* [gentoo-commits] proj/sci:master commit in: sci-biology/stringtie/, sci-biology/stringtie/files/
@ 2018-06-25 21:33 Martin Mokrejs
0 siblings, 0 replies; 4+ messages in thread
From: Martin Mokrejs @ 2018-06-25 21:33 UTC (permalink / raw
To: gentoo-commits
commit: ea5a2c0348666f4e6ff00c25a5597d4e5c0fd084
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Jun 25 21:33:33 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Jun 25 21:33:33 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ea5a2c03
sci-biology/stringtie: drop bundled samtools-0.18.1, fix Makefile
Also use properly named CXX and CXXFLAGS variables, respect their initial
values.
Package-Manager: Portage-2.3.40, Repoman-2.3.9
sci-biology/stringtie/files/Makefile.patch | 122 +++++++++++++++++++++++++++
sci-biology/stringtie/stringtie-1.2.2.ebuild | 9 +-
2 files changed, 130 insertions(+), 1 deletion(-)
diff --git a/sci-biology/stringtie/files/Makefile.patch b/sci-biology/stringtie/files/Makefile.patch
new file mode 100644
index 000000000..8f5379b6b
--- /dev/null
+++ b/sci-biology/stringtie/files/Makefile.patch
@@ -0,0 +1,122 @@
+--- 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
+@@ -1,13 +1,15 @@
+-BAM := ./samtools-0.1.18
++BAM_INC = $(EPREFIX)/usr/include/bam-0.1-legacy
++BAM_LIB = # or -L/some/path
++BAM_LIBS = -lbam-0.1-legacy
+ #path to the directory where the samtools package was built (in place)
+ #so libbam.a and *.h files MUST be in here
+
+ GDIR :=./gclib
+
+-INCDIRS := -I. -I${GDIR} -I${BAM}
++INCDIRS := -I. -I${GDIR} -I${BAM_INC}
+
+-#CC := clang++
+-CC := g++
++#CXX := clang++
++CXX ?= g++
+
+
+ ifneq (,$(findstring nothreads,$(MAKECMDGOALS)))
+@@ -15,12 +17,12 @@
+ endif
+
+ #detect MinGW (Windows environment)
+-ifneq (,$(findstring mingw,$(shell ${CC} -dumpmachine)))
++ifneq (,$(findstring mingw,$(shell ${CXX} -dumpmachine)))
+ WINDOWS=1
+ endif
+
+ LFLAGS =
+-# MinGW32 GCC 4.5 link problem fix
++# MinGW32 GCXX 4.5 link problem fix
+ #ifdef WINDOWS
+ ifneq (,$(findstring 4.5.,$(shell g++ -dumpversion)))
+ LFLAGS += -static-libstdc++ -static-libgcc
+@@ -50,7 +52,7 @@
+ #LINKER := clang++
+ LINKER := g++
+
+-LIBS := -lbam -lz
++LIBS := ${BAM_LIBS} -lz
+
+ # Non-windows systems need pthread
+ ifndef WINDOWS
+@@ -68,27 +70,27 @@
+ #ifneq (,$(findstring release,$(MAKECMDGOALS)))
+ ifneq (,$(filter %release %static, $(MAKECMDGOALS)))
+ # -- release build
+- CFLAGS := -O3 -DNDEBUG -g $(BASEFLAGS)
+- LDFLAGS := -g -L${BAM} ${LFLAGS}
++ CXXFLAGS += -DNDEBUG -g $(BASEFLAGS)
++ 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"
+ $(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"
+- 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}
+ #LIBS := -Wl,-Bstatic -lasan -lubsan -Wl,-Bdynamic -ldl $(LIBS)
+ LIBS := -lasan -lubsan -ldl $(LIBS)
+ else
+@@ -97,13 +99,13 @@
+ 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}
+ endif
+ 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 +132,7 @@
+ 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, $^} ${LIBS}
+
+ .PHONY : clean cleanall cleanAll allclean
+@@ -143,7 +143,6 @@
+ @${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.*
+
diff --git a/sci-biology/stringtie/stringtie-1.2.2.ebuild b/sci-biology/stringtie/stringtie-1.2.2.ebuild
index 4bcc049de..1f38bf7cd 100644
--- a/sci-biology/stringtie/stringtie-1.2.2.ebuild
+++ b/sci-biology/stringtie/stringtie-1.2.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -17,6 +17,13 @@ IUSE=""
DEPEND="sci-biology/samtools:0.1-legacy" # bundled samtools-0.1.18
RDEPEND="${DEPEND}"
+PATCHES=( "${FILESDIR}"/Makefile.patch )
+
+src_prepare(){
+ default
+ rm -r samtools-0.1.18 || die
+}
+
src_compile(){
emake release
}
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/stringtie/, sci-biology/stringtie/files/
@ 2018-06-26 8:15 Martin Mokrejs
0 siblings, 0 replies; 4+ messages in thread
From: Martin Mokrejs @ 2018-06-26 8:15 UTC (permalink / raw
To: gentoo-commits
commit: 989059eec92c6fda0890e076cb9fc70fc994ed3f
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jun 26 08:15:28 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jun 26 08:15:28 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=989059ee
sci-biology/stringtie: keep modified bundled copy of samtools-0.1.18
https://github.com/gpertea/stringtie/issues/185#issuecomment-400128090
https://github.com/gpertea/stringtie/issues/186#issuecomment-400131844
Therefore, keep local copy of gclib and samtools.
Still it does not compile for me with gcc-7.3.0
Package-Manager: Portage-2.3.40, Repoman-2.3.9
sci-biology/stringtie/files/Makefile.patch | 6 +++---
sci-biology/stringtie/stringtie-1.2.2.ebuild | 18 +++++++-----------
2 files changed, 10 insertions(+), 14 deletions(-)
diff --git a/sci-biology/stringtie/files/Makefile.patch b/sci-biology/stringtie/files/Makefile.patch
index 7db068985..a7ca43c39 100644
--- a/sci-biology/stringtie/files/Makefile.patch
+++ b/sci-biology/stringtie/files/Makefile.patch
@@ -2,9 +2,9 @@
+++ stringtie-1.2.2/Makefile 2018-06-26 00:46:43.406712302 +0200
@@ -1,13 +1,15 @@
-BAM := ./samtools-0.1.18
-+BAM_INC = -I$(EPREFIX)/usr/include/bam-0.1-legacy
-+BAM_LIB = # or -L/some/path
-+BAM_LIBS = -lbam-0.1-legacy
++BAM_INC = -I./samtools-0.1.18
++BAM_LIB = -L./samtools-0.1.18
++BAM_LIBS = -lbam
#path to the directory where the samtools package was built (in place)
#so libbam.a and *.h files MUST be in here
diff --git a/sci-biology/stringtie/stringtie-1.2.2.ebuild b/sci-biology/stringtie/stringtie-1.2.2.ebuild
index 37c0f26cf..953999e87 100644
--- a/sci-biology/stringtie/stringtie-1.2.2.ebuild
+++ b/sci-biology/stringtie/stringtie-1.2.2.ebuild
@@ -8,25 +8,21 @@ HOMEPAGE="https://ccb.jhu.edu/software/stringtie
https://github.com/gpertea/stringtie"
SRC_URI="http://ccb.jhu.edu/software/stringtie/dl/${P}.tar.gz"
-LICENSE="Artistic-2"
+LICENSE="Artistic-2 MIT" # MIT from bundled samtools-0.1.18
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE=""
-# contains bundled gclib (0.9.8?), well they are just headers
-DEPEND="
- sci-biology/gclib
- sci-biology/samtools:0.1-legacy" # bundled samtools-0.1.18
+# contains bundled and modified samtools-0.1.18
+# https://github.com/gpertea/stringtie/issues/185#issuecomment-400128090
+#
+# contains bundled gclib (0.9.8?), a modified version?
+# https://github.com/gpertea/stringtie/issues/186#issuecomment-400131844
+DEPEND=""
RDEPEND="${DEPEND}"
PATCHES=( "${FILESDIR}"/Makefile.patch )
-src_prepare(){
- default
- rm -r samtools-0.1.18 || die
- # TODO: `rm -rf ./gclib' and fix Makefile
-}
-
src_compile(){
emake release
}
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/stringtie/, sci-biology/stringtie/files/
@ 2018-06-27 12:37 Martin Mokrejs
0 siblings, 0 replies; 4+ messages in thread
From: Martin Mokrejs @ 2018-06-27 12:37 UTC (permalink / raw
To: gentoo-commits
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/${P}.tar.gz"
LICENSE="Artistic-2 MIT" # MIT from bundled samtools-0.1.18
SLOT="0"
-KEYWORDS="" # gclib/GThreads.h:804:19: error: conflicting declaration
-# 'typedef long long int __intmax_t'
+KEYWORDS="~amd64 ~x86"
IUSE=""
# contains bundled and modified samtools-0.1.18
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/stringtie/, sci-biology/stringtie/files/
@ 2021-03-06 14:55 Andrew Ammerlaan
0 siblings, 0 replies; 4+ messages in thread
From: Andrew Ammerlaan @ 2021-03-06 14:55 UTC (permalink / raw
To: gentoo-commits
commit: d5262133d2c941fbbf3995e7512d6d98df6fb250
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Mar 6 14:55:12 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Mar 6 14:55:12 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=d5262133
sci-biology/stringtie: cleanup old
Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/stringtie/files/Makefile.patch | 112 --------------------------
sci-biology/stringtie/stringtie-1.3.4d.ebuild | 33 --------
2 files changed, 145 deletions(-)
diff --git a/sci-biology/stringtie/files/Makefile.patch b/sci-biology/stringtie/files/Makefile.patch
deleted file mode 100644
index b7efa605c..000000000
--- a/sci-biology/stringtie/files/Makefile.patch
+++ /dev/null
@@ -1,112 +0,0 @@
---- stringtie-1.3.4d/Makefile 2018-06-26 00:36:17.119583211 +0200
-+++ stringtie-1.3.4d/Makefile 2018-06-26 00:46:43.406712302 +0200
-@@ -1,28 +1,32 @@
--BAM := ./samtools-0.1.18
--#path to the directory where the samtools package was built (in place)
--#so libbam.a and *.h files MUST be in here
-+#-- for now these MUST point to the included samtools-0.x.x and gclib subdirectories
-+BAM := ./samtools-0.1.18
-+GDIR := ./gclib
-+#--
-
--GDIR :=./gclib
-+INCDIRS := -I. -I${GDIR} -I${BAM}
-
--INCDIRS := -I. -I${GDIR} -I${BAM}
--
--CC := g++
-+#CXX ?= g++
-+CXX := $(if $(CXX),$(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)))
- NOTHREADS=1
- endif
-
- #detect MinGW (Windows environment)
--ifneq (,$(findstring mingw,$(shell ${CC} -dumpmachine)))
-+ifneq (,$(findstring mingw,$(shell ${CXX} -dumpmachine)))
- WINDOWS=1
- endif
-
-@@ -63,7 +67,8 @@ endif
- ifneq (,$(filter %release %static, $(MAKECMDGOALS)))
- # -- release build
- RELEASE_BUILD=1
-- CFLAGS := -DNDEBUG -g $(BASEFLAGS) $(CFLAGS) -O3
-+ CXXFLAGS := $(if $(CXXFLAGS),$(CXXFLAGS),-g -O3)
-+ CXXFLAGS += -DNDEBUG $(BASEFLAGS)
- else
- ifneq (,$(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"
-- CFLAGS += -fsanitize=bounds -fsanitize=float-divide-by-zero -fsanitize=vptr
-- CFLAGS += -fsanitize=float-cast-overflow -fsanitize=object-size
-- #CFLAGS += -fcheck-pointer-bounds -mmpx
-+ 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)
-+ CXXFLAGS += -DDEBUG -D_DEBUG -DGDEBUG -fno-common -fstack-protector
- LIBS := -lasan -lubsan -ldl $(LIBS)
- else
-- ifeq (,$(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 $@
-
- OBJS += rlink.o tablemaker.o tmerge.o
-
diff --git a/sci-biology/stringtie/stringtie-1.3.4d.ebuild b/sci-biology/stringtie/stringtie-1.3.4d.ebuild
deleted file mode 100644
index 953999e87..000000000
--- a/sci-biology/stringtie/stringtie-1.3.4d.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="Transcriptome assembler and RNA-Seq analysis on BAM files aka cufflinks"
-HOMEPAGE="https://ccb.jhu.edu/software/stringtie
- https://github.com/gpertea/stringtie"
-SRC_URI="http://ccb.jhu.edu/software/stringtie/dl/${P}.tar.gz"
-
-LICENSE="Artistic-2 MIT" # MIT from bundled samtools-0.1.18
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-# contains bundled and modified samtools-0.1.18
-# https://github.com/gpertea/stringtie/issues/185#issuecomment-400128090
-#
-# contains bundled gclib (0.9.8?), a modified version?
-# https://github.com/gpertea/stringtie/issues/186#issuecomment-400131844
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-PATCHES=( "${FILESDIR}"/Makefile.patch )
-
-src_compile(){
- emake release
-}
-
-src_install(){
- dobin stringtie
- dodoc README
-}
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2021-03-06 14:55 [gentoo-commits] proj/sci:master commit in: sci-biology/stringtie/, sci-biology/stringtie/files/ Andrew Ammerlaan
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2018-06-27 12:37 Martin Mokrejs
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