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commit c9e7274217070fbb5db69f827f5f8c98a8ef913c Author: Alexandre Mestiashvili <[email protected]> Date: Sun May 10 09:51:09 2015 +0200 d/patches/gcc_flags_cleanup.patch: remove -mtune=core2 and mmmx,msse* flags see #784780 d/patches/inject_hardening_flags.patch: refreshed d/rules: use override_dh_installexamples-indep, fixes #784782 d/README.Debian-source: mention doc/SubreadUserGuide.pdf removal --- debian/README.Debian-source | 2 ++ debian/patches/gcc_flags_cleanup.patch | 18 ++++++++++++++++++ debian/patches/inject_hardening_flags.patch | 8 ++++---- debian/patches/series | 1 + debian/rules | 2 +- 5 files changed, 26 insertions(+), 5 deletions(-) diff --git a/debian/README.Debian-source b/debian/README.Debian-source new file mode 100644 index 0000000..c009f5b --- /dev/null +++ b/debian/README.Debian-source @@ -0,0 +1,2 @@ + This source package doesn't contain the pdf documentation + /doc/SubreadUserGuide.pdf shiped with the original tarball. diff --git a/debian/patches/gcc_flags_cleanup.patch b/debian/patches/gcc_flags_cleanup.patch new file mode 100644 index 0000000..72a5dd6 --- /dev/null +++ b/debian/patches/gcc_flags_cleanup.patch @@ -0,0 +1,18 @@ +Description: remove too specific -mtune and -msse* flags +Origin: Debian Med Packaging Team <[email protected]> +--- subread.orig/src/Makefile.Linux ++++ subread/src/Makefile.Linux +@@ -2,10 +2,10 @@ + + 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 = -O9 -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} -lpthread -lz -lm -O9 -DMAKE_FOR_EXON -D MAKE_STANDALONE # -DREPORT_ALL_THE_BEST ++CC = gcc ${CCFLAGS} -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 + + + ALL_LIBS= core core-junction core-indel sambam-file sublog gene-algorithms hashtable input-files sorted-hashtable gene-value-index exon-algorithms HelperFunctions interval_merge long-hashtable diff --git a/debian/patches/inject_hardening_flags.patch b/debian/patches/inject_hardening_flags.patch index 63585ab..81859b5 100644 --- a/debian/patches/inject_hardening_flags.patch +++ b/debian/patches/inject_hardening_flags.patch @@ -4,10 +4,10 @@ Origin: Debian Med Packaging Team <[email protected]> +++ subread/src/Makefile.Linux @@ -4,7 +4,7 @@ - CCFLAGS = -mtune=core2 ${MACOS} -O9 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\"${SUBREAD_VERSION}\" -D_FILE_OFFSET_BITS=64 + CCFLAGS = -O9 -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 -+LDFLAGS = ${STATIC_MAKE} ${EXTRA_FLAGS} -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} -lpthread -lz -lm -O9 -DMAKE_FOR_EXON -D MAKE_STANDALONE # -DREPORT_ALL_THE_BEST ++LDFLAGS = ${STATIC_MAKE} ${EXTRA_FLAGS} -lpthread -lz -lm -O9 -DMAKE_FOR_EXON -D MAKE_STANDALONE # -DREPORT_ALL_THE_BEST + CC = gcc ${CCFLAGS} -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 diff --git a/debian/patches/series b/debian/patches/series index c3feeb9..c7d6d2a 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,2 +1,3 @@ +gcc_flags_cleanup.patch fix_syntax.patch inject_hardening_flags.patch diff --git a/debian/rules b/debian/rules index 14ec560..62dd948 100755 --- a/debian/rules +++ b/debian/rules @@ -65,7 +65,7 @@ DNA-seq reads and RNA-seq reads (for the purpose of expression analysis)' \ dh_auto_install -override_dh_installexamples: +override_dh_installexamples-indep: tar -cJf $(CURDIR)/debian/subread-data/usr/share/doc/subread/examples/test.tar.xz test/ override_dh_compress: -- 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
