From d703c5a43cf46b3e7228f8beaeb66b7bba525638 Mon Sep 17 00:00:00 2001 From: Andrew Ammerlaan Date: Wed, 26 Jan 2022 11:02:49 +0100 Subject: sci-biology/bambus: fix PMS violation Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan --- sci-biology/bambus/bambus-2.33-r1.ebuild | 99 ------------------------------ sci-biology/bambus/bambus-2.33-r2.ebuild | 100 +++++++++++++++++++++++++++++++ 2 files changed, 100 insertions(+), 99 deletions(-) delete mode 100644 sci-biology/bambus/bambus-2.33-r1.ebuild create mode 100644 sci-biology/bambus/bambus-2.33-r2.ebuild (limited to 'sci-biology') diff --git a/sci-biology/bambus/bambus-2.33-r1.ebuild b/sci-biology/bambus/bambus-2.33-r1.ebuild deleted file mode 100644 index 1e2078c94..000000000 --- a/sci-biology/bambus/bambus-2.33-r1.ebuild +++ /dev/null @@ -1,99 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit perl-module toolchain-funcs - -DESCRIPTION="Scaffolding Polymorphic Genomes and Metagenomes, a part of AMOS bundle" -HOMEPAGE=" - https://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS - https://sourceforge.net/projects/amos/files/bambus" -SRC_URI=" - https://sourceforge.net/projects/amos/files/bambus/${PV}/${P}.tar.gz - http://mira-assembler.sourceforge.net/docs/scaffolding_MIRA_BAMBUS.pdf" # no https - -LICENSE="Artistic" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - sci-biology/tigr-foundation-libs - dev-perl/XML-Parser - dev-perl/Config-IniFiles - dev-perl/GraphViz" -DEPEND="${RDEPEND}" - -PATCHES=( - "${FILESDIR}"/TigrFoundation-all-patches.patch -) - -src_prepare() { - default -# eapply "${FILESDIR}"/amos-2.0.8-gcc44.patch - sed -e 's:BASEDIR = /usr/local/packages/bambus:BASEDIR = /usr:' -i Makefile || die - sed -e 's:PERL = /usr/local/bin/perl:PERL = /usr/bin/perl:' -i Makefile || die - sed \ - -e 's:INSTDIR:DESTDIR:g' \ - -i Makefile src/Makefile doc/Makefile || die - sed -e 's:make all;:make all || exit 255;:' -i src/Makefile || die - sed \ - -e 's:INSTDIR:DESTDIR:g' \ - -i src/IO/Makefile src/DotLib/Makefile src/grommit/Makefile || die - sed -e "s:^CC\t=:CC=$(tc-getCXX):" -i Makefile || die - sed -e "s:^CXX\t=:CXX=$(tc-getCXX):" -i Makefile || die - sed -e "s:^LD\t:LD=$(tc-getCXX):" -i Makefile || die - sed -e 's:^AR\t=:#AR=:' -i Makefile || die - sed -e 's:^export:#export:' -i Makefile || die - sed -e 's:-Wl::' -i src/grommit/Makefile || die - # sed -e 's:-L../TIGR_Foundation_CC/:-L../TIGR_Foundation_CC/:' -i src/grommit/Makefile || die - sed -e 's:make all:make all DESTDIR=$(DESTDIR):' -i Makefile || die - sed -e 's:make install:make install DESTDIR=$(DESTDIR):' -i Makefile || die - sed -e "s:# Main targets:LD=$(tc-getCXX):" -i src/grommit/Makefile || die - sed -e 's:^LDFLAGS =$(STATIC_$(OSTYPE)):LDFLAGS += $(STATIC_$(OSTYPE)):' -i src/grommit/Makefile || die - sed -e 's:CFLAGS = $(HEADERS) -g:CFLAGS += $(HEADERS) -fPIC:' -i src/grommit/Makefile || die - sed -e 's:^$ENV{PERLLIB}:$ENV{PERL5LIB}:' -i src/goBambus.pl || die - sed -e 's:^#!.*:#!/usr/bin/perl:' -i src/goBambus.pl || die - sed -e 's:^#!.*:#!/usr/bin/perl:' -i src/IO/*.pl || die - einfo "Argh, cannot delete src/TIGR_Foundation_CC/ because it has some extra files getopt.* not present" - einfo "in sci-biology/tigr-foundation-libs. It seems bambus-2.33/src/TIGR_Foundation_CC/ contains" - einfo "the following 3 files getopt.cc getopt.hh getopt1.cc which were possibly copied" - einfo "over from some old GNU libc and maybe could be completely dropped?" - einfo "Affected would be:" - einfo "bambus-2.33/src/grommit/newgrp.cc:#include " - einfo "bambus-2.33/src/TIGR_Foundation_CC/Options.hh:#include " - einfo "bambus-2.33/src/TIGR_Foundation_CC/Options.hh:#include \"getopt.hh\"" - einfo "bambus-2.33/src/TIGR_Foundation_CC/OptionResult.cc:/*! Uses same syntax as getopt" - #rm -rf src/TIGR_Foundation_CC || die "Failed to rm -rf src/TIGR_Foundation_CC/, we use it from sci-biology/tigr-foundation-libs" - #sed -i 's:TIGR_Foundation_CC::' src/Makefile || die "Failed to zap last pointer to local copy of tigr-foundation-libs" - cd src/TIGR_Foundation_CC || die "Failed to cd src/TIGR_Foundation_CC/" - sed -e "s:/export/usr/local:${ED}/usr:g" -i Makefile || die -} - -src_install() { - emake DESTDIR="${ED}/usr" install - # cvs HEAD of amos now contains even more updated files: /usr/bin/printScaff /usr/bin/untangle /usr/lib/TIGR/AsmLib.pm - for f in FASTArecord.pm FASTAreader.pm Foundation.pm FASTAgrammar.pm AsmLib.pm; do rm "${ED}"/usr/lib/TIGR/$f; done || die - for f in printScaff untangle; do rm "${ED}"/usr/bin/$f; done || die - - # we compiled using locally provided TIGR_Foundation_CC/{cc,.hh} files but - # link against the libTigrFoundation.a provided by sci-biology/tigr-foundation-libs package - for f in CategoryInformation.hh MessageLevel.hh ConfigFile.hh LogCategory.hh \ - ConfigSection.hh TIGR_Foundation.hh OptionResult.hh Exceptions.hh \ - LogMsg.hh Options.hh Logger.hh FileSystem.hh; do - rm "${ED}"/usr/include/$f || die - done - rm "${ED}"/usr/lib/libTigrFoundation.a || die - - dodir /usr/share/doc/${PF} - mv "${ED}"/usr/doc/* "${ED}"/usr/share/doc/${PF} || die - rmdir "${ED}"/usr/doc || die - - dobin "${FILESDIR}"/goBambus.pl - dodoc "${DISTDIR}"/scaffolding_MIRA_BAMBUS.pdf - rm -r "${ED}"/usr/lib || die -} - -pkg_postinst(){ - einfo "For manual see http://mira-assembler.sourceforge.net/docs/scaffolding_MIRA_BAMBUS.pdf" -} diff --git a/sci-biology/bambus/bambus-2.33-r2.ebuild b/sci-biology/bambus/bambus-2.33-r2.ebuild new file mode 100644 index 000000000..475c7f0b1 --- /dev/null +++ b/sci-biology/bambus/bambus-2.33-r2.ebuild @@ -0,0 +1,100 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit perl-module toolchain-funcs + +DESCRIPTION="Scaffolding Polymorphic Genomes and Metagenomes, a part of AMOS bundle" +HOMEPAGE=" + https://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS + https://sourceforge.net/projects/amos/files/bambus" +SRC_URI=" + https://sourceforge.net/projects/amos/files/bambus/${PV}/${P}.tar.gz + http://mira-assembler.sourceforge.net/docs/scaffolding_MIRA_BAMBUS.pdf" # no https + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + sci-biology/tigr-foundation-libs + dev-perl/XML-Parser + dev-perl/Config-IniFiles + dev-perl/GraphViz" +DEPEND="${RDEPEND}" + +PATCHES=( + "${FILESDIR}"/TigrFoundation-all-patches.patch +) + +src_prepare() { + default +# eapply "${FILESDIR}"/amos-2.0.8-gcc44.patch + sed -e 's:BASEDIR = /usr/local/packages/bambus:BASEDIR = /usr:' -i Makefile || die + sed -e 's:PERL = /usr/local/bin/perl:PERL = /usr/bin/perl:' -i Makefile || die + sed \ + -e 's:INSTDIR:DESTDIR:g' \ + -i Makefile src/Makefile doc/Makefile || die + sed -e 's:make all;:make all || exit 255;:' -i src/Makefile || die + sed \ + -e 's:INSTDIR:DESTDIR:g' \ + -i src/IO/Makefile src/DotLib/Makefile src/grommit/Makefile || die + sed -e "s:^CC\t=:CC=$(tc-getCXX):" -i Makefile || die + sed -e "s:^CXX\t=:CXX=$(tc-getCXX):" -i Makefile || die + sed -e "s:^LD\t:LD=$(tc-getCXX):" -i Makefile || die + sed -e 's:^AR\t=:#AR=:' -i Makefile || die + sed -e 's:^export:#export:' -i Makefile || die + sed -e 's:-Wl::' -i src/grommit/Makefile || die + # sed -e 's:-L../TIGR_Foundation_CC/:-L../TIGR_Foundation_CC/:' -i src/grommit/Makefile || die + sed -e 's:make all:make all DESTDIR=$(DESTDIR):' -i Makefile || die + sed -e 's:make install:make install DESTDIR=$(DESTDIR):' -i Makefile || die + sed -e "s:# Main targets:LD=$(tc-getCXX):" -i src/grommit/Makefile || die + sed -e 's:^LDFLAGS =$(STATIC_$(OSTYPE)):LDFLAGS += $(STATIC_$(OSTYPE)):' -i src/grommit/Makefile || die + sed -e 's:CFLAGS = $(HEADERS) -g:CFLAGS += $(HEADERS) -fPIC:' -i src/grommit/Makefile || die + sed -e 's:^$ENV{PERLLIB}:$ENV{PERL5LIB}:' -i src/goBambus.pl || die + sed -e 's:^#!.*:#!/usr/bin/perl:' -i src/goBambus.pl || die + sed -e 's:^#!.*:#!/usr/bin/perl:' -i src/IO/*.pl || die + einfo "Argh, cannot delete src/TIGR_Foundation_CC/ because it has some extra files getopt.* not present" + einfo "in sci-biology/tigr-foundation-libs. It seems bambus-2.33/src/TIGR_Foundation_CC/ contains" + einfo "the following 3 files getopt.cc getopt.hh getopt1.cc which were possibly copied" + einfo "over from some old GNU libc and maybe could be completely dropped?" + einfo "Affected would be:" + einfo "bambus-2.33/src/grommit/newgrp.cc:#include " + einfo "bambus-2.33/src/TIGR_Foundation_CC/Options.hh:#include " + einfo "bambus-2.33/src/TIGR_Foundation_CC/Options.hh:#include \"getopt.hh\"" + einfo "bambus-2.33/src/TIGR_Foundation_CC/OptionResult.cc:/*! Uses same syntax as getopt" + #rm -rf src/TIGR_Foundation_CC || die "Failed to rm -rf src/TIGR_Foundation_CC/, we use it from sci-biology/tigr-foundation-libs" + #sed -i 's:TIGR_Foundation_CC::' src/Makefile || die "Failed to zap last pointer to local copy of tigr-foundation-libs" +} + +src_install() { + pushd src/TIGR_Foundation_CC || die + sed -e "s:/export/usr/local:${ED}/usr:g" -i Makefile || die + popd || die + emake DESTDIR="${ED}/usr" install + # cvs HEAD of amos now contains even more updated files: /usr/bin/printScaff /usr/bin/untangle /usr/lib/TIGR/AsmLib.pm + for f in FASTArecord.pm FASTAreader.pm Foundation.pm FASTAgrammar.pm AsmLib.pm; do rm "${ED}"/usr/lib/TIGR/$f; done || die + for f in printScaff untangle; do rm "${ED}"/usr/bin/$f; done || die + + # we compiled using locally provided TIGR_Foundation_CC/{cc,.hh} files but + # link against the libTigrFoundation.a provided by sci-biology/tigr-foundation-libs package + for f in CategoryInformation.hh MessageLevel.hh ConfigFile.hh LogCategory.hh \ + ConfigSection.hh TIGR_Foundation.hh OptionResult.hh Exceptions.hh \ + LogMsg.hh Options.hh Logger.hh FileSystem.hh; do + rm "${ED}"/usr/include/$f || die + done + rm "${ED}"/usr/lib/libTigrFoundation.a || die + + dodir /usr/share/doc/${PF} + mv "${ED}"/usr/doc/* "${ED}"/usr/share/doc/${PF} || die + rmdir "${ED}"/usr/doc || die + + dobin "${FILESDIR}"/goBambus.pl + dodoc "${DISTDIR}"/scaffolding_MIRA_BAMBUS.pdf + rm -r "${ED}"/usr/lib || die +} + +pkg_postinst(){ + einfo "For manual see http://mira-assembler.sourceforge.net/docs/scaffolding_MIRA_BAMBUS.pdf" +} -- cgit v1.2.3-65-gdbad