commit: 25c5b41b494d8cd66bf5c552b35b78acc484f07e Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Wed Jun 27 12:36:48 2018 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Wed Jun 27 12:36:48 2018 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=25c5b41b
sci-biology/stringtie: version bump, accepted new upstream patch, works CXX/CXXFLAGS are still not respected for bundled samtools subdirectory. https://github.com/gpertea/stringtie/issues/185#issuecomment-400637035 Package-Manager: Portage-2.3.40, Repoman-2.3.9 sci-biology/stringtie/files/Makefile.patch | 140 ++++++++++----------- ...ingtie-1.2.2.ebuild => stringtie-1.3.4d.ebuild} | 3 +- 2 files changed, 69 insertions(+), 74 deletions(-) diff --git a/sci-biology/stringtie/files/Makefile.patch b/sci-biology/stringtie/files/Makefile.patch index a7ca43c39..b7efa605c 100644 --- a/sci-biology/stringtie/files/Makefile.patch +++ b/sci-biology/stringtie/files/Makefile.patch @@ -1,26 +1,41 @@ ---- stringtie-1.2.2/Makefile 2018-06-26 00:36:17.119583211 +0200 -+++ stringtie-1.2.2/Makefile 2018-06-26 00:46:43.406712302 +0200 -@@ -1,13 +1,15 @@ +--- stringtie-1.3.4d/Makefile 2018-06-26 00:36:17.119583211 +0200 ++++ stringtie-1.3.4d/Makefile 2018-06-26 00:46:43.406712302 +0200 +@@ -1,28 +1,32 @@ -BAM := ./samtools-0.1.18 -+BAM_INC = -I./samtools-0.1.18 -+BAM_LIB = -L./samtools-0.1.18 -+BAM_LIBS = -lbam - #path to the directory where the samtools package was built (in place) - #so libbam.a and *.h files MUST be in here +-#path to the directory where the samtools package was built (in place) +-#so libbam.a and *.h files MUST be in here ++#-- for now these MUST point to the included samtools-0.x.x and gclib subdirectories ++BAM := ./samtools-0.1.18 ++GDIR := ./gclib ++#-- - GDIR :=./gclib +-GDIR :=./gclib ++INCDIRS := -I. -I${GDIR} -I${BAM} --INCDIRS := -I. -I${GDIR} -I${BAM} -+INCDIRS := -I. -I${GDIR} ${BAM_INC} +-INCDIRS := -I. -I${GDIR} -I${BAM} +- +-CC := g++ ++#CXX ?= g++ ++CXX := $(if $(CXX),$(CXX),g++) --#CC := clang++ --CC := g++ -+#CXX := clang++ -+CXX ?= g++ + BASEFLAGS := -Wall -Wextra ${INCDIRS} -fsigned-char -D_FILE_OFFSET_BITS=64 \ + -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti ++#for gcc 8+ add: -Wno-class-memaccess ++ ++ ++LINKER := $(if $(LINKER),$(LINKER),g++) +-LINKER := g++ ++LDFLAGS := $(if $(LDFLAGS),$(LDFLAGS),-g) + +-LDFLAGS := -g -L${BAM} $(LDFLAGS) ++LDFLAGS += -L${BAM} + +-LIBS := -lbam -lz ++LIBS := -lbam -lz ifneq (,$(findstring nothreads,$(MAKECMDGOALS))) -@@ -15,7 +17,7 @@ + NOTHREADS=1 endif #detect MinGW (Windows environment) @@ -29,36 +44,22 @@ WINDOWS=1 endif -@@ -48,9 +50,9 @@ - # C/C++ linker - - #LINKER := clang++ --LINKER := g++ -+LINKER ?= g++ - --LIBS := -lbam -lz -+LIBS := ${BAM_LIBS} -lz - - # Non-windows systems need pthread - ifndef WINDOWS -@@ -68,8 +70,10 @@ - #ifneq (,$(findstring release,$(MAKECMDGOALS))) +@@ -63,7 +67,8 @@ endif ifneq (,$(filter %release %static, $(MAKECMDGOALS))) # -- release build -- CFLAGS := -O3 -DNDEBUG -g $(BASEFLAGS) -- LDFLAGS := -g -L${BAM} ${LFLAGS} -+ CXXFLAGS ?= -O3 -g + RELEASE_BUILD=1 +- CFLAGS := -DNDEBUG -g $(BASEFLAGS) $(CFLAGS) -O3 ++ CXXFLAGS := $(if $(CXXFLAGS),$(CXXFLAGS),-g -O3) + CXXFLAGS += -DNDEBUG $(BASEFLAGS) -+ LDFLAGS ?= -g -+ LDFLAGS += ${BAM_LIB} ${LFLAGS} - ifneq (,$(findstring static,$(MAKECMDGOALS))) - LDFLAGS += -static-libstdc++ -static-libgcc - endif -@@ -80,15 +84,16 @@ + else + ifneq (,$(filter %memcheck %memdebug, $(MAKECMDGOALS))) + #use sanitizer in gcc 4.9+ +@@ -72,21 +77,21 @@ else ifeq "$(GCCVER49)" "0" $(error gcc version 4.9 or greater is required for this build target) endif - CFLAGS := -fno-omit-frame-pointer -fsanitize=undefined -fsanitize=address $(BASEFLAGS) ++ CXXFLAGS := $(if $(CXXFLAGS),$(CXXFLAGS),-g -O0) + CXXFLAGS += -fno-omit-frame-pointer -fsanitize=undefined -fsanitize=address $(BASEFLAGS) GCCVER5 := $(shell expr `g++ -dumpversion | cut -f1 -d.` \>= 5) ifeq "$(GCCVER5)" "1" @@ -70,47 +71,42 @@ + #CXXFLAGS += -fcheck-pointer-bounds -mmpx endif - CFLAGS := -g -DDEBUG -D_DEBUG -DGDEBUG -fno-common -fstack-protector $(CFLAGS) -- LDFLAGS := -g -L${BAM} -+ CXXFLAGS ?= -g + CXXFLAGS += -DDEBUG -D_DEBUG -DGDEBUG -fno-common -fstack-protector -+ LDFLAGS += -g ${BAM_LIB} - #LIBS := -Wl,-Bstatic -lasan -lubsan -Wl,-Bdynamic -ldl $(LIBS) LIBS := -lasan -lubsan -ldl $(LIBS) else -@@ -97,13 +102,14 @@ - GMEMTRACE=1 - endif - #just plain debug build -- CFLAGS := -g -DDEBUG -D_DEBUG -DGDEBUG $(BASEFLAGS) -- LDFLAGS := -g -L${BAM} -+ CXXFLAGS ?= -g -+ CXXFLAGS += -DDEBUG -D_DEBUG -DGDEBUG $(BASEFLAGS) -+ LDFLAGS += ${BAM_LIB} +- ifeq (,$(findstring clean,$(MAKECMDGOALS))) + #just plain debug build + DEBUG_BUILD=1 +- CFLAGS := -g -DDEBUG -D_DEBUG -DGDEBUG $(BASEFLAGS) +- endif ++ CXXFLAGS := $(if $(CXXFLAGS),$(CXXFLAGS),-g -O0) ++ CXXFLAGS += -DDEBUG -D_DEBUG -DGDEBUG $(BASEFLAGS) endif endif +@@ -106,23 +111,20 @@ ifdef DEBUG_BUILD + DBG_WARN+='WARNING: built DEBUG version [much slower], use "make clean release" for a faster, optimized version of the program.' + endif + +- + OBJS := ${GDIR}/GBase.o ${GDIR}/GArgs.o ${GDIR}/GStr.o ${GDIR}/GBam.o \ + ${GDIR}/gdna.o ${GDIR}/codons.o ${GDIR}/GFaSeqGet.o ${GDIR}/gff.o + +- + ifneq (,$(filter %memtrace %memusage %memuse, $(MAKECMDGOALS))) +- CFLAGS += -DGMEMTRACE ++ CXXFLAGS += -DGMEMTRACE + OBJS += ${GDIR}/proc_mem.o + endif + + ifndef NOTHREADS + OBJS += ${GDIR}/GThreads.o + endif + +- %.o : %.cpp - ${CC} ${CFLAGS} -c $< -o $@ + ${CXX} ${CXXFLAGS} -c $< -o $@ - OBJS := ${GDIR}/GBase.o ${GDIR}/GArgs.o ${GDIR}/GStr.o ${GDIR}/GBam.o \ - ${GDIR}/gdna.o ${GDIR}/codons.o ${GDIR}/GFaSeqGet.o ${GDIR}/gff.o -@@ -130,9 +136,7 @@ - rlink.o : rlink.h tablemaker.h $(GDIR)/GBam.h $(GDIR)/GBitVec.h - tmerge.o : rlink.h tmerge.h - tablemaker.o : tablemaker.h rlink.h --${BAM}/libbam.a: -- cd ${BAM} && make lib --stringtie: ${BAM}/libbam.a $(OBJS) stringtie.o -+stringtie: $(OBJS) stringtie.o - ${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} - - .PHONY : clean cleanall cleanAll allclean -@@ -143,7 +147,6 @@ - @${RM} stringtie stringtie.o* stringtie.exe $(OBJS) - @${RM} core.* - allclean cleanAll cleanall: -- cd ${BAM} && make clean - @${RM} stringtie stringtie.o* stringtie.exe $(OBJS) - @${RM} core.* + OBJS += rlink.o tablemaker.o tmerge.o diff --git a/sci-biology/stringtie/stringtie-1.2.2.ebuild b/sci-biology/stringtie/stringtie-1.3.4d.ebuild similarity index 84% rename from sci-biology/stringtie/stringtie-1.2.2.ebuild rename to sci-biology/stringtie/stringtie-1.3.4d.ebuild index cb26b6961..953999e87 100644 --- a/sci-biology/stringtie/stringtie-1.2.2.ebuild +++ b/sci-biology/stringtie/stringtie-1.3.4d.ebuild @@ -10,8 +10,7 @@ SRC_URI="http://ccb.jhu.edu/software/stringtie/dl/${P}.tar.gz"; LICENSE="Artistic-2 MIT" # MIT from bundled samtools-0.1.18 SLOT="0" -KEYWORDS="" # gclib/GThreads.h:804:19: error: conflicting declaration -# 'typedef long long int __intmax_t' +KEYWORDS="~amd64 ~x86" IUSE="" # contains bundled and modified samtools-0.1.18
