[med-svn] [subread] 03/05: Refresh and update patches

[Alex Mestiashvili]

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

commit ee4a168a4cbe1cc1d77ca25d8604bf1252dfbc4b
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Tue Mar 21 15:42:12 2017 +0100

    Refresh and update patches
---
 debian/patches/arch_specific_flags.patch | 19 +++++++++----------
 debian/patches/fix_ftbfs_kfreebsd.patch  |  4 ++--
 2 files changed, 11 insertions(+), 12 deletions(-)

diff --git a/debian/patches/arch_specific_flags.patch b/debian/patches/arch_specific_flags.patch
index 6de2c62..e52df1a 100644
--- a/debian/patches/arch_specific_flags.patch
+++ b/debian/patches/arch_specific_flags.patch
@@ -1,26 +1,25 @@
 Description: Inject architecture specific flags:
  - For amd64 and i386 add -mtune=generic and -msse3,
  - use -fsigned-char for all architectures and place it in the very beginning
-   of CFLAGS, otherwise test fail on architecrures with unsigned char 
+   of CFLAGS, otherwise test fail on architecrures with unsigned char
    signedness
  - Change -O9 to -O3 because -O levels higher than 3 have no effect
- - Append CFLAGS and LDFLAGS instead of hardcoding the values, this way the 
+ - Append CFLAGS and LDFLAGS instead of hardcoding the values, this way the
    hardening flags are set correctly
 Author: Alex Mestiashvili <alex at biotec.tu-dresden.de>
---- a/src/Makefile.Linux
-+++ b/src/Makefile.Linux
-@@ -2,10 +2,10 @@
- 
+--- subread.orig/src/Makefile.Linux
++++ subread/src/Makefile.Linux
+@@ -3,10 +3,10 @@
  include makefile.version
  
--OPT_LEVEL = 9
+ 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
--CC = gcc ${CCFLAGS} -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -mmmx -msse -msse2 -msse3 -fmessage-length=0 
-+OPT_LEVEL = 3
 +CCFLAGS += -O${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
-+CC = gcc ${CFLAGS} ${CPPFLAGS} ${CCFLAGS} -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0
+ 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} ${CFLAGS} ${CPPFLAGS} ${CCFLAGS} -ggdb -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 core-bigtable seek-zlib
diff --git a/debian/patches/fix_ftbfs_kfreebsd.patch b/debian/patches/fix_ftbfs_kfreebsd.patch
index 2b79fb4..e4307a6 100644
--- a/debian/patches/fix_ftbfs_kfreebsd.patch
+++ b/debian/patches/fix_ftbfs_kfreebsd.patch
@@ -2,7 +2,7 @@ Subject: Fix ftbfs on kfreebsd
 From: Alex Mestiashvili <alex at biotec.tu-dresden.de>
 --- subread.orig/src/HelperFunctions.c
 +++ subread/src/HelperFunctions.c
-@@ -770,6 +770,9 @@
+@@ -771,6 +771,9 @@
  #ifdef FREEBSD
  	return 1;
  #else
@@ -12,7 +12,7 @@ From: Alex Mestiashvili <alex at biotec.tu-dresden.de>
  #ifdef MACOS
      int         mib[6], x1, ret = 1;
  	size_t		len;
-@@ -860,6 +863,7 @@
+@@ -861,6 +864,7 @@
  	return 1;
  #endif
  #endif

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