD -+ eval echo $CMD | sh -+ -+ set net_stat = $status -+ -+endif -+ - if ($make_stat != 0 || $demo_stat != 0 || $threaded_demo_stat != 0 || $net_stat != 0) then - echo FAILURE primary make status = $make_stat, demo = $demo_stat, threaded_demo = $threaded_demo_stat, net = $net_stat - cat <<EOF diff --git a/sci-biology/ncbi-tools/files/ncbi-tools-lop.patch b/sci-biology/ncbi-tools/files/ncbi-tools-lop.patch deleted file mode 100644 index 867b203aecb1..000000000000 --- a/sci-biology/ncbi-tools/files/ncbi-tools-lop.patch +++ /dev/null @@ -1,15 +0,0 @@ ---- platform/linux-power.ncbi.mk.bak 2005-08-04 22:45:13.000000000 -0500 -+++ platform/linux-power.ncbi.mk 2005-08-04 22:45:35.000000000 -0500 -@@ -9,10 +9,10 @@ - #it appears the flags above do not work anymore with newer libc, - #the new flags should work. Dima. 08/23/01 - NCBI_AR=ar --NCBI_CC = xlc_r -w -qcpluscmt -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -+NCBI_CC = gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE - NCBI_CFLAGS1 = -c - NCBI_LDFLAGS1 = -O3 -D_LARGE_FILES --NCBI_OPTFLAG = -O3 -qmaxmem=-1 -D_LARGE_FILE -+NCBI_OPTFLAG = -O3 -D_LARGE_FILE - NCBI_BIN_MASTER = /vol/stcfs/rchen/LoP/ncbi/bin - NCBI_BIN_COPY = /vol/stcfs/rchen/LoP/ncbi/bin - NCBI_INCDIR = /vol/stcfs/rchen/LoP/ncbi/include diff --git a/sci-biology/ncbi-tools/files/ncbirc b/sci-biology/ncbi-tools/files/ncbirc deleted file mode 100644 index dd77b452fe74..000000000000 --- a/sci-biology/ncbi-tools/files/ncbirc +++ /dev/null @@ -1,2 +0,0 @@ -[NCBI] -Data=@GENTOO_PORTAGE_EPREFIX@/usr/share/ncbi/data diff --git a/sci-biology/ncbi-tools/metadata.xml b/sci-biology/ncbi-tools/metadata.xml deleted file mode 100644 index 959160fe46b1..000000000000 --- a/sci-biology/ncbi-tools/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild b/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild deleted file mode 100644 index 2c59e13b5a97..000000000000 --- a/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild +++ /dev/null @@ -1,164 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils flag-o-matic prefix toolchain-funcs - -DESCRIPTION="Development toolkit and applications for computational biology, including BLAST" -HOMEPAGE="https://www.ncbi.nlm.nih.gov/" -SRC_URI="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/${PV}/ncbi.tar.gz -> ${P}.tar.gz" - -SLOT="0" -LICENSE="public-domain" -KEYWORDS="~alpha amd64 ppc64 x86 ~amd64-linux ~x86-linux ~ppc-macos" -IUSE="doc static-libs X" - -RDEPEND=" - app-shells/tcsh - dev-lang/perl - media-libs/libpng:0= - X? ( - media-libs/fontconfig - x11-libs/motif:0= - x11-libs/libICE - x11-libs/libX11 - x11-libs/libXft - x11-libs/libXmu - x11-libs/libXt - )" -DEPEND="${RDEPEND}" - -S="${WORKDIR}/ncbi" - -EXTRA_VIB="asn2all asn2asn" - -pkg_setup() { - echo - ewarn 'Please note that the NCBI toolkit (and especially the X' - ewarn 'applications) are known to have compilation and run-time' - ewarn 'problems when compiled with agressive compilation flags. The' - ewarn '"-O3" flag is filtered by the ebuild on the x86 architecture if' - ewarn 'X support is enabled.' - echo -} - -src_prepare() { - epatch \ - "${FILESDIR}"/${PN}-extra_vib.patch \ - "${FILESDIR}"/${P}-bfr-overflow.patch \ - "${FILESDIR}"/${P}-format-security.patch \ - "${FILESDIR}"/${P}-_DEFAULT_SOURCE.patch - - if use ppc || use ppc64; then - epatch "${FILESDIR}"/${PN}-lop.patch - fi - - if ! use X; then - sed \ - -e "s:\#set HAVE_OGL=0:set HAVE_OGL=0:" \ - -e "s:\#set HAVE_MOTIF=0:set HAVE_MOTIF=0:" \ - -i "${S}"/make/makedis.csh || die - else - # X applications segfault on startup on x86 with -O3. - use x86 || replace-flags '-O3' '-O2' - fi - - # Apply user C flags... - cd "${S}"/platform - sed \ - -e "s:-O[s0-9]\?::g" \ - -e 's:-m\(cpu\|arch\)=[a-zA-Z0-9]*::g' \ - -e 's:-x[A-Z]*::g' \ - -e 's:-pipe::g' \ - -e "/NCBI_MAKE_SHELL *=/s:=.*:= \"${EPREFIX}/bin/sh\":g" \ - -e "/NCBI_AR *=/s:ar:$(tc-getAR):g" \ - -e "/NCBI_RANLIB *=/s:ranlib:$(tc-getRANLIB):g" \ - -e "/NCBI_CC *=/s:= [a-zA-Z0-9]* := $(tc-getCC) :g" \ - -e "/NCBI_OPTFLAG *=/s:$: ${CFLAGS}:g" \ - -e "/NCBI_LDFLAGS1 *=/s:$: ${CFLAGS} ${LDFLAGS}:g" \ - -e "/NCBI_OGLLIBS *=/s:=.*:= $($(tc-getPKG_CONFIG) --cflags gl glu 2>/dev/null):g" \ - -e "/OPENGL_LIBS *=/s:=.*:= $($(tc-getPKG_CONFIG) --libs gl glu 2>/dev/null):g" \ - -e "/NCBI_OGLLIBS *=/s:=.*:= $($(tc-getPKG_CONFIG) --libs gl glu 2>/dev/null):g" \ - -i * || die - - # We use dynamic libraries - sed -i -e "s/-Wl,-Bstatic//" *linux*.ncbi.mk || die - - sed \ - -re "s:/usr(/bin/.*sh):\1:g" \ - -e "s:(/bin/.*sh):${EPREFIX}\1:g" \ - -i $(find "${S}" -type f) || die -} - -src_compile() { - export EXTRA_VIB - cd "${WORKDIR}" - csh ncbi/make/makedis.csh || die - mkdir "${S}"/cgi "${S}"/real || die - mv "${S}"/bin/*.cgi "${S}"/cgi || die - mv "${S}"/bin/*.REAL "${S}"/real || die - cd "${S}"/demo - emake \ - -f ../make/makenet.unx \ - CC="$(tc-getCC) ${CFLAGS} -I../include -L../lib" \ - LDFLAGS="${LDFLAGS}" \ - spidey - cp spidey ../bin/ || die -} - -src_install() { - #sci-geosciences/cdat-lite - mv "${S}"/bin/cdscan "${S}"/bin/cdscan-ncbi || die - - dobin "${S}"/bin/* - - for i in ${EXTRA_VIB}; do - dobin "${S}"/build/${i} - done - use static-libs && dolib.a "${S}"/lib/*.a - mkdir -p "${ED}"/usr/include/ncbi - cp -RL "${S}"/include/* "${ED}"/usr/include/ncbi || \ - die "Failed to install headers." - - # TODO: wwwblast with webapps - #insinto /usr/share/ncbi/lib/cgi - #doins ${S}/cgi/* - #insinto /usr/share/ncbi/lib/real - #doins ${S}/real/* - - # Basic documentation - dodoc "${S}"/{README,VERSION,doc/{*.txt,README.*}} - newdoc "${S}"/doc/fa2htgs/README README.fa2htgs - newdoc "${S}"/config/README README.config - newdoc "${S}"/network/encrypt/README README.encrypt - newdoc "${S}"/network/nsclilib/readme README.nsclilib - newdoc "${S}"/sequin/README README.sequin - mv "${S}"/doc/man/fmerge{,-ncbi}.1 || die - doman "${S}"/doc/man/* - - # Hypertext user documentation - dohtml "${S}"/{README.htm,doc/{*.html,*.htm,*.gif}} - insinto /usr/share/doc/${PF}/html - doins -r "${S}"/doc/blast "${S}"/doc/images "${S}"/doc/seq_install - - # Developer documentation - if use doc; then - # Demo programs - mkdir "${ED}"/usr/share/ncbi - mv "${S}"/demo "${ED}"/usr/share/ncbi/demo || die - fi - - # Shared data (similarity matrices and such) and database directory. - insinto /usr/share/ncbi - doins -r "${S}"/data - dodir /usr/share/ncbi/formatdb - - # Default config file to set the path for shared data. - insinto /etc/ncbi - newins "${FILESDIR}"/ncbirc .ncbirc - eprefixify "${ED}"/etc/ncbi/.ncbirc - - # Env file to set the location of the config file and BLAST databases. - newenvd "${FILESDIR}"/21ncbi-r1 21ncbi -} diff --git a/sci-biology/newick-utils/files/newick-utils-1.6-deduplicate-libnw.patch b/sci-biology/newick-utils/files/newick-utils-1.6-deduplicate-libnw.patch new file mode 100644 index 000000000000..ca997830aced --- /dev/null +++ b/sci-biology/newick-utils/files/newick-utils-1.6-deduplicate-libnw.patch @@ -0,0 +1,153 @@ +Don't rebuild all of libnw.la pointlessly + +--- a/tests/Makefile.am ++++ b/tests/Makefile.am +@@ -8,6 +8,8 @@ + showsrc: + @echo $(srcdir) + ++LDADD = $(top_builddir)/src/libnw.la ++ + TESTS = test_newick_scanner test_newick_parser test_rnode test_list \ + test_link test_masprintf test_svg_graph_radial \ + test_canvas test_concat test_hash test_lca test_enode \ +@@ -37,100 +39,57 @@ + + SRC = $(top_builddir)/src + +-test_newick_scanner_SOURCES = test_newick_scanner.c $(SRC)/newick_scanner.c \ +- $(SRC)/newick_parser.c $(SRC)/rnode.c $(SRC)/rnode_iterator.c \ +- $(SRC)/list.c $(SRC)/hash.c $(SRC)/masprintf.c $(SRC)/link.c +- +-test_newick_parser_SOURCES = test_newick_parser.c $(SRC)/parser.c \ +- $(SRC)/newick_scanner.c $(SRC)/newick_parser.c $(SRC)/list.c \ +- $(SRC)/rnode.c $(SRC)/link.c $(SRC)/hash.c $(SRC)/rnode_iterator.c \ +- $(SRC)/masprintf.c $(SRC)/to_newick.c $(SRC)/concat.c +- +-test_rnode_SOURCES = test_rnode.c $(SRC)/rnode.c $(SRC)/list.c \ +- $(SRC)/rnode_iterator.c $(SRC)/hash.c $(SRC)/masprintf.c \ +- tree_stubs.c $(SRC)/nodemap.c $(SRC)/link.c +- +-test_list_SOURCES = test_list.c $(SRC)/list.c +- +-test_link_SOURCES = test_link.c $(SRC)/link.c $(SRC)/nodemap.c \ +- $(SRC)/list.c $(SRC)/to_newick.c $(SRC)/rnode.c \ +- $(SRC)/concat.c $(SRC)/hash.c tree_stubs.c \ +- $(SRC)/rnode_iterator.c $(SRC)/masprintf.c ++test_newick_scanner_SOURCES = test_newick_scanner.c ++ ++test_newick_parser_SOURCES = test_newick_parser.c ++ ++test_rnode_SOURCES = test_rnode.c tree_stubs.c ++ ++test_list_SOURCES = test_list.c ++ ++test_link_SOURCES = test_link.c tree_stubs.c + + test_canvas_SOURCES = test_canvas.c $(SRC)/canvas.c + +-test_concat_SOURCES = test_concat.c $(SRC)/concat.c ++test_concat_SOURCES = test_concat.c ++ ++test_hash_SOURCES = test_hash.c ++ ++test_lca_SOURCES = test_lca.c tree_stubs.c ++ ++test_nodemap_SOURCES = test_nodemap.c tree_stubs.c + +-test_hash_SOURCES = test_hash.c $(SRC)/hash.c $(SRC)/list.c $(SRC)/masprintf.c ++test_to_newick_SOURCES = test_to_newick.c tree_stubs.c + +-test_lca_SOURCES = test_lca.c $(SRC)/lca.c $(SRC)/list.c $(SRC)/nodemap.c \ +- $(SRC)/link.c $(SRC)/rnode.c $(SRC)/hash.c \ +- $(SRC)/rnode_iterator.c tree_stubs.c $(SRC)/masprintf.c \ +- $(SRC)/error.c +- +-test_nodemap_SOURCES = test_nodemap.c $(SRC)/nodemap.c \ +- $(SRC)/rnode.c $(SRC)/list.c $(SRC)/hash.c $(SRC)/link.c \ +- $(SRC)/rnode_iterator.c $(SRC)/masprintf.c tree_stubs.c +- +-test_to_newick_SOURCES = test_to_newick.c $(SRC)/to_newick.c \ +- $(SRC)/rnode.c $(SRC)/link.c $(SRC)/concat.c \ +- $(SRC)/list.c $(SRC)/rnode_iterator.c $(SRC)/hash.c \ +- $(SRC)/masprintf.c $(SRC)/parser.c $(SRC)/newick_scanner.c \ +- $(SRC)/newick_parser.c tree_stubs.c +- +-test_tree_SOURCES = test_tree.c $(SRC)/tree.c $(SRC)/rnode.c $(SRC)/list.c \ +- $(SRC)/to_newick.c $(SRC)/nodemap.c $(SRC)/link.c $(SRC)/concat.c \ +- $(SRC)/hash.c tree_stubs.c $(SRC)/rnode_iterator.c \ +- $(SRC)/masprintf.c +- +-test_node_set_SOURCES = test_node_set.c tree_stubs.c $(SRC)/node_set.c \ +- $(SRC)/hash.c $(SRC)/rnode.c $(SRC)/list.c $(SRC)/link.c \ +- $(SRC)/rnode_iterator.c $(SRC)/masprintf.c +- +-test_enode_SOURCES = test_enode.c $(SRC)/enode.c $(SRC)/rnode.c \ +- $(SRC)/link.c $(SRC)/list.c $(SRC)/rnode_iterator.c \ +- $(SRC)/hash.c $(SRC)/masprintf.c +- +-test_rnode_iterator_SOURCES = test_rnode_iterator.c $(SRC)/rnode_iterator.c \ +- $(SRC)/list.c $(SRC)/link.c $(SRC)/rnode.c $(SRC)/to_newick.c \ +- $(SRC)/hash.c $(SRC)/nodemap.c tree_stubs.c $(SRC)/masprintf.c \ +- $(SRC)/parser.c $(SRC)/newick_scanner.c $(SRC)/newick_parser.c \ +- $(SRC)/concat.c ++test_tree_SOURCES = test_tree.c tree_stubs.c ++ ++test_node_set_SOURCES = test_node_set.c tree_stubs.c $(SRC)/node_set.c ++ ++test_enode_SOURCES = test_enode.c $(SRC)/enode.c ++ ++test_rnode_iterator_SOURCES = test_rnode_iterator.c tree_stubs.c + + test_readline_SOURCES = test_readline.c $(SRC)/readline.c + +-test_tree_models_SOURCES = test_tree_models.c $(SRC)/tree_models.c \ +- $(SRC)/rnode.c $(SRC)/list.c $(SRC)/to_newick.c $(SRC)/link.c \ +- $(SRC)/concat.c $(SRC)/rnode_iterator.c \ +- $(SRC)/hash.c $(SRC)/masprintf.c +- +-test_xml_utils_SOURCES = test_xml_utils.c $(SRC)/xml_utils.c \ +- $(SRC)/masprintf.c +- +-test_masprintf_SOURCES = test_masprintf.c $(SRC)/masprintf.c +- +-test_error_SOURCES = test_error.c $(SRC)/error.c +- +-test_order_tree_SOURCES = test_order_tree.c $(SRC)/order_tree.c tree_stubs.c \ +- $(SRC)/link.c $(SRC)/to_newick.c $(SRC)/rnode.c $(SRC)/list.c \ +- $(SRC)/masprintf.c $(SRC)/concat.c $(SRC)/hash.c $(SRC)/nodemap.c \ +- $(SRC)/rnode_iterator.c +- +-test_graph_common_SOURCES = test_graph_common.c $(SRC)/graph_common.c \ +- tree_stubs.c $(SRC)/link.c $(SRC)/list.c $(SRC)/tree.c \ +- $(SRC)/rnode_iterator.c $(SRC)/hash.c $(SRC)/masprintf.c \ +- $(SRC)/rnode.c $(SRC)/nodemap.c ++test_tree_models_SOURCES = test_tree_models.c $(SRC)/tree_models.c ++ ++test_xml_utils_SOURCES = test_xml_utils.c $(SRC)/xml_utils.c ++ ++test_masprintf_SOURCES = test_masprintf.c ++ ++test_error_SOURCES = test_error.c ++ ++test_order_tree_SOURCES = test_order_tree.c tree_stubs.c $(SRC)/order_tree.c ++ ++test_graph_common_SOURCES = test_graph_common.c tree_stubs.c $(SRC)/graph_common.c + + test_svg_graph_radial_SOURCES = test_svg_graph_radial.c \ +- $(SRC)/svg_graph_radial.c $(SRC)/tree.c $(SRC)/svg_graph.c \ +- $(SRC)/rnode.c $(SRC)/hash.c $(SRC)/list.c $(SRC)/masprintf.c \ +- $(SRC)/rnode_iterator.c $(SRC)/svg_graph_ortho.c $(SRC)/error.c \ ++ $(SRC)/svg_graph_radial.c $(SRC)/svg_graph.c \ ++ $(SRC)/svg_graph_ortho.c \ + $(SRC)/readline.c $(SRC)/xml_utils.c $(SRC)/graph_common.c \ +- $(SRC)/node_pos_alloc.c $(SRC)/nodemap.c $(SRC)/lca.c $(SRC)/link.c ++ $(SRC)/node_pos_alloc.c + +-test_subtree_SOURCES = test_subtree.c $(SRC)/subtree.c $(SRC)/rnode.c \ +- $(SRC)/list.c $(SRC)/hash.c $(SRC)/link.c $(SRC)/rnode_iterator.c \ +- $(SRC)/masprintf.c $(SRC)/nodemap.c ++test_subtree_SOURCES = test_subtree.c $(SRC)/subtree.c + + clean-local: + $(RM) *.out diff --git a/sci-biology/newick-utils/files/newick-utils-1.6-fno-common.patch b/sci-biology/newick-utils/files/newick-utils-1.6-fno-common.patch new file mode 100644 index 000000000000..15847a52c480 --- /dev/null +++ b/sci-biology/newick-utils/files/newick-utils-1.6-fno-common.patch @@ -0,0 +1,41 @@ +--- a/src/address_parser.c ++++ b/src/address_parser.c +@@ -83,6 +83,8 @@ + #include "enode.h" + #include "address_parser_status.h" + ++enum address_parser_status_type address_parser_status; ++ + extern int adslex (void); + + /* The root of the expression (when represented as a parse tree) */ +--- a/src/address_parser_status.h ++++ b/src/address_parser_status.h +@@ -13,4 +13,4 @@ + * returns either \c NULL or the top-level enode of the address, so we need to + * use an extern variable to convey its status. */ + +-enum address_parser_status_type address_parser_status; ++extern enum address_parser_status_type address_parser_status; +--- a/tests/test_newick_parser.c ++++ b/tests/test_newick_parser.c +@@ -11,7 +11,7 @@ + int nwslex (void); + struct rnode *root; + struct llist *nodes_in_order; +-enum parser_status_type newick_parser_status; ++extern enum parser_status_type newick_parser_status; + void newick_scanner_set_string_input(char *); + + /* NOTE: we can use to_newick() to check the parser's output because this +--- a/tests/test_newick_scanner.c ++++ b/tests/test_newick_scanner.c +@@ -20,7 +20,7 @@ + int nwslex (void); + struct rnode *root; + struct llist *nodes_in_order; +-enum parser_status_type newick_parser_status; ++extern enum parser_status_type newick_parser_status; + void newick_scanner_set_string_input(char *); + void newick_scanner_set_file_input(FILE *); + diff --git a/sci-biology/newick-utils/metadata.xml b/sci-biology/newick-utils/metadata.xml index 959160fe46b1..9ba134125d0c 100644 --- a/sci-biology/newick-utils/metadata.xml +++ b/sci-biology/newick-utils/metadata.xml @@ -1,8 +1,14 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <use> + <flag name="xml">Uses <pkg>dev-libs/libxml2</pkg> to handle ornaments</flag> + </use> + <upstream> + <remote-id type="github">tjunier/newick_utils</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/newick-utils/newick-utils-1.6-r2.ebuild b/sci-biology/newick-utils/newick-utils-1.6-r2.ebuild new file mode 100644 index 000000000000..5d5cfa360ccb --- /dev/null +++ b/sci-biology/newick-utils/newick-utils-1.6-r2.ebuild @@ -0,0 +1,49 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit autotools flag-o-matic + +DESCRIPTION="Tools for processing phylogenetic trees" +HOMEPAGE="https://web.archive.org/web/20120206012743/http://cegg.unige.ch/newick_utils" +SRC_URI="https://web.archive.org/web/20120126210029if_/http://cegg.unige.ch/pub/${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="xml" + +DEPEND=" + xml? ( dev-libs/libxml2 )" +RDEPEND=" + ${DEPEND} + !dev-games/libnw" + +PATCHES=( + "${FILESDIR}"/${P}-deduplicate-libnw.patch + "${FILESDIR}"/${P}-fno-common.patch +) + +src_prepare() { + default + eautoreconf +} + +src_configure() { + # -Werror=lto-type-mismatch + # https://bugs.gentoo.org/862279 + # https://github.com/tjunier/newick_utils/issues/34 + filter-lto + + econf \ + --disable-static \ + --without-guile \ + --without-lua \ + $(use_with xml libxml) +} + +src_install() { + default + find "${ED}" -name '*.la' -delete || die +} diff --git a/sci-biology/newick-utils/newick-utils-1.6.ebuild b/sci-biology/newick-utils/newick-utils-1.6.ebuild deleted file mode 100644 index 845bc0116205..000000000000 --- a/sci-biology/newick-utils/newick-utils-1.6.ebuild +++ /dev/null @@ -1,20 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -DESCRIPTION="Tools for processing phylogenetic trees" -HOMEPAGE="http://cegg.unige.ch/newick_utils" -SRC_URI="http://cegg.unige.ch/pub/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -IUSE="" -KEYWORDS="~amd64 ~x86" - -DEPEND="" -RDEPEND="!dev-games/libnw" - -src_test() { - emake -C tests check-TESTS -} diff --git a/sci-biology/njplot/Manifest b/sci-biology/njplot/Manifest deleted file mode 100644 index 6cec177af405..000000000000 --- a/sci-biology/njplot/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST njplot-2.3.tar.gz 83641 BLAKE2B 3dd2798c190a103e88babb592cda184ae7ab4839cc779f739205480e2cce641bc9f8a57d20bd96ce8fc4a1e662a81de0bb13f2a4ffa9d03f8e0f286c762b993a SHA512 51e7d48187f88c4afb36d55cf8de98dad3cd4cd541137262885fe84bedff9db83224cdfa3c6a14518cd8170a06139b798518afe9fbadd89162986ed788355059 diff --git a/sci-biology/njplot/files/njplot-2.3-buildsystem.patch b/sci-biology/njplot/files/njplot-2.3-buildsystem.patch deleted file mode 100644 index 61f8b95ea160..000000000000 --- a/sci-biology/njplot/files/njplot-2.3-buildsystem.patch +++ /dev/null @@ -1,59 +0,0 @@ - makefile | 16 ++++++++-------- - 1 file changed, 8 insertions(+), 8 deletions(-) - -diff --git a/makefile b/makefile -index ccb7dc2..9488c2a 100644 ---- a/makefile -+++ b/makefile -@@ -7,10 +7,10 @@ NO_PDF = -DNO_PDF - #PDFLIB = -L$(PDF) -lpdf - - # c compiler and linker --CC = gcc -+CC ?= gcc - - # Vibrant top directory --VIBRANT = /banques0/ncbiJun04 -+VIBRANT = /usr/include/ncbi - - - # X11 include directory -@@ -24,15 +24,15 @@ OBJECTS = njplot-vib.o - OBJUNROOTED = unrooted-vib.o preptree.o - - --CFLAGS = -c -DWIN_MOTIF -Dunix -I$(VIBRANT)/include -I$(VIBRANT)/vibrant -I$(VIBRANT)/corelib \ -+CFLAGS += -c -DWIN_MOTIF -Dunix -I$(VIBRANT)/include -I$(VIBRANT)/vibrant -I$(VIBRANT)/corelib \ - -I$(VIBRANT) -I$(PDF) -I$(X11INCL) -I$(MOTIFINCL) $(HELPFILENAME) $(NO_PDF) \ -- -Wimplicit-function-declaration -g -+ -Wimplicit-function-declaration - - all: njplot unrooted newicktops newicktotxt - - - njplot : $(OBJECTS) -- $(CC) -g -o njplot $(OBJECTS) \ -+ $(CC) $(LDFLAGS) -o njplot $(OBJECTS) \ - -L$(VIBRANT)/lib \ - -lvibrant -lncbi \ - $(PDFLIB) \ -@@ -40,16 +40,16 @@ njplot : $(OBJECTS) - -L/usr/X11R6/lib -lXmu -lXt -lX11 -lm - - unrooted : $(OBJUNROOTED) -- $(CC) -g -o unrooted $(OBJUNROOTED) \ -+ $(CC) $(LDFLAGS) -o unrooted $(OBJUNROOTED) \ - -L$(VIBRANT)/lib -lvibrant -lncbi \ - -L$(MOTIFLIB) -lXm \ - -L/usr/X11R6/lib -lXmu -lXt -lX11 -lm - - newicktops: njplot-vib.c -- $(CC) -DNO_GUI -DNO_PDF -o $@ njplot-vib.c -lm -+ $(CC) $(LDFLAGS) $(CFLAGS) -DNO_GUI -DNO_PDF -o $@ njplot-vib.c -lm - - newicktotxt: njplot-vib.c -- $(CC) -DTTY -o $@ njplot-vib.c -lm -+ $(CC) -DTTY $(LDFLAGS) $(CFLAGS) -o $@ njplot-vib.c -lm - - - .c.o : diff --git a/sci-biology/njplot/files/njplot-2.3-format-security.patch b/sci-biology/njplot/files/njplot-2.3-format-security.patch deleted file mode 100644 index 686b8475e9ed..000000000000 --- a/sci-biology/njplot/files/njplot-2.3-format-security.patch +++ /dev/null @@ -1,16 +0,0 @@ - njplot-vib.c | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/njplot-vib.c b/njplot-vib.c -index fe55609..63fd3b6 100644 ---- a/njplot-vib.c -+++ b/njplot-vib.c -@@ -1976,7 +1976,7 @@ PDFONLY" no window interface, just write the PDF/PostScript tree plot\n" - #else - fprintf(stderr, - #endif -- message); -+ "%s", message); - exit(0); - } - } diff --git a/sci-biology/njplot/metadata.xml b/sci-biology/njplot/metadata.xml deleted file mode 100644 index 2a3eb3140966..000000000000 --- a/sci-biology/njplot/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <longdescription> - NJplot is a tree drawing program able to draw any phylogenetic tree - expressed in the Newick phylogenetic tree format (e.g., the format used - by the PHYLIP package). NJplot is especially convenient for rooting the - unrooted trees obtained from parsimony, distance or maximum likelihood - tree-building methods. - </longdescription> -</pkgmetadata> diff --git a/sci-biology/njplot/njplot-2.3-r2.ebuild b/sci-biology/njplot/njplot-2.3-r2.ebuild deleted file mode 100644 index 420861dac42b..000000000000 --- a/sci-biology/njplot/njplot-2.3-r2.ebuild +++ /dev/null @@ -1,38 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit toolchain-funcs - -DESCRIPTION="A phylogenetic tree drawing program which supports tree rooting" -HOMEPAGE="http://pbil.univ-lyon1.fr/software/njplot.html" -SRC_URI="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/archive/njplot-${PV}.tar.gz" - -LICENSE="public-domain" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -RDEPEND=" - sci-biology/ncbi-tools[X,static-libs] - x11-libs/libXmu" -DEPEND="${RDEPEND}" - -PATCHES=( - "${FILESDIR}"/${P}-format-security.patch - "${FILESDIR}"/${P}-buildsystem.patch -) - -src_prepare() { - default - sed -i -e "s:njplot.help:${EPREFIX}/usr/share/doc/${PF}/njplot.help:" njplot-vib.c || die - - tc-export CC -} - -src_install() { - dobin newicktops newicktotxt njplot unrooted - doman *.1 - dodoc README njplot.help -} diff --git a/sci-biology/pals/metadata.xml b/sci-biology/pals/metadata.xml index 959160fe46b1..ccdff086e20b 100644 --- a/sci-biology/pals/metadata.xml +++ b/sci-biology/pals/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/pals/pals-1.0-r1.ebuild b/sci-biology/pals/pals-1.0-r2.ebuild index 32579b9d0757..94f972567ea7 100644 --- a/sci-biology/pals/pals-1.0-r1.ebuild +++ b/sci-biology/pals/pals-1.0-r2.ebuild @@ -1,23 +1,18 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit toolchain-funcs DESCRIPTION="Pairwise Aligner for Long Sequences" -HOMEPAGE="http://www.drive5.com/pals/" -SRC_URI="http://www.drive5.com/pals/pals_source.tar.gz -> ${P}.tar.gz" +HOMEPAGE="https://www.drive5.com/pals/" +SRC_URI="https://www.drive5.com/pals/pals_source.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}" LICENSE="public-domain" SLOT="0" -KEYWORDS="amd64 x86" -IUSE="" - -RDEPEND="" -DEPEND="${RDEPEND}" - -S=${WORKDIR} +KEYWORDS="amd64 ~x86" PATCHES=( "${FILESDIR}"/${PN}-1.0-fix-build-system.patch ) diff --git a/sci-biology/paml/Manifest b/sci-biology/paml/Manifest index ca4a6f9a9d8b..4e828eff1360 100644 --- a/sci-biology/paml/Manifest +++ b/sci-biology/paml/Manifest @@ -1 +1,2 @@ -DIST paml4.4c.tar.gz 2891715 BLAKE2B 04449b80e4fec080eabb69108d399a32278fcc79221e3c0d087ad1d978517ae2655bce8c300260dfb99d4d60700369ec338fa71c1d48f41a82017dbd3cae2397 SHA512 6a5f6d5baa91afa924ea392b76e59db6691fa9d6ee13a248dfe6e46d3fc83178ce41c2991de1c4cdb21952ee53771298aa0c62060f47d0dd84eaa76eb533498a +DIST paml-4.10.7.tar.gz 5250841 BLAKE2B 4d2a7fdc8eb93abe200165f7805520a02f4251dc651f26c4e1bf6fb11eee3d0721fd9d6f3c96979bae0f51b77f168e8d8a12f3dd3cbbfec7e8210a70b7c4bb9e SHA512 e450c0a28ecef946279fd92834eb5ddfb50805167655364cc959ef21839a75280a37d79209918373e80dacb0fc35decaccdb1477e53a81fd99fb140a0ce839fe +DIST paml4.9j.tgz 6380272 BLAKE2B 58fc40904aff6ae539613e772fc0525b557c1e72c1a7a1d95176987bafed8771624ae6c53803bc71c5821a52de8212a49ad99c02c408870ec929c15b6bf217e0 SHA512 c5f3c42409bbaf5ac67c816a245f1d3175ee449dcf10232d9de539130341f80f85ae53518cbca549b1f42ddf64a6e8140a22b9da091d458b425512f11f8c1758 diff --git a/sci-biology/paml/files/paml-4.10.7-LDFLAGS.patch b/sci-biology/paml/files/paml-4.10.7-LDFLAGS.patch new file mode 100644 index 000000000000..492396a0fd83 --- /dev/null +++ b/sci-biology/paml/files/paml-4.10.7-LDFLAGS.patch @@ -0,0 +1,60 @@ +https://github.com/abacus-gene/paml/pull/46 +--- a/src/Makefile ++++ b/src/Makefile +@@ -9,39 +9,39 @@ LIBS = -lm # -lM + all : $(PRGS) + + baseml : baseml.o tools.o treesub.c treespace.c paml.h +- $(CC) $(CFLAGS) -o $@ baseml.o tools.o $(LIBS) ++ $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ baseml.o tools.o $(LIBS) + basemlg : basemlg.o tools.o treesub.c treespace.c paml.h +- $(CC) $(CFLAGS) -o $@ basemlg.o tools.o $(LIBS) ++ $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ basemlg.o tools.o $(LIBS) + codeml : codeml.o tools.o treesub.c treespace.c paml.h +- $(CC) $(CFLAGS) -o $@ codeml.o tools.o $(LIBS) ++ $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ codeml.o tools.o $(LIBS) + evolver : evolver.o tools.o treesub.c treespace.c paml.h +- $(CC) $(CFLAGS) -o $@ evolver.o tools.o $(LIBS) ++ $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ evolver.o tools.o $(LIBS) + pamp : pamp.o tools.o treesub.c treespace.c paml.h +- $(CC) $(CFLAGS) -o $@ pamp.o tools.o $(LIBS) ++ $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ pamp.o tools.o $(LIBS) + mcmctree : mcmctree.o tools.o treesub.c treespace.c paml.h +- $(CC) $(CFLAGS) -o $@ mcmctree.c tools.o $(LIBS) +- $(CC) $(CFLAGS) -o infinitesites -D INFINITESITES mcmctree.c tools.o $(LIBS) ++ $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ mcmctree.c tools.o $(LIBS) ++ $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o infinitesites -D INFINITESITES mcmctree.c tools.o $(LIBS) + yn00: yn00.o tools.o paml.h +- $(CC) $(CFLAGS) -o $@ yn00.o tools.o $(LIBS) ++ $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ yn00.o tools.o $(LIBS) + chi2 : chi2.o +- $(CC) $(CFLAGS) -o $@ chi2.c $(LIBS) ++ $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ chi2.c $(LIBS) + + tools.o : paml.h tools.c +- $(CC) $(CFLAGS) -c tools.c ++ $(CC) $(CPPFLAGS) $(CFLAGS) -c tools.c + baseml.o : paml.h baseml.c treesub.c treespace.c +- $(CC) $(CFLAGS) -c baseml.c ++ $(CC) $(CPPFLAGS) $(CFLAGS) -c baseml.c + basemlg.o : paml.h basemlg.c treesub.c +- $(CC) $(CFLAGS) -c basemlg.c ++ $(CC) $(CPPFLAGS) $(CFLAGS) -c basemlg.c + codeml.o : paml.h codeml.c treesub.c treespace.c +- $(CC) $(CFLAGS) -c codeml.c ++ $(CC) $(CPPFLAGS) $(CFLAGS) -c codeml.c + evolver.o: evolver.c treesub.c treespace.c +- $(CC) $(CFLAGS) -c evolver.c ++ $(CC) $(CPPFLAGS) $(CFLAGS) -c evolver.c + mcmctree.o : paml.h mcmctree.c treesub.c treespace.c +- $(CC) $(CFLAGS) -c mcmctree.c ++ $(CC) $(CPPFLAGS) $(CFLAGS) -c mcmctree.c + pamp.o : paml.h pamp.c treesub.c treespace.c +- $(CC) $(CFLAGS) -c pamp.c ++ $(CC) $(CPPFLAGS) $(CFLAGS) -c pamp.c + yn00.o : paml.h yn00.c +- $(CC) $(CFLAGS) -c yn00.c ++ $(CC) $(CPPFLAGS) $(CFLAGS) -c yn00.c + + clean : + -rm *.o $(PRGS) diff --git a/sci-biology/paml/files/paml-4.9j-fno-common.patch b/sci-biology/paml/files/paml-4.9j-fno-common.patch new file mode 100644 index 000000000000..66eeb8a56b86 --- /dev/null +++ b/sci-biology/paml/files/paml-4.9j-fno-common.patch @@ -0,0 +1,14 @@ +--- a/src/paml.h ++++ b/src/paml.h +@@ -372,9 +372,9 @@ + void printSptree(void); + + +-enum {BASEseq=0, CODONseq, AAseq, CODON2AAseq, BINARYseq, BASE5seq} SeqTypes; ++typedef enum {BASEseq=0, CODONseq, AAseq, CODON2AAseq, BINARYseq, BASE5seq} SeqTypes; + +-enum {PrBranch=1, PrNodeNum=2, PrLabel=4, PrNodeStr=8, PrAge=16, PrOmega=32} OutTreeOptions; ++typedef enum {PrBranch=1, PrNodeNum=2, PrLabel=4, PrNodeStr=8, PrAge=16, PrOmega=32} OutTreeOptions; + + + /* use mean (0; default) for discrete gamma instead of median (1) */ diff --git a/sci-biology/paml/files/paml-4.9j-makefile.patch b/sci-biology/paml/files/paml-4.9j-makefile.patch new file mode 100644 index 000000000000..611b80444c89 --- /dev/null +++ b/sci-biology/paml/files/paml-4.9j-makefile.patch @@ -0,0 +1,42 @@ +--- a/src/Makefile ++++ b/src/Makefile +@@ -1,27 +1,18 @@ +-PRGS = baseml codeml basemlg mcmctree pamp evolver yn00 chi2
+-CC = cc # cc, gcc, cl
++PRGS = baseml basemlg codeml evolver pamp mcmctree infinitesites yn00 chi2
+
+-CFLAGS = -O3
++CFLAGS += -Wno-unused-result
+ #CFLAGS = -fast
+
+-LIBS = -lm # -lM
++LDLIBS = -lm
+
+ all : $(PRGS)
+
+-baseml : baseml.c tools.c treesub.c treespace.c paml.h
+- $(CC) $(CFLAGS) -o $@ baseml.c tools.c $(LIBS)
+-basemlg : basemlg.c tools.c treesub.c treespace.c paml.h
+- $(CC) $(CFLAGS) -o $@ basemlg.c tools.c $(LIBS)
+-codeml : codeml.c tools.c treesub.c treespace.c paml.h
+- $(CC) $(CFLAGS) -o $@ codeml.c tools.c $(LIBS)
+-evolver : evolver.c tools.c treesub.c treespace.c paml.h
+- $(CC) $(CFLAGS) -o $@ evolver.c tools.c $(LIBS)
+-pamp : pamp.c tools.c treesub.c treespace.c paml.h
+- $(CC) $(CFLAGS) -o $@ pamp.c tools.c $(LIBS)
+-mcmctree : mcmctree.c tools.c treesub.c treespace.c paml.h
+- $(CC) $(CFLAGS) -o $@ mcmctree.c tools.c $(LIBS)
+- $(CC) $(CFLAGS) -o infinitesites -D INFINITESITES mcmctree.c tools.c $(LIBS)
+-yn00: yn00.c tools.c paml.h
+- $(CC) $(CFLAGS) -o $@ yn00.c tools.c $(LIBS)
+-chi2 : chi2.c
+- $(CC) $(CFLAGS) -o $@ chi2.c $(LIBS)
++baseml: tools.o paml.h
++basemlg: tools.o paml.h
++codeml: tools.o paml.h
++evolver: tools.o paml.h
++pamp: tools.o paml.h
++mcmctree: tools.o paml.h
++infinitesites: tools.o paml.h
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -DINFINITESITES mcmctree.c -o infinitesites tools.o $(LDLIBS)
++yn00: tools.o paml.h
diff --git a/sci-biology/paml/metadata.xml b/sci-biology/paml/metadata.xml index 959160fe46b1..1407729820e0 100644 --- a/sci-biology/paml/metadata.xml +++ b/sci-biology/paml/metadata.xml @@ -1,8 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">abacus-gene/paml</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/paml/paml-4.10.7.ebuild b/sci-biology/paml/paml-4.10.7.ebuild new file mode 100644 index 000000000000..3291f74efcad --- /dev/null +++ b/sci-biology/paml/paml-4.10.7.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit toolchain-funcs + +DESCRIPTION="Phylogenetic Analysis by Maximum Likelihood" +HOMEPAGE="https://abacus.gene.ucl.ac.uk/software/paml.html" +SRC_URI="https://github.com/abacus-gene/${PN}/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="free-noncomm" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +PATCHES=( + "${FILESDIR}"/${PN}-4.10.7-LDFLAGS.patch +) + +src_compile() { + emake -C src CC="$(tc-getCC)" CFLAGS="${CFLAGS}" LDFLAGS="${LDFLAGS}" +} + +src_install() { + dobin src/{baseml,basemlg,codeml,evolver,pamp,mcmctree,infinitesites,yn00,chi2} + + dodoc -r README.md doc/. + + insinto /usr/share/${PN}/control + doins examples/*.ctl + + insinto /usr/share/${PN}/dat + doins -r examples/stewart* examples/*.dat dat/. + + insinto /usr/share/${PN} + doins -r examples +} diff --git a/sci-biology/paml/paml-4.4c-r1.ebuild b/sci-biology/paml/paml-4.4c-r1.ebuild deleted file mode 100644 index 27fe5ed4c769..000000000000 --- a/sci-biology/paml/paml-4.4c-r1.ebuild +++ /dev/null @@ -1,47 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit toolchain-funcs versionator - -MY_P=$(version_format_string '${PN}$1$2') - -DESCRIPTION="Phylogenetic Analysis by Maximum Likelihood" -HOMEPAGE="http://abacus.gene.ucl.ac.uk/software/paml.html" -SRC_URI="http://abacus.gene.ucl.ac.uk/software/${PN}${PV}.tar.gz" - -LICENSE="free-noncomm" -SLOT="0" -KEYWORDS="amd64 x86" -IUSE="" - -S=${WORKDIR}/${MY_P} - -src_prepare() { - # Notice send by mail to prof. Ziheng Yang - sed -i "s/\$(CC)/& \$(LDFLAGS)/" src/Makefile || die #335608 -} - -src_compile() { - emake -C src \ - CC="$(tc-getCC)" \ - CFLAGS="${CFLAGS} -Wno-unused-result" \ - LDFLAGS="${LDFLAGS}" -} - -src_install() { - dodoc README.txt doc/* - - insinto /usr/share/${PN}/control - doins *.ctl - - insinto /usr/share/${PN}/dat - doins stewart* *.dat dat/* - - insinto /usr/share/${PN} - doins -r examples/ - - cd src || die - dobin baseml codeml basemlg mcmctree pamp evolver yn00 chi2 -} diff --git a/sci-biology/paml/paml-4.9j.ebuild b/sci-biology/paml/paml-4.9j.ebuild new file mode 100644 index 000000000000..e8a5d07ee40c --- /dev/null +++ b/sci-biology/paml/paml-4.9j.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +inherit toolchain-funcs + +DESCRIPTION="Phylogenetic Analysis by Maximum Likelihood" +HOMEPAGE="http://abacus.gene.ucl.ac.uk/software/paml.html" +SRC_URI="http://abacus.gene.ucl.ac.uk/software/${P/-/}.tgz" + +LICENSE="free-noncomm" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +S="${WORKDIR}/${P/-/}" +PATCHES=( + "${FILESDIR}"/${PN}-4.9j-makefile.patch + "${FILESDIR}"/${PN}-4.9j-fno-common.patch +) + +src_configure() { + tc-export CC +} + +src_compile() { + emake -C src +} + +src_install() { + dobin src/{baseml,basemlg,codeml,evolver,pamp,mcmctree,infinitesites,yn00,chi2} + + dodoc -r README.txt doc/. + + insinto /usr/share/${PN}/control + doins *.ctl + + insinto /usr/share/${PN}/dat + doins -r stewart* *.dat dat/. + + insinto /usr/share/${PN} + doins -r examples +} diff --git a/sci-biology/phrap/Manifest b/sci-biology/phrap/Manifest deleted file mode 100644 index 12d65a0b5974..000000000000 --- a/sci-biology/phrap/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST phrap-1.080812-distrib.tar.gz 317350 BLAKE2B 9cc53d05184b4a55a9a80e6112498f91a622b98a853b255daedd57c892b7c2bb8ef3091ed3d141e297864c158b7e03d02313a272448d2e0fb80e1c51a906e00a SHA512 6b125b9a99b6180eb5de16bccfe068abefdb59237fd3295924c418749f2f2d6e39cdbcecc6786e42738846975334c4d8a645eae8fd0fcbda6b0e99241deb15ca diff --git a/sci-biology/phrap/files/phrap-1.080812-fix-build-system.patch b/sci-biology/phrap/files/phrap-1.080812-fix-build-system.patch deleted file mode 100644 index 6d30c2ce326a..000000000000 --- a/sci-biology/phrap/files/phrap-1.080812-fix-build-system.patch +++ /dev/null @@ -1,100 +0,0 @@ -* Fix perl shebang to be portable -* Make build system honour LDFLAGS - ---- a/makefile -+++ b/makefile -@@ -25,9 +25,8 @@ - # Makefile for swat, phrap, cross_match, phrapview; also swprobs (currently inactivated) - #CC= icc - #CFLAGS= -O2 -wd266,880 --CC= cc --CFLAGS= -O2 --LFLAGS= -lm -+CC ?= cc -+LIBS = -lm - - SWATOBJS= swat.o weibull.o - -@@ -96,46 +95,46 @@ - chmod a+x phrapview - - swat: makefile $(SWATOBJS) $(SWOBJS) -- $(CC) $(CFLAGS) -o $@ $(SWATOBJS) $(SWOBJS) $(LFLAGS) -+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(SWATOBJS) $(SWOBJS) $(LIBS) - chmod o-r swat - - alpha_swat: makefile $(ALPHOBJS) $(SWOBJS) -- $(CC) $(CFLAGS) -o $@ $(ALPHOBJS) $(SWOBJS) $(LFLAGS) -+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(ALPHOBJS) $(SWOBJS) $(LIBS) - chmod o-r alpha_swat - - swat_counts: makefile $(COUNOBJS) $(SWOBJS) -- $(CC) $(CFLAGS) -o $@ $(COUNOBJS) $(SWOBJS) $(LFLAGS) -+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(COUNOBJS) $(SWOBJS) $(LIBS) - chmod o-r swat_counts - - swprobs: makefile $(PROBOBJS) -- $(CC) $(CFLAGS) -o $@ $(PROBOBJS) $(LFLAGS) -+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(PROBOBJS) $(LIBS) - - phrap: makefile phrap.o call_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) -- $(CC) $(CFLAGS) -o $@ phrap.o call_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(LFLAGS) -+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ phrap.o call_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(LIBS) - chmod o-r phrap - - gcphrap: makefile gcphrap.o gccall_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) -- $(CC) $(CFLAGS) -o $@ gcphrap.o gccall_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) $(LFLAGS) -+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ gcphrap.o gccall_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) $(LIBS) - chmod o-r gcphrap - - cross_match: makefile cross_match.o call_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) -- $(CC) $(CFLAGS) -o $@ cross_match.o call_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(LFLAGS) -+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ cross_match.o call_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(LIBS) - chmod o-r cross_match - - gccross_match: makefile gccross_match.o gccall_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) -- $(CC) $(CFLAGS) -o $@ gccross_match.o gccall_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) $(LFLAGS) -+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ gccross_match.o gccall_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) $(LIBS) - chmod o-r gccross_match - - cluster: makefile $(CLOBJS) call_subs.o $(SCANOBJS) $(SWOBJS) -- $(CC) $(CFLAGS) -o $@ $(CLOBJS) call_subs.o $(SCANOBJS) $(SWOBJS) $(LFLAGS) -+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(CLOBJS) call_subs.o $(SCANOBJS) $(SWOBJS) $(LIBS) - chmod o-r cluster - - loco: makefile $(LOCOOBJS) $(SWOBJS) -- $(CC) $(CFLAGS) -o $@ $(LOCOOBJS) $(SWOBJS) $(LFLAGS) -+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(LOCOOBJS) $(SWOBJS) $(LIBS) - chmod o-r loco - - erf_test: $(ERFOBJS) -- $(CC) $(CFLAGS) -o $@ $(ERFOBJS) $(LFLAGS) -+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(ERFOBJS) $(LIBS) - - loco.o: swat.h - -@@ -228,7 +227,7 @@ - anomalies.o: swat.h - - fast_smith_wat.s: fast_smith_wat.c -- cc -S -machine_code -source_listing -O3 fast_smith_wat.c -+ $(CC) $(CFLAGS) -S -machine_code -source_listing fast_smith_wat.c - #N.B. fast_smith_wat.s MUST BE EDITTED BEFORE USE!!! - - tig_node.o: swat.h ---- a/phrapview -+++ b/phrapview -@@ -1,4 +1,4 @@ --#!/usr/local/bin/perl -w -+#!/usr/bin/env perl - - - #/***************************************************************************** -@@ -25,6 +25,7 @@ - # - #*****************************************************************************/ - -+use warnings; - use strict; - use Tk; - #phrapview version 0.960731 diff --git a/sci-biology/phrap/metadata.xml b/sci-biology/phrap/metadata.xml deleted file mode 100644 index 959160fe46b1..000000000000 --- a/sci-biology/phrap/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/phrap/phrap-1.080812-r2.ebuild b/sci-biology/phrap/phrap-1.080812-r2.ebuild deleted file mode 100644 index 08ea5a1fb71f..000000000000 --- a/sci-biology/phrap/phrap-1.080812-r2.ebuild +++ /dev/null @@ -1,47 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit toolchain-funcs - -DESCRIPTION="Shotgun assembly and alignment utilities" -HOMEPAGE="http://www.phrap.org/" -SRC_URI="phrap-${PV}-distrib.tar.gz" - -LICENSE="phrap" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND="" -RDEPEND=" - dev-lang/perl - dev-perl/Tk" - -S="${WORKDIR}" - -RESTRICT="fetch" -PATCHES=( "${FILESDIR}/${PN}-1.080812-fix-build-system.patch" ) - -pkg_nofetch() { - einfo "Please visit http://www.phrap.org/phredphrapconsed.html and obtain the file" - einfo "\"distrib.tar.gz\", then rename it to \"phrap-${PV}-distrib.tar.gz\"" - einfo "and put it into your DISTDIR directory." -} - -src_compile() { - emake CC="$(tc-getCC)" \ - CFLAGS="${CFLAGS}" \ - LDFLAGS="${LDFLAGS}" -} - -src_install() { - dobin cross_match loco phrap phrapview swat - newbin cluster cluster_phrap - - local i - for i in {general,phrap,swat}.doc; do - newdoc ${i} ${i}.txt - done -} diff --git a/sci-biology/phred/Manifest b/sci-biology/phred/Manifest deleted file mode 100644 index 1c0aa1a3ee91..000000000000 --- a/sci-biology/phred/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST phred-dist-071220.b-acd.tar.gz 357767 BLAKE2B ae1180f54eaa3631a4e32c2ffe388b35745302e3d014c8fa893119e7e488d4bb4316f7ee0588cd12db5cbbc23033f689f4a0a487cdc7fe42e8c7a67ceb3c43ae SHA512 0a6b0a733e6dcc0495eaab720b75f8e5815df494d0a773b8b8336d5208321c2ba475921084835a769367ec51aed156585ab97346a510100d4337e3215ec75276 diff --git a/sci-biology/phred/files/phred-071220-fix-build-system.patch b/sci-biology/phred/files/phred-071220-fix-build-system.patch deleted file mode 100644 index 997f39941a07..000000000000 --- a/sci-biology/phred/files/phred-071220-fix-build-system.patch +++ /dev/null @@ -1,82 +0,0 @@ -* Fix build system to honour CC, CFLAGS, CPPFLAGS and LDFLAGS -* Specify a default target, in order to keep the ebuild slim - ---- a/Makefile -+++ b/Makefile -@@ -12,9 +12,9 @@ - - # UNIX specific definitions (default) - # --CC= cc --CFLAGS= -O -DANSI_C $(LXFLAGS) --CLIB= -lm -+CC ?= cc -+CPPFLAGS += -DANSI_C $(LXFLAGS) -+LIBS += -lm - - # Windows 'nmake' specific definitions - # -@@ -133,9 +133,6 @@ - $(objdir)writeSDF.o \ - $(objdir)writeSeq.o - --SRCS = $(OBJS:.o=.c) --WOBJ = $(OBJS:.o=.obj) -- - INCS = \ - $(incdir)chromatData.h \ - $(incdir)freeChromatData.h \ -@@ -179,48 +176,18 @@ - # UNIX make specific phred target - # note: a horizontal tab character must precede `$(CC)' - # --phred: $(OBJS) -- $(CC) $(CFLAGS) -o phred $(OBJS) $(CLIB) - - --# Windows nmake specific phred target --# --forwindows: $(WOBJ) -- $(CC) $(CFLAGS) /Fephred $(WOBJ) --# $(CC) $(CFLAGS) /Fedaev daev.c -+.PHONY: all -+all: phred daev - - --# test CC: refuse to compile if --# --# o SunOS --# --# AND --# --# o using /usr/ucb/cc compiler --# --# NOTE: this compiler causes problems: see PHRED.DOC --# --test_cc: -- @if [ `uname` = SunOS ] ; \ -- then \ -- if [ `which $(CC)` = "/usr/ucb/cc" ] ; \ -- then \ -- echo ""; \ -- echo "============================================================"; \ -- echo "| |"; \ -- echo "| This SUN C compiler produces a bad phred executable. |"; \ -- echo "| |"; \ -- echo "| Please see the PHRED.DOC file for more information. |"; \ -- echo "| |"; \ -- echo "============================================================"; \ -- echo ""; \ -- exit 1; \ -- fi \ -- fi -+phred: $(OBJS) -+ $(CC) $(LDFLAGS) $(CFLAGS) -o phred $^ $(LIBS) - - - daev: daev.o -- $(CC) $(CFLAGS) -o daev daev.o -lm -+ $(CC) $(LDFLAGS) $(CFLAGS) -o daev $^ $(LIBS) - - - clean: diff --git a/sci-biology/phred/files/phred-071220-fix-qa.patch b/sci-biology/phred/files/phred-071220-fix-qa.patch deleted file mode 100644 index ab4d2ea023f6..000000000000 --- a/sci-biology/phred/files/phred-071220-fix-qa.patch +++ /dev/null @@ -1,36 +0,0 @@ -Fix implicit declarations: -* daev.c: In function ‘processParameters’: -* daev.c:849:14: warning: implicit declaration of function ‘isdigit’ [-Wimplicit-function-declaration] -* if( !isdigit( argv[iarg][0] ) ) - ---- a/autoPhred.c -+++ b/autoPhred.c -@@ -57,6 +57,7 @@ - static int xstrcmp(); - #endif - -+int freeMBRData( MBRData *mbrData ); - #ifdef ANSI_C - int autoPhred( Option *option ) - #else ---- a/daev.c -+++ b/daev.c -@@ -58,6 +58,7 @@ - #include <sys/stat.h> - #include <time.h> - #include <math.h> -+#include <ctype.h> - - #ifndef _WIN32 - #include <dirent.h> ---- a/mergedBaseRead.c -+++ b/mergedBaseRead.c -@@ -63,7 +63,7 @@ - Peak *peak; - Observed_peak *obs_peak; - -- static initFlag = 0; -+ static int initFlag = 0; - static char mchar[256][256]; - - if( initFlag == 0 ) diff --git a/sci-biology/phred/metadata.xml b/sci-biology/phred/metadata.xml deleted file mode 100644 index 959160fe46b1..000000000000 --- a/sci-biology/phred/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/phred/phred-071220-r1.ebuild b/sci-biology/phred/phred-071220-r1.ebuild deleted file mode 100644 index bf7a0c7338cb..000000000000 --- a/sci-biology/phred/phred-071220-r1.ebuild +++ /dev/null @@ -1,50 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit toolchain-funcs - -DESCRIPTION="A base caller for Sanger DNA sequencing" -HOMEPAGE="http://phrap.org/phredphrapconsed.html" -SRC_URI="phred-dist-071220.b-acd.tar.gz" - -LICENSE="phrap" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND="" -RDEPEND="" - -S="${WORKDIR}" - -RESTRICT="fetch" -PATCHES=( - "${FILESDIR}/${PN}-071220-fix-build-system.patch" - "${FILESDIR}/${PN}-071220-fix-qa.patch" -) - -pkg_nofetch() { - einfo "Please visit ${HOMEPAGE} and obtain the file" - einfo "${SRC_URI}, then place it into your DISTDIR directory." -} - -src_compile() { - emake CC="$(tc-getCC)" \ - CFLAGS="${CFLAGS}" \ - LDFLAGS="${LDFLAGS}" -} - -src_install() { - dobin phred daev - - insinto /usr/share/${PN} - doins phredpar.dat - - echo "PHRED_PARAMETER_FILE=${EPREFIX}/usr/share/${PN}/phredpar.dat" > 99phred || die - doenvd 99phred - - newdoc DAEV.DOC DAEV.DOC.txt - newdoc PHRED.DOC PHRED.DOC.txt -} diff --git a/sci-biology/phylip/Manifest b/sci-biology/phylip/Manifest index 5a714766bc16..444e3d45e356 100644 --- a/sci-biology/phylip/Manifest +++ b/sci-biology/phylip/Manifest @@ -1,2 +1 @@ -DIST phylip-3.69.tar.gz 1511935 BLAKE2B 76aa5a79d2553c6f269c011f633d1101ee4d85ac398a36dd463e5605d90833ecb1e5f6c21edba3e142e2d4ab5ef034fa739e52e0ab3f941a7987915ae352be0b SHA512 e36d12bfe597896b4298c1d0e3b0b7bd783573dc03e861b9472d8284391b2339cb3fb58eb6580298724bbd516127b68925815455514f939da9272fcfed7e229d -DIST phylip-3.696.tar.gz 3955721 BLAKE2B dc75fc442eb63e44bc2e68e5dc97b3ff8f741bfa53740ed57ca114b53dcb71db9baeb9a96c3e693f7fae92afbaa71c7b5acfb39e7770bacb6aafa8c33b355be6 SHA512 711a9a34be72b0f63c746733cd1384f091b7cc597dbd9a40c130e074efbf0a0ecc30e5a6b3452bb73dc69cddbdae2fc07d1c0a68f0be207471eab73ab876c6be +DIST phylip-3.698.zip 9675991 BLAKE2B 8d020cf17b3245b9827af4bdd1d17167c3e1a41ae805766c4b72f09de107775314a2a296c00f84f928487403cc02741fd46ae73585d0dba143f4b926777e9add SHA512 7f822dabd1ffdb6a689e0c308f5a3ae129bd86e305086a18c0c755ac3c6ca28a4337d52ced76b280706926370e23f19f304851ef82e32833d1945ed277f7d70d diff --git a/sci-biology/phylip/files/phylip-3.698-fno-common.patch b/sci-biology/phylip/files/phylip-3.698-fno-common.patch new file mode 100644 index 000000000000..986b1d9650ab --- /dev/null +++ b/sci-biology/phylip/files/phylip-3.698-fno-common.patch @@ -0,0 +1,70 @@ +--- a/src/draw.c ++++ b/src/draw.c +@@ -34,6 +34,11 @@ +
+ char fontname[LARGE_BUF_LENGTH];
+
++long treecolor, namecolor, backcolor, bottomcolor, vrmlskycolornear, vrmlskycolorfar,
++ vrmlgroundcolornear, vrmlgroundcolorfar, vrmlplotcolor;
++
++char afmfile[FNMLNGTH];
++
+ /* format of matrix: capheight, length[32],length[33],..length[256]*/
+
+ byte *full_pic ;
+--- a/src/draw.h ++++ b/src/draw.h +@@ -52,10 +52,10 @@ + double intensity, x, y, z;
+ } vrmllighttype;
+
+-long treecolor, namecolor, backcolor, bottomcolor, vrmlskycolornear, vrmlskycolorfar,
++extern long treecolor, namecolor, backcolor, bottomcolor, vrmlskycolornear, vrmlskycolorfar,
+ vrmlgroundcolornear, vrmlgroundcolorfar, vrmlplotcolor;
+
+-char afmfile[FNMLNGTH];
++extern char afmfile[FNMLNGTH];
+
+ double lengthtext(char *, long, char *, fonttype);
+ double heighttext(fonttype, char *);
+--- a/src/drawtree.c ++++ b/src/drawtree.c +@@ -69,7 +69,7 @@ + uselengths, regular, rotate, empty, rescaled,
+ notfirst, improve, nbody, firstscreens, labelavoid;
+ boolean pictbold,pictitalic,pictshadow,pictoutline;
+-boolean javarun;
++extern boolean javarun;
+
+ striptype stripe;
+ plottertype plotter, oldplotter;
+--- a/src/phylip.c ++++ b/src/phylip.c +@@ -34,6 +34,8 @@ +
+ #include "phylip.h"
+
++boolean javarun;
++
+ #ifdef WIN32
+ #include <windows.h>
+ /* for console code (clear screen, text color settings) */
+--- a/src/phylip.h ++++ b/src/phylip.h +@@ -331,7 +331,7 @@ + /* Lower-triangular format. */
+ #define MAT_LOWERTRI (MAT_LOWER | MAT_MACHINE)
+
+-boolean javarun;
++extern boolean javarun;
+
+ typedef long *steptr;
+ typedef long longer[6];
+@@ -351,7 +351,6 @@ + extern long spp, words, bits;
+ extern boolean ibmpc, ansi, tranvsp;
+ extern naym *nayme; /* names of species */
+-boolean firstplotblock; // for debugging BMP output
+
+ #define ebcdic EBCDIC
+
diff --git a/sci-biology/phylip/files/phylip-3.698-makefile.patch b/sci-biology/phylip/files/phylip-3.698-makefile.patch new file mode 100644 index 000000000000..f55ab98dd9cb --- /dev/null +++ b/sci-biology/phylip/files/phylip-3.698-makefile.patch @@ -0,0 +1,266 @@ +--- a/src/Makefile.unx ++++ b/src/Makefile.unx +@@ -81,7 +81,6 @@ + #CC = cc + # + # To use GCC instead: +-CC = gcc + # + # ---------------------------------------------------------------------------- + # +@@ -91,7 +90,6 @@ + # + # + #A minimal one +-CFLAGS = + # + # A basic one for debugging + #CFLAGS = -g +@@ -220,7 +218,7 @@ + @echo "Done." + @echo "" + +-put: ++put: all + @echo "Installing PHYLIP v3.6 binaries in $(EXEDIR)" + @mkdir -p $(EXEDIR) + @cp $(PROGS) $(EXEDIR) +@@ -270,195 +268,195 @@ + clique.o: clique.c disc.h phylip.h + + clique: clique.o disc.o phylip.o +- $(CC) $(CFLAGS) clique.o disc.o phylip.o $(LIBS) -o clique ++ $(CC) $(LDFLAGS) clique.o disc.o phylip.o $(LIBS) -o clique + + cons.o: cons.c cons.h phylip.h + + consense.o: consense.c cons.h phylip.h + + consense: consense.o phylip.o cons.o +- $(CC) $(CFLAGS) consense.o phylip.o cons.o $(LIBS) -o consense ++ $(CC) $(LDFLAGS) consense.o phylip.o cons.o $(LIBS) -o consense + + contml.o: contml.c cont.h phylip.h + + contml: contml.o cont.o phylip.o +- $(CC) $(CFLAGS) contml.o cont.o phylip.o $(LIBS) -o contml ++ $(CC) $(LDFLAGS) contml.o cont.o phylip.o $(LIBS) -o contml + + contrast.o: contrast.c cont.h phylip.h + + contrast: contrast.o cont.o phylip.o +- $(CC) $(CFLAGS) contrast.o cont.o phylip.o $(LIBS) -o contrast ++ $(CC) $(LDFLAGS) contrast.o cont.o phylip.o $(LIBS) -o contrast + + dnacomp.o: dnacomp.c seq.h phylip.h + + dnacomp: dnacomp.o seq.o phylip.o +- $(CC) $(CFLAGS) dnacomp.o seq.o phylip.o $(LIBS) -o dnacomp ++ $(CC) $(LDFLAGS) dnacomp.o seq.o phylip.o $(LIBS) -o dnacomp + + dnadist.o: dnadist.c seq.h phylip.h + + dnadist: dnadist.o seq.o phylip.o +- $(CC) $(CFLAGS) dnadist.o seq.o phylip.o $(LIBS) -o dnadist ++ $(CC) $(LDFLAGS) dnadist.o seq.o phylip.o $(LIBS) -o dnadist + + dnainvar.o: dnainvar.c seq.h phylip.h + + dnainvar: dnainvar.o seq.o phylip.o +- $(CC) $(CFLAGS) dnainvar.o seq.o phylip.o $(LIBS) -o dnainvar ++ $(CC) $(LDFLAGS) dnainvar.o seq.o phylip.o $(LIBS) -o dnainvar + + dnaml.o: dnaml.c seq.h phylip.h + + dnaml: dnaml.o seq.o phylip.o +- $(CC) $(CFLAGS) dnaml.o seq.o phylip.o $(LIBS) -o dnaml ++ $(CC) $(LDFLAGS) dnaml.o seq.o phylip.o $(LIBS) -o dnaml + + dnamlk.o: dnamlk.c seq.h phylip.h mlclock.h printree.h + + dnamlk: dnamlk.o seq.o phylip.o mlclock.o printree.o +- $(CC) $(CFLAGS) dnamlk.o seq.o phylip.o mlclock.o printree.o $(LIBS) -o dnamlk ++ $(CC) $(LDFLAGS) dnamlk.o seq.o phylip.o mlclock.o printree.o $(LIBS) -o dnamlk + + dnamove.o: dnamove.c seq.h moves.h phylip.h + + dnamove: dnamove.o seq.o moves.o phylip.o +- $(CC) $(CFLAGS) dnamove.o seq.o moves.o phylip.o $(LIBS) -o dnamove ++ $(CC) $(LDFLAGS) dnamove.o seq.o moves.o phylip.o $(LIBS) -o dnamove + + dnapenny.o: dnapenny.c seq.h phylip.h + + dnapenny: dnapenny.o seq.o phylip.o +- $(CC) $(CFLAGS) dnapenny.o seq.o phylip.o $(LIBS) -o dnapenny ++ $(CC) $(LDFLAGS) dnapenny.o seq.o phylip.o $(LIBS) -o dnapenny + + dnapars.o: dnapars.c seq.h phylip.h + + dnapars: dnapars.o seq.o phylip.o +- $(CC) $(CFLAGS) dnapars.o seq.o phylip.o $(LIBS) -o dnapars ++ $(CC) $(LDFLAGS) dnapars.o seq.o phylip.o $(LIBS) -o dnapars + + dolmove.o: dolmove.c disc.h moves.h dollo.h phylip.h + + dolmove: dolmove.o disc.o moves.o dollo.o phylip.o +- $(CC) $(CFLAGS) dolmove.o disc.o moves.o dollo.o phylip.o $(LIBS) -o dolmove ++ $(CC) $(LDFLAGS) dolmove.o disc.o moves.o dollo.o phylip.o $(LIBS) -o dolmove + + dollop.o: dollop.c disc.h dollo.h phylip.h + + dollop: dollop.o disc.o dollo.o phylip.o +- $(CC) $(CFLAGS) dollop.o disc.o dollo.o phylip.o $(LIBS) -o dollop ++ $(CC) $(LDFLAGS) dollop.o disc.o dollo.o phylip.o $(LIBS) -o dollop + + dolpenny.o: dolpenny.c disc.h dollo.h phylip.h + + dolpenny: dolpenny.o disc.o dollo.o phylip.o +- $(CC) $(CFLAGS) dolpenny.o disc.o dollo.o phylip.o $(LIBS) -o dolpenny ++ $(CC) $(LDFLAGS) dolpenny.o disc.o dollo.o phylip.o $(LIBS) -o dolpenny + + draw.o: draw.c draw.h phylip.h +- $(CC) $(DFLAGS) -c draw.c ++ $(CC) $(DFLAGS) $(CPPFLAGS) -c draw.c + + draw2.o: draw2.c draw.h phylip.h +- $(CC) $(DFLAGS) -c draw2.c ++ $(CC) $(DFLAGS) $(CPPFLAGS) -c draw2.c + + drawgram.o: drawgram.c draw.h phylip.h +- $(CC) $(DFLAGS) -c drawgram.c ++ $(CC) $(DFLAGS) $(CPPFLAGS) -c drawgram.c + + drawgram: drawgram.o draw.o draw2.o phylip.o +- $(CC) $(DFLAGS) draw.o draw2.o drawgram.o phylip.o $(DLIBS) -o drawgram ++ $(CC) $(LDFLAGS) draw.o draw2.o drawgram.o phylip.o $(DLIBS) -o drawgram + + # needed by java +-libdrawgram.so: drawgram.o draw.o draw2.o phylip.o +- $(CC) $(CFLAGS) -o libdrawgram.so -shared -fPIC drawgram.c draw.c draw2.c phylip.c $(CLIBS) ++libdrawgram.so: ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o libdrawgram.so -Wl,-soname,libdrawgram.so -shared -fPIC drawgram.c draw.c draw2.c phylip.c $(CLIBS) + + drawtree.o: drawtree.c draw.h phylip.h +- $(CC) $(DFLAGS) -shared -fPIC -c drawtree.c ++ $(CC) $(DFLAGS) $(CPPFLAGS) -c drawtree.c + + drawtree: drawtree.o draw.o draw2.o phylip.o +- $(CC) $(DFLAGS) draw.o draw2.o drawtree.o phylip.o $(DLIBS) -o drawtree ++ $(CC) $(LDFLAGS) draw.o draw2.o drawtree.o phylip.o $(DLIBS) -o drawtree + + # needed by java +-libdrawtree.so: drawtree.o draw.o draw2.o phylip.o +- $(CC) $(CFLAGS) -o libdrawtree.so -shared -fPIC drawtree.c draw.c draw2.c phylip.c $(CLIBS) ++libdrawtree.so: ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o libdrawtree.so -Wl,-soname,libdrawtree.so -shared -fPIC drawtree.c draw.c draw2.c phylip.c $(CLIBS) + + factor.o: factor.c phylip.h + + factor: factor.o phylip.o +- $(CC) $(CFLAGS) factor.o phylip.o $(LIBS) -o factor ++ $(CC) $(LDFLAGS) factor.o phylip.o $(LIBS) -o factor + + fitch.o: fitch.c dist.h phylip.h + + fitch: fitch.o dist.o phylip.o +- $(CC) $(CFLAGS) fitch.o dist.o phylip.o $(LIBS) -o fitch ++ $(CC) $(LDFLAGS) fitch.o dist.o phylip.o $(LIBS) -o fitch + + gendist.o: gendist.c phylip.h + + gendist: gendist.o phylip.o +- $(CC) $(CFLAGS) gendist.o phylip.o $(LIBS) -o gendist ++ $(CC) $(LDFLAGS) gendist.o phylip.o $(LIBS) -o gendist + + kitsch.o: kitsch.c dist.h phylip.h + + kitsch: kitsch.o dist.o phylip.o +- $(CC) $(CFLAGS) kitsch.o dist.o phylip.o $(LIBS) -o kitsch ++ $(CC) $(LDFLAGS) kitsch.o dist.o phylip.o $(LIBS) -o kitsch + + mix.o: mix.c disc.h wagner.h phylip.h + + mix: mix.o disc.o wagner.o phylip.o +- $(CC) $(CFLAGS) mix.o disc.o wagner.o phylip.o $(LIBS) -o mix ++ $(CC) $(LDFLAGS) mix.o disc.o wagner.o phylip.o $(LIBS) -o mix + + move.o: move.c disc.h moves.h wagner.h phylip.h + + move: move.o disc.o moves.o wagner.o phylip.o +- $(CC) $(CFLAGS) move.o disc.o moves.o wagner.o phylip.o $(LIBS) -o move ++ $(CC) $(LDFLAGS) move.o disc.o moves.o wagner.o phylip.o $(LIBS) -o move + + neighbor.o: neighbor.c dist.h phylip.h + + neighbor: neighbor.o dist.o phylip.o +- $(CC) $(CFLAGS) neighbor.o dist.o phylip.o $(LIBS) -o neighbor ++ $(CC) $(LDFLAGS) neighbor.o dist.o phylip.o $(LIBS) -o neighbor + + pars.o: pars.c discrete.h phylip.h + + pars: pars.o discrete.o phylip.o +- $(CC) $(CFLAGS) pars.o discrete.o phylip.o $(LIBS) -o pars ++ $(CC) $(LDFLAGS) pars.o discrete.o phylip.o $(LIBS) -o pars + + penny.o: penny.c disc.h wagner.h phylip.h + + penny: penny.o disc.o wagner.o phylip.o +- $(CC) $(CFLAGS) penny.o disc.o wagner.o phylip.o $(LIBS) -o penny ++ $(CC) $(LDFLAGS) penny.o disc.o wagner.o phylip.o $(LIBS) -o penny + + proml.o: proml.c seq.h phylip.h + + proml: proml.o seq.o phylip.o +- $(CC) $(CFLAGS) proml.o seq.o phylip.o $(LIBS) -o proml ++ $(CC) $(LDFLAGS) proml.o seq.o phylip.o $(LIBS) -o proml + + promlk.o: promlk.c seq.h phylip.h mlclock.h printree.h + + promlk: promlk.o seq.o phylip.o mlclock.o printree.o +- $(CC) $(CFLAGS) promlk.o seq.o phylip.o mlclock.o printree.o $(LIBS) -o promlk ++ $(CC) $(LDFLAGS) promlk.o seq.o phylip.o mlclock.o printree.o $(LIBS) -o promlk + + protdist.o: protdist.c seq.h phylip.h + + protdist: protdist.o seq.o phylip.o +- $(CC) $(CFLAGS) protdist.o seq.o phylip.o $(LIBS) -o protdist ++ $(CC) $(LDFLAGS) protdist.o seq.o phylip.o $(LIBS) -o protdist + + protpars.o: protpars.c seq.h phylip.h + + protpars: protpars.o seq.o phylip.o +- $(CC) $(CFLAGS) protpars.o seq.o phylip.o $(LIBS) -o protpars ++ $(CC) $(LDFLAGS) protpars.o seq.o phylip.o $(LIBS) -o protpars + + restdist.o: restdist.c seq.h phylip.h + + restdist: restdist.o seq.o phylip.o +- $(CC) $(CFLAGS) restdist.o seq.o phylip.o $(LIBS) -o restdist ++ $(CC) $(LDFLAGS) restdist.o seq.o phylip.o $(LIBS) -o restdist + + restml.o: restml.c seq.h phylip.h + + restml: restml.o seq.o phylip.o +- $(CC) $(CFLAGS) restml.o seq.o phylip.o $(LIBS) -o restml ++ $(CC) $(LDFLAGS) restml.o seq.o phylip.o $(LIBS) -o restml + + retree.o: retree.c moves.h phylip.h + + retree: retree.o moves.o phylip.o +- $(CC) $(CFLAGS) retree.o moves.o phylip.o $(LIBS) -o retree ++ $(CC) $(LDFLAGS) retree.o moves.o phylip.o $(LIBS) -o retree + + seqboot.o: seqboot.c phylip.h + + seqboot: seqboot.o seq.o phylip.o +- $(CC) $(CFLAGS) seqboot.o seq.o phylip.o $(LIBS) -o seqboot ++ $(CC) $(LDFLAGS) seqboot.o seq.o phylip.o $(LIBS) -o seqboot + + treedist.o: treedist.c cons.h phylip.h + + treedist: treedist.o phylip.o cons.o +- $(CC) $(CFLAGS) treedist.o cons.o phylip.o $(LIBS) -o treedist ++ $(CC) $(LDFLAGS) treedist.o cons.o phylip.o $(LIBS) -o treedist + + + # ---------------------------------------------------------------------------- diff --git a/sci-biology/phylip/metadata.xml b/sci-biology/phylip/metadata.xml index 959160fe46b1..ccdff086e20b 100644 --- a/sci-biology/phylip/metadata.xml +++ b/sci-biology/phylip/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/phylip/phylip-3.69-r1.ebuild b/sci-biology/phylip/phylip-3.69-r1.ebuild deleted file mode 100644 index e54c75d9b356..000000000000 --- a/sci-biology/phylip/phylip-3.69-r1.ebuild +++ /dev/null @@ -1,51 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit toolchain-funcs - -DESCRIPTION=" The PHYLogeny Inference Package" -HOMEPAGE="http://evolution.genetics.washington.edu/phylip.html" -SRC_URI="http://evolution.gs.washington.edu/${PN}/download/${P}.tar.gz" - -SLOT="0" -LICENSE="free-noncomm" -IUSE="" -KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos" - -RDEPEND="x11-libs/libXaw" -DEPEND="${RDEPEND} - x11-base/xorg-proto" - -S="${WORKDIR}/${P}/src" - -src_prepare() { - sed \ - -e "s/CFLAGS = -O3 -fomit-frame-pointer/CFLAGS = ${CFLAGS}/" \ - -e "s/CC = cc/CC = $(tc-getCC)/" \ - -e "s/DC = cc/DC = $(tc-getCC)/" \ - -e "/ -o /s:\(\$(CC)\):\1 ${LDFLAGS}:g" \ - -i Makefile || die "Patching Makefile failed." - mkdir ../fonts || die -} - -src_compile() { - emake -j1 all put -} - -src_install() { - cd "${WORKDIR}/${P}" || die - - mv exe/font* fonts || die "Font move failed." - mv exe/factor exe/factor-${PN} || die "Renaming factor failed." - - dobin exe/* - - dodoc "${FILESDIR}"/README.Gentoo - - dohtml -r phylip.html doc - - insinto /usr/share/${PN}/ - doins -r fonts -} diff --git a/sci-biology/phylip/phylip-3.696-r1.ebuild b/sci-biology/phylip/phylip-3.696-r1.ebuild deleted file mode 100644 index 85150acaf9cb..000000000000 --- a/sci-biology/phylip/phylip-3.696-r1.ebuild +++ /dev/null @@ -1,54 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit toolchain-funcs - -DESCRIPTION=" The PHYLogeny Inference Package" -HOMEPAGE="http://evolution.genetics.washington.edu/phylip.html" -SRC_URI="http://evolution.gs.washington.edu/${PN}/download/${P}.tar.gz" - -SLOT="0" -LICENSE="BSD-2" -IUSE="" -KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" - -RDEPEND="x11-libs/libXaw" -DEPEND="${RDEPEND} - x11-base/xorg-proto" - -S="${WORKDIR}/${P}/src" - -src_prepare() { - mv Makefile.unx Makefile || die - sed \ - -e "/ -o /s:\(\$(CC)\):\1 ${LDFLAGS}:g" \ - -i Makefile || die "Patching Makefile failed." - mkdir ../fonts || die -} - -src_compile() { - emake -j1 \ - CC="$(tc-getCC)" \ - DC="$(tc-getCC)" \ - CFLAGS="${CFLAGS} -Wno-unused-result" \ - all put -} - -src_install() { - cd "${WORKDIR}/${P}" || die - - mv exe/font* fonts || die "Font move failed." - mv exe/factor exe/factor-${PN} || die "Renaming factor failed." - - dolib.so exe/*so && rm exe/*so - dobin exe/* - - dodoc "${FILESDIR}"/README.Gentoo - - dohtml -r phylip.html doc - - insinto /usr/share/${PN}/ - doins -r fonts -} diff --git a/sci-biology/phylip/phylip-3.696-r2.ebuild b/sci-biology/phylip/phylip-3.696-r2.ebuild deleted file mode 100644 index 66391e0e662d..000000000000 --- a/sci-biology/phylip/phylip-3.696-r2.ebuild +++ /dev/null @@ -1,55 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit toolchain-funcs - -DESCRIPTION=" The PHYLogeny Inference Package" -HOMEPAGE="http://evolution.genetics.washington.edu/phylip.html" -SRC_URI="http://evolution.gs.washington.edu/${PN}/download/${P}.tar.gz" - -SLOT="0" -LICENSE="BSD-2" -IUSE="" -KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" -# 'mix' tool collides with dev-lang/elixir, bug #537514 -RDEPEND="x11-libs/libXaw - !!dev-lang/elixir" -DEPEND="${RDEPEND} - x11-base/xorg-proto" - -S="${WORKDIR}/${P}/src" - -src_prepare() { - mv Makefile.unx Makefile || die - sed \ - -e "/ -o /s:\(\$(CC)\):\1 ${LDFLAGS}:g" \ - -i Makefile || die "Patching Makefile failed." - mkdir ../fonts || die -} - -src_compile() { - emake -j1 \ - CC="$(tc-getCC)" \ - DC="$(tc-getCC)" \ - CFLAGS="${CFLAGS} -Wno-unused-result" \ - all put -} - -src_install() { - cd "${WORKDIR}/${P}" || die - - mv exe/font* fonts || die "Font move failed." - mv exe/factor exe/factor-${PN} || die "Renaming factor failed." - - dolib.so exe/*so && rm exe/*so - dobin exe/* - - dodoc "${FILESDIR}"/README.Gentoo - - dohtml -r phylip.html doc - - insinto /usr/share/${PN}/ - doins -r fonts -} diff --git a/sci-biology/phylip/phylip-3.698.ebuild b/sci-biology/phylip/phylip-3.698.ebuild new file mode 100644 index 000000000000..34bfd5699b03 --- /dev/null +++ b/sci-biology/phylip/phylip-3.698.ebuild @@ -0,0 +1,60 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +inherit flag-o-matic toolchain-funcs + +DESCRIPTION="The PHYLogeny Inference Package" +HOMEPAGE="http://evolution.genetics.washington.edu/phylip.html" +SRC_URI="http://evolution.gs.washington.edu/${PN}/download/${P}.zip" + +LICENSE="BSD-2" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" + +# 'mix' tool collides with dev-lang/elixir, bug #537514 +RDEPEND=" + x11-libs/libXaw + !dev-lang/elixir" +DEPEND="${RDEPEND} + x11-base/xorg-proto" +BDEPEND="app-arch/unzip" + +PATCHES=( + "${FILESDIR}"/${P}-makefile.patch + "${FILESDIR}"/${P}-fno-common.patch +) + +src_prepare() { + default + + mkdir fonts || die + # clear out old binaries + rm -r exe || die +} + +src_configure() { + tc-export CC + append-cflags -Wno-unused-result +} + +src_compile() { + emake -C src -f Makefile.unx all put +} + +src_install() { + mv exe/font* fonts || die "Font move failed" + mv exe/factor exe/factor-${PN} || die "Renaming factor failed" + + dolib.so exe/*so + rm exe/*so || die + dobin exe/* + + dodoc "${FILESDIR}"/README.Gentoo + docinto html + dodoc -r phylip.html doc + + insinto /usr/share/phylip + doins -r fonts +} diff --git a/sci-biology/phyml/metadata.xml b/sci-biology/phyml/metadata.xml index d4e4a77f868c..e8a2d7c4a3b0 100644 --- a/sci-biology/phyml/metadata.xml +++ b/sci-biology/phyml/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/phyml/phyml-2.4.5-r3.ebuild b/sci-biology/phyml/phyml-2.4.5-r4.ebuild index 098771430632..c0e9c38caf92 100644 --- a/sci-biology/phyml/phyml-2.4.5-r3.ebuild +++ b/sci-biology/phyml/phyml-2.4.5-r4.ebuild @@ -1,27 +1,24 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit toolchain-funcs -MY_P=${PN}_v${PV} +MY_P="${PN}_v${PV}" DESCRIPTION="Estimation of large phylogenies by maximum likelihood" HOMEPAGE="http://atgc.lirmm.fr/phyml/" SRC_URI="http://www.lirmm.fr/~guindon/${MY_P}.tar.gz" +S="${WORKDIR}/${MY_P}" LICENSE="GPL-2" SLOT="0" -KEYWORDS="amd64 ppc x86" -IUSE="" - -S=${WORKDIR}/${MY_P} +KEYWORDS="amd64 ~ppc ~x86" PATCHES=( "${FILESDIR}"/${PN}-2.4.5-fix-build-system.patch ) -src_prepare() { - default +src_configure() { tc-export CC } diff --git a/sci-biology/picard/Manifest b/sci-biology/picard/Manifest deleted file mode 100644 index 62dd6475dcea..000000000000 --- a/sci-biology/picard/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST picard-1.103.tar.bz2 15037887 BLAKE2B a4df3aad9242749964a997698d80634e14ce19af575de9609655483eba247d0968cbdc856dbf00d854ec7eae37da8f3d047c50e4b78843e9d08441d9ef18eff6 SHA512 f8db38a8fee278868cd2ea11f78275a5defadf36e053703133f0f90836df8e3a3ca08635fd7c02967ed99b52bc5baffa600a34b58a94288d3eede7f5c3dd79ca diff --git a/sci-biology/picard/files/1.103-gentoo.patch b/sci-biology/picard/files/1.103-gentoo.patch deleted file mode 100644 index 00e89b95056a..000000000000 --- a/sci-biology/picard/files/1.103-gentoo.patch +++ /dev/null @@ -1,131 +0,0 @@ -diff --git a/build.xml b/build.xml -index fca2271..11f4fbd 100755 ---- a/build.xml -+++ b/build.xml -@@ -52,9 +52,6 @@ - <property name="testng.verbosity" value="2"/> - <property name="test.debug.port" value="5005" /> <!-- override on the command line if desired --> - -- <property environment="env"/> -- <property name="java6.home" value="${env.JAVA6_HOME}"/> -- - <condition property="isUnix"> - <os family="unix"/> - </condition> -@@ -78,9 +75,6 @@ - <pathelement location="${classes}"/> - </path> - -- <path id="java6.lib.ref"> -- <fileset dir="${java6.home}/lib" includes="*.jar"/> -- </path> - </target> - - <!-- CLEAN --> -@@ -94,10 +88,6 @@ - </target> - - <!-- COMPILE --> -- <target name="compile" depends="compile-src, compile-tests" -- description="Compile files without cleaning"> -- </target> -- - <target name="compile-src" depends="compile-sam-jdk, compile-picard, compile-tribble, compile-variant" description="Compile files without cleaning"/> - - <target name="compile-sam-jdk" depends="init" description="Compile sam-jdk files without cleaning"> -@@ -138,7 +128,7 @@ - </target> - - <!-- TEST --> -- <target name="test" depends="compile, set_excluded_test_groups" description="Run unit tests"> -+ <target name="test" depends="compile-tests, set_excluded_test_groups" description="Run unit tests"> - <taskdef resource="testngtasks" classpathref="classpath"/> - <testng suitename="picard-tests" classpathref="classpath" outputdir="${test.output}" - failureproperty="tests.failed" excludedgroups="${excludedTestGroups}" workingDir="${basedir}" -@@ -151,6 +141,8 @@ - <classfileset dir="${classes.test}"> - <include name="**/Test*.class"/> - <include name="**/*Test.class"/> -+ <exclude name="**/ValidateSamFileTest.class" /> -+ <exclude name="**/VCFWriterUnitTest.class" /> - </classfileset> - <jvmarg value="-Xmx2G"/> - </testng> -@@ -165,7 +157,7 @@ - </target> - - <target name="single-test" -- depends="compile, compile-tests" -+ depends="compile-tests" - description="Compile and run a single test."> - <taskdef resource="testngtasks" classpathref="classpath"/> - <fail unless="name" message="Please provide input test: -Dname=..." /> -@@ -200,13 +192,12 @@ - </jar> - </target> - -- <target name="picard-jar" depends="compile" -+ <target name="picard-jar" depends="compile-src" - description="Builds picard-${picard-version}.jar for inclusion in other projects"> - <mkdir dir="${dist}"/> - <jar destfile="${dist}/picard-${picard-version}.jar" compress="no"> - <fileset dir="${classes}" includes ="net/sf/picard/**/*.*"/> - <fileset dir="${src.scripts}" includes="**/*.R"/> -- <zipfileset src="${lib}/apache-ant-1.8.2-bzip2.jar"/> - <manifest> - <attribute name="Implementation-Version" value="${picard-version}(${repository.revision})"/> - <attribute name="Implementation-Vendor" value="Broad Institute"/> -@@ -214,7 +205,7 @@ - </jar> - </target> - -- <target name="tribble-jar" depends="compile" -+ <target name="tribble-jar" depends="compile-src" - description="Builds tribble-${tribble-version}.jar for inclusion in other projects"> - <mkdir dir="${dist}"/> - <jar destfile="${dist}/tribble-${tribble-version}.jar" compress="no"> -@@ -225,7 +216,7 @@ - </copy> - </target> - -- <target name="variant-jar" depends="compile" -+ <target name="variant-jar" depends="compile-src" - description="Builds variant-${variant-version}.jar for inclusion in other projects"> - <mkdir dir="${dist}"/> - <jar destfile="${dist}/variant-${variant-version}.jar" compress="no"> -@@ -262,7 +253,7 @@ - </javadoc> - </target> - -- <target name="package-commands" depends="compile, sam-jar, picard-jar, tribble-jar, variant-jar"> -+ <target name="package-commands" depends="compile-src, sam-jar, picard-jar, tribble-jar, variant-jar"> - <delete dir="${command_tmp}"/> - - <mkdir dir="${command_tmp}"/> -@@ -344,7 +335,7 @@ - </target> - - <!-- ALL --> -- <target name="all" depends="compile, sam-jar, picard-jar, tribble-jar, variant-jar, package-commands, document-standard-options" description="Default build target"> -+ <target name="all" depends="compile-src, sam-jar, picard-jar, tribble-jar, variant-jar, package-commands, document-standard-options" description="Default build target"> - <zip zipfile="${dist}/picard-tools-${picard-version}.zip"> - <zipfileset dir="${dist}" includes="*.jar" prefix="picard-tools-${picard-version}"/> - <zipfileset dir="${lib}" includes="snappy*.jar"/> -@@ -468,8 +459,6 @@ - target="${javac.target}"> - <classpath refid="@{compile.classpath}"/> - <compilerarg line="@{compiler.args}" /> -- <!-- ensure that Java 6 bootclasspath is used --> -- <compilerarg value="-Xbootclasspath/p:${toString:java6.lib.ref}"/> - </javac> - </sequential> - </macrodef> -@@ -494,8 +483,6 @@ - <pathelement location="${classes}"/> - </classpath> - <compilerarg line="@{compiler.args}"/> -- <!-- ensure that Java 6 bootclasspath is used --> -- <compilerarg value="-Xbootclasspath/p:${toString:java6.lib.ref}"/> - </javac> - </sequential> - </macrodef> diff --git a/sci-biology/picard/metadata.xml b/sci-biology/picard/metadata.xml deleted file mode 100644 index 34f79a25054b..000000000000 --- a/sci-biology/picard/metadata.xml +++ /dev/null @@ -1,11 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">picard</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/picard/picard-1.103.ebuild b/sci-biology/picard/picard-1.103.ebuild deleted file mode 100644 index 7a6111c87746..000000000000 --- a/sci-biology/picard/picard-1.103.ebuild +++ /dev/null @@ -1,69 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI="5" - -JAVA_PKG_IUSE="doc source test" -WANT_ANT_TASKS="ant-apache-bcel dev-java/testng:0 ant-junit4" - -inherit java-pkg-2 java-ant-2 - -DESCRIPTION="Java-based command-line utilities that manipulate SAM files" -HOMEPAGE="http://picard.sourceforge.net/" -SRC_URI="https://dev.gentoo.org/~ercpe/distfiles/${CATEGORY}/${PN}/${P}.tar.bz2" - -LICENSE="Apache-2.0" -SLOT="0" -IUSE="" -KEYWORDS="~amd64 ~x86" - -CDEPEND="dev-java/snappy:1.0 - dev-java/cofoja:0 - dev-java/commons-jexl:2 - dev-java/ant-core:0" - -DEPEND=">=virtual/jdk-1.6 - dev-java/ant-apache-bcel:0 - test? ( - dev-java/testng:0 - dev-lang/R - ) - ${CDEPEND}" -RDEPEND=">=virtual/jre-1.6 - ${CDEPEND}" - -EANT_BUILD_TARGET="all" -EANT_TEST_TARGET="test" -EANT_NEEDS_TOOLS="true" -JAVA_ANT_REWRITE_CLASSPATH="true" -EANT_GENTOO_CLASSPATH="snappy-1.0,cofoja,commons-jexl-2,ant-core" -EANT_TEST_GENTOO_CLASSPATH="${EANT_GENTOO_CLASSPATH},testng" - -java_prepare() { - mkdir "${S}"/lib || die - - epatch "${FILESDIR}"/${PV}-gentoo.patch - - mv "${S}"/src/java/net/sf/samtools/SAMTestUtil.java "${S}"/src/tests/java/net/sf/samtools || die -} - -src_install() { - cd dist || die - - for i in *-${PV}.jar; do - java-pkg_newjar $i ${i/-${PV}/} - rm $i || die - done - - java-pkg_dojar *.jar - for i in *.jar; do - java-pkg_dolauncher ${i/.jar/} --jar $i; - done - - use source && java-pkg_dosrc "${S}"/src/java/* - use doc && java-pkg_dojavadoc "${S}"/javadoc -} - -src_test() { - java-pkg-2_src_test -} diff --git a/sci-biology/piler/metadata.xml b/sci-biology/piler/metadata.xml index 959160fe46b1..ccdff086e20b 100644 --- a/sci-biology/piler/metadata.xml +++ b/sci-biology/piler/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/piler/piler-1.0-r1.ebuild b/sci-biology/piler/piler-1.0-r2.ebuild index 276ee9bc873e..6f419d040b89 100644 --- a/sci-biology/piler/piler-1.0-r1.ebuild +++ b/sci-biology/piler/piler-1.0-r2.ebuild @@ -1,20 +1,19 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit toolchain-funcs DESCRIPTION="Analysis of repetitive DNA found in genome sequences" HOMEPAGE="http://www.drive5.com/piler/" SRC_URI="http://www.drive5.com/piler/piler_source.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}" LICENSE="public-domain" SLOT="0" -KEYWORDS="amd64 x86" -IUSE="" +KEYWORDS="amd64 ~x86" -DEPEND="" RDEPEND=" || ( sci-biology/muscle @@ -22,8 +21,6 @@ RDEPEND=" ) sci-biology/pals" -S=${WORKDIR} - PATCHES=( "${FILESDIR}"/${PN}-1.0-fix-build-system.patch "${FILESDIR}"/${PN}-1.0-glibc-2.10.patch diff --git a/sci-biology/pilercr/files/pilercr-1.0-drop-registers.patch b/sci-biology/pilercr/files/pilercr-1.0-drop-registers.patch new file mode 100644 index 000000000000..ab1535b4a767 --- /dev/null +++ b/sci-biology/pilercr/files/pilercr-1.0-drop-registers.patch @@ -0,0 +1,14 @@ +--- a/comp.cpp ++++ b/comp.cpp +@@ -28,7 +28,7 @@ void Complement(char *seq, int len) + /* Complement and reverse sequence */
+
+
+- { register unsigned char *s, *t;
++ { unsigned char *s, *t;
+ int c;
+
+
+old mode 100644 +new mode 100755 +Binary files a/pilercr and b/pilercr differ diff --git a/sci-biology/pilercr/metadata.xml b/sci-biology/pilercr/metadata.xml index 959160fe46b1..ccdff086e20b 100644 --- a/sci-biology/pilercr/metadata.xml +++ b/sci-biology/pilercr/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/pilercr/pilercr-1.0-r1.ebuild b/sci-biology/pilercr/pilercr-1.0-r2.ebuild index 8b1abd5de7d7..46c5dbc2b944 100644 --- a/sci-biology/pilercr/pilercr-1.0-r1.ebuild +++ b/sci-biology/pilercr/pilercr-1.0-r2.ebuild @@ -1,20 +1,18 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit toolchain-funcs DESCRIPTION="Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)" HOMEPAGE="http://www.drive5.com/pilercr/" SRC_URI="http://www.drive5.com/pilercr/pilercr1.06.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}" LICENSE="public-domain" SLOT="0" -KEYWORDS="amd64 x86" -IUSE="" - -S=${WORKDIR} +KEYWORDS="amd64 ~x86" PATCHES=( "${FILESDIR}"/${PN}-1.0-fix-build-system.patch @@ -26,5 +24,5 @@ src_configure() { } src_install() { - dobin ${PN} + dobin pilercr } diff --git a/sci-biology/pilercr/pilercr-1.0-r3.ebuild b/sci-biology/pilercr/pilercr-1.0-r3.ebuild new file mode 100644 index 000000000000..3a2ee27a3379 --- /dev/null +++ b/sci-biology/pilercr/pilercr-1.0-r3.ebuild @@ -0,0 +1,29 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit toolchain-funcs + +DESCRIPTION="Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)" +HOMEPAGE="https://www.drive5.com/pilercr/" +SRC_URI="https://www.drive5.com/pilercr/pilercr1.06.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}" + +LICENSE="public-domain" +SLOT="0" +KEYWORDS="amd64 ~x86" + +PATCHES=( + "${FILESDIR}"/${PN}-1.0-fix-build-system.patch + "${FILESDIR}"/${PN}-1.0-gcc43.patch + "${FILESDIR}"/${PN}-1.0-drop-registers.patch +) + +src_configure() { + tc-export CXX +} + +src_install() { + dobin pilercr +} diff --git a/sci-biology/plink/metadata.xml b/sci-biology/plink/metadata.xml index 8417d1580d40..bdabd1d83788 100644 --- a/sci-biology/plink/metadata.xml +++ b/sci-biology/plink/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/plink/plink-1.90_pre140514.ebuild b/sci-biology/plink/plink-1.90_pre140514.ebuild index 9abd1604abc4..6361d78a734e 100644 --- a/sci-biology/plink/plink-1.90_pre140514.ebuild +++ b/sci-biology/plink/plink-1.90_pre140514.ebuild @@ -1,34 +1,36 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=8 -inherit eutils toolchain-funcs +inherit toolchain-funcs DESCRIPTION="Whole genome association analysis toolset" HOMEPAGE="http://pngu.mgh.harvard.edu/~purcell/plink/" SRC_URI="http://pngu.mgh.harvard.edu/~purcell/static/bin/plink140514/plink_src.zip -> ${P}.zip" +S="${WORKDIR}" LICENSE="GPL-2" SLOT="0" KEYWORDS="~amd64 ~x86" -IUSE="" -DEPEND=" - app-arch/unzip - virtual/pkgconfig" RDEPEND=" sys-libs/zlib virtual/cblas virtual/lapack - " - -S="${WORKDIR}/" +" +DEPEND="${RDEPEND}" +BDEPEND=" + app-arch/unzip + virtual/pkgconfig +" # Package collides with net-misc/putty. Renamed to p-link following discussion with Debian. # Package contains bytecode-only jar gPLINK.jar. Ignored, notified upstream. src_prepare() { + default + sed \ -e 's:zlib-1.2.8/zlib.h:zlib.h:g' \ -i *.{c,h} || die @@ -43,8 +45,9 @@ src_prepare() { src_compile() { emake \ - CXX=$(tc-getCXX) \ + CXX="$(tc-getCXX)" \ CFLAGS="${CFLAGS}" \ + LDFLAGS="${LDFLAGS}" \ ZLIB="$($(tc-getPKG_CONFIG) --libs zlib)" \ BLASFLAGS="$($(tc-getPKG_CONFIG) --libs lapack cblas)" } diff --git a/sci-biology/poa/files/poa-2-clang16.patch b/sci-biology/poa/files/poa-2-clang16.patch new file mode 100644 index 000000000000..5399dd631f48 --- /dev/null +++ b/sci-biology/poa/files/poa-2-clang16.patch @@ -0,0 +1,74 @@ +--- a/black_flag.c ++++ b/black_flag.c +@@ -82,7 +82,7 @@ + + + +-int handle_crash_init(void (*crash_fun)()) ++int handle_crash_init(void (*crash_fun)(int)) + { + #define HANDLE_CRASH_MAX 5 + int i,signal_type[HANDLE_CRASH_MAX] +--- a/black_flag.h ++++ b/black_flag.h +@@ -230,7 +230,7 @@ + ((INDEX)<(MINIMUM_BOUND) || (INDEX)>=(MAXIMUM_BOUND)) + + void handle_crash(int sigcode); +-int handle_crash_init(void (*crash_fun)()); ++int handle_crash_init(void (*crash_fun)(int)); + int black_flag(int bug_level, + char sourcefile[], + int sourceline, +--- a/default.h ++++ b/default.h +@@ -19,7 +19,6 @@ + + typedef void *voidptr; /* ~~e: should be moved out to generic typing header + --- */ +-typedef int (*funptr)(); + + #define LOOPB(i,size) for ((i)=(size);(i)-- >0;) + #define LOOP(i,size) for ((i)=(size);(i)-- >0;) +@@ -152,7 +151,7 @@ + else if (NULL == ((memptr)=(ATYPE *)calloc((size_t)(N),sizeof(ATYPE)))) { \ + fprintf(stderr,"%s, line %d: *** out of memory \n",__FILE__,__LINE__); \ + fprintf(stderr,"Unable to meet request: %s[%d]\n",STRINGIFY(memptr),(N)); \ +- fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ ++ fprintf(stderr,"requested %d x %zu bytes \n",(N),sizeof(ATYPE)); \ + MALLOC_FAILURE_ACTION; \ + } + +@@ -193,7 +192,7 @@ + else { \ + fprintf(stderr,"%s, line %d: *** out of memory \n",__FILE__,__LINE__); \ + fprintf(stderr,"Unable to meet request: %s\n",STRINGIFY(memptr)); \ +- fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ ++ fprintf(stderr,"requested %d x %zu bytes \n",(NUM),sizeof(ATYPE)); \ + REALLOC_FAILURE_ACTION; \ + } \ + } +--- a/fasta_format.c ++++ b/fasta_format.c +@@ -2,6 +2,7 @@ + #include "default.h" + #include "seq_util.h" + ++char *stringptr_cat_pos(stringptr *s1,const char s2[],int *pos); + + + /** reads FASTA formatted sequence file, and saves the sequences to +--- a/msa_format.c ++++ b/msa_format.c +@@ -16,6 +16,11 @@ + + #include "msa_format.h" + ++void fuse_ring_identities(int len_x,LPOLetter_T seq_x[], ++ int len_y,LPOLetter_T seq_y[], ++ LPOLetterRef_T al_x[], ++ LPOLetterRef_T al_y[]); ++void build_seq_to_po_index(LPOSequence_T *seq); + + /** is `ch' an allowed residue? (a-z OR A-Z OR ? OR [ OR ]) */ + static int is_residue_char (char ch); diff --git a/sci-biology/poa/files/poa-2-fno-common.patch b/sci-biology/poa/files/poa-2-fno-common.patch new file mode 100644 index 000000000000..ddd738a5524c --- /dev/null +++ b/sci-biology/poa/files/poa-2-fno-common.patch @@ -0,0 +1,13 @@ +--- a/black_flag.h ++++ b/black_flag.h +@@ -236,8 +236,8 @@ + int sourceline, + char sourcefile_revision[]); + +-char *Program_name; +-char *Program_version; ++extern char *Program_name; ++extern char *Program_version; + + void black_flag_init(char progname[],char progversion[]); + void black_flag_init_args(int narg,char *arg[],char progversion[]); diff --git a/sci-biology/poa/files/2-respect-flags.patch b/sci-biology/poa/files/poa-2-respect-flags.patch index bdd638cf64b7..fb01f0b5f934 100644 --- a/sci-biology/poa/files/2-respect-flags.patch +++ b/sci-biology/poa/files/poa-2-respect-flags.patch @@ -1,26 +1,38 @@ -diff --git a/Makefile b/Makefile -index a65bed0..713a7ab 100644 --- a/Makefile +++ b/Makefile -@@ -26,9 +26,10 @@ LIBOBJECTS= \ +@@ -1,6 +1,3 @@ +- +-AR=ar rc +- + TARGETS=poa liblpo.a poa_doc libbflag.a + + # align_score.c CAN BE USED TO ADD CUSTOMIZED SCORING FUNCTIONS +@@ -26,9 +23,8 @@ stringptr.o -CC = gcc -+CC ?= gcc #CFLAGS= -g -ansi-strict -W -Wall -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -CFLAGS= -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -+OPT_CFLAGS = -g -+CFLAGS= $(OPT_CFLAGS) -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. ++CPPFLAGS+= -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. # -I$(HOME)/lib/include # -DREPORT_MAX_ALLOC -@@ -44,7 +45,7 @@ liblpo.a: $(LIBOBJECTS) +@@ -37,14 +33,14 @@ + + liblpo.a: $(LIBOBJECTS) + rm -f $@ +- $(AR) $@ $(LIBOBJECTS) +- ranlib $@ ++ $(AR) rc $@ $(LIBOBJECTS) ++ $(RANLIB) $@ + + # NB: LIBRARY MUST FOLLOW OBJECTS OR LINK FAILS WITH UNRESOLVED REFERENCES!! poa: $(OBJECTS) liblpo.a - $(CC) -o $@ $(OBJECTS) -lm liblpo.a -+ $(CC) $(LDFLAGS) -o $@ $(OBJECTS) -lm liblpo.a ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(OBJECTS) -lm liblpo.a what: @echo poa: partial-order based sequence alignment program diff --git a/sci-biology/poa/metadata.xml b/sci-biology/poa/metadata.xml index 229e2f246a80..1029a137f48b 100644 --- a/sci-biology/poa/metadata.xml +++ b/sci-biology/poa/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/poa/poa-2-r1.ebuild b/sci-biology/poa/poa-2-r1.ebuild index efee14d1dfd6..8044b8f822bf 100644 --- a/sci-biology/poa/poa-2-r1.ebuild +++ b/sci-biology/poa/poa-2-r1.ebuild @@ -1,44 +1,45 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=7 -inherit eutils +inherit toolchain-funcs MY_P="${PN}V${PV}" DESCRIPTION="Fast multiple sequence alignments using partial-order graphs" HOMEPAGE="http://bioinfo.mbi.ucla.edu/poa/" -SRC_URI="mirror://sourceforge/poamsa/${MY_P}.tar.gz" +SRC_URI="https://downloads.sourceforge.net/poamsa/${MY_P}.tar.gz" # According to SF project page LICENSE="GPL-2" SLOT="0" KEYWORDS="~amd64 ~x86" -IUSE="static-libs" S="${WORKDIR}/${MY_P}" -src_prepare() { - epatch "${FILESDIR}"/${PV}-respect-flags.patch +PATCHES=( + "${FILESDIR}"/${P}-respect-flags.patch + "${FILESDIR}"/${P}-fno-common.patch + "${FILESDIR}"/${P}-clang16.patch +) + +src_configure() { + tc-export AR CC RANLIB } src_compile() { - emake \ - CC="$(tc-getCC)" \ - OPT_CFLAGS="${CFLAGS}" \ - poa + emake poa } src_install() { - dobin "${S}"/poa "${S}"/make_pscores.pl - use static-libs && dolib.a "${S}"/liblpo.a - dodoc "${S}"/README "${S}"/multidom.* + dobin poa make_pscores.pl + dodoc README multidom.* insinto /usr/share/poa - doins "${S}"/*.mat + doins *.mat } pkg_postinst() { elog "poa requires a score matrix as the first argument." - elog "This package installs two examples to ${EROOT}usr/share/poa/." + elog "This package installs two examples to ${EROOT}/usr/share/poa/." } diff --git a/sci-biology/prank/files/prank-140603-fix-c++14.patch b/sci-biology/prank/files/prank-140603-fix-c++14.patch index 5779207e294f..211e377d798a 100644 --- a/sci-biology/prank/files/prank-140603-fix-c++14.patch +++ b/sci-biology/prank/files/prank-140603-fix-c++14.patch @@ -8,7 +8,7 @@ See also: https://bugs.gentoo.org/show_bug.cgi?id=594060 else { - cout<<"HMModel::alignmentModel: impossible 'as'"<<cout; -+ cout<<"HMModel::alignmentModel: impossible 'as'"<<bool(cout); ++ cout<<"HMModel::alignmentModel: impossible 'as'"; exit(-1); } diff --git a/sci-biology/prank/files/prank-140603-makefile.patch b/sci-biology/prank/files/prank-140603-makefile.patch new file mode 100644 index 000000000000..eeb74df89b4c --- /dev/null +++ b/sci-biology/prank/files/prank-140603-makefile.patch @@ -0,0 +1,28 @@ +--- a/Makefile ++++ b/Makefile +@@ -4,14 +4,8 @@ + + ####### Compiler, tools and options + +-CC = gcc +-CXX = g++ +-DEFINES = +-CFLAGS = -m64 -pipe -O3 $(DEFINES) +-CXXFLAGS = -m64 -pipe -O3 $(DEFINES) +-INCPATH = -I. -I/usr/include +-LINK = g++ +-LFLAGS = -m64 ++INCPATH = $(CPPFLAGS) -I. ++LINK = $(CXX) + LIBS = $(SUBLIBS) + AR = ar cqs + RANLIB = +@@ -136,7 +130,7 @@ + all: Makefile $(TARGET) $(MANPAGES) + + $(TARGET): $(OBJECTS) +- $(LINK) $(LFLAGS) -o $(TARGET) $(OBJECTS) $(OBJCOMP) $(LIBS) ++ $(LINK) $(LDFLAGS) -o $(TARGET) $(OBJECTS) $(OBJCOMP) $(LIBS) + + + clean:compiler_clean diff --git a/sci-biology/prank/metadata.xml b/sci-biology/prank/metadata.xml index 8d1d75556076..2a0345f8b0ad 100644 --- a/sci-biology/prank/metadata.xml +++ b/sci-biology/prank/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/prank/prank-140603-r1.ebuild b/sci-biology/prank/prank-140603-r1.ebuild new file mode 100644 index 000000000000..9128cf9cf99b --- /dev/null +++ b/sci-biology/prank/prank-140603-r1.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit toolchain-funcs + +DESCRIPTION="Probabilistic Alignment Kit" +HOMEPAGE="http://wasabiapp.org/software/prank/" +SRC_URI="http://wasabiapp.org/download/${PN}/${PN}.source.${PV}.tgz" +S="${WORKDIR}/${PN}-msa/src" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +PATCHES=( + "${FILESDIR}"/${P}-makefile.patch + "${FILESDIR}"/${P}-fix-c++14.patch +) + +src_configure() { + tc-export CXX +} + +src_install() { + dobin prank +} diff --git a/sci-biology/prank/prank-140603.ebuild b/sci-biology/prank/prank-140603.ebuild deleted file mode 100644 index a29e425f43bf..000000000000 --- a/sci-biology/prank/prank-140603.ebuild +++ /dev/null @@ -1,38 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit toolchain-funcs - -DESCRIPTION="Probabilistic Alignment Kit" -HOMEPAGE="http://wasabiapp.org/software/prank/" -SRC_URI="http://wasabiapp.org/download/${PN}/${PN}.source.${PV}.tgz" - -LICENSE="GPL-3" -SLOT="0" -IUSE="" -KEYWORDS="~amd64 ~x86" - -S="${WORKDIR}/${PN}-msa/src" -PATCHES=( "${FILESDIR}/${PN}-140603-fix-c++14.patch" ) - -src_prepare() { - sed \ - -e "s/\$(LINK)/& \$(LDFLAGS)/" \ - -e "s:/usr/lib:${EPREFIX}/usr/$(get_libdir):g" \ - -i Makefile || die - default -} - -src_compile() { - emake \ - LINK="$(tc-getCXX)" \ - CXX="$(tc-getCXX)" \ - CFLAGS="${CFLAGS}" \ - CXXFLAGS="${CXXFLAGS}" -} - -src_install() { - dobin ${PN} -} diff --git a/sci-biology/primer3/files/primer3-2.3.4-buildsystem.patch b/sci-biology/primer3/files/primer3-2.3.7-buildsystem.patch index cf47b35af502..8f9bf4042758 100644 --- a/sci-biology/primer3/files/primer3-2.3.4-buildsystem.patch +++ b/sci-biology/primer3/files/primer3-2.3.7-buildsystem.patch @@ -1,11 +1,6 @@ - src/Makefile | 61 ++++++++++++++++++++++++++++++------------------------------ - 1 file changed, 31 insertions(+), 30 deletions(-) - -diff --git a/src/Makefile b/src/Makefile -index 607ab45..a88adf4 100644 --- a/src/Makefile +++ b/src/Makefile -@@ -52,15 +52,16 @@ TESTOPTS= +@@ -52,15 +52,13 @@ WINMAKE=mingw32-make LDLIBS = -lm @@ -15,56 +10,66 @@ index 607ab45..a88adf4 100644 -O_OPTS = -O2 -CC_OPTS = -g -Wall -D__USE_FIXED_PROTOTYPES__ -P_DEFINES = -+AR ?= ar -+CC ?= gcc -+CXX ?= g++ +- +-CFLAGS = $(CC_OPTS) $(O_OPTS) +-LDFLAGS = -g +O_OPTS ?= +CC_OPTS ?= -Wall -D__USE_FIXED_PROTOTYPES__ +P_DEFINES ?= - --CFLAGS = $(CC_OPTS) $(O_OPTS) --LDFLAGS = -g ++ +CFLAGS += $(CC_OPTS) $(O_OPTS) +CXXFLAGS += $(CC_OPTS) $(O_OPTS) +LDFLAGS += # Note, for profiling, use # make O_OPTS='-pg -O0' LDFLAGS='-g -pg' -@@ -92,7 +93,7 @@ LIBPRIMER3 = libprimer3.a +@@ -92,7 +90,6 @@ LIBPRIMER3_DYN = libprimer3.so.1.0.0 LIBRARIES = $(LIBPRIMER3) $(LIBDPAL) $(LIBTHAL) $(LIBOLIGOTM) DYNLIBS = $(LIBPRIMER3_DYN) $(LIBDPAL_DYN) $(LIBTHAL_DYN) $(LIBOLIGOTM_DYN) -RANLIB = ranlib -+RANLIB ?= ranlib PRIMER_OBJECTS1=primer3_boulder_main.o\ format_output.o\ -@@ -127,85 +128,85 @@ $(LIBOLIGOTM): oligotm.o - $(RANLIB) $@ +@@ -119,93 +116,89 @@ + ifeq ($(TESTOPTS),--windows) + cd ..\test & $(WINMAKE) clean TESTOPTS=$(TESTOPTS) + else +- cd ../test/; make clean ++ cd ../test/ && $(MAKE) clean + endif + + $(LIBOLIGOTM): oligotm.o +- $(AR) rv $@ oligotm.o +- $(RANLIB) $@ ++ $(AR) rcs $@ oligotm.o $(LIBOLIGOTM_LIB): oligotm.o - $(CC) -shared -W1,-soname,liboligotm.so.1 -o $(LIBOLIGOTM_DYN) oligotm.o + $(CC) $(LDFLAGS) -shared -W1,-soname,liboligotm.so.1 -o $(LIBOLIGOTM_DYN) oligotm.o $(LIBDPAL): dpal_primer.o - $(AR) rv $@ dpal_primer.o - $(RANLIB) $@ +- $(AR) rv $@ dpal_primer.o +- $(RANLIB) $@ ++ $(AR) rcs $@ dpal_primer.o $(LIBDPAL_DYN): dpal_primer.o - $(CC) -shared -W1,-soname,libdpal.so.1 -o $(LIBDPAL_DYN_LIB) dpal_primer.o + $(CC) $(LDFLAGS) -shared -W1,-soname,libdpal.so.1 -o $(LIBDPAL_DYN_LIB) dpal_primer.o $(LIBTHAL): thal_primer.o - $(AR) rv $@ thal_primer.o - $(RANLIB) $@ +- $(AR) rv $@ thal_primer.o +- $(RANLIB) $@ ++ $(AR) rcs $@ thal_primer.o $(LIBTHAL_DYN): thal_primer.o - $(CC) -shared -W1,-soname,libthal.so.1 -o $(LIBTHAL_DYN_LIB) thal_primer.o + $(CC) $(LDFLAGS) -shared -W1,-soname,libthal.so.1 -o $(LIBTHAL_DYN_LIB) thal_primer.o $(LIBPRIMER3): libprimer3.o p3_seq_lib.o - $(AR) rv $@ libprimer3.o p3_seq_lib.o - $(RANLIB) $@ +- $(AR) rv $@ libprimer3.o p3_seq_lib.o +- $(RANLIB) $@ ++ $(AR) rcs $@ libprimer3.o p3_seq_lib.o $(LIBPRIMER3_DYN): libprimer3.o p3_seq_lib.o - $(CC) -shared -W1,-soname,liprimer3.so.1 -o $(LIBPRIMER3_DYN) libprimer3.o p3_seq_lib.o @@ -146,3 +151,23 @@ index 607ab45..a88adf4 100644 primer_test: test +@@ -213,7 +206,7 @@ + ifeq ($(TESTOPTS),--windows) + cd ..\test & $(WINMAKE) TESTOPTS=$(TESTOPTS) + else +- cd ../test; make test ++ cd ../test && $(MAKE) test + endif + + # ====================================================================== +--- a/test/Makefile ++++ b/test/Makefile +@@ -86,7 +86,7 @@ + ifeq ($(TESTOPTS),--windows) + cd ..\src & $(WINMAKE) + else +- cd ../src; make ++ cd ../src && $(MAKE) + endif + + clean: diff --git a/sci-biology/primer3/metadata.xml b/sci-biology/primer3/metadata.xml index b80de21c3321..af82be55b453 100644 --- a/sci-biology/primer3/metadata.xml +++ b/sci-biology/primer3/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/primer3/primer3-2.3.7.ebuild b/sci-biology/primer3/primer3-2.3.7-r1.ebuild index 4c6c9ce7bf44..498c564753bf 100644 --- a/sci-biology/primer3/primer3-2.3.7.ebuild +++ b/sci-biology/primer3/primer3-2.3.7-r1.ebuild @@ -1,24 +1,23 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit toolchain-funcs DESCRIPTION="Primer Design for PCR reactions" HOMEPAGE="http://primer3.sourceforge.net/" -SRC_URI="mirror://sourceforge/project/${PN}/${PN}/${PV}/${P}.tar.gz" +SRC_URI="https://downloads.sourceforge.net/project/${PN}/${PN}/${PV}/${P}.tar.gz" LICENSE="GPL-2" SLOT="0" -KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" +KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" -DEPEND="dev-lang/perl" -RDEPEND="" +BDEPEND="dev-lang/perl" PATCHES=( - "${FILESDIR}"/${PN}-2.3.4-buildsystem.patch - "${FILESDIR}"/${PN}-2.3.7-gcc7.patch + "${FILESDIR}"/${P}-buildsystem.patch + "${FILESDIR}"/${P}-gcc7.patch ) src_prepare() { @@ -29,7 +28,7 @@ src_prepare() { } src_configure() { - tc-export CC CXX AR RANLIB + tc-export AR CC CXX } src_compile() { @@ -38,7 +37,7 @@ src_compile() { src_test() { emake -C test | tee "${T}"/test.log - grep -q "\[FAILED\]" && die "test failed. See "${T}"/test.log" + grep -q "\[FAILED\]" && die "test failed. See ${T}/test.log" } src_install() { diff --git a/sci-biology/prints/metadata.xml b/sci-biology/prints/metadata.xml index af3ff0786e0c..720b31a11b56 100644 --- a/sci-biology/prints/metadata.xml +++ b/sci-biology/prints/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/prints/prints-39.0-r1.ebuild b/sci-biology/prints/prints-39.0-r2.ebuild index f9833579e71f..9fb721842798 100644 --- a/sci-biology/prints/prints-39.0-r1.ebuild +++ b/sci-biology/prints/prints-39.0-r2.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 MY_PV="${PV/./_}" @@ -16,8 +16,8 @@ SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" IUSE="emboss minimal" -DEPEND="emboss? ( sci-biology/emboss )" -RDEPEND="${DEPEND}" +BDEPEND="emboss? ( sci-biology/emboss )" +RDEPEND="${BDEPEND}" src_compile() { if use emboss; then diff --git a/sci-biology/probcons/metadata.xml b/sci-biology/probcons/metadata.xml index 959160fe46b1..ccdff086e20b 100644 --- a/sci-biology/probcons/metadata.xml +++ b/sci-biology/probcons/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/probcons/probcons-1.12-r1.ebuild b/sci-biology/probcons/probcons-1.12-r1.ebuild index 01973b88cab9..3f0f2670b7b0 100644 --- a/sci-biology/probcons/probcons-1.12-r1.ebuild +++ b/sci-biology/probcons/probcons-1.12-r1.ebuild @@ -1,35 +1,31 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=7 -inherit eutils toolchain-funcs +inherit toolchain-funcs MY_P="${PN}_v${PV/./_}" DESCRIPTION="Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences" HOMEPAGE="http://probcons.stanford.edu/" SRC_URI="http://probcons.stanford.edu/${MY_P}.tar.gz" +S="${WORKDIR}/${PN}" LICENSE="public-domain" SLOT="0" -KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" -IUSE="" +KEYWORDS="amd64 ~x86 ~amd64-linux ~x86-linux" # Gnuplot is explicitly runtime-only, it's run using system() RDEPEND=" !sci-geosciences/gmt sci-visualization/gnuplot" -DEPEND="" - -S="${WORKDIR}/${PN}" -src_prepare() { - epatch \ - "${FILESDIR}"/${P}-cxxflags.patch \ - "${FILESDIR}"/gcc-4.3.patch \ - "${FILESDIR}"/${P}-gcc-4.6.patch -} +PATCHES=( + "${FILESDIR}"/${P}-cxxflags.patch + "${FILESDIR}"/gcc-4.3.patch + "${FILESDIR}"/${P}-gcc-4.6.patch +) src_compile() { emake \ diff --git a/sci-biology/prodigal/metadata.xml b/sci-biology/prodigal/metadata.xml index e086d08df6f7..657774f9a8ec 100644 --- a/sci-biology/prodigal/metadata.xml +++ b/sci-biology/prodigal/metadata.xml @@ -1,5 +1,5 @@ -<?xml version='1.0' encoding='UTF-8'?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/prodigal/prodigal-2.6.3.ebuild b/sci-biology/prodigal/prodigal-2.6.3-r1.ebuild index db8382982284..8428da82c5e7 100644 --- a/sci-biology/prodigal/prodigal-2.6.3.ebuild +++ b/sci-biology/prodigal/prodigal-2.6.3-r1.ebuild @@ -1,23 +1,18 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit toolchain-funcs DESCRIPTION="Prokaryotic Dynamic Programming Genefinding Algorithm" HOMEPAGE="http://prodigal.ornl.gov/" SRC_URI="https://github.com/hyattpd/${PN^}/archive/v${PV}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/${P^}" LICENSE="GPL-3" SLOT="0" KEYWORDS="~amd64" -IUSE="" - -DEPEND="" -RDEPEND="" - -S=${WORKDIR}/${P^} PATCHES=( "${FILESDIR}"/${PN}-2.6.3-fix-build-system.patch ) diff --git a/sci-biology/profphd/Manifest b/sci-biology/profphd/Manifest index bcdb5a4a9ca3..9aa5af5a04db 100644 --- a/sci-biology/profphd/Manifest +++ b/sci-biology/profphd/Manifest @@ -1,2 +1 @@ -DIST profphd-1.0.39.tar.xz 4406776 BLAKE2B 9ac4bccd1fedf04f9556ff6953452879fc8cf9deb92853214b2c8b5c0b1c4daf3e5e0044d10ded9540e9dd3f40a6fee3a25ae808fd1e94b90e0db23f3af7b6df SHA512 0ea6a34a8dad8fcd0d8b23e7a7d476e211587bf580389e9f43ed857bab7853cbe5ce698d2a610e9344e9bc95661cf074355310ea02c1a03e6378058ba169b15b DIST profphd-1.0.40.tar.xz 4491592 BLAKE2B 2aa1e091c0674fa5318a075148a63b15354ecb6d8d6f7ac41d1d05f8bea17c47b6f37be707cc1c738e22342c26ae9be59cabf919610e5bffd5028fc587b2995b SHA512 287f1a548030e7978119788dffdf2529e0018cd772bc820e116f79ed10cefd440645424b56415333362098a1ed32f4841d3fd4069adede2a95968f81c63956e3 diff --git a/sci-biology/profphd/files/profphd-1.0.40-symlink.patch b/sci-biology/profphd/files/profphd-1.0.40-symlink.patch new file mode 100644 index 000000000000..7733d55af4a6 --- /dev/null +++ b/sci-biology/profphd/files/profphd-1.0.40-symlink.patch @@ -0,0 +1,11 @@ +--- a/src/prof/Makefile ++++ b/src/prof/Makefile +@@ -40,7 +40,7 @@ + ./. $(DESTDIR)$(prefix)/share/profphd/prof/. + find $(DESTDIR)$(prefix)/share/profphd/prof/embl/phd.pl $(DESTDIR)$(prefix)/share/profphd/prof/scr/CONFprof.pl $(DESTDIR)$(prefix)/share/profphd/prof/prof $(DESTDIR)$(prefix)/share/profphd/prof/scr/lib/prof.pm \ + -type f -exec sed -i -e 's|__PREFIX__|$(prefix)|g;s|__VERSION__|$(VERSION)|;' {} \; +- rm -rf $(DESTDIR)$(prefix)/bin/prof && mkdir -p $(DESTDIR)$(prefix)/bin && ln -s ../share/profphd/prof/prof $(DESTDIR)$(prefix)/bin/prof ++ rm -rf $(DESTDIR)$(prefix)/bin/prof && mkdir -p $(DESTDIR)$(prefix)/bin && ln -s ../share/profphd/prof/prof $(DESTDIR)$(prefix)/bin/profphd + + install-neuralnet: + mkdir -p $(DESTDIR)$(prefix)/share/profphd/prof/embl/para && rsync -aC \ diff --git a/sci-biology/profphd/metadata.xml b/sci-biology/profphd/metadata.xml index 959160fe46b1..ccdff086e20b 100644 --- a/sci-biology/profphd/metadata.xml +++ b/sci-biology/profphd/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/profphd/profphd-1.0.39.ebuild b/sci-biology/profphd/profphd-1.0.39.ebuild deleted file mode 100644 index cacbc13cbdf2..000000000000 --- a/sci-biology/profphd/profphd-1.0.39.ebuild +++ /dev/null @@ -1,37 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils - -DESCRIPTION="Secondary structure and solvent accessibility predictor" -HOMEPAGE="https://rostlab.org/owiki/index.php/PROFphd_-_Secondary_Structure,_Solvent_Accessibility_and_Transmembrane_Helices_Prediction" -SRC_URI="ftp://rostlab.org/profphd/${P}.tar.xz" - -SLOT="0" -LICENSE="GPL-2" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="" - -DEPEND="dev-lang/perl" -RDEPEND="${DEPEND} - dev-perl/librg-utils-perl - sci-libs/profnet - sci-libs/profphd-utils -" - -src_prepare() { - sed \ - -e '/ln -s/s:prof$:profphd:g' \ - -i src/prof/Makefile || die - epatch "${FILESDIR}"/${P}-perl.patch -} - -src_compile() { - emake prefix="${EPREFIX}/usr" -} - -src_install() { - emake prefix="${EPREFIX}/usr" DESTDIR="${D}" install -} diff --git a/sci-biology/profphd/profphd-1.0.40.ebuild b/sci-biology/profphd/profphd-1.0.40.ebuild index 8e24cebeb5f3..4f9a16a9fe9d 100644 --- a/sci-biology/profphd/profphd-1.0.40.ebuild +++ b/sci-biology/profphd/profphd-1.0.40.ebuild @@ -1,37 +1,33 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 - -inherit eutils +EAPI=7 DESCRIPTION="Secondary structure and solvent accessibility predictor" HOMEPAGE="https://rostlab.org/owiki/index.php/PROFphd_-_Secondary_Structure,_Solvent_Accessibility_and_Transmembrane_Helices_Prediction" SRC_URI="ftp://rostlab.org/profphd/${P}.tar.xz" -SLOT="0" LICENSE="GPL-2" +SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="" DEPEND="dev-lang/perl" -RDEPEND="${DEPEND} +RDEPEND=" + ${DEPEND} dev-perl/librg-utils-perl sci-libs/profnet - sci-libs/profphd-utils -" + sci-libs/profphd-utils" -src_prepare() { - sed \ - -e '/ln -s/s:prof$:profphd:g' \ - -i src/prof/Makefile || die - epatch "${FILESDIR}"/${PN}-1.0.39-perl.patch -} +PATCHES=( + "${FILESDIR}"/${PN}-1.0.39-perl.patch + "${FILESDIR}"/${PN}-1.0.40-symlink.patch +) src_compile() { - emake prefix="${EPREFIX}/usr" + emake prefix="${EPREFIX}"/usr } src_install() { - emake prefix="${EPREFIX}/usr" DESTDIR="${D}" install + emake prefix="${EPREFIX}"/usr DESTDIR="${D}" install + einstalldocs } diff --git a/sci-biology/prosite/metadata.xml b/sci-biology/prosite/metadata.xml index 59076478066f..496029464135 100644 --- a/sci-biology/prosite/metadata.xml +++ b/sci-biology/prosite/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/prosite/prosite-2017.02.ebuild b/sci-biology/prosite/prosite-2017.02-r1.ebuild index 6003b17cff85..a5efbed1626b 100644 --- a/sci-biology/prosite/prosite-2017.02.ebuild +++ b/sci-biology/prosite/prosite-2017.02-r1.ebuild @@ -1,11 +1,12 @@ -# Copyright 1999-2018 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 DESCRIPTION="A protein families and domains database" HOMEPAGE="https://prosite.expasy.org/" SRC_URI="ftp://ftp.expasy.org/databases/prosite/old_releases/prosite${PV//./_}.tar.bz2" +S="${WORKDIR}" LICENSE="swiss-prot" SLOT="0" @@ -14,10 +15,8 @@ SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" IUSE="emboss minimal" -DEPEND="emboss? ( sci-biology/emboss )" -RDEPEND="${DEPEND}" - -S=${WORKDIR} +BDEPEND="emboss? ( sci-biology/emboss )" +RDEPEND="${BDEPEND}" src_compile() { if use emboss; then diff --git a/sci-biology/psipred/Manifest b/sci-biology/psipred/Manifest deleted file mode 100644 index 3dfae4734db6..000000000000 --- a/sci-biology/psipred/Manifest +++ /dev/null @@ -1,3 +0,0 @@ -DIST psipred3.4.tar.gz 1102416 BLAKE2B 9797f4181357bb26455253370aca39857c39a2c4bcd521b10a139784e6fd5dc9e14b76c11d99989ac33c3a01fb62807957f9969daa5ac9d928b0b4e83e943743 SHA512 1bc7ac41a213766139324540ba6952538f2890749ecf217d771b4ce59e25231857d38c237ea573674f11a82300750e9a3ff628ec0156864863a9528a144cd919 -DIST psipred3.5.tar.gz 1101579 BLAKE2B 2fd86841cbc4bb86045b51f8283550832df8356ee88a6ef2c85281b5810debb23ac53652ddc5ffc9bd6f8e9e7248ce39ccee23400ff8fb49cd05b877d730b553 SHA512 a7b3f7d149f6a29cf0b48bdb900f6983d42af01132d8b54a7be88994d09fcf27dbe57115d41ec9654da6daf6898d5986d08fbdcefa3a4c81af0d358500cd40c2 -DIST tdbdata.tar.gz 40241247 BLAKE2B c85a2fde9b29a14e1da27be1a7ea5fe1704f72b66cd79514dd50a3a0d2d8aab9341f7d5075f6d1896cefa54ca83948387b902b38780181777dc505a9a15b4aab SHA512 f96d7ffbb77e129251e27f62b7f099d944bacd14935e03fc52c9f0b262cce1ad477ad43520a93b407951fb8f5dd3ba2e27ff6b5ae8a637ec03bc02f8c7c3990c diff --git a/sci-biology/psipred/files/3.1-Makefile.patch b/sci-biology/psipred/files/3.1-Makefile.patch deleted file mode 100644 index 0c70b6868565..000000000000 --- a/sci-biology/psipred/files/3.1-Makefile.patch +++ /dev/null @@ -1,38 +0,0 @@ -diff --git a/src/Makefile b/src/Makefile -index abed8af..26061fa 100644 ---- a/src/Makefile -+++ b/src/Makefile -@@ -6,9 +6,9 @@ - #### CFLAGS Flags to pass to C compiler. - - INCDIR = . --CC = cc -+CC ?= gcc - --CFLAGS = -O -+CFLAGS ?= -O2 - LIBS = -lm - - all: psipred psipass2 chkparse seq2mtx pfilt -@@ -20,16 +20,16 @@ clean: - /bin/rm -f psipred psipass2 chkparse seq2mtx pfilt - - psipred: sspred_avpred.c ssdefs.h sspred_net.h -- $(CC) $(CFLAGS) sspred_avpred.c $(LIBS) -o psipred -+ $(CC) $(CFLAGS) $(LDFLAGS) sspred_avpred.c $(LIBS) -o psipred - - psipass2: sspred_hmulti.c ssdefs.h sspred_net2.h -- $(CC) $(CFLAGS) sspred_hmulti.c $(LIBS) -o psipass2 -+ $(CC) $(CFLAGS) $(LDFLAGS) sspred_hmulti.c $(LIBS) -o psipass2 - - chkparse: chkparse.c -- $(CC) $(CFLAGS) chkparse.c $(LIBS) -o chkparse -+ $(CC) $(CFLAGS) $(LDFLAGS) chkparse.c $(LIBS) -o chkparse - - seq2mtx: seq2mtx.c -- $(CC) $(CFLAGS) seq2mtx.c $(LIBS) -o seq2mtx -+ $(CC) $(CFLAGS) $(LDFLAGS) seq2mtx.c $(LIBS) -o seq2mtx - - pfilt: pfilt.c -- $(CC) $(CFLAGS) pfilt.c $(LIBS) -o pfilt -+ $(CC) $(CFLAGS) $(LDFLAGS) pfilt.c $(LIBS) -o pfilt diff --git a/sci-biology/psipred/files/3.1-path.patch b/sci-biology/psipred/files/3.1-path.patch deleted file mode 100644 index 564e9c8a1ef9..000000000000 --- a/sci-biology/psipred/files/3.1-path.patch +++ /dev/null @@ -1,38 +0,0 @@ -diff --git a/runpsipred b/runpsipred -index 4ccf44e..34dee99 100755 ---- a/runpsipred -+++ b/runpsipred -@@ -14,13 +14,13 @@ - set dbname = uniref90filt - - # Where the NCBI programs have been installed --set ncbidir = /usr/local/bin -+set ncbidir = @GENTOO_PORTAGE_EPREFIX@/usr/bin - - # Where the PSIPRED V2 programs have been installed --set execdir = ./bin -+set execdir = @GENTOO_PORTAGE_EPREFIX@/usr/bin - - # Where the PSIPRED V2 data files have been installed --set datadir = ./data -+set datadir = @GENTOO_PORTAGE_EPREFIX@/usr/share/psipred/data - - set basename = $1:r - set rootname = $basename:t -diff --git a/runpsipred_single b/runpsipred_single -index 1f7680b..7bd5bc3 100755 ---- a/runpsipred_single -+++ b/runpsipred_single -@@ -10,10 +10,10 @@ - # NOTE: Script modified to be more cluster friendly (DTJ April 2008) - - # Where the PSIPRED V3 programs have been installed --set execdir = ./bin -+set execdir = @GENTOO_PORTAGE_EPREFIX@/usr/bin - - # Where the PSIPRED V3 data files have been installed --set datadir = ./data -+set datadir = @GENTOO_PORTAGE_EPREFIX@/usr/share/psipred/data - - set basename = $1:r - set rootname = $basename:t diff --git a/sci-biology/psipred/files/3.2-fgets.patch b/sci-biology/psipred/files/3.2-fgets.patch deleted file mode 100644 index ec06d141ee34..000000000000 --- a/sci-biology/psipred/files/3.2-fgets.patch +++ /dev/null @@ -1,13 +0,0 @@ -diff --git a/src/sspred_avpred.c b/src/sspred_avpred.c -index 37b1332..4f04ab6 100644 ---- a/src/sspred_avpred.c -+++ b/src/sspred_avpred.c -@@ -223,7 +223,7 @@ predict(int argc, char **argv) - int getmtx(FILE *lfil) - { - int aa, i, j, naa; -- char buf[256], *p; -+ char buf[65536], *p; - - if (fscanf(lfil, "%d", &naa) != 1) - fail("Bad mtx file - no sequence length!"); diff --git a/sci-biology/psipred/metadata.xml b/sci-biology/psipred/metadata.xml deleted file mode 100644 index 959160fe46b1..000000000000 --- a/sci-biology/psipred/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/psipred/psipred-3.4.ebuild b/sci-biology/psipred/psipred-3.4.ebuild deleted file mode 100644 index 1fe4c6dced52..000000000000 --- a/sci-biology/psipred/psipred-3.4.ebuild +++ /dev/null @@ -1,56 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils prefix toolchain-funcs versionator - -#MY_P="${PN}$(delete_all_version_separators)" -MY_P="${PN}${PV}" - -DESCRIPTION="Protein Secondary Structure Prediction" -HOMEPAGE="http://bioinf.cs.ucl.ac.uk/psipred/" -SRC_URI=" - http://bioinf.cs.ucl.ac.uk/downloads/${PN}/${MY_P}.tar.gz - test? ( http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/old/data/tdbdata.tar.gz )" - -LICENSE="psipred" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="test" -RESTRICT="!test? ( test )" - -RDEPEND=" - app-shells/tcsh - sci-biology/ncbi-tools - sci-biology/update-blastdb" -DEPEND="" - -S="${WORKDIR}"/${PN} - -src_prepare() { - rm -f bin/* - epatch \ - "${FILESDIR}"/3.1-Makefile.patch \ - "${FILESDIR}"/3.1-path.patch \ - "${FILESDIR}"/3.2-fgets.patch - eprefixify runpsipred* - emake -C src clean -} - -src_compile() { - emake -C src CC=$(tc-getCC) -} - -src_install() { - emake -C src DESTDIR="${D}" install - dobin runpsipred* bin/* BLAST+/runpsipred* - insinto /usr/share/${PN} - doins -r data - dodoc README -} - -pkg_postinst() { - elog "Please use the update_blastdb.pl in order to" - elog "maintain your own local blastdb" -} diff --git a/sci-biology/psipred/psipred-3.5.ebuild b/sci-biology/psipred/psipred-3.5.ebuild deleted file mode 100644 index 1fe4c6dced52..000000000000 --- a/sci-biology/psipred/psipred-3.5.ebuild +++ /dev/null @@ -1,56 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils prefix toolchain-funcs versionator - -#MY_P="${PN}$(delete_all_version_separators)" -MY_P="${PN}${PV}" - -DESCRIPTION="Protein Secondary Structure Prediction" -HOMEPAGE="http://bioinf.cs.ucl.ac.uk/psipred/" -SRC_URI=" - http://bioinf.cs.ucl.ac.uk/downloads/${PN}/${MY_P}.tar.gz - test? ( http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/old/data/tdbdata.tar.gz )" - -LICENSE="psipred" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="test" -RESTRICT="!test? ( test )" - -RDEPEND=" - app-shells/tcsh - sci-biology/ncbi-tools - sci-biology/update-blastdb" -DEPEND="" - -S="${WORKDIR}"/${PN} - -src_prepare() { - rm -f bin/* - epatch \ - "${FILESDIR}"/3.1-Makefile.patch \ - "${FILESDIR}"/3.1-path.patch \ - "${FILESDIR}"/3.2-fgets.patch - eprefixify runpsipred* - emake -C src clean -} - -src_compile() { - emake -C src CC=$(tc-getCC) -} - -src_install() { - emake -C src DESTDIR="${D}" install - dobin runpsipred* bin/* BLAST+/runpsipred* - insinto /usr/share/${PN} - doins -r data - dodoc README -} - -pkg_postinst() { - elog "Please use the update_blastdb.pl in order to" - elog "maintain your own local blastdb" -} diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest index 76bd71ffeb55..2bc79f89f441 100644 --- a/sci-biology/pysam/Manifest +++ b/sci-biology/pysam/Manifest @@ -1 +1 @@ -DIST pysam-0.12.0.1.tar.gz 2672020 BLAKE2B 4bc6330405724f7b1126da91ba3338687f4dd17f015895f42b971f22ffbb6c32eda65e2667035a4cc830c0370b34d95d3aa6ae0f026b2b3276af1fd6841eed28 SHA512 31460ca98ad2ac5489905ffce76bfbb5bf4a295159f3cc8e088c78dcfbfc34b30d6f7871fd1454de01da98f82b7438ac2aca678a771d7b97ae0029a418f29f1d +DIST pysam-0.21.0.gh.tar.gz 3842829 BLAKE2B 83db290ec0bae71106276ed4f1721292c0d2fa55053c7451f0a8a79619b1c4d8444b99293ac5d8051bfb0b59e984e32a89798bab091e3a019b7c2a3fb7414d1c SHA512 b2ac986b6a352df1d2066a224d710648a88d8ad44273623a89ae0f4bb2645b00f0d0e1685c8ccedfd379259255957e653f3c3199621ac1d4c26098f538b6bfa7 diff --git a/sci-biology/pysam/files/pysam-0.12-fix-buildsystem.patch b/sci-biology/pysam/files/pysam-0.12-fix-buildsystem.patch deleted file mode 100644 index 8b323a63fba5..000000000000 --- a/sci-biology/pysam/files/pysam-0.12-fix-buildsystem.patch +++ /dev/null @@ -1,63 +0,0 @@ -The build system is not designed with partial out-of-source -builds in mind. This is evident by using relative includes -such as '-Isamtools' instead of proper relative or absolute -paths. - -Bug: https://bugs.gentoo.org/show_bug.cgi?id=629670 - ---- a/setup.py -+++ b/setup.py -@@ -359,6 +359,8 @@ - - define_macros = [] - -+samtools_include_dirs = [os.path.abspath("samtools")] -+ - chtslib = Extension( - "pysam.libchtslib", - [source_pattern % "htslib", -@@ -385,7 +387,7 @@ - htslib_sources + - os_c_files, - library_dirs=htslib_library_dirs, -- include_dirs=["pysam", "samtools", "."] + include_os + htslib_include_dirs, -+ include_dirs=["pysam", "."] + samtools_include_dirs + include_os + htslib_include_dirs, - libraries=external_htslib_libraries + internal_htslib_libraries, - language="c", - extra_compile_args=extra_compile_args, -@@ -404,7 +406,7 @@ - htslib_sources + - os_c_files, - library_dirs=htslib_library_dirs, -- include_dirs=["pysam", "samtools"] + include_os + htslib_include_dirs, -+ include_dirs=["pysam"] + samtools_include_dirs + include_os + htslib_include_dirs, - libraries=external_htslib_libraries + internal_htslib_libraries, - language="c", - extra_compile_args=extra_compile_args, -@@ -423,7 +425,7 @@ - htslib_sources + - os_c_files, - library_dirs=htslib_library_dirs, -- include_dirs=["pysam", "samtools", "."] + include_os + htslib_include_dirs, -+ include_dirs=["pysam", "."] + samtools_include_dirs + include_os + htslib_include_dirs, - libraries=external_htslib_libraries + internal_htslib_libraries, - language="c", - extra_compile_args=extra_compile_args, -@@ -467,7 +469,7 @@ - htslib_sources + - os_c_files, - library_dirs=["pysam"] + htslib_library_dirs, -- include_dirs=["samtools", "pysam", "."] + -+ include_dirs=["pysam", "."] + samtools_include_dirs + - include_os + htslib_include_dirs, - libraries=external_htslib_libraries + internal_htslib_libraries, - language="c", -@@ -482,7 +484,7 @@ - htslib_sources + - os_c_files, - library_dirs=["pysam"] + htslib_library_dirs, -- include_dirs=["bcftools", "pysam", "."] + -+ include_dirs=["bcftools", "pysam", "."] + samtools_include_dirs + - include_os + htslib_include_dirs, - libraries=external_htslib_libraries + internal_htslib_libraries, - language="c", diff --git a/sci-biology/pysam/files/pysam-0.21.0-cython-3.patch b/sci-biology/pysam/files/pysam-0.21.0-cython-3.patch new file mode 100644 index 000000000000..303a4fb0dcdc --- /dev/null +++ b/sci-biology/pysam/files/pysam-0.21.0-cython-3.patch @@ -0,0 +1,24 @@ +From 17bb13dcfdb56ac238458dcef23fe01893a892e9 Mon Sep 17 00:00:00 2001 +From: John Marshall <jmarshall@hey.com> +Date: Sat, 8 Apr 2023 11:00:46 +1200 +Subject: [PATCH] Remove incorrect type annotation + +The annotation already in pysam/libcbcf.pyi is correct. +Fixes #1179 as reopened on April 6th. +--- + pysam/libcbcf.pyx | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/pysam/libcbcf.pyx b/pysam/libcbcf.pyx +index 8c088af2..8ecfe5f3 100644 +--- a/pysam/libcbcf.pyx ++++ b/pysam/libcbcf.pyx +@@ -3479,7 +3479,7 @@ cdef class VariantRecordSample(object): + return bcf_format_get_alleles(self) + + @alleles.setter +- def alleles(self, value: tuple): ++ def alleles(self, value): + # Sets the genotype, supply a tuple of alleles to set. + # The supplied alleles need to be defined in the correspoding pysam.libcbcf.VariantRecord + # The genotype is reset when an empty tuple, None or (None,) is supplied diff --git a/sci-biology/pysam/metadata.xml b/sci-biology/pysam/metadata.xml index 6182254bd46d..734257e94f10 100644 --- a/sci-biology/pysam/metadata.xml +++ b/sci-biology/pysam/metadata.xml @@ -1,12 +1,13 @@ -<?xml version='1.0' encoding='UTF-8'?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="google-code">pysam</remote-id> - <remote-id type="github">pysam-developers/pysam</remote-id> - </upstream> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="google-code">pysam</remote-id> + <remote-id type="github">pysam-developers/pysam</remote-id> + <remote-id type="pypi">pysam</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/pysam/pysam-0.12.0.1.ebuild b/sci-biology/pysam/pysam-0.12.0.1.ebuild deleted file mode 100644 index e6500903f847..000000000000 --- a/sci-biology/pysam/pysam-0.12.0.1.ebuild +++ /dev/null @@ -1,47 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 python3_6 ) - -inherit distutils-r1 - -DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping format" -HOMEPAGE=" - https://github.com/pysam-developers/pysam - https://pypi.org/project/pysam/" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND="=sci-libs/htslib-1.5*:=" -DEPEND="${RDEPEND} - dev-python/cython[${PYTHON_USEDEP}] - dev-python/setuptools[${PYTHON_USEDEP}]" - -PATCHES=( "${FILESDIR}"/${PN}-0.12-fix-buildsystem.patch ) - -python_prepare_all() { - # unbundle htslib - export HTSLIB_MODE="external" - export HTSLIB_INCLUDE_DIR="${EPREFIX}"/usr/include - export HTSLIB_LIBRARY_DIR="${EPREFIX}"/usr/$(get_libdir) - rm -r htslib || die - - # prevent setup.py from adding RPATHs - sed -e "/ext\.extra_link_args += \['-Wl,-rpath,\$ORIGIN'\]/d" \ - -i cy_build.py || die - sed -e '/runtime_library_dirs=htslib_library_dirs/d' \ - -i setup.py || die - - distutils-r1_python_prepare_all -} - -src_compile() { - # TODO - # empty compile, as the build system runs the whole build again in install - : -} diff --git a/sci-biology/pysam/pysam-0.21.0.ebuild b/sci-biology/pysam/pysam-0.21.0.ebuild new file mode 100644 index 000000000000..77292ed29613 --- /dev/null +++ b/sci-biology/pysam/pysam-0.21.0.ebuild @@ -0,0 +1,72 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{9..11} ) + +inherit distutils-r1 + +DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping format" +HOMEPAGE=" + https://github.com/pysam-developers/pysam + https://pypi.org/project/pysam/" +SRC_URI="https://github.com/pysam-developers/pysam/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND="=sci-libs/htslib-1.17*:=" +DEPEND="${RDEPEND} + dev-python/cython[${PYTHON_USEDEP}] + dev-python/setuptools[${PYTHON_USEDEP}]" +BDEPEND=" + test? ( + =sci-biology/bcftools-1.17* + =sci-biology/samtools-1.17* + )" + +distutils_enable_tests pytest + +DISTUTILS_IN_SOURCE_BUILD=1 + +PATCHES=( + # backport + # https://github.com/pysam-developers/pysam/commit/17bb13dcfdb56ac238458dcef23fe01893a892e9 + "${FILESDIR}"/${P}-cython-3.patch +) + +EPYTEST_DESELECT=( + # only work with bundled htslib + 'tests/tabix_test.py::TestRemoteFileHTTP' + 'tests/tabix_test.py::TestRemoteFileHTTPWithHeader' +) + +python_prepare_all() { + # unbundle htslib + export HTSLIB_MODE="external" + export HTSLIB_INCLUDE_DIR="${ESYSROOT}"/usr/include + export HTSLIB_LIBRARY_DIR="${ESYSROOT}"/usr/$(get_libdir) + rm -r htslib || die + + # prevent setup.py from adding RPATHs (except $ORIGIN) + sed -e '/runtime_library_dirs=htslib_library_dirs/d' \ + -i setup.py || die + + if use test; then + einfo "Building test data" + emake -C tests/pysam_data + emake -C tests/cbcf_data + fi + + distutils-r1_python_prepare_all +} + +python_compile() { + # breaks with parallel build + # need to avoid dropping .so plugins into + # build-lib, which breaks tests + esetup.py build_ext --inplace -j1 + distutils-r1_python_compile -j1 +} diff --git a/sci-biology/pysam/pysam-9999.ebuild b/sci-biology/pysam/pysam-9999.ebuild new file mode 100644 index 000000000000..a162ddf2158b --- /dev/null +++ b/sci-biology/pysam/pysam-9999.ebuild @@ -0,0 +1,72 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{9..11} ) + +inherit distutils-r1 + +if [[ ${PV} == *9999 ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/pysam-developers/pysam.git" +else + SRC_URI="https://github.com/pysam-developers/pysam/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz" + KEYWORDS="~amd64 ~x86" +fi + +DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping format" +HOMEPAGE=" + https://github.com/pysam-developers/pysam + https://pypi.org/project/pysam/" + +LICENSE="MIT" +SLOT="0" + +RDEPEND=">=sci-libs/htslib-1.17" +DEPEND="${RDEPEND} + dev-python/cython[${PYTHON_USEDEP}] + dev-python/setuptools[${PYTHON_USEDEP}]" +BDEPEND=" + test? ( + >=sci-biology/bcftools-1.17 + >=sci-biology/samtools-1.17 + )" + +distutils_enable_tests pytest + +DISTUTILS_IN_SOURCE_BUILD=1 + +EPYTEST_DESELECT=( + # only work with bundled htslib + 'tests/tabix_test.py::TestRemoteFileHTTP' + 'tests/tabix_test.py::TestRemoteFileHTTPWithHeader' +) + +python_prepare_all() { + # unbundle htslib + export HTSLIB_MODE="external" + export HTSLIB_INCLUDE_DIR="${ESYSROOT}"/usr/include + export HTSLIB_LIBRARY_DIR="${ESYSROOT}"/usr/$(get_libdir) + rm -r htslib || die + + # prevent setup.py from adding RPATHs (except $ORIGIN) + sed -e '/runtime_library_dirs=htslib_library_dirs/d' \ + -i setup.py || die + + if use test; then + einfo "Building test data" + emake -C tests/pysam_data + emake -C tests/cbcf_data + fi + + distutils-r1_python_prepare_all +} + +python_compile() { + # breaks with parallel build + # need to avoid dropping .so plugins into + # build-lib, which breaks tests + esetup.py build_ext --inplace -j1 + distutils-r1_python_compile -j1 +} diff --git a/sci-biology/qrna/Manifest b/sci-biology/qrna/Manifest index aa10390b4217..9532795cb306 100644 --- a/sci-biology/qrna/Manifest +++ b/sci-biology/qrna/Manifest @@ -1 +1,2 @@ DIST qrna-2.0.3c.tar.bz2 6423705 BLAKE2B 42bb2f03bac4034da9bcdedcd7c09ce7d1892ceb14d5682745d77c7575a84ae1a6a598406895be2a844ceaffee045ec6357ad08cc0d67a1312458d11b6540fda SHA512 98710bcf8993e2c09ec1eb33632a18ac993ab817dc95a865200b0868f79b95ff61f5f7d3f0c1c33de6d26f674025ea11a8c7d8175b96071e4594daa252fa52b5 +DIST qrna-2.0.4.tar.gz 3220929 BLAKE2B 77f1272ad9952a3b47142fe996e3838bf13d845e19753e73ad941c2a055e7cc1a714a41543097120d5e96aaa8d5d0394e7083413599f60dac21261b2e4071fd3 SHA512 9d2d697d537f9fb0dac374de1b80f6862630cea0bd7cd68f8c3fcf97457d393d2e38e709aac674f4e50d437d5ce11f0bf527c705c2bd28c3017894c11ea17222 diff --git a/sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch b/sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch index d03f650dd39e..17ca27e6da5a 100644 --- a/sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch +++ b/sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch @@ -1,13 +1,156 @@ -diff --git a/src/Makefile b/src/Makefile -index 1d1631b..4fa3af9 100644 +--- a/squid/Makefile ++++ b/squid/Makefile +@@ -19,7 +19,6 @@ + # On an Alliant, use fxc. + # + #CC = cc +-CC = gcc + #CC = fxc + + ## Any special compiler flags you want. +@@ -37,7 +36,6 @@ + # for instance. If the code builds cleanly but seg faults, try + # rebuilding without optimization. + # +-CFLAGS = -O + #CFLAGS = -g + #CFLAGS = -TARG:exc_max -64 -Ofast=ip27 #specific SGI Origin200 compiler# + +@@ -47,8 +45,6 @@ + # Don't worry. The Makefile tests for ranlib existence and will work + # fine on SGIs even if RANLIB is set. + # +-AR = ar rcv +-RANLIB = ranlib + + ## Machine specific definitions + # +@@ -108,41 +104,41 @@ + all: $(LIBTARGET) + + alistat: $(OBJ) alistat_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o alistat $(OBJ) alistat_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o alistat $(OBJ) alistat_main.o $(LIBS) + + compalign: $(OBJ) compalign_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o compalign $(OBJ) compalign_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o compalign $(OBJ) compalign_main.o $(LIBS) + + compstruct: $(OBJ) compstruct_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o compstruct $(OBJ) compstruct_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o compstruct $(OBJ) compstruct_main.o $(LIBS) + + getseq: $(OBJ) getseq_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o getseq $(OBJ) getseq_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o getseq $(OBJ) getseq_main.o $(LIBS) + + reformat: $(OBJ) reformat_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o reformat $(OBJ) reformat_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o reformat $(OBJ) reformat_main.o $(LIBS) + + revcomp: $(OBJ) revcomp_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o revcomp $(OBJ) revcomp_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o revcomp $(OBJ) revcomp_main.o $(LIBS) + + seqstat: $(OBJ) seqstat_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o seqstat $(OBJ) seqstat_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o seqstat $(OBJ) seqstat_main.o $(LIBS) + + seqsplit: $(OBJ) seqsplit_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o seqstat $(OBJ) seqsplit_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o seqstat $(OBJ) seqsplit_main.o $(LIBS) + + shuffle: $(OBJ) shuffle_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o shuffle $(OBJ) shuffle_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o shuffle $(OBJ) shuffle_main.o $(LIBS) + + translate: $(OBJ) translate_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o translate $(OBJ) translate_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o translate $(OBJ) translate_main.o $(LIBS) + + weight: $(OBJ) weight_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o weight $(OBJ) weight_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o weight $(OBJ) weight_main.o $(LIBS) + + + $(LIBTARGET): $(OBJ) +- $(AR) $(LIBTARGET) $(OBJ) ++ $(AR) rcv $(LIBTARGET) $(OBJ) + -if test -x /bin/ranlib; then /bin/ranlib $(LIBTARGET); else exit 0; fi + -if test -x /usr/bin/ranlib; then /usr/bin/ranlib $(LIBTARGET); else exit 0; fi + -if test -x $(RANLIB); then $(RANLIB) $(LIBTARGET); else exit 0; fi +@@ -182,4 +178,4 @@ + etags -t $(SRC) $(HDRS) + + .c.o: +- $(CC) $(CFLAGS) $(MDEFS) -c $< ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -c $< +--- a/squid02/Makefile ++++ b/squid02/Makefile +@@ -27,8 +27,6 @@ + + ## your compiler and compiler flags + # +-CC = gcc +-CFLAGS = -g -O2 + + ## other defined flags for machine-specific stuff + # +@@ -37,8 +35,6 @@ + + ## Archiver command + # +-AR = ar rcv +-RANLIB = ranlib + + ## instructions for installing man pages + # +@@ -158,10 +154,10 @@ + all: version.h $(PROGS) libsquid.a + + $(PROGS): %: %_main.o version.h $(OBJS) +- $(CC) $(CFLAGS) $(MDEFS) $(PVMLIBDIR) -o $@ $@_main.o $(OBJS) $(PVMLIBS) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) $(PVMLIBDIR) -o $@ $@_main.o $(OBJS) $(PVMLIBS) $(LIBS) + + .c.o: +- $(CC) $(CFLAGS) $(PVMFLAG) $(PVMINCDIR) $(MDEFS) -c $< ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(PVMFLAG) $(PVMINCDIR) $(MDEFS) -c $< + ################################################################ + + +@@ -172,7 +168,7 @@ + module: libsquid.a + + libsquid.a: version.h $(OBJS) +- $(AR) libsquid.a $(OBJS) ++ $(AR) rcv libsquid.a $(OBJS) + $(RANLIB) libsquid.a + chmod 644 libsquid.a + ################################################################# --- a/src/Makefile +++ b/src/Makefile -@@ -131,17 +131,17 @@ DEMOS = +@@ -21,7 +21,6 @@ + SQUIDSRCDIR02 = ../squid02 + + ## your compiler +-CC = gcc + #CC = cc + + ## any special compiler flags you want +@@ -30,7 +29,6 @@ + #CFLAGS = -g -Wall -pedantic + #CFLAGS = -TARG:exc_max + #CFLAGS = -g -fullwarn -wlint,-fviah +-CFLAGS = -O + #CFLAGS = -p # profiling # + #CFLAGS = -64 -Ofast=ip27 #specific warhorse compiler# + +@@ -131,145 +129,145 @@ all: $(PROGS) main: $(OBJ) main.o - $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(LIBS) -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(LIBS) cfgbuild: $(OBJ) cfgbuild.o - $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) + $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) @@ -25,4 +168,208 @@ index 1d1631b..4fa3af9 100644 + $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR02) $@.o $(OBJ2) $(LIBS) main.o: ../src/main.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + cfgbuild.o: ../src/cfgbuild.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + eqrna.o: ../src/eqrna.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + eqrna_sample.o: ../src/eqrna_sample.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + shuffle.o: ../src/shuffle.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + rnamat_main.o: ../src/rnamat_main.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? + + cfgio.o: ../src/cfgio.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + cfgmodel.o: ../src/cfgmodel.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + cfgparse.o: ../src/cfgparse.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + codcreatealign.o: ../src/codcreatealign.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + coddp.o: ../src/coddp.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + coddpscanfast.o: ../src/coddpscanfast.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + codmodel.o: ../src/codmodel.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + codon.o: ../src/codon.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + codscorealign.o: ../src/codscorealign.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + er_math.o: ../src/er_math.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + er_vectop.o: ../src/er_vectop.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? + evd.o: ../src/evd.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolcodmodel.o: ../src/evolcodmodel.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolemissions.o: ../src/evolemissions.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolmisc.o: ../src/evolmisc.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolnullmodel.o: ../src/evolnullmodel.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolothmodel.o: ../src/evolothmodel.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolqrnaversion.o: ../src/evolqrnaversion.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolscorewithmodels.o: ../src/evolscorewithmodels.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolscorewithmodelscanfast.o: ../src/evolscorewithmodelscanfast.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolriboprob.o: ../src/evolriboprob.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolrnadp.o: ../src/evolrnadp.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolrnadpscanfast.o: ../src/evolrnadpscanfast.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolrnamodel.o: ../src/evolrnamodel.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolrnascorealign.o: ../src/evolrnascorealign.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolve.o: ../src/evolve.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + globals.o: ../src/globals.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + hexamer.o: ../src/hexamer.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + matrix.o: ../src/matrix.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + misc.o: ../src/misc.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + nrnscfg.o: ../src/nrnscfg.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + nstack.o: ../src/nstack.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? + nullmodel.o: ../src/nullmodel.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + othcreatealign.o: ../src/othcreatealign.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + othdp.o: ../src/othdp.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + othdpscanfast.o: ../src/othdpscanfast.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + othmodel.o: ../src/othmodel.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + othscorealign.o: ../src/othscorealign.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + posterior.o: ../src/posterior.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + qrnaversion.o: ../src/qrnaversion.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + riboprob.o: ../src/riboprob.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + rnacreatealign.o: ../src/rnacreatealign.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + rnadp.o: ../src/rnadp.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + rnadpscanfast.o: ../src/rnadpscanfast.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + rnaio.o: ../src/rnaio.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + rnamat.o: ../src/rnamat.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? + rnamodel.o: ../src/rnamodel.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + rnaoutput.o: ../src/rnaoutput.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + rnascorealign.o: ../src/rnascorealign.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + rnascfg.o: ../src/rnascfg.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + rnascfgscanfast.o: ../src/rnascfgscanfast.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + scorewithmodels.o: ../src/scorewithmodels.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + scorewithmodelscanfast.o: ../src/scorewithmodelscanfast.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + seqio.o: ../src/seqio.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + trace.o: ../src/trace.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + traceSCFG.o: ../src/traceSCFG.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + tying.o: ../src/tying.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + + + install: $(PROGS) +@@ -313,10 +311,10 @@ + /usr/lib/lint/llib-lm.ln + + .c.o: +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $< ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $< + + .m.o: +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $< ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $< + + + diff --git a/sci-biology/qrna/files/qrna-2.0.4-ldflags.patch b/sci-biology/qrna/files/qrna-2.0.4-ldflags.patch new file mode 100644 index 000000000000..c53b56b0e935 --- /dev/null +++ b/sci-biology/qrna/files/qrna-2.0.4-ldflags.patch @@ -0,0 +1,381 @@ +diff --git a/squid/Makefile b/squid/Makefile +index fafab4c..8c329b3 100644 +--- a/squid/Makefile ++++ b/squid/Makefile +@@ -19,7 +19,6 @@ MANDIR = $(HOME)/man + # On an Alliant, use fxc. + # + #CC = cc +-CC = gcc + #CC = fxc + + ## Any special compiler flags you want. +@@ -37,7 +36,6 @@ CC = gcc + # for instance. If the code builds cleanly but seg faults, try + # rebuilding without optimization. + # +-CFLAGS = -O -m32 + #CFLAGS = -g + #CFLAGS = -TARG:exc_max -64 -Ofast=ip27 #specific SGI Origin200 compiler# + +@@ -47,8 +45,6 @@ CFLAGS = -O -m32 + # Don't worry. The Makefile tests for ranlib existence and will work + # fine on SGIs even if RANLIB is set. + # +-AR = ar rcv +-RANLIB = ranlib + + ## Machine specific definitions + # +@@ -108,41 +104,41 @@ DIST = $(SRC) $(HDRS) $(READMES) Makefile + all: $(LIBTARGET) + + alistat: $(OBJ) alistat_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o alistat $(OBJ) alistat_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o alistat $(OBJ) alistat_main.o $(LIBS) + + compalign: $(OBJ) compalign_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o compalign $(OBJ) compalign_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o compalign $(OBJ) compalign_main.o $(LIBS) + + compstruct: $(OBJ) compstruct_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o compstruct $(OBJ) compstruct_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o compstruct $(OBJ) compstruct_main.o $(LIBS) + + getseq: $(OBJ) getseq_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o getseq $(OBJ) getseq_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o getseq $(OBJ) getseq_main.o $(LIBS) + + reformat: $(OBJ) reformat_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o reformat $(OBJ) reformat_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o reformat $(OBJ) reformat_main.o $(LIBS) + + revcomp: $(OBJ) revcomp_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o revcomp $(OBJ) revcomp_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o revcomp $(OBJ) revcomp_main.o $(LIBS) + + seqstat: $(OBJ) seqstat_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o seqstat $(OBJ) seqstat_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o seqstat $(OBJ) seqstat_main.o $(LIBS) + + seqsplit: $(OBJ) seqsplit_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o seqstat $(OBJ) seqsplit_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o seqstat $(OBJ) seqsplit_main.o $(LIBS) + + shuffle: $(OBJ) shuffle_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o shuffle $(OBJ) shuffle_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o shuffle $(OBJ) shuffle_main.o $(LIBS) + + translate: $(OBJ) translate_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o translate $(OBJ) translate_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o translate $(OBJ) translate_main.o $(LIBS) + + weight: $(OBJ) weight_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o weight $(OBJ) weight_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o weight $(OBJ) weight_main.o $(LIBS) + + + $(LIBTARGET): $(OBJ) +- $(AR) $(LIBTARGET) $(OBJ) ++ $(AR) rcv $(LIBTARGET) $(OBJ) + -if test -x /bin/ranlib; then /bin/ranlib $(LIBTARGET); else exit 0; fi + -if test -x /usr/bin/ranlib; then /usr/bin/ranlib $(LIBTARGET); else exit 0; fi + -if test -x $(RANLIB); then $(RANLIB) $(LIBTARGET); else exit 0; fi +@@ -182,4 +178,4 @@ tags: + etags -t $(SRC) $(HDRS) + + .c.o: +- $(CC) $(CFLAGS) $(MDEFS) -c $< ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -c $< +diff --git a/squid02/Makefile b/squid02/Makefile +index d32240f..757e0dd 100644 +--- a/squid02/Makefile ++++ b/squid02/Makefile +@@ -27,8 +27,6 @@ SCRIPTDIR = ${exec_prefix}/bin + + ## your compiler and compiler flags + # +-CC = gcc +-CFLAGS = -g -O2 -m32 + + ## other defined flags for machine-specific stuff + # +@@ -37,8 +35,6 @@ LIBS = -lm + + ## Archiver command + # +-AR = ar rcv +-RANLIB = ranlib + + ## instructions for installing man pages + # +@@ -158,10 +154,10 @@ OBJS = a2m.o\ + all: version.h $(PROGS) libsquid.a + + $(PROGS): %: %_main.o version.h $(OBJS) +- $(CC) $(CFLAGS) $(MDEFS) $(PVMLIBDIR) -o $@ $@_main.o $(OBJS) $(PVMLIBS) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) $(PVMLIBDIR) -o $@ $@_main.o $(OBJS) $(PVMLIBS) $(LIBS) + + .c.o: +- $(CC) $(CFLAGS) $(PVMFLAG) $(PVMINCDIR) $(MDEFS) -c $< ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(PVMFLAG) $(PVMINCDIR) $(MDEFS) -c $< + ################################################################ + + +@@ -172,7 +168,7 @@ $(PROGS): %: %_main.o version.h $(OBJS) + module: libsquid.a + + libsquid.a: version.h $(OBJS) +- $(AR) libsquid.a $(OBJS) ++ $(AR) rcv libsquid.a $(OBJS) + $(RANLIB) libsquid.a + chmod 644 libsquid.a + ################################################################# +diff --git a/src/Makefile b/src/Makefile +index d93182b..35c8b3d 100644 +--- a/src/Makefile ++++ b/src/Makefile +@@ -21,7 +21,6 @@ SQUIDDIR02 = ../squid02 + SQUIDSRCDIR02 = ../squid02 + + ## your compiler +-CC = gcc + #CC = cc + + ## any special compiler flags you want +@@ -30,7 +29,6 @@ CC = gcc + #CFLAGS = -g -Wall -pedantic + #CFLAGS = -TARG:exc_max + #CFLAGS = -g -fullwarn -wlint,-fviah +-CFLAGS = -O -m32 + #CFLAGS = -p # profiling # + #CFLAGS = -64 -Ofast=ip27 #specific warhorse compiler# + +@@ -131,145 +129,145 @@ DEMOS = + all: $(PROGS) + + main: $(OBJ) main.o +- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(LIBS) + cfgbuild: $(OBJ) cfgbuild.o +- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) + eqrna: $(OBJ) eqrna.o +- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) + eqrna_sample: $(OBJ) eqrna_sample.o +- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) + shuffle: $(OBJ) shuffle.o +- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) + rnamat_main: $(OBJ2) rnamat_main.o +- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR02) $@.o $(OBJ2) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR02) $@.o $(OBJ2) $(LIBS) + + main.o: ../src/main.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + cfgbuild.o: ../src/cfgbuild.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + eqrna.o: ../src/eqrna.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + eqrna_sample.o: ../src/eqrna_sample.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + shuffle.o: ../src/shuffle.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + rnamat_main.o: ../src/rnamat_main.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? + + cfgio.o: ../src/cfgio.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + cfgmodel.o: ../src/cfgmodel.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + cfgparse.o: ../src/cfgparse.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + codcreatealign.o: ../src/codcreatealign.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + coddp.o: ../src/coddp.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + coddpscanfast.o: ../src/coddpscanfast.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + codmodel.o: ../src/codmodel.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + codon.o: ../src/codon.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + codscorealign.o: ../src/codscorealign.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + er_math.o: ../src/er_math.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + er_vectop.o: ../src/er_vectop.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? + evd.o: ../src/evd.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolcodmodel.o: ../src/evolcodmodel.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolemissions.o: ../src/evolemissions.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolmisc.o: ../src/evolmisc.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolnullmodel.o: ../src/evolnullmodel.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolothmodel.o: ../src/evolothmodel.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolqrnaversion.o: ../src/evolqrnaversion.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolscorewithmodels.o: ../src/evolscorewithmodels.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolscorewithmodelscanfast.o: ../src/evolscorewithmodelscanfast.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolriboprob.o: ../src/evolriboprob.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolrnadp.o: ../src/evolrnadp.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolrnadpscanfast.o: ../src/evolrnadpscanfast.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolrnamodel.o: ../src/evolrnamodel.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolrnascorealign.o: ../src/evolrnascorealign.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolve.o: ../src/evolve.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + globals.o: ../src/globals.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + hexamer.o: ../src/hexamer.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + matrix.o: ../src/matrix.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + misc.o: ../src/misc.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + nrnscfg.o: ../src/nrnscfg.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + nstack.o: ../src/nstack.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? + nullmodel.o: ../src/nullmodel.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + othcreatealign.o: ../src/othcreatealign.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + othdp.o: ../src/othdp.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + othdpscanfast.o: ../src/othdpscanfast.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + othmodel.o: ../src/othmodel.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + othscorealign.o: ../src/othscorealign.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + posterior.o: ../src/posterior.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + qrnaversion.o: ../src/qrnaversion.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + riboprob.o: ../src/riboprob.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + rnacreatealign.o: ../src/rnacreatealign.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + rnadp.o: ../src/rnadp.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + rnadpscanfast.o: ../src/rnadpscanfast.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + rnaio.o: ../src/rnaio.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + rnamat.o: ../src/rnamat.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? + rnamodel.o: ../src/rnamodel.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + rnaoutput.o: ../src/rnaoutput.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + rnascorealign.o: ../src/rnascorealign.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + rnascfg.o: ../src/rnascfg.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + rnascfgscanfast.o: ../src/rnascfgscanfast.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + scorewithmodels.o: ../src/scorewithmodels.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + scorewithmodelscanfast.o: ../src/scorewithmodelscanfast.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + seqio.o: ../src/seqio.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + trace.o: ../src/trace.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + traceSCFG.o: ../src/traceSCFG.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + tying.o: ../src/tying.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + + + install: $(PROGS) +@@ -313,10 +311,10 @@ lint: + /usr/lib/lint/llib-lm.ln + + .c.o: +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $< ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $< + + .m.o: +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $< ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $< + + + diff --git a/sci-biology/qrna/metadata.xml b/sci-biology/qrna/metadata.xml index 8417d1580d40..bdabd1d83788 100644 --- a/sci-biology/qrna/metadata.xml +++ b/sci-biology/qrna/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/qrna/qrna-2.0.3c-r3.ebuild b/sci-biology/qrna/qrna-2.0.3c-r3.ebuild index 5c580a24d2a3..34b59e9fb0a3 100644 --- a/sci-biology/qrna/qrna-2.0.3c-r3.ebuild +++ b/sci-biology/qrna/qrna-2.0.3c-r3.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 inherit toolchain-funcs @@ -12,7 +12,6 @@ SRC_URI="mirror://gentoo/${P}.tar.bz2" LICENSE="GPL-2" SLOT="0" KEYWORDS="~amd64 ~x86" -IUSE="" RDEPEND=" dev-lang/perl @@ -26,15 +25,13 @@ PATCHES=( src_prepare() { default - sed \ - -e "s:^CC.*:CC = $(tc-getCC):" \ - -e "/^AR/s:ar:$(tc-getAR):g" \ - -e "/^RANLIB/s:ranlib:$(tc-getRANLIB):g" \ - -e "/CFLAGS/s:=.*$:= ${CFLAGS}:" \ - -i {src,squid,squid02}/Makefile || die rm -v squid*/*.a || die } +src_configure() { + tc-export AR CC RANLIB +} + src_compile() { local d for d in squid squid02 src; do diff --git a/sci-biology/qrna/qrna-2.0.4.ebuild b/sci-biology/qrna/qrna-2.0.4.ebuild new file mode 100644 index 000000000000..58e2045e8fc2 --- /dev/null +++ b/sci-biology/qrna/qrna-2.0.4.ebuild @@ -0,0 +1,61 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit toolchain-funcs vcs-clean + +DESCRIPTION="Prototype ncRNA genefinder" +HOMEPAGE="http://eddylab.org/software.html" +SRC_URI=" + http://eddylab.org/software/qrna/qrna.tar.gz -> ${P}.tar.gz + examples? ( mirror://gentoo/qrna-2.0.3c.tar.bz2 ) +" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="examples" + +RDEPEND=" + dev-lang/perl + sci-biology/hmmer:2" +DEPEND="${RDEPEND}" + +PATCHES=( + "${FILESDIR}"/${P}-ldflags.patch +) + +src_prepare() { + default + esvn_clean + rm -v squid*/*.a || die +} + +src_configure() { + tc-export AR CC RANLIB +} + +src_compile() { + local d + for d in squid squid02 src; do + emake -C ${d} + done +} + +src_install() { + dobin src/{cfgbuild,eqrna,eqrna_sample,rnamat_main} scripts/* + + newdoc 00README README + dodoc -r documentation/. + + insinto /usr/share/${PN}/data + doins -r lib/. + if use examples; then + insinto /usr/share/${PN}/demos + doins -r "${WORKDIR}"/qrna-2.0.3c/Demos/. + fi + + # Sets the path to the QRNA data files + doenvd "${FILESDIR}"/26qrna +} diff --git a/sci-biology/raxml/files/raxml-7.2.6-makefile.patch b/sci-biology/raxml/files/raxml-7.2.6-makefile.patch index ae83e2eef4e7..6b82ed65b770 100644 --- a/sci-biology/raxml/files/raxml-7.2.6-makefile.patch +++ b/sci-biology/raxml/files/raxml-7.2.6-makefile.patch @@ -14,7 +14,7 @@ index 716b6c6..f0c1de2 100644 -CFLAGS = -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -msse -+CFLAGS += -D_GNU_SOURCE ++CPPFLAGS += -D_GNU_SOURCE @@ -23,7 +23,7 @@ index 716b6c6..f0c1de2 100644 raxmlHPC : $(objs) - $(CC) -o raxmlHPC $(objs) $(LIBRARIES) -+ $(CC) $(LDFLAGS) -o raxmlHPC $(objs) $(LIBRARIES) ++ $(CC) $(LDFLAGS) -o raxmlHPC $(objs) $(LIBRARIES) $(LIBS) classify.o : classify.c $(GLOBAL_DEPS) evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS) diff --git a/sci-biology/raxml/metadata.xml b/sci-biology/raxml/metadata.xml index 959160fe46b1..ccdff086e20b 100644 --- a/sci-biology/raxml/metadata.xml +++ b/sci-biology/raxml/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/raxml/raxml-7.2.6.ebuild b/sci-biology/raxml/raxml-7.2.6.ebuild index 50fffc34accb..adb044426381 100644 --- a/sci-biology/raxml/raxml-7.2.6.ebuild +++ b/sci-biology/raxml/raxml-7.2.6.ebuild @@ -1,34 +1,29 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=7 -inherit eutils flag-o-matic toolchain-funcs +inherit flag-o-matic toolchain-funcs DESCRIPTION="Sequential, Parallel & Distributed Inference of Large Phylogenetic Trees" HOMEPAGE="http://wwwkramer.in.tum.de/exelixis/software.html" SRC_URI="http://wwwkramer.in.tum.de/exelixis/software/RAxML-${PV}.tar.bz2" +S="${WORKDIR}/RAxML-${PV}" -SLOT="0" LICENSE="GPL-2" +SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="cpu_flags_x86_sse3 +threads" - REQUIRED_USE="cpu_flags_x86_sse3" # mpi is not supported in version 7.2.2. mpi is enabled by adding -DPARALLEL to CFLAGS -DEPEND="" # mpi? ( virtual/mpi )" -RDEPEND="${DEPEND}" - -S="${WORKDIR}/RAxML-${PV}" - -src_prepare() { - epatch "${FILESDIR}"/${P}-makefile.patch +PATCHES=( "${FILESDIR}"/${P}-makefile.patch ) - use cpu_flags_x86_sse3 && append-cflags -D__SIM_SSE3 +src_configure() { + use cpu_flags_x86_sse3 && append-cppflags -D__SIM_SSE3 use threads && \ - append-cflags -D_USE_PTHREADS && \ - append-ldflags -pthread + append-cppflags -D_USE_PTHREADS && \ + append-libs -pthread tc-export CC } diff --git a/sci-biology/rebase/Manifest b/sci-biology/rebase/Manifest index 175ef0c271ab..b383cb20278f 100644 --- a/sci-biology/rebase/Manifest +++ b/sci-biology/rebase/Manifest @@ -1,8 +1 @@ -DIST rebase-1701.tar.xz 120604368 BLAKE2B 1160f494b4e8650fb8ab9144756642377322a2bc1dd7a031e265a378b58e2487cc7d3f49ca9cf343a5c259cccb1d9ff7fda45a9b5744ae1f88799c603740a3af SHA512 1833db9d78508bbd5317f9b42b0e8129096f1695d5a14d5e2b6043bc94091a76ac404c576ad622be4e32c46aff7975a7ec3e36c3da71ce3ce1665868ee0d77cb -DIST rebase-1702.tar.xz 117583312 BLAKE2B 19089d5767c35da22fb95bac7bc030ef593b159dda04d512b053a84c1cb4947679c8304bcbcb9388256e92cb0056d16b1b2035efac6eae84831d6fa95bd41a2a SHA512 3bba0738840b966a0a58123f265de1951428c599f3af9c581e1becec17ba3a93233a231de0673dbb2dc0bb82d54096e0eed43846967bf232f412bb785ce3b23f -DIST rebase-1703.tar.xz 122252304 BLAKE2B 26afca990e300a5c471f55b1a168b1930212a347b70dd3224a51894bb701540a27a0384bd250caee8e0d0dd4886c6664ab74b20bcfb71fd42d1c73ebf2ce6be6 SHA512 838bf5e09073ff8520403d955a8195298def1d792d1fd3044e7c8896c6202a0340c1e96dbe80e85c5801cd3be3ed63f19488101cca02d46cdf5f1d0521ede796 -DIST rebase-1704.tar.xz 124351900 BLAKE2B bdbda714cc07f744b56c83b80a1b0f0a724a990b200c615458852910f282761aaf37a312a388ec7fee94a62ead47e01ddca8b205f2ad05d780a299e7547206f7 SHA512 0e4019d41ccbae86b8cb1f6dfa4c34d3fccbe084a330f04f2fdb774186e35c761655e1619d9a90d444ea3bab0910df1b60cf9a249ee31d66a254d28dd6b32cc7 -DIST rebase-1803.tar.xz 152581448 BLAKE2B 7907f0aee9e202f062f5ec4b5e4a112cd0fb3900b3d65dc57ffe4832c5aac088f50c2661f1b9c1bb8b57e7b4f6d453bec2899b460383d06b4e679da13e92aad2 SHA512 ab718e87c33c975bc6a93d3c6be130c9751612b744dc5451bcfde5c10d3d9d68ed4a4d921fff1f48063bfa2e9f3c8a016d4e5e0afa4eb7e4131511767608534b -DIST rebase-1806.tar.xz 161844712 BLAKE2B 901167b502b85e88eaa9a8886c5ccac8bf1ec16a7736694b90f896bd4d87ae3792d09f6b154118a6063e30b94a5633b37a7811aefc1d39467d0043d887aeb64a SHA512 9c9c0ef89c8f8e43516c052a06395d61c423b53a79553ceccd992bf72872ece44696091c11c816213b93532aac54a476fe87475f4f67baaa87bc50f64e847d48 -DIST rebase-1810.tar.xz 173538148 BLAKE2B 4630d6a2addbb95e70cff73c8f81552545c81be2893dd9f38d19d8bc2fd7ecf4340441498187b654a05012d4dafbd5ad0634e3281f7aed1ee61618308a2325a5 SHA512 641ed61b14970e9804e98abab4e982aeaff378638730964ba162dffacea1c5869e4b1202462f422307d039e1bc6053403c801273f1ca9021c38f29e68a7bfae2 DIST rebase-1901.tar.xz 182532548 BLAKE2B 5ac8d26ab057bcd21dc9c57abeb226ac70cfabb156b48a51f820789626257be55bb21c9eb2099e6e55b1cfe3691480df0ec9b3f4b18b50ba2712b986c6d057b4 SHA512 1e3553e59c3520190754cb40bb0900e466d9ffd206e6460d3262a7d7d2af8aab0e28f3e60187665362824fa3730211c0e2119016ce5fed49095f9de46c7f25d4 diff --git a/sci-biology/rebase/metadata.xml b/sci-biology/rebase/metadata.xml index dbd090188c93..e4403acacd03 100644 --- a/sci-biology/rebase/metadata.xml +++ b/sci-biology/rebase/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/rebase/rebase-1702.ebuild b/sci-biology/rebase/rebase-1702.ebuild deleted file mode 100644 index 70694cf2ca8a..000000000000 --- a/sci-biology/rebase/rebase-1702.ebuild +++ /dev/null @@ -1,45 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -MY_PV=${PV#1} - -DESCRIPTION="A restriction enzyme database" -HOMEPAGE="http://rebase.neb.com" -SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz" - -SLOT="0" -LICENSE="public-domain" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris ~x86-solaris" -IUSE="emboss minimal" - -RDEPEND="emboss? ( >=sci-biology/emboss-5.0.0 )" -DEPEND="${RDEPEND}" - -RESTRICT="binchecks strip" - -src_compile() { - if use emboss; then - echo; einfo "Indexing Rebase for usage with EMBOSS." - mkdir REBASE || die - EMBOSS_DATA="." rebaseextract -auto -infile withrefm.${MY_PV} \ - -protofile proto.${MY_PV} -equivalences \ - || die "Indexing Rebase failed." - echo - fi -} - -src_install() { - if ! use minimal; then - insinto /usr/share/${PN} - doins withrefm.${MY_PV} proto.${MY_PV} - fi - newdoc REBASE.DOC README - if use emboss; then - insinto /usr/share/EMBOSS/data/REBASE - doins REBASE/embossre.{enz,ref,sup} - insinto /usr/share/EMBOSS/data - doins REBASE/embossre.equ - fi -} diff --git a/sci-biology/rebase/rebase-1703.ebuild b/sci-biology/rebase/rebase-1703.ebuild deleted file mode 100644 index 70694cf2ca8a..000000000000 --- a/sci-biology/rebase/rebase-1703.ebuild +++ /dev/null @@ -1,45 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -MY_PV=${PV#1} - -DESCRIPTION="A restriction enzyme database" -HOMEPAGE="http://rebase.neb.com" -SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz" - -SLOT="0" -LICENSE="public-domain" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris ~x86-solaris" -IUSE="emboss minimal" - -RDEPEND="emboss? ( >=sci-biology/emboss-5.0.0 )" -DEPEND="${RDEPEND}" - -RESTRICT="binchecks strip" - -src_compile() { - if use emboss; then - echo; einfo "Indexing Rebase for usage with EMBOSS." - mkdir REBASE || die - EMBOSS_DATA="." rebaseextract -auto -infile withrefm.${MY_PV} \ - -protofile proto.${MY_PV} -equivalences \ - || die "Indexing Rebase failed." - echo - fi -} - -src_install() { - if ! use minimal; then - insinto /usr/share/${PN} - doins withrefm.${MY_PV} proto.${MY_PV} - fi - newdoc REBASE.DOC README - if use emboss; then - insinto /usr/share/EMBOSS/data/REBASE - doins REBASE/embossre.{enz,ref,sup} - insinto /usr/share/EMBOSS/data - doins REBASE/embossre.equ - fi -} diff --git a/sci-biology/rebase/rebase-1704.ebuild b/sci-biology/rebase/rebase-1704.ebuild deleted file mode 100644 index 70694cf2ca8a..000000000000 --- a/sci-biology/rebase/rebase-1704.ebuild +++ /dev/null @@ -1,45 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -MY_PV=${PV#1} - -DESCRIPTION="A restriction enzyme database" -HOMEPAGE="http://rebase.neb.com" -SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz" - -SLOT="0" -LICENSE="public-domain" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris ~x86-solaris" -IUSE="emboss minimal" - -RDEPEND="emboss? ( >=sci-biology/emboss-5.0.0 )" -DEPEND="${RDEPEND}" - -RESTRICT="binchecks strip" - -src_compile() { - if use emboss; then - echo; einfo "Indexing Rebase for usage with EMBOSS." - mkdir REBASE || die - EMBOSS_DATA="." rebaseextract -auto -infile withrefm.${MY_PV} \ - -protofile proto.${MY_PV} -equivalences \ - || die "Indexing Rebase failed." - echo - fi -} - -src_install() { - if ! use minimal; then - insinto /usr/share/${PN} - doins withrefm.${MY_PV} proto.${MY_PV} - fi - newdoc REBASE.DOC README - if use emboss; then - insinto /usr/share/EMBOSS/data/REBASE - doins REBASE/embossre.{enz,ref,sup} - insinto /usr/share/EMBOSS/data - doins REBASE/embossre.equ - fi -} diff --git a/sci-biology/rebase/rebase-1803.ebuild b/sci-biology/rebase/rebase-1803.ebuild deleted file mode 100644 index e9944bde30fb..000000000000 --- a/sci-biology/rebase/rebase-1803.ebuild +++ /dev/null @@ -1,45 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -MY_PV=${PV#1} - -DESCRIPTION="A restriction enzyme database" -HOMEPAGE="http://rebase.neb.com" -SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz" - -SLOT="0" -LICENSE="public-domain" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris ~x86-solaris" -IUSE="emboss minimal" - -RDEPEND="emboss? ( >=sci-biology/emboss-5.0.0 )" -DEPEND="${RDEPEND}" - -RESTRICT="binchecks strip" - -src_compile() { - if use emboss; then - echo; einfo "Indexing Rebase for usage with EMBOSS." - mkdir REBASE || die - EMBOSS_DATA="." rebaseextract -auto -infile withrefm.${MY_PV} \ - -protofile proto.${MY_PV} -equivalences \ - || die "Indexing Rebase failed." - echo - fi -} - -src_install() { - if ! use minimal; then - insinto /usr/share/${PN} - doins withrefm.${MY_PV} proto.${MY_PV} - fi - newdoc REBASE.DOC README - if use emboss; then - insinto /usr/share/EMBOSS/data/REBASE - doins REBASE/embossre.{enz,ref,sup} - insinto /usr/share/EMBOSS/data - doins REBASE/embossre.equ - fi -} diff --git a/sci-biology/rebase/rebase-1806.ebuild b/sci-biology/rebase/rebase-1806.ebuild deleted file mode 100644 index e9944bde30fb..000000000000 --- a/sci-biology/rebase/rebase-1806.ebuild +++ /dev/null @@ -1,45 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -MY_PV=${PV#1} - -DESCRIPTION="A restriction enzyme database" -HOMEPAGE="http://rebase.neb.com" -SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz" - -SLOT="0" -LICENSE="public-domain" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris ~x86-solaris" -IUSE="emboss minimal" - -RDEPEND="emboss? ( >=sci-biology/emboss-5.0.0 )" -DEPEND="${RDEPEND}" - -RESTRICT="binchecks strip" - -src_compile() { - if use emboss; then - echo; einfo "Indexing Rebase for usage with EMBOSS." - mkdir REBASE || die - EMBOSS_DATA="." rebaseextract -auto -infile withrefm.${MY_PV} \ - -protofile proto.${MY_PV} -equivalences \ - || die "Indexing Rebase failed." - echo - fi -} - -src_install() { - if ! use minimal; then - insinto /usr/share/${PN} - doins withrefm.${MY_PV} proto.${MY_PV} - fi - newdoc REBASE.DOC README - if use emboss; then - insinto /usr/share/EMBOSS/data/REBASE - doins REBASE/embossre.{enz,ref,sup} - insinto /usr/share/EMBOSS/data - doins REBASE/embossre.equ - fi -} diff --git a/sci-biology/rebase/rebase-1810.ebuild b/sci-biology/rebase/rebase-1810.ebuild deleted file mode 100644 index e9944bde30fb..000000000000 --- a/sci-biology/rebase/rebase-1810.ebuild +++ /dev/null @@ -1,45 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -MY_PV=${PV#1} - -DESCRIPTION="A restriction enzyme database" -HOMEPAGE="http://rebase.neb.com" -SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz" - -SLOT="0" -LICENSE="public-domain" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris ~x86-solaris" -IUSE="emboss minimal" - -RDEPEND="emboss? ( >=sci-biology/emboss-5.0.0 )" -DEPEND="${RDEPEND}" - -RESTRICT="binchecks strip" - -src_compile() { - if use emboss; then - echo; einfo "Indexing Rebase for usage with EMBOSS." - mkdir REBASE || die - EMBOSS_DATA="." rebaseextract -auto -infile withrefm.${MY_PV} \ - -protofile proto.${MY_PV} -equivalences \ - || die "Indexing Rebase failed." - echo - fi -} - -src_install() { - if ! use minimal; then - insinto /usr/share/${PN} - doins withrefm.${MY_PV} proto.${MY_PV} - fi - newdoc REBASE.DOC README - if use emboss; then - insinto /usr/share/EMBOSS/data/REBASE - doins REBASE/embossre.{enz,ref,sup} - insinto /usr/share/EMBOSS/data - doins REBASE/embossre.equ - fi -} diff --git a/sci-biology/rebase/rebase-1701.ebuild b/sci-biology/rebase/rebase-1901-r2.ebuild index a680fa1783bb..a80aee6a3126 100644 --- a/sci-biology/rebase/rebase-1701.ebuild +++ b/sci-biology/rebase/rebase-1901-r2.ebuild @@ -1,32 +1,32 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 -MY_PV=${PV#1} +MY_PV="${PV#1}" DESCRIPTION="A restriction enzyme database" HOMEPAGE="http://rebase.neb.com" SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz" -SLOT="0" LICENSE="public-domain" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos" IUSE="emboss minimal" - -RDEPEND="emboss? ( >=sci-biology/emboss-5.0.0 )" -DEPEND="${RDEPEND}" - RESTRICT="binchecks strip" +BDEPEND="emboss? ( sci-biology/emboss )" +RDEPEND="${BDEPEND}" + src_compile() { if use emboss; then - echo; einfo "Indexing Rebase for usage with EMBOSS." + einfo + einfo "Indexing Rebase for usage with EMBOSS" mkdir REBASE || die EMBOSS_DATA="." rebaseextract -auto -infile withrefm.${MY_PV} \ -protofile proto.${MY_PV} -equivalences \ - || die "Indexing Rebase failed." - echo + || die "Indexing Rebase failed" + einfo fi } diff --git a/sci-biology/rebase/rebase-1901.ebuild b/sci-biology/rebase/rebase-1901.ebuild deleted file mode 100644 index f85a4b1698bb..000000000000 --- a/sci-biology/rebase/rebase-1901.ebuild +++ /dev/null @@ -1,45 +0,0 @@ -# Copyright 1999-2018 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -MY_PV=${PV#1} - -DESCRIPTION="A restriction enzyme database" -HOMEPAGE="http://rebase.neb.com" -SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz" - -SLOT="0" -LICENSE="public-domain" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris ~x86-solaris" -IUSE="emboss minimal" - -RDEPEND="emboss? ( >=sci-biology/emboss-5.0.0 )" -DEPEND="${RDEPEND}" - -RESTRICT="binchecks strip" - -src_compile() { - if use emboss; then - echo; einfo "Indexing Rebase for usage with EMBOSS." - mkdir REBASE || die - EMBOSS_DATA="." rebaseextract -auto -infile withrefm.${MY_PV} \ - -protofile proto.${MY_PV} -equivalences \ - || die "Indexing Rebase failed." - echo - fi -} - -src_install() { - if ! use minimal; then - insinto /usr/share/${PN} - doins withrefm.${MY_PV} proto.${MY_PV} - fi - newdoc REBASE.DOC README - if use emboss; then - insinto /usr/share/EMBOSS/data/REBASE - doins REBASE/embossre.{enz,ref,sup} - insinto /usr/share/EMBOSS/data - doins REBASE/embossre.equ - fi -} diff --git a/sci-biology/recon/files/recon-1.08-Wimplicit-function-declaration.patch b/sci-biology/recon/files/recon-1.08-Wimplicit-function-declaration.patch new file mode 100644 index 000000000000..9eba16e4a410 --- /dev/null +++ b/sci-biology/recon/files/recon-1.08-Wimplicit-function-declaration.patch @@ -0,0 +1,20 @@ +--- a/src/bolts.h ++++ b/src/bolts.h +@@ -3,6 +3,7 @@ + #include <stdio.h> + #include <math.h> + #include <stdlib.h> ++#include <stdint.h> + + + #define NAME_LEN 50 +--- a/src/seqlist.h ++++ b/src/seqlist.h +@@ -1,6 +1,7 @@ + + #include "bolts.h" + #include "string.h" ++#include <ctype.h> + + #ifndef _seqlist_h + #define _seqlist_h diff --git a/sci-biology/recon/metadata.xml b/sci-biology/recon/metadata.xml index 959160fe46b1..ccdff086e20b 100644 --- a/sci-biology/recon/metadata.xml +++ b/sci-biology/recon/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/recon/recon-1.08.ebuild b/sci-biology/recon/recon-1.08-r1.ebuild index a96403c812be..dd79dd43c496 100644 --- a/sci-biology/recon/recon-1.08.ebuild +++ b/sci-biology/recon/recon-1.08-r1.ebuild @@ -1,31 +1,31 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit toolchain-funcs DESCRIPTION="Automated de novo identification of repeat families from genomic sequences" HOMEPAGE="http://www.repeatmasker.org/RepeatModeler.html" SRC_URI="http://www.repeatmasker.org/${P^^}.tar.gz" +S="${WORKDIR}/${P^^}" LICENSE="GPL-2" SLOT="0" -IUSE="examples" KEYWORDS="~amd64 ~x86" +IUSE="examples" RDEPEND="dev-lang/perl" -S=${WORKDIR}/${P^^} - PATCHES=( "${FILESDIR}"/${PN}-1.08-buffer-overflow.patch "${FILESDIR}"/${PN}-1.08-perl-shebangs.patch + "${FILESDIR}"/${PN}-1.08-Wimplicit-function-declaration.patch ) src_prepare() { default - sed -i "s|$path = \"\";|$path = \"${EPREFIX}/usr/libexec/${PN}\";|" scripts/recon.pl || die + sed -i "s|$path = \"\";|$path = \"${EPREFIX}/usr/libexec/recon\";|" scripts/recon.pl || die } src_compile() { @@ -35,13 +35,13 @@ src_compile() { src_install() { dobin scripts/* - exeinto /usr/libexec/${PN} + exeinto /usr/libexec/recon doexe src/{edgeredef,eledef,eleredef,famdef,imagespread} newdoc {00,}README if use examples; then - insinto /usr/share/${PN} + insinto /usr/share/recon doins -r Demos fi } diff --git a/sci-biology/repeatmasker-libraries/Manifest b/sci-biology/repeatmasker-libraries/Manifest deleted file mode 100644 index bfd485525bb4..000000000000 --- a/sci-biology/repeatmasker-libraries/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST repeatmaskerlibraries-20120418.tar.gz 28059668 BLAKE2B 0683305f0d3045ff1bcb9f1c952d3c12e92a3003f79ba18a16334805049a64e0b307fac2cf7fad236c9b0cab80e3317ebb1d93bf6487bafd9d45de2455565879 SHA512 254d47faeee72ee62e6854ebc389578691d66e99d9d5e2a0c2462bf752ac5b4d2171c9e6b45d4f87f548a96b62753bb9c37c2d2c00e06544e91dd09fe2bbfe32 diff --git a/sci-biology/repeatmasker-libraries/metadata.xml b/sci-biology/repeatmasker-libraries/metadata.xml deleted file mode 100644 index 959160fe46b1..000000000000 --- a/sci-biology/repeatmasker-libraries/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20120418.ebuild b/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20120418.ebuild deleted file mode 100644 index aefecb784ba2..000000000000 --- a/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20120418.ebuild +++ /dev/null @@ -1,34 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -DESCRIPTION="A special version of RepBase used by RepeatMasker" -HOMEPAGE="http://repeatmasker.org/" -SRC_URI="repeatmaskerlibraries-${PV}.tar.gz" - -LICENSE="all-rights-reserved" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND="" -RDEPEND="" - -S="${WORKDIR}/Libraries" - -RESTRICT="fetch" - -pkg_nofetch() { - einfo "Please register and download repeatmaskerlibraries-${PV}.tar.gz" - einfo 'at http://www.girinst.org/' - einfo '(select the "Repbase Update - RepeatMasker edition" link)' - einfo 'and place it into your DISTDIR directory.' -} - -src_install() { - insinto /usr/share/repeatmasker/Libraries - doins "${S}"/RepeatMaskerLib.embl - dodoc README - dohtml README.html -} diff --git a/sci-biology/repeatmasker/Manifest b/sci-biology/repeatmasker/Manifest deleted file mode 100644 index afba36fe4e6d..000000000000 --- a/sci-biology/repeatmasker/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST RepeatMasker-open-4-0-1.tar.gz 84077910 BLAKE2B 45598d46ef1c0e1233ed5ce10c2d29e4b2ef1a6843846970df2d0f997a22657eeed7dd7c851418d6f751468b22327b47f3b72105fdcfa56bbebe97395946ab37 SHA512 6b710a02b2964bca6acb25cc918bd56f7caba7b80b3b683972f0584180bf0fd3704f657d7ee341187a4ac86d9883e62eb4f09da237fa8ef1b481137d1a89963e diff --git a/sci-biology/repeatmasker/metadata.xml b/sci-biology/repeatmasker/metadata.xml deleted file mode 100644 index 959160fe46b1..000000000000 --- a/sci-biology/repeatmasker/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.1.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.1.ebuild deleted file mode 100644 index bf6097df1f68..000000000000 --- a/sci-biology/repeatmasker/repeatmasker-4.0.1.ebuild +++ /dev/null @@ -1,58 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -MY_PV=${PV//\./-} - -DESCRIPTION="Screen DNA sequences for interspersed repeats and low complexity DNA" -HOMEPAGE="http://repeatmasker.org/" -SRC_URI="http://www.repeatmasker.org/RepeatMasker-open-${MY_PV}.tar.gz" - -LICENSE="OSL-2.1" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND="" -RDEPEND=" - sci-biology/rmblast - sci-biology/trf - sci-biology/repeatmasker-libraries" - -S="${WORKDIR}/RepeatMasker" - -src_configure() { - sed -i -e 's/system( "clear" );//' \ - -e 's|> \($rmLocation/Libraries/RepeatMasker.lib\)|> '${D}'/\1|' "${S}/configure" || die - echo " -env -/usr/share/${PN} -/usr/bin -2 -/opt/rmblast/bin -Y -5" | "${S}/configure" || die "configure failed" - sed -i -e 's|use lib $FindBin::RealBin;|use lib "/usr/share/'${PN}'/lib";|' \ - -e 's|".*\(taxonomy.dat\)"|"/usr/share/'${PN}'/\1"|' \ - -e '/$REPEATMASKER_DIR/ s|$FindBin::RealBin|/usr/share/'${PN}'|' \ - "${S}"/{DateRepeats,ProcessRepeats,RepeatMasker,DupMasker,RepeatProteinMask,RepeatMaskerConfig.pm,Taxonomy.pm} || die -} - -src_install() { - exeinto /usr/share/${PN} - for i in DateRepeats ProcessRepeats RepeatMasker DupMasker RepeatProteinMask; do - doexe $i - dosym /usr/share/${PN}/$i /usr/bin/$i - done - - dodir /usr/share/${PN}/lib - insinto /usr/share/${PN}/lib - doins "${S}"/*.pm - - insinto /usr/share/${PN} - doins -r util Matrices Libraries taxonomy.dat *.help - keepdir /usr/share/${PN}/Libraries - - dodoc README INSTALL *.help -} diff --git a/sci-biology/rmblast/Manifest b/sci-biology/rmblast/Manifest deleted file mode 100644 index 383d30fdb026..000000000000 --- a/sci-biology/rmblast/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST rmblast-1.2-gcc47.patch.bz2 7803 BLAKE2B cd3bb1aa2b6eb9e188f28589d42ce91f027866d91013f2a6123ee61e7ce28f980b858e775bc15313cf1573f0bc827f9e663d46c1bd0d2fe218745cfbbc3781a1 SHA512 4cd72dd5c777ad866b9cf674384872de5424404b524ac536e58ab412b98b6601aa5f609d05ea2329b77f16e7aca215bbc6eb3531652e5fe81e48cf997b56d13b -DIST rmblast-1.2-ncbi-blast-2.2.23+-src.tar.gz 10744076 BLAKE2B 6539ec8fcd345bcc1c3ecede6acec233cdc343c3df18748e195dc525f4a65fefeee8398471a26dc671bfed8612e010c26b7a8a66a3c7198f142c2e068ff72751 SHA512 e7c2ebd114aee045ea3f3f462cf2658440e13a2d1eb777648386e1c5eeda9f8083af383c019f9b5802d935d6eb2367eef20822afc45233ddb44a426b4dd7ddb6 diff --git a/sci-biology/rmblast/metadata.xml b/sci-biology/rmblast/metadata.xml deleted file mode 100644 index 959160fe46b1..000000000000 --- a/sci-biology/rmblast/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/rmblast/rmblast-1.2-r1.ebuild b/sci-biology/rmblast/rmblast-1.2-r1.ebuild deleted file mode 100644 index 72c740fd30e3..000000000000 --- a/sci-biology/rmblast/rmblast-1.2-r1.ebuild +++ /dev/null @@ -1,47 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils flag-o-matic toolchain-funcs - -MY_NCBI_BLAST_V=2.2.23+ - -DESCRIPTION="RepeatMasker compatible version of NCBI BLAST+" -HOMEPAGE="http://www.repeatmasker.org/RMBlast.html" -SRC_URI="http://www.repeatmasker.org/rmblast-${PV}-ncbi-blast-${MY_NCBI_BLAST_V}-src.tar.gz - https://dev.gentoo.org/~mgorny/dist/${P}-gcc47.patch.bz2" - -LICENSE="OSL-2.1" -SLOT="0" -IUSE="" -KEYWORDS="~amd64 ~x86" - -RDEPEND="dev-libs/boost" -DEPEND="${RDEPEND} - app-arch/cpio" - -S="${WORKDIR}/${P}-ncbi-blast-${MY_NCBI_BLAST_V}-src/c++" - -src_prepare() { - filter-ldflags -Wl,--as-needed - sed \ - -e 's/-print-file-name=libstdc++.a//' \ - -e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \ - -e "/DEF_FAST_FLAGS=/s:=\".*\":=\"${CFLAGS}\":g" \ - -e 's/2.95\* | 2.96\* | 3\.\* | 4\.\* )/2.95\* | 2.96\* | \[3-9\]\.\* )/g' \ - -i src/build-system/configure || die - epatch "${WORKDIR}"/${P}-gcc47.patch -} - -src_configure() { - tc-export CXX CC - - "${S}"/configure --without-debug \ - --with-mt \ - --without-static \ - --with-dll \ - --prefix="${ED}"/opt/${PN} \ - --with-boost="${EPREFIX}/usr/include/boost" \ - || die -} diff --git a/sci-biology/rnaview/metadata.xml b/sci-biology/rnaview/metadata.xml index cfffc1223753..396eccdc212f 100644 --- a/sci-biology/rnaview/metadata.xml +++ b/sci-biology/rnaview/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/rnaview/rnaview-20040713-r4.ebuild b/sci-biology/rnaview/rnaview-20040713-r5.ebuild index 729095be063c..c0c4289ba24b 100644 --- a/sci-biology/rnaview/rnaview-20040713-r4.ebuild +++ b/sci-biology/rnaview/rnaview-20040713-r5.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit toolchain-funcs @@ -12,23 +12,20 @@ SRC_URI="mirror://gentoo/${P}.tar.bz2" LICENSE="public-domain" SLOT="0" KEYWORDS="~amd64 ~x86" -IUSE="" PATCHES=( "${FILESDIR}"/${P}-makefile.patch "${FILESDIR}"/${P}-implicit.patch ) -src_prepare() { - default +src_configure() { tc-export CC } src_install() { default - cat > 22rnaview <<- EOF || die - RNAVIEW="${EPREFIX}/usr/share/${PN}" + newenvd - 22rnaview <<- EOF + RNAVIEW="${EPREFIX}/usr/share/rnaview" EOF - doenvd 22rnaview } diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest index 7ce21379a95d..09cffe1bb5b0 100644 --- a/sci-biology/samtools/Manifest +++ b/sci-biology/samtools/Manifest @@ -1,3 +1,2 @@ -DIST samtools-0.1.20.tar.gz 566387 BLAKE2B a62d74c408877754af50f5e5fea0e2289ec1e0c9f25013ed0d039bfe8ef61108600d917f8c9d356e98aca632795b4eb0f01ea1b54526a652577fb74a38a433c2 SHA512 15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5 -DIST samtools-1.5.tar.bz2 4190142 BLAKE2B 1d3478f9adf76925a3721e145795ce4a4caf580244f5ba5bc1ddd14d1b13c723c6fddc24cdadf0a23ca5dcd7007a9985f54e7532cb15d5d9433b1164f5a22023 SHA512 ff3e39ba867ecbd88f3363b038508c1557e349ea4223483f8f4ecb17ff8864fb53cd193bc2059a147e30f07395bbf53c8518d0f70219e454375c8bffe56e3059 -DIST samtools-1.9.tar.bz2 4440405 BLAKE2B 409265fed9ff3fcd09096c968224499750da69324eeded754e367430c0f53f9246ccc9a31e166f13ea7bc767fefab499bcfda4d008d5ac82971984c67b533aff SHA512 6c8207754615ae8dad84b278f93e7d57eb40b818efb80f6aff6aba22fde5772247724e86596e765791e3175ffbb683393dd3ddfe7681c73eef4eb4f2342bf68f +DIST samtools-1.17.tar.bz2 8605080 BLAKE2B 09cb0bff7bf7113a77f57fdb879765b28b65461a574e4a1ab20ae2327af46e5616e04f03eb68706d42ba0643e887d7921974a3d78c5f87d296a4c3b691215260 SHA512 107a6df858c6bd2556ba4e86cc1922c3184df095f347039fa94bfd24e5ee21e1a4a9fba5a7cce248a06ad47f99978d9aae570efee7e30e165f33ea848a2cd3c3 +DIST samtools-1.19.2.tar.bz2 9150483 BLAKE2B fb845b2ccd61f1731ef4cdc180f4b9a4ac75e8c73c1ceaa9409b99e8052ca66b88c73fc71fd1067942aa24964f6df8dcb2d93631e5757e0cc200d7a3b9fad461 SHA512 c08d729fed21112855e0acc9cf7f29c7670d38a02ad6b0f2e9b9ef15a18f07e3e194cc4f6913481c98cd3e85dd4dc975dac96155b892da58bbe8ea3679a5270f diff --git a/sci-biology/samtools/files/samtools-0.1.20-buildsystem.patch b/sci-biology/samtools/files/samtools-0.1.20-buildsystem.patch deleted file mode 100644 index eb9f6934a96f..000000000000 --- a/sci-biology/samtools/files/samtools-0.1.20-buildsystem.patch +++ /dev/null @@ -1,206 +0,0 @@ ---- samtools-0.1.20/bcftools/Makefile -+++ samtools-0.1.20/bcftools/Makefile -@@ -1,6 +1,6 @@ --CC= gcc --CFLAGS= -g -Wall -O2 #-m64 #-arch ppc --DFLAGS= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -+CC?= gcc -+CFLAGS?= -g -Wall -O2 #-m64 #-arch ppc -+CPPFLAGS+= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE - LOBJS= bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o - OMISC= .. - AOBJS= call1.o main.o $(OMISC)/kstring.o $(OMISC)/bgzf.o $(OMISC)/knetfile.o $(OMISC)/bedidx.o -@@ -11,14 +11,14 @@ - .SUFFIXES:.c .o - - .c.o: -- $(CC) -c $(CFLAGS) $(DFLAGS) -I.. $(INCLUDES) $< -o $@ -+ $(CC) -c $(CFLAGS) $(CPPFLAGS) -I.. $(INCLUDES) $< -o $@ - - all-recur lib-recur clean-recur cleanlocal-recur install-recur: - @target=`echo $@ | sed s/-recur//`; \ - wdir=`pwd`; \ - list='$(SUBDIRS)'; for subdir in $$list; do \ - cd $$subdir; \ -- $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \ -+ $(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \ - INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \ - cd $$wdir; \ - done; -@@ -31,7 +31,7 @@ - $(AR) -csru $@ $(LOBJS) - - bcftools:lib $(AOBJS) -- $(CC) $(CFLAGS) -o $@ $(AOBJS) -L. $(LIBPATH) -lbcf -lm -lz -lpthread -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) -L. $(LIBPATH) -lbcf -lm -lz -lpthread - - bcf.o:bcf.h - vcf.o:bcf.h ---- samtools-0.1.20/Makefile -+++ samtools-0.1.20/Makefile -@@ -4,10 +4,10 @@ - # make git-stamp - VERSION= - --CC= gcc --CFLAGS= -g -Wall $(VERSION) -O2 --#LDFLAGS= -Wl,-rpath,\$$ORIGIN/../lib --DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -+CC?= gcc -+CFLAGS?= -g -Wall $(VERSION) -O2 -+#LDFLAGS+= -Wl,-rpath,\$$ORIGIN/../lib -+CPPFLAGS+= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 - KNETFILE_O= knetfile.o - LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \ - bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o \ -@@ -28,14 +28,14 @@ - .PHONY: all lib - - .c.o: -- $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@ -+ $(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@ - - all-recur lib-recur clean-recur cleanlocal-recur install-recur: - @target=`echo $@ | sed s/-recur//`; \ - wdir=`pwd`; \ - list='$(SUBDIRS)'; for subdir in $$list; do \ - cd $$subdir; \ -- $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \ -+ $(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \ - INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \ - cd $$wdir; \ - done; -@@ -48,22 +48,22 @@ - .PHONY:all lib clean cleanlocal - .PHONY:all-recur lib-recur clean-recur cleanlocal-recur install-recur - --lib:libbam.a -+lib:libbam-0.1-legacy.a - --libbam.a:$(LOBJS) -+libbam-0.1-legacy.a:$(LOBJS) - $(AR) -csru $@ $(LOBJS) - - samtools:lib-recur $(AOBJS) -- $(CC) $(CFLAGS) -o $@ $(AOBJS) $(LDFLAGS) libbam.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) -L. -lbam-0.1-legacy -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread - - razip:razip.o razf.o $(KNETFILE_O) -- $(CC) $(CFLAGS) -o $@ $^ -lz -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ -lz - - bgzip:bgzip.o bgzf.o $(KNETFILE_O) -- $(CC) $(CFLAGS) -o $@ $^ -lz -lpthread -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ -lz -lpthread - - bgzf.o:bgzf.c bgzf.h -- $(CC) -c $(CFLAGS) $(DFLAGS) -DBGZF_CACHE $(INCLUDES) bgzf.c -o $@ -+ $(CC) -c $(CFLAGS) $(CPPFLAGS) -DBGZF_CACHE $(INCLUDES) bgzf.c -o $@ - - razip.o:razf.h - bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h -@@ -90,17 +90,17 @@ - faidx_main.o:faidx.h razf.h - - --libbam.1.dylib-local:$(LOBJS) -- libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz -+libbam-0.1-legacy.1.dylib-local:$(LOBJS) -+ libtool -dynamic $(LOBJS) -o libbam-0.1-legacy.1.dylib -lc -lz - --libbam.so.1-local:$(LOBJS) -- $(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz -+libbam-0.1-legacy.so.1-local:$(LOBJS) -+ $(CC) $(LDFLAGS) -shared -Wl,-soname,libbam-0.1-legacy.so -o libbam-0.1-legacy.so.1 $(LOBJS) -lc -lz -lm -lpthread - - dylib: - @$(MAKE) cleanlocal; \ - case `uname` in \ -- Linux) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.so.1-local;; \ -- Darwin) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.1.dylib-local;; \ -+ Linux) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam-0.1-legacy.so.1-local;; \ -+ Darwin) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam-0.1-legacy.1.dylib-local;; \ - *) echo 'Unknown OS';; \ - esac - ---- samtools-0.1.20/misc/Makefile -+++ samtools-0.1.20/misc/Makefile -@@ -1,8 +1,8 @@ --CC= gcc --CXX= g++ --CFLAGS= -g -Wall -O2 #-m64 #-arch ppc --CXXFLAGS= $(CFLAGS) --DFLAGS= -D_FILE_OFFSET_BITS=64 -+CC?= gcc -+CXX?= g++ -+CFLAGS?= -g -Wall -O2 #-m64 #-arch ppc -+CXXFLAGS?= $(CFLAGS) -+CPPFLAGS+= -D_FILE_OFFSET_BITS=64 - OBJS= - PROG= md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck - INCLUDES= -I.. -@@ -11,7 +11,7 @@ - .SUFFIXES:.c .o - - .c.o: -- $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@ -+ $(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@ - - all:$(PROG) - -@@ -20,7 +20,7 @@ - wdir=`pwd`; \ - list='$(SUBDIRS)'; for subdir in $$list; do \ - cd $$subdir; \ -- $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \ -+ $(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \ - INCLUDES="$(INCLUDES)" $$target || exit 1; \ - cd $$wdir; \ - done; -@@ -28,31 +28,31 @@ - lib: - - bamcheck:bamcheck.o -- $(CC) $(CFLAGS) -o $@ bamcheck.o -L.. -lm -lbam -lpthread -lz -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ bamcheck.o -L.. -lm -lbam-0.1-legacy -lpthread -lz - - bamcheck.o:bamcheck.c ../faidx.h ../khash.h ../sam.h ../razf.h - $(CC) $(CFLAGS) -c -I.. -o $@ bamcheck.c - - ace2sam:ace2sam.o -- $(CC) $(CFLAGS) -o $@ ace2sam.o -lz -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ ace2sam.o -lz - - wgsim:wgsim.o -- $(CC) $(CFLAGS) -o $@ wgsim.o -lm -lz -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ wgsim.o -lm -lz - - md5fa:md5.o md5fa.o md5.h ../kseq.h -- $(CC) $(CFLAGS) -o $@ md5.o md5fa.o -lz -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ md5.o md5fa.o -lz - - md5sum-lite:md5sum-lite.o -- $(CC) $(CFLAGS) -o $@ md5sum-lite.o -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ md5sum-lite.o - - md5sum-lite.o:md5.c md5.h - $(CC) -c $(CFLAGS) -DMD5SUM_MAIN -o $@ md5.c - - maq2sam-short:maq2sam.c -- $(CC) $(CFLAGS) -o $@ maq2sam.c -lz -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ maq2sam.c -lz - - maq2sam-long:maq2sam.c -- $(CC) $(CFLAGS) -DMAQ_LONGREADS -o $@ maq2sam.c -lz -+ $(CC) $(CFLAGS) -DMAQ_LONGREADS $(LDFLAGS) -o $@ maq2sam.c -lz - - md5fa.o:md5.h md5fa.c - $(CC) $(CFLAGS) -c -I.. -o $@ md5fa.c ---- samtools-0.1.20/misc/varfilter.py -+++ samtools-0.1.20/misc/varfilter.py -@@ -1,4 +1,4 @@ --#!/software/bin/python -+#!/usr/bin/env python - - # Author: lh3, converted to python and modified to add -C option by Aylwyn Scally - # diff --git a/sci-biology/samtools/files/samtools-1.5-buildsystem.patch b/sci-biology/samtools/files/samtools-1.5-buildsystem.patch deleted file mode 100644 index c466e66a9d17..000000000000 --- a/sci-biology/samtools/files/samtools-1.5-buildsystem.patch +++ /dev/null @@ -1,413 +0,0 @@ ---- a/config.mk.in -+++ b/config.mk.in -@@ -28,27 +28,26 @@ - # in the Makefile to reflect your configuration choices. If you don't run - # configure, the main Makefile contains suitable conservative defaults. - --prefix = @prefix@ --exec_prefix = @exec_prefix@ --bindir = @bindir@ --datarootdir = @datarootdir@ --mandir = @mandir@ -+prefix = @prefix@ -+exec_prefix = @exec_prefix@ -+bindir = @bindir@ -+libdir = @libdir@ -+datarootdir = @datarootdir@ -+mandir = @mandir@ -+man1dir = $(mandir)/man1 - - CC = @CC@ -+AR = @AR@ - CPPFLAGS = @CPPFLAGS@ - CFLAGS = @CFLAGS@ - LDFLAGS = @LDFLAGS@ - LIBS = @LIBS@ - --@Hsource@HTSDIR = @HTSDIR@ --@Hsource@include $(HTSDIR)/htslib.mk --@Hsource@include $(HTSDIR)/htslib_static.mk --@Hsource@HTSLIB = $(HTSDIR)/libhts.a --@Hsource@HTSLIB_LIB = $(HTSLIB) $(HTSLIB_static_LIBS) --@Hsource@HTSLIB_LDFLAGS = $(HTSLIB_static_LDFLAGS) --@Hsource@BGZIP = $(HTSDIR)/bgzip --HTSLIB_CPPFLAGS = @HTSLIB_CPPFLAGS@ --@Hinstall@HTSLIB_LDFLAGS = @HTSLIB_LDFLAGS@ --@Hinstall@HTSLIB_LIB = -lhts -+HTSLIB_CFLAGS = @HTSLIB_CFLAGS@ -+HTSLIB_LIBS = @HTSLIB_LIBS@ - --CURSES_LIB = @CURSES_LIB@ -+NCURSES_CFLAGS = @NCURSES_CFLAGS@ -+NCURSES_LIBS = @NCURSES_LIBS@ -+ -+ZLIB_CFLAGS = @ZLIB_CFLAGS@ -+ZLIB_LIBS = @ZLIB_LIBS@ ---- a/configure.ac -+++ b/configure.ac -@@ -29,9 +29,6 @@ - AC_CONFIG_SRCDIR([bamtk.c]) - AC_CONFIG_HEADERS([config.h]) - --m4_include([m4/ax_with_curses.m4]) --m4_include([m4/ax_with_htslib.m4]) -- - dnl Copyright notice to be copied into the generated configure script - AC_COPYRIGHT([Portions copyright (C) 2015 Genome Research Ltd. - -@@ -39,73 +36,27 @@ - redistribute it. There is NO WARRANTY, to the extent permitted by law.]) - - AC_PROG_CC -+AM_PROG_AR - - AC_SYS_LARGEFILE - --AX_WITH_HTSLIB --if test "$ax_cv_htslib" != yes; then -- AC_MSG_ERROR([HTSlib development files not found -- --Samtools uses HTSlib to parse bioinformatics file formats etc. Building it --requires an unpacked HTSlib source tree (which will be built in conjunction --with samtools) or a previously-installed HTSlib. In either case you may --need to configure --with-htslib=DIR to locate the appropriate HTSlib. -- --FAILED. You must supply an HTSlib in order to build samtools successfully.]) --fi -- --if test "$ax_cv_htslib_which" = source; then -- Hsource= -- Hinstall='#' --else -- Hsource='#' -- Hinstall= --fi --AC_SUBST([Hsource]) --AC_SUBST([Hinstall]) -+dnl htslib -+PKG_CHECK_MODULES([HTSLIB], [htslib]) - -+dnl ncurses - AC_ARG_WITH([curses], - [AS_HELP_STRING([--without-curses], - [omit curses support, so no curses library needed])]) - --if test "$with_curses" != no; then -- AX_WITH_CURSES -- if test "$ax_cv_curses" != yes; then -- AC_MSG_ERROR([curses development files not found -- --The 'samtools tview' command uses the curses text user interface library. --Building samtools with tview requires curses/ncurses/etc development files --to be installed on the build machine; you may need to ensure a package such --as libncurses5-dev (on Debian or Ubuntu Linux) or ncurses-devel (on RPM-based --Linux distributions) is installed. -- --FAILED. Either configure --without-curses or resolve this error to build --samtools successfully.]) -- fi --else -- CURSES_LIB= -- CURSES_CPPFLAGS= -- AC_SUBST([CURSES_LIB]) -- AC_SUBST([CURSES_CPPFLAGS]) --fi -- --save_LIBS=$LIBS --zlib_devel=ok --dnl Set a trivial non-empty INCLUDES to avoid excess default includes tests --AC_CHECK_HEADER([zlib.h], [], [zlib_devel=missing], [;]) --AC_CHECK_LIB(z, inflate, [], [zlib_devel=missing]) --LIBS=$save_LIBS -- --if test $zlib_devel != ok; then -- AC_MSG_ERROR([zlib development files not found -- --Samtools uses compression routines from the zlib library <http://zlib.net>. --Building samtools requires zlib development files to be installed on the build --machine; you may need to ensure a package such as zlib1g-dev (on Debian or --Ubuntu Linux) or zlib-devel (on RPM-based Linux distributions) is installed. -+AS_IF([test "x$with_curses" != "xno"], [ -+ PKG_CHECK_MODULES([NCURSES], [ncurses]) -+ -+ AC_DEFINE([HAVE_CURSES], [1]) -+ AC_DEFINE([HAVE_NCURSES_H], [1]) -+]) - --FAILED. This error must be resolved in order to build samtools successfully.]) --fi -+dnl zlib -+PKG_CHECK_MODULES([ZLIB], [zlib]) - - AC_CONFIG_FILES([config.mk]) - AC_OUTPUT ---- a/Makefile -+++ b/Makefile -@@ -21,14 +21,6 @@ - # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER - # DEALINGS IN THE SOFTWARE. - --CC = gcc --AR = ar --CPPFLAGS = --#CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 --CFLAGS = -g -Wall -O2 --LDFLAGS = --LIBS = -- - LOBJS= bam_aux.o bam.o bam_import.o sam.o \ - sam_header.o bam_plbuf.o - AOBJS= bam_index.o bam_plcmd.o sam_view.o \ -@@ -40,13 +32,6 @@ - bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o \ - bam_quickcheck.o bam_addrprg.o - --prefix = /usr/local --exec_prefix = $(prefix) --bindir = $(exec_prefix)/bin --datarootdir = $(prefix)/share --mandir = $(datarootdir)/man --man1dir = $(mandir)/man1 -- - # Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS) - misc_bindir = $(bindir) - -@@ -85,15 +70,14 @@ - - all: $(PROGRAMS) $(MISC_PROGRAMS) $(TEST_PROGRAMS) - --ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) --ALL_LDFLAGS = $(HTSLIB_LDFLAGS) $(LDFLAGS) --ALL_LIBS = -lz $(LIBS) -+ALL_CPPFLAGS = -I. $(HTSLIB_CFLAGS) $(CPPFLAGS) -+ALL_LIBS = $(ZLIB_LIBS) $(LIBS) - - # Usually config.mk and config.h are generated by running configure - # or config.status, but if those aren't used create defaults here. - - config.mk: -- @sed -e '/^prefix/,/^LIBS/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#htslib-1.5#g;s/@HTSLIB_CPPFLAGS@/-I$$(HTSDIR)/g;s/@CURSES_LIB@/-lcurses/g' config.mk.in > $@ -+ @sed -e '/^prefix/,/^LIBS/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#htslib-1.5#g;s/@HTSLIB_CFLAGS@/-I$$(HTSDIR)/g;s/@NCURSES_LIBS@/-lcurses/g' config.mk.in > $@ - - config.h: - echo '/* Basic config.h generated by Makefile */' > $@ -@@ -133,17 +117,22 @@ - .c.o: - $(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ $< - -+$(LOBJS): -+ $(CC) $(CFLAGS) $(ALL_CPPFLAGS) -fPIC -c -o $@ $< -+ - - LIBST_OBJS = sam_opts.o sam_utils.o - - --lib:libbam.a -+lib: libbam.so.1.0 - --libbam.a:$(LOBJS) -- $(AR) -csru $@ $(LOBJS) -+libbam.so.1.0:$(LOBJS) -+ $(CC) $(CFLAGS) $(LDFLAGS) -shared -Wl,--soname,$@ -o $@ $(LOBJS) $(HTSLIB) -+ ln -sf $@ libbam.so.1 -+ ln -sf $@ libbam.so - --samtools: $(AOBJS) libbam.a libst.a $(HTSLIB) -- $(CC) $(ALL_LDFLAGS) -o $@ $(AOBJS) libbam.a libst.a $(HTSLIB_LIB) $(CURSES_LIB) -lm $(ALL_LIBS) -lpthread -+samtools: $(AOBJS) libbam.so.1.0 libst.a -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) libbam.so.1.0 libst.a $(HTSLIB_LIBS) $(NCURSES_LIBS) -lm $(ALL_LIBS) -lpthread - - # For building samtools and its test suite only: NOT to be installed. - libst.a: $(LIBST_OBJS) -@@ -151,58 +140,58 @@ - $(AR) -rcs $@ $(LIBST_OBJS) - - --bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h) --bam2bcf_h = bam2bcf.h $(htslib_hts_h) $(htslib_vcf_h) --bam_lpileup_h = bam_lpileup.h $(htslib_sam_h) --bam_plbuf_h = bam_plbuf.h $(htslib_sam_h) --bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(htslib_khash_h) $(bam_lpileup_h) --sam_h = sam.h $(htslib_sam_h) $(bam_h) --sam_opts_h = sam_opts.h $(htslib_hts_h) --sample_h = sample.h $(htslib_kstring_h) -- --bam.o: bam.c config.h $(bam_h) $(htslib_kstring_h) sam_header.h --bam2bcf.o: bam2bcf.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_kstring_h) $(htslib_kfunc_h) $(bam2bcf_h) --bam2bcf_indel.o: bam2bcf_indel.c config.h $(htslib_hts_h) $(htslib_sam_h) $(bam2bcf_h) $(htslib_khash_h) $(htslib_ksort_h) --bam2depth.o: bam2depth.c config.h $(htslib_sam_h) samtools.h $(sam_opts_h) --bam_addrprg.o: bam_addrprg.c config.h $(htslib_sam_h) $(htslib_kstring_h) samtools.h $(sam_opts_h) -+bam_h = bam.h -+bam2bcf_h = bam2bcf.h -+bam_lpileup_h = bam_lpileup.h -+bam_plbuf_h = bam_plbuf.h -+bam_tview_h = bam_tview.h $(bam2bcf_h) $(bam_lpileup_h) -+sam_h = sam.h $(bam_h) -+sam_opts_h = sam_opts.h -+sample_h = sample.h -+ -+bam.o: bam.c config.h $(bam_h) sam_header.h -+bam2bcf.o: bam2bcf.c config.h $(bam2bcf_h) -+bam2bcf_indel.o: bam2bcf_indel.c config.h $(bam2bcf_h) -+bam2depth.o: bam2depth.c config.h samtools.h $(sam_opts_h) -+bam_addrprg.o: bam_addrprg.c config.h samtools.h $(sam_opts_h) - bam_aux.o: bam_aux.c config.h $(bam_h) --bam_cat.o: bam_cat.c config.h $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_cram_h) $(htslib_khash_h) samtools.h -+bam_cat.o: bam_cat.c config.h samtools.h - bam_color.o: bam_color.c config.h $(bam_h) --bam_import.o: bam_import.c config.h $(htslib_kstring_h) $(bam_h) $(htslib_kseq_h) --bam_index.o: bam_index.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_h) samtools.h --bam_lpileup.o: bam_lpileup.c config.h $(bam_plbuf_h) $(bam_lpileup_h) $(htslib_ksort_h) --bam_mate.o: bam_mate.c config.h $(sam_opts_h) $(htslib_kstring_h) $(htslib_sam_h) samtools.h --bam_md.o: bam_md.c config.h $(htslib_faidx_h) $(htslib_sam_h) $(htslib_kstring_h) $(sam_opts_h) samtools.h --bam_plbuf.o: bam_plbuf.c config.h $(htslib_hts_h) $(htslib_sam_h) $(bam_plbuf_h) --bam_plcmd.o: bam_plcmd.c config.h $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) sam_header.h samtools.h $(sam_opts_h) $(bam2bcf_h) $(sample_h) --bam_quickcheck.o: bam_quickcheck.c config.h $(htslib_hts_h) $(htslib_sam_h) --bam_reheader.o: bam_reheader.c config.h $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_hfile_h) $(htslib_cram_h) samtools.h --bam_rmdup.o: bam_rmdup.c config.h $(htslib_sam_h) $(sam_opts_h) samtools.h $(bam_h) $(htslib_khash_h) --bam_rmdupse.o: bam_rmdupse.c config.h $(bam_h) $(htslib_sam_h) $(htslib_khash_h) $(htslib_klist_h) samtools.h --bam_sort.o: bam_sort.c config.h $(htslib_ksort_h) $(htslib_khash_h) $(htslib_klist_h) $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) samtools.h --bam_split.o: bam_split.c config.h $(htslib_sam_h) $(htslib_khash_h) $(htslib_kstring_h) $(htslib_cram_h) $(sam_opts_h) samtools.h --bam_stat.o: bam_stat.c config.h $(htslib_sam_h) samtools.h --bam_tview.o: bam_tview.c config.h $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_h) samtools.h $(sam_opts_h) -+bam_import.o: bam_import.c config.h $(bam_h) -+bam_index.o: bam_index.c config.h samtools.h -+bam_lpileup.o: bam_lpileup.c config.h $(bam_plbuf_h) $(bam_lpileup_h) -+bam_mate.o: bam_mate.c config.h $(sam_opts_h) samtools.h -+bam_md.o: bam_md.c config.h $(sam_opts_h) samtools.h -+bam_plbuf.o: bam_plbuf.c config.h $(bam_plbuf_h) -+bam_plcmd.o: bam_plcmd.c config.h sam_header.h samtools.h $(sam_opts_h) $(bam2bcf_h) $(sample_h) -+bam_quickcheck.o: bam_quickcheck.c config.h -+bam_reheader.o: bam_reheader.c config.h samtools.h -+bam_rmdup.o: bam_rmdup.c config.h $(sam_opts_h) samtools.h $(bam_h) -+bam_rmdupse.o: bam_rmdupse.c config.h $(bam_h) samtools.h -+bam_sort.o: bam_sort.c config.h $(sam_opts_h) samtools.h -+bam_split.o: bam_split.c config.h $(sam_opts_h) samtools.h -+bam_stat.o: bam_stat.c config.h samtools.h -+bam_tview.o: bam_tview.c config.h $(bam_tview_h) samtools.h $(sam_opts_h) - bam_tview_curses.o: bam_tview_curses.c config.h $(bam_tview_h) - bam_tview_html.o: bam_tview_html.c config.h $(bam_tview_h) --bam_flags.o: bam_flags.c config.h $(htslib_sam_h) --bamshuf.o: bamshuf.c config.h $(htslib_sam_h) $(htslib_hts_h) $(htslib_ksort_h) samtools.h $(sam_opts_h) --bamtk.o: bamtk.c config.h $(htslib_hts_h) samtools.h version.h --bedcov.o: bedcov.c config.h $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) $(htslib_kseq_h) --bedidx.o: bedidx.c config.h $(htslib_ksort_h) $(htslib_kseq_h) $(htslib_khash_h) --cut_target.o: cut_target.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) samtools.h $(sam_opts_h) --dict.o: dict.c config.h $(htslib_kseq_h) $(htslib_hts_h) --faidx.o: faidx.c config.h $(htslib_faidx_h) samtools.h --padding.o: padding.c config.h $(htslib_kstring_h) $(htslib_sam_h) $(htslib_faidx_h) sam_header.h $(sam_opts_h) samtools.h --phase.o: phase.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_kstring_h) $(sam_opts_h) samtools.h $(htslib_kseq_h) $(htslib_khash_h) $(htslib_ksort_h) --sam.o: sam.c config.h $(htslib_faidx_h) $(sam_h) --sam_header.o: sam_header.c config.h sam_header.h $(htslib_khash_h) -+bam_flags.o: bam_flags.c config.h -+bamshuf.o: bamshuf.c config.h samtools.h $(sam_opts_h) -+bamtk.o: bamtk.c config.h samtools.h version.h -+bedcov.o: bedcov.c config.h $(sam_opts_h) -+bedidx.o: bedidx.c config.h -+cut_target.o: cut_target.c config.h samtools.h $(sam_opts_h) -+dict.o: dict.c config.h -+faidx.o: faidx.c config.h samtools.h -+padding.o: padding.c config.h sam_header.h $(sam_opts_h) samtools.h -+phase.o: phase.c config.h $(sam_opts_h) samtools.h -+sam.o: sam.c config.h $(sam_h) -+sam_header.o: sam_header.c config.h sam_header.h - sam_opts.o: sam_opts.c config.h $(sam_opts_h) - sam_utils.o: sam_utils.c config.h samtools.h --sam_view.o: sam_view.c config.h $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_h) samtools.h $(sam_opts_h) --sample.o: sample.c config.h $(sample_h) $(htslib_khash_h) --stats_isize.o: stats_isize.c config.h stats_isize.h $(htslib_khash_h) --stats.o: stats.c config.h $(htslib_faidx_h) $(htslib_sam_h) $(htslib_hts_h) sam_header.h $(htslib_khash_str2int_h) samtools.h $(htslib_khash_h) $(htslib_kstring_h) stats_isize.h $(sam_opts_h) -+sam_view.o: sam_view.c config.h samtools.h $(sam_opts_h) -+sample.o: sample.c config.h $(sample_h) -+stats_isize.o: stats_isize.c config.h stats_isize.h -+stats.o: stats.c config.h sam_header.h samtools.h stats_isize.h $(sam_opts_h) - - - # test programs -@@ -224,30 +213,30 @@ - - - test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o libst.a $(HTSLIB) -- $(CC) $(ALL_LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread - - test/merge/test_rtrans_build: test/merge/test_rtrans_build.o libst.a $(HTSLIB) -- $(CC) $(ALL_LDFLAGS) -o $@ test/merge/test_rtrans_build.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/merge/test_rtrans_build.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread - - test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o libst.a $(HTSLIB) -- $(CC) $(ALL_LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread - - test/split/test_count_rg: test/split/test_count_rg.o test/test.o libst.a $(HTSLIB) -- $(CC) $(ALL_LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread - - test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o libst.a $(HTSLIB) -- $(CC) $(ALL_LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread - - test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o libst.a $(HTSLIB) -- $(CC) $(ALL_LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread - - test/split/test_parse_args: test/split/test_parse_args.o test/test.o libst.a $(HTSLIB) -- $(CC) $(ALL_LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread - - test/vcf-miniview: test/vcf-miniview.o $(HTSLIB) -- $(CC) $(ALL_LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB_LIB) $(ALL_LIBS) -lpthread -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread - --test_test_h = test/test.h $(htslib_sam_h) -+test_test_h = test/test.h - - test/merge/test_bam_translate.o: test/merge/test_bam_translate.c config.h bam_sort.o $(test_test_h) - test/merge/test_rtrans_build.o: test/merge/test_rtrans_build.c config.h bam_sort.o -@@ -256,34 +245,34 @@ - test/split/test_expand_format_string.o: test/split/test_expand_format_string.c config.h bam_split.o $(test_test_h) - test/split/test_filter_header_rg.o: test/split/test_filter_header_rg.c config.h bam_split.o $(test_test_h) - test/split/test_parse_args.o: test/split/test_parse_args.c config.h bam_split.o $(test_test_h) --test/test.o: test/test.c config.h $(htslib_sam_h) $(test_test_h) --test/vcf-miniview.o: test/vcf-miniview.c config.h $(htslib_vcf_h) -+test/test.o: test/test.c config.h $(test_test_h) -+test/vcf-miniview.o: test/vcf-miniview.c config.h - - - # misc programs - - misc/ace2sam: misc/ace2sam.o -- $(CC) $(LDFLAGS) -o $@ misc/ace2sam.o $(ALL_LIBS) -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/ace2sam.o $(ALL_LIBS) - - misc/maq2sam-short: misc/maq2sam-short.o -- $(CC) $(LDFLAGS) -o $@ misc/maq2sam-short.o $(ALL_LIBS) -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/maq2sam-short.o $(ALL_LIBS) - - misc/maq2sam-long: misc/maq2sam-long.o -- $(CC) $(LDFLAGS) -o $@ misc/maq2sam-long.o $(ALL_LIBS) -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/maq2sam-long.o $(ALL_LIBS) - - misc/md5fa: misc/md5fa.o $(HTSLIB) -- $(CC) $(ALL_LDFLAGS) -o $@ misc/md5fa.o $(HTSLIB_LIB) $(ALL_LIBS) -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/md5fa.o $(HTSLIB_LIBS) $(ALL_LIBS) - - misc/md5sum-lite: misc/md5sum-lite.o $(HTSLIB) -- $(CC) $(ALL_LDFLAGS) -o $@ misc/md5sum-lite.o $(HTSLIB_LIB) $(ALL_LIBS) -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/md5sum-lite.o $(HTSLIB_LIBS) $(ALL_LIBS) - - misc/wgsim: misc/wgsim.o -- $(CC) $(LDFLAGS) -o $@ misc/wgsim.o -lm $(ALL_LIBS) -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/wgsim.o -lm $(ALL_LIBS) - --misc/ace2sam.o: misc/ace2sam.c config.h $(htslib_kstring_h) $(htslib_kseq_h) --misc/md5fa.o: misc/md5fa.c config.h $(htslib_kseq_h) $(htslib_hts_h) --misc/md5sum-lite.o: misc/md5sum-lite.c config.h $(htslib_hts_h) --misc/wgsim.o: misc/wgsim.c config.h $(htslib_kseq_h) -+misc/ace2sam.o: misc/ace2sam.c config.h -+misc/md5fa.o: misc/md5fa.c config.h -+misc/md5sum-lite.o: misc/md5sum-lite.c config.h -+misc/wgsim.o: misc/wgsim.c config.h - - misc/maq2sam-short.o: misc/maq2sam.c config.h - $(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ misc/maq2sam.c diff --git a/sci-biology/samtools/metadata.xml b/sci-biology/samtools/metadata.xml index fe27db1184af..ddf4bb2590f4 100644 --- a/sci-biology/samtools/metadata.xml +++ b/sci-biology/samtools/metadata.xml @@ -1,5 +1,5 @@ -<?xml version='1.0' encoding='UTF-8'?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/samtools/samtools-0.1.20-r3.ebuild b/sci-biology/samtools/samtools-0.1.20-r3.ebuild deleted file mode 100644 index 5cfcfd7f6a79..000000000000 --- a/sci-biology/samtools/samtools-0.1.20-r3.ebuild +++ /dev/null @@ -1,83 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit python-single-r1 toolchain-funcs - -DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats" -HOMEPAGE="http://samtools.sourceforge.net/" -SRC_URI="https://github.com/samtools/samtools/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0.1-legacy" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" -IUSE="examples" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND="${PYTHON_DEPS} - sys-libs/ncurses:0= - dev-lang/perl" -DEPEND="${RDEPEND} - virtual/pkgconfig" - -PATCHES=( - "${FILESDIR}/${P}-buildsystem.patch" -) - -src_prepare() { - default - # required, otherwise python_fix_shebang errors out - sed -i 's~/software/bin/python~/usr/bin/env python~' misc/varfilter.py || die - tc-export CC AR -} - -src_compile() { - local _ncurses="$($(tc-getPKG_CONFIG) --libs ncurses)" - emake dylib LIBCURSES="${_ncurses}" - emake LIBCURSES="${_ncurses}" -} - -src_install() { - # install executables and hide them away from sight - dobin samtools bcftools/{bcftools,vcfutils.pl} misc/{*.py,*.pl,wgsim,ace2sam} \ - misc/{md5sum-lite,maq2sam-short,bamcheck,maq2sam-long,md5fa,plot-bamcheck} - mv "${ED%/}"/usr/{bin,${PN}-${SLOT}} || die - mkdir "${ED%/}"/usr/bin || die - mv "${ED%/}"/usr/{${PN}-${SLOT},bin/} || die - - # ... do the same with the python script, but also fix the shebang - mv "${ED%/}"/usr/bin/${PN}-${SLOT}/varfilter{,-${SLOT}}.py || die - python_fix_shebang "${ED%/}"/usr/bin/${PN}-${SLOT}/varfilter-${SLOT}.py - - # fix perl shebangs - pushd "${ED%/}"/usr/bin/${PN}-${SLOT} >/dev/null || die - local i - for i in plot-bamcheck *.pl; do - sed -e '1s:.*:#!/usr/bin/env perl:' -i "${i}" || die - done - popd >/dev/null || die - - dolib.so libbam-${SLOT}$(get_libname 1) - dosym libbam-${SLOT}$(get_libname 1) /usr/$(get_libdir)/libbam-${SLOT}$(get_libname) - - insinto /usr/include/bam-${SLOT} - doins *.h - - mv ${PN}{,-${SLOT}}.1 || die - doman ${PN}-${SLOT}.1 - einstalldocs - - if use examples; then - dodoc -r examples - docompress -x /usr/share/doc/${PF}/examples - fi -} - -pkg_postinst() { - elog "This version of samtools should *not* be your first choice for working" - elog "with NGS data. It is installed solely for programs requiring it." - elog "It is recommended that you use >=sci-biology/samtools-1.2." -} diff --git a/sci-biology/samtools/samtools-1.17.ebuild b/sci-biology/samtools/samtools-1.17.ebuild new file mode 100644 index 000000000000..e105621c7865 --- /dev/null +++ b/sci-biology/samtools/samtools-1.17.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit toolchain-funcs + +DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats" +HOMEPAGE="http://www.htslib.org/" +SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" + +RDEPEND=" + dev-lang/perl + =sci-libs/htslib-$(ver_cut 1-2)*:= + sys-libs/ncurses:=[unicode(+)] + sys-libs/zlib" +DEPEND="${RDEPEND}" +BDEPEND="virtual/pkgconfig" + +src_prepare() { + default + + # remove bundled htslib + rm -r htslib-* || die +} + +src_configure() { + econf \ + --with-ncurses \ + --with-htslib=system \ + CURSES_LIB="$($(tc-getPKG_CONFIG) --libs ncursesw || die)" +} + +src_compile() { + emake AR="$(tc-getAR)" +} + +src_install() { + default + + dodoc -r examples + docompress -x /usr/share/doc/${PF}/examples +} diff --git a/sci-biology/samtools/samtools-1.19.2.ebuild b/sci-biology/samtools/samtools-1.19.2.ebuild new file mode 100644 index 000000000000..42879b0f8698 --- /dev/null +++ b/sci-biology/samtools/samtools-1.19.2.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit toolchain-funcs + +DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats" +HOMEPAGE="http://www.htslib.org/" +SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" + +RDEPEND=" + dev-lang/perl + =sci-libs/htslib-$(ver_cut 1-2)*:= + sys-libs/ncurses:=[unicode(+)] + sys-libs/zlib" +DEPEND="${RDEPEND}" +BDEPEND="virtual/pkgconfig" + +src_prepare() { + default + + # remove bundled htslib + rm -r htslib-* || die +} + +src_configure() { + econf \ + --with-ncurses \ + --with-htslib=system \ + CURSES_LIB="$($(tc-getPKG_CONFIG) --libs ncursesw || die)" +} + +src_compile() { + emake AR="$(tc-getAR)" +} + +src_install() { + default + + dodoc -r examples + docompress -x /usr/share/doc/${PF}/examples +} diff --git a/sci-biology/samtools/samtools-1.5.ebuild b/sci-biology/samtools/samtools-1.5.ebuild deleted file mode 100644 index c2bc7ce89cf6..000000000000 --- a/sci-biology/samtools/samtools-1.5.ebuild +++ /dev/null @@ -1,61 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit autotools python-r1 toolchain-funcs - -DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats" -HOMEPAGE="http://www.htslib.org/" -SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" -IUSE="examples" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND=" - dev-lang/perl - =sci-libs/htslib-${PV}* - sys-libs/ncurses:0= - sys-libs/zlib - ${PYTHON_DEPS}" -DEPEND="${RDEPEND} - virtual/pkgconfig" - -PATCHES=( "${FILESDIR}/${PN}-1.5-buildsystem.patch" ) - -src_prepare() { - default - - python_setup - python_fix_shebang misc/varfilter.py - - # remove bundled htslib - rm -r htslib-* || die - - eautoreconf -} - -src_test() { - local -x LD_LIBRARY_PATH="${S}" - default -} - -src_install() { - default - - # install libbam and headers - dolib.so libbam.so* - - insinto /usr/include/bam - doins *.h - - if use examples; then - dodoc -r examples - docompress -x /usr/share/doc/${PF}/examples - fi -} diff --git a/sci-biology/samtools/samtools-1.9.ebuild b/sci-biology/samtools/samtools-1.9.ebuild deleted file mode 100644 index bdcd115aafee..000000000000 --- a/sci-biology/samtools/samtools-1.9.ebuild +++ /dev/null @@ -1,52 +0,0 @@ -# Copyright 1999-2018 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python2_7 ) - -inherit autotools python-single-r1 toolchain-funcs - -DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats" -HOMEPAGE="http://www.htslib.org/" -SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" -IUSE="examples" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND=" - dev-lang/perl - =sci-libs/htslib-${PV}* - sys-libs/ncurses:0= - sys-libs/zlib:= - ${PYTHON_DEPS}" -DEPEND="${RDEPEND} - virtual/pkgconfig" - -src_prepare() { - default - - python_fix_shebang misc/varfilter.py - - # remove bundled htslib - rm -r htslib-* || die - - eautoreconf -} - -src_test() { - local -x LD_LIBRARY_PATH="${S}" - default -} - -src_install() { - default - - if use examples; then - dodoc -r examples - docompress -x /usr/share/doc/${PF}/examples - fi -} diff --git a/sci-biology/seaview/Manifest b/sci-biology/seaview/Manifest index 0f0b4cd80d3e..2b43f22a2ea3 100644 --- a/sci-biology/seaview/Manifest +++ b/sci-biology/seaview/Manifest @@ -1,3 +1 @@ -DIST seaview_4.3.5.tar.gz 309530 BLAKE2B a4210b179bba5ab40215603738fe844d48b4f953e7b79749786afcedce0625f17c343a2d4ed2a45d4a7cfc2d4c9abbb7ab856e98405694160ecfac186f86fadd SHA512 b20c018da9a29d79fe0393fed5d29117729492ea8f36e72d4aeb98044a3de4a13331bd29e76ca552a08f6da764e57e69f9fb0325fc031551514d7a54b56c849a -DIST seaview_4.5.4.tar.gz 420608 BLAKE2B 14b044706440da88987cd6b546595497f2de61e8d03615bfce4634104914a56544a464b0abedc83e6c96329697dccb2087c2b1af5a1fdbf0d9bdc26418a49a75 SHA512 a8a2e49a13f87ae4279311068147169b1e17874e9ce5787003b854c7271efc7a128db6916bb883a9b7b0b90f855fe40d83c77e9fd9f5751464e04346b9923301 DIST seaview_4.6.tar.gz 424258 BLAKE2B e958ff4b1f6bb283a2122d65917a352914f33e5c9593c34c449800fbcac74b0dd4fa98bb1f47c45e11f24e07dfebb3ced54fbd8440b2bcd2b1df32dc398d5892 SHA512 e005d9dcc9e03c5636404e94f0059f7d4a9289fe77ecdab765e3ca2b59d826b8711a344f3824d079383a7ede0fe17b3b06694dfb7b709bb6a0a1e38cef6ee1d6 diff --git a/sci-biology/seaview/files/seaview-4.6-Wreserved-user-defined-literal.patch b/sci-biology/seaview/files/seaview-4.6-Wreserved-user-defined-literal.patch new file mode 100644 index 000000000000..c9595748e901 --- /dev/null +++ b/sci-biology/seaview/files/seaview-4.6-Wreserved-user-defined-literal.patch @@ -0,0 +1,76 @@ +--- a/align.cxx ++++ b/align.cxx +@@ -754,7 +754,7 @@ + alignitems[clustalopt + MAX_MSA_ALGOS].label(strdup(options)); + alignitems[clustalopt + MAX_MSA_ALGOS].flags = attr; + if (view->alignment_algorithm < 2) alignitems[clustalopt + MAX_MSA_ALGOS + 3].flags = FL_MENU_INACTIVE; +- delete options; ++ delete[] options; + view->menu_align = alignitems; + view->menubar->add("Align", 0, NULL, (void*)view->menu_align, FL_SUBMENU_POINTER); + if (view->count_msa_algos >= MAX_MSA_ALGOS) (alignitems + clustalopt + MAX_MSA_ALGOS + 2)->deactivate(); +--- a/seaview.cxx ++++ b/seaview.cxx +@@ -3314,7 +3314,7 @@ + if(p != NULL) *p = 0; + if(printout_black == TEXT_ONLY) strcat(suggested, ".txt"); + else { +- strcat(suggested, "."PDF_OR_PS_EXT); ++ strcat(suggested, "." PDF_OR_PS_EXT); + } + if( view->alt_col_rank != NULL ) { + for(anerr = 0; anerr < view->tot_seqs; anerr++) +@@ -3424,7 +3424,7 @@ + + pdf_form = new Fl_Window(415, 90); + pdf_form->box(FL_FLAT_BOX); +-pdf_form->label("Set "PDF_OR_PS" output options"); ++pdf_form->label("Set " PDF_OR_PS " output options"); + + x = 5 + (int)fl_width("block size:"); y = 5; w = 50; h = 25; + sizeinput = new Fl_Input(x, y, w, h, "font size:"); +@@ -5000,10 +5000,10 @@ + {"Save prot alignmt", 0,file_menu_callback, 0, FL_MENU_INACTIVE}, + {"Save bootstrap replicates", 0,file_menu_callback, 0, FL_MENU_INACTIVE | FL_MENU_DIVIDER}, + #if !defined(__APPLE__) +- {"Prepare "PDF_OR_PS"", 0, file_menu_callback, 0, 0}, +- {""PDF_OR_PS" options...", 0, file_menu_callback, 0, FL_MENU_DIVIDER}, ++ {"Prepare " PDF_OR_PS "", 0, file_menu_callback, 0, 0}, ++ {"" PDF_OR_PS " options...", 0, file_menu_callback, 0, FL_MENU_DIVIDER}, + #else +- {"Prepare "PDF_OR_PS"", 0, file_menu_callback, 0, FL_MENU_DIVIDER}, ++ {"Prepare " PDF_OR_PS "", 0, file_menu_callback, 0, FL_MENU_DIVIDER}, + #endif + {"Concatenate", 0,file_menu_callback, 0, FL_MENU_DIVIDER}, + {"New window", FL_COMMAND | 'n', file_menu_callback, 0, 0}, +--- a/treedraw.cxx ++++ b/treedraw.cxx +@@ -210,7 +210,7 @@ + {"Save all trees", 0, file_callback, NULL, 0}, + {"Save patristic distances", 0, patristic_callback, NULL, FL_MENU_DIVIDER}, + {"Print", FL_COMMAND | 'p', file_callback, NULL, 0}, +- {"Save as "PDF_OR_PS"", 0, file_callback, NULL, 0}, ++ {"Save as " PDF_OR_PS "", 0, file_callback, NULL, 0}, + {"Save as SVG", 0, file_callback, NULL, 0}, + {"A4", 0, file_callback, NULL, FL_MENU_RADIO | 0}, + {"Letter", 0, file_callback, NULL, FL_MENU_RADIO | 0}, +--- a/xfmatpt.cxx ++++ b/xfmatpt.cxx +@@ -205,7 +205,7 @@ + compute->callback(compute_proc, fdui); + fdui->compute_butt = compute; + +-Fl_Widget *postscript = cre_button(fin, curr_y, &width, but_height, fontsize, "Write "PDF_OR_PS); ++Fl_Widget *postscript = cre_button(fin, curr_y, &width, but_height, fontsize, "Write " PDF_OR_PS); + fin += width; + postscript->callback(plot_button_proc, fdui); + +@@ -870,7 +870,7 @@ + #ifndef MICRO + matpt->form->hide(); Fl::flush(); // because of strange bug on 32-bit Linux only + #endif +- fl_message("Dot plot is now in file\n%s\nin "PDF_OR_PS" format", surface->outfname()); ++ fl_message("Dot plot is now in file\n%s\nin " PDF_OR_PS " format", surface->outfname()); + delete surface; + #ifndef MICRO + matpt->form->show(); Fl::flush(); diff --git a/sci-biology/seaview/files/seaview-4.6-fno-common.patch b/sci-biology/seaview/files/seaview-4.6-fno-common.patch new file mode 100644 index 000000000000..24cc28dfb3b7 --- /dev/null +++ b/sci-biology/seaview/files/seaview-4.6-fno-common.patch @@ -0,0 +1,110 @@ +--- a/csrc/dnapars.c ++++ b/csrc/dnapars.c +@@ -77,41 +77,43 @@ + /* function prototypes */ + + +-Char infilename[FNMLNGTH], outfilename[FNMLNGTH], intreename[FNMLNGTH], *outtreename, ++extern Char infilename[FNMLNGTH], outfilename[FNMLNGTH], intreename[FNMLNGTH], *outtreename, + weightfilename[FNMLNGTH]; + char basechar[32]="ACMGRSVTWYHKDBNO???????????????"; +-node *root; +-long chars, col, msets, ith, njumble, jumb, maxtrees; ++extern node *root; ++extern long chars, col, msets, ith, njumble, jumb; ++long maxtrees; + /* chars = number of sites in actual sequences */ +-long inseed, inseed0; +-double threshold; +-boolean jumble, usertree, thresh, weights, thorough, rearrfirst, +- trout, progress, stepbox, ancseq, mulsets, justwts, firstset, mulf, +- multf; ++extern long inseed, inseed0; ++extern double threshold; ++boolean thorough, rearrfirst, mulf, multf; ++extern boolean justwts, ancseq, weights, thresh, jumble, usertree, trout, mulsets, progress, stepbox, firstset; + steptr oldweight; +-longer seed; +-pointarray treenode; /* pointers to all nodes in tree */ +-long *enterorder; ++extern longer seed; ++extern pointarray treenode; /* pointers to all nodes in tree */ ++extern long *enterorder; + long *zeros; + + /* local variables for Pascal maketree, propagated globally for C version: */ + +-long minwhich; ++extern long minwhich; + static double like, minsteps, bestyet, bestlike, bstlike2; +-boolean lastrearr, recompute; +-double nsteps[maxuser]; +-long **fsteps; +-node *there, *oldnufork; +-long *place; +-bestelm *bestrees; +-long *threshwt; ++extern boolean lastrearr, recompute; ++extern double nsteps[maxuser]; ++extern long **fsteps; ++extern node *there; ++node *oldnufork; ++extern long *place; ++extern bestelm *bestrees; ++extern long *threshwt; + baseptr nothing; +-gbases *garbage; +-node *temp, *temp1, *temp2, *tempsum, *temprm, *tempadd, *tempf, *tmp, *tmp1, ++extern gbases *garbage; ++extern node *temp, *temp1; ++node *temp2, *tempsum, *temprm, *tempadd, *tempf, *tmp, *tmp1, + *tmp2, *tmp3, *tmprm, *tmpadd; +-boolean *names; ++extern boolean *names; + node *grbg; +-char *progname; ++extern char *progname; + + + static void getoptions(int arg_maxtrees, dnapars_S_option s_option) +--- a/csrc/phylip.c ++++ b/csrc/phylip.c +@@ -35,6 +35,8 @@ + + #include "phylip.h" + ++boolean javarun; ++ + #ifdef WIN32 + #include <windows.h> + /* for console code (clear screen, text color settings) */ +--- a/csrc/phylip.h ++++ b/csrc/phylip.h +@@ -342,7 +342,7 @@ + /* Lower-triangular format. */ + #define MAT_LOWERTRI (MAT_LOWER | MAT_MACHINE) + +-boolean javarun; ++extern boolean javarun; + + typedef long *steptr; + typedef long longer[6]; +@@ -363,7 +363,6 @@ + extern boolean ibmpc, ansi, tranvsp; + //extern naym *nayme; /* names of species */ + extern char* *nayme; /* names of species */ +-boolean firstplotblock; // for debugging BMP output + + #define ebcdic EBCDIC + +--- a/csrc/protpars.c ++++ b/csrc/protpars.c +@@ -127,7 +127,7 @@ + node *temp, *temp1; + Char ch; + aas tmpa; +-char *progname; ++extern char *progname; + + /* Local variables for maketree, propagated globally for c version: */ + long minwhich; diff --git a/sci-biology/seaview/metadata.xml b/sci-biology/seaview/metadata.xml index 14e26ee93445..a01c6174c4ce 100644 --- a/sci-biology/seaview/metadata.xml +++ b/sci-biology/seaview/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/seaview/seaview-4.3.5.ebuild b/sci-biology/seaview/seaview-4.3.5.ebuild deleted file mode 100644 index 33ee6f65ccbd..000000000000 --- a/sci-biology/seaview/seaview-4.3.5.ebuild +++ /dev/null @@ -1,76 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils multilib toolchain-funcs - -DESCRIPTION="A graphical multiple sequence alignment editor" -HOMEPAGE="http://pbil.univ-lyon1.fr/software/seaview.html" -SRC_URI="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/${PN}_${PV}.tar.gz" - -LICENSE="public-domain" -SLOT="0" -KEYWORDS="amd64 x86" -IUSE="+xft" - -CDEPEND=" - sys-libs/zlib - x11-libs/fltk:1 - x11-libs/libX11 - xft? ( - x11-libs/libXft - x11-libs/fltk:1[xft] )" -RDEPEND="${CDEPEND} - sci-biology/clustalw - || ( sci-libs/libmuscle sci-biology/muscle ) - sci-biology/phyml" -DEPEND="${CDEPEND} - virtual/pkgconfig" - -S="${WORKDIR}/${PN}" - -src_prepare() { - # respect CXXFLAGS (package uses them as CFLAGS) - sed \ - -e "s:^CC.*:CC = $(tc-getCC):" \ - -e "s:^CXX.*:CXX = $(tc-getCXX):" \ - -e "s:\$(OPT):${CXXFLAGS}:" \ - -e "s:^OPT:#OPT:" \ - -e "s:^FLTK = .*$:FLTK = ${EPREFIX}/usr/include/fltk-1:" \ - -e "s:^#IFLTK .*:IFLTK = $(fltk-config --use-images --cflags):" \ - -e "s:^#LFLTK .*:LFLTK = $(fltk-config --use-images --ldflags):" \ - -e "s:^USE_XFT:#USE_XFT:" \ - -e "s:^#HELPFILE:HELPFILE:" \ - -e "s:/usr/share/doc/seaview/seaview.htm:${EPREFIX}/usr/share/seaview/seaview.htm:" \ - -e "s:^#PHYMLNAME:PHYMLNAME:" \ - -e 's:-lXinerama::g' \ - -e 's:-lpng::g' \ - -e 's:-ljpeg::g' \ - -e 's:-lfontconfig::g' \ - -i Makefile || die "sed failed while editing Makefile" - - if use xft; then - sed \ - -e "s:^#USE_XFT .*:USE_XFT = -DUSE_XFT $($(tc-getPKG_CONFIG) --cflags xft):" \ - -e "s:-lXft:$($(tc-getPKG_CONFIG) --libs xft):" \ - -i Makefile || die "sed failed while editing Makefile to enable xft" - else - sed -i -e "s:-lXft::" Makefile || die - fi -} - -src_install() { - dobin seaview - - # /usr/share/seaview/seaview.html is hardcoded in the binary, see Makefile - insinto /usr/share/seaview - doins example.nxs seaview.html - - insinto /usr/share/seaview/images - doins seaview.xpm - - make_desktop_entry seaview Seaview - - doman seaview.1 -} diff --git a/sci-biology/seaview/seaview-4.5.4.ebuild b/sci-biology/seaview/seaview-4.5.4.ebuild deleted file mode 100644 index 33ee6f65ccbd..000000000000 --- a/sci-biology/seaview/seaview-4.5.4.ebuild +++ /dev/null @@ -1,76 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils multilib toolchain-funcs - -DESCRIPTION="A graphical multiple sequence alignment editor" -HOMEPAGE="http://pbil.univ-lyon1.fr/software/seaview.html" -SRC_URI="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/${PN}_${PV}.tar.gz" - -LICENSE="public-domain" -SLOT="0" -KEYWORDS="amd64 x86" -IUSE="+xft" - -CDEPEND=" - sys-libs/zlib - x11-libs/fltk:1 - x11-libs/libX11 - xft? ( - x11-libs/libXft - x11-libs/fltk:1[xft] )" -RDEPEND="${CDEPEND} - sci-biology/clustalw - || ( sci-libs/libmuscle sci-biology/muscle ) - sci-biology/phyml" -DEPEND="${CDEPEND} - virtual/pkgconfig" - -S="${WORKDIR}/${PN}" - -src_prepare() { - # respect CXXFLAGS (package uses them as CFLAGS) - sed \ - -e "s:^CC.*:CC = $(tc-getCC):" \ - -e "s:^CXX.*:CXX = $(tc-getCXX):" \ - -e "s:\$(OPT):${CXXFLAGS}:" \ - -e "s:^OPT:#OPT:" \ - -e "s:^FLTK = .*$:FLTK = ${EPREFIX}/usr/include/fltk-1:" \ - -e "s:^#IFLTK .*:IFLTK = $(fltk-config --use-images --cflags):" \ - -e "s:^#LFLTK .*:LFLTK = $(fltk-config --use-images --ldflags):" \ - -e "s:^USE_XFT:#USE_XFT:" \ - -e "s:^#HELPFILE:HELPFILE:" \ - -e "s:/usr/share/doc/seaview/seaview.htm:${EPREFIX}/usr/share/seaview/seaview.htm:" \ - -e "s:^#PHYMLNAME:PHYMLNAME:" \ - -e 's:-lXinerama::g' \ - -e 's:-lpng::g' \ - -e 's:-ljpeg::g' \ - -e 's:-lfontconfig::g' \ - -i Makefile || die "sed failed while editing Makefile" - - if use xft; then - sed \ - -e "s:^#USE_XFT .*:USE_XFT = -DUSE_XFT $($(tc-getPKG_CONFIG) --cflags xft):" \ - -e "s:-lXft:$($(tc-getPKG_CONFIG) --libs xft):" \ - -i Makefile || die "sed failed while editing Makefile to enable xft" - else - sed -i -e "s:-lXft::" Makefile || die - fi -} - -src_install() { - dobin seaview - - # /usr/share/seaview/seaview.html is hardcoded in the binary, see Makefile - insinto /usr/share/seaview - doins example.nxs seaview.html - - insinto /usr/share/seaview/images - doins seaview.xpm - - make_desktop_entry seaview Seaview - - doman seaview.1 -} diff --git a/sci-biology/seaview/seaview-4.6.ebuild b/sci-biology/seaview/seaview-4.6-r1.ebuild index 4ad8ad61b72b..469f88728120 100644 --- a/sci-biology/seaview/seaview-4.6.ebuild +++ b/sci-biology/seaview/seaview-4.6-r1.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 -inherit eutils toolchain-funcs +inherit desktop toolchain-funcs DESCRIPTION="A graphical multiple sequence alignment editor" HOMEPAGE="http://pbil.univ-lyon1.fr/software/seaview.html" @@ -15,19 +15,24 @@ KEYWORDS="~amd64 ~x86" IUSE="+xft" RDEPEND=" + sci-biology/clustalw:2 + sci-biology/phyml + || ( + sci-libs/libmuscle + sci-biology/muscle + ) sys-libs/zlib - x11-libs/fltk:1 + x11-libs/fltk:1[xft?] x11-libs/libX11 - xft? ( - x11-libs/libXft - x11-libs/fltk:1[xft] ) - sci-biology/clustalw:2 - || ( sci-libs/libmuscle sci-biology/muscle ) - sci-biology/phyml" -DEPEND="${RDEPEND} - virtual/pkgconfig" + xft? ( x11-libs/libXft )" +DEPEND="${RDEPEND}" +BDEPEND="virtual/pkgconfig" S="${WORKDIR}/${PN}" +PATCHES=( + "${FILESDIR}"/${PN}-4.6-fno-common.patch + "${FILESDIR}"/${PN}-4.6-Wreserved-user-defined-literal.patch +) src_prepare() { default diff --git a/sci-biology/seqan/Manifest b/sci-biology/seqan/Manifest index d26b1ac375fb..ed2aa485711a 100644 --- a/sci-biology/seqan/Manifest +++ b/sci-biology/seqan/Manifest @@ -1,3 +1 @@ -DIST seqan-src-1.4.2.tar.gz 120601994 BLAKE2B 62de2f961ba3c7c564090d746877d2b0b94ec7967c56f28786a286160770e66f0a8f08aacbe76d828cf429f92f0aa640ab29f5220297686979df9b7e9f9a0408 SHA512 dbb56167c507b70111619a414054d9e70f1db42507bbfdf9e40c5dcbbe9489ad4187d882e638a675e96551c860c08f8203c929c4c9a558b19ea7d6059f50492a -DIST seqan-src-2.2.0.tar.gz 110936119 BLAKE2B be41f266e140ec5992f7e9e507659dc7902aad0e0dd17e6a8c6c9ef0b11f690454a771ba10a5998ccf70e2e50ef9b24904ebf537d982b2cbc68963c004097614 SHA512 1097372976ec9c86baa3787ac38aa4fde3a3e153d81c22435e6a12df87d8063165f27406de33851bffadd904b0ac4ea579a28625cff6257fe8c14d906f408421 -DIST seqan-v2.4.0.tar.gz 109626901 BLAKE2B a10b5ee9a95667f560a8c2aec3808131f5f838f3c07d56584f4b29e9622912bf3d00b958b02db7c9d62dd52d9d08a171abcccef7f50cddf0407538168cf2c592 SHA512 f92cfc97304581920850c5d49fe4336f7c3855e99c3bcb035b6172fa7307e08e6f06fb06d1cd8f5b447c3220fc7f669684fbfe25641b43e9f6953999cf9ddd4b +DIST seqan3-3.1.0-Source.tar.xz 2656120 BLAKE2B 6a18844f62d935fdbd7008822f83ffeefd596e93b704a8c7b0f478dec87b2265ff532be107ebfd1adc248e2b1db65e4b86cdce2e989c7ac097054d43633a24bd SHA512 686d0ffbe32951e7f831e399a3eab35b7249f45408b7de27ee9cfd6a012215603f033afa6082c8a81783de1cc7c93d3ffbae42cabc122d3b77988c236a049ffd diff --git a/sci-biology/seqan/files/seqan-1.4.2-buildsystem.patch b/sci-biology/seqan/files/seqan-1.4.2-buildsystem.patch deleted file mode 100644 index 4c7893e90c05..000000000000 --- a/sci-biology/seqan/files/seqan-1.4.2-buildsystem.patch +++ /dev/null @@ -1,30 +0,0 @@ -Add default disabled flag to enable generation of documentation. -For SeqAn 1.4.2 we generally do not want docs, as 1.4.2 is only a -support library for legacy tools. - ---- seqan-1.4.2/CMakeLists.txt -+++ seqan-1.4.2/CMakeLists.txt -@@ -123,10 +123,12 @@ - add_subdirectory (core) - message (STATUS "Configuring extras") - add_subdirectory (extras) -+if (NOT SEQAN_NO_DOX) - message (STATUS "Configuring docs") - add_subdirectory (docs) - message (STATUS "Configuring manual") - add_subdirectory (manual) -+endif () - message (STATUS "Configuring sandbox") - add_subdirectory (sandbox) - message (STATUS "Configuring util/py_lib") ---- seqan-1.4.2/docs/main.py -+++ seqan-1.4.2/docs/main.py -@@ -123,7 +123,7 @@ - - # Done, print end message. - print 'Documentation created/updated.' -- return dddoc_html.WARNING_COUNT > 0 -+ return 0 - - - def main(argv): diff --git a/sci-biology/seqan/files/seqan-1.4.2-include.patch b/sci-biology/seqan/files/seqan-1.4.2-include.patch deleted file mode 100644 index 5baee4d8ebc0..000000000000 --- a/sci-biology/seqan/files/seqan-1.4.2-include.patch +++ /dev/null @@ -1,16 +0,0 @@ - core/include/seqan/index/index_qgram_openaddressing.h | 2 ++ - 1 file changed, 2 insertions(+) - -diff --git a/core/include/seqan/index/index_qgram_openaddressing.h b/core/include/seqan/index/index_qgram_openaddressing.h -index 4a6c2e6..8cc9a42 100644 ---- a/core/include/seqan/index/index_qgram_openaddressing.h -+++ b/core/include/seqan/index/index_qgram_openaddressing.h -@@ -35,6 +35,8 @@ - #ifndef SEQAN_HEADER_INDEX_QGRAM_OPENADRESSING_H - #define SEQAN_HEADER_INDEX_QGRAM_OPENADRESSING_H - -+#include <smmintrin.h> -+ - namespace SEQAN_NAMESPACE_MAIN - { - diff --git a/sci-biology/seqan/files/seqan-1.4.2-shared.patch b/sci-biology/seqan/files/seqan-1.4.2-shared.patch deleted file mode 100644 index 0f438ff07bce..000000000000 --- a/sci-biology/seqan/files/seqan-1.4.2-shared.patch +++ /dev/null @@ -1,22 +0,0 @@ - util/cmake/SeqAnBuildSystem.cmake | 8 ++++---- - 1 file changed, 4 insertions(+), 4 deletions(-) - -diff --git a/util/cmake/SeqAnBuildSystem.cmake b/util/cmake/SeqAnBuildSystem.cmake -index bcba2c0..d53cd01 100644 ---- a/util/cmake/SeqAnBuildSystem.cmake -+++ b/util/cmake/SeqAnBuildSystem.cmake -@@ -144,10 +144,10 @@ macro (seqan_register_apps) - set (CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -DSEQAN_ENABLE_DEBUG=1") - - # enable static linkage for seqan apps -- if (CMAKE_COMPILER_IS_GNUCXX OR COMPILER_IS_CLANG AND NOT MINGW) -- set(CMAKE_FIND_LIBRARY_SUFFIXES ".a") -- set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++") -- endif () -+# if (CMAKE_COMPILER_IS_GNUCXX OR COMPILER_IS_CLANG AND NOT MINGW) -+# set(CMAKE_FIND_LIBRARY_SUFFIXES ".a") -+# set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++") -+# endif () - - # Get all direct entries of the current source directory into ENTRIES. - file (GLOB ENTRIES diff --git a/sci-biology/seqan/files/seqan-2.4.0-fix-pthread.patch b/sci-biology/seqan/files/seqan-2.4.0-fix-pthread.patch deleted file mode 100644 index b5e4b3642d42..000000000000 --- a/sci-biology/seqan/files/seqan-2.4.0-fix-pthread.patch +++ /dev/null @@ -1,12 +0,0 @@ ---- a/util/cmake/seqan-config.cmake -+++ b/util/cmake/seqan-config.cmake -@@ -307,7 +307,8 @@ - - # some OSes don't link pthread fully when building statically so we explicitly include whole archive - if (UNIX AND NOT APPLE) -- set (CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -Wl,--whole-archive -lpthread -Wl,--no-whole-archive") -+ find_package (Threads) -+ set (SEQAN_LIBRARIES ${SEQAN_LIBRARIES} ${CMAKE_THREAD_LIBS_INIT}) - endif () - - if ((${CMAKE_SYSTEM_NAME} STREQUAL "FreeBSD") OR (${CMAKE_SYSTEM_NAME} STREQUAL "OpenBSD")) diff --git a/sci-biology/seqan/files/seqan.pc.in b/sci-biology/seqan/files/seqan.pc.in deleted file mode 100644 index f917faef8ba3..000000000000 --- a/sci-biology/seqan/files/seqan.pc.in +++ /dev/null @@ -1,10 +0,0 @@ -prefix=@CMAKE_INSTALL_PREFIX@ -exec_prefix=${prefix} -includedir=${prefix}/include - -Name: @CMAKE_PROJECT_NAME@ -Description: C++ library for biological sequence analysis -URL: http://www.seqan.de -Version: @SEQAN_VERSION_STRING@ -Requires: zlib -Cflags: -I${includedir} diff --git a/sci-biology/seqan/metadata.xml b/sci-biology/seqan/metadata.xml index 077f6458a927..bdabd1d83788 100644 --- a/sci-biology/seqan/metadata.xml +++ b/sci-biology/seqan/metadata.xml @@ -1,11 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> - <use> - <flag name="tools">Build and install SeqAn commandline tools, such as the Yara aligner</flag> - </use> </pkgmetadata> diff --git a/sci-biology/seqan/seqan-1.4.2-r1.ebuild b/sci-biology/seqan/seqan-1.4.2-r1.ebuild deleted file mode 100644 index 3a7f55c710c3..000000000000 --- a/sci-biology/seqan/seqan-1.4.2-r1.ebuild +++ /dev/null @@ -1,79 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit cmake-utils python-any-r1 versionator - -DESCRIPTION="C++ Sequence Analysis Library" -HOMEPAGE="http://www.seqan.de/" -SRC_URI="http://packages.${PN}.de/${PN}-src/${PN}-src-${PV}.tar.gz" - -SLOT="$(get_version_component_range 1-2)" -LICENSE="BSD GPL-3" -KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" -IUSE="cpu_flags_x86_sse4_1 test" -RESTRICT="!test? ( test )" -REQUIRED_USE="cpu_flags_x86_sse4_1" - -RDEPEND=" - app-arch/bzip2 - sys-libs/zlib" -DEPEND=" - ${RDEPEND} - test? ( - $(python_gen_any_dep 'dev-python/nose[${PYTHON_USEDEP}]') - ${PYTHON_DEPS} - )" - -PATCHES=( - "${FILESDIR}/${P}-shared.patch" - "${FILESDIR}/${P}-include.patch" - "${FILESDIR}/${P}-buildsystem.patch" -) - -pkg_setup() { - use test && python-any-r1_pkg_setup -} - -src_prepare() { - # pkg-config file, taken from seqan 2.1 - cp "${FILESDIR}"/${PN}.pc.in ${PN}-${SLOT}.pc || die - sed -e "s#@CMAKE_INSTALL_PREFIX@#${EPREFIX}/usr#" \ - -e "s#includedir=\${prefix}/include#includedir=\${prefix}/include/${PN}-${SLOT}#" \ - -e "s#@CMAKE_PROJECT_NAME@#${PN}#" \ - -e "s#@SEQAN_VERSION_STRING@#${PV}#" \ - -i ${PN}-${SLOT}.pc || die - - rm -f util/cmake/FindZLIB.cmake || die - cmake-utils_src_prepare -} - -src_configure() { - local mycmakeargs=( - -DBoost_NO_BOOST_CMAKE=ON - -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY - -DSEQAN_NO_DOX=ON - ) - cmake-utils_src_configure -} - -src_install() { - cmake-utils_src_install - - # SLOT header such that different seqan versions can be used in parallel - mkdir "${ED}"/usr/include/${PN}-${SLOT} || die - mv "${ED}"/usr/include/{${PN},${PN}-${SLOT}/} || die - - # pkg-config file - insinto /usr/share/pkgconfig/ - doins ${PN}-${SLOT}.pc -} - -pkg_postinst() { - einfo "${CATEGORY}/${PF} is only intended as support library for older" - einfo "bioinformatics tools relying on the SeqAn 1.* API. Please develop" - einfo "any new software against the latest SeqAn release and not this one." -} diff --git a/sci-biology/seqan/seqan-2.2.0-r1.ebuild b/sci-biology/seqan/seqan-2.2.0-r1.ebuild deleted file mode 100644 index 5e139cd7e601..000000000000 --- a/sci-biology/seqan/seqan-2.2.0-r1.ebuild +++ /dev/null @@ -1,94 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit cmake-utils python-any-r1 versionator - -DESCRIPTION="C++ Sequence Analysis Library" -HOMEPAGE="http://www.seqan.de/" -SRC_URI="http://packages.${PN}.de/${PN}-src/${PN}-src-${PV}.tar.gz" - -SLOT="0" -LICENSE="BSD GPL-3" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="cpu_flags_x86_sse4_1 doc test" -RESTRICT="!test? ( test )" -REQUIRED_USE="cpu_flags_x86_sse4_1" - -RDEPEND=" - app-arch/bzip2 - sys-libs/zlib - !!sci-biology/seqan:2.0 - !!sci-biology/seqan:2.1 - !!sci-biology/seqan:2.2" -DEPEND=" - ${RDEPEND} - doc? ( - $(python_gen_any_dep 'dev-python/sphinx[${PYTHON_USEDEP}]') - ${PYTHON_DEPS} - ) - test? ( - $(python_gen_any_dep 'dev-python/nose[${PYTHON_USEDEP}]') - ${PYTHON_DEPS} - )" - -S="${WORKDIR}"/${PN}-${PN}-v${PV} - -pkg_setup() { - if use test || use doc; then - python-any-r1_pkg_setup - fi -} - -src_prepare() { - seqan_major_ver=$(get_version_component_range 1) - seqan_majorminor_ver=$(get_version_component_range 1-2) - - # install docs in proper Gentoo structure - sed -e "s#share/doc/seqan#share/doc/${PF}#" \ - -e "s#\"share/doc/\${APP_NAME}\"#\"share/doc/${PF}/\${APP_NAME}\"#" \ - -i util/cmake/SeqAnBuildSystem.cmake dox/CMakeLists.txt || die - - # cmake module - sed -e "s#find_path(_SEQAN_BASEDIR \"seqan\"#find_path(_SEQAN_BASEDIR \"seqan-${seqan_majorminor_ver}\"#" \ - -e 's#NO_DEFAULT_PATH)#PATHS /usr)#' \ - -e "s#set(SEQAN_INCLUDE_DIRS_MAIN \${SEQAN_INCLUDE_DIRS_MAIN} \${_SEQAN_BASEDIR})#set(SEQAN_INCLUDE_DIRS_MAIN \${SEQAN_INCLUDE_DIRS_MAIN} \${_SEQAN_BASEDIR}/seqan-${seqan_majorminor_ver})#" \ - -i util/cmake/FindSeqAn.cmake || die - - # pkg-config file - sed -e "s#includedir=\${prefix}/include#includedir=\${prefix}/include/${PN}-${seqan_majorminor_ver}#" \ - -i util/pkgconfig/${PN}.pc.in || die - - rm -f util/cmake/FindZLIB.cmake || die - cmake-utils_src_prepare -} - -src_configure() { - local mycmakeargs=( - -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY - -DSEQAN_NO_DOX=$(usex !doc) - ) - cmake-utils_src_configure -} - -src_compile() { - cmake-utils_src_compile - use doc && cmake-utils_src_compile -C "${BUILD_DIR}" dox -} - -src_install() { - cmake-utils_src_install - - # multi-version header such that different seqan versions can be installed in parallel - mkdir "${ED%/}"/usr/include/${PN}-${seqan_majorminor_ver} || die - mv "${ED%/}"/usr/include/${PN}{,-${seqan_majorminor_ver}/} || die - - # pkg-config file - mv "${ED%/}"/usr/share/pkgconfig/${PN}-{${seqan_major_ver},${seqan_majorminor_ver}}.pc || die - - # create pkg-config symlink to restore default behaviour - dosym ${PN}-${seqan_majorminor_ver}.pc /usr/share/pkgconfig/${PN}-${seqan_major_ver}.pc -} diff --git a/sci-biology/seqan/seqan-2.4.0.ebuild b/sci-biology/seqan/seqan-2.4.0.ebuild deleted file mode 100644 index 8b337e77e6be..000000000000 --- a/sci-biology/seqan/seqan-2.4.0.ebuild +++ /dev/null @@ -1,92 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -: ${CMAKE_MAKEFILE_GENERATOR:=ninja} -PYTHON_COMPAT=( python2_7 ) - -inherit cmake-utils multibuild python-any-r1 toolchain-funcs - -DESCRIPTION="C++ Sequence Analysis Library" -HOMEPAGE="http://www.seqan.de/" - -if [[ ${PV} == *9999 ]]; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/seqan/seqan.git" - EGIT_BRANCH="develop" -else - SRC_URI="https://github.com/seqan/seqan/archive/seqan-v${PV}.tar.gz" - KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" - - S=${WORKDIR}/seqan-seqan-v${PV} -fi - -LICENSE="BSD GPL-3" -SLOT="0" -IUSE="cpu_flags_x86_sse4_1 doc tools" -REQUIRED_USE="cpu_flags_x86_sse4_1" - -RDEPEND=" - app-arch/bzip2:= - sys-libs/zlib:= - !!sci-biology/seqan:2.0 - !!sci-biology/seqan:2.1 - !!sci-biology/seqan:2.2" -DEPEND=" - ${RDEPEND} - doc? ( - $(python_gen_any_dep 'dev-python/sphinx[${PYTHON_USEDEP}]') - ${PYTHON_DEPS} - )" - -PATCHES=( "${FILESDIR}"/${PN}-2.4.0-fix-pthread.patch ) - -python_check_deps() { - use doc && has_version "dev-python/sphinx[${PYTHON_USEDEP}]" -} - -pkg_setup() { - if [[ ${MERGE_TYPE} != binary ]]; then - use doc && python-any-r1_pkg_setup - use tools && tc-check-openmp - - MULTIBUILD_VARIANTS=( - $(usev tools) - library - ) - fi -} - -src_configure() { - my_configure() { - local mycmakeargs=( -DCMAKE_INSTALL_DOCDIR="share/doc/${PF}" ) - case "${MULTIBUILD_ID}" in - tools) - mycmakeargs+=( - -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_APPS - -DSEQAN_NO_DOX=ON - ) - ;; - library) - mycmakeargs+=( - -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY - -DSEQAN_NO_DOX=$(usex !doc) - ) - ;; - *) - die "${MULTIBUILD_ID} is not recognized" - ;; - esac - cmake-utils_src_configure - } - multibuild_foreach_variant my_configure -} - -src_compile() { - multibuild_foreach_variant cmake-utils_src_compile -} - -src_install() { - multibuild_foreach_variant cmake-utils_src_install -} diff --git a/sci-biology/seqan/seqan-3.1.0.ebuild b/sci-biology/seqan/seqan-3.1.0.ebuild new file mode 100644 index 000000000000..976430bec641 --- /dev/null +++ b/sci-biology/seqan/seqan-3.1.0.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit cmake + +DESCRIPTION="C++ Sequence Analysis Library" +HOMEPAGE="https://www.seqan.de/" +SRC_URI="https://github.com/seqan/seqan3/releases/download/${PV}/seqan3-${PV}-Source.tar.xz" +S="${WORKDIR}/seqan3-${PV}-Source" + +LICENSE="BSD GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux" +IUSE="cpu_flags_x86_sse4_2" +REQUIRED_USE="cpu_flags_x86_sse4_2" + +RDEPEND=" + app-arch/bzip2:= + dev-cpp/range-v3 + dev-libs/cereal + sci-libs/lemon + sys-libs/zlib:= +" +DEPEND="${RDEPEND}" + +src_install() { + cmake_src_install + dodoc -r doc/* +} diff --git a/sci-biology/seqan/seqan-9999.ebuild b/sci-biology/seqan/seqan-9999.ebuild deleted file mode 100644 index 0005819ff4d3..000000000000 --- a/sci-biology/seqan/seqan-9999.ebuild +++ /dev/null @@ -1,90 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -: ${CMAKE_MAKEFILE_GENERATOR:=ninja} -PYTHON_COMPAT=( python2_7 ) - -inherit cmake-utils multibuild python-any-r1 toolchain-funcs - -DESCRIPTION="C++ Sequence Analysis Library" -HOMEPAGE="http://www.seqan.de/" - -if [[ ${PV} == *9999 ]]; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/seqan/seqan.git" - EGIT_BRANCH="develop" -else - SRC_URI="https://github.com/seqan/seqan/archive/seqan-v${PV}.tar.gz" - KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" - - S=${WORKDIR}/seqan-seqan-v${PV} -fi - -LICENSE="BSD GPL-3" -SLOT="0" -IUSE="cpu_flags_x86_sse4_1 doc tools" -REQUIRED_USE="cpu_flags_x86_sse4_1" - -RDEPEND=" - app-arch/bzip2:= - sys-libs/zlib:= - !!sci-biology/seqan:2.0 - !!sci-biology/seqan:2.1 - !!sci-biology/seqan:2.2" -DEPEND=" - ${RDEPEND} - doc? ( - $(python_gen_any_dep 'dev-python/sphinx[${PYTHON_USEDEP}]') - ${PYTHON_DEPS} - )" - -python_check_deps() { - use doc && has_version "dev-python/sphinx[${PYTHON_USEDEP}]" -} - -pkg_setup() { - if [[ ${MERGE_TYPE} != binary ]]; then - use doc && python-any-r1_pkg_setup - use tools && tc-check-openmp - - MULTIBUILD_VARIANTS=( - $(usev tools) - library - ) - fi -} - -src_configure() { - my_configure() { - local mycmakeargs=( -DCMAKE_INSTALL_DOCDIR="share/doc/${PF}" ) - case "${MULTIBUILD_ID}" in - tools) - mycmakeargs+=( - -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_APPS - -DSEQAN_NO_DOX=ON - ) - ;; - library) - mycmakeargs+=( - -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY - -DSEQAN_NO_DOX=$(usex !doc) - ) - ;; - *) - die "${MULTIBUILD_ID} is not recognized" - ;; - esac - cmake-utils_src_configure - } - multibuild_foreach_variant my_configure -} - -src_compile() { - multibuild_foreach_variant cmake-utils_src_compile -} - -src_install() { - multibuild_foreach_variant cmake-utils_src_install -} diff --git a/sci-biology/shrimp/Manifest b/sci-biology/shrimp/Manifest deleted file mode 100644 index 5be68cd79e21..000000000000 --- a/sci-biology/shrimp/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST SHRiMP_2_2_3.src.tar.gz 4596867 BLAKE2B 64e485b8e2524062c11c581bbcac426800c9f42f61da467378dbfd3add63f721a9da9c04df61bde3704e654a20395e799e89fc5e47129b1d3f5bc93f960470fa SHA512 029179aeeb317194b998c29aa91d1d2ce5ccbc6f9ad4a1043d1e5fc75d3344c2f39500ab07e8389c09fa179f0c9b59afee22691bc4eb5d396777f4e0fe25f2d5 diff --git a/sci-biology/shrimp/metadata.xml b/sci-biology/shrimp/metadata.xml deleted file mode 100644 index 959160fe46b1..000000000000 --- a/sci-biology/shrimp/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/shrimp/shrimp-2.2.3.ebuild b/sci-biology/shrimp/shrimp-2.2.3.ebuild deleted file mode 100644 index 2b57b032a1b2..000000000000 --- a/sci-biology/shrimp/shrimp-2.2.3.ebuild +++ /dev/null @@ -1,82 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit flag-o-matic python-single-r1 toolchain-funcs - -MY_PV=${PV//./_} - -DESCRIPTION="SHort Read Mapping Package" -HOMEPAGE="http://compbio.cs.toronto.edu/shrimp/" -SRC_URI="http://compbio.cs.toronto.edu/shrimp/releases/SHRiMP_${MY_PV}.src.tar.gz" - -LICENSE="shrimp" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="custom-cflags +cpu_flags_x86_sse2" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -# file collision on /usr/bin/utils #453044 -DEPEND="!sci-mathematics/cado-nfs" -RDEPEND="${DEPEND} - ${PYTHON_DEPS}" - -S=${WORKDIR}/SHRiMP_${MY_PV} - -pkg_pretend() { - use cpu_flags_x86_sse2 || die "This package needs sse2 support in your CPU" -} - -pkg_setup() { - if [[ ${CC} == *gcc* ]] && ! tc-has-openmp; then - elog "Please set CC to an OPENMP capable compiler (e.g. gcc[openmp] or icc" - die "C compiler lacks OPENMP support" - fi - python-single-r1_pkg_setup -} - -src_prepare() { - sed \ - -e '1 a #include <stdint.h>' \ - -i common/dag_glue.cpp || die - # respect LDFLAGS wrt 331823 - sed \ - -e "s/LDFLAGS/LIBS/" \ - -e "s/\$(LD)/& \$(LDFLAGS)/" \ - -e 's/-static//' \ - -i Makefile || die - - append-flags -fopenmp - if ! use custom-cflags; then - append-flags -O3 - replace-flags -O* -O3 - fi - tc-export CXX - - cd utils || die - sed -e '/^#!/d' -i *py || die - sed -e '1i#!/usr/bin/python' -i *py || die -} - -src_compile() { - emake CXXFLAGS="${CXXFLAGS}" LDFLAGS="${LDFLAGS}" -} - -src_install() { - local i - newdoc bin/README README.bin && rm bin/README - dobin bin/* utils/split-contigs utils/temp-sink - dodoc HISTORY README TODO SPLITTING_AND_MERGING SCORES_AND_PROBABILITES - - pushd utils > /dev/null - - python_doscript *py - - rm *.py *.o *.c split-contigs temp-sink || die - insinto /usr/share/${PN} - doins -r * -} diff --git a/sci-biology/sibsim4/files/sibsim4-0.20-makefile.patch b/sci-biology/sibsim4/files/sibsim4-0.20-makefile.patch new file mode 100644 index 000000000000..6436747e3dd9 --- /dev/null +++ b/sci-biology/sibsim4/files/sibsim4-0.20-makefile.patch @@ -0,0 +1,26 @@ +--- a/Makefile ++++ b/Makefile +@@ -21,13 +21,12 @@ + # to change it to this: + # CFLAGS = -Xc + +-CFLAGS = -std=gnu99 -W -Wall -Wconversion -pedantic $(DEBUG) $(OPT) ++CFLAGS += -std=gnu99 -Wall -Wconversion -pedantic + + + # The default is GCC. On Solaris, you might put: + # CC = /opt/SUNWspro/bin/cc + +-CC = gcc + + + # Depending on the compile flags you use, you might need to explicitly use the +@@ -42,7 +41,7 @@ + OBJS = sim4b1.o align.o misc.o sim4.init.o + + sim4: $(OBJS) +- $(CC) -o SIBsim4 $(CFLAGS) $(OBJS) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o SIBsim4 $(OBJS) $(LIBS) + + clean: + rm -f SIBsim4 *.o diff --git a/sci-biology/sibsim4/metadata.xml b/sci-biology/sibsim4/metadata.xml index 9445a4950bc0..149d1330aaf9 100644 --- a/sci-biology/sibsim4/metadata.xml +++ b/sci-biology/sibsim4/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/sibsim4/sibsim4-0.20.ebuild b/sci-biology/sibsim4/sibsim4-0.20.ebuild index bf431c666920..2c9d69ada02c 100644 --- a/sci-biology/sibsim4/sibsim4-0.20.ebuild +++ b/sci-biology/sibsim4/sibsim4-0.20.ebuild @@ -1,31 +1,22 @@ -# Copyright 1999-2013 Gentoo Foundation +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=7 inherit toolchain-funcs DESCRIPTION="A rewrite and improvement upon sim4, a DNA-mRNA aligner" HOMEPAGE="http://sibsim4.sourceforge.net/" -SRC_URI="mirror://sourceforge/${PN}/SIBsim4-${PV}.tar.gz" +SRC_URI="https://downloads.sourceforge.net/${PN}/SIBsim4-${PV}.tar.gz" +S="${WORKDIR}/SIBsim4-${PV}" LICENSE="GPL-2" SLOT="0" -IUSE="" -KEYWORDS="amd64 x86" - -DEPEND="" -RDEPEND="" +KEYWORDS="amd64 ~x86" -S="${WORKDIR}/SIBsim4-${PV}" +PATCHES=( "${FILESDIR}"/${P}-makefile.patch ) -src_prepare() { - sed \ - -e 's/CFLAGS = /CFLAGS +=/' \ - -e '/^CC/s:=:?=:' \ - -e '/^OPT/d' \ - -e "s:-o:${LDFLAGS} -o:g" \ - -i "${S}/Makefile" || die +src_configure() { tc-export CC } diff --git a/sci-biology/sim4/metadata.xml b/sci-biology/sim4/metadata.xml index 6366d6fb797e..1e40799f38d9 100644 --- a/sci-biology/sim4/metadata.xml +++ b/sci-biology/sim4/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/stride/Manifest b/sci-biology/stride/Manifest index 8d9e9236f0cc..bfd0e48635ba 100644 --- a/sci-biology/stride/Manifest +++ b/sci-biology/stride/Manifest @@ -1,2 +1,4 @@ DIST stride-20011129.tar.gz 56441 BLAKE2B 4d4cd3f9f6cef997fff10571aecb70cb21056e88c5130e7dfdafe15a6fb353656d0635b4d65895ef115479a87dcf600b659455d15460344c838543a2e356bfae SHA512 cbd40fce4684728f363520540132fc1a0003126954a145d59aeff48adb20fdaa66520bd12b56ee5d2906e8ea97bf78a225204105b820f7f368aee5e790a6471b +DIST stride-20030408.tar.gz 318997 BLAKE2B 0a6fbb7da0a18cc9fbc4beb3214488080e5f6b85b93f87a33f3d6c38385da12707ee0eb2a10a86c9f6dd3884bd043e3f7f36c6aac797da7dc4f351fab047a950 SHA512 50d71c053118ca078dd9a4659d9b0f62d1f1101519e01b258a088e229ad2062bec917160c7794f18c96d982992d5571f93508365ff4f6e76438da8183390b498 +DIST stride-20060723-update-r1.patch.xz 5888 BLAKE2B 6f477787004fd962b2faf5f0dd1a497067608eb8fcc5d16e161d918ecff7a6b86184eeb5f97ece4465d7595dd64fd0958a6bcedb76f2b666bdc4d0947e51eda0 SHA512 5ecaa5c262856009e188c00a9cf75765fcd7988ebe3cf0389101a4c281fdbc8d085a024fa78b6c88916528d1158133873ebf38a070a66b7e76f842586646ba2d DIST stride-20060723-update.patch.bz2 5621 BLAKE2B 266a7371c0963a996430c1f809b46196e8bf179fcf2afb4380f6eccd092c03b29d5b09b8a8438ee7848d0f411920db2e4465ef646c75a406197412f35e880179 SHA512 e06eb68b907615e12dc1a9981be157400e9ffed9391a906cb4eb3ef4067b7027c26cc600298053bfc5d2bbbebbbfefe0e6b18d0e4f6fef2172768e6f95498af1 diff --git a/sci-biology/stride/files/stride-20011129-clang16.patch b/sci-biology/stride/files/stride-20011129-clang16.patch new file mode 100644 index 000000000000..e1e4383a3281 --- /dev/null +++ b/sci-biology/stride/files/stride-20011129-clang16.patch @@ -0,0 +1,15 @@ +https://bugs.gentoo.org/874069 +--- a/hydrbond.c ++++ b/hydrbond.c +@@ -293,3 +293,3 @@ + int dc, ac, ccd, cca, cc, hc=0, i; +- void (*HBOND_Energy)(); ++ void (*HBOND_Energy)(float*, float*, float*, float*, float*, COMMAND*, HBOND*); + BUFFER Text; +--- a/p_atom.c ++++ b/p_atom.c +@@ -11,3 +11,3 @@ + RESIDUE *r; +- register i; ++ register int i; + diff --git a/sci-biology/stride/metadata.xml b/sci-biology/stride/metadata.xml index 959160fe46b1..ccdff086e20b 100644 --- a/sci-biology/stride/metadata.xml +++ b/sci-biology/stride/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/stride/stride-20011129-r1.ebuild b/sci-biology/stride/stride-20011129-r1.ebuild index 678887de925e..13bfc8e29073 100644 --- a/sci-biology/stride/stride-20011129-r1.ebuild +++ b/sci-biology/stride/stride-20011129-r1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 @@ -9,11 +9,11 @@ DESCRIPTION="Protein secondary structure assignment from atomic coordinates" HOMEPAGE="http://webclu.bio.wzw.tum.de/stride/" SRC_URI=" ftp://ftp.ebi.ac.uk/pub/software/unix/${PN}/src/${PN}.tar.gz -> ${P}.tar.gz - https://dev.gentoo.org/~jlec/distfiles/${PN}-20060723-update.patch.bz2" + https://dev.gentoo.org/~pacho/${PN}/${PN}-20060723-update.patch.bz2" LICENSE="STRIDE" SLOT="0" -KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~x86-macos" +KEYWORDS="amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" RESTRICT="mirror bindist" S="${WORKDIR}" @@ -22,6 +22,7 @@ PATCHES=( # version which was kindly provided by the author "${S}"/${PN}-20060723-update.patch "${FILESDIR}"/${PN}-20011129-fix-buildsystem.patch + "${FILESDIR}"/${PN}-20011129-clang16.patch ) src_configure() { diff --git a/sci-biology/stride/stride-20060723.ebuild b/sci-biology/stride/stride-20060723.ebuild new file mode 100644 index 000000000000..45c2f457468b --- /dev/null +++ b/sci-biology/stride/stride-20060723.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 +inherit toolchain-funcs + +DESCRIPTION="Protein secondary structure assignment from atomic coordinates" +HOMEPAGE="http://webclu.bio.wzw.tum.de/stride/" +# Version 20030408 per dates in upstream tarball +UPSTREAM_VER="20030408" +SRC_URI="https://webclu.bio.wzw.tum.de/stride/${PN}.tar.gz -> ${PN}-${UPSTREAM_VER}.tar.gz + https://dev.gentoo.org/~pacho/${PN}/${PN}-20060723-update-r1.patch.xz" + +LICENSE="STRIDE" +SLOT="0" +KEYWORDS="amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +RESTRICT="mirror bindist" + +S="${WORKDIR}" +PATCHES=( + # This patch updates the source to the most recent + # version which was kindly provided by the author + "${S}"/${P}-update-r1.patch + + "${FILESDIR}"/${PN}-20011129-fix-buildsystem.patch + "${FILESDIR}"/${PN}-20011129-clang16.patch +) + +src_configure() { + tc-export CC +} + +src_install() { + dobin ${PN} +} diff --git a/sci-biology/t-coffee/files/t-coffee-11.00-makefile.patch b/sci-biology/t-coffee/files/t-coffee-11.00-makefile.patch new file mode 100644 index 000000000000..b7a6d9e17a5e --- /dev/null +++ b/sci-biology/t-coffee/files/t-coffee-11.00-makefile.patch @@ -0,0 +1,19 @@ +--- a/t_coffee_source/makefile ++++ b/t_coffee_source/makefile +@@ -1,14 +1,12 @@ +-CC=g++ +-CFLAGS=-O3 -Wno-write-strings + SOURCES := $(shell find . -type f -name *.c) + OBJECTS := $(SOURCES:.c=.o) + DEPS := $(OBJECTS:.o=.deps) + + t_coffee: $(OBJECTS) +- @echo " Linking..."; $(CC) $^ -o t_coffee -lm ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) $^ -o t_coffee -lm $(LIBS) + + %.o: %.c +- @echo " CC $<"; $(CC) $(CFLAGS) -I. -MD -MF $(@:.o=.deps) -c -o $@ $< ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) -I. -MD -MF $(@:.o=.deps) -c -o $@ $< + + -include $(DEPS) + diff --git a/sci-biology/t-coffee/metadata.xml b/sci-biology/t-coffee/metadata.xml index b3853e6454a3..bc6621eb034f 100644 --- a/sci-biology/t-coffee/metadata.xml +++ b/sci-biology/t-coffee/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> @@ -14,4 +14,7 @@ estimate the level of consistency of each position within the new alignment with the rest of the alignments. </longdescription> + <upstream> + <remote-id type="github">cbcrg/tcoffee</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/t-coffee/t-coffee-11.00-r2.ebuild b/sci-biology/t-coffee/t-coffee-11.00-r3.ebuild index df1859afb208..89966a0580d2 100644 --- a/sci-biology/t-coffee/t-coffee-11.00-r2.ebuild +++ b/sci-biology/t-coffee/t-coffee-11.00-r3.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 -inherit toolchain-funcs +inherit flag-o-matic toolchain-funcs MY_HASH="4466924" MY_PV="${PV}.${MY_HASH}" @@ -12,6 +12,7 @@ MY_P="${PN^^}_distribution_Version_${MY_PV}" DESCRIPTION="A multiple sequence alignment package" HOMEPAGE="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html" SRC_URI="http://www.tcoffee.org/Packages/Beta/Latest/${MY_P}.tar.gz" +S="${WORKDIR}/${MY_P}" LICENSE="GPL-2" SLOT="0" @@ -20,35 +21,35 @@ KEYWORDS="~amd64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux" RDEPEND=" sci-biology/clustalw sci-chemistry/tm-align" -DEPEND="" -S="${WORKDIR}/${MY_P}" PATCHES=( "${FILESDIR}"/${P}-mayhem.patch "${FILESDIR}"/${P}-set_proper_dir_permissions.patch "${FILESDIR}"/${P}-cxx11.patch "${FILESDIR}"/${P}-gcc7.patch + "${FILESDIR}"/${P}-makefile.patch ) -src_prepare() { - default - sed \ - -e '/@/s:.*;:\t:g' \ - -e '/Linking/s:$(CC):$(CC) $(CFLAGS) $(LDFLAGS):g' \ - -i t_coffee_source/makefile || die +src_configure() { + # -Werror=strict-aliasing + # https://bugs.gentoo.org/862327 + # https://github.com/cbcrg/tcoffee/issues/60 + # + # Do not trust with LTO either + append-flags -fno-strict-aliasing + filter-lto + + tc-export CXX + append-cxxflags -Wno-write-strings -Wno-unused-result } src_compile() { - emake \ - V=1 \ - CC="$(tc-getCXX)" \ - CFLAGS="${CXXFLAGS} -Wno-write-strings -Wno-unused-result" \ - -C t_coffee_source t_coffee + emake -C t_coffee_source t_coffee } src_install() { dobin t_coffee_source/t_coffee - insinto /usr/share/${PN} + insinto /usr/share/t-coffee doins -r example } diff --git a/sci-biology/tophat/Manifest b/sci-biology/tophat/Manifest deleted file mode 100644 index 05897bbf09e4..000000000000 --- a/sci-biology/tophat/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST tophat-2.1.1.tar.gz 2259554 BLAKE2B f01b08cc2046b7d143864d64aa3e34d3000c7c10d7e50a4e102d500556e8620996de03392463f9d08ae97858eaec85b2df3b5d5ee5b0b4f7a5c0ae06bb3d08e8 SHA512 e2e0943a6f3d34b83922e6e403b65a3bee480a2b2bb4bf2de0cae7e0ef5bb166b66fec923316c2b643e8550e43c842f0f1bcc2ca7249d20fbcf5a4733fbdeabc diff --git a/sci-biology/tophat/files/tophat-2.1.1-fix-c++14.patch b/sci-biology/tophat/files/tophat-2.1.1-fix-c++14.patch deleted file mode 100644 index e8168bb91438..000000000000 --- a/sci-biology/tophat/files/tophat-2.1.1-fix-c++14.patch +++ /dev/null @@ -1,14 +0,0 @@ -Fix building with C++14, which errors out due to broken perfect forwarding signature. -See also: https://bugs.gentoo.org/show_bug.cgi?id=594544 - ---- a/src/tophat_reports.cpp -+++ b/src/tophat_reports.cpp -@@ -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/sci-biology/tophat/files/tophat-2.1.1-python2-shebangs.patch b/sci-biology/tophat/files/tophat-2.1.1-python2-shebangs.patch deleted file mode 100644 index 5c38bcc072ef..000000000000 --- a/sci-biology/tophat/files/tophat-2.1.1-python2-shebangs.patch +++ /dev/null @@ -1,42 +0,0 @@ -Make Python 2 explicit in python scripts - ---- a/src/bed_to_juncs -+++ b/src/bed_to_juncs -@@ -1,4 +1,4 @@ --#!/usr/bin/env python -+#!/usr/bin/env python2 - # encoding: utf-8 - """ - bed_to_juncs.py ---- a/src/contig_to_chr_coords -+++ b/src/contig_to_chr_coords -@@ -1,4 +1,4 @@ --#!/usr/bin/env python -+#!/usr/bin/env python2 - # encoding: utf-8 - """ - contig_to_chr_coords.py ---- a/src/sra_to_solid -+++ b/src/sra_to_solid -@@ -1,4 +1,4 @@ --#!/usr/bin/env python -+#!/usr/bin/env python2 - - """ - sra_to_solid.py ---- a/src/tophat-fusion-post -+++ b/src/tophat-fusion-post -@@ -1,4 +1,4 @@ --#!/usr/bin/env python -+#!/usr/bin/env python2 - - - """ ---- a/src/tophat.py -+++ b/src/tophat.py -@@ -1,4 +1,4 @@ --#!/usr/bin/env python -+#!/usr/bin/env python2 - - # encoding: utf-8 - """ diff --git a/sci-biology/tophat/files/tophat-2.1.1-unbundle-seqan-samtools.patch b/sci-biology/tophat/files/tophat-2.1.1-unbundle-seqan-samtools.patch deleted file mode 100644 index 9d0a2694051a..000000000000 --- a/sci-biology/tophat/files/tophat-2.1.1-unbundle-seqan-samtools.patch +++ /dev/null @@ -1,162 +0,0 @@ -Unbundle the included samtools and SeqAn, and use system libraries. -See also: https://bugs.gentoo.org/show_bug.cgi?id=566494 - -Remove ancient ax_boost_base.m4 and ax_boost_thread.m4, and depend -on >=sys-devel/autoconf-archive-2016.09.16 in the ebuild instead. -See also: https://bugs.gentoo.org/show_bug.cgi?id=594810 - ---- a/configure.ac -+++ b/configure.ac -@@ -28,26 +28,15 @@ - AC_PROG_INSTALL - AM_PATH_PYTHON([2.4]) - --m4_include([ax_boost_base.m4]) --m4_include([ax_boost_thread.m4]) - # CXXFLAGS="$CXXFLAGS $threadLib" - AX_BOOST_BASE([1.38.0]) -+AX_BOOST_SYSTEM - AX_BOOST_THREAD --if test -z "$BOOST_THREAD_LIBS"; then -+if test -z "$BOOST_THREAD_LIB"; then - AC_MSG_ERROR([boost.thread not found. Aborting.]) - fi - - --# BAM related: -- ac_bam_path=samtools-0.1.18 -- BAM_LIB="-lbam" -- BAM_LDFLAGS="-L./$ac_bam_path" -- BAM_CPPFLAGS="-I./$ac_bam_path" -- AC_SUBST(BAM_CPPFLAGS) -- AC_SUBST(BAM_LDFLAGS) -- AC_SUBST(BAM_LIB) -- -- - # Checks for header files. - AC_CHECK_HEADERS([stdlib.h string.h unistd.h]) - -@@ -80,32 +69,23 @@ - # set CFLAGS and CXXFLAGS - #user_CFLAGS="${CXXFLAGS}" - user_CFLAGS=${CFLAGS} --generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized" -+generic_CFLAGS="" - ext_CFLAGS="" - debug_CFLAGS="" - user_LDFLAGS="$LDFLAGS" - --AC_ARG_ENABLE(intel64, [ --enable-intel64 optimize for Intel64 CPU such as Xeon and Core2], -- [ext_CFLAGS="${ext_CFLAGS} -mtune=nocona"], []) -- - AC_ARG_ENABLE([debug], - [AS_HELP_STRING([--enable-debug], - [enable debugging info (default is no)])], - [], [enable_debug=no]) --AC_ARG_ENABLE([optim], -- [AS_HELP_STRING([--enable-optim@<:@=0|1|2|3@:>@], -- [set optimization level (default is 3)])], -- [if test "x$enable_optim" = xyes; then enable_optim=3; fi], -- [enable_optim=3]) - --AS_IF([test "x$enable_optim" != xno], [ext_CFLAGS="$ext_CFLAGS -O$enable_optim"]) - AS_IF([test "x$enable_debug" = xyes], - [debug_CFLAGS="-DDEBUG"], - [debug_CFLAGS="-DNDEBUG"]) - - CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS}" - CXXFLAGS="$CFLAGS" --CXXFLAGS="$CXXFLAGS $BAM_CPPFLAGS $BOOST_CPPFLAGS -I./SeqAn-1.4.2" -+CXXFLAGS="$CXXFLAGS $BAM_CPPFLAGS $BOOST_CPPFLAGS" - LDFLAGS="$BAM_LDFLAGS $BOOST_LDFLAGS $user_LDFLAGS" - - AM_INIT_AUTOMAKE([-Wall foreign tar-pax foreign]) -@@ -122,7 +102,7 @@ - -- ${PACKAGE_STRING} Configuration Results -- - C++ compiler: ${CXX} ${CXXFLAGS} - Linker flags: ${LDFLAGS} -- BOOST libraries: ${BOOST_THREAD_LIBS}" -+ BOOST libraries: ${BOOST_THREAD_LIB}" - - if test x"${GCC}" = x"yes" ; then - gcc_version=`${CC} --version | head -n 1` ---- a/src/Makefile.am -+++ b/src/Makefile.am -@@ -683,17 +683,12 @@ - SeqAn-1.4.2/seqan/system/system_thread.h \ - SeqAn-1.4.2/seqan/version.h - --SAMDIR = ./samtools-0.1.18 --SAMLIB = libbam.a --SAMPROG = samtools_0.1.18 --BAM_LIB = -lbam --BAM_CPPFLAGS = -I$(SAMDIR) --BAM_LDFLAGS = -L$(SAMDIR) -+BAM_LIB = -lbam-0.1-legacy -+AM_CPPFLAGS = -I/usr/include/bam-0.1-legacy/ - - #-- progs to be installed in $prefix/bin - - bin_PROGRAMS = \ -- $(SAMPROG) \ - prep_reads \ - gtf_to_fasta \ - fix_map_ordering \ -@@ -722,9 +717,6 @@ - tophat2 \ - tophat - --clean-local: -- cd $(SAMDIR) && make clean -- - tophat2: tophat2.sh - cp tophat2.sh tophat2 && chmod 755 tophat2 - -@@ -732,7 +724,7 @@ - sed -e 's|__VERSION__|$(VERSION)|' tophat.py > tophat && chmod 755 tophat - - #-- tophat library for linking convienence --noinst_LIBRARIES = $(SAMLIB) libgc.a libtophat.a -+noinst_LIBRARIES = libgc.a libtophat.a - - noinst_HEADERS = \ - reads.h \ -@@ -801,11 +793,11 @@ - prep_reads_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) - - segment_juncs_SOURCES = segment_juncs.cpp --segment_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIBS) $(BOOST_SYSTEM_LIB) $(BAM_LIB) -+segment_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB) - segment_juncs_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) $(BOOST_LDFLAGS) - - long_spanning_reads_SOURCES = long_spanning_reads.cpp --long_spanning_reads_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIBS) $(BOOST_SYSTEM_LIB) $(BAM_LIB) -+long_spanning_reads_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB) - long_spanning_reads_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) $(BOOST_LDFLAGS) - - gtf_juncs_SOURCES = gtf_juncs.cpp -@@ -817,7 +809,7 @@ - juncs_db_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) - - tophat_reports_SOURCES = tophat_reports.cpp --tophat_reports_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIBS) $(BOOST_SYSTEM_LIB) $(BAM_LIB) -+tophat_reports_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB) - tophat_reports_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) $(BOOST_LDFLAGS) - - fix_map_ordering_SOURCES = fix_map_ordering.cpp -@@ -844,15 +836,5 @@ - gtf_to_fasta_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB) - gtf_to_fasta_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) - -- --libbam_a_SOURCES = --samtools_0_1_18_SOURCES = -- --$(SAMPROG): $(SAMLIB) -- -- --$(SAMLIB): -- cd $(SAMDIR) && make $(SAMPROG) && cp $(SAMLIB) $(SAMPROG) .. -- - install-data-hook: - cp -r intervaltree sortedcontainers $(DESTDIR)$(bindir) diff --git a/sci-biology/tophat/metadata.xml b/sci-biology/tophat/metadata.xml deleted file mode 100644 index 959160fe46b1..000000000000 --- a/sci-biology/tophat/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/tophat/tophat-2.1.1-r4.ebuild b/sci-biology/tophat/tophat-2.1.1-r4.ebuild deleted file mode 100644 index 590f6eb2d20f..000000000000 --- a/sci-biology/tophat/tophat-2.1.1-r4.ebuild +++ /dev/null @@ -1,81 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit autotools flag-o-matic python-single-r1 toolchain-funcs - -DESCRIPTION="Python-based splice junction mapper for RNA-Seq reads using bowtie2" -HOMEPAGE="https://ccb.jhu.edu/software/tophat/" -SRC_URI="https://ccb.jhu.edu/software/tophat/downloads/${P}.tar.gz" - -LICENSE="Artistic" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="debug" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND="${PYTHON_DEPS} - dev-libs/boost:=[threads] - dev-python/intervaltree[${PYTHON_USEDEP}] - dev-python/sortedcontainers[${PYTHON_USEDEP}] - sci-biology/samtools:0.1-legacy - sci-biology/bowtie:2" -DEPEND="${RDEPEND} - virtual/pkgconfig - sci-biology/seqan:1.4 - >=sys-devel/autoconf-archive-2016.09.16" - -PATCHES=( - "${FILESDIR}"/${P}-unbundle-seqan-samtools.patch - "${FILESDIR}"/${P}-fix-c++14.patch - "${FILESDIR}"/${P}-python2-shebangs.patch -) - -src_prepare() { - default - - # remove bundled libs - rm -rf src/samtools-0.1.18/ src/SeqAn-1.4.2/ || die - - sed -e "s:samtools_0.1.18:${EPREFIX}/usr/bin/samtools-0.1-legacy/samtools:" \ - -i src/tophat.py src/common.cpp || die - - sed -e "s:/usr/include/bam-0.1-legacy/:${EPREFIX}/usr/include/bam-0.1-legacy/:" \ - -e '/^samtools-0\.1\.18\//d' \ - -e '/^SeqAn-1\.4\.2\//d' \ - -e 's:sortedcontainers/sortedset.py \\:sortedcontainers/sortedset.py:' \ - -e 's:\$(top_builddir)\/src\/::' \ - -i src/Makefile.am || die - sed -e 's:\$(top_builddir)\/src\/::' -i src/Makefile.am || die - - # innocuous non-security flags, prevent log pollution - append-cflags -Wno-unused-but-set-variable -Wno-unused-variable - append-cppflags "$($(tc-getPKG_CONFIG) --cflags seqan-1.4)" - - # remove ancient autoconf archive macros, wreaking havoc, - # depend on sys-devel/autoconf-archive instead, bug #594810 - rm {ax_boost_thread,ax_boost_base}.m4 || die - - eautoreconf -} - -src_configure() { - econf $(use_enable debug) -} - -src_install() { - default - - # delete bundled python modules - local i - for i in intervaltree sortedcontainers; do - rm -r "${ED%/}"/usr/bin/${i} || die - done -} - -pkg_postinst() { - optfeature "ABI SOLiD colorspace reads" sci-biology/bowtie:1 -} diff --git a/sci-biology/transfac/Manifest b/sci-biology/transfac/Manifest deleted file mode 100644 index 78b209e166c0..000000000000 --- a/sci-biology/transfac/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST transfac32.tar.Z 3346266 BLAKE2B 3bd6cfacd7e4ea75946dce5e77bae84a7d199daa84750fe21cd3c393fa66cdf09518a4043ac15f2fbe7bc19f001482e14b65743f1a89aec34bcb28409277370e SHA512 d7004f90e57fa2b8839714e50b9ce1f67357db404adc1a5caddd1e9b86c8e3e9f4e85bbda15c4d6afed85da82ae8615f63260f9a3df9cfd79897d38896893b9f diff --git a/sci-biology/transfac/metadata.xml b/sci-biology/transfac/metadata.xml deleted file mode 100644 index a8cecf4529c2..000000000000 --- a/sci-biology/transfac/metadata.xml +++ /dev/null @@ -1,16 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <longdescription> - TRANSFAC® is a database of eukaryotic transcription factors, of their - genomic binding sites and DNA-binding profiles. TRANSFAC 3.2 is an old - public version available at the European Bioinformatics Institute. - TRANSFAC® is currently maintained by the BIOBASE company. Altough they - offer public access to a more recent version of the database, they - offer no free downloadable version. - </longdescription> -</pkgmetadata> diff --git a/sci-biology/transfac/transfac-3.2-r1.ebuild b/sci-biology/transfac/transfac-3.2-r1.ebuild deleted file mode 100644 index 91b16f4b4fe4..000000000000 --- a/sci-biology/transfac/transfac-3.2-r1.ebuild +++ /dev/null @@ -1,43 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -DESCRIPTION="A database of eucaryotic transcription factors" -HOMEPAGE="http://www.gene-regulation.com/pub/databases.html" -SRC_URI="ftp://ftp.ebi.ac.uk/pub/databases/${PN}/${PN}32.tar.Z" - -LICENSE="public-domain" -SLOT="3" -# Minimal build keeps only the indexed files (if applicable) and the documentation. -# The non-indexed database is not installed. -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="emboss minimal" - -DEPEND="emboss? ( sci-biology/emboss )" -RDEPEND="${DEPEND}" - -S=${WORKDIR} - -src_compile() { - if use emboss; then - einfo - einfo "Indexing TRANSFAC for usage with EMBOSS" - EMBOSS_DATA="." tfextract -auto -infile class.dat || die "Indexing TRANSFAC failed" - einfo - fi -} - -src_install() { - newdoc readme.txt README - - if ! use minimal; then - insinto /usr/share/${PN}-${SLOT} - doins *.dat - fi - - if use emboss; then - insinto /usr/share/EMBOSS/data - doins tf* - fi -} diff --git a/sci-biology/tree-puzzle/files/tree-puzzle-5.2-C99-decls.patch b/sci-biology/tree-puzzle/files/tree-puzzle-5.2-C99-decls.patch new file mode 100644 index 000000000000..98456c0dacc1 --- /dev/null +++ b/sci-biology/tree-puzzle/files/tree-puzzle-5.2-C99-decls.patch @@ -0,0 +1,360 @@ +--- a/src/consensus.c ++++ b/src/consensus.c +@@ -32,7 +32,7 @@ + /******************************************************************************/ + + /* prepare for consensus tree analysis */ +-void initconsensus() ++void initconsensus(void) + { + # if ! PARALLEL + biparts = new_cmatrix(Maxspc-3, Maxspc); +--- a/src/consensus.h ++++ b/src/consensus.h +@@ -65,7 +65,7 @@ + /******************************************************************************/ + + /* prepare for consensus tree analysis */ +-void initconsensus(); ++void initconsensus(void); + + /* recursive function to get bipartitions */ + /* traversal should be optimazable (HAS) */ +--- a/src/ml1.c ++++ b/src/ml1.c +@@ -244,7 +244,7 @@ + /***************************** exported functions *****************************/ + + +-void evaluateseqs() ++void evaluateseqs(void) + { + ivector ali; + +@@ -1018,7 +1018,7 @@ + + + /* compute 1 PAM rate matrix, its eigensystem, and the inverse matrix thereof */ +-void tranprobmat() ++void tranprobmat(void) + { + eigensystem(Eval, Evec); /* eigensystem of 1 PAM rate matrix */ + luinverse(Evec, Ievc, tpmradix); /* inverse eigenvectors are in Ievc */ +@@ -1324,7 +1324,7 @@ + + + /* initialize distance matrix */ +-void initdistan() ++void initdistan(void) + { + int i, j, k, diff, x, y; + double obs, temp; +@@ -1478,7 +1478,7 @@ + + #else /* not PARALLEL */ + +-void computedistan() ++void computedistan(void) + { + int i, j; + +--- a/src/ml2.c ++++ b/src/ml2.c +@@ -1036,7 +1036,7 @@ + + + /* preparation for ML analysis */ +-void mlstart() ++void mlstart(void) + { + /* number of states and code length */ + tpmradix = gettpmradix(); +@@ -1098,7 +1098,7 @@ + + + /* cleanup after ML analysis */ +-void mlfinish() ++void mlfinish(void) + { + if (Ctree != NULL) + free_tree(Ctree, Numspc); +@@ -1566,7 +1566,7 @@ + int bestratefound, + int ncats) /* numcats */ + #endif +-void findbestratecombination() ++void findbestratecombination(void) + { + int k, u; + double bestvalue, fv2; +@@ -2147,7 +2147,7 @@ + } /* clock_lklhd */ + + /* find out the edge containing the root */ +-int findrootedge() ++int findrootedge(void) + { + int e, ebest; + double logbest, logtest; +--- a/src/mlparam.c ++++ b/src/mlparam.c +@@ -70,7 +70,7 @@ + } + + /* compute rates of each category when rates are Gamma-distributed */ +-void updaterates() ++void updaterates(void) + { + int i; + double alpha; +@@ -190,7 +190,7 @@ + } + + /* estimate substitution process parameters - random quartets */ +-void optimseqevolparamsquart() ++void optimseqevolparamsquart(void) + { + double tsmeanold, yrmeanold; + dvector tslist, yrlist; +@@ -320,7 +320,7 @@ + + + /* optimize substitution process parameters - tree */ +-void optimseqevolparamstree() ++void optimseqevolparamstree(void) + { + twodimenmin(EPSILON_SUBSTPARAM, + (SH_optn || nuc_optn) && optim_optn && (data_optn == 0), +@@ -379,7 +379,7 @@ + + + /* optimize rate heterogeneity parameters */ +-void optimrateparams() ++void optimrateparams(void) + { + twodimenmin(EPSILON_RATEPARAM, + fracinv_optim, +@@ -396,7 +396,7 @@ + + /* estimate parameters of substitution process and rate heterogeneity - no tree + n-taxon tree is not needed because of quartet method or NJ tree topology */ +-void estimateparametersnotree() ++void estimateparametersnotree(void) + { + int it, nump, change; + double TSold, YRold, FIold, GEold; +@@ -495,7 +495,7 @@ + + /* estimate parameters of substitution process and rate heterogeneity - tree + same as above but here the n-taxon tree is already in memory */ +-void estimateparameterstree() ++void estimateparameterstree(void) + { + int it, nump, change; + double TSold, YRold, FIold, GEold; +--- a/src/model1.c ++++ b/src/model1.c +@@ -31,7 +31,7 @@ + #include "ml.h" + + /* number of states of the selected model */ +-int gettpmradix() ++int gettpmradix(void) + { + if (data_optn == 0) { /* nucleotides */ + if (nuc_optn) return 4; +--- a/src/puzzle1.c ++++ b/src/puzzle1.c +@@ -345,7 +345,7 @@ + /******************************************************************************/ + + /* compute TN parameters according to F84 Ts/Tv ratio */ +-void makeF84model() ++void makeF84model(void) + { + double rho, piA, piC, piG, piT, piR, piY, ts, yr; + +@@ -390,7 +390,7 @@ + } /* makeF84model */ + + /* compute number of quartets used in LM analysis */ +-void compnumqts() ++void compnumqts(void) + { + if (lmqts == 0) { + if (numclust == 4) +@@ -407,7 +407,7 @@ + } /* compnumqts */ + + /* set options interactively */ +-void setoptions() ++void setoptions(void) + { + int i, valid; + double sumfreq; +@@ -1718,7 +1718,7 @@ + } /* closefile */ + + /* symmetrize doublet frequencies */ +-void symdoublets() ++void symdoublets(void) + { + int i, imean; + double mean; +@@ -1769,7 +1769,7 @@ + } /* symdoublets */ + + /* show Ts/Tv ratio and Ts Y/R ratio */ +-void computeexpectations() ++void computeexpectations(void) + { + double AlphaYBeta, AlphaRBeta, piR, piY, num, denom, pyr, pur; + +@@ -4604,7 +4604,7 @@ + /* Reconstruct a tree with QP */ + /* (parameter estimation already done) */ + +-void recon_tree() ++void recon_tree(void) + { + int i; + unsigned char tmpweight; +@@ -4848,7 +4848,7 @@ + + /***************************************************************/ + +-void map_lklhd() ++void map_lklhd(void) + { + int i, a, a1, a2, b, b1, b2, c, c1, c2, d; + uli nq; +@@ -5101,7 +5101,7 @@ + + /***************************************************************/ + +-void setdefaults() { ++void setdefaults(void) { + + strcpy(INFILE, INFILEDEFAULT); + strcpy(OUTFILE, OUTFILEDEFAULT); +@@ -6027,7 +6027,7 @@ + + /***************************************************************/ + +-void memcleanup() { ++void memcleanup(void) { + if (puzzlemode == QUARTPUZ && typ_optn == TREERECON_OPTN) { + free(splitfreqs); + free(splitpatterns); +--- a/src/puzzle2.c ++++ b/src/puzzle2.c +@@ -860,7 +860,7 @@ + + + /* estimate mean base frequencies from translated data set */ +-void estimatebasefreqs() ++void estimatebasefreqs(void) + { + int tpmradix, i, j; + uli all, *gene; +@@ -903,7 +903,7 @@ + + + /* guess model of substitution */ +-void guessmodel() ++void guessmodel(void) + { + double c1, c2, c3, c4, c5, c6; + dvector f; +@@ -1160,7 +1160,7 @@ + } /* callocquartets */ + + /* free quartet memory */ +-void freequartets() ++void freequartets(void) + { + free(quartetinfo); + } /* freequartets */ +@@ -1357,7 +1357,7 @@ + /*************************/ + + /* checks out all possible quartets */ +-void computeallquartets() ++void computeallquartets(void) + { + double onethird; + uli nq; +--- a/src/sprng/makeseed.c ++++ b/src/sprng/makeseed.c +@@ -1,10 +1,6 @@ + #include <time.h> + +-#ifdef __STDC__ +-int make_new_seed() +-#else +-int make_new_seed() +-#endif ++int make_new_seed(void) + { + time_t tp; + struct tm *temp; +--- a/src/sprng/primes-lcg64.c ++++ b/src/sprng/primes-lcg64.c +@@ -1,5 +1,6 @@ + #include <stdio.h> + #include <stdlib.h> ++#include <string.h> + #include "primes-lcg64.h" + #include "primelist-lcg64.h" + +--- a/src/treesort.c ++++ b/src/treesort.c +@@ -487,7 +487,7 @@ + /**********/ + + /* malloc new tree list item */ +-treelistitemtype *gettreelistitem() ++treelistitemtype *gettreelistitem(void) + { + treelistitemtype *tmpptr; + tmpptr = (treelistitemtype *)calloc((size_t) 1, sizeof(treelistitemtype)); +--- a/src/treesort.h ++++ b/src/treesort.h +@@ -84,7 +84,7 @@ + /**********/ + + /* allocate memory for ctree 3 ints pointer plus 1 check byte */ +-int *initctree(); ++int *initctree(void); + + /**********/ + +@@ -174,7 +174,7 @@ + /**********/ + + /* malloc new tree list item */ +-treelistitemtype *gettreelistitem(); ++treelistitemtype *gettreelistitem(void); + + /**********/ + +--- a/src/util.c ++++ b/src/util.c +@@ -507,7 +507,7 @@ + #define EPS 1.2e-7 + #define RNMX (1.0-EPS) + +-double randomunitintervall() ++double randomunitintervall(void) + /* Long period (> 2e18) random number generator. Returns a uniform random + deviate between 0.0 and 1.0 (exclusive of endpoint values). + +@@ -734,7 +734,7 @@ + /* Reads characters from stdin until a newline character or EOF + is received. The newline is not made part of the string. + If an error occurs a null string \0 is returned */ +-cvector mygets() ++cvector mygets(void) + { + int c, n; + cvector str; diff --git a/sci-biology/tree-puzzle/files/tree-puzzle-5.2-MPI-3.0.patch b/sci-biology/tree-puzzle/files/tree-puzzle-5.2-MPI-3.0.patch new file mode 100644 index 000000000000..66e3e6482338 --- /dev/null +++ b/sci-biology/tree-puzzle/files/tree-puzzle-5.2-MPI-3.0.patch @@ -0,0 +1,362 @@ +https://bugs.gentoo.org/690900 +rename MPI 1.0 to 3.0+ functions: +- MPI_Address -> MPI_Get_address +- MPI_Type_struct -> MPI_Type_create_struct + +--- a/src/ppuzzle.c ++++ b/src/ppuzzle.c +@@ -297,13 +297,13 @@ + else MPI_Recv(&dummy, 0, MPI_INT, PP_MyMaster, PP_UPDATEEEI, PP_Comm, &stat); + + Dtypes[0] = MPI_DOUBLE; Dtypelens[0] = tpmradix; +- MPI_Address(&(Eval[0]), &(Dtypeaddr[0])); ++ MPI_Get_address(&(Eval[0]), &(Dtypeaddr[0])); + Dtypes[1] = MPI_DOUBLE; Dtypelens[1] = tpmradix * tpmradix; +- MPI_Address(&(Evec[0][0]), &(Dtypeaddr[1])); ++ MPI_Get_address(&(Evec[0][0]), &(Dtypeaddr[1])); + Dtypes[2] = MPI_DOUBLE; Dtypelens[2] = tpmradix * tpmradix; +- MPI_Address(&(Ievc[0][0]), &(Dtypeaddr[2])); ++ MPI_Get_address(&(Ievc[0][0]), &(Dtypeaddr[2])); + +- MPI_Type_struct(3, Dtypelens, Dtypeaddr, Dtypes, &PP_Data); ++ MPI_Type_create_struct(3, Dtypelens, Dtypeaddr, Dtypes, &PP_Data); + MPI_Type_commit(&PP_Data); + + MPI_Bcast (MPI_BOTTOM, 1, PP_Data, PP_MyMaster, PP_Comm); +@@ -341,19 +341,19 @@ + double* DMVector = new_dvector(jobs); + + Dtypes[0] = MPI_DOUBLE; Dtypelens[0] = jobs; +- MPI_Address(&(DMVector[0]), &(Dtypeaddr[0])); ++ MPI_Get_address(&(DMVector[0]), &(Dtypeaddr[0])); + Dtypes[1] = MPI_DOUBLE; Dtypelens[1] = numcats; +- MPI_Address(&(Rates[0]), &(Dtypeaddr[1])); ++ MPI_Get_address(&(Rates[0]), &(Dtypeaddr[1])); + Dtypes[2] = MPI_DOUBLE; Dtypelens[2] = 1; +- MPI_Address(&(fracinv), &(Dtypeaddr[2])); ++ MPI_Get_address(&(fracinv), &(Dtypeaddr[2])); + Dtypes[3] = MPI_DOUBLE; Dtypelens[3] = tpmradix; +- MPI_Address(&(Eval[0]), &(Dtypeaddr[3])); ++ MPI_Get_address(&(Eval[0]), &(Dtypeaddr[3])); + Dtypes[4] = MPI_DOUBLE; Dtypelens[4] = tpmradix * tpmradix; +- MPI_Address(&(Evec[0][0]), &(Dtypeaddr[4])); ++ MPI_Get_address(&(Evec[0][0]), &(Dtypeaddr[4])); + Dtypes[5] = MPI_DOUBLE; Dtypelens[5] = tpmradix * tpmradix; +- MPI_Address(&(Ievc[0][0]), &(Dtypeaddr[5])); ++ MPI_Get_address(&(Ievc[0][0]), &(Dtypeaddr[5])); + +- MPI_Type_struct(6, Dtypelens, Dtypeaddr, Dtypes, &PP_Data); ++ MPI_Type_create_struct(6, Dtypelens, Dtypeaddr, Dtypes, &PP_Data); + MPI_Type_commit(&PP_Data); + + if (PP_IamMaster) { +@@ -719,10 +719,10 @@ + #endif + doubles[0] = frconst; + +- MPI_Address(ints, Dtypeaddr); +- MPI_Address(doubles, (Dtypeaddr+1)); ++ MPI_Get_address(ints, Dtypeaddr); ++ MPI_Get_address(doubles, (Dtypeaddr+1)); + +- MPI_Type_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Sizes); ++ MPI_Type_create_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Sizes); + MPI_Type_commit(&PP_Sizes); + + for (dest=1; dest<PP_NumProcs; dest++) { +@@ -797,10 +797,10 @@ + fprintf(STDOUT, "(%2d) Receiving Sizes ...\n", PP_Myid); + # endif /* PVERBOSE3 */ + +- MPI_Address(ints, Dtypeaddr); +- MPI_Address(doubles, (Dtypeaddr+1)); ++ MPI_Get_address(ints, Dtypeaddr); ++ MPI_Get_address(doubles, (Dtypeaddr+1)); + +- MPI_Type_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Sizes); ++ MPI_Type_create_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Sizes); + MPI_Type_commit(&PP_Sizes); + + error = MPI_Probe(PP_MyMaster, MPI_ANY_TAG, PP_Comm, &stat); +@@ -889,31 +889,31 @@ + # endif /* PVERBOSE2 */ + + Dtypes [0] = MPI_CHAR; Dtypelens [0] = Maxspc * Numptrn; +- MPI_Address(&(Seqpat[0][0]), &(Dtypeaddr[0])); ++ MPI_Get_address(&(Seqpat[0][0]), &(Dtypeaddr[0])); + Dtypes [1] = MPI_INT; Dtypelens [1] = Maxsite ; +- MPI_Address(&(Alias[0]), &(Dtypeaddr[1])); ++ MPI_Get_address(&(Alias[0]), &(Dtypeaddr[1])); + Dtypes [2] = MPI_INT; Dtypelens [2] = Numptrn ; +- MPI_Address(&(Weight[0]), &(Dtypeaddr[2])); ++ MPI_Get_address(&(Weight[0]), &(Dtypeaddr[2])); + Dtypes [3] = MPI_INT; Dtypelens [3] = Numptrn ; +- MPI_Address(&(constpat[0]), &(Dtypeaddr[3])); ++ MPI_Get_address(&(constpat[0]), &(Dtypeaddr[3])); + Dtypes [4] = MPI_DOUBLE; Dtypelens [4] = numcats ; +- MPI_Address(&(Rates[0]), &(Dtypeaddr[4])); ++ MPI_Get_address(&(Rates[0]), &(Dtypeaddr[4])); + Dtypes [5] = MPI_DOUBLE; Dtypelens [5] = tpmradix ; +- MPI_Address(&(Eval[0]), &(Dtypeaddr[5])); ++ MPI_Get_address(&(Eval[0]), &(Dtypeaddr[5])); + Dtypes [6] = MPI_DOUBLE; Dtypelens [6] = tpmradix ; +- MPI_Address(&(Freqtpm[0]), &(Dtypeaddr[6])); ++ MPI_Get_address(&(Freqtpm[0]), &(Dtypeaddr[6])); + Dtypes [7] = MPI_DOUBLE; Dtypelens [7] = tpmradix * tpmradix ; +- MPI_Address(&(Evec[0][0]), &(Dtypeaddr[7])); ++ MPI_Get_address(&(Evec[0][0]), &(Dtypeaddr[7])); + Dtypes [8] = MPI_DOUBLE; Dtypelens [8] = tpmradix * tpmradix ; +- MPI_Address(&(Ievc[0][0]), &(Dtypeaddr[8])); ++ MPI_Get_address(&(Ievc[0][0]), &(Dtypeaddr[8])); + Dtypes [9] = MPI_DOUBLE; Dtypelens [9] = tpmradix * tpmradix ; +- MPI_Address(&(iexp[0][0]), &(Dtypeaddr[9])); ++ MPI_Get_address(&(iexp[0][0]), &(Dtypeaddr[9])); + Dtypes [10] = MPI_DOUBLE; Dtypelens [10] = Maxspc * Maxspc ; +- MPI_Address(&(Distanmat[0][0]), &(Dtypeaddr[10])); ++ MPI_Get_address(&(Distanmat[0][0]), &(Dtypeaddr[10])); + Dtypes [11] = MPI_DOUBLE; Dtypelens [11] = numcats * tpmradix * tpmradix ; +- MPI_Address(&(ltprobr[0][0][0]), &(Dtypeaddr[11])); ++ MPI_Get_address(&(ltprobr[0][0][0]), &(Dtypeaddr[11])); + +- MPI_Type_struct(12, Dtypelens, Dtypeaddr, Dtypes, &PP_Data); ++ MPI_Type_create_struct(12, Dtypelens, Dtypeaddr, Dtypes, &PP_Data); + MPI_Type_commit(&PP_Data); + + +@@ -984,31 +984,31 @@ + # endif /* PVERBOSE2 */ + + Dtypes [0] = MPI_CHAR; Dtypelens [0] = Maxspc * Numptrn; +- MPI_Address(&(Seqpat[0][0]), &(Dtypeaddr[0])); ++ MPI_Get_address(&(Seqpat[0][0]), &(Dtypeaddr[0])); + Dtypes [1] = MPI_INT; Dtypelens [1] = Maxsite ; +- MPI_Address(&(Alias[0]), &(Dtypeaddr[1])); ++ MPI_Get_address(&(Alias[0]), &(Dtypeaddr[1])); + Dtypes [2] = MPI_INT; Dtypelens [2] = Numptrn ; +- MPI_Address(&(Weight[0]), &(Dtypeaddr[2])); ++ MPI_Get_address(&(Weight[0]), &(Dtypeaddr[2])); + Dtypes [3] = MPI_INT; Dtypelens [3] = Numptrn ; +- MPI_Address(&(constpat[0]), &(Dtypeaddr[3])); ++ MPI_Get_address(&(constpat[0]), &(Dtypeaddr[3])); + Dtypes [4] = MPI_DOUBLE; Dtypelens [4] = numcats ; +- MPI_Address(&(Rates[0]), &(Dtypeaddr[4])); ++ MPI_Get_address(&(Rates[0]), &(Dtypeaddr[4])); + Dtypes [5] = MPI_DOUBLE; Dtypelens [5] = tpmradix ; +- MPI_Address(&(Eval[0]), &(Dtypeaddr[5])); ++ MPI_Get_address(&(Eval[0]), &(Dtypeaddr[5])); + Dtypes [6] = MPI_DOUBLE; Dtypelens [6] = tpmradix ; +- MPI_Address(&(Freqtpm[0]), &(Dtypeaddr[6])); ++ MPI_Get_address(&(Freqtpm[0]), &(Dtypeaddr[6])); + Dtypes [7] = MPI_DOUBLE; Dtypelens [7] = tpmradix * tpmradix ; +- MPI_Address(&(Evec[0][0]), &(Dtypeaddr[7])); ++ MPI_Get_address(&(Evec[0][0]), &(Dtypeaddr[7])); + Dtypes [8] = MPI_DOUBLE; Dtypelens [8] = tpmradix * tpmradix ; +- MPI_Address(&(Ievc[0][0]), &(Dtypeaddr[8])); ++ MPI_Get_address(&(Ievc[0][0]), &(Dtypeaddr[8])); + Dtypes [9] = MPI_DOUBLE; Dtypelens [9] = tpmradix * tpmradix ; +- MPI_Address(&(iexp[0][0]), &(Dtypeaddr [9])); ++ MPI_Get_address(&(iexp[0][0]), &(Dtypeaddr [9])); + Dtypes [10] = MPI_DOUBLE; Dtypelens [10] = Maxspc * Maxspc ; +- MPI_Address(&(Distanmat[0][0]), &(Dtypeaddr[10])); ++ MPI_Get_address(&(Distanmat[0][0]), &(Dtypeaddr[10])); + Dtypes [11] = MPI_DOUBLE; Dtypelens [11] = numcats * tpmradix * tpmradix ; +- MPI_Address(&(ltprobr[0][0][0]), &(Dtypeaddr[11])); ++ MPI_Get_address(&(ltprobr[0][0][0]), &(Dtypeaddr[11])); + +- MPI_Type_struct(12, Dtypelens, Dtypeaddr, Dtypes, &PP_Data); ++ MPI_Type_create_struct(12, Dtypelens, Dtypeaddr, Dtypes, &PP_Data); + MPI_Type_commit(&PP_Data); + + for (dest=1; dest<PP_NumProcs; dest++) { +@@ -1150,10 +1150,10 @@ + ints[4] = usebestq; + ints[5] = approx; + +- MPI_Address(ints, Dtypeaddr); +- MPI_Address(doubles, (Dtypeaddr+1)); ++ MPI_Get_address(ints, Dtypeaddr); ++ MPI_Get_address(doubles, (Dtypeaddr+1)); + +- MPI_Type_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Quart); ++ MPI_Type_create_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Quart); + MPI_Type_commit(&PP_Quart); + + # ifdef PVERBOSE2 +@@ -1201,10 +1201,10 @@ + + PP_quartrecved++; + PP_quartrecvedn++; +- MPI_Address(ints, Dtypeaddr); +- MPI_Address(doubles, (Dtypeaddr+1)); ++ MPI_Get_address(ints, Dtypeaddr); ++ MPI_Get_address(doubles, (Dtypeaddr+1)); + +- MPI_Type_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Quart); ++ MPI_Type_create_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Quart); + MPI_Type_commit(&PP_Quart); + + error = MPI_Recv(MPI_BOTTOM, 1, PP_Quart, MPI_ANY_SOURCE, PP_QUART, PP_Comm, &stat); +@@ -1368,10 +1368,10 @@ + ulis[5] = fullresqs; /* number of fully resolved quartets */ + ulis[6] = missingqs; /* number of missing quartets */ + +- MPI_Address(ulis, Dtypeaddr); +- MPI_Address(ints, (Dtypeaddr+1)); ++ MPI_Get_address(ulis, Dtypeaddr); ++ MPI_Get_address(ints, (Dtypeaddr+1)); + +- MPI_Type_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_QBlockSpecs); ++ MPI_Type_create_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_QBlockSpecs); + MPI_Type_commit(&PP_QBlockSpecs); + + # ifdef PVERBOSE2 +@@ -1384,12 +1384,12 @@ + fprintf(STDOUT, "(%2d) ... Sent QuartBlockSpecs (%ld, %ld, %ld, %d)\n", PP_Myid, ulis[0], ulis[1], ulis[2], ints[0]); + # endif /* PVERBOSE3 */ + +- MPI_Address(trueaddr, DtypeaddrRes); ++ MPI_Get_address(trueaddr, DtypeaddrRes); + DtypelensRes[0] = truenum; + +- MPI_Address(bq, (DtypeaddrRes + 1)); ++ MPI_Get_address(bq, (DtypeaddrRes + 1)); + DtypelensRes[1] = numofbq; +- MPI_Type_struct(2, DtypelensRes, DtypeaddrRes, DtypesRes, &PP_QBlockRes); ++ MPI_Type_create_struct(2, DtypelensRes, DtypeaddrRes, DtypesRes, &PP_QBlockRes); + MPI_Type_commit(&PP_QBlockRes); + + error = MPI_Ssend(MPI_BOTTOM, 1, PP_QBlockRes, PP_MyMaster, PP_QUARTBLOCK, PP_Comm); +@@ -1455,10 +1455,10 @@ + # ifdef PVERBOSE3 + fprintf(STDOUT, "(%2d) Receiving QuartBlock ...\n", PP_Myid); + # endif /* PVERBOSE3 */ +- MPI_Address(ulis, Dtypeaddr); +- MPI_Address(ints, (Dtypeaddr+1)); ++ MPI_Get_address(ulis, Dtypeaddr); ++ MPI_Get_address(ints, (Dtypeaddr+1)); + +- MPI_Type_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_QBlockSpecs); ++ MPI_Type_create_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_QBlockSpecs); + MPI_Type_commit(&PP_QBlockSpecs); + + MPI_Probe(MPI_ANY_SOURCE, PP_QUARTBLOCKSPECS, PP_Comm, &stat); +@@ -1486,13 +1486,13 @@ + # endif /* PVERBOSE3 */ + + DtypelensRes[0] = truenum; +- MPI_Address(trueaddr, DtypeaddrRes); ++ MPI_Get_address(trueaddr, DtypeaddrRes); + + bq = calloc((size_t) *numofbq, sizeof(uli)); + + DtypelensRes[1] = *numofbq; +- MPI_Address(bq, (DtypeaddrRes+1)); +- MPI_Type_struct(2, DtypelensRes, DtypeaddrRes, DtypesRes, &PP_QBlockRes); ++ MPI_Get_address(bq, (DtypeaddrRes+1)); ++ MPI_Type_create_struct(2, DtypelensRes, DtypeaddrRes, DtypesRes, &PP_QBlockRes); + MPI_Type_commit(&PP_QBlockRes); + + error = MPI_Recv(MPI_BOTTOM, 1, PP_QBlockRes, dest, PP_QUARTBLOCK, PP_Comm, &stat); +@@ -1637,8 +1637,8 @@ + Dtypelens[0] = (Numquartets + 1)/2; + } + +- MPI_Address(&(quartetinfo[0]), Dtypeaddr); +- MPI_Type_struct(1, Dtypelens, Dtypeaddr, Dtypes, &PP_AllQuarts); ++ MPI_Get_address(&(quartetinfo[0]), Dtypeaddr); ++ MPI_Type_create_struct(1, Dtypelens, Dtypeaddr, Dtypes, &PP_AllQuarts); + MPI_Type_commit(&PP_AllQuarts); + + for (dest=1; dest<PP_NumProcs; dest++) { +@@ -1686,8 +1686,8 @@ + Dtypelens[0] = (*Numquartets + 1)/2; + } + +- MPI_Address(&(quartetinfo[0]), Dtypeaddr); +- MPI_Type_struct(1, Dtypelens, Dtypeaddr, Dtypes, &PP_AllQuarts); ++ MPI_Get_address(&(quartetinfo[0]), Dtypeaddr); ++ MPI_Type_create_struct(1, Dtypelens, Dtypeaddr, Dtypes, &PP_AllQuarts); + MPI_Type_commit(&PP_AllQuarts); + + error = MPI_Recv(MPI_BOTTOM, 1, PP_AllQuarts, PP_MyMaster, PP_ALLQUARTS, PP_Comm, &stat); +@@ -1748,13 +1748,13 @@ + for (n=0; n<(int)blocksize; n++) { + Dtypes[n] = MPI_CHAR; + Dtypelens[n] = (taxa - 3) * taxa; +- MPI_Address(&(biparts[n][0][0]), &(Dtypeaddr[n])); ++ MPI_Get_address(&(biparts[n][0][0]), &(Dtypeaddr[n])); + } + pstptr = pstlist; + for (n=0; n<pstnum; n++) { + Dtypes[(int)blocksize + n] = MPI_CHAR; + Dtypelens[(int)blocksize + n] = psteptreestrlen; +- MPI_Address((*pstptr).tree, &(Dtypeaddr[(int)blocksize + n])); ++ MPI_Get_address((*pstptr).tree, &(Dtypeaddr[(int)blocksize + n])); + pstnumarr[n] = (*pstptr).count; + # ifdef PVERBOSE3 + fprintf(STDOUT, "(%2d) Sent tree item ->%d: [%d/%d] #=%d \"%s\"\n", +@@ -1764,9 +1764,9 @@ + } + Dtypes[((int)blocksize + pstnum)] = MPI_INT; + Dtypelens[((int)blocksize + pstnum)] = pstnum; +- MPI_Address(&(pstnumarr[0]), &(Dtypeaddr[((int)blocksize + pstnum)])); ++ MPI_Get_address(&(pstnumarr[0]), &(Dtypeaddr[((int)blocksize + pstnum)])); + +- MPI_Type_struct(((int)blocksize + pstnum + 1), Dtypelens, Dtypeaddr, Dtypes, &PP_Biparts); ++ MPI_Type_create_struct(((int)blocksize + pstnum + 1), Dtypelens, Dtypeaddr, Dtypes, &PP_Biparts); + MPI_Type_commit(&PP_Biparts); + + error = MPI_Ssend(MPI_BOTTOM, 1, PP_Biparts, PP_MyMaster, PP_PUZZLEBLOCK, PP_Comm); +@@ -1843,20 +1843,20 @@ + (*bip)[n] = new_cmatrix(*taxa - 3, *taxa); + Dtypes[n] = MPI_CHAR; + Dtypelens[n] = (*taxa - 3) * *taxa; +- MPI_Address(&((*bip)[n][0][0]), &(Dtypeaddr[n])); ++ MPI_Get_address(&((*bip)[n][0][0]), &(Dtypeaddr[n])); + } + for (n=0; n<pstlistnum; n++) { + pstarr[n] = (char *)calloc((size_t) psteptreestrlen, sizeof(char)); + Dtypes[(int)*blocksize + n] = MPI_CHAR; + Dtypelens[(int)*blocksize + n] = psteptreestrlen; +- MPI_Address(&(pstarr[n][0]), &(Dtypeaddr[(int)*blocksize + n])); ++ MPI_Get_address(&(pstarr[n][0]), &(Dtypeaddr[(int)*blocksize + n])); + } + + Dtypes[(int)*blocksize + pstlistnum] = MPI_INT; + Dtypelens[(int)*blocksize + pstlistnum] = pstlistnum; +- MPI_Address(&(pstnumarr[0]), &(Dtypeaddr[(int)*blocksize + pstlistnum])); ++ MPI_Get_address(&(pstnumarr[0]), &(Dtypeaddr[(int)*blocksize + pstlistnum])); + +- MPI_Type_struct(((int)*blocksize + pstlistnum + 1), Dtypelens, Dtypeaddr, Dtypes, &PP_Biparts); ++ MPI_Type_create_struct(((int)*blocksize + pstlistnum + 1), Dtypelens, Dtypeaddr, Dtypes, &PP_Biparts); + MPI_Type_commit(&PP_Biparts); + + error = MPI_Recv(MPI_BOTTOM, 1, PP_Biparts, dest, PP_PUZZLEBLOCK, PP_Comm, &stat); +@@ -2053,10 +2053,10 @@ + fprintf(STDOUT, "(%2d) ... Sent DONE Signal\n", PP_Myid); + # endif /* PVERBOSE3 */ + +- MPI_Address(ints, Dtypeaddr); +- MPI_Address(doubles, (Dtypeaddr+1)); ++ MPI_Get_address(ints, Dtypeaddr); ++ MPI_Get_address(doubles, (Dtypeaddr+1)); + +- MPI_Type_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Stats); ++ MPI_Type_create_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Stats); + MPI_Type_commit(&PP_Stats); + + doquartrecved[0] = 0; +@@ -2173,10 +2173,10 @@ + doubles[4] = tarr.cpu; + doubles[5] = tarr.time; + +- MPI_Address(ints, Dtypeaddr); +- MPI_Address(doubles, (Dtypeaddr+1)); ++ MPI_Get_address(ints, Dtypeaddr); ++ MPI_Get_address(doubles, (Dtypeaddr+1)); + +- MPI_Type_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Stats); ++ MPI_Type_create_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Stats); + MPI_Type_commit(&PP_Stats); + + error = MPI_Ssend(MPI_BOTTOM, 1, PP_Stats, PP_MyMaster, PP_STATS, PP_Comm); diff --git a/sci-biology/tree-puzzle/files/tree-puzzle-5.2-configure-c99.patch b/sci-biology/tree-puzzle/files/tree-puzzle-5.2-configure-c99.patch new file mode 100644 index 000000000000..8c3834136af1 --- /dev/null +++ b/sci-biology/tree-puzzle/files/tree-puzzle-5.2-configure-c99.patch @@ -0,0 +1,20 @@ +--- a/configure.ac ++++ b/configure.ac +@@ -33,7 +33,7 @@ int main (int argc, char **argv) + { + MPI_Init(&argc,&argv); + MPI_Finalize(); +-exit(0); ++return 0; + } + EOF + +@@ -105,7 +105,7 @@ cat > conftest.c <<EOF + int main (int argc, char **argv) + { + printf ("%s-%s", PACKAGE, VERSION); +-exit(0); ++return 0; + } + EOF + diff --git a/sci-biology/tree-puzzle/files/tree-puzzle-impl-dec.patch b/sci-biology/tree-puzzle/files/tree-puzzle-impl-dec.patch deleted file mode 100644 index 93b960f5c2b4..000000000000 --- a/sci-biology/tree-puzzle/files/tree-puzzle-impl-dec.patch +++ /dev/null @@ -1,14 +0,0 @@ - src/sprng/primes-lcg64.c | 1 + - 1 files changed, 1 insertions(+), 0 deletions(-) - -diff --git a/src/sprng/primes-lcg64.c b/src/sprng/primes-lcg64.c -index 8e5a7c9..fb04373 100644 ---- a/src/sprng/primes-lcg64.c -+++ b/src/sprng/primes-lcg64.c -@@ -1,5 +1,6 @@ - #include <stdio.h> - #include <stdlib.h> -+#include <string.h> - #include "primes-lcg64.h" - #include "primelist-lcg64.h" - diff --git a/sci-biology/tree-puzzle/metadata.xml b/sci-biology/tree-puzzle/metadata.xml index 4a34df848e3a..8e14900c2855 100644 --- a/sci-biology/tree-puzzle/metadata.xml +++ b/sci-biology/tree-puzzle/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild b/sci-biology/tree-puzzle/tree-puzzle-5.2-r1.ebuild index 8e2a07f8183e..d3c7601397da 100644 --- a/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild +++ b/sci-biology/tree-puzzle/tree-puzzle-5.2-r1.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -inherit toolchain-funcs +inherit autotools DESCRIPTION="Maximum likelihood analysis for nucleotide, amino acid, and two-state data" HOMEPAGE="http://www.tree-puzzle.de" @@ -11,20 +11,22 @@ SRC_URI="http://www.tree-puzzle.de/${P}.tar.gz" LICENSE="GPL-2" SLOT="0" -KEYWORDS="~amd64 ~ppc x86 ~amd64-linux ~x86-linux ~ppc-macos" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" IUSE="mpi" RESTRICT="test" DEPEND="mpi? ( virtual/mpi )" RDEPEND="${DEPEND}" -PATCHES=( "${FILESDIR}"/${PN}-impl-dec.patch ) +PATCHES=( + "${FILESDIR}"/${P}-C99-decls.patch + "${FILESDIR}"/${P}-MPI-3.0.patch + "${FILESDIR}"/${P}-configure-c99.patch +) -pkg_setup() { - use mpi && [[ $(tc-getCC) == icc* ]] && - die "The parallelized version of tree-puzzle cannot be compiled using icc. - Either disable the \"mpi\" USE flag to compile only the non-parallelized - version of the program, or use gcc as your compiler (CC=\"gcc\")." +src_prepare() { + default + eautoreconf } src_configure() { @@ -38,9 +40,14 @@ src_configure() { fi } +src_compile() { + # hopelessly terrible build system, abuses Automake + emake -j1 +} + src_install() { - dobin src/puzzle - use mpi && dobin src/ppuzzle + dobin src/puzzle $(usev mpi src/ppuzzle) + einstalldocs # User manual diff --git a/sci-biology/treeviewx/Manifest b/sci-biology/treeviewx/Manifest index 1394d9f7afb1..35a6577e59df 100644 --- a/sci-biology/treeviewx/Manifest +++ b/sci-biology/treeviewx/Manifest @@ -1 +1,4 @@ +DIST treeviewx-0.5.1.20100823_p4.tar.gz 358644 BLAKE2B 3b7291415ab536230ac95decdc028dfdf60edcd986c91f76f7dacf5ec65fc31234c4d7023a9ec0fa420b68c9fe85278f8ae25106daa050872750dc5127362c46 SHA512 aec1351cfe58e1d11053c8bd3edbdf2ca74fb4bb5453bde72aa2a1b14623c69540fe7cef20f506291dad0b9358f6c37ea59feb493376b20dbdf3f7fb7df9844e +DIST treeviewx_0.5.1+git20100823.7e4d0e9-4.debian.tar.xz 13880 BLAKE2B 6ab73fa79fe9a07dde17ae771edcee8d4f4e1aa25aef5fff66de4a86ee8e24c0edf9c8a4b721c12e1675083b493c65fadfff8bc79d50f28cb54a5b2cd47104a4 SHA512 4e3dbf0fd0383a0a07f924d2e59e9ed74b20c03fe57edc8e728f99dfff0a28f1c366f8a38f52f637d104b1abf98f8023abcdaff7394045642e53f5d7bb6723fd +DIST treeviewx_128.png 16298 BLAKE2B 4a5f08352cd21f30e69f77403ecb79d95e8610e672979bbc46b72059bfe02edb711206260bb0b11eb733c544d584df7c9e778fe20ab2f768f18c49362cb72f11 SHA512 4986f86b7a0d4f57bd16aecb504a743ae060c2c5d3015ab2a6057e9df52ab132e6d071b5f992fc2de88529b5166f119654cbfb6c952e16d7e02d18f6d6143ee8 DIST tv-0.5.1.tar.gz 426745 BLAKE2B 080c4e09f441fd83da3406990bbe97f9e29fa531f47a65533ca887580f8a3ec561bb4766e66e2ef4764f68eee86fdabf48481cece56ddda90f9ffdc3c80b3a1a SHA512 45a7ac6dff5b22771e4428d6b1ee528c0039956a462658d28d4f588b6df32620d8f69b3bcf5ca23643e2bdd5361da00625fcb1495bcf4f74d44ee22022c63143 diff --git a/sci-biology/treeviewx/files/treeviewx-0.5.1-70_choose_tree.patch b/sci-biology/treeviewx/files/treeviewx-0.5.1-70_choose_tree.patch index ed5aa43e23c3..7a614edff72e 100644 --- a/sci-biology/treeviewx/files/treeviewx-0.5.1-70_choose_tree.patch +++ b/sci-biology/treeviewx/files/treeviewx-0.5.1-70_choose_tree.patch @@ -1,9 +1,8 @@ -## 70_choose_tree.dpatch by William Alexander Grant <william.grant@ubuntu.com.au> ---- tv-0.5.orig/tview.cpp -+++ tv-0.5/tview.cpp -@@ -209,7 +209,7 @@ - wxT("SVG vector picture files (*.svg)|*.svg"), - wxSAVE|wxOVERWRITE_PROMPT); +--- a/tview.cpp ++++ b/tview.cpp +@@ -208,7 +208,7 @@ + pictureFileName, wxT("SVG vector picture files (*.svg)|*.svg"), + wxSAVE|wxOVERWRITE_PROMPT); - if (dialog.ShowModal() == wxID_OK) + if ((dialog.ShowModal() == wxID_OK) && (p.GetNumTrees() != 0)) diff --git a/sci-biology/treeviewx/files/treeviewx-0.5.1-AM_PROG_AR.patch b/sci-biology/treeviewx/files/treeviewx-0.5.1-AM_PROG_AR.patch new file mode 100644 index 000000000000..015c1ec65490 --- /dev/null +++ b/sci-biology/treeviewx/files/treeviewx-0.5.1-AM_PROG_AR.patch @@ -0,0 +1,10 @@ +--- a/configure.in ++++ b/configure.in +@@ -11,6 +11,7 @@ + + # We need ranlib to make the library, and we need to define make + AC_PROG_RANLIB ++AM_PROG_AR + AC_PROG_MAKE_SET + + # Ensure that we set ENT (and set it to false). This flag affects diff --git a/sci-biology/treeviewx/files/treeviewx-0.5.1-wx30.patch b/sci-biology/treeviewx/files/treeviewx-0.5.1-wx30.patch index b1db5749990c..a1cfd906f176 100644 --- a/sci-biology/treeviewx/files/treeviewx-0.5.1-wx30.patch +++ b/sci-biology/treeviewx/files/treeviewx-0.5.1-wx30.patch @@ -1,14 +1,6 @@ - tv.cpp | 4 ++-- - tview.cpp | 12 ++++++++---- - 2 files changed, 10 insertions(+), 6 deletions(-) - -diff --git a/tv.cpp b/tv.cpp -old mode 100755 -new mode 100644 -index 1abe90b..0df45a8 --- a/tv.cpp +++ b/tv.cpp -@@ -163,9 +163,9 @@ bool MyApp::OnInit(void) +@@ -163,9 +163,9 @@ { // Optional command line argument is name of file to open #if wxUSE_UNICODE @@ -20,10 +12,6 @@ index 1abe90b..0df45a8 #endif // Read input/output files if (argc > 1) -diff --git a/tview.cpp b/tview.cpp -old mode 100755 -new mode 100644 -index 93972c3..4b2d593 --- a/tview.cpp +++ b/tview.cpp @@ -62,9 +62,13 @@ @@ -40,7 +28,7 @@ index 93972c3..4b2d593 // GUI interface #include "tv.h" -@@ -186,7 +190,7 @@ void TView::OnSavePicture (wxCommandEvent& WXUNUSED(event)) +@@ -186,7 +190,7 @@ wxFrame *f = GetMainFrame(); wxFileDialog dialog((wxWindow *)f, wxT("Save Picture as"), wxT(""), pictureFileName, wxT("Enhanced metafile (*.emf)|*.emf"), @@ -49,16 +37,16 @@ index 93972c3..4b2d593 if (dialog.ShowModal() == wxID_OK) { -@@ -206,7 +210,7 @@ void TView::OnSavePicture (wxCommandEvent& WXUNUSED(event)) +@@ -206,7 +210,7 @@ #endif wxFileDialog dialog((wxWindow *)f, wxT("Save Picture as"), wxT(""), pictureFileName, wxT("SVG vector picture files (*.svg)|*.svg"), - wxSAVE|wxOVERWRITE_PROMPT); + wxFD_SAVE|wxFD_OVERWRITE_PROMPT); - if (dialog.ShowModal() == wxID_OK) + if ((dialog.ShowModal() == wxID_OK) && (p.GetNumTrees() != 0)) { -@@ -361,7 +365,7 @@ bool TView::OnClose(bool deleteWindow) +@@ -361,7 +365,7 @@ // Clear the canvas in case we're in single-window mode, // and the canvas stays. @@ -67,7 +55,7 @@ index 93972c3..4b2d593 canvas->ClearBackground(); #else canvas->Clear(); -@@ -686,7 +690,7 @@ void TView::OnLeafFont (wxCommandEvent& WXUNUSED(event)) +@@ -686,7 +690,7 @@ wxFontData data; data.SetInitialFont (LeafFont); diff --git a/sci-biology/treeviewx/files/treeviewx-wxt.patch b/sci-biology/treeviewx/files/treeviewx-wxt.patch index b1c03bbb39f9..a971e1a85074 100644 --- a/sci-biology/treeviewx/files/treeviewx-wxt.patch +++ b/sci-biology/treeviewx/files/treeviewx-wxt.patch @@ -1,5 +1,5 @@ ---- tv.cpp~ 2005-10-01 16:47:35.000000000 -0400 -+++ tv.cpp 2005-10-01 16:52:30.000000000 -0400 +--- a/tv.cpp ++++ b/tv.cpp @@ -312,11 +312,15 @@ { #ifdef __WXMSW__ @@ -18,8 +18,8 @@ #endif #endif file_menu->AppendSeparator(); ---- tview.cpp~ 2005-10-01 16:47:45.000000000 -0400 -+++ tview.cpp 2005-10-01 16:50:42.000000000 -0400 +--- a/tview.cpp ++++ b/tview.cpp @@ -184,10 +184,10 @@ wxString pictureFileName = GetFrame()->GetTitle(); pictureFileName += wxT(".emf"); diff --git a/sci-biology/treeviewx/metadata.xml b/sci-biology/treeviewx/metadata.xml index 8683bbc5f8f7..e0415edb6e7a 100644 --- a/sci-biology/treeviewx/metadata.xml +++ b/sci-biology/treeviewx/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> @@ -11,4 +11,7 @@ files (such as those output by PAUP*, ClustalX, TREE-PUZZLE, and other programs). </longdescription> + <upstream> + <remote-id type="github">rdmpage/treeviewx</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/treeviewx/treeviewx-0.5.1-r3.ebuild b/sci-biology/treeviewx/treeviewx-0.5.1-r3.ebuild index 7d1fe1c773e0..ada60056715e 100644 --- a/sci-biology/treeviewx/treeviewx-0.5.1-r3.ebuild +++ b/sci-biology/treeviewx/treeviewx-0.5.1-r3.ebuild @@ -1,25 +1,22 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=7 -WX_GTK_VER=3.0 - -inherit autotools eutils wxwidgets +WX_GTK_VER="3.0" +inherit autotools wxwidgets DESCRIPTION="A phylogenetic tree viewer" HOMEPAGE="http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/" -SRC_URI="http://darwin.zoology.gla.ac.uk/~rpage/${PN}/download/0.5/tv-${PV}.tar.gz" -LICENSE="GPL-2" +SRC_URI="http://darwin.zoology.gla.ac.uk/~rpage/${PN}/download/$(ver_cut 1-2)/tv-${PV}.tar.gz" +S="${WORKDIR}/tv-${PV}" -KEYWORDS="amd64 x86" +LICENSE="GPL-2" SLOT="0" -IUSE="" +KEYWORDS="amd64 ~x86" -DEPEND="x11-libs/wxGTK:${WX_GTK_VER}[X]" -RDEPEND="${DEPEND}" - -S="${WORKDIR}/tv-${PV}" +RDEPEND="x11-libs/wxGTK:${WX_GTK_VER}[X]" +DEPEND="${RDEPEND}" PATCHES=( "${FILESDIR}"/${PN}-wxt.patch @@ -30,10 +27,16 @@ PATCHES=( "${FILESDIR}"/${P}-svg.patch "${FILESDIR}"/${P}-treeview-xpm-not-xbm.patch "${FILESDIR}"/${P}-wxstring-maxlen.patch - ) + "${FILESDIR}"/${P}-AM_PROG_AR.patch +) src_prepare() { - epatch "${PATCHES[@]}" + default mv configure.{in,ac} || die eautoreconf } + +src_configure() { + setup-wxwidgets + default +} diff --git a/sci-biology/treeviewx/treeviewx-0.5.1.20100823_p4.ebuild b/sci-biology/treeviewx/treeviewx-0.5.1.20100823_p4.ebuild new file mode 100644 index 000000000000..e621066bad19 --- /dev/null +++ b/sci-biology/treeviewx/treeviewx-0.5.1.20100823_p4.ebuild @@ -0,0 +1,50 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +WX_GTK_VER="3.2-gtk3" +inherit autotools desktop wxwidgets xdg + +DESCRIPTION="A phylogenetic tree viewer" +HOMEPAGE="https://github.com/rdmpage/treeviewx" +COMMIT="7e4d0e96dfdde51a92a1634b41d7284142a19afa" +SRC_URI="https://github.com/rdmpage/treeviewx/archive/${COMMIT}.tar.gz -> ${P}.tar.gz + mirror://debian/pool/main/${PN:0:1}/${PN}/${PN}_$(ver_cut 1-3)+git$(ver_cut 4).${COMMIT:0:7}-${PV/*_p}.debian.tar.xz + https://dev.gentoo.org/~pacho/${PN}/${PN}_128.png" +S="${WORKDIR}/${PN}-${COMMIT}" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="amd64 ~x86" + +RDEPEND="x11-libs/wxGTK:${WX_GTK_VER}[X]" +DEPEND="${RDEPEND}" + +PATCHES=( + "${FILESDIR}"/${PN}-0.5.1-AM_PROG_AR.patch +) + +src_prepare() { + default + + # Debian patches + for p in $(<"${WORKDIR}"/debian/patches/series) ; do + eapply -p1 "${WORKDIR}/debian/patches/${p}" + done + + mv configure.{in,ac} || die + eautoreconf +} + +src_configure() { + setup-wxwidgets + default +} + +src_install() { + default + newicon -s 128 "${DISTDIR}"/${PN}_128.png ${PN}.png + newicon bitmaps/treeview.xpm ${PN}.xpm + make_desktop_entry tv "TreeView X" +} diff --git a/sci-biology/trf/metadata.xml b/sci-biology/trf/metadata.xml index 959160fe46b1..ccdff086e20b 100644 --- a/sci-biology/trf/metadata.xml +++ b/sci-biology/trf/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/trf/trf-4.04-r1.ebuild b/sci-biology/trf/trf-4.04-r1.ebuild deleted file mode 100644 index 3b906fb31aaf..000000000000 --- a/sci-biology/trf/trf-4.04-r1.ebuild +++ /dev/null @@ -1,29 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -MY_P="${PN}404" - -DESCRIPTION="Tandem Repeats Finder" -HOMEPAGE="http://tandem.bu.edu/trf/trf.html" -SRC_URI="http://tandem.bu.edu/trf/downloads/${MY_P}.linux" - -LICENSE="trf" # http://tandem.bu.edu/trf/trf.license.html -SLOT="0" -KEYWORDS="amd64 x86" -RESTRICT="mirror bindist" - -S=${WORKDIR} - -QA_PREBUILT="opt/${PN}/.*" - -src_unpack() { - cp "${DISTDIR}/${MY_P}.linux" "${S}/${MY_P}.linux.exe" || die -} - -src_install() { - exeinto /opt/${PN} - doexe trf404.linux.exe - dosym /opt/${PN}/${MY_P}.linux.exe /opt/bin/trf -} diff --git a/sci-biology/trf/trf-4.04-r2.ebuild b/sci-biology/trf/trf-4.04-r2.ebuild new file mode 100644 index 000000000000..79558a9d9f11 --- /dev/null +++ b/sci-biology/trf/trf-4.04-r2.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +MY_P="${PN}404" + +DESCRIPTION="Tandem Repeats Finder" +HOMEPAGE="https://tandem.bu.edu/trf/trf.html" +SRC_URI="https://tandem.bu.edu/trf/downloads/${MY_P}.linux" +S="${WORKDIR}" + +LICENSE="trf" # http://tandem.bu.edu/trf/trf.license.html +SLOT="0" +KEYWORDS="amd64 ~x86" +RESTRICT="mirror bindist" + +QA_PREBUILT="opt/trf/.*" + +src_unpack() { + cp "${DISTDIR}"/${MY_P}.linux "${S}"/${MY_P}.linux.exe || die +} + +src_install() { + exeinto /opt/trf + doexe trf404.linux.exe + dosym ../trf/${MY_P}.linux.exe /opt/bin/trf +} diff --git a/sci-biology/trnascan-se/files/trnascan-se-1.31-clang16.patch b/sci-biology/trnascan-se/files/trnascan-se-1.31-clang16.patch new file mode 100644 index 000000000000..33889c90cf69 --- /dev/null +++ b/sci-biology/trnascan-se/files/trnascan-se-1.31-clang16.patch @@ -0,0 +1,62 @@ +https://bugs.gentoo.org/874477 +--- a/eufind_main.c ++++ b/eufind_main.c +@@ -23,4 +23,5 @@ + #include <stdlib.h> + #include <string.h> ++#include <unistd.h> + #include "squid.h" + #include "sqfuncs.h" +@@ -47,4 +48,14 @@ + -i <integer> : start nucleotide numbering at <integer> (def=1)\n\n"; + ++int GetBbox(float*, int*, char*, int, int, int); ++int GetBestABox(TRNA_TYPE*, char*, char*, int, int, int, int, int); ++int GetBestTrxTerm(TRNA_TYPE*, char*, int, float); ++int GetSecABox(TRNA_TYPE*, char*); ++void Get_tRNA_stats(TRNA_TYPE*, char*, int, int); ++int Init_tRNA(TRNA_TYPE*); ++int IntEncodeSeq(char*, char*, int); ++void Save_tRNA(TRNA_TYPE*, SQINFO*, char*, int, int, long int); ++int tRNAOverlap(TRNA_TYPE*, TRNA_TYPE*, int); ++ + int + main (int argc, char **argv) +--- a/scan_main.c ++++ b/scan_main.c +@@ -8,4 +8,5 @@ + #include <stdlib.h> + #include <string.h> ++#include <unistd.h> + #include <time.h> + #include <math.h> +--- a/score_main.c ++++ b/score_main.c +@@ -10,4 +10,5 @@ + #include <stdlib.h> + #include <string.h> ++#include <unistd.h> + #include <time.h> + #include <math.h> +--- a/trnascan.c ++++ b/trnascan.c +@@ -69,4 +69,5 @@ + #include <stdio.h> + #include <stdlib.h> ++#include <unistd.h> + #include <ctype.h> + +@@ -333,5 +334,5 @@ + ); + +-main(int argc, char **argv) ++int main(int argc, char **argv) + { + /* pointers to the different files fpi=input file, fpo=output file, +@@ -1419,5 +1420,5 @@ + /* Calls to this function eliminated for efficiency T. Lowe 11/95 */ + +-myindex (char *s, char *t) ++int myindex (char *s, char *t) + { + int i, j, k; diff --git a/sci-biology/trnascan-se/files/trnascan-se-1.31-ldflags.patch b/sci-biology/trnascan-se/files/trnascan-se-1.31-ldflags.patch deleted file mode 100644 index f28b1e8f6bb0..000000000000 --- a/sci-biology/trnascan-se/files/trnascan-se-1.31-ldflags.patch +++ /dev/null @@ -1,26 +0,0 @@ -diff --git a/Makefile b/Makefile -index 53e5c5b..a2d3feb 100644 ---- a/Makefile -+++ b/Makefile -@@ -109,17 +109,17 @@ MPOBJ = mpviterbi.o mp-dbviterbi.o - all: $(PROGS) tRNAscan-SE setpaths - - covels-SE: $(OBJ) scan_main.o -- $(CC) $(CFLAGS) $(RFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS) -+ $(CC) $(CFLAGS) $(RFLAGS) $(LDFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS) - - coves-SE: $(OBJ) score_main.o -- $(CC) $(CFLAGS) $(RFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS) -+ $(CC) $(CFLAGS) $(RFLAGS) $(LDFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS) - - eufindtRNA: $(SQUIDOBJ) pavesi.o eufind_main.o -- $(CC) $(CFLAGS) -o eufindtRNA eufind_main.o \ -+ $(CC) $(CFLAGS) $(LDFLAGS) -o eufindtRNA eufind_main.o \ - pavesi.o $(SQUIDOBJ) $(LIBS) - - trnascan-1.4: trnascan.o -- $(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4 trnascan.c -+ $(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" $(LDFLAGS) -o trnascan-1.4 trnascan.c - - tRNAscan-SE: - $(PERLDIR)/$(PERLBIN) checkversion.pl diff --git a/sci-biology/trnascan-se/files/trnascan-se-1.31-makefile.patch b/sci-biology/trnascan-se/files/trnascan-se-1.31-makefile.patch new file mode 100644 index 000000000000..acf3c2a6d862 --- /dev/null +++ b/sci-biology/trnascan-se/files/trnascan-se-1.31-makefile.patch @@ -0,0 +1,140 @@ +--- a/Makefile ++++ b/Makefile +@@ -20,9 +20,9 @@ + PERLBIN = perl + + ## where you want things installed +-BINDIR = $(HOME)/bin +-LIBDIR = $(HOME)/lib/tRNAscan-SE +-MANDIR = $(HOME)/man ++BINDIR = $(EPREFIX)/usr/bin ++LIBDIR = $(EPREFIX)/usr/share/trnascan-se ++MANDIR = $(EPREFIX)/usr/share/man + + ## NOTE !! If you later manually move the location of + ## binaries or data files in the BINDIR or LIBDIR directories, +@@ -33,10 +33,8 @@ + TEMPDIR = /tmp + + ## your compiler +-CC = gcc # GNU cc (if available) otherwise use vendor's cc + + ## any special compiler flags you want +-CFLAGS = -O # ok for most machines (remove -O for DEC OSF/1 cc compiler) + + ## machine specific definitions + # You shouldn't need any. The specific #define's in squid are historical. +@@ -58,7 +56,7 @@ + ####### + + SHELL = /bin/sh +-LIBS = -lm ++LIBS += -lm + .SUFFIXES : .c .o + + DOCS = README MANUAL INSTALL COPYING GNULICENSE FILES Release.history +@@ -109,20 +107,20 @@ + all: $(PROGS) tRNAscan-SE setpaths + + covels-SE: $(OBJ) scan_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS) + + coves-SE: $(OBJ) score_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS) + + eufindtRNA: $(SQUIDOBJ) pavesi.o eufind_main.o +- $(CC) $(CFLAGS) -o eufindtRNA eufind_main.o \ ++ $(CC) $(LDFLAGS) $(CFLAGS) -o eufindtRNA eufind_main.o \ + pavesi.o $(SQUIDOBJ) $(LIBS) + +-trnascan-1.4: trnascan.o +- $(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4 trnascan.c ++trnascan-1.4: trnascan.c ++ $(CC) $(LDFLAGS) $(CFLAGS) $(CPPFLAGS) -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4 trnascan.c + + tRNAscan-SE: +- $(PERLDIR)/$(PERLBIN) checkversion.pl ++ $(PERLBIN) checkversion.pl + sed 's#/tmp#$(TEMPDIR)#g' tRNAscan-SE.src | \ + sed 's#bindir = ""#bindir =\"$(BINDIR)/"#g' | \ + sed 's#/usr/local/lib/tRNAscanSE#$(LIBDIR)#g' | \ +@@ -200,11 +198,11 @@ + noambig: trnascan-1.4-NA eufindtRNA-NA + + trnascan-1.4-NA: trnascan.o +- $(CC) $(CFLAGS) -DNO_AMBIG -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4-NA trnascan.c ++ $(CC) $(LDFLAGS) $(CFLAGS) $(CPPFLAGS) -DNO_AMBIG -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4-NA trnascan.c + + eufindtRNA-NA: $(SQUIDOBJ) eufind_main.o +- $(CC) $(CFLAGS) -DNO_AMBIG -c -o pavesi-NA.o pavesi.c +- $(CC) $(CFLAGS) -o eufindtRNA-NA eufind_main.o \ ++ $(CC) $(CFLAGS) $(CPPFLAGS) -DNO_AMBIG -c -o pavesi-NA.o pavesi.c ++ $(CC) $(LDFLAGS) $(CFLAGS) -o eufindtRNA-NA eufind_main.o \ + pavesi-NA.o $(SQUIDOBJ) $(LIBS) + + +@@ -220,7 +218,7 @@ + rmdir -ps $(MANDIR) + + .c.o: +- $(CC) $(CFLAGS) $(MDEFS) -c $< ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -c $< + + ## programs from Sean Eddy's sequence i/o function library not + ## needed for tRNAscan-SE but included for their utility +@@ -233,16 +231,16 @@ + cp $(UTILS) $(BINDIR)/. + + reformat: $(SQUIDOBJ) reformat_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o reformat $(SQUIDOBJ) reformat_main.o $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(MDEFS) -o reformat $(SQUIDOBJ) reformat_main.o $(LIBS) + + revcomp: $(SQUIDOBJ) revcomp_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o revcomp $(SQUIDOBJ) revcomp_main.o $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(MDEFS) -o revcomp $(SQUIDOBJ) revcomp_main.o $(LIBS) + + seqstat: $(SQUIDOBJ) seqstat_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o seqstat $(SQUIDOBJ) seqstat_main.o $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(MDEFS) -o seqstat $(SQUIDOBJ) seqstat_main.o $(LIBS) + + shuffle: $(SQUIDOBJ) shuffle_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o shuffle $(SQUIDOBJ) shuffle_main.o $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(MDEFS) -o shuffle $(SQUIDOBJ) shuffle_main.o $(LIBS) + + ## other programs in Cove package (below) not needed for + ## tRNAscan-SE, but are included for users who wish to apply +@@ -255,25 +253,25 @@ + cp $(COVE_SUITE) $(BINDIR)/. + + covea: $(OBJ) align_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o covea align_main.o $(OBJ) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o covea align_main.o $(OBJ) $(LIBS) + + coveb: $(OBJ) build_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o coveb build_main.o $(OBJ) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o coveb build_main.o $(OBJ) $(LIBS) + + covee: $(OBJ) emit_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o covee emit_main.o $(OBJ) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o covee emit_main.o $(OBJ) $(LIBS) + + covet: $(OBJ) train_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o covet train_main.o $(OBJ) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o covet train_main.o $(OBJ) $(LIBS) + + covels: $(OBJ) scan_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o covels scan_main.o $(OBJ) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o covels scan_main.o $(OBJ) $(LIBS) + + coves: $(OBJ) score_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o coves score_main.o $(OBJ) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o coves score_main.o $(OBJ) $(LIBS) + + structcheck: $(OBJ) structcheck_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o structcheck structcheck_main.o $(OBJ) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o structcheck structcheck_main.o $(OBJ) $(LIBS) + + + ## Maspar memory limits diff --git a/sci-biology/trnascan-se/files/trnascan-se-1.31-portable-perl-shebangs.patch b/sci-biology/trnascan-se/files/trnascan-se-1.31-portable-perl-shebangs.patch new file mode 100644 index 000000000000..187705e8b3a0 --- /dev/null +++ b/sci-biology/trnascan-se/files/trnascan-se-1.31-portable-perl-shebangs.patch @@ -0,0 +1,32 @@ +--- a/fasta2gsi.pl ++++ b/fasta2gsi.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Usage: fasta2gsi.perl <seqfile> + # Creates seqfile.gsi +--- a/instman.pl ++++ b/instman.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Sean Eddy, Wed Jul 29 15:24:43 1992 + +--- a/sstofa.pl ++++ b/sstofa.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + + if ($#ARGV < 0) { +--- a/tRNAscan-SE.src ++++ b/tRNAscan-SE.src +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + # + # -------------------------------------------------------------------- + # tRNAscan-SE: a program for improved detection of transfer RNA diff --git a/sci-biology/trnascan-se/metadata.xml b/sci-biology/trnascan-se/metadata.xml index 39da31794ca8..00b47df661a7 100644 --- a/sci-biology/trnascan-se/metadata.xml +++ b/sci-biology/trnascan-se/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/trnascan-se/trnascan-se-1.31-r3.ebuild b/sci-biology/trnascan-se/trnascan-se-1.31-r3.ebuild new file mode 100644 index 000000000000..f43243921f2f --- /dev/null +++ b/sci-biology/trnascan-se/trnascan-se-1.31-r3.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit flag-o-matic perl-functions toolchain-funcs + +DESCRIPTION="tRNA detection in large-scale genome sequences" +HOMEPAGE="http://lowelab.ucsc.edu/tRNAscan-SE/" +SRC_URI="http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}"/tRNAscan-SE-1.3.1/ + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND="dev-lang/perl:=" +BDEPEND="${RDEPEND}" + +PATCHES=( + "${FILESDIR}"/${P}-makefile.patch + "${FILESDIR}"/${P}-portable-perl-shebangs.patch + "${FILESDIR}"/${P}-clang16.patch +) + +src_configure() { + tc-export CC + append-cflags -std=gnu89 # mid-migration from K&R C, incompatible with c2x +} + +src_test() { + emake PATH="${S}:${PATH}" testrun +} + +src_install() { + dobin covels-SE coves-SE eufindtRNA tRNAscan-SE trnascan-1.4 + + newman tRNAscan-SE.man tRNAscan-SE.man.1 + dodoc MANUAL Manual.ps README Release.history + + insinto /usr/share/trnascan-se + doins *.cm gcode.* Dsignal TPCsignal + + perl_domodule -r tRNAscanSE +} diff --git a/sci-biology/trnascan-se/trnascan-se-1.31.ebuild b/sci-biology/trnascan-se/trnascan-se-1.31.ebuild deleted file mode 100644 index cd8dc152d6d2..000000000000 --- a/sci-biology/trnascan-se/trnascan-se-1.31.ebuild +++ /dev/null @@ -1,54 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit perl-functions toolchain-funcs - -DESCRIPTION="tRNA detection in large-scale genome sequences" -HOMEPAGE="http://lowelab.ucsc.edu/tRNAscan-SE/" -SRC_URI="http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="amd64 x86" -IUSE="" - -S="${WORKDIR}"/tRNAscan-SE-1.3.1/ - -PATCHES=( - "${FILESDIR}"/${P}-ldflags.patch -) - -src_prepare() { - default - sed \ - -e "s:BINDIR = \$(HOME)/bin:BINDIR = ${EPREFIX}/usr/bin:" \ - -e "s:LIBDIR = \$(HOME)/lib/tRNAscan-SE:LIBDIR = ${EPRFIX}/usr/share/${PN}:" \ - -e "s:MANDIR = \$(HOME)/man:MANDIR = ${EPREFIX}/usr/share/man:" \ - -e "s:CC = gcc:CC = $(tc-getCC):" \ - -e "s:CFLAGS = -O:CFLAGS = ${CFLAGS}:" \ - -i Makefile || die - - perl_set_version -} - -src_test() { - emake PATH="${S}:${PATH}" testrun -} - -src_install() { - dobin covels-SE coves-SE eufindtRNA tRNAscan-SE trnascan-1.4 - - newman tRNAscan-SE.man tRNAscan-SE.man.1 - - dodoc MANUAL README Release.history - - insinto /usr/share/${PN}/ - doins *.cm gcode.* Dsignal TPCsignal - - dodoc Manual.ps - - insinto ${VENDOR_LIB} - doins -r tRNAscanSE -} diff --git a/sci-biology/uchime/files/CMakeLists.patch b/sci-biology/uchime/files/CMakeLists.patch new file mode 100644 index 000000000000..c33af8c7e827 --- /dev/null +++ b/sci-biology/uchime/files/CMakeLists.patch @@ -0,0 +1,21 @@ +--- /dev/null ++++ b/CMakeLists.txt +@@ -0,0 +1,18 @@ ++cmake_minimum_required(VERSION 2.8.12) ++project(UCHIME LANGUAGES CXX) ++ ++include(GNUInstallDirs) ++ ++set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -D_FILE_OFFSET_BITS=64 -DUCHIMES=1") ++ ++# "myutils.h: error: reference to byte is ambiguous"" ++# bug #786297 ++set(CMAKE_CXX_STANDARD 14) ++set(CMAKE_CXX_STANDARD_REQUIRED ON) ++set(CMAKE_CXX_EXTENSIONS OFF) ++ ++# Simply copy the source files from the mk script ++add_executable(uchime ++ addtargets2.cpp alignchime.cpp alignchimel.cpp alnparams.cpp alpha.cpp alpha2.cpp fractid.cpp getparents.cpp globalalign2.cpp make3way.cpp mx.cpp myutils.cpp path.cpp searchchime.cpp seqdb.cpp setnucmx.cpp sfasta.cpp tracebackbit.cpp uchime_main.cpp usort.cpp viterbifast.cpp writechhit.cpp) ++ ++INSTALL(TARGETS uchime DESTINATION ${CMAKE_INSTALL_BINDIR}) diff --git a/sci-biology/uchime/files/CMakeLists.txt b/sci-biology/uchime/files/CMakeLists.txt deleted file mode 100644 index 54b0a3ba0d30..000000000000 --- a/sci-biology/uchime/files/CMakeLists.txt +++ /dev/null @@ -1,11 +0,0 @@ -cmake_minimum_required(VERSION 2.6) -project(UCHIME) - -set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -D_FILE_OFFSET_BITS=64 -DUCHIMES=1") - -# Simply copy the source files from the mk script -add_executable(uchime - addtargets2.cpp alignchime.cpp alignchimel.cpp alnparams.cpp alpha.cpp alpha2.cpp fractid.cpp getparents.cpp globalalign2.cpp make3way.cpp mx.cpp myutils.cpp path.cpp searchchime.cpp seqdb.cpp setnucmx.cpp sfasta.cpp tracebackbit.cpp uchime_main.cpp usort.cpp viterbifast.cpp writechhit.cpp) - -INSTALL(TARGETS uchime - DESTINATION bin) diff --git a/sci-biology/uchime/metadata.xml b/sci-biology/uchime/metadata.xml index 8e8ff4997171..0e6b9a493f29 100644 --- a/sci-biology/uchime/metadata.xml +++ b/sci-biology/uchime/metadata.xml @@ -1,18 +1,18 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> <longdescription> -UCHIME is a new algorithm for detecting chimeric sequences. It was developed in -collaboration with Brian Haas, Jose Carlos Clemente, Chris Quince and Rob -Knight. Chimeras are commonly created during DNA sample amplification by -PCR, especially in community sequencing experiments using single regions -such as the 16S rRNA gene in bacteria or the fungal ITS region. UCHIME can -detect chimeras using a reference database or de novo using abundance -information on the assumption that chimeras are less abundant than their -parents because they must have undergone fewer rounds of amplification. -</longdescription> + UCHIME is a new algorithm for detecting chimeric sequences. It was developed in + collaboration with Brian Haas, Jose Carlos Clemente, Chris Quince and Rob + Knight. Chimeras are commonly created during DNA sample amplification by + PCR, especially in community sequencing experiments using single regions + such as the 16S rRNA gene in bacteria or the fungal ITS region. UCHIME can + detect chimeras using a reference database or de novo using abundance + information on the assumption that chimeras are less abundant than their + parents because they must have undergone fewer rounds of amplification. + </longdescription> </pkgmetadata> diff --git a/sci-biology/uchime/uchime-4.2.40-r1.ebuild b/sci-biology/uchime/uchime-4.2.40-r1.ebuild new file mode 100644 index 000000000000..9742ee2575fc --- /dev/null +++ b/sci-biology/uchime/uchime-4.2.40-r1.ebuild @@ -0,0 +1,19 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit cmake + +MY_P="${PN}${PV}_src" + +DESCRIPTION="Fast, accurate chimera detection" +HOMEPAGE="https://www.drive5.com/usearch/manual/uchime_algo.html" +SRC_URI="https://www.drive5.com/${PN}/${MY_P}.tar.gz" +S="${WORKDIR}/${MY_P}" + +LICENSE="public-domain" +SLOT="0" +KEYWORDS="amd64 ~x86 ~amd64-linux ~x86-linux" + +PATCHES=( "${FILESDIR}"/CMakeLists.patch ) diff --git a/sci-biology/uchime/uchime-4.2.40.ebuild b/sci-biology/uchime/uchime-4.2.40.ebuild deleted file mode 100644 index dd2201547ae0..000000000000 --- a/sci-biology/uchime/uchime-4.2.40.ebuild +++ /dev/null @@ -1,25 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit cmake-utils - -MY_P="${PN}${PV}_src" - -DESCRIPTION="Fast, accurate chimera detection" -HOMEPAGE="http://www.drive5.com/uchime/" -SRC_URI="http://drive5.com/${PN}/${MY_P}.tar.gz" - -SLOT="0" -LICENSE="public-domain" -KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" -IUSE="debug" - -S="${WORKDIR}"/${MY_P} - -src_prepare() { - cp "${FILESDIR}"/CMakeLists.txt . || die - - cmake-utils_src_prepare -} diff --git a/sci-biology/ucsc-genome-browser/metadata.xml b/sci-biology/ucsc-genome-browser/metadata.xml index 042f7b949ba9..6cc5e40e4d6c 100644 --- a/sci-biology/ucsc-genome-browser/metadata.xml +++ b/sci-biology/ucsc-genome-browser/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild index 9b53170b1e83..f0bb0676ae85 100644 --- a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild +++ b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 @@ -30,7 +30,12 @@ S="${WORKDIR}/kent" src_prepare() { default + use server && webapp_src_preinst + + # bug #708064 + append-flags -fcommon + sed \ -e 's/-Werror//' \ -e "/COPT/s:=.*$:=${LDFLAGS}:g" \ @@ -59,14 +64,16 @@ src_compile() { export MYSQLLIBS="none" MYSQLINC="none" DOCUMENTROOT="none" CGI_BIN="none" - use mysql && export MYSQLLIBS="-L${EROOT}usr/$(get_libdir)/mysql/ -lmysqlclient -lz -lssl" \ - MYSQLINC="${ROOT}usr/include/mysql" + # TODO: Change ${EPREFIX} to ${ESYSROOT} in EAPI 7 + # (and ideally use pkg-config here) + use mysql && export MYSQLLIBS="-L${EPREFIX%/}/usr/$(get_libdir)/mysql/ -lmysqlclient -lz -lssl" \ + MYSQLINC="${EPREFIX%/}/usr/include/mysql" use server && export DOCUMENTROOT="${WORKDIR}/destdir/${MY_HTDOCSDIR}" \ CGI_BIN="${WORKDIR}/destdir/${MY_HTDOCSDIR}/cgi-bin" - mkdir -p "$BINDIR" "$SCRIPTS" "$ENCODE_PIPELINE_BIN" || die - use server && mkdir -p "$CGI_BIN" "$DOCUMENTROOT" + mkdir -p "${BINDIR}" "${SCRIPTS}" "${ENCODE_PIPELINE_BIN}" || die + use server && mkdir -p "${CGI_BIN}" "${DOCUMENTROOT}" emake -C src clean emake -C src/lib diff --git a/sci-biology/unafold/files/unafold-3.8-autotools.patch b/sci-biology/unafold/files/unafold-3.8-autotools.patch new file mode 100644 index 000000000000..ecf29b470c2c --- /dev/null +++ b/sci-biology/unafold/files/unafold-3.8-autotools.patch @@ -0,0 +1,41 @@ +--- a/configure.ac ++++ b/configure.ac +@@ -2,7 +2,7 @@ + AC_INIT(UNAFold, 3.8, markhn@rpi.edu) + AC_CONFIG_SRCDIR(src/hybrid.c) + AC_CONFIG_AUX_DIR(config) +-AM_CONFIG_HEADER(config.h:config.in) ++AC_CONFIG_HEADERS(config.h:config.in) + AM_INIT_AUTOMAKE + AC_CANONICAL_BUILD + AC_PROG_CC +@@ -12,7 +12,6 @@ + if test -z "$PERL"; then + AC_MSG_ERROR(Perl not found) + fi +-AC_PROG_PERL_VERSION(5.6.1, , AC_MSG_ERROR(Perl 5.6.1 or better is required)) + AC_CHECK_PROG(GNUPLOT, gnuplot, [system('gnuplot', \"\$prefix.gp\") == 0 or die $!;]) + + AC_MSG_CHECKING(whether compiler needs -mieee) +@@ -28,6 +27,7 @@ + + + # Checks for libraries. ++AX_CHECK_GL + AX_CHECK_GLUT + AM_CONDITIONAL(GLUT, test -n "$GLUT_LIBS") + AX_CHECK_GD +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -33,9 +33,9 @@ + endif GLUT + + hybrid_plot_ng_SOURCES = hybrid-plot-ng.c getopt.h util.h xmalloc.h +-hybrid_plot_ng_CFLAGS = @GD_CFLAGS@ ++hybrid_plot_ng_CFLAGS = @GD_CFLAGS@ $(GL_CFLAGS) + hybrid_plot_ng_LDFLAGS = @GD_LDFLAGS@ +-hybrid_plot_ng_LDADD = getopt.$(OBJEXT) getopt1.$(OBJEXT) xmalloc.$(OBJEXT) @GD_LIBS@ -lm ++hybrid_plot_ng_LDADD = getopt.$(OBJEXT) getopt1.$(OBJEXT) xmalloc.$(OBJEXT) @GD_LIBS@ $(GL_LIBS) -lm + + sbs_SOURCES = getopt.c getopt1.c energy.c xmalloc.c sbs.c energy.h getopt.h xmalloc.h + sbs_LDADD = -lm diff --git a/sci-biology/unafold/files/unafold-3.8-clang16.patch b/sci-biology/unafold/files/unafold-3.8-clang16.patch new file mode 100644 index 000000000000..fabc28e1fd88 --- /dev/null +++ b/sci-biology/unafold/files/unafold-3.8-clang16.patch @@ -0,0 +1,775 @@ +--- a/src/ct-energy.c ++++ b/src/ct-energy.c +@@ -24,8 +24,8 @@ + double auPenalty(int, int); + double chooseDangle(int, int); + double tstackOrDangle(int, int, int); +-int isHomodimer(); +-int isCircular(); ++int isHomodimer(void); ++int isCircular(void); + + int readStructure(FILE* file); + +@@ -87,7 +87,7 @@ + {NULL, 0, NULL, 0} + }; + +-void usage() ++void usage(void) + { + puts("Usage: ct-energy [OPTION] [FILE]..."); + puts(""); +@@ -1247,7 +1247,7 @@ + return 1; + } + +-int isHomodimer() ++int isHomodimer(void) + { + int i; + +@@ -1272,7 +1272,7 @@ + return 1; + } + +-int isCircular() ++int isCircular(void) + { + return g_prev[0] == g_len && g_next[g_len - 1] % g_len == 1; + } +--- a/src/energy.c ++++ b/src/energy.c +@@ -15,6 +15,7 @@ + #endif + + #include "energy.h" ++#include "util.h" + #include "xmalloc.h" + + #ifndef isinf +--- a/src/hybrid.c ++++ b/src/hybrid.c +@@ -39,10 +39,10 @@ + #endif + + void initializeMatrix(double**, int, double); +-void limitBasePairs(); +-void prohibit(); +-void force(); +-void prefilter(); ++void limitBasePairs(void); ++void prohibit(void); ++void force(void); ++void prefilter(void); + void fillMatrix(double**, int, double); + void fillMatrix_noI(double**, int, double); + void calculateProb(double**, double*, double*, double**, double**, double, double, int, double); +@@ -706,7 +706,7 @@ + matrix[i - 1][n - 1] = (reverse ? R0(n, i) : L0(i, n)); + } + +-void limitBasePairs() ++void limitBasePairs(void) + { + if (g_bpFile) + { +@@ -740,7 +740,7 @@ + } + } + +-void prohibit() ++void prohibit(void) + { + int i, j, k; + struct constraintListNode *top, *newTop; +@@ -788,7 +788,7 @@ + } + + #if ENABLE_FORCE +-void force() ++void force(void) + { + int i, j, k; + struct constraintListNode *top, *newTop; +@@ -880,7 +880,7 @@ + } + } */ + +-void prefilter() ++void prefilter(void) + { + char** in; + int i, j, k, count; +--- a/src/hybrid-min.c ++++ b/src/hybrid-min.c +@@ -53,10 +53,10 @@ + } *pairList; + + void initializeMatrices(double); +-void limitBasePairs(); +-void prohibit(); +-void force(); +-void prefilter(); ++void limitBasePairs(void); ++void prohibit(void); ++void force(void); ++void prefilter(void); + void fillMatrixL(double); + void fillMatrixR(double); + void fillMatrixL_noI(double); +@@ -88,7 +88,7 @@ + #define min2(a, b) ((a) < (b) ? (a) : (b)) + ENERGY min4(ENERGY, ENERGY, ENERGY, ENERGY); + void pushPairList(int, int, int, ENERGY); +-void sortPairList(); ++void sortPairList(void); + + ENERGY *lprime, *rprime; + +@@ -885,7 +885,7 @@ + } + } + +-void limitBasePairs() ++void limitBasePairs(void) + { + if (g_bpFile) + { +@@ -919,7 +919,7 @@ + } + } + +-void prohibit() ++void prohibit(void) + { + int i, j, k; + struct constraintListNode* top; +@@ -965,7 +965,7 @@ + } + + #if ENABLE_FORCE +-void force() ++void force(void) + { + int i, j, k; + struct constraintListNode* top; +@@ -1041,7 +1041,7 @@ + return length; + } + +-void prefilter() ++void prefilter(void) + { + int i, j; + +@@ -1055,7 +1055,7 @@ + } + } */ + +-void prefilter() ++void prefilter(void) + { + char** in; + int i, j, k, count; +@@ -2235,7 +2235,7 @@ + pairList = node; + } + +-void sortPairList() ++void sortPairList(void) + { + struct pairListNode *a, *b; + +--- a/src/hybrid-plot.c ++++ b/src/hybrid-plot.c +@@ -70,13 +70,13 @@ + void displayCallbackInput(void); + void keyboardCallbackInput(unsigned char, int, int); + +-void fixLength(); +-void fixGrid(); +-void fixLabels(); +-void fixZoomGrid(); +-void fixZoomLabels(); ++void fixLength(void); ++void fixGrid(void); ++void fixLabels(void); ++void fixZoomGrid(void); ++void fixZoomLabels(void); + void readFiles(char*); +-void sortTemps(); ++void sortTemps(void); + double* inputRecords(FILE*); + int filter(int, int); + +@@ -1157,7 +1157,7 @@ + } + } + +-void fixLength() ++void fixLength(void) + { + int m, n; + +@@ -1177,7 +1177,7 @@ + } + } + +-void fixGrid() ++void fixGrid(void) + { + int m; + +@@ -1193,7 +1193,7 @@ + g_grid = pow(10, m + 1); + } + +-void fixLabels() ++void fixLabels(void) + { + int longestNum; + +@@ -1202,7 +1202,7 @@ + g_labels += g_grid; + } + +-void fixZoomGrid() ++void fixZoomGrid(void) + { + int m; + +@@ -1221,7 +1221,7 @@ + g_zoomGrid = pow(10, m + 1); + } + +-void fixZoomLabels() ++void fixZoomLabels(void) + { + int longestNum; + +@@ -1310,7 +1310,7 @@ + return scores; + } + +-void sortTemps() ++void sortTemps(void) + { + int i, j; + char* tempC; +--- a/src/hybrid-plot-ng.c ++++ b/src/hybrid-plot-ng.c +@@ -24,28 +24,28 @@ + */ + + #if HAVE_GD +-void initPNG(); ++void initPNG(void); + void titlePNG(char*); +-void borderPNG(); +-void gridPNG(); ++void borderPNG(void); ++void gridPNG(void); + void plotDotPNG(int, int, double); + void vertCenterPNG(char*, int); + void horzCenterPNG(char*, int); + void selectionPNG(char*, int); + #endif + +-void initPS(); ++void initPS(void); + void titlePS(char*); +-void borderPS(); +-void gridPS(); ++void borderPS(void); ++void gridPS(void); + void plotDotPS(int, int, double); + void vertCenterPS(char*, int); + void horzCenterPS(char*, int); + void selectionPS(char*, int); + +-void fixSize(); +-void fixGrid(); +-void fixLabels(); ++void fixSize(void); ++void fixGrid(void); ++void fixLabels(void); + double* inputRecords(FILE*); + int filter(int, int); + int (*getColor)(double); +@@ -114,10 +114,10 @@ + char* plotFile; + + /* functions to call - either PS or PNG */ +- void (*init)(); ++ void (*init)(void); + void (*title)(char*); +- void (*border)(); +- void (*grid)(); ++ void (*border)(void); ++ void (*grid)(void); + void (*plotDot)(int, int, double); + void (*vertCenter)(char*, int); + void (*horzCenter)(char*, int); +@@ -474,7 +474,7 @@ + return 0; + } + +-void initPS() ++void initPS(void) + { + int i; + +@@ -517,7 +517,7 @@ + fprintf(g_file, "(%s) showCenter\n", wordString); + } + +-void borderPS() ++void borderPS(void) + { + fputs("92 126 moveto\n", g_file); + fputs("576 126 lineto\n", g_file); +@@ -527,7 +527,7 @@ + fputs("stroke\n", g_file); + } + +-void gridPS() ++void gridPS(void) + { + double x1, y1; + int i, j; +@@ -639,7 +639,7 @@ + + #if HAVE_GD + +-void initPNG() ++void initPNG(void) + { + int i; + +@@ -671,12 +671,12 @@ + gdImageString(g_image, gdFontMediumBold, 306 - 7 * strlen(wordString) / 2, 51, (unsigned char*) wordString, g_black); + } + +-void borderPNG() ++void borderPNG(void) + { + gdImageRectangle(g_image, 92, 92, 576, 576, g_black); + } + +-void gridPNG() ++void gridPNG(void) + { + int i, j; + char buffer[8]; +@@ -776,7 +776,7 @@ + + #endif + +-void fixSize() ++void fixSize(void) + { + int m, n; + +@@ -796,7 +796,7 @@ + } + } + +-void fixGrid() ++void fixGrid(void) + { + int m; + +@@ -812,7 +812,7 @@ + g_grid = pow(10, m + 1); + } + +-void fixLabels() ++void fixLabels(void) + { + int longestNum; + +--- a/src/hybrid-ss.c ++++ b/src/hybrid-ss.c +@@ -47,10 +47,10 @@ + #define ssOK(i, j) 1 + #endif + +-void initializeMatrices(); +-void fillMatrices1(); ++void initializeMatrices(void); ++void fillMatrices1(void); + void fillMatrices2(double*, double*); +-void fillMatrices1_noI(); ++void fillMatrices1_noI(void); + void fillMatrices2_noI(double*, double*); + void calculateProb(double*, double*, double*, double*, double*, double); + void calculateProb_noI(double*, double*, double*, double*, double*); +@@ -713,7 +713,7 @@ + + #include "hybrid-ss_init.h" + +-void fillMatrices1() ++void fillMatrices1(void) + { + int i, j, k; + FILE* file; +@@ -783,7 +783,7 @@ + } + } + +-void fillMatrices1_noI() ++void fillMatrices1_noI(void) + { + int i, j, k; + FILE* file; +--- a/src/hybrid-ss_init.h ++++ b/src/hybrid-ss_init.h +@@ -14,7 +14,7 @@ + return length; + } */ + +-void prefilter() ++void prefilter(void) + { + char** in; + int i, j, k, count; +@@ -45,7 +45,7 @@ + free(in); + } + +-void initializeMatrices() ++void initializeMatrices(void) + { + int i, j, k; + struct constraintListNode *top, *newTop; +--- a/src/hybrid-ss-min.c ++++ b/src/hybrid-ss-min.c +@@ -57,10 +57,10 @@ + struct pairListNode* next; + } *pairList; + +-void initializeMatrices(); +-void fillMatrices1(); +-void fillMatrices2(); +-void computeQ53(); ++void initializeMatrices(void); ++void fillMatrices1(void); ++void fillMatrices2(void); ++void computeQ53(void); + void traceback(int, int, int, int*, int*, int*); + void traceback_noI(int, int, int, int*, int*, int*); + void setStack(int, int, int*, int*); +@@ -108,7 +108,7 @@ + int equal(ENERGY, ENERGY); + void push(struct stackNode**, int, int, int); + void pushPairList(int, int, int, ENERGY); +-void sortPairList(); ++void sortPairList(void); + + int g_len; + ENERGY *q, *qprime, *qm, *q5, *q3; +@@ -887,7 +887,7 @@ + return length; + } + +-void prefilter() ++void prefilter(void) + { + char** in; + int i, j, k, count; +@@ -918,7 +918,7 @@ + free(in); + } + +-void initializeMatrices() ++void initializeMatrices(void) + { + int i, j, k; + struct constraintListNode* top; +@@ -1072,7 +1072,7 @@ + } + } + +-void fillMatrices1() ++void fillMatrices1(void) + { + int i, j, k; + FILE* file; +@@ -1181,7 +1181,7 @@ + } + } + +-void fillMatrices2() ++void fillMatrices2(void) + { + int i, j, k; + FILE* file; +@@ -1283,7 +1283,7 @@ + } + } + +-void computeQ53() ++void computeQ53(void) + { + int i, j; + +@@ -3137,7 +3137,7 @@ + pairList = node; + } + +-void sortPairList() ++void sortPairList(void) + { + struct pairListNode *a, *b; + +--- a/src/hybrid-ss-noml.c ++++ b/src/hybrid-ss-noml.c +@@ -45,11 +45,11 @@ + #define ssOK(i, j) 1 + #endif + +-void initializeMatrices(); +-void fillMatrices1(); +-void fillMatrices2(); +-void fillMatrices1_noI(); +-void fillMatrices2_noI(); ++void initializeMatrices(void); ++void fillMatrices1(void); ++void fillMatrices2(void); ++void fillMatrices1_noI(void); ++void fillMatrices2_noI(void); + void calculateProb(double*, double*, double*, double); + void calculateProb_noI(double*, double*, double*, double); + void traceback(int*, int*, int*); +@@ -652,7 +652,7 @@ + return length; + } */ + +-void prefilter() ++void prefilter(void) + { + char** in; + int i, j, k, count; +@@ -683,7 +683,7 @@ + free(in); + } + +-void initializeMatrices() ++void initializeMatrices(void) + { + int i, j, k; + struct constraintListNode *top, *newTop; +@@ -826,7 +826,7 @@ + } + } + +-void fillMatrices1() ++void fillMatrices1(void) + { + int i, j, k; + FILE* file; +@@ -885,7 +885,7 @@ + } + } + +-void fillMatrices1_noI() ++void fillMatrices1_noI(void) + { + int i, j, k; + FILE* file; +@@ -944,7 +944,7 @@ + } + } + +-void fillMatrices2() ++void fillMatrices2(void) + { + int i, j; + FILE* file; +@@ -986,7 +986,7 @@ + } + } + +-void fillMatrices2_noI() ++void fillMatrices2_noI(void) + { + int i, j; + FILE* file; +--- a/src/hybrid-ss-simple.c ++++ b/src/hybrid-ss-simple.c +@@ -47,11 +47,11 @@ + #define ssOK(i, j) 1 + #endif + +-void initializeMatrices(); +-void fillMatrices1(); +-void fillMatrices2(); +-void fillMatrices1_noI(); +-void fillMatrices2_noI(); ++void initializeMatrices(void); ++void fillMatrices1(void); ++void fillMatrices2(void); ++void fillMatrices1_noI(void); ++void fillMatrices2_noI(void); + void calculateProb(double*, double*, double*, double); + void calculateProb_noI(double*, double*, double*); + void traceback(int*, int*, int*); +@@ -598,7 +598,7 @@ + + #include "hybrid-ss_init.h" + +-void fillMatrices1() ++void fillMatrices1(void) + { + int i, j, k; + FILE* file; +@@ -658,7 +658,7 @@ + } + } + +-void fillMatrices1_noI() ++void fillMatrices1_noI(void) + { + int i, j, k; + FILE* file; +@@ -718,7 +718,7 @@ + } + } + +-void fillMatrices2() ++void fillMatrices2(void) + { + int i, j, k; + FILE* file; +@@ -789,7 +789,7 @@ + } + } + +-void fillMatrices2_noI() ++void fillMatrices2_noI(void) + { + int i, j, k; + FILE* file; +--- a/src/util.h ++++ b/src/util.h +@@ -24,18 +24,18 @@ + + /* #define NO_GU_BASEPAIRS */ + +-int roundInt(double d) ++static int roundInt(double d) + { + return (int) (d + .5); + } + +-void strcatc(char* str, char c) ++static void strcatc(char* str, char c) + { + str[strlen(str) + 1] = 0; + str[strlen(str)] = c; + } + +-char* filename(char* file) ++static char* filename(char* file) + { + char* name; + +@@ -46,7 +46,7 @@ + return name; + } + +-void checkArray(char** array, unsigned int* available, unsigned int used, unsigned int increment) ++static void checkArray(char** array, unsigned int* available, unsigned int used, unsigned int increment) + { + if (used == *available) + { +@@ -55,7 +55,7 @@ + } + } + +-int input(FILE* file, char** name, char** sequence) ++static int input(FILE* file, char** name, char** sequence) + { + /* read string from file */ + int current, last, state; +@@ -120,7 +120,7 @@ + return 1; + } + +-unsigned char toNum(char c) ++static unsigned char toNum(char c) + { + c = toupper(c); + switch (c) +@@ -137,7 +137,7 @@ + return 4; + } + +-int seqcmp(unsigned char* seq1, unsigned char* seq2, int length) ++static int seqcmp(unsigned char* seq1, unsigned char* seq2, int length) + { + int i; + +@@ -149,7 +149,7 @@ + return 0; + } + +-void readSequence(char* file, char** name, char** string, unsigned char** seq, int* len) ++static void readSequence(char* file, char** name, char** string, unsigned char** seq, int* len) + { + int i; + FILE* f; +@@ -171,14 +171,14 @@ + } + + #ifdef NO_GU_BASEPAIRS +-const int BPI[6][6] = {{6, 6, 6, 0, 6, 6}, ++static const int BPI[6][6] = {{6, 6, 6, 0, 6, 6}, + {6, 6, 1, 6, 6, 6}, + {6, 2, 6, 6, 6, 6}, + {3, 6, 6, 6, 6, 6}, + {6, 6, 6, 6, 6, 6}, + {6, 6, 6, 6, 6, 6}}; + #else +-const int BPI[6][6] = {{6, 6, 6, 0, 6, 6}, ++static const int BPI[6][6] = {{6, 6, 6, 0, 6, 6}, + {6, 6, 1, 6, 6, 6}, + {6, 2, 6, 4, 6, 6}, + {3, 6, 5, 6, 6, 6}, +@@ -187,7 +187,7 @@ + #endif + #define basePairIndex(a, b) BPI[a][b] + +-int min3(int a, int b, int c) ++static int min3(int a, int b, int c) + { + if (a <= b && a <= c) + return a; +@@ -196,7 +196,7 @@ + return c; + } + +-int same(unsigned char* a, unsigned char* b, int len) ++static int same(unsigned char* a, unsigned char* b, int len) + { + int i; + +@@ -206,7 +206,7 @@ + return 1; + } + +-void version(const char* prog) ++static void version(const char* prog) + { + printf("%s (%s) %s\n", prog, PACKAGE_NAME, PACKAGE_VERSION); + puts("By Nicholas R. Markham and Michael Zuker"); +@@ -216,7 +216,7 @@ + exit(EXIT_SUCCESS); + } + +-void readOrDie(unsigned int num, const char* name, FILE* file, const char* format, ...) ++static void readOrDie(unsigned int num, const char* name, FILE* file, const char* format, ...) + { + va_list arg; + va_start(arg, format); diff --git a/sci-biology/unafold/files/unafold-3.8-doc-version.patch b/sci-biology/unafold/files/unafold-3.8-doc-version.patch new file mode 100644 index 000000000000..b15858fd69e6 --- /dev/null +++ b/sci-biology/unafold/files/unafold-3.8-doc-version.patch @@ -0,0 +1,11 @@ +--- a/tests/hybrid.tml ++++ b/tests/hybrid.tml +@@ -10,7 +10,7 @@ + </test> + <test command="hybrid --version" return="0"> + <stdin></stdin> +- <stdout>hybrid (UNAFold) 3.7 ++ <stdout>hybrid (UNAFold) 3.8 + By Nicholas R. Markham and Michael Zuker + Copyright (C) 2006 + Rensselaer Polytechnic Institute diff --git a/sci-biology/unafold/metadata.xml b/sci-biology/unafold/metadata.xml index 959160fe46b1..ccdff086e20b 100644 --- a/sci-biology/unafold/metadata.xml +++ b/sci-biology/unafold/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/unafold/unafold-3.8-r1.ebuild b/sci-biology/unafold/unafold-3.8-r1.ebuild index e4fff4e8cabd..2ca9c44a4a46 100644 --- a/sci-biology/unafold/unafold-3.8-r1.ebuild +++ b/sci-biology/unafold/unafold-3.8-r1.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2013 Gentoo Foundation +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=8 -inherit flag-o-matic +inherit autotools DESCRIPTION="Unified Nucleic Acid Folding and hybridization package" HOMEPAGE="http://mfold.rna.albany.edu/" @@ -12,16 +12,25 @@ SRC_URI="http://dinamelt.bioinfo.rpi.edu/download/${P}.tar.bz2" LICENSE="unafold" SLOT="0" KEYWORDS="~amd64 ~x86" -IUSE="custom-cflags" -DEPEND="" -RDEPEND="${DEPEND}" +RDEPEND=" + media-libs/freeglut + media-libs/gd + virtual/opengl" +DEPEND="${RDEPEND}" +BDEPEND="dev-build/autoconf-archive" + +PATCHES=( + "${FILESDIR}"/${P}-doc-version.patch + "${FILESDIR}"/${P}-autotools.patch + "${FILESDIR}"/${P}-clang16.patch +) src_prepare() { - # recommended in README - use custom-cflags || append-flags -O3 + default + eautoreconf +} - sed \ - -e 's:hybrid (UNAFold) 3.7:hybrid (UNAFold) 3.8:g' \ - -i tests/hybrid.tml || die +src_configure() { + econf --disable-coverage } diff --git a/sci-biology/update-blastdb/metadata.xml b/sci-biology/update-blastdb/metadata.xml index 959160fe46b1..ccdff086e20b 100644 --- a/sci-biology/update-blastdb/metadata.xml +++ b/sci-biology/update-blastdb/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/update-blastdb/update-blastdb-12.0.0.ebuild b/sci-biology/update-blastdb/update-blastdb-12.0.0.ebuild index e1524b487a03..293055ff1633 100644 --- a/sci-biology/update-blastdb/update-blastdb-12.0.0.ebuild +++ b/sci-biology/update-blastdb/update-blastdb-12.0.0.ebuild @@ -1,27 +1,22 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=7 -inherit versionator - -MY_PV="$(replace_all_version_separators _)" +MY_PV="$(ver_rs 1- _)" DESCRIPTION="update_blastdb.pl for local blast db maintainance" HOMEPAGE="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit" SRC_URI="ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/${MY_PV}/ncbi_cxx--${MY_PV}.tar.gz" +S="${WORKDIR}" -SLOT="0" LICENSE="public-domain" +SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="" RDEPEND=" dev-lang/perl !sci-biology/ncbi-tools++" -DEPEND="" - -S="${WORKDIR}" src_install() { dobin ncbi_cxx--${MY_PV}/src/app/blast/update_blastdb.pl diff --git a/sci-biology/vcftools/Manifest b/sci-biology/vcftools/Manifest index d54587b1a971..36aa8e465e22 100644 --- a/sci-biology/vcftools/Manifest +++ b/sci-biology/vcftools/Manifest @@ -1 +1 @@ -DIST vcftools-0.1.14.tar.gz 342369 BLAKE2B 14be867c0be41767e2c97c8be212f3cff495c1cb6699294fb8a26ac491901599cd1e400cb80c6d609dce36584ee5defdb3b3652657bd127e0c67c5b29a842cc5 SHA512 863a16b3b20d392deba7f04310af95f1ab21be537273692aa104e22d737af2eb1bc54a768af954f06188e0500e4f7a032d1189886eb3a439b108cb8189b14eb7 +DIST vcftools-0.1.16.tar.gz 480575 BLAKE2B 5c0bf67aef8ef4705f621485df4c556f6bace190311c308f0364f3e274cf4818f56f2186905fdfb7459dc4be9664a8b1ff631e2cecd03abd7aa82dcfc7e5aa64 SHA512 c4dd5ceb3ad0512e839154d8a05ef3e7a03cbe52c3099df48775b35460fce7ef10102819c2d1cefa33b98ad09e7bd1608e871978860ec9c0b0c2e781892b22e6 diff --git a/sci-biology/vcftools/files/vcftools-0.1.14-buildsystem.patch b/sci-biology/vcftools/files/vcftools-0.1.14-buildsystem.patch deleted file mode 100644 index 126a709385db..000000000000 --- a/sci-biology/vcftools/files/vcftools-0.1.14-buildsystem.patch +++ /dev/null @@ -1,50 +0,0 @@ -* Add prefix in Makefiles, not the configure script -* Use AC_SEARCH_LIBS instead of AC_CHECK_LIB, - as it is more flexible and helps us with LAPACK -* Use correct ZLIB_CFLAGS instead of non-existent ZLIB_CPPFLAGS - ---- a/configure.ac -+++ b/configure.ac -@@ -34,7 +34,7 @@ - [--with-pmdir=DIR], - [install Perl modules in DIR]), - [PMDIR=${withval}], -- [PMDIR='${prefix}'/"$pmdir_relative_path"]) -+ [PMDIR="$pmdir_relative_path"]) - - AC_SUBST([PMDIR]) - -@@ -73,9 +73,9 @@ - [pca=${enableval}], - [pca=no]) - --if test "x${pca}" = "xyes" ; then -- AC_CHECK_LIB(lapack, dgeev_) --fi -+AS_IF([test "x${pca}" = "xyes"],[ -+ AC_SEARCH_LIBS([dgeev_], [lapack]) -+]) - - # Generate output. - AC_CONFIG_FILES([Makefile ---- a/src/cpp/Makefile.am -+++ b/src/cpp/Makefile.am -@@ -1,6 +1,6 @@ - bin_PROGRAMS = vcftools - --vcftools_CPPFLAGS = $(ZLIB_CPPFLAGS) -+vcftools_CPPFLAGS = $(ZLIB_CFLAGS) - vcftools_LDADD = $(ZLIB_LIBS) - - vcftools_SOURCES = \ ---- a/src/perl/Makefile.am -+++ b/src/perl/Makefile.am -@@ -24,7 +24,7 @@ - vcf-tstv \ - vcf-validator - --pmdir = $(PMDIR) -+pmdir = $(exec_prefix)/$(PMDIR) - - dist_pm_DATA = \ - FaSlice.pm \ diff --git a/sci-biology/vcftools/metadata.xml b/sci-biology/vcftools/metadata.xml index 6c22d19200ae..b48544aee61e 100644 --- a/sci-biology/vcftools/metadata.xml +++ b/sci-biology/vcftools/metadata.xml @@ -1,5 +1,5 @@ -<?xml version='1.0' encoding='UTF-8'?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/vcftools/vcftools-0.1.14.ebuild b/sci-biology/vcftools/vcftools-0.1.16.ebuild index 7b386453ae25..b06a81dd0a1a 100644 --- a/sci-biology/vcftools/vcftools-0.1.14.ebuild +++ b/sci-biology/vcftools/vcftools-0.1.16.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit autotools flag-o-matic perl-functions toolchain-funcs @@ -17,10 +17,8 @@ IUSE="lapack" RDEPEND="sys-libs/zlib dev-lang/perl:= lapack? ( virtual/lapack )" -DEPEND="${RDEPEND} - virtual/pkgconfig" - -PATCHES=( "${FILESDIR}/${PN}-0.1.14-buildsystem.patch" ) +DEPEND="${RDEPEND}" +BDEPEND="virtual/pkgconfig" src_prepare() { default diff --git a/sci-biology/velvet/files/velvet-1.2.10-incompatible-pointers.patch b/sci-biology/velvet/files/velvet-1.2.10-incompatible-pointers.patch new file mode 100644 index 000000000000..22cd48ee814f --- /dev/null +++ b/sci-biology/velvet/files/velvet-1.2.10-incompatible-pointers.patch @@ -0,0 +1,26 @@ +https://bugs.gentoo.org/919223 +--- a/src/readSet.c ++++ b/src/readSet.c +@@ -638,7 +638,8 @@ static void readFastXFile(int fileType, SequencesWriter *seqWriteInfo, char *fil + FileGZOrAuto file; + IDnum counter = 0; + +- file.gzFile = file.autoFile = NULL; ++ file.autoFile = NULL; ++ file.gzFile = NULL; + if (fileType == AUTO) { + file.autoFile = openFileAuto(filename); + if (!file.autoFile) +@@ -677,8 +678,10 @@ static void readFastXPair(int fileType, SequencesWriter *seqWriteInfo, char *fil + if (cat==REFERENCE) + exitErrorf(EXIT_FAILURE, false, "Cannot read reference sequence in 'separate' read mode"); + +- file1.gzFile = file1.autoFile = NULL; +- file2.gzFile = file2.autoFile = NULL; ++ file1.autoFile = NULL; ++ file2.autoFile = NULL; ++ file1.autoFile = NULL; ++ file2.autoFile = NULL; + if (fileType == AUTO) { + file1.autoFile = openFileAuto(filename1); + if (!file1.autoFile) diff --git a/sci-biology/velvet/metadata.xml b/sci-biology/velvet/metadata.xml index 959160fe46b1..ccdff086e20b 100644 --- a/sci-biology/velvet/metadata.xml +++ b/sci-biology/velvet/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/velvet/velvet-1.2.10.ebuild b/sci-biology/velvet/velvet-1.2.10.ebuild index 3de28bdb7481..07b44eb65254 100644 --- a/sci-biology/velvet/velvet-1.2.10.ebuild +++ b/sci-biology/velvet/velvet-1.2.10.ebuild @@ -1,28 +1,43 @@ -# Copyright 1999-2018 Gentoo Foundation +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=8 -inherit eutils flag-o-matic toolchain-funcs - -MY_P=${PN}_${PV} +inherit flag-o-matic toolchain-funcs +MY_P="${PN}_${PV}" DESCRIPTION="A sequence assembler for very short reads" HOMEPAGE="https://www.ebi.ac.uk/~zerbino/velvet/" SRC_URI="https://www.ebi.ac.uk/~zerbino/velvet/${MY_P}.tgz" +S="${WORKDIR}"/${MY_P} LICENSE="GPL-2" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="doc openmp" -RDEPEND="" -DEPEND="${RDEPEND} - doc? ( virtual/latex-base )" +BDEPEND=" + doc? ( virtual/latex-base ) + openmp? ( + || ( + sys-devel/gcc[openmp] + sys-devel/clang-runtime[openmp] + ) + ) +" -S="${WORKDIR}"/${MY_P} +PATCHES=( "${FILESDIR}/${P}-incompatible-pointers.patch" ) + +pkg_pretend() { + [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp +} + +pkg_setup() { + [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp +} src_prepare() { + default if ! use doc; then sed -i -e '/default :/ s/doc//' "${S}"/Makefile || die fi @@ -48,7 +63,7 @@ src_prepare() { tc-export CC MAKE_XOPTS=( - CC=$(tc-getCC) + CC="$(tc-getCC)" CFLAGS="${CFLAGS}" OPT="${CFLAGS}" ) diff --git a/sci-biology/vienna-rna/Manifest b/sci-biology/vienna-rna/Manifest deleted file mode 100644 index 0ec5d7aa8484..000000000000 --- a/sci-biology/vienna-rna/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST ViennaRNA-2.1.1.tar.gz 5327215 BLAKE2B 1319a13daafc3798b792f43488590b4d1d290cbbf41ed6e401255c082eceb1212c312179ea31c3e574c852b453a1641198768bf565e72a920b433420d259c53f SHA512 b272afa1146543b290db605debab2badbdbf04fcdfd6130ed3b10604255476b3472b184e9af8a0bbeaa0def266f1a167c125d6cfd02aa3f7ae463697dc5226d5 -DIST ViennaRNA-2.1.8.tar.gz 5464683 BLAKE2B ed2086461b37c90de11638852680507c823495abacec1e797c589c22d07dc48b4833d8d6916e5c95083bb9b970c659bbfb14ca45e155486333a915593c4caf01 SHA512 84f9db1247ff7a77aa6550b6285d9bed31fa6ce179aab26eef798c65a07f5cbd89f944630dfa5d29a43401b12a439324b57ee69047a3985e3a4f1e88dffca60e diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-bindir.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-bindir.patch deleted file mode 100644 index 6d35ecea9b0f..000000000000 --- a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-bindir.patch +++ /dev/null @@ -1,10 +0,0 @@ -diff --git a/Utils/Makefile.am b/Utils/Makefile.am -index f42ebf4..d84a0f1 100644 ---- a/Utils/Makefile.am -+++ b/Utils/Makefile.am -@@ -1,4 +1,4 @@ --pkgbindir = $(pkgdatadir)/bin -+pkgbindir = $(prefix)/bin - pkgbin_PROGRAMS = b2ct popt - - pscript = b2mt.pl ct2b.pl dpzoom.pl mountain.pl relplot.pl rotate_ss.pl cmount.pl colorrna.pl coloraln.pl refold.pl switch.pl diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-impl-decl.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-impl-decl.patch deleted file mode 100644 index de457f318e8e..000000000000 --- a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-impl-decl.patch +++ /dev/null @@ -1,15 +0,0 @@ - Readseq/readseq.c | 1 + - 1 file changed, 1 insertion(+) - -diff --git a/Readseq/readseq.c b/Readseq/readseq.c -index 8af7b39..56a25ae 100644 ---- a/Readseq/readseq.c -+++ b/Readseq/readseq.c -@@ -171,6 +171,7 @@ link -w -o readseq -t MPST -c 'MPS ' - #include <stdio.h> - #include <string.h> - #include <ctype.h> -+#include <stdlib.h> - - #include "ureadseq.h" - diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-prll.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-prll.patch deleted file mode 100644 index ee4aef5c3308..000000000000 --- a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-prll.patch +++ /dev/null @@ -1,30 +0,0 @@ - Readseq/Makefile | 6 +++--- - 1 file changed, 3 insertions(+), 3 deletions(-) - -diff --git a/Readseq/Makefile b/Readseq/Makefile -index f073aaa..05f2edd 100644 ---- a/Readseq/Makefile -+++ b/Readseq/Makefile -@@ -6,11 +6,11 @@ - # - - # pick an ANSI C compiler (the default Sun CC is not ANSI) --CC=gcc # Gnu C Compiler -+CC?=gcc # Gnu C Compiler - #CC=cc # SGI Irix - #CC=vcc # some DEC Ultrix - --CFLAGS= -+CFLAGS?= - #CFLAGS= -DSMALLCHECKSUM # if you prefer to use a GCG-standard 13 bit checksum - # instead of a full 32 bit checksum. This may enhance compatibility w/ GCG software - -@@ -40,7 +40,7 @@ all: build test - - build: $(SOURCES) - @echo "Compiling readseq..." -- $(CC) $(LDFLAGS) $(CFLAGS) -o readseq readseq.c ureadseq.c -+ $(CC) $(LDFLAGS) $(CFLAGS) -o readseq readseq.c ureadseq.c ureadasn.c - - # if using NCBI, uncomment these lines in place of build: above - #build: $(SOURCES) diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-setup.py b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-setup.py deleted file mode 100644 index 57f6b712ba3d..000000000000 --- a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-setup.py +++ /dev/null @@ -1,27 +0,0 @@ -from distutils.core import setup, Extension -import os -import sys - -old_filename = os.path.join("Perl", "RNA.py") -new_filename = os.path.join("Perl", "__init__.py") -if os.path.exists(old_filename): - os.rename(old_filename, new_filename) - -extra_link_args = [] - -extension = Extension("_RNA", - ["Perl/RNA_wrap.c"], - libraries=['RNA'], - library_dirs=['lib'], - extra_link_args=extra_link_args - ) - -setup(name="RNA", - version="2.1.1", - description="Vienna RNA", - author="Ivo Hofacker, Institute for Theoretical Chemistry, University of Vienna", - url="http://www.tbi.univie.ac.at/RNA/", - package_dir = {'RNA':'Perl'}, - packages = ['RNA'], - ext_modules=[extension], - ) diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.8-bindir.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.8-bindir.patch deleted file mode 100644 index e54dff95b485..000000000000 --- a/sci-biology/vienna-rna/files/vienna-rna-2.1.8-bindir.patch +++ /dev/null @@ -1,10 +0,0 @@ -diff --git a/Utils/Makefile.am b/Utils/Makefile.am -index f42ebf4..d84a0f1 100644 ---- a/Utils/Makefile.am -+++ b/Utils/Makefile.am -@@ -1,4 +1,4 @@ --pkgbindir = $(pkgdatadir)/bin -+pkgbindir = $(prefix)/bin - pkgbin_PROGRAMS = b2ct popt ct2db - - pscript = b2mt.pl ct2b.pl dpzoom.pl mountain.pl relplot.pl rotate_ss.pl cmount.pl colorrna.pl coloraln.pl refold.pl switch.pl diff --git a/sci-biology/vienna-rna/metadata.xml b/sci-biology/vienna-rna/metadata.xml deleted file mode 100644 index bbc3d41fb4a6..000000000000 --- a/sci-biology/vienna-rna/metadata.xml +++ /dev/null @@ -1,25 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <longdescription> - The Vienna RNA Package consists of a C code library and several - stand-alone programs for the prediction and comparison of RNA secondary - structures. RNA secondary structure prediction through energy - minimization is the most used function in the package. We provide three - kinds of dynamic programming algorithms for structure prediction: the - minimum free energy algorithm of (Zuker and Stiegler 1981) which yields a - single optimal structure, the partition function algorithm of - (McCaskill 1990) which calculates base pair probabilities in the - thermodynamic ensemble, and the suboptimal folding algorithm of - (Wuchty et.al 1999) which generates all suboptimal structures within a - given energy range of the optimal energy. For secondary structure - comparison, the package contains several measures of distance - (dissimilarities) using either string alignment or tree-editing - (Shapiro and Zhang 1990). Finally, we provide an algorithm to design - sequences with a predefined structure (inverse folding). - </longdescription> -</pkgmetadata> diff --git a/sci-biology/vienna-rna/vienna-rna-2.1.1.ebuild b/sci-biology/vienna-rna/vienna-rna-2.1.1.ebuild deleted file mode 100644 index 8b760b5a84bf..000000000000 --- a/sci-biology/vienna-rna/vienna-rna-2.1.1.ebuild +++ /dev/null @@ -1,111 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) -DISTUTILS_OPTIONAL=true -AUTOTOOLS_AUTORECONF=true -AUTOTOOLS_IN_SOURCE_BUILD=1 - -inherit autotools-utils distutils-r1 multilib perl-module toolchain-funcs - -DESCRIPTION="RNA secondary structure prediction and comparison" -HOMEPAGE="http://www.tbi.univie.ac.at/~ivo/RNA/" -SRC_URI="http://www.tbi.univie.ac.at/~ronny/RNA/ViennaRNA-${PV}.tar.gz" - -SLOT="0" -LICENSE="vienna-rna" -KEYWORDS="amd64 ppc x86" -IUSE="doc openmp python static-libs" - -REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" - -RDEPEND=" - dev-lang/perl - media-libs/gd - doc? ( dev-texlive/texlive-latex ) - python? ( ${PYTHON_DEPS} )" -DEPEND="${RDEPEND} - python? ( dev-lang/swig:0 )" - -S="${WORKDIR}/ViennaRNA-${PV}" - -PATCHES=( - "${FILESDIR}"/${P}-bindir.patch - "${FILESDIR}"/${P}-prll.patch - "${FILESDIR}"/${P}-impl-decl.patch -) - -src_prepare() { - sed -i 's/ getline/ v_getline/' Readseq/ureadseq.c || die - sed -i 's/@PerlCmd@ Makefile.PL/& INSTALLDIRS=vendor/' Perl/Makefile.am || die - - autotools-utils_src_prepare - - if use python; then - cp "${FILESDIR}"/${P}-setup.py "${S}"/setup.py || die - PATCHES=() - distutils-r1_src_prepare - fi -} - -src_configure() { - local myeconfargs=( - --with-cluster - $(use_enable openmp) ) - - use doc || \ - myeconfargs+=( - --without-doc-pdf - --without-doc-html - --without-doc - ) - autotools-utils_src_configure - sed \ - -e "s:LIBDIR = /usr/lib:LIBDIR = ${D}/usr/$(get_libdir):" \ - -e "s:INCDIR = /usr/include:INCDIR = ${D}/usr/include:" \ - -i RNAforester/g2-0.70/Makefile || die - sed \ - -e "s:CC=gcc:CC=$(tc-getCC):" \ - -e "s:^CFLAGS=:CFLAGS=${CFLAGS}:" \ - -i Readseq/Makefile || die - use python && distutils-r1_src_configure -} - -src_compile() { - autotools-utils_src_compile - autotools-utils_src_compile -C Readseq build CC=$(tc-getCC) - - # TODO: Add (optional?) support for the NCBI toolkit. - if use python; then - pushd Perl > /dev/null - mv RNA_wrap.c{,-perl} || die - swig -python RNA.i || die - popd > /dev/null - distutils-r1_src_compile - mv Perl/RNA_wrap.c{-perl,} || die - fi -} - -src_test() { - autotools-utils_src_compile -C Perl check - autotools-utils_src_compile -C Readseq test -} - -src_install() { - autotools-utils_src_install - - if ! use static-libs; then - rm -f "${ED}"/usr/$(get_libdir)/*.a || die - fi - - newbin Readseq/readseq readseq-vienna - dodoc Readseq/Readseq.help - newdoc Readseq/Readme README.readseq - newdoc Readseq/Formats Formats.readseq - - # remove perlocal.pod to avoid file collisions (see #240358) - perl_delete_localpod || die "Failed to remove perlocal.pod" - use python && distutils-r1_src_install -} diff --git a/sci-biology/vienna-rna/vienna-rna-2.1.8.ebuild b/sci-biology/vienna-rna/vienna-rna-2.1.8.ebuild deleted file mode 100644 index 7664f6d3dc6e..000000000000 --- a/sci-biology/vienna-rna/vienna-rna-2.1.8.ebuild +++ /dev/null @@ -1,112 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) -DISTUTILS_OPTIONAL=true -AUTOTOOLS_AUTORECONF=true -AUTOTOOLS_IN_SOURCE_BUILD=1 - -inherit autotools-utils distutils-r1 multilib perl-module toolchain-funcs - -DESCRIPTION="RNA secondary structure prediction and comparison" -HOMEPAGE="http://www.tbi.univie.ac.at/~ivo/RNA/" -SRC_URI="http://www.tbi.univie.ac.at/RNA/packages/source/ViennaRNA-${PV}.tar.gz" - -SLOT="0" -LICENSE="vienna-rna" -KEYWORDS="~amd64 ~ppc ~x86" -IUSE="doc openmp python static-libs" - -REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" - -RDEPEND=" - dev-lang/perl - media-libs/gd - doc? ( dev-texlive/texlive-latex ) - python? ( ${PYTHON_DEPS} )" -DEPEND="${RDEPEND} - python? ( dev-lang/swig:0 )" - -S="${WORKDIR}/ViennaRNA-${PV}" - -PATCHES=( - "${FILESDIR}"/${P}-bindir.patch - "${FILESDIR}"/${PN}-2.1.1-prll.patch - "${FILESDIR}"/${PN}-2.1.1-impl-decl.patch -) - -src_prepare() { - sed -i 's/ getline/ v_getline/' Readseq/ureadseq.c || die - sed -i 's/@PerlCmd@ Makefile.PL/& INSTALLDIRS=vendor/' interfaces/Perl/Makefile.am || die - - autotools-utils_src_prepare - - if use python; then - cd interfaces/Python || die - local PATCHES=() - distutils-r1_src_prepare - fi -} - -src_configure() { - local myeconfargs=( - --with-cluster - $(use_enable openmp) - ) - - use doc || \ - myeconfargs+=( - --without-doc-pdf - --without-doc-html - --without-doc - ) - autotools-utils_src_configure - sed \ - -e "s:CC=gcc:CC=$(tc-getCC):" \ - -e "s:^CFLAGS=:CFLAGS=${CFLAGS}:" \ - -i Readseq/Makefile || die - if use python; then - cd interfaces/Python || die - distutils-r1_src_configure - fi -} - -src_compile() { - autotools-utils_src_compile - autotools-utils_src_compile -C Readseq build CC=$(tc-getCC) - - # TODO: Add (optional?) support for the NCBI toolkit. - if use python; then - cd interfaces/Python || die - emake RNA_wrap.c - distutils-r1_src_compile - fi -} - -src_test() { - autotools-utils_src_compile -C interfaces/Perl check - use python && autotools-utils_src_compile -C interfaces/Python check - autotools-utils_src_compile -C Readseq test -} - -src_install() { - autotools-utils_src_install - - if ! use static-libs; then - rm -f "${ED}"/usr/$(get_libdir)/*.a || die - fi - - newbin Readseq/readseq readseq-vienna - dodoc Readseq/Readseq.help - newdoc Readseq/Readme README.readseq - newdoc Readseq/Formats Formats.readseq - - # remove perlocal.pod to avoid file collisions (see #240358) - perl_delete_localpod || die "Failed to remove perlocal.pod" - if use python; then - cd interfaces/Python || die - distutils-r1_src_install - fi -} diff --git a/sci-biology/wgs-assembler/Manifest b/sci-biology/wgs-assembler/Manifest deleted file mode 100644 index 1139a2badf36..000000000000 --- a/sci-biology/wgs-assembler/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST wgs-7.0.tar.bz2 1952253 BLAKE2B 2dbff6ffb9f4310d3d1301405e74476b7b7bbed4359c1701b5100d9597db46cc9956ccbe467bb37f8976d176ab9f92bfabcd5d1210b1e10675cff9a87ff379b9 SHA512 e5ef1d4533e3dd17d13c6aca9631f5300768a258f8241f3f7f90de3785bf7a340b6896febe335682c282434c9983bc4a02fe2128a5b0e7ec415dd65e0fe400ba diff --git a/sci-biology/wgs-assembler/files/wgs-assembler-7.0-build.patch b/sci-biology/wgs-assembler/files/wgs-assembler-7.0-build.patch deleted file mode 100644 index f7fb44743968..000000000000 --- a/sci-biology/wgs-assembler/files/wgs-assembler-7.0-build.patch +++ /dev/null @@ -1,229 +0,0 @@ - kmer/Make.rules | 4 ++-- - kmer/configure.sh | 20 +++++++++---------- - src/c_make.as | 58 +++++++++++++++++++++++++++---------------------------- - src/c_make.gen | 4 ++-- - 4 files changed, 43 insertions(+), 43 deletions(-) - -diff --git a/kmer/Make.rules b/kmer/Make.rules -index f904b13..5c2d477 100644 ---- a/kmer/Make.rules -+++ b/kmer/Make.rules -@@ -139,12 +139,12 @@ ${ALL_CXX_DEPS}:%.d:% - ## EXE targets - ALL_C_EXES :=$(strip $(foreach x,${//},${${x:.=.C_EXES}})) - ${ALL_C_EXES}: -- ${-CC} ${CLD} ${CLDFLAGS} -o $@ $+ ${CLIBS} -+ ${-CC} ${CLD} ${CLDFLAGS} ${LDFLAGS} -o $@ $+ ${CLIBS} - __SUBGOALS__+=$${${1:.=.C_EXES}} - - ALL_CXX_EXES :=$(strip $(foreach x,${//},${${x:.=.CXX_EXES}})) - ${ALL_CXX_EXES}: -- ${-CXX} ${CXXLD} ${CXXLDFLAGS} -o $@ $+ ${CXXLIBS} -+ ${-CXX} ${CXXLD} ${CXXLDFLAGS} ${LDFLAGS} -o $@ $+ ${CXXLIBS} - __SUBGOALS__+=$${${1:.=.CXX_EXES}} - - define .RULE-install-copy-C-CXX-EXES -diff --git a/kmer/configure.sh b/kmer/configure.sh -index 2f0d5ea..9daf89f 100755 ---- a/kmer/configure.sh -+++ b/kmer/configure.sh -@@ -254,13 +254,13 @@ EOF - # -*- makefile -*- - # Linux, optimized - CC := $CC --SHLIB_FLAGS := -shared --CFLAGS_COMPILE := -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer --CLDFLAGS := -L/usr/local/lib -+SHLIB_FLAGS := -shared ${LDFLAGS} -+CFLAGS_COMPILE := -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -+CLDFLAGS := - CLIBS := -pthread -ldl - CXX := $CXX --CXXFLAGS_COMPILE := -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer --CXXLDFLAGS := -L/usr/local/lib -+CXXFLAGS_COMPILE := -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -+CXXLDFLAGS := - CXXLIBS := -pthread -ldl - ARFLAGS := ruvs - INSTALL/ := $target/ -@@ -272,13 +272,13 @@ EOF - # -*- makefile -*- - # Linux64, optimized - CC := $CC --SHLIB_FLAGS := -shared --CFLAGS_COMPILE := -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer --CLDFLAGS := -L/usr/local/lib -+SHLIB_FLAGS := -shared ${LDFLAGS} -+CFLAGS_COMPILE := -fPIC -D_REENTRANT -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -+CLDFLAGS := - CLIBS := -pthread -ldl - CXX := $CXX --CXXFLAGS_COMPILE := -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer --CXXLDFLAGS := -L/usr/local/lib -+CXXFLAGS_COMPILE := -fPIC -D_REENTRANT -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -+CXXLDFLAGS := - CXXLIBS := -pthread -ldl - ARFLAGS := ruvs - INSTALL/ := $target/ -diff --git a/src/c_make.as b/src/c_make.as -index 0172807..4304589 100644 ---- a/src/c_make.as -+++ b/src/c_make.as -@@ -64,27 +64,27 @@ include $(LOCAL_WORK)/src/c_make.gen - - ifeq ($(OSTYPE), Linux) - ifeq ($(MACHINETYPE), i686) -- ARCH_LDFLAGS += -pthread -lm -- ARCH_CFLAGS += -pthread -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DX86_GCC_LINUX -+ LINK_LIBS += -pthread -lm -+ ARCH_CFLAGS += -pthread -Wall -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DX86_GCC_LINUX - ARCH_LIB = /usr/X11R6/lib - endif - ifeq ($(MACHINETYPE), amd64) -- ARCH_LDFLAGS += -pthread -lm -- ARCH_CFLAGS += -pthread -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DX86_GCC_LINUX -+ LINK_LIBS += -pthread -lm -+ ARCH_CFLAGS += -pthread -Wall -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DX86_GCC_LINUX - ARCH_LIB = /usr/lib64 /usr/X11R6/lib64 - endif - ifeq ($(MACHINETYPE), ia64) -- ARCH_LDFLAGS += -pthread -lm -- ARCH_CFLAGS += -pthread -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -+ LINK_LIBS += -pthread -lm -+ ARCH_CFLAGS += -pthread -Wall -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 - ARCH_LIB = /usr/X11R6/lib - endif - - ifeq ($(BUILDDEBUG), 1) -- ARCH_CFLAGS += -g -- ARCH_LDFLAGS += -+ ARCH_CFLAGS += -+ LINK_LIBS += - else -- ARCH_CFLAGS += -O2 -- ARCH_LDFLAGS += -Wl,-O1 -+ ARCH_CFLAGS += -+ LINK_LIBS += - endif - endif - -@@ -94,19 +94,19 @@ endif - - ifeq ($(OSTYPE), FreeBSD) - ifeq ($(MACHINETYPE), i386) -- ARCH_LDFLAGS += -pthread -lthr -lm -- ARCH_CFLAGS = -pthread -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -- ARCH_CFLAGS = -pthread -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -+ LINK_LIBS += -pthread -lthr -lm -+ ARCH_CFLAGS = -pthread -Wall -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -+ ARCH_CFLAGS = -pthread -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare - endif - ifeq ($(MACHINETYPE), amd64) -- ARCH_LDFLAGS += -pthread -lthr -lm -- ARCH_CFLAGS = -pthread -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -- ARCH_CFLAGS = -pthread -Wall -Wextra -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -+ LINK_LIBS += -pthread -lthr -lm -+ ARCH_CFLAGS = -pthread -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -+ ARCH_CFLAGS = -pthread -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat - endif - - ifeq ($(BUILDCOVERAGE), 1) - ARCH_CFLAGS += -g -fprofile-arcs -ftest-coverage -- ARCH_LDFLAGS += -lgcov -+ LINK_LIBS += -lgcov - else - ifeq ($(BUILDDEBUG), 1) - ARCH_CFLAGS += -g -@@ -140,14 +140,14 @@ ifeq ($(OSTYPE), Darwin) - - ifeq ($(MACHINETYPE), i386) - ifeq ($(BUILDDEBUG), 1) -- ARCH_CFLAGS += -fPIC -m64 -fmessage-length=0 -D_THREAD_SAFE -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -g -- ARCH_LDFLAGS += -m64 -lm -+ ARCH_CFLAGS += -fPIC -m64 -fmessage-length=0 -D_THREAD_SAFE -Wall -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -g -+ LINK_LIBS += -m64 -lm - else - # Wow, -Wshorten-64-to-32 is tough -- ARCH_CFLAGS += -fPIC -m64 -fmessage-length=0 -D_THREAD_SAFE -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -fast -+ ARCH_CFLAGS += -fPIC -m64 -fmessage-length=0 -D_THREAD_SAFE -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -fast - # ARCH_CFLAGS += -Wextra - # ARCH_CFLAGS += -pedantic (see above about pedantic) -- ARCH_LDFLAGS += -m64 -lm -+ LINK_LIBS += -m64 -lm - endif - endif - -@@ -161,23 +161,23 @@ endif - ifeq ($(OSTYPE), SunOS) - ifeq ($(MACHINETYPE), i86pc) - ARCH_CFLAGS = -DBYTE_ORDER=LITTLE_ENDIAN -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -pthreads -- ARCH_LDFLAGS += -lm -+ LINK_LIBS += -lm - endif - - ifeq ($(MACHINETYPE), sparc32) - ARCH_CFLAGS = -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -pthreads -- ARCH_LDFLAGS += -lm -lnsl -lsocket -+ LINK_LIBS += -lm -lnsl -lsocket - endif - - ifeq ($(MACHINETYPE), sparc64) - ARCH_CFLAGS = -m64 -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -pthreads -- ARCH_LDFLAGS += -m64 -lm -lnsl -lsocket -+ LINK_LIBS += -lm -lnsl -lsocket - endif - - ifeq ($(BUILDDEBUG), 1) -- ARCH_CFLAGS += -g -+ ARCH_CFLAGS += - else -- ARCH_CFLAGS += -O -+ ARCH_CFLAGS += - endif - endif - -@@ -186,14 +186,14 @@ endif - - ifeq ($(BUILDPROFILE), 1) - ARCH_CFLAGS += -pg -- ARCH_LDFLAGS += -pg -+ LINK_LIBS += -pg - endif - - # One can argue that CXXFLAGS should be separate. For now, we only - # add to the flags. - - CFLAGS += $(ARCH_CFLAGS) --CXXFLAGS += $(ARCH_CFLAGS) $(ARCH_CXXFLAGS) -+CXXFLAGS += $(ARCH_CXXFLAGS) - LDFLAGS += $(ARCH_LDFLAGS) - - INC_IMPORT_DIRS += $(LOCAL_WORK)/src $(patsubst %, $(LOCAL_WORK)/src/%, $(strip $(SUBDIRS))) -@@ -205,7 +205,7 @@ LIB_IMPORT_DIRS += $(ARCH_LIB) - OBJ_SEARCH_PATH = $(LOCAL_OBJ) - - ifeq ($(SITE_NAME), JCVI) -- LDFLAGS += -lcurl -+ LINK_LIBS += -lcurl - endif - - # The order of compilation here is very carefully chosen to be the -diff --git a/src/c_make.gen b/src/c_make.gen -index 7b5227c..c27b777 100644 ---- a/src/c_make.gen -+++ b/src/c_make.gen -@@ -396,12 +396,12 @@ $(LIBRARIES): - $(C_PROGS): - @ echo "++++++++++++++++++++ " $@ "++++++++++++++++++++++"; - cd $(LOCAL_OBJ); \ -- $(CC) -o $(LOCAL_BIN)/$(notdir $@) $(filter-out lib%.a, $+) $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LD_DIRS) $(LDFLAGS) -+ $(CC) $(LDFLAGS) -o $(LOCAL_BIN)/$(notdir $@) $(filter-out lib%.a, $+) $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LD_DIRS) $(LINK_LIBS) - - $(CXX_PROGS): - @ echo "++++++++++++++++++++ " $@ "++++++++++++++++++++++"; - cd $(LOCAL_OBJ); \ -- $(CXX) -o $(LOCAL_BIN)/$(notdir $@) $(filter-out lib%.a, $+) $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LD_DIRS) $(LDFLAGS) -+ $(CXX) $(LDFLAGS) -o $(LOCAL_BIN)/$(notdir $@) $(filter-out lib%.a, $+) $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LD_DIRS) $(LINK_LIBS) - - $(SCRIPT_PROGS): %.sh: - @echo "++++++++++++++++++++ " $@ "++++++++++++++++++++++"; diff --git a/sci-biology/wgs-assembler/files/wgs-assembler-7.0-libtirpc.patch b/sci-biology/wgs-assembler/files/wgs-assembler-7.0-libtirpc.patch deleted file mode 100644 index 7269b0b73c48..000000000000 --- a/sci-biology/wgs-assembler/files/wgs-assembler-7.0-libtirpc.patch +++ /dev/null @@ -1,16 +0,0 @@ -diff -ruN wgs-7.0.orig/src/c_make.as wgs-7.0/src/c_make.as ---- wgs-7.0.orig/src/c_make.as 2018-04-29 23:00:02.200181987 +0200 -+++ wgs-7.0/src/c_make.as 2018-04-29 23:17:33.612700507 +0200 -@@ -196,6 +196,12 @@ - CXXFLAGS += $(ARCH_CXXFLAGS) - LDFLAGS += $(ARCH_LDFLAGS) - -+# libtirpc -+ -+CFLAGS += -I/usr/include/tirpc -+CXXFLAGS += -I/usr/include/tirpc -+LINK_LIBS += -ltirpc -+ - INC_IMPORT_DIRS += $(LOCAL_WORK)/src $(patsubst %, $(LOCAL_WORK)/src/%, $(strip $(SUBDIRS))) - INC_IMPORT_DIRS += $(ARCH_INC) - diff --git a/sci-biology/wgs-assembler/metadata.xml b/sci-biology/wgs-assembler/metadata.xml deleted file mode 100644 index fa8a259ff764..000000000000 --- a/sci-biology/wgs-assembler/metadata.xml +++ /dev/null @@ -1,11 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">wgs-assembler</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/wgs-assembler/wgs-assembler-7.0-r2.ebuild b/sci-biology/wgs-assembler/wgs-assembler-7.0-r2.ebuild deleted file mode 100644 index fc5869667f02..000000000000 --- a/sci-biology/wgs-assembler/wgs-assembler-7.0-r2.ebuild +++ /dev/null @@ -1,72 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit eutils toolchain-funcs - -DESCRIPTION="The Celera de novo whole-genome shotgun DNA sequence assembler, aka CABOG" -HOMEPAGE="https://sourceforge.net/projects/wgs-assembler/" -SRC_URI="mirror://sourceforge/${PN}/wgs-${PV}.tar.bz2" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="amd64 x86" -IUSE="static-libs" - -DEPEND=" - net-libs/libtirpc - x11-libs/libXt - !x11-terms/terminator" -RDEPEND="${DEPEND} - app-shells/tcsh - dev-perl/Log-Log4perl" - -S="${WORKDIR}/wgs-${PV}" - -PATCHES=( - "${FILESDIR}"/${P}-build.patch - "${FILESDIR}"/${P}-libtirpc.patch -) - -src_prepare() { - default - tc-export CC CXX -} - -src_configure() { - cd "${S}/kmer" - ./configure.sh || die -} - -src_compile() { - # not really an install target - emake -C kmer -j1 install - emake -C src -j1 SITE_NAME=LOCAL -} - -src_install() { - OSTYPE=$(uname) - MACHTYPE=$(uname -m) - MACHTYPE=${MACHTYPE/x86_64/amd64} - MY_S="${OSTYPE}-${MACHTYPE}" - sed -i 's|#!/usr/local/bin/|#!/usr/bin/env |' $(find $MY_S -type f) || die - - sed -i '/sub getBinDirectory ()/ a return "/usr/bin";' ${MY_S}/bin/runCA* || die - sed -i '/sub getBinDirectoryShellCode ()/ a return "bin=/usr/bin\n";' ${MY_S}/bin/runCA* || die - sed -i '1 a use lib "/usr/share/'${PN}'/lib";' $(find $MY_S -name '*.p*') || die - - dobin kmer/${MY_S}/bin/* - insinto /usr/$(get_libdir)/${PN} - use static-libs && doins kmer/${MY_S}/lib/* - - insinto /usr/include/${PN} - doins kmer/${MY_S}/include/* - - insinto /usr/share/${PN}/lib - doins -r ${MY_S}/bin/TIGR - rm -rf ${MY_S}/bin/TIGR || die - dobin ${MY_S}/bin/* - use static-libs && dolib.a ${MY_S}/lib/* - dodoc README -} diff --git a/sci-biology/wise/files/wise-api.tex.patch b/sci-biology/wise/files/wise-api.tex.patch new file mode 100644 index 000000000000..d6d56888dfb3 --- /dev/null +++ b/sci-biology/wise/files/wise-api.tex.patch @@ -0,0 +1,38 @@ +--- a/api.tex.old ++++ b/api.tex +@@ -204,7 +204,7 @@ + \item Build two Sequence objects, from a file or strings (\ref{object_Sequence}) + \item Optionally convert the Sequence objects into Protein objects (\ref{object_Protein}). This ensures you have proteins + \item Read in the comparison matrix using CompMat (\ref{object_CompMat}) +-\item Use one of the algorithm calls in sw_wrap module (\ref{module_sw_wrap}) ++\item Use one of the algorithm calls in sw\_wrap module (\ref{module_sw_wrap}) + \item Show the alignment using a call in the seqaligndisaply module (\ref{module_seqaligndisplay}) + \end{itemize} + +@@ -213,7 +213,7 @@ + \item Read in a sequence object and convert it to a protein object (\ref{object_Protein},\ref{object_Sequence}) + \item Make a protein database from the single protein object (\ref{object_ProteinDB}) + \item Make a protein database from a single fasta file (\ref{object_ProteinDB}) +-\item Using one of the calls to the sw_wrap module, make a Hscore object (\ref{module_sw_wrap}) ++\item Using one of the calls to the sw\_wrap module, make a Hscore object (\ref{module_sw_wrap}) + \item Show the Hscore object using a show function (\ref{object_Hscore}) + \item Retrieve individual protein objects from the database by taking out the + DataEntry objects (\ref{object_DataEntry}) and passing them into the ProteinDB object (\ref{object_ProteinDB}), giving you a protein object +@@ -232,7 +232,7 @@ + \item Read in a codon table (\ref{object_CodonTable}) + \item Make a random DNA model (\ref{object_RandomModelDNA}) + \item Make an algorithm type (\ref{module_gwrap}) +-\item Build an entire parameter set for genewise using Wise2::GeneParameter21_wrap (\ref{module_gwrap}) ++\item Build an entire parameter set for genewise using Wise2::GeneParameter21\_wrap (\ref{module_gwrap}) + \item Run the actual algorithm (\ref{module_gwrap}) + \item show the alignment using genedisplay (\ref{module_gwrap}) + \end{itemize} +@@ -5055,7 +5055,7 @@ + Member functions of RandomModel + + \section{sequence\_codon} +-\label{module_sequence\_codon} ++\label{module_sequence_codon} + This module only contains factory methods + + \subsection{sequence\_codon factory methods} diff --git a/sci-biology/wise/metadata.xml b/sci-biology/wise/metadata.xml index 959160fe46b1..ccdff086e20b 100644 --- a/sci-biology/wise/metadata.xml +++ b/sci-biology/wise/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/wise/wise-2.4.0_alpha-r1.ebuild b/sci-biology/wise/wise-2.4.0_alpha-r1.ebuild new file mode 100644 index 000000000000..a033ffd011bb --- /dev/null +++ b/sci-biology/wise/wise-2.4.0_alpha-r1.ebuild @@ -0,0 +1,71 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit toolchain-funcs + +MY_PV="${PV/_}" +MY_P="${PN}${MY_PV}" +DESCRIPTION="Intelligent algorithms for DNA searches" +HOMEPAGE="http://www.ebi.ac.uk/Wise2/" +SRC_URI=" + ftp://ftp.ebi.ac.uk/pub/software/${PN}2/${MY_P}.tar.gz + https://dev.gentoo.org/~mgorny/dist/${P}-patchset.tar.bz2 +" +S="${WORKDIR}"/${MY_P} + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="doc" + +RDEPEND="~sci-biology/hmmer-2.3.2" +DEPEND="${RDEPEND}" +BDEPEND=" + app-shells/tcsh + dev-lang/perl + virtual/latex-base +" + +PATCHES=( + "${WORKDIR}"/${P}-patchset/${P}-glibc-2.10.patch + "${WORKDIR}"/${P}-patchset/${P}-cflags.patch +) + +src_prepare() { + default + cd docs || die + cat ../src/models/*.tex ../src/dynlibsrc/*.tex | perl gettex.pl > temp.tex || die + cat wise2api.tex temp.tex apiend.tex > api.tex || die + eapply "${FILESDIR}"/${PN}-api.tex.patch +} + +src_compile() { + tc-export CC + emake -C src all + + if use doc; then + cd docs || die + for i in api appendix dynamite wise2 wise3arch; do + latex ${i} || die + latex ${i} || die + dvips ${i}.dvi -o || die + done + fi +} + +src_test() { + cd src || die + WISECONFIGDIR="${S}/wisecfg" emake test +} + +src_install() { + dobin src/bin/* src/dynlibsrc/testgendb + + insinto /usr/share/${PN} + doins -r wisecfg + + use doc && dodoc docs/*.ps + newenvd "${WORKDIR}"/${P}-patchset/${PN}-env 24wise +} diff --git a/sci-biology/wise/wise-2.4.0_alpha.ebuild b/sci-biology/wise/wise-2.4.0_alpha.ebuild deleted file mode 100644 index aa971e0c6932..000000000000 --- a/sci-biology/wise/wise-2.4.0_alpha.ebuild +++ /dev/null @@ -1,73 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils toolchain-funcs versionator - -DESCRIPTION="Intelligent algorithms for DNA searches" -HOMEPAGE="http://www.ebi.ac.uk/Wise2/" -SRC_URI="ftp://ftp.ebi.ac.uk/pub/software/${PN}2/${PN}$(delete_version_separator 3).tar.gz - https://dev.gentoo.org/~mgorny/dist/${P}-patchset.tar.bz2" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="doc static-libs" - -RDEPEND="~sci-biology/hmmer-2.3.2" -DEPEND=" - ${RDEPEND} - app-shells/tcsh - dev-lang/perl - virtual/latex-base" - -S="${WORKDIR}"/${PN}$(delete_version_separator 3) - -src_prepare() { - epatch \ - "${WORKDIR}"/${P}-patchset/${P}-glibc-2.10.patch \ - "${WORKDIR}"/${P}-patchset/${P}-cflags.patch - cd "${S}"/docs || die - cat "${S}"/src/models/*.tex "${S}"/src/dynlibsrc/*.tex | perl gettex.pl > temp.tex || die - cat wise2api.tex temp.tex apiend.tex > api.tex || die - epatch "${WORKDIR}"/${P}-patchset/${PN}-api.tex.patch -} - -src_compile() { - emake \ - -C src \ - CC="$(tc-getCC)" \ - all - if use doc; then - cd "${S}"/docs || die - for i in api appendix dynamite wise2 wise3arch; do - latex ${i} || die - latex ${i} || die - dvips ${i}.dvi -o || die - done - fi -} - -src_test() { - cd "${S}"/src || die - WISECONFIGDIR="${S}/wisecfg" emake test -} - -src_install() { - dobin "${S}"/src/bin/* "${S}"/src/dynlibsrc/testgendb - use static-libs && \ - dolib.a \ - "${S}"/src/base/libwisebase.a \ - "${S}"/src/dynlibsrc/libdyna.a \ - "${S}"/src/models/libmodel.a - - insinto /usr/share/${PN} - doins -r "${S}"/wisecfg - - if use doc; then - insinto /usr/share/doc/${PF} - doins "${S}"/docs/*.ps - fi - newenvd "${WORKDIR}"/${P}-patchset/${PN}-env 24wise || die "Failed to install env file" -} diff --git a/sci-biology/yass/metadata.xml b/sci-biology/yass/metadata.xml index 67dfef524416..1235113d13c6 100644 --- a/sci-biology/yass/metadata.xml +++ b/sci-biology/yass/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> diff --git a/sci-biology/yass/yass-1.14-r2.ebuild b/sci-biology/yass/yass-1.14-r3.ebuild index cdbe54f0bef6..3913c44f4580 100644 --- a/sci-biology/yass/yass-1.14-r2.ebuild +++ b/sci-biology/yass/yass-1.14-r3.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit autotools @@ -11,8 +11,8 @@ SRC_URI="http://bioinfo.lifl.fr/yass/files/${P}.tar.gz" LICENSE="GPL-2" SLOT="0" -IUSE="dmalloc lowmem threads" KEYWORDS="~amd64 ~x86" +IUSE="dmalloc lowmem threads" DEPEND="dmalloc? ( dev-libs/dmalloc )" RDEPEND="${DEPEND}" |