[med-svn] [rna-star] 03/06: New upstream version + adapted patches

Andreas Tille tille at debian.org
Thu Dec 31 11:54:07 UTC 2015 

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository rna-star.

commit 0e2f079947b9100407b819c894156995eaab2368
Author: Andreas Tille <tille at debian.org>
Date:   Thu Dec 31 12:40:42 2015 +0100

    New upstream version + adapted patches
---
 debian/changelog                         |  5 ++--
 debian/patches/compilationstuff.patch    | 48 +++++++++++++++-----------------
 debian/patches/donotuse_own_htslib.patch | 44 ++++++++++++++---------------
 debian/patches/mips_shm_noreserve.patch  |  2 +-
 4 files changed, 49 insertions(+), 50 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index d8b175a..a7ef197 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,8 +1,9 @@
-rna-star (2.4.2a+dfsg-2) UNRELEASED; urgency=medium
+rna-star (2.5.0a+dfsg-1) UNRELEASED; urgency=medium
 
   * Packaging moved from svn to git
+  * New upstream version
 
- -- Andreas Tille <tille at debian.org>  Thu, 31 Dec 2015 12:16:39 +0100
+ -- Andreas Tille <tille at debian.org>  Thu, 31 Dec 2015 12:27:01 +0100
 
 rna-star (2.4.2a+dfsg-1) unstable; urgency=medium
 
diff --git a/debian/patches/compilationstuff.patch b/debian/patches/compilationstuff.patch
index d2594e7..419927e 100644
--- a/debian/patches/compilationstuff.patch
+++ b/debian/patches/compilationstuff.patch
@@ -4,7 +4,7 @@ Description: Setting some compile options, fix some gcc errors
 
 --- a/source/Parameters.h
 +++ b/source/Parameters.h
-@@ -56,7 +56,7 @@ class Parameters {
+@@ -60,7 +60,7 @@ class Parameters {
          int readFilesIndex;
          uint32 readFilesN;
          vector <string> readFilesIn, readFilesInTmp;
@@ -15,7 +15,7 @@ Description: Setting some compile options, fix some gcc errors
          vector <string> readFilesCommand;
 --- a/source/STAR.cpp
 +++ b/source/STAR.cpp
-@@ -361,7 +361,7 @@ int main(int argInN, char* argIn[]) {
+@@ -386,7 +386,7 @@ int main(int argInN, char* argIn[]) {
          vector <string> bamBinNamesV;
          for (uint32 ibin=0; ibin<nBins; ibin++) {
              
@@ -26,42 +26,40 @@ Description: Setting some compile options, fix some gcc errors
                  bamBinNamesV.pop_back();
 --- a/source/Makefile
 +++ b/source/Makefile
-@@ -18,29 +18,29 @@ OBJECTS = SharedMemory.o PackedArray.o S
-         bam_cat.o
- SOURCES := $(wildcard *.cpp) $(wildcard *.c)
+@@ -12,17 +12,17 @@ CXXFLAGSextra ?=
+ CXX ?= g++
  
--LDFLAGS := -pthread -Bstatic -lhts -Bdynamic -lz -lrt
+ # pre-defined flags
+-LDFLAGS_shared := -pthread -Bstatic -lhts -Bdynamic -lz -lrt
 -LDFLAGS_static := -static -static-libgcc -pthread -Lhtslib -lhts -lz
-+LDFLAGS := -pthread -lhts -Bdynamic $(LDFLAGS_add)
-+LDFLAGS_static += -static -static-libgcc -pthread -lhts -lz
++LDFLAGS_shared := -pthread -Bstatic -lhts -Bdynamic $(LDFLAGS_add)
++LDFLAGS_static := -static -static-libgcc -pthread -lhts -lz
  LDFLAGS_Mac :=-pthread -lz htslib/libhts.a
  LDFLAGS_Mac_static :=-pthread -lz -static-libgcc htslib/libhts.a
- 
--LDFLAGS_gdb := $(LDFLAGS_static)
--LDFLAGS_gdb := $(LDFLAGS)
-+LDFLAGS_gdb += $(LDFLAGS_static)
-+LDFLAGS_gdb += $(LDFLAGS)
+-LDFLAGS_gdb := $(LDFLAGS_shared)
++LDFLAGS_gdb += $(LDFLAGS_shared)
  
  COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE="$(shell echo `date` $(HOSTNAME):`pwd`)"'
- EXTRAFLAGS := 
  
--CCFLAGS_common := -pipe -std=c++0x -Wall -Wextra -fopenmp $(COMPTIMEPLACE) $(OPTIMFLAGS) $(OPTIMFLAGS1) $(EXTRAFLAGS)
--CCFLAGS_main := -O3 $(CCFLAGS_common)
--CCFLAGS_gdb :=  -O0 -g $(CCFLAGS_common)
-+CCFLAGS_common := -pipe -std=c++0x -Wall -Wextra -fopenmp $(COMPTIMEPLACE) $(OPTIMFLAGS) $(OPTIMFLAGS1) $(EXTRAFLAGS) $(CCFLAGS_common_add)
-+CCFLAGS_main += -O3 $(CCFLAGS_common)
-+CCFLAGS_gdb +=  -O0 -g $(CCFLAGS_common)
+-CXXFLAGS_common := -pipe -std=c++11 -Wall -Wextra -fopenmp $(COMPTIMEPLACE)
+-CXXFLAGS_main := -O3 $(CXXFLAGS_common)
+-CXXFLAGS_gdb :=  -O0 -g $(CXXFLAGS_common)
++CXXFLAGS_common := -pipe -std=c++11 -Wall -Wextra -fopenmp $(COMPTIMEPLACE) $(CCFLAGS_common_add)
++CXXFLAGS_main += -O3 $(CXXFLAGS_common)
++CXXFLAGS_gdb +=  -O0 -g $(CXXFLAGS_common)
+ 
+ CFLAGS := -O3 -pipe -Wall -Wextra $(CFLAGS)
  
- CXX ?=g++
+@@ -54,10 +54,10 @@ SOURCES := $(wildcard *.cpp) $(wildcard
  
  
  %.o : %.cpp
--	$(CXX) -c $(CCFLAGS) $<
-+	$(CXX) -c $(CCFLAGS) $(COMPTIMEPLACE) $<
+-	$(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $<
++	$(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(COMPTIMEPLACE) $<
  
  %.o : %.c
--	$(CXX) -c $(CCFLAGS) $<
-+	$(CXX) -c $(CCFLAGS) $(COMPTIMEPLACE) $<
+-	$(CXX) -c $(CPPFLAGS) $(CFLAGS) $<
++	$(CXX) -c $(CPPFLAGS) $(CFLAGS) $(COMPTIMEPLACE) $<
  
  all: STAR
  
diff --git a/debian/patches/donotuse_own_htslib.patch b/debian/patches/donotuse_own_htslib.patch
index 1e1c180..ad30c2c 100644
--- a/debian/patches/donotuse_own_htslib.patch
+++ b/debian/patches/donotuse_own_htslib.patch
@@ -4,16 +4,16 @@ Description: Use Debian packaged htslib
 
 --- a/source/Makefile
 +++ b/source/Makefile
-@@ -18,7 +18,7 @@ OBJECTS = SharedMemory.o PackedArray.o S
-         bam_cat.o
- SOURCES := $(wildcard *.cpp) $(wildcard *.c)
+@@ -12,7 +12,7 @@ CXXFLAGSextra ?=
+ CXX ?= g++
  
--LDFLAGS := -pthread -Lhtslib -Bstatic -lhts -Bdynamic -lz -lrt
-+LDFLAGS := -pthread -Bstatic -lhts -Bdynamic -lz -lrt
+ # pre-defined flags
+-LDFLAGS_shared := -pthread -Lhtslib -Bstatic -lhts -Bdynamic -lz -lrt
++LDFLAGS_shared := -pthread -Bstatic -lhts -Bdynamic -lz -lrt
  LDFLAGS_static := -static -static-libgcc -pthread -Lhtslib -lhts -lz
  LDFLAGS_Mac :=-pthread -lz htslib/libhts.a
  LDFLAGS_Mac_static :=-pthread -lz -static-libgcc htslib/libhts.a
-@@ -51,20 +51,17 @@ clean:
+@@ -68,20 +68,17 @@ clean:
  .PHONY: CLEAN
  CLEAN:
  	rm -f *.o STAR Depend.list
@@ -34,8 +34,8 @@ Description: Use Debian packaged htslib
 +Depend.list: $(SOURCES) parametersDefault.xxd
  	echo $(SOURCES)
  	/bin/rm -f ./Depend.list
- 	$(CXX) $(CCFLAGS_common) -MM $^ >> Depend.list
-@@ -75,11 +72,6 @@ endif
+ 	$(CXX) $(CXXFLAGS_common) -MM $^ >> Depend.list
+@@ -92,11 +89,6 @@ endif
  endif
  endif
  
@@ -47,17 +47,6 @@ Description: Use Debian packaged htslib
  parametersDefault.xxd: parametersDefault
  	xxd -i parametersDefault > parametersDefault.xxd
  
---- a/source/STAR.cpp
-+++ b/source/STAR.cpp
-@@ -28,7 +28,7 @@
- #include "sjdbInsertJunctions.h"
- 
- 
--#include "htslib/htslib/sam.h"
-+#include <htslib/sam.h>
- extern int bam_cat(int nfn, char * const *fn, const bam_hdr_t *h, const char* outbam);
- 
- int main(int argInN, char* argIn[]) {
 --- a/source/bamRemoveDuplicates.cpp
 +++ b/source/bamRemoveDuplicates.cpp
 @@ -1,7 +1,7 @@
@@ -71,7 +60,7 @@ Description: Use Debian packaged htslib
  #include "ErrorWarning.h"
 --- a/source/bam_cat.c
 +++ b/source/bam_cat.c
-@@ -49,8 +49,8 @@ THE SOFTWARE.
+@@ -52,8 +52,8 @@ THE SOFTWARE.
  #include <stdlib.h>
  #include <unistd.h>
  
@@ -94,8 +83,8 @@ Description: Use Debian packaged htslib
  #include "Stats.h"
 --- a/source/IncludeDefine.h
 +++ b/source/IncludeDefine.h
-@@ -26,8 +26,8 @@
- #include "VERSION"
+@@ -28,8 +28,8 @@
+ #define ERROR_OUT string ( __FILE__ ) +":"+ to_string ( (uint) __LINE__ ) +":"+ string ( __FUNCTION__ )
  
  //external libs
 -#define SAMTOOLS_BGZF_H "htslib/htslib/bgzf.h"
@@ -114,3 +103,14 @@ Description: Use Debian packaged htslib
  
  string bam_cigarString (bam1_t *b) {//output CIGAR string
  //    kstring_t strK;
+--- a/source/STAR.cpp
++++ b/source/STAR.cpp
+@@ -26,7 +26,7 @@
+ #include "sjdbInsertJunctions.h"
+ #include "bam_cat.h"
+ 
+-#include "htslib/htslib/sam.h"
++#include <htslib/sam.h>
+ #include "parametersDefault.xxd"
+ 
+ 
diff --git a/debian/patches/mips_shm_noreserve.patch b/debian/patches/mips_shm_noreserve.patch
index 2dff645..30da5bf 100644
--- a/debian/patches/mips_shm_noreserve.patch
+++ b/debian/patches/mips_shm_noreserve.patch
@@ -5,7 +5,7 @@ Description: resolves build issue for mipsel, until this issue gets fixed in gli
 
 --- a/source/IncludeDefine.h
 +++ b/source/IncludeDefine.h
-@@ -36,6 +36,10 @@ using namespace std;
+@@ -38,6 +38,10 @@ using namespace std;
    #define SHM_NORESERVE 0
  #endif
  

-- 
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