commit: f8ed4029d610b62eb95b85692efd9396ab8fd933 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Fri May 5 09:19:58 2023 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Fri May 5 09:19:58 2023 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f8ed4029
sci-biology/samtools: drop 0.1.20-r4 Closes: https://bugs.gentoo.org/862288 Signed-off-by: David Seifert <soap <AT> gentoo.org> profiles/package.mask | 6 - sci-biology/samtools/Manifest | 1 - .../files/samtools-0.1.20-buildsystem.patch | 206 --------------------- sci-biology/samtools/samtools-0.1.20-r4.ebuild | 73 -------- 4 files changed, 286 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index f381e12c4b19..5b737647d95d 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -283,12 +283,6 @@ dev-ruby/allison # Removal on 2023-05-07. Bug #878655. app-misc/wildq -# David Seifert <s...@gentoo.org> (2023-04-06) -# Last release over 7 years ago, abandoned upstream, still depends on -# dead 0.1-legacy samtools slot. No revdeps in tree. -# Removal on 2023-05-06. Bug #862288. -sci-biology/samtools:0.1-legacy - # Ionen Wolkens <io...@gentoo.org> (2023-03-30) # NVIDIA dropped support for the 390.xx branch in December 2022[1]. # diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest index 5787a3bb63e6..72408c9c9544 100644 --- a/sci-biology/samtools/Manifest +++ b/sci-biology/samtools/Manifest @@ -1,2 +1 @@ -DIST samtools-0.1.20.tar.gz 566387 BLAKE2B a62d74c408877754af50f5e5fea0e2289ec1e0c9f25013ed0d039bfe8ef61108600d917f8c9d356e98aca632795b4eb0f01ea1b54526a652577fb74a38a433c2 SHA512 15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5 DIST samtools-1.17.tar.bz2 8605080 BLAKE2B 09cb0bff7bf7113a77f57fdb879765b28b65461a574e4a1ab20ae2327af46e5616e04f03eb68706d42ba0643e887d7921974a3d78c5f87d296a4c3b691215260 SHA512 107a6df858c6bd2556ba4e86cc1922c3184df095f347039fa94bfd24e5ee21e1a4a9fba5a7cce248a06ad47f99978d9aae570efee7e30e165f33ea848a2cd3c3 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 $@ md5fa.c ---- samtools-0.1.20/misc/varfilter.py -+++ samtools-0.1.20/misc/varfilter.py -@@ -1,4 +1,4 @@ --#!/software/bin/python -+#!/usr/bin/env python - - # Author: lh3, converted to python and modified to add -C option by Aylwyn Scally - # diff --git a/sci-biology/samtools/samtools-0.1.20-r4.ebuild b/sci-biology/samtools/samtools-0.1.20-r4.ebuild deleted file mode 100644 index f4b779aa838b..000000000000 --- a/sci-biology/samtools/samtools-0.1.20-r4.ebuild +++ /dev/null @@ -1,73 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit multilib toolchain-funcs - -DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats" -HOMEPAGE="http://samtools.sourceforge.net/"; -SRC_URI="https://github.com/samtools/samtools/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0.1-legacy" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" - -RDEPEND=" - sys-libs/ncurses:0= - dev-lang/perl" -DEPEND="${RDEPEND}" -BDEPEND="virtual/pkgconfig" - -PATCHES=( "${FILESDIR}"/${P}-buildsystem.patch ) - -src_prepare() { - default - 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}-${SLOT},bin/} || die - - # remove py2 script, has been removed upstream anyways - # https://github.com/samtools/samtools/issues/1125 - rm "${ED}"/usr/bin/${PN}-${SLOT}/varfilter.py || die - - # 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 - - dodoc -r examples - docompress -x /usr/share/doc/${PF}/examples -} - -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-1.10." -}
