From 752d6256e5204b958b0ef7905675a940b5e9172f Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Thu, 12 May 2022 16:42:50 +0300 Subject: gentoo resync : 12.05.2022 --- sci-biology/STAR/Manifest | 6 +- sci-biology/STAR/STAR-2.5.3a.ebuild | 42 ------- sci-biology/STAR/STAR-2.7.10a.ebuild | 5 +- .../STAR/files/STAR-2.5.3a-fix-build-system.patch | 123 --------------------- .../STAR/files/STAR-2.7.10a-missing-include.patch | 22 ++++ 5 files changed, 28 insertions(+), 170 deletions(-) delete mode 100644 sci-biology/STAR/STAR-2.5.3a.ebuild delete mode 100644 sci-biology/STAR/files/STAR-2.5.3a-fix-build-system.patch create mode 100644 sci-biology/STAR/files/STAR-2.7.10a-missing-include.patch (limited to 'sci-biology/STAR') diff --git a/sci-biology/STAR/Manifest b/sci-biology/STAR/Manifest index 8f7c05fc8c7f..74eeb0bb4086 100644 --- a/sci-biology/STAR/Manifest +++ b/sci-biology/STAR/Manifest @@ -1,7 +1,5 @@ -AUX STAR-2.5.3a-fix-build-system.patch 5318 BLAKE2B 28a839eb61a5b1adef804249328c7917dca2ec765f00a48b90aa42d7da3ca393f7726b7aafdb6d0429a55fe696bd51b0e06d85ef6e50a3a4f5874c731b194f1e SHA512 412bdf74c50869f470f3d7452d3799e92a45da198e50ecad63688e4c24444a25f044d464e462e19ba41c5abf590865e43542cd1b60a1f3948bf357be468e8441 AUX STAR-2.7.10a-fix-build-system.patch 7176 BLAKE2B 24a14d2d8af26565a3a7f754e9633c54c2cdaf72bf4e3b4fe3390a3790be16620117f576abf82d91e8816478fc1a012e7424ab6d93bb6161b975acd08627d3f0 SHA512 4d854336b2e0c61ca1ac604cded7f08e484974e1ec6d78928e5eb21eb7adb0ae3f6ec9deb3dc050dcffe1732f9076f2b4cddad7aa18ccad20f9232c9e11d1856 -DIST STAR-2.5.3a.tar.gz 9857460 BLAKE2B 32cc633862e6e81f5a5bdfc59986dca74e8adc4970a11a06c501065c5ad9cb37fc788f8e67ab2353292e683c8c385778cd0ffee69c0b15803796dbc445013a43 SHA512 8bd86ad384f2c0331fd701873b02641301f4205a5ff0fceeb800d425da42c53b6c61a74500d37fee7fc13a5bff10e1fb44b9142811883b8f5cd012f51f1f9fdf +AUX STAR-2.7.10a-missing-include.patch 568 BLAKE2B 90d86e5bde440771edc60fb61f7d2f6ed2cd6cfbaff795725dfafe33213fa6eac86ac5cb90ba4df98e72b55fccd68bb6e1b6512cde3843fea05da53e271d8d5e SHA512 5ee3c977af62038014cf4aee31a03c534579a9e6846ad12ab32cd548ac18167816d7f4facedffae20a3e2f61b08c5325fea16969b9b1107a8bd0837d94453b7c DIST STAR-2.7.10a.tar.gz 12270915 BLAKE2B 51a9cf2c838cfeb313df9e5024b53cd5a89088f08ac88c8dc57a9e08cd3ba394e46ffe86a8ff3b9484b25b681ecd960098c06d879e772d21afe8cc2d0d35175d SHA512 19a5f3c25d147bcd96cf68249d275dad7fd11425031a40c97c7ae15846f55839ced897d541ed60b426a6bf089d968ac86625af774db3950dc459035ac2b659c9 -EBUILD STAR-2.5.3a.ebuild 881 BLAKE2B 692466b512aaa3da2e2323f90576d47c2f5e694a4ac8ee8ce2d887435a1ef964dcab9adbdb3c3f88b43cc5463b258635be0f2b542485ee16bc9ec32b655fcf65 SHA512 9b8a80c19b0da8e697c913a8401c08a71a07511477c71b1dd20748e5487e8bb5ab870c37058d49abc27a5ac56722e98b2d784431c19f7173275b82f41f9a2663 -EBUILD STAR-2.7.10a.ebuild 970 BLAKE2B 63bc2b4656d4e672faf819f83bd2a930851e0b5c2d1ff422c5a72b655d5c68515a317675c59df2ff9256e4653351f1f180d9c94dbd256c89810d31ca3940b9ad SHA512 76841ebb6bb3a7c15da15c2124287959938beeb1c6e1a5fa362c476283b51dca49bcca83be9e10d5f39702f23b01ee131f8ab2f568b986e529fc006e65a25ffb +EBUILD STAR-2.7.10a.ebuild 1022 BLAKE2B bfd279163ccdd54b834a5ca50b8ee5b09548a7370dbaa632d01f6cf7b2b9d013aa40419790f1b558dbc27dabd1ad55b3c8eb833321084925125db55647b6e020 SHA512 6a86e78d98ea727598cfcc281713caaacd910c1f48c9d711af47ca44b1f51e5c880a3490910f9547517c7bb783d817e32436f86e35e166661bc41f57492f6314 MISC metadata.xml 341 BLAKE2B 5cf54dcbc5013bbebd80edd8d03456553ec6f7f52527d076f921916ebe9b862c97aae6f641741b81ac44cfc84356ca13e19dd3be2b63c075923a701c22e695c1 SHA512 888d00d5873390206f21aa9daaf78fc8c3f9b88e528c38ca7696779b221fd21acc6beadf543c14e16f74cb600cab479bc3f9bba8625214480583f369e6ea67a8 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() { - [[ ${MERGE_TYPE} != binary ]] && tc-check-openmp -} - -src_configure() { - tc-export CC CXX PKG_CONFIG -} - -src_compile() { - emake -C source STAR -} - -src_install() { - dobin source/STAR - einstalldocs -} diff --git a/sci-biology/STAR/STAR-2.7.10a.ebuild b/sci-biology/STAR/STAR-2.7.10a.ebuild index 7239efcfe45c..c3deb5a94b0a 100644 --- a/sci-biology/STAR/STAR-2.7.10a.ebuild +++ b/sci-biology/STAR/STAR-2.7.10a.ebuild @@ -17,7 +17,10 @@ RDEPEND="sci-libs/htslib:=" DEPEND="${RDEPEND}" BDEPEND="virtual/pkgconfig" -PATCHES=( "${FILESDIR}"/${PN}-2.7.10a-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() { 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-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 +Date: Sat, 7 May 2022 15:06:11 +0200 +Subject: [PATCH] Add missing `#include ` (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 + #include + + typedef struct{ -- cgit v1.2.3