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=
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