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 <[email protected]> Mon, 25 May 2015 11:27:31 +0900 + [ Andreas Tille ] + * New upstream version + -- Andreas Tille <[email protected]> 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) _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
