[med-svn] [subread] 04/06: Refresh and update paches

[Alex Mestiashvili]

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

commit 8dbd32f4f5d0a64d3bb82ee78550c82dd8a8b7f0
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Fri Jul 28 11:21:05 2017 +0200

    Refresh and update paches
---
 debian/patches/arch_specific_flags.patch | 8 ++++----
 debian/patches/fix_ftbfs_kfreebsd.patch  | 6 +++---
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/debian/patches/arch_specific_flags.patch b/debian/patches/arch_specific_flags.patch
index e52df1a..484b5b4 100644
--- a/debian/patches/arch_specific_flags.patch
+++ b/debian/patches/arch_specific_flags.patch
@@ -13,12 +13,12 @@ Author: Alex Mestiashvili <alex at biotec.tu-dresden.de>
  include makefile.version
  
  OPT_LEVEL = 3
--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
+-CCFLAGS = -mtune=core2 ${MACOS} -O${OPT_LEVEL} -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\"${SUBREAD_VERSION}\"  -D_FILE_OFFSET_BITS=64 # -w
+-LDFLAGS = ${STATIC_MAKE} -pthread -lz -lm ${MACOS} -O${OPT_LEVEL} -DMAKE_FOR_EXON -D MAKE_STANDALONE 
 +CCFLAGS += -O${OPT_LEVEL} -fsigned-char -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\"${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
++LDFLAGS += ${STATIC_MAKE} -pthread -lz -lm -O${OPT_LEVEL} -DMAKE_FOR_EXON -D MAKE_STANDALONE
  CC_EXEC = gcc
--CC = ${CC_EXEC}  ${CCFLAGS}  -fmessage-length=0  -ggdb # -fomit-frame-pointer -ffast-math -funroll-loops -mmmx -msse -msse2 -msse3 -fmessage-length=0
+-CC = ${CC_EXEC}  ${CCFLAGS}  -fmessage-length=0  -ggdb 
 +CC = ${CC_EXEC} ${CFLAGS} ${CPPFLAGS} ${CCFLAGS} -ggdb -fmessage-length=0
  
  
diff --git a/debian/patches/fix_ftbfs_kfreebsd.patch b/debian/patches/fix_ftbfs_kfreebsd.patch
index e4307a6..aab5386 100644
--- a/debian/patches/fix_ftbfs_kfreebsd.patch
+++ b/debian/patches/fix_ftbfs_kfreebsd.patch
@@ -2,8 +2,8 @@ Subject: Fix ftbfs on kfreebsd
 From: Alex Mestiashvili <alex at biotec.tu-dresden.de>
 --- subread.orig/src/HelperFunctions.c
 +++ subread/src/HelperFunctions.c
-@@ -771,6 +771,9 @@
- #ifdef FREEBSD
+@@ -773,6 +773,9 @@
+ #if defined(FREEBSD) || defined(__MINGW32__)
  	return 1;
  #else
 +#ifdef KFREEBSD
@@ -12,7 +12,7 @@ From: Alex Mestiashvili <alex at biotec.tu-dresden.de>
  #ifdef MACOS
      int         mib[6], x1, ret = 1;
  	size_t		len;
-@@ -861,6 +864,7 @@
+@@ -863,6 +866,7 @@
  	return 1;
  #endif
  #endif

-- 
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