[med-svn] r19549 - in trunk/packages/rna-star/trunk/debian: . patches

Andreas Tille tille at moszumanska.debian.org
Mon Jul 6 17:46:50 UTC 2015 

Author: tille
Date: 2015-07-06 17:46:49 +0000 (Mon, 06 Jul 2015)
New Revision: 19549

Modified:
   trunk/packages/rna-star/trunk/debian/changelog
   trunk/packages/rna-star/trunk/debian/patches/compilationstuff.patch
   trunk/packages/rna-star/trunk/debian/patches/donotuse_own_htslib.patch
   trunk/packages/rna-star/trunk/debian/patches/mips_shm_noreserve.patch
   trunk/packages/rna-star/trunk/debian/watch
Log:
New upstream version with adapted patches


Modified: trunk/packages/rna-star/trunk/debian/changelog
===================================================================
--- trunk/packages/rna-star/trunk/debian/changelog	2015-07-06 17:23:09 UTC (rev 19548)
+++ trunk/packages/rna-star/trunk/debian/changelog	2015-07-06 17:46:49 UTC (rev 19549)
@@ -1,9 +1,13 @@
-rna-star (2.4.0k-2) UNRELEASED; urgency=medium
+rna-star (2.4.2a+dfsg-1) unstable; urgency=medium
 
+  [ Charles Plessy ]
   * Remove large GENCODE file, found in later upstream versions.
 
- -- Charles Plessy <plessy at debian.org>  Mon, 25 May 2015 11:27:31 +0900
+  [ Andreas Tille ]
+  * New upstream version
 
+ -- Andreas Tille <tille at debian.org>  Mon, 06 Jul 2015 19:28:49 +0200
+
 rna-star (2.4.0k-1) unstable; urgency=medium
 
   * New upstream version (adapted patches)

Modified: trunk/packages/rna-star/trunk/debian/patches/compilationstuff.patch
===================================================================
--- trunk/packages/rna-star/trunk/debian/patches/compilationstuff.patch	2015-07-06 17:23:09 UTC (rev 19548)
+++ trunk/packages/rna-star/trunk/debian/patches/compilationstuff.patch	2015-07-06 17:46:49 UTC (rev 19549)
@@ -4,7 +4,7 @@
 
 --- a/source/Parameters.h
 +++ b/source/Parameters.h
-@@ -54,7 +54,7 @@ class Parameters {
+@@ -56,7 +56,7 @@ class Parameters {
          int readFilesIndex;
          uint32 readFilesN;
          vector <string> readFilesIn, readFilesInTmp;
@@ -13,22 +13,33 @@
          uint readNmates;
          string readMatesLengthsIn;
          vector <string> readFilesCommand;
+--- a/source/STAR.cpp
++++ b/source/STAR.cpp
+@@ -361,7 +361,7 @@ int main(int argInN, char* argIn[]) {
+         vector <string> bamBinNamesV;
+         for (uint32 ibin=0; ibin<nBins; ibin++) {
+             
+-            bamBinNamesV.push_back(P->outBAMsortTmpDir+"/b"+to_string((uint) ibin));            
++            bamBinNamesV.push_back(P->outBAMsortTmpDir+"/b"+std::to_string((uint) ibin));            
+             struct stat buffer;
+             if (stat (bamBinNamesV.back().c_str(), &buffer) != 0) {//check if file exists
+                 bamBinNamesV.pop_back();
 --- a/source/Makefile
 +++ b/source/Makefile
-@@ -17,28 +17,28 @@ OBJECTS = PackedArray.o SuffixArrayFuns.
+@@ -18,29 +18,29 @@ OBJECTS = SharedMemory.o PackedArray.o S
          bam_cat.o
  SOURCES := $(wildcard *.cpp) $(wildcard *.c)
  
--LDFLAGS := -pthread -Bstatic -lhts -Bdynamic -lz
+-LDFLAGS := -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
-+LDFLAGS := -pthread -lhts -lz $(LDFLAGS_add)
-+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
++LDFLAGS := -pthread -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)
  
  COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE="$(shell echo `date` $(HOSTNAME):`pwd`)"'
@@ -41,7 +52,7 @@
 +CCFLAGS_main += -O3 $(CCFLAGS_common)
 +CCFLAGS_gdb +=  -O0 -g $(CCFLAGS_common)
  
- CXX :=g++
+ CXX ?=g++
  
  
  %.o : %.cpp
@@ -54,14 +65,3 @@
  
  all: STAR
  
---- a/source/STAR.cpp
-+++ b/source/STAR.cpp
-@@ -331,7 +331,7 @@ int main(int argInN, char* argIn[]) {
-         vector <string> bamBinNamesV;
-         for (uint32 ibin=0; ibin<nBins; ibin++) {
-             
--            bamBinNamesV.push_back(P->outBAMsortTmpDir+"/b"+to_string((uint) ibin));            
-+            bamBinNamesV.push_back(P->outBAMsortTmpDir+"/b"+std::to_string((uint) ibin));            
-             struct stat buffer;
-             if (stat (bamBinNamesV.back().c_str(), &buffer) != 0) {//check if file exists
-                 bamBinNamesV.pop_back();

Modified: trunk/packages/rna-star/trunk/debian/patches/donotuse_own_htslib.patch
===================================================================
--- trunk/packages/rna-star/trunk/debian/patches/donotuse_own_htslib.patch	2015-07-06 17:23:09 UTC (rev 19548)
+++ trunk/packages/rna-star/trunk/debian/patches/donotuse_own_htslib.patch	2015-07-06 17:46:49 UTC (rev 19549)
@@ -4,16 +4,16 @@
 
 --- a/source/Makefile
 +++ b/source/Makefile
-@@ -17,7 +17,7 @@ OBJECTS = PackedArray.o SuffixArrayFuns.
+@@ -18,7 +18,7 @@ OBJECTS = SharedMemory.o PackedArray.o S
          bam_cat.o
  SOURCES := $(wildcard *.cpp) $(wildcard *.c)
  
--LDFLAGS := -pthread -Lhtslib -Bstatic -lhts -Bdynamic -lz
-+LDFLAGS := -pthread -Bstatic -lhts -Bdynamic -lz
+-LDFLAGS := -pthread -Lhtslib -Bstatic -lhts -Bdynamic -lz -lrt
++LDFLAGS := -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
-@@ -49,20 +49,17 @@ clean:
+@@ -51,20 +51,17 @@ clean:
  .PHONY: CLEAN
  CLEAN:
  	rm -f *.o STAR Depend.list
@@ -35,7 +35,7 @@
  	echo $(SOURCES)
  	/bin/rm -f ./Depend.list
  	$(CXX) $(CCFLAGS_common) -MM $^ >> Depend.list
-@@ -73,11 +70,6 @@ endif
+@@ -75,11 +72,6 @@ endif
  endif
  endif
  
@@ -49,10 +49,10 @@
  
 --- a/source/STAR.cpp
 +++ b/source/STAR.cpp
-@@ -23,7 +23,7 @@
- #include "mapThreadsSpawn.h"
- #include "ErrorWarning.h"
+@@ -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);
@@ -94,7 +94,7 @@
  #include "Stats.h"
 --- a/source/IncludeDefine.h
 +++ b/source/IncludeDefine.h
-@@ -24,8 +24,8 @@
+@@ -26,8 +26,8 @@
  #include "VERSION"
  
  //external libs

Modified: trunk/packages/rna-star/trunk/debian/patches/mips_shm_noreserve.patch
===================================================================
--- trunk/packages/rna-star/trunk/debian/patches/mips_shm_noreserve.patch	2015-07-06 17:23:09 UTC (rev 19548)
+++ trunk/packages/rna-star/trunk/debian/patches/mips_shm_noreserve.patch	2015-07-06 17:46:49 UTC (rev 19549)
@@ -5,7 +5,7 @@
 
 --- a/source/IncludeDefine.h
 +++ b/source/IncludeDefine.h
-@@ -34,6 +34,10 @@ using namespace std;
+@@ -36,6 +36,10 @@ using namespace std;
    #define SHM_NORESERVE 0
  #endif
  

Modified: trunk/packages/rna-star/trunk/debian/watch
===================================================================
--- trunk/packages/rna-star/trunk/debian/watch	2015-07-06 17:23:09 UTC (rev 19548)
+++ trunk/packages/rna-star/trunk/debian/watch	2015-07-06 17:46:49 UTC (rev 19549)
@@ -1,3 +1,4 @@
 version=3
 
-https://github.com/alexdobin/STAR/releases .*/archive/STAR_(\d[\d.a-z]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g" \
+  https://github.com/alexdobin/STAR/releases .*/archive/STAR_(\d[\d.a-z]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)

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