[med-svn] [subread] 01/02: 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

[Alex Mestiashvili]

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malex-guest pushed a commit to branch master
in repository subread.

commit c9e7274217070fbb5db69f827f5f8c98a8ef913c
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
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 <debian-med-packaging at lists.alioth.debian.org>
+--- 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 <debian-med-packaging at lists.alioth.debian.org>
 +++ 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:

-- 
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