[med-svn] r14274 - trunk/packages/mothur/trunk/debian/patches

[Andreas Tille]

Author: tille
Date: 2013-07-30 12:39:10 +0000 (Tue, 30 Jul 2013)
New Revision: 14274

Modified:
   trunk/packages/mothur/trunk/debian/patches/build_without_tty.patch
   trunk/packages/mothur/trunk/debian/patches/catchall_fix.patch
   trunk/packages/mothur/trunk/debian/patches/drop_sse_option.patch
   trunk/packages/mothur/trunk/debian/patches/makefile.patch
   trunk/packages/mothur/trunk/debian/patches/no_lcurses.patch
   trunk/packages/mothur/trunk/debian/patches/uchime_link_dynamically
Log:
Refresh patches


Modified: trunk/packages/mothur/trunk/debian/patches/build_without_tty.patch
===================================================================
--- trunk/packages/mothur/trunk/debian/patches/build_without_tty.patch	2013-07-30 12:35:22 UTC (rev 14273)
+++ trunk/packages/mothur/trunk/debian/patches/build_without_tty.patch	2013-07-30 12:39:10 UTC (rev 14274)
@@ -1,6 +1,6 @@
 --- a/uchime_src/mk
 +++ b/uchime_src/mk
-@@ -6,7 +6,7 @@
+@@ -6,7 +6,7 @@ rm -f *.o mk.stdout mk.stderr tmp.stderr
  
  for CPPName in $CPPNames
  do

Modified: trunk/packages/mothur/trunk/debian/patches/catchall_fix.patch
===================================================================
--- trunk/packages/mothur/trunk/debian/patches/catchall_fix.patch	2013-07-30 12:35:22 UTC (rev 14273)
+++ trunk/packages/mothur/trunk/debian/patches/catchall_fix.patch	2013-07-30 12:39:10 UTC (rev 14274)
@@ -4,7 +4,7 @@
 
 --- a/catchallcommand.cpp
 +++ b/catchallcommand.cpp
-@@ -190,6 +190,7 @@
+@@ -198,6 +198,7 @@ int CatchAllCommand::execute() {
  		
  		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
  		
@@ -12,7 +12,7 @@
  		//get location of catchall
  		path = m->argv;
  		path = path.substr(0, (path.find_last_of("othur")-5));
-@@ -238,6 +239,11 @@
+@@ -246,6 +247,11 @@ int CatchAllCommand::execute() {
          
  		//prepare full output directory
  		outputDir = m->getFullPathName(outputDir);

Modified: trunk/packages/mothur/trunk/debian/patches/drop_sse_option.patch
===================================================================
--- trunk/packages/mothur/trunk/debian/patches/drop_sse_option.patch	2013-07-30 12:35:22 UTC (rev 14273)
+++ trunk/packages/mothur/trunk/debian/patches/drop_sse_option.patch	2013-07-30 12:39:10 UTC (rev 14274)
@@ -4,7 +4,7 @@
 Description: Fix for FTBFS: cc1plus: error: unrecognized command line option '-msse2'
 --- a/uchime_src/mk
 +++ b/uchime_src/mk
-@@ -7,7 +7,7 @@
+@@ -7,7 +7,7 @@ rm -f *.o mk.stdout mk.stderr tmp.stderr
  for CPPName in $CPPNames
  do
    echo $CPPName >> /dev/tty

Modified: trunk/packages/mothur/trunk/debian/patches/makefile.patch
===================================================================
--- trunk/packages/mothur/trunk/debian/patches/makefile.patch	2013-07-30 12:35:22 UTC (rev 14273)
+++ trunk/packages/mothur/trunk/debian/patches/makefile.patch	2013-07-30 12:39:10 UTC (rev 14274)
@@ -3,7 +3,7 @@
   Set -m64 but not -march=native for 64-bit build
 --- a/makefile
 +++ b/makefile
-@@ -21,14 +21,15 @@
+@@ -21,14 +21,15 @@ FORTAN_COMPILER = gfortran
  FORTRAN_FLAGS = 
  
  # Optimize to level 3:
@@ -21,7 +21,7 @@
  	
  	#if you using cygwin to build Windows the following line
  	#CXX = x86_64-w64-mingw32-g++
-@@ -38,6 +39,10 @@
+@@ -38,6 +39,10 @@ ifeq  ($(strip $(64BIT_VERSION)),yes)
  
  	#if you are a linux user use the following line
  	#CXXFLAGS += -mtune=native -march=native -m64
@@ -31,8 +31,8 @@
 +	CXXFLAGS += -m64
  	
  	CXXFLAGS += -DBIT_VERSION 
-     	FORTRAN_FLAGS = -m64
-@@ -120,4 +125,3 @@
+     FORTRAN_FLAGS = -m64
+@@ -120,4 +125,3 @@ install : mothur
  clean :
  	@rm -f $(OBJECTS)
  	@rm -f uchime

Modified: trunk/packages/mothur/trunk/debian/patches/no_lcurses.patch
===================================================================
--- trunk/packages/mothur/trunk/debian/patches/no_lcurses.patch	2013-07-30 12:35:22 UTC (rev 14273)
+++ trunk/packages/mothur/trunk/debian/patches/no_lcurses.patch	2013-07-30 12:39:10 UTC (rev 14274)
@@ -3,7 +3,7 @@
 Dscription: There is no need to link against lncurses because its symbols are not used
 --- a/makefile
 +++ b/makefile
-@@ -63,8 +63,7 @@
+@@ -68,8 +68,7 @@ endif
  ifeq  ($(strip $(USEREADLINE)),yes)
      CXXFLAGS += -DUSE_READLINE
      LIBS = \

Modified: trunk/packages/mothur/trunk/debian/patches/uchime_link_dynamically
===================================================================
--- trunk/packages/mothur/trunk/debian/patches/uchime_link_dynamically	2013-07-30 12:35:22 UTC (rev 14273)
+++ trunk/packages/mothur/trunk/debian/patches/uchime_link_dynamically	2013-07-30 12:39:10 UTC (rev 14274)
@@ -3,7 +3,7 @@
 
 --- a/uchime_src/mk
 +++ b/uchime_src/mk
-@@ -14,9 +14,9 @@
+@@ -14,9 +14,9 @@ do
  done
  
  LINK_OPTS=