[med-svn] r10297 - trunk/packages/probcons/trunk/debian/patches

Andreas Tille tille at alioth.debian.org
Tue Apr 3 20:32:52 UTC 2012 

Author: tille
Date: 2012-04-03 20:32:52 +0000 (Tue, 03 Apr 2012)
New Revision: 10297

Added:
   trunk/packages/probcons/trunk/debian/patches/10_add-RNA-in-Makefile.patch
   trunk/packages/probcons/trunk/debian/patches/11-Rename-programs-in-Makefile.patch
Removed:
   trunk/packages/probcons/trunk/debian/patches/10_add-RNA-in-Makefile.diff
   trunk/packages/probcons/trunk/debian/patches/11-Rename-programs-in-Makefile.diff
Modified:
   trunk/packages/probcons/trunk/debian/patches/series
Log:
Patches not executable (so worked arround svn issue to not be able to handle this correctly and rm + recreate - now with the extension patch)


Deleted: trunk/packages/probcons/trunk/debian/patches/10_add-RNA-in-Makefile.diff
===================================================================
--- trunk/packages/probcons/trunk/debian/patches/10_add-RNA-in-Makefile.diff	2012-04-03 20:27:04 UTC (rev 10296)
+++ trunk/packages/probcons/trunk/debian/patches/10_add-RNA-in-Makefile.diff	2012-04-03 20:32:52 UTC (rev 10297)
@@ -1,40 +0,0 @@
-The purpose of this patch is to add a rule for the building of probcons-RNA.
-
---- probcons-1.10/Makefile	2006-05-07 13:45:26.000000000 +0900
-+++ probcons-1.10.modified/Makefile	2006-05-07 13:51:20.000000000 +0900
-@@ -16,6 +16,7 @@
- ################################################################################
- 
- OTHERFLAGS = -DNumInsertStates=2 -DVERSION="1.12"
-+OTHERFLAGS-RNA = -DNumInsertStates=1 -DVERSION="1.12"
- 
- # debug mode    
- #CXXFLAGS = -g -W -Wall -pedantic -DENABLE_CHECKS -fno-inline $(OTHERFLAGS)
-@@ -25,13 +26,16 @@
- 
- # release mode
- #CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -mmmx -msse -msse2 -mfpmath=sse -march=pentium4 -mcpu=pentium4 -funroll-loops -fomit-frame-pointer 
-+
- CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -funroll-loops
-+CXXFLAGS-RNA = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS-RNA) -funroll-loops
-+
- 
- ################################################################################
- # 3) Dependencies
- ################################################################################
- 
--TARGETS = probcons compare project makegnuplot
-+TARGETS = probcons probcons-RNA compare project makegnuplot
- 
- .PHONY : all
- all : $(TARGETS)
-@@ -42,6 +46,9 @@
- compare : MultiSequence.h Sequence.h FileBuffer.h SafeVector.h CompareToRef.cc
- 	$(CXX) $(CXXFLAGS) -o compare CompareToRef.cc
- 
-+probcons-RNA : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults-RNA.h SafeVector.h Main-RNA.cc
-+	$(CXX) $(CXXFLAGS-RNA) -lm -o probcons-RNA Main-RNA.cc 
-+
- fixref : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h FixRef.cc
- 	$(CXX) $(CXXFLAGS) -o fixref FixRef.cc
- 

Added: trunk/packages/probcons/trunk/debian/patches/10_add-RNA-in-Makefile.patch
===================================================================
--- trunk/packages/probcons/trunk/debian/patches/10_add-RNA-in-Makefile.patch	                        (rev 0)
+++ trunk/packages/probcons/trunk/debian/patches/10_add-RNA-in-Makefile.patch	2012-04-03 20:32:52 UTC (rev 10297)
@@ -0,0 +1,40 @@
+The purpose of this patch is to add a rule for the building of probcons-RNA.
+
+--- probcons-1.10/Makefile	2006-05-07 13:45:26.000000000 +0900
++++ probcons-1.10.modified/Makefile	2006-05-07 13:51:20.000000000 +0900
+@@ -16,6 +16,7 @@
+ ################################################################################
+ 
+ OTHERFLAGS = -DNumInsertStates=2 -DVERSION="1.12"
++OTHERFLAGS-RNA = -DNumInsertStates=1 -DVERSION="1.12"
+ 
+ # debug mode    
+ #CXXFLAGS = -g -W -Wall -pedantic -DENABLE_CHECKS -fno-inline $(OTHERFLAGS)
+@@ -25,13 +26,16 @@
+ 
+ # release mode
+ #CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -mmmx -msse -msse2 -mfpmath=sse -march=pentium4 -mcpu=pentium4 -funroll-loops -fomit-frame-pointer 
++
+ CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -funroll-loops
++CXXFLAGS-RNA = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS-RNA) -funroll-loops
++
+ 
+ ################################################################################
+ # 3) Dependencies
+ ################################################################################
+ 
+-TARGETS = probcons compare project makegnuplot
++TARGETS = probcons probcons-RNA compare project makegnuplot
+ 
+ .PHONY : all
+ all : $(TARGETS)
+@@ -42,6 +46,9 @@
+ compare : MultiSequence.h Sequence.h FileBuffer.h SafeVector.h CompareToRef.cc
+ 	$(CXX) $(CXXFLAGS) -o compare CompareToRef.cc
+ 
++probcons-RNA : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults-RNA.h SafeVector.h Main-RNA.cc
++	$(CXX) $(CXXFLAGS-RNA) -lm -o probcons-RNA Main-RNA.cc 
++
+ fixref : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h FixRef.cc
+ 	$(CXX) $(CXXFLAGS) -o fixref FixRef.cc
+ 

Deleted: trunk/packages/probcons/trunk/debian/patches/11-Rename-programs-in-Makefile.diff
===================================================================
--- trunk/packages/probcons/trunk/debian/patches/11-Rename-programs-in-Makefile.diff	2012-04-03 20:27:04 UTC (rev 10296)
+++ trunk/packages/probcons/trunk/debian/patches/11-Rename-programs-in-Makefile.diff	2012-04-03 20:32:52 UTC (rev 10297)
@@ -1,41 +0,0 @@
-The purpose of this patch is to rename programs with a too generic name, to avoid
-conflicts on file names.
-
---- probcons-1.10-orig/Makefile	2006-06-04 22:01:10.000000000 +0900
-+++ probcons-1.10/Makefile	2006-06-04 21:53:30.000000000 +0900
-@@ -35,7 +35,7 @@
- # 3) Dependencies
- ################################################################################
- 
--TARGETS = probcons probcons-RNA compare project makegnuplot
-+TARGETS = probcons probcons-RNA pc-compare pc-project pc-makegnuplot
- 
- .PHONY : all
- all : $(TARGETS)
-@@ -43,8 +43,8 @@
- probcons : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h Main.cc
- 	$(CXX) $(CXXFLAGS) -lm -o probcons Main.cc 
- 
--compare : MultiSequence.h Sequence.h FileBuffer.h SafeVector.h CompareToRef.cc
--	$(CXX) $(CXXFLAGS) -o compare CompareToRef.cc
-+pc-compare : MultiSequence.h Sequence.h FileBuffer.h SafeVector.h CompareToRef.cc
-+	$(CXX) $(CXXFLAGS) -o pc-compare CompareToRef.cc
- 
- probcons-RNA : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults-RNA.h SafeVector.h Main-RNA.cc
- 	$(CXX) $(CXXFLAGS-RNA) -lm -o probcons-RNA Main-RNA.cc 
-@@ -52,11 +52,11 @@
- fixref : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h FixRef.cc
- 	$(CXX) $(CXXFLAGS) -o fixref FixRef.cc
- 
--project : MultiSequence.h Sequence.h SafeVector.h ProjectPairwise.cc
--	$(CXX) $(CXXFLAGS) -o project ProjectPairwise.cc
-+pc-project : MultiSequence.h Sequence.h SafeVector.h ProjectPairwise.cc
-+	$(CXX) $(CXXFLAGS) -o pc-project ProjectPairwise.cc
- 
--makegnuplot : MakeGnuPlot.cc
--	$(CXX) $(CXXFLAGS) -o makegnuplot MakeGnuPlot.cc
-+pc-makegnuplot : MakeGnuPlot.cc
-+	$(CXX) $(CXXFLAGS) -o pc-makegnuplot MakeGnuPlot.cc
- 
- .PHONY : clean
- clean:

Added: trunk/packages/probcons/trunk/debian/patches/11-Rename-programs-in-Makefile.patch
===================================================================
--- trunk/packages/probcons/trunk/debian/patches/11-Rename-programs-in-Makefile.patch	                        (rev 0)
+++ trunk/packages/probcons/trunk/debian/patches/11-Rename-programs-in-Makefile.patch	2012-04-03 20:32:52 UTC (rev 10297)
@@ -0,0 +1,41 @@
+The purpose of this patch is to rename programs with a too generic name, to avoid
+conflicts on file names.
+
+--- probcons-1.10-orig/Makefile	2006-06-04 22:01:10.000000000 +0900
++++ probcons-1.10/Makefile	2006-06-04 21:53:30.000000000 +0900
+@@ -35,7 +35,7 @@
+ # 3) Dependencies
+ ################################################################################
+ 
+-TARGETS = probcons probcons-RNA compare project makegnuplot
++TARGETS = probcons probcons-RNA pc-compare pc-project pc-makegnuplot
+ 
+ .PHONY : all
+ all : $(TARGETS)
+@@ -43,8 +43,8 @@
+ probcons : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h Main.cc
+ 	$(CXX) $(CXXFLAGS) -lm -o probcons Main.cc 
+ 
+-compare : MultiSequence.h Sequence.h FileBuffer.h SafeVector.h CompareToRef.cc
+-	$(CXX) $(CXXFLAGS) -o compare CompareToRef.cc
++pc-compare : MultiSequence.h Sequence.h FileBuffer.h SafeVector.h CompareToRef.cc
++	$(CXX) $(CXXFLAGS) -o pc-compare CompareToRef.cc
+ 
+ probcons-RNA : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults-RNA.h SafeVector.h Main-RNA.cc
+ 	$(CXX) $(CXXFLAGS-RNA) -lm -o probcons-RNA Main-RNA.cc 
+@@ -52,11 +52,11 @@
+ fixref : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h FixRef.cc
+ 	$(CXX) $(CXXFLAGS) -o fixref FixRef.cc
+ 
+-project : MultiSequence.h Sequence.h SafeVector.h ProjectPairwise.cc
+-	$(CXX) $(CXXFLAGS) -o project ProjectPairwise.cc
++pc-project : MultiSequence.h Sequence.h SafeVector.h ProjectPairwise.cc
++	$(CXX) $(CXXFLAGS) -o pc-project ProjectPairwise.cc
+ 
+-makegnuplot : MakeGnuPlot.cc
+-	$(CXX) $(CXXFLAGS) -o makegnuplot MakeGnuPlot.cc
++pc-makegnuplot : MakeGnuPlot.cc
++	$(CXX) $(CXXFLAGS) -o pc-makegnuplot MakeGnuPlot.cc
+ 
+ .PHONY : clean
+ clean:

Modified: trunk/packages/probcons/trunk/debian/patches/series
===================================================================
--- trunk/packages/probcons/trunk/debian/patches/series	2012-04-03 20:27:04 UTC (rev 10296)
+++ trunk/packages/probcons/trunk/debian/patches/series	2012-04-03 20:32:52 UTC (rev 10297)
@@ -1,4 +1,4 @@
-10_add-RNA-in-Makefile.diff
-11-Rename-programs-in-Makefile.diff
+10_add-RNA-in-Makefile.patch
+11-Rename-programs-in-Makefile.patch
 fix-gcc-4.5-headers
 fix-gcc-4.6.patch

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