commit: bcd5ba73fe296ee35a11a3ee96a62a35afa4ac0a Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sat May 7 11:01:01 2022 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sat May 7 11:01:01 2022 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=bcd5ba73
sci-biology/STAR: drop 2.5.3a Closes: https://bugs.gentoo.org/716300 Closes: https://bugs.gentoo.org/736056 Closes: https://bugs.gentoo.org/741152 Signed-off-by: David Seifert <soap <AT> gentoo.org> sci-biology/STAR/Manifest | 1 - sci-biology/STAR/STAR-2.5.3a.ebuild | 42 ------- .../STAR/files/STAR-2.5.3a-fix-build-system.patch | 123 --------------------- 3 files changed, 166 deletions(-) diff --git a/sci-biology/STAR/Manifest b/sci-biology/STAR/Manifest index d8457898903d..d97c61cb21c0 100644 --- a/sci-biology/STAR/Manifest +++ b/sci-biology/STAR/Manifest @@ -1,2 +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-2.5.3a.ebuild deleted file mode 100644 index 73743cbb4e59..000000000000 --- a/sci-biology/STAR/STAR-2.5.3a.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit toolchain-funcs - -DESCRIPTION="STAR aligner: align RNA-seq reads to reference genome uncompressed suffix arrays" -HOMEPAGE="https://github.com/alexdobin/STAR"; -SRC_URI="https://github.com/alexdobin/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64" - -RDEPEND="sci-libs/htslib:=" -DEPEND="${RDEPEND} - virtual/pkgconfig" - -PATCHES=( "${FILESDIR}"/${PN}-2.5.3a-fix-build-system.patch ) -DOCS=( README.md CHANGES.md RELEASEnotes.md doc/STARmanual.pdf ) - -pkg_pretend() { - [[ ${MERGE_TYPE} != binary ]] && tc-check-openmp -} - -pkg_setup() { - [[ ${MERGE_TYPE} != binary ]] && tc-check-openmp -} - -src_configure() { - tc-export CC CXX PKG_CONFIG -} - -src_compile() { - emake -C source STAR -} - -src_install() { - dobin source/STAR - einstalldocs -} 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) - -
