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authorMartin Mokrejs <mmokrejs@fold.natur.cuni.cz>2018-06-27 14:36:48 +0200
committerMartin Mokrejs <mmokrejs@fold.natur.cuni.cz>2018-06-27 14:36:48 +0200
commit25c5b41b494d8cd66bf5c552b35b78acc484f07e (patch)
tree9a246d5fdb5322fe40b48b97dae9007fdb313367
parentCorrected hard masking dates (diff)
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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
-rw-r--r--sci-biology/stringtie/Manifest2
-rw-r--r--sci-biology/stringtie/files/Makefile.patch140
-rw-r--r--sci-biology/stringtie/stringtie-1.3.4d.ebuild (renamed from sci-biology/stringtie/stringtie-1.2.2.ebuild)3
3 files changed, 70 insertions, 75 deletions
diff --git a/sci-biology/stringtie/Manifest b/sci-biology/stringtie/Manifest
index 74fcf6481..1e23e3aa7 100644
--- a/sci-biology/stringtie/Manifest
+++ b/sci-biology/stringtie/Manifest
@@ -1 +1 @@
-DIST stringtie-1.2.2.tar.gz 410898 BLAKE2B 78525aa436b0b2fce4a12fca3adff4972cab887bfca18d992a16b70e168832d831365f22e6a6eae5974883ff2be8dcb82e5e4972fe3f5b6c53f1912486f96031 SHA512 b84d30dc84d4e4793619ff50751b7918e410adfafdc7cfe3e08c9b51e6a09c952e430d799d3adbd003089f1eb58d7ce9e428f24ba44529d3ef1b5ff7aa43da8e
+DIST stringtie-1.3.4d.tar.gz 438025 BLAKE2B e9ea21f9d42cc90cb1fba200f13e840061bb8b34e1c3217aeaaee16edc2e2ededd5bae93d9575a7e198590d8ac8c4ba2d85f282a829d53296fd3edcd221a2d9a SHA512 450790af11536f1d9ac90e45af719b25bf7bd3a3123dcf8173b31e64446e650acb89bc9c9424c6fd0d527722fe204f510955308123f167ebd1c4334368fa2a4f
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
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