* [gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/files/, profiles/, sci-biology/samtools/
@ 2023-05-05 9:20 David Seifert
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From: David Seifert @ 2023-05-05 9:20 UTC (permalink / raw
To: gentoo-commits
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 <soap@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 <ionen@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."
-}
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