This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository rna-star.
commit cc4e99e3fce15c11fc9349be43fd22d751edc6b8 Author: Andreas Tille <[email protected]> Date: Thu May 19 18:06:43 2016 +0200 Update patches --- debian/patches/compilationstuff.patch | 31 --------------------- debian/patches/donotuse_own_htslib.patch | 48 +++++++++++--------------------- debian/patches/mips_shm_noreserve.patch | 6 ++-- debian/patches/series | 1 - 4 files changed, 19 insertions(+), 67 deletions(-) diff --git a/debian/patches/compilationstuff.patch b/debian/patches/compilationstuff.patch deleted file mode 100644 index cbf80d4..0000000 --- a/debian/patches/compilationstuff.patch +++ /dev/null @@ -1,31 +0,0 @@ -Author: Steffen Moeller <[email protected]>, -Last-Changed: Thu, 29 Jan 2015 14:18:44 +0100 -Description: Setting some compile options, fix some gcc errors - -Index: rna-star/source/Parameters.h -=================================================================== ---- rna-star.orig/source/Parameters.h -+++ rna-star/source/Parameters.h -@@ -61,7 +61,7 @@ class Parameters { - int readFilesIndex; - uint32 readFilesN; - vector <string> readFilesIn, readFilesInTmp; -- vector <vector <string>> readFilesNames; -+ vector <vector <string> > readFilesNames; - uint readNmates; - string readMatesLengthsIn; - vector <string> readFilesCommand; -Index: rna-star/source/STAR.cpp -=================================================================== ---- rna-star.orig/source/STAR.cpp -+++ rna-star/source/STAR.cpp -@@ -386,7 +386,7 @@ 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(); - diff --git a/debian/patches/donotuse_own_htslib.patch b/debian/patches/donotuse_own_htslib.patch index f274ea7..2eeb604 100644 --- a/debian/patches/donotuse_own_htslib.patch +++ b/debian/patches/donotuse_own_htslib.patch @@ -2,10 +2,8 @@ Author: Steffen Moeller <[email protected]>, Last-Changed: Thu, 29 Jan 2015 14:18:44 +0100 Description: Use Debian packaged htslib -Index: rna-star/source/Makefile -=================================================================== ---- rna-star.orig/source/Makefile -+++ rna-star/source/Makefile +--- a/source/Makefile ++++ b/source/Makefile @@ -12,17 +12,17 @@ CXXFLAGSextra ?= CXX ?= g++ @@ -77,10 +75,8 @@ Index: rna-star/source/Makefile parametersDefault.xxd: parametersDefault xxd -i parametersDefault > parametersDefault.xxd -Index: rna-star/source/bamRemoveDuplicates.cpp -=================================================================== ---- rna-star.orig/source/bamRemoveDuplicates.cpp -+++ rna-star/source/bamRemoveDuplicates.cpp +--- a/source/bamRemoveDuplicates.cpp ++++ b/source/bamRemoveDuplicates.cpp @@ -1,7 +1,7 @@ #include <unordered_map> #include "bamRemoveDuplicates.h" @@ -90,10 +86,8 @@ Index: rna-star/source/bamRemoveDuplicates.cpp #include "IncludeDefine.h" #include SAMTOOLS_BGZF_H #include "ErrorWarning.h" -Index: rna-star/source/bam_cat.c -=================================================================== ---- rna-star.orig/source/bam_cat.c -+++ rna-star/source/bam_cat.c +--- a/source/bam_cat.c ++++ b/source/bam_cat.c @@ -52,8 +52,8 @@ THE SOFTWARE. #include <stdlib.h> #include <unistd.h> @@ -105,10 +99,8 @@ Index: rna-star/source/bam_cat.c #include <cstring> #define BUF_SIZE 0x10000 -Index: rna-star/source/signalFromBAM.h -=================================================================== ---- rna-star.orig/source/signalFromBAM.h -+++ rna-star/source/signalFromBAM.h +--- a/source/signalFromBAM.h ++++ b/source/signalFromBAM.h @@ -1,6 +1,6 @@ #ifndef CODE_signalFromBAM #define CODE_signalFromBAM @@ -117,10 +109,8 @@ Index: rna-star/source/signalFromBAM.h #include <fstream> #include <string> #include "Stats.h" -Index: rna-star/source/IncludeDefine.h -=================================================================== ---- rna-star.orig/source/IncludeDefine.h -+++ rna-star/source/IncludeDefine.h +--- a/source/IncludeDefine.h ++++ b/source/IncludeDefine.h @@ -28,8 +28,8 @@ #define ERROR_OUT string ( __FILE__ ) +":"+ to_string ( (uint) __LINE__ ) +":"+ string ( __FUNCTION__ ) @@ -132,10 +122,8 @@ Index: rna-star/source/IncludeDefine.h using namespace std; -Index: rna-star/source/BAMfunctions.cpp -=================================================================== ---- rna-star.orig/source/BAMfunctions.cpp -+++ rna-star/source/BAMfunctions.cpp +--- a/source/BAMfunctions.cpp ++++ b/source/BAMfunctions.cpp @@ -1,5 +1,5 @@ #include "BAMfunctions.h" -#include "htslib/htslib/kstring.h" @@ -143,10 +131,8 @@ Index: rna-star/source/BAMfunctions.cpp string bam_cigarString (bam1_t *b) {//output CIGAR string // kstring_t strK; -Index: rna-star/source/STAR.cpp -=================================================================== ---- rna-star.orig/source/STAR.cpp -+++ rna-star/source/STAR.cpp +--- a/source/STAR.cpp ++++ b/source/STAR.cpp @@ -26,7 +26,7 @@ #include "sjdbInsertJunctions.h" #include "bam_cat.h" @@ -156,10 +142,8 @@ Index: rna-star/source/STAR.cpp #include "parametersDefault.xxd" -Index: rna-star/source/bam_cat.h -=================================================================== ---- rna-star.orig/source/bam_cat.h -+++ rna-star/source/bam_cat.h +--- a/source/bam_cat.h ++++ b/source/bam_cat.h @@ -1,7 +1,7 @@ #ifndef CODE_bam_cat #define CODE_bam_cat diff --git a/debian/patches/mips_shm_noreserve.patch b/debian/patches/mips_shm_noreserve.patch index 30da5bf..36ae29b 100644 --- a/debian/patches/mips_shm_noreserve.patch +++ b/debian/patches/mips_shm_noreserve.patch @@ -5,8 +5,8 @@ Description: resolves build issue for mipsel, until this issue gets fixed in gli --- a/source/IncludeDefine.h +++ b/source/IncludeDefine.h -@@ -38,6 +38,10 @@ using namespace std; - #define SHM_NORESERVE 0 +@@ -42,6 +42,10 @@ using namespace std; + #define SHM_NORESERVE 010000 #endif +#if defined(__mips__) && !defined(SHM_NORESERVE) @@ -14,5 +14,5 @@ Description: resolves build issue for mipsel, until this issue gets fixed in gli +#endif + typedef int8_t int8; - typedef uint8_t uint8; + typedef uint8_t uint8; diff --git a/debian/patches/series b/debian/patches/series index 2d31638..4abc50b 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,3 +1,2 @@ donotuse_own_htslib.patch -compilationstuff.patch mips_shm_noreserve.patch -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/rna-star.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
