commit: 3208b43922f41181f1109b3bf33d922eb16cc9fd
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Jun 25 22:51:11 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Jun 25 22:51:11 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=3208b439
sci-biology/stringtie: patch cleanup
Package-Manager: Portage-2.3.40, Repoman-2.3.9
sci-biology/stringtie/files/Makefile.patch | 62 ++++++++++++++----------------
1 file changed, 28 insertions(+), 34 deletions(-)
diff --git a/sci-biology/stringtie/files/Makefile.patch
b/sci-biology/stringtie/files/Makefile.patch
index 8f5379b6b..7db068985 100644
--- a/sci-biology/stringtie/files/Makefile.patch
+++ b/sci-biology/stringtie/files/Makefile.patch
@@ -1,8 +1,8 @@
---- stringtie-1.2.2/Makefile 2018-06-25 23:28:55.558150677 +0200
-+++ stringtie-1.2.2/Makefile 2018-06-25 23:29:55.819798846 +0200
+--- 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 @@
-BAM := ./samtools-0.1.18
-+BAM_INC = $(EPREFIX)/usr/include/bam-0.1-legacy
++BAM_INC = -I$(EPREFIX)/usr/include/bam-0.1-legacy
+BAM_LIB = # or -L/some/path
+BAM_LIBS = -lbam-0.1-legacy
#path to the directory where the samtools package was built (in place)
@@ -11,7 +11,7 @@
GDIR :=./gclib
-INCDIRS := -I. -I${GDIR} -I${BAM}
-+INCDIRS := -I. -I${GDIR} -I${BAM_INC}
++INCDIRS := -I. -I${GDIR} ${BAM_INC}
-#CC := clang++
-CC := g++
@@ -20,7 +20,7 @@
ifneq (,$(findstring nothreads,$(MAKECMDGOALS)))
-@@ -15,12 +17,12 @@
+@@ -15,7 +17,7 @@
endif
#detect MinGW (Windows environment)
@@ -29,69 +29,63 @@
WINDOWS=1
endif
- LFLAGS =
--# MinGW32 GCC 4.5 link problem fix
-+# MinGW32 GCXX 4.5 link problem fix
- #ifdef WINDOWS
- ifneq (,$(findstring 4.5.,$(shell g++ -dumpversion)))
- LFLAGS += -static-libstdc++ -static-libgcc
-@@ -50,7 +52,7 @@
+@@ -48,9 +50,9 @@
+ # C/C++ linker
+
#LINKER := clang++
- LINKER := g++
+-LINKER := g++
++LINKER ?= g++
-LIBS := -lbam -lz
+LIBS := ${BAM_LIBS} -lz
# Non-windows systems need pthread
ifndef WINDOWS
-@@ -68,27 +70,27 @@
+@@ -68,8 +70,10 @@
#ifneq (,$(findstring release,$(MAKECMDGOALS)))
ifneq (,$(filter %release %static, $(MAKECMDGOALS)))
# -- release build
- CFLAGS := -O3 -DNDEBUG -g $(BASEFLAGS)
- LDFLAGS := -g -L${BAM} ${LFLAGS}
-+ CXXFLAGS += -DNDEBUG -g $(BASEFLAGS)
++ CXXFLAGS ?= -O3 -g
++ CXXFLAGS += -DNDEBUG $(BASEFLAGS)
++ LDFLAGS ?= -g
+ LDFLAGS += ${BAM_LIB} ${LFLAGS}
ifneq (,$(findstring static,$(MAKECMDGOALS)))
LDFLAGS += -static-libstdc++ -static-libgcc
endif
- else
- ifneq (,$(filter %memcheck %memdebug, $(MAKECMDGOALS)))
- #make memcheck : use the statically linked address sanitizer in gcc 4.9.x
-- GCCVER49 := $(shell expr `g++ -dumpversion | cut -f1,2 -d.` \>= 4.9)
-- ifeq "$(GCCVER49)" "0"
-+ GCXXVER49 := $(shell expr `g++ -dumpversion | cut -f1,2 -d.` \>= 4.9)
-+ ifeq "$(GCXXVER49)" "0"
+@@ -80,15 +84,16 @@
+ 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)
-- GCCVER5 := $(shell expr `g++ -dumpversion | cut -f1 -d.` \>= 5)
-- ifeq "$(GCCVER5)" "1"
++ CXXFLAGS += -fno-omit-frame-pointer -fsanitize=undefined
-fsanitize=address $(BASEFLAGS)
+ GCCVER5 := $(shell expr `g++ -dumpversion | cut -f1 -d.` \>= 5)
+ ifeq "$(GCCVER5)" "1"
- CFLAGS += -fsanitize=bounds -fsanitize=float-divide-by-zero
-fsanitize=vptr
- CFLAGS += -fsanitize=float-cast-overflow -fsanitize=object-size
- #CFLAGS += -fcheck-pointer-bounds -mmpx
-+ CXXFLAGS := -fno-omit-frame-pointer -fsanitize=undefined
-fsanitize=address $(BASEFLAGS)
-+ GCXXVER5 := $(shell expr `g++ -dumpversion | cut -f1 -d.` \>= 5)
-+ ifeq "$(GCXXVER5)" "1"
+ CXXFLAGS += -fsanitize=bounds -fsanitize=float-divide-by-zero
-fsanitize=vptr
+ CXXFLAGS += -fsanitize=float-cast-overflow -fsanitize=object-size
+ #CXXFLAGS += -fcheck-pointer-bounds -mmpx
endif
- CFLAGS := -g -DDEBUG -D_DEBUG -DGDEBUG -fno-common -fstack-protector
$(CFLAGS)
- LDFLAGS := -g -L${BAM}
-+ CXXFLAGS += -DDEBUG -D_DEBUG -DGDEBUG -fno-common -fstack-protector
$(CXXFLAGS)
-+ LDFLAGS += ${BAM_LIB}
++ 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 +99,13 @@
+@@ -97,13 +102,14 @@
GMEMTRACE=1
endif
#just plain debug build
- CFLAGS := -g -DDEBUG -D_DEBUG -DGDEBUG $(BASEFLAGS)
- LDFLAGS := -g -L${BAM}
-+ CXXFLAGS += -DDEBUG -D_DEBUG -DGDEBUG $(BASEFLAGS)
-+ LDFLAGS += ${BAM_LIB}
++ CXXFLAGS ?= -g
++ CXXFLAGS += -DDEBUG -D_DEBUG -DGDEBUG $(BASEFLAGS)
++ LDFLAGS += ${BAM_LIB}
endif
endif
@@ -101,7 +95,7 @@
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 +132,7 @@
+@@ -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
@@ -112,7 +106,7 @@
${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
.PHONY : clean cleanall cleanAll allclean
-@@ -143,7 +143,6 @@
+@@ -143,7 +147,6 @@
@${RM} stringtie stringtie.o* stringtie.exe $(OBJS)
@${RM} core.*
allclean cleanAll cleanall:
