diff options
author | V3n3RiX <venerix@redcorelinux.org> | 2017-10-09 18:53:29 +0100 |
---|---|---|
committer | V3n3RiX <venerix@redcorelinux.org> | 2017-10-09 18:53:29 +0100 |
commit | 4f2d7949f03e1c198bc888f2d05f421d35c57e21 (patch) | |
tree | ba5f07bf3f9d22d82e54a462313f5d244036c768 /sci-biology/wgs-assembler/files |
reinit the tree, so we can have metadata
Diffstat (limited to 'sci-biology/wgs-assembler/files')
-rw-r--r-- | sci-biology/wgs-assembler/files/wgs-assembler-7.0-build.patch | 229 |
1 files changed, 229 insertions, 0 deletions
diff --git a/sci-biology/wgs-assembler/files/wgs-assembler-7.0-build.patch b/sci-biology/wgs-assembler/files/wgs-assembler-7.0-build.patch new file mode 100644 index 000000000000..f7fb44743968 --- /dev/null +++ b/sci-biology/wgs-assembler/files/wgs-assembler-7.0-build.patch @@ -0,0 +1,229 @@ + kmer/Make.rules | 4 ++-- + kmer/configure.sh | 20 +++++++++---------- + src/c_make.as | 58 +++++++++++++++++++++++++++---------------------------- + src/c_make.gen | 4 ++-- + 4 files changed, 43 insertions(+), 43 deletions(-) + +diff --git a/kmer/Make.rules b/kmer/Make.rules +index f904b13..5c2d477 100644 +--- a/kmer/Make.rules ++++ b/kmer/Make.rules +@@ -139,12 +139,12 @@ ${ALL_CXX_DEPS}:%.d:% + ## EXE targets + ALL_C_EXES :=$(strip $(foreach x,${//},${${x:.=.C_EXES}})) + ${ALL_C_EXES}: +- ${-CC} ${CLD} ${CLDFLAGS} -o $@ $+ ${CLIBS} ++ ${-CC} ${CLD} ${CLDFLAGS} ${LDFLAGS} -o $@ $+ ${CLIBS} + __SUBGOALS__+=$${${1:.=.C_EXES}} + + ALL_CXX_EXES :=$(strip $(foreach x,${//},${${x:.=.CXX_EXES}})) + ${ALL_CXX_EXES}: +- ${-CXX} ${CXXLD} ${CXXLDFLAGS} -o $@ $+ ${CXXLIBS} ++ ${-CXX} ${CXXLD} ${CXXLDFLAGS} ${LDFLAGS} -o $@ $+ ${CXXLIBS} + __SUBGOALS__+=$${${1:.=.CXX_EXES}} + + define .RULE-install-copy-C-CXX-EXES +diff --git a/kmer/configure.sh b/kmer/configure.sh +index 2f0d5ea..9daf89f 100755 +--- a/kmer/configure.sh ++++ b/kmer/configure.sh +@@ -254,13 +254,13 @@ EOF + # -*- makefile -*- + # Linux, optimized + CC := $CC +-SHLIB_FLAGS := -shared +-CFLAGS_COMPILE := -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer +-CLDFLAGS := -L/usr/local/lib ++SHLIB_FLAGS := -shared ${LDFLAGS} ++CFLAGS_COMPILE := -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts ++CLDFLAGS := + CLIBS := -pthread -ldl + CXX := $CXX +-CXXFLAGS_COMPILE := -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer +-CXXLDFLAGS := -L/usr/local/lib ++CXXFLAGS_COMPILE := -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts ++CXXLDFLAGS := + CXXLIBS := -pthread -ldl + ARFLAGS := ruvs + INSTALL/ := $target/ +@@ -272,13 +272,13 @@ EOF + # -*- makefile -*- + # Linux64, optimized + CC := $CC +-SHLIB_FLAGS := -shared +-CFLAGS_COMPILE := -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer +-CLDFLAGS := -L/usr/local/lib ++SHLIB_FLAGS := -shared ${LDFLAGS} ++CFLAGS_COMPILE := -fPIC -D_REENTRANT -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts ++CLDFLAGS := + CLIBS := -pthread -ldl + CXX := $CXX +-CXXFLAGS_COMPILE := -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer +-CXXLDFLAGS := -L/usr/local/lib ++CXXFLAGS_COMPILE := -fPIC -D_REENTRANT -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts ++CXXLDFLAGS := + CXXLIBS := -pthread -ldl + ARFLAGS := ruvs + INSTALL/ := $target/ +diff --git a/src/c_make.as b/src/c_make.as +index 0172807..4304589 100644 +--- a/src/c_make.as ++++ b/src/c_make.as +@@ -64,27 +64,27 @@ include $(LOCAL_WORK)/src/c_make.gen + + ifeq ($(OSTYPE), Linux) + ifeq ($(MACHINETYPE), i686) +- ARCH_LDFLAGS += -pthread -lm +- ARCH_CFLAGS += -pthread -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DX86_GCC_LINUX ++ LINK_LIBS += -pthread -lm ++ ARCH_CFLAGS += -pthread -Wall -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DX86_GCC_LINUX + ARCH_LIB = /usr/X11R6/lib + endif + ifeq ($(MACHINETYPE), amd64) +- ARCH_LDFLAGS += -pthread -lm +- ARCH_CFLAGS += -pthread -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DX86_GCC_LINUX ++ LINK_LIBS += -pthread -lm ++ ARCH_CFLAGS += -pthread -Wall -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DX86_GCC_LINUX + ARCH_LIB = /usr/lib64 /usr/X11R6/lib64 + endif + ifeq ($(MACHINETYPE), ia64) +- ARCH_LDFLAGS += -pthread -lm +- ARCH_CFLAGS += -pthread -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 ++ LINK_LIBS += -pthread -lm ++ ARCH_CFLAGS += -pthread -Wall -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 + ARCH_LIB = /usr/X11R6/lib + endif + + ifeq ($(BUILDDEBUG), 1) +- ARCH_CFLAGS += -g +- ARCH_LDFLAGS += ++ ARCH_CFLAGS += ++ LINK_LIBS += + else +- ARCH_CFLAGS += -O2 +- ARCH_LDFLAGS += -Wl,-O1 ++ ARCH_CFLAGS += ++ LINK_LIBS += + endif + endif + +@@ -94,19 +94,19 @@ endif + + ifeq ($(OSTYPE), FreeBSD) + ifeq ($(MACHINETYPE), i386) +- ARCH_LDFLAGS += -pthread -lthr -lm +- ARCH_CFLAGS = -pthread -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare +- ARCH_CFLAGS = -pthread -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare ++ LINK_LIBS += -pthread -lthr -lm ++ ARCH_CFLAGS = -pthread -Wall -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare ++ ARCH_CFLAGS = -pthread -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare + endif + ifeq ($(MACHINETYPE), amd64) +- ARCH_LDFLAGS += -pthread -lthr -lm +- ARCH_CFLAGS = -pthread -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat +- ARCH_CFLAGS = -pthread -Wall -Wextra -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat ++ LINK_LIBS += -pthread -lthr -lm ++ ARCH_CFLAGS = -pthread -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat ++ ARCH_CFLAGS = -pthread -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat + endif + + ifeq ($(BUILDCOVERAGE), 1) + ARCH_CFLAGS += -g -fprofile-arcs -ftest-coverage +- ARCH_LDFLAGS += -lgcov ++ LINK_LIBS += -lgcov + else + ifeq ($(BUILDDEBUG), 1) + ARCH_CFLAGS += -g +@@ -140,14 +140,14 @@ ifeq ($(OSTYPE), Darwin) + + ifeq ($(MACHINETYPE), i386) + ifeq ($(BUILDDEBUG), 1) +- ARCH_CFLAGS += -fPIC -m64 -fmessage-length=0 -D_THREAD_SAFE -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -g +- ARCH_LDFLAGS += -m64 -lm ++ ARCH_CFLAGS += -fPIC -m64 -fmessage-length=0 -D_THREAD_SAFE -Wall -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -g ++ LINK_LIBS += -m64 -lm + else + # Wow, -Wshorten-64-to-32 is tough +- ARCH_CFLAGS += -fPIC -m64 -fmessage-length=0 -D_THREAD_SAFE -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -fast ++ ARCH_CFLAGS += -fPIC -m64 -fmessage-length=0 -D_THREAD_SAFE -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -fast + # ARCH_CFLAGS += -Wextra + # ARCH_CFLAGS += -pedantic (see above about pedantic) +- ARCH_LDFLAGS += -m64 -lm ++ LINK_LIBS += -m64 -lm + endif + endif + +@@ -161,23 +161,23 @@ endif + ifeq ($(OSTYPE), SunOS) + ifeq ($(MACHINETYPE), i86pc) + ARCH_CFLAGS = -DBYTE_ORDER=LITTLE_ENDIAN -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -pthreads +- ARCH_LDFLAGS += -lm ++ LINK_LIBS += -lm + endif + + ifeq ($(MACHINETYPE), sparc32) + ARCH_CFLAGS = -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -pthreads +- ARCH_LDFLAGS += -lm -lnsl -lsocket ++ LINK_LIBS += -lm -lnsl -lsocket + endif + + ifeq ($(MACHINETYPE), sparc64) + ARCH_CFLAGS = -m64 -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -pthreads +- ARCH_LDFLAGS += -m64 -lm -lnsl -lsocket ++ LINK_LIBS += -lm -lnsl -lsocket + endif + + ifeq ($(BUILDDEBUG), 1) +- ARCH_CFLAGS += -g ++ ARCH_CFLAGS += + else +- ARCH_CFLAGS += -O ++ ARCH_CFLAGS += + endif + endif + +@@ -186,14 +186,14 @@ endif + + ifeq ($(BUILDPROFILE), 1) + ARCH_CFLAGS += -pg +- ARCH_LDFLAGS += -pg ++ LINK_LIBS += -pg + endif + + # One can argue that CXXFLAGS should be separate. For now, we only + # add to the flags. + + CFLAGS += $(ARCH_CFLAGS) +-CXXFLAGS += $(ARCH_CFLAGS) $(ARCH_CXXFLAGS) ++CXXFLAGS += $(ARCH_CXXFLAGS) + LDFLAGS += $(ARCH_LDFLAGS) + + INC_IMPORT_DIRS += $(LOCAL_WORK)/src $(patsubst %, $(LOCAL_WORK)/src/%, $(strip $(SUBDIRS))) +@@ -205,7 +205,7 @@ LIB_IMPORT_DIRS += $(ARCH_LIB) + OBJ_SEARCH_PATH = $(LOCAL_OBJ) + + ifeq ($(SITE_NAME), JCVI) +- LDFLAGS += -lcurl ++ LINK_LIBS += -lcurl + endif + + # The order of compilation here is very carefully chosen to be the +diff --git a/src/c_make.gen b/src/c_make.gen +index 7b5227c..c27b777 100644 +--- a/src/c_make.gen ++++ b/src/c_make.gen +@@ -396,12 +396,12 @@ $(LIBRARIES): + $(C_PROGS): + @ echo "++++++++++++++++++++ " $@ "++++++++++++++++++++++"; + cd $(LOCAL_OBJ); \ +- $(CC) -o $(LOCAL_BIN)/$(notdir $@) $(filter-out lib%.a, $+) $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LD_DIRS) $(LDFLAGS) ++ $(CC) $(LDFLAGS) -o $(LOCAL_BIN)/$(notdir $@) $(filter-out lib%.a, $+) $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LD_DIRS) $(LINK_LIBS) + + $(CXX_PROGS): + @ echo "++++++++++++++++++++ " $@ "++++++++++++++++++++++"; + cd $(LOCAL_OBJ); \ +- $(CXX) -o $(LOCAL_BIN)/$(notdir $@) $(filter-out lib%.a, $+) $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LD_DIRS) $(LDFLAGS) ++ $(CXX) $(LDFLAGS) -o $(LOCAL_BIN)/$(notdir $@) $(filter-out lib%.a, $+) $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LD_DIRS) $(LINK_LIBS) + + $(SCRIPT_PROGS): %.sh: + @echo "++++++++++++++++++++ " $@ "++++++++++++++++++++++"; |