[med-svn] r15701 - in trunk/packages/bitseq/trunk/debian: . patches

Andreas Tille tille at moszumanska.debian.org
Wed Jan 1 18:45:43 UTC 2014 

Author: tille
Date: 2014-01-01 18:45:43 +0000 (Wed, 01 Jan 2014)
New Revision: 15701

Added:
   trunk/packages/bitseq/trunk/debian/patches/link_against_system_samtools.patch
Removed:
   trunk/packages/bitseq/trunk/debian/patches/link_against_system_samtools
Modified:
   trunk/packages/bitseq/trunk/debian/control
   trunk/packages/bitseq/trunk/debian/patches/series
Log:
Add hardening options


Modified: trunk/packages/bitseq/trunk/debian/control
===================================================================
--- trunk/packages/bitseq/trunk/debian/control	2014-01-01 18:34:23 UTC (rev 15700)
+++ trunk/packages/bitseq/trunk/debian/control	2014-01-01 18:45:43 UTC (rev 15701)
@@ -17,7 +17,7 @@
 Architecture: any
 Depends: ${shlibs:Depends},
          ${misc:Depends},
-         python-minimal
+         python
 Suggests: samtools
 Description: Bayesian Inference of Transcripts from Sequencing Data
  BitSeq is an application for inferring expression levels of individual

Deleted: trunk/packages/bitseq/trunk/debian/patches/link_against_system_samtools
===================================================================
--- trunk/packages/bitseq/trunk/debian/patches/link_against_system_samtools	2014-01-01 18:34:23 UTC (rev 15700)
+++ trunk/packages/bitseq/trunk/debian/patches/link_against_system_samtools	2014-01-01 18:45:43 UTC (rev 15701)
@@ -1,51 +0,0 @@
-Author: Tim Booth <tbooth at ceh.ac.uk>
-Last-Update: Wed, 01 Jan 2014 19:04:47 +0100 (by Andreas Tille)
-Description: link against Debian packaged samtools
-
---- BitSeq-0.7.0.orig/ReadDistribution.h
-+++ BitSeq-0.7.0/ReadDistribution.h
-@@ -21,8 +21,8 @@
- 
- #else
- 
--#include "bam.h"
--#include "sam.h"
-+#include <samtools/bam.h>
-+#include <samtools/sam.h>
- 
- //#define bam_init1() ((bam1_t*)calloc(1, sizeof(bam1_t)))
- /*
---- BitSeq-0.7.0.orig/Makefile
-+++ BitSeq-0.7.0/Makefile
-@@ -63,8 +63,8 @@
- getWithinGeneExpression: getWithinGeneExpression.cpp $(COMMON_DEPS) PosteriorSamples.o TranscriptInfo.o
- 	$(CXX) $(CXXFLAGS) $(LDFLAGS) getWithinGeneExpression.cpp $(COMMON_DEPS) PosteriorSamples.o TranscriptInfo.o -o getWithinGeneExpression
- 
--parseAlignment: parseAlignment.cpp $(COMMON_DEPS) ReadDistribution.o samtools/sam.o TranscriptExpression.o TranscriptInfo.o TranscriptSequence.o
--	$(CXX) $(CXXFLAGS) $(OPENMP) $(LDFLAGS) -pthread -Isamtools parseAlignment.cpp $(COMMON_DEPS) ReadDistribution.o samtools/*.o TranscriptExpression.o TranscriptInfo.o TranscriptSequence.o -lz -o parseAlignment
-+parseAlignment: parseAlignment.cpp $(COMMON_DEPS) ReadDistribution.o TranscriptExpression.o TranscriptInfo.o TranscriptSequence.o
-+	$(CXX) $(CXXFLAGS) $(OPENMP) $(LDFLAGS) -pthread parseAlignment.cpp $(COMMON_DEPS) ReadDistribution.o TranscriptExpression.o TranscriptInfo.o TranscriptSequence.o -lz -lbam -o parseAlignment
- 
- transposeLargeFile: transposeLargeFile.cpp $(COMMON_DEPS) transposeFiles.o
- 	$(CXX) $(CXXFLAGS) $(LDFLAGS) transposeLargeFile.cpp $(COMMON_DEPS) transposeFiles.o -o transposeLargeFile
-@@ -92,7 +92,7 @@
- 	$(CXX) $(CXXFLAGS) -ffunction-sections -fdata-sections -c PosteriorSamples.cpp
- 
- ReadDistribution.o: ReadDistribution.cpp ReadDistribution.h TranscriptExpression.h TranscriptInfo.h TranscriptSequence.h 
--	$(CXX) $(CXXFLAGS) $(OPENMP) -Isamtools -c ReadDistribution.cpp
-+	$(CXX) $(CXXFLAGS) $(OPENMP) -c ReadDistribution.cpp
- 
- Sampler.o: Sampler.cpp Sampler.h GibbsParameters.h
- 	$(CXX) $(CXXFLAGS) $(BOOSTFLAGS) -c Sampler.cpp
-@@ -116,10 +116,7 @@
- asa103/asa103.o:
- 	make --directory asa103
- 
--samtools/sam.o:
--	make --directory samtools
--
- # CLEAN:
- clean:
--	rm asa103/*.o samtools/*.o *.o $(PROGRAMS)
-+	rm -f asa103/*.o samtools/*.o *.o $(PROGRAMS)
- 

Copied: trunk/packages/bitseq/trunk/debian/patches/link_against_system_samtools.patch (from rev 15698, trunk/packages/bitseq/trunk/debian/patches/link_against_system_samtools)
===================================================================
--- trunk/packages/bitseq/trunk/debian/patches/link_against_system_samtools.patch	                        (rev 0)
+++ trunk/packages/bitseq/trunk/debian/patches/link_against_system_samtools.patch	2014-01-01 18:45:43 UTC (rev 15701)
@@ -0,0 +1,51 @@
+Author: Tim Booth <tbooth at ceh.ac.uk>
+Last-Update: Wed, 01 Jan 2014 19:04:47 +0100 (by Andreas Tille)
+Description: link against Debian packaged samtools
+
+--- BitSeq-0.7.0.orig/ReadDistribution.h
++++ BitSeq-0.7.0/ReadDistribution.h
+@@ -21,8 +21,8 @@
+ 
+ #else
+ 
+-#include "bam.h"
+-#include "sam.h"
++#include <samtools/bam.h>
++#include <samtools/sam.h>
+ 
+ //#define bam_init1() ((bam1_t*)calloc(1, sizeof(bam1_t)))
+ /*
+--- BitSeq-0.7.0.orig/Makefile
++++ BitSeq-0.7.0/Makefile
+@@ -63,8 +63,8 @@
+ getWithinGeneExpression: getWithinGeneExpression.cpp $(COMMON_DEPS) PosteriorSamples.o TranscriptInfo.o
+ 	$(CXX) $(CXXFLAGS) $(LDFLAGS) getWithinGeneExpression.cpp $(COMMON_DEPS) PosteriorSamples.o TranscriptInfo.o -o getWithinGeneExpression
+ 
+-parseAlignment: parseAlignment.cpp $(COMMON_DEPS) ReadDistribution.o samtools/sam.o TranscriptExpression.o TranscriptInfo.o TranscriptSequence.o
+-	$(CXX) $(CXXFLAGS) $(OPENMP) $(LDFLAGS) -pthread -Isamtools parseAlignment.cpp $(COMMON_DEPS) ReadDistribution.o samtools/*.o TranscriptExpression.o TranscriptInfo.o TranscriptSequence.o -lz -o parseAlignment
++parseAlignment: parseAlignment.cpp $(COMMON_DEPS) ReadDistribution.o TranscriptExpression.o TranscriptInfo.o TranscriptSequence.o
++	$(CXX) $(CXXFLAGS) $(OPENMP) $(LDFLAGS) -pthread parseAlignment.cpp $(COMMON_DEPS) ReadDistribution.o TranscriptExpression.o TranscriptInfo.o TranscriptSequence.o -lz -lbam -o parseAlignment
+ 
+ transposeLargeFile: transposeLargeFile.cpp $(COMMON_DEPS) transposeFiles.o
+ 	$(CXX) $(CXXFLAGS) $(LDFLAGS) transposeLargeFile.cpp $(COMMON_DEPS) transposeFiles.o -o transposeLargeFile
+@@ -92,7 +92,7 @@
+ 	$(CXX) $(CXXFLAGS) -ffunction-sections -fdata-sections -c PosteriorSamples.cpp
+ 
+ ReadDistribution.o: ReadDistribution.cpp ReadDistribution.h TranscriptExpression.h TranscriptInfo.h TranscriptSequence.h 
+-	$(CXX) $(CXXFLAGS) $(OPENMP) -Isamtools -c ReadDistribution.cpp
++	$(CXX) $(CXXFLAGS) $(OPENMP) -c ReadDistribution.cpp
+ 
+ Sampler.o: Sampler.cpp Sampler.h GibbsParameters.h
+ 	$(CXX) $(CXXFLAGS) $(BOOSTFLAGS) -c Sampler.cpp
+@@ -116,10 +116,7 @@
+ asa103/asa103.o:
+ 	make --directory asa103
+ 
+-samtools/sam.o:
+-	make --directory samtools
+-
+ # CLEAN:
+ clean:
+-	rm asa103/*.o samtools/*.o *.o $(PROGRAMS)
++	rm -f asa103/*.o samtools/*.o *.o $(PROGRAMS)
+ 

Modified: trunk/packages/bitseq/trunk/debian/patches/series
===================================================================
--- trunk/packages/bitseq/trunk/debian/patches/series	2014-01-01 18:34:23 UTC (rev 15700)
+++ trunk/packages/bitseq/trunk/debian/patches/series	2014-01-01 18:45:43 UTC (rev 15701)
@@ -1 +1,2 @@
-link_against_system_samtools
+link_against_system_samtools.patch
+hardening.patch

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