* [gentoo-commits] repo/gentoo:master commit in: sci-biology/STAR/, sci-biology/STAR/files/
@ 2017-11-16 13:17 David Seifert
0 siblings, 0 replies; 3+ messages in thread
From: David Seifert @ 2017-11-16 13:17 UTC (permalink / raw
To: gentoo-commits
commit: acd76729254ed012b6898eb33fcc59ab8c2076e4
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Thu Nov 16 12:32:54 2017 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Thu Nov 16 13:16:45 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=acd76729
sci-biology/STAR: Initial addition
Closes: https://github.com/gentoo/sci/pull/814
Package-Manager: Portage-2.3.14, Repoman-2.3.6
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 +++++++++++++++++++++
sci-biology/STAR/metadata.xml | 19 ++++
4 files changed, 185 insertions(+)
diff --git a/sci-biology/STAR/Manifest b/sci-biology/STAR/Manifest
new file mode 100644
index 00000000000..0ec6da1a3d9
--- /dev/null
+++ b/sci-biology/STAR/Manifest
@@ -0,0 +1 @@
+DIST STAR-2.5.3a.tar.gz 9857460 SHA256 2a258e77cda103aa293e528f8597f25dc760cba188d0a7bc7c9452f4698e7c04 SHA512 8bd86ad384f2c0331fd701873b02641301f4205a5ff0fceeb800d425da42c53b6c61a74500d37fee7fc13a5bff10e1fb44b9142811883b8f5cd012f51f1f9fdf WHIRLPOOL 64bb7dc68e24ecd7d198d281e98042fd1463fc96af8ab8be9cab8e1588c2d08ab7cd1435187f2e0ebe870da11ab607c8f8a981d76360c55dd76e1fb4bb304006
diff --git a/sci-biology/STAR/STAR-2.5.3a.ebuild b/sci-biology/STAR/STAR-2.5.3a.ebuild
new file mode 100644
index 00000000000..73743cbb4e5
--- /dev/null
+++ b/sci-biology/STAR/STAR-2.5.3a.ebuild
@@ -0,0 +1,42 @@
+# 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
new file mode 100644
index 00000000000..8e504fa429e
--- /dev/null
+++ b/sci-biology/STAR/files/STAR-2.5.3a-fix-build-system.patch
@@ -0,0 +1,123 @@
+* 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) $(LIBS_common)
+
+
diff --git a/sci-biology/STAR/metadata.xml b/sci-biology/STAR/metadata.xml
new file mode 100644
index 00000000000..22727da1cad
--- /dev/null
+++ b/sci-biology/STAR/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>proxy-maint@gentoo.org</email>
+ <name>Proxy Maintainers</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-biology@gentoo.org</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">alexdobin/STAR</remote-id>
+ </upstream>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/STAR/, sci-biology/STAR/files/
@ 2022-02-19 19:56 David Seifert
0 siblings, 0 replies; 3+ messages in thread
From: David Seifert @ 2022-02-19 19:56 UTC (permalink / raw
To: gentoo-commits
commit: 49b36caac2597482c792bee0884ae34bea231806
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Feb 19 19:56:01 2022 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Feb 19 19:56:01 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=49b36caa
sci-biology/STAR: unbundle htslib properly
Closes: https://bugs.gentoo.org/833770
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/STAR/STAR-2.7.10a.ebuild | 8 +
.../STAR/files/STAR-2.7.10a-fix-build-system.patch | 195 +++++++++++++++++++++
2 files changed, 203 insertions(+)
diff --git a/sci-biology/STAR/STAR-2.7.10a.ebuild b/sci-biology/STAR/STAR-2.7.10a.ebuild
index 6b1c5b15d482..7239efcfe45c 100644
--- a/sci-biology/STAR/STAR-2.7.10a.ebuild
+++ b/sci-biology/STAR/STAR-2.7.10a.ebuild
@@ -17,6 +17,7 @@ RDEPEND="sci-libs/htslib:="
DEPEND="${RDEPEND}"
BDEPEND="virtual/pkgconfig"
+PATCHES=( "${FILESDIR}"/${PN}-2.7.10a-fix-build-system.patch )
DOCS=( README.md CHANGES.md RELEASEnotes.md doc/STARmanual.pdf )
pkg_pretend() {
@@ -27,6 +28,13 @@ pkg_setup() {
[[ ${MERGE_TYPE} != binary ]] && tc-check-openmp
}
+src_prepare() {
+ default
+
+ # remove bundled htslib
+ rm -r source/htslib || die
+}
+
src_configure() {
tc-export CC CXX PKG_CONFIG
}
diff --git a/sci-biology/STAR/files/STAR-2.7.10a-fix-build-system.patch b/sci-biology/STAR/files/STAR-2.7.10a-fix-build-system.patch
new file mode 100644
index 000000000000..0f06c94fb109
--- /dev/null
+++ b/sci-biology/STAR/files/STAR-2.7.10a-fix-build-system.patch
@@ -0,0 +1,195 @@
+--- a/source/bam_cat.c
++++ b/source/bam_cat.c
+@@ -52,8 +52,8 @@
+ #include <stdlib.h>
+ #include <unistd.h>
+
+-#include "htslib/htslib/bgzf.h"
+-#include "htslib/htslib/sam.h"
++#include <htslib/bgzf.h>
++#include <htslib/sam.h>
+ #include <cstring>
+
+ #define BUF_SIZE 0x10000
+--- a/source/bam_cat.h
++++ b/source/bam_cat.h
+@@ -1,7 +1,7 @@
+ #ifndef CODE_bam_cat
+ #define CODE_bam_cat
+
+-#include "htslib/htslib/sam.h"
++#include <htslib/sam.h>
+
+ int bam_cat(int nfn, char * const *fn, const bam_hdr_t *h, const char* outbam);
+
+--- a/source/BAMfunctions.cpp
++++ b/source/BAMfunctions.cpp
+@@ -1,5 +1,5 @@
+ #include "BAMfunctions.h"
+-#include "htslib/htslib/kstring.h"
++#include <htslib/kstring.h>
+
+
+ string bam_cigarString (bam1_t *b) {//output CIGAR string
+--- a/source/bamRemoveDuplicates.cpp
++++ b/source/bamRemoveDuplicates.cpp
+@@ -1,7 +1,7 @@
+ #include <unordered_map>
+ #include "bamRemoveDuplicates.h"
+ #include <iostream>
+-#include "htslib/htslib/sam.h"
++#include <htslib/sam.h>
+ #include "IncludeDefine.h"
+ #include SAMTOOLS_BGZF_H
+ #include "ErrorWarning.h"
+--- a/source/IncludeDefine.h
++++ b/source/IncludeDefine.h
+@@ -30,8 +30,8 @@
+ #define ERROR_OUT string ( __FILE__ ) +":"+ to_string ( (uint) __LINE__ ) +":"+ string ( __FUNCTION__ )
+
+ //external libs
+-#define SAMTOOLS_BGZF_H "htslib/htslib/bgzf.h"
+-#define SAMTOOLS_SAM_H "htslib/htslib/sam.h"
++#define SAMTOOLS_BGZF_H <htslib/bgzf.h>
++#define SAMTOOLS_SAM_H <htslib/sam.h>
+
+ using namespace std;
+
+--- a/source/Makefile
++++ b/source/Makefile
+@@ -12,11 +12,7 @@
+ CXX ?= g++
+
+ # pre-defined flags
+-LDFLAGS_shared := -pthread -Lhtslib -Bstatic -lhts -Bdynamic -lz
+-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)
++LIBS := -pthread -lhts -lz
+
+ DATE_FMT = --iso-8601=seconds
+ ifdef SOURCE_DATE_EPOCH
+@@ -27,7 +23,7 @@
+
+ BUILD_PLACE ?= $(HOSTNAME):$(shell pwd)
+
+-COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE="$(BUILD_DATE) $(BUILD_PLACE)"'
++COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE=""'
+
+
+ GIT_CHECK := $(shell git status 1> /dev/null 2> /dev/null && echo 0)
+@@ -41,13 +37,13 @@
+
+ # Defaults, can be overridden by make arguments or environment
+ CXXFLAGS ?= -pipe -Wall -Wextra
+-CFLAGS ?= -pipe -Wall -Wextra -O3
++CFLAGS ?= -pipe -Wall -Wextra
+ CXXFLAGS_SIMD ?= -mavx2
+
+ # Unconditionally set essential flags and optimization options
+ CXXFLAGS_common := -std=c++11 -fopenmp $(COMPTIMEPLACE) $(GIT_BRANCH_COMMIT_DIFF)
+-CXXFLAGS_main := -O3 $(CXXFLAGS_common)
+-CXXFLAGS_gdb := -O0 -g3 $(CXXFLAGS_common)
++CXXFLAGS_main := $(CXXFLAGS_common)
++CXXFLAGS_gdb := $(CXXFLAGS_common)
+
+ ##########################################################################################################
+ OBJECTS = SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall_multiMappers.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o \
+@@ -130,7 +126,7 @@
+ ifneq ($(MAKECMDGOALS),clean_solo)
+ ifneq ($(MAKECMDGOALS),STARforMac)
+ ifneq ($(MAKECMDGOALS),STARforMacGDB)
+-Depend.list: $(SOURCES) parametersDefault.xxd htslib
++Depend.list: $(SOURCES) parametersDefault.xxd
+ echo $(SOURCES)
+ 'rm' -f ./Depend.list
+ $(CXX) $(CXXFLAGS_common) -MM $^ >> Depend.list
+@@ -142,57 +138,43 @@
+ endif
+ endif
+
+-htslib : htslib/libhts.a
+-
+-htslib/libhts.a :
+- $(MAKE) -C htslib lib-static
+-
+ parametersDefault.xxd: parametersDefault
+ xxd -i parametersDefault > parametersDefault.xxd
+
+ STAR$(SFX) : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) $(CXXFLAGS)
+-STAR$(SFX) : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS)
+ STAR$(SFX) : Depend.list parametersDefault.xxd $(OBJECTS)
+- $(CXX) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
++ $(CXX) $(LDFLAGS) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LIBS)
+
+ STARstatic$(SFX) : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) $(CXXFLAGS)
+-STARstatic$(SFX) : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_static) $(LDFLAGS)
+ STARstatic$(SFX) : Depend.list parametersDefault.xxd $(OBJECTS)
+- $(CXX) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
++ $(CXX) $(LDFLAGS) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LIBS)
+
+ STARlong$(SFX) : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_LONG_READS' $(CXXFLAGS)
+-STARlong$(SFX) : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS)
+ STARlong$(SFX) : Depend.list parametersDefault.xxd $(OBJECTS)
+- $(CXX) -o STARlong$(SFX) $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
++ $(CXX) $(LDFLAGS) -o STARlong$(SFX) $(CXXFLAGS) $(OBJECTS) $(LIBS)
+
+ STARlongStatic$(SFX) : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_LONG_READS' $(CXXFLAGS)
+-STARlongStatic$(SFX) : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_static) $(LDFLAGS)
+ STARlongStatic$(SFX) : Depend.list parametersDefault.xxd $(OBJECTS)
+- $(CXX) -o STARlong$(SFX) $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
++ $(CXX) $(LDFLAGS) -o STARlong$(SFX) $(CXXFLAGS) $(OBJECTS) $(LIBS)
+
+
+
+ POSIXSHARED : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -DPOSIX_SHARED_MEM $(CXXFLAGS)
+-POSIXSHARED : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS)
+ POSIXSHARED : Depend.list parametersDefault.xxd $(OBJECTS)
+- $(CXX) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
++ $(CXX) $(LDFLAGS) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LIBS)
+
+ 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) $(LDFLAGS) -o STAR $(CXXFLAGS) $(OBJECTS) $(LIBS)
+
+ 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) $(LDFLAGS) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LIBS)
+
+ 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) $(LDFLAGS) -o STAR $(CXXFLAGS) $(OBJECTS) $(LIBS)
+
+ 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) $(LDFLAGS) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LIBS)
+--- a/source/signalFromBAM.h
++++ b/source/signalFromBAM.h
+@@ -1,6 +1,6 @@
+ #ifndef CODE_signalFromBAM
+ #define CODE_signalFromBAM
+-#include "htslib/htslib/sam.h"
++#include <htslib/sam.h>
+ #include <fstream>
+ #include <string>
+ #include "Stats.h"
+--- a/source/STAR.cpp
++++ b/source/STAR.cpp
+@@ -29,7 +29,7 @@
+
+ #include "twoPassRunPass1.h"
+
+-#include "htslib/htslib/sam.h"
++#include <htslib/sam.h>
+ #include "parametersDefault.xxd"
+
+ void usage(int usageType) {
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/STAR/, sci-biology/STAR/files/
@ 2022-05-07 13:13 David Seifert
0 siblings, 0 replies; 3+ messages in thread
From: David Seifert @ 2022-05-07 13:13 UTC (permalink / raw
To: gentoo-commits
commit: 1f20252245bf55c15c8664783024d06c1eaf6c6a
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat May 7 13:13:13 2022 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat May 7 13:13:13 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1f202522
sci-biology/STAR: fix GCC 12 build
Closes: https://bugs.gentoo.org/840586
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/STAR/STAR-2.7.10a.ebuild | 5 ++++-
.../STAR/files/STAR-2.7.10a-missing-include.patch | 22 ++++++++++++++++++++++
2 files changed, 26 insertions(+), 1 deletion(-)
diff --git a/sci-biology/STAR/STAR-2.7.10a.ebuild b/sci-biology/STAR/STAR-2.7.10a.ebuild
index 7239efcfe45c..c3deb5a94b0a 100644
--- a/sci-biology/STAR/STAR-2.7.10a.ebuild
+++ b/sci-biology/STAR/STAR-2.7.10a.ebuild
@@ -17,7 +17,10 @@ RDEPEND="sci-libs/htslib:="
DEPEND="${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-2.7.10a-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 <soap@gentoo.org>
+Date: Sat, 7 May 2022 15:06:11 +0200
+Subject: [PATCH] Add missing `#include <array>` (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 <array>
+ #include <unordered_map>
+
+ typedef struct{
^ permalink raw reply related [flat|nested] 3+ messages in thread
end of thread, other threads:[~2022-05-07 13:13 UTC | newest]
Thread overview: 3+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2017-11-16 13:17 [gentoo-commits] repo/gentoo:master commit in: sci-biology/STAR/, sci-biology/STAR/files/ David Seifert
-- strict thread matches above, loose matches on Subject: below --
2022-02-19 19:56 David Seifert
2022-05-07 13:13 David Seifert
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox