[med-svn] r18835 - trunk/packages/vsearch/trunk/debian/patches

Sat Feb 21 19:04:04 UTC 2015

Author: tille
Date: 2015-02-21 19:04:03 +0000 (Sat, 21 Feb 2015)
New Revision: 18835

Modified:
   trunk/packages/vsearch/trunk/debian/patches/fix_optimisation_flags.patch
   trunk/packages/vsearch/trunk/debian/patches/hardening.patch
   trunk/packages/vsearch/trunk/debian/patches/sysconf_memory_sizing.patch
   trunk/packages/vsearch/trunk/debian/patches/x86_spezific_opts.patch
Log:
Refresh patches


Modified: trunk/packages/vsearch/trunk/debian/patches/fix_optimisation_flags.patch
===================================================================

--- trunk/packages/vsearch/trunk/debian/patches/fix_optimisation_flags.patch	2015-02-21 17:50:03 UTC (rev 18834)
+++ trunk/packages/vsearch/trunk/debian/patches/fix_optimisation_flags.patch	2015-02-21 19:04:03 UTC (rev 18835)
@@ -4,9 +4,9 @@
 Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2015-February/031414.html
 Description: Drop -msse2 flag
 
---- a/src/Makefile.BZLIB
-+++ b/src/Makefile.BZLIB
-@@ -27,7 +27,7 @@ WARN=-Wall -Wsign-compare
+--- vsearch-1.1.1.orig/src/Makefile.BZLIB
++++ vsearch-1.1.1/src/Makefile.BZLIB
+@@ -27,7 +27,7 @@
  #WARN=-Weverything
  
  CXX=g++
@@ -15,9 +15,9 @@
  LINKFLAGS=$(PROFILING)
  LIBS=-lpthread -lbz2
  
---- a/src/Makefile.ZLIB
-+++ b/src/Makefile.ZLIB
-@@ -27,7 +27,7 @@ WARN=-Wall -Wsign-compare
+--- vsearch-1.1.1.orig/src/Makefile.ZLIB
++++ vsearch-1.1.1/src/Makefile.ZLIB
+@@ -27,7 +27,7 @@
  #WARN=-Weverything
  
  CXX=g++
@@ -26,9 +26,9 @@
  LINKFLAGS=$(PROFILING)
  LIBS=-lpthread -lz
  
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -27,7 +27,7 @@ WARN=-Wall -Wsign-compare
+--- vsearch-1.1.1.orig/src/Makefile
++++ vsearch-1.1.1/src/Makefile
+@@ -27,7 +27,7 @@
  #WARN=-Weverything
  
  CXX=g++

Modified: trunk/packages/vsearch/trunk/debian/patches/hardening.patch
===================================================================
--- trunk/packages/vsearch/trunk/debian/patches/hardening.patch	2015-02-21 17:50:03 UTC (rev 18834)
+++ trunk/packages/vsearch/trunk/debian/patches/hardening.patch	2015-02-21 19:04:03 UTC (rev 18835)
@@ -3,9 +3,9 @@
 Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2015-February/031414.html
 Description: Propagate hardening options
 
---- a/src/Makefile.BZLIB
-+++ b/src/Makefile.BZLIB
-@@ -34,7 +34,7 @@ endif
+--- vsearch-1.1.1.orig/src/Makefile.BZLIB
++++ vsearch-1.1.1/src/Makefile.BZLIB
+@@ -34,7 +34,7 @@
  
  CXX=g++
  CXXFLAGS=-O3 -DHAVE_BZLIB $(MTUNE) -Icityhash $(WARN) $(PROFILING)
@@ -14,9 +14,9 @@
  LIBS=-lpthread -lbz2
  
  PROG=vsearch-bz
---- a/src/Makefile.ZLIB
-+++ b/src/Makefile.ZLIB
-@@ -34,7 +34,7 @@ endif
+--- vsearch-1.1.1.orig/src/Makefile.ZLIB
++++ vsearch-1.1.1/src/Makefile.ZLIB
+@@ -34,7 +34,7 @@
  
  CXX=g++
  CXXFLAGS=-O3 -DHAVE_ZLIB $(MTUNE) -Icityhash $(WARN) $(PROFILING)
@@ -25,9 +25,9 @@
  LIBS=-lpthread -lz
  
  PROG=vsearch-gz
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -34,7 +34,7 @@ endif
+--- vsearch-1.1.1.orig/src/Makefile
++++ vsearch-1.1.1/src/Makefile
+@@ -34,7 +34,7 @@
  
  CXX=g++
  CXXFLAGS=-O3 $(MTUNE) -Icityhash $(WARN) $(PROFILING)

Modified: trunk/packages/vsearch/trunk/debian/patches/sysconf_memory_sizing.patch
===================================================================
--- trunk/packages/vsearch/trunk/debian/patches/sysconf_memory_sizing.patch	2015-02-21 17:50:03 UTC (rev 18834)
+++ trunk/packages/vsearch/trunk/debian/patches/sysconf_memory_sizing.patch	2015-02-21 19:04:03 UTC (rev 18835)
@@ -7,8 +7,8 @@
 Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2015-February/031414.html
 Last-Update: Thu, 19 Feb 2015 16:07:52 +0100 (Andreas Tille <tille at debian.org>)
 
---- a/src/arch.cc
-+++ b/src/arch.cc
+--- vsearch-1.1.1.orig/src/arch.cc
++++ vsearch-1.1.1/src/arch.cc
 @@ -21,6 +21,8 @@
  
  #include "vsearch.h"
@@ -18,7 +18,7 @@
  unsigned long arch_get_memused()
  {
    struct rusage r_usage;
-@@ -63,7 +65,15 @@ unsigned long arch_get_memtotal()
+@@ -63,7 +65,15 @@
    if(-1 == sysctl(mib, 2, &ram, &length, NULL, 0))
      fatal("Cannot determine amount of RAM");
    return ram;

Modified: trunk/packages/vsearch/trunk/debian/patches/x86_spezific_opts.patch
===================================================================
--- trunk/packages/vsearch/trunk/debian/patches/x86_spezific_opts.patch	2015-02-21 17:50:03 UTC (rev 18834)
+++ trunk/packages/vsearch/trunk/debian/patches/x86_spezific_opts.patch	2015-02-21 19:04:03 UTC (rev 18835)
@@ -4,9 +4,9 @@
 Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2015-February/031414.html
 Description: Conditional use of -mtune flag
 
---- a/src/Makefile.BZLIB
-+++ b/src/Makefile.BZLIB
-@@ -26,8 +26,14 @@ PROFILING=-g
+--- vsearch-1.1.1.orig/src/Makefile.BZLIB
++++ vsearch-1.1.1/src/Makefile.BZLIB
+@@ -26,8 +26,14 @@
  WARN=-Wall -Wsign-compare
  #WARN=-Weverything
  
@@ -22,9 +22,9 @@
  LINKFLAGS=$(PROFILING)
  LIBS=-lpthread -lbz2
  
---- a/src/Makefile.ZLIB
-+++ b/src/Makefile.ZLIB
-@@ -26,8 +26,14 @@ PROFILING=-g
+--- vsearch-1.1.1.orig/src/Makefile.ZLIB
++++ vsearch-1.1.1/src/Makefile.ZLIB
+@@ -26,8 +26,14 @@
  WARN=-Wall -Wsign-compare
  #WARN=-Weverything
  
@@ -40,9 +40,9 @@
  LINKFLAGS=$(PROFILING)
  LIBS=-lpthread -lz
  
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -26,8 +26,14 @@ PROFILING=-g
+--- vsearch-1.1.1.orig/src/Makefile
++++ vsearch-1.1.1/src/Makefile
+@@ -26,8 +26,14 @@
  WARN=-Wall -Wsign-compare
  #WARN=-Weverything
  


