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commit 1e72b13c2eed9ee7733a469ad4370c8d07aabef0 Author: Alexandre Mestiashvili <[email protected]> Date: Thu May 21 17:40:32 2015 +0200 d/rules: export -fsigned-char only once d/patches/arch_specific_flags.patch: use -O2 instead of -O9, remove duplicated options d/README.source: merge with d/README.Debian-source describe why powerpc, mips and s390x are excluded --- debian/README.Debian-source | 2 -- debian/README.source | 15 +++++++++++++++ debian/patches/arch_specific_flags.patch | 8 ++++---- debian/rules | 1 + 4 files changed, 20 insertions(+), 6 deletions(-) diff --git a/debian/README.Debian-source b/debian/README.Debian-source deleted file mode 100644 index c009f5b..0000000 --- a/debian/README.Debian-source +++ /dev/null @@ -1,2 +0,0 @@ - This source package doesn't contain the pdf documentation - /doc/SubreadUserGuide.pdf shiped with the original tarball. diff --git a/debian/README.source b/debian/README.source new file mode 100644 index 0000000..aafb435 --- /dev/null +++ b/debian/README.source @@ -0,0 +1,15 @@ + + The source package of subread doesn't include the pdf documentation + /doc/SubreadUserGuide.pdf shiped with the original tarball. + + In order to get the +dfsg tarball use get-orig-source target in d/rules + + The subread package is currently build only for the following architectures: + + arm64 armel armhf hurd-i386 i386 kfreebsd-amd64 kfreebsd-i386 mipsel ppc64elo + + It is possible to built subread also on powerpc, mips and s390x, + but a few core tools of subread suite fail on these architectures. + exactSNP can't read the input BAM file and subjunc segfaults. + + -- Alex Mestiashvili <[email protected]> Thu, 21 May 2015 16:15:30 +0200 diff --git a/debian/patches/arch_specific_flags.patch b/debian/patches/arch_specific_flags.patch index bb06253..722caa8 100644 --- a/debian/patches/arch_specific_flags.patch +++ b/debian/patches/arch_specific_flags.patch @@ -1,7 +1,7 @@ Description: inject architecture specific flags: for amd64 and i386 add -mtune=generic and -msse3, - for architectures where char is by default unsigned - use -fsigned-char gcc option + use -fsigned-char for all architectures + change -O9 to -O2 as I couldn't fine -O9 in gcc options Author: Alex Mestiashvili <[email protected]> --- subread.orig/src/Makefile.Linux +++ subread/src/Makefile.Linux @@ -10,11 +10,11 @@ Author: Alex Mestiashvili <[email protected]> include makefile.version -CCFLAGS = -mtune=core2 ${MACOS} -O9 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\"${SUBREAD_VERSION}\" -D_FILE_OFFSET_BITS=64 -+CCFLAGS = ${EXTRA_CC_FLAGS} -O9 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\"${SUBREAD_VERSION}\" -D_FILE_OFFSET_BITS=64 ++CCFLAGS = ${EXTRA_CC_FLAGS} -O2 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\"${SUBREAD_VERSION}\" -D_FILE_OFFSET_BITS=64 #CCFLAGS = -D_FORTIFY_SOURCE=2 -mtune=core2 ${MACOS} -O2 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\"${SUBREAD_VERSION}\" # -DREPORT_ALL_THE_BEST -LDFLAGS = ${STATIC_MAKE} -lpthread -lz -lm ${MACOS} -O9 -DMAKE_FOR_EXON -D MAKE_STANDALONE # -DREPORT_ALL_THE_BEST -CC = gcc ${CCFLAGS} -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -mmmx -msse -msse2 -msse3 -fmessage-length=0 -+LDFLAGS = ${STATIC_MAKE} ${EXTRA_LD_FLAGS} -lpthread -lz -lm -O9 -DMAKE_FOR_EXON -D MAKE_STANDALONE # -DREPORT_ALL_THE_BEST ++LDFLAGS = ${STATIC_MAKE} ${EXTRA_LD_FLAGS} -lpthread -lz -lm # -DREPORT_ALL_THE_BEST +CC = gcc ${CCFLAGS} -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 diff --git a/debian/rules b/debian/rules index 16c77ef..cef5aab 100755 --- a/debian/rules +++ b/debian/rules @@ -11,6 +11,7 @@ bindir := $(CURDIR)/bin utildir := $(CURDIR)/bin/utilities DEB_HOST_ARCH := $(shell dpkg-architecture -qDEB_HOST_ARCH) +EXTRA_CC_FLAGS = ifeq ($(DEB_HOST_ARCH),$(filter $(DEB_HOST_ARCH),amd64 i386)) EXTRA_CC_FLAGS = -mtune=generic -msse3 endif -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/subread.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
