[med-svn] [subread] 05/14: Refresh quilt patches

[Alex Mestiashvili]

This is an automated email from the git hooks/post-receive script.

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

commit e55fbcee6e17df2392f54c87c449892abb2ae1c5
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Fri Apr 22 18:08:58 2016 +0200

    Refresh quilt patches
---
 debian/patches/arch_specific_flags.patch | 12 ++++++------
 debian/patches/series                    |  2 +-
 debian/patches/syntax_err.patch          |  2 +-
 3 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/debian/patches/arch_specific_flags.patch b/debian/patches/arch_specific_flags.patch
index 96134e1..0ec3215 100644
--- a/debian/patches/arch_specific_flags.patch
+++ b/debian/patches/arch_specific_flags.patch
@@ -9,13 +9,13 @@ Author: Alex Mestiashvili <alex at biotec.tu-dresden.de>
  
  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 =  -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
+-OPT_LEVEL = 9
+-CCFLAGS = -mtune=core2 ${MACOS} -O${OPT_LEVEL} -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\"${SUBREAD_VERSION}\"  -D_FILE_OFFSET_BITS=64
+-LDFLAGS = ${STATIC_MAKE} -lpthread -lz -lm ${MACOS} -O${OPT_LEVEL} -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 
-+CCFLAGS = ${EXTRA_CC_FLAGS} -O3 -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\"${SUBREAD_VERSION}\"  -D_FILE_OFFSET_BITS=64
-+#CCFLAGS =  -D_FORTIFY_SOURCE=2 -mtune=core2 ${MACOS} -O9 -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\"${SUBREAD_VERSION}\"  # -DREPORT_ALL_THE_BEST
-+LDFLAGS = ${STATIC_MAKE} ${EXTRA_LD_FLAGS} -lpthread -lz -lm # -DREPORT_ALL_THE_BEST
++OPT_LEVEL = 3
++CCFLAGS = ${EXTRA_CC_FLAGS} -O${OPT_LEVEL} -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\"${SUBREAD_VERSION}\"  -D_FILE_OFFSET_BITS=64
++LDFLAGS = ${STATIC_MAKE} -lpthread -lz -lm -O${OPT_LEVEL} -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 98d6178..1a235aa 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,2 @@
-syntax_err.patch
 arch_specific_flags.patch
+syntax_err.patch
diff --git a/debian/patches/syntax_err.patch b/debian/patches/syntax_err.patch
index 41b12ef..d92a48a 100644
--- a/debian/patches/syntax_err.patch
+++ b/debian/patches/syntax_err.patch
@@ -2,7 +2,7 @@ Description: spelling-error-in-binary featureCounts s/requried/required/
 Origin: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 --- subread.orig/src/readSummary.c
 +++ subread/src/readSummary.c
-@@ -3427,7 +3427,7 @@
+@@ -3511,7 +3511,7 @@
  	SUBREADputs("  --largestOverlap    Assign reads to a meta-feature/feature that has the ");
  	SUBREADputs("                      largest number of overlapping bases.");
  	SUBREADputs("");

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/subread.git