[med-svn] [subread] 02/04: d/rules: add -msse3 and -mtune=generic for i386/amd64 d/patches: merge hardening and gcc_flags_cleanup patches

[Alex Mestiashvili]

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

commit 5395d60d291ae5f024fa605ecd1f87914943250c
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Fri May 15 15:15:56 2015 +0200

    d/rules: add -msse3 and -mtune=generic for i386/amd64
    d/patches: merge hardening and gcc_flags_cleanup patches
---
 debian/patches/gcc_flags_cleanup.patch      |  9 +++++----
 debian/patches/inject_hardening_flags.patch | 13 -------------
 debian/patches/series                       |  1 -
 debian/rules                                | 10 ++++++++++
 4 files changed, 15 insertions(+), 18 deletions(-)

diff --git a/debian/patches/gcc_flags_cleanup.patch b/debian/patches/gcc_flags_cleanup.patch
index 72a5dd6..100ace3 100644
--- a/debian/patches/gcc_flags_cleanup.patch
+++ b/debian/patches/gcc_flags_cleanup.patch
@@ -1,4 +1,5 @@
-Description: remove too specific -mtune and -msse* flags
+Description: remove too specific -mtune and -msse* flags and inject hardening 
+ flags, add -msse3 flag for i386/AMD64
 Origin: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 --- subread.orig/src/Makefile.Linux
 +++ subread/src/Makefile.Linux
@@ -7,12 +8,12 @@ Origin: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
  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 = ${MTUNE} -O9 -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\"${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 
++LDFLAGS = ${STATIC_MAKE} ${EXTRA_FLAGS} -lpthread -lz -lm -O9 -DMAKE_FOR_EXON -D MAKE_STANDALONE # -DREPORT_ALL_THE_BEST
++CC = gcc ${CCFLAGS} ${SSE_FLAGS} -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
deleted file mode 100644
index 81859b5..0000000
--- a/debian/patches/inject_hardening_flags.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-Description: Inject hardening LDFLAGS
-Origin: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
---- subread.orig/src/Makefile.Linux
-+++ subread/src/Makefile.Linux
-@@ -4,7 +4,7 @@
- 
- 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 -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 741e6f6..bd566ca 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,4 +1,3 @@
 getopt4exactSNP.patch
 gcc_flags_cleanup.patch
 fix_syntax.patch
-inject_hardening_flags.patch
diff --git a/debian/rules b/debian/rules
index 62dd948..55276a5 100755
--- a/debian/rules
+++ b/debian/rules
@@ -10,6 +10,16 @@ mandir := $(CURDIR)/debian/$(pkg)/usr/share/man/man1
 bindir := $(CURDIR)/bin
 utildir := $(CURDIR)/bin/utilities
 
+SSE_FLAGS =
+MTUNE =
+DEB_HOST_ARCH := $(shell dpkg-architecture -qDEB_HOST_ARCH)
+ifeq ($(DEB_HOST_ARCH),$(filter $(DEB_HOST_ARCH),amd64 i386))
+SSE_FLAGS = -msse3 
+MTUNE = -mtune=generic
+endif
+export SSE_FLAGS
+export MTUNE
+
 %:
 	dh $@
 

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