[med-svn] [rna-star] 04/05: Adjusted patches for 2.5.1
Steffen Möller
moeller at moszumanska.debian.org
Tue Feb 23 18:15:38 UTC 2016
This is an automated email from the git hooks/post-receive script.
moeller pushed a commit to branch master
in repository rna-star.
commit 8b3467af27a6436089584a7f4a36fe4144165bb6
Author: Steffen Moeller <moeller at debian.org>
Date: Tue Feb 23 18:09:00 2016 +0100
Adjusted patches for 2.5.1
---
debian/patches/compilationstuff.patch | 52 ++++--------------
debian/patches/donotuse_own_htslib.patch | 92 +++++++++++++++++++++++---------
2 files changed, 77 insertions(+), 67 deletions(-)
diff --git a/debian/patches/compilationstuff.patch b/debian/patches/compilationstuff.patch
index 419927e..cbf80d4 100644
--- a/debian/patches/compilationstuff.patch
+++ b/debian/patches/compilationstuff.patch
@@ -2,9 +2,11 @@ Author: Steffen Moeller <moeller at debian.org>,
Last-Changed: Thu, 29 Jan 2015 14:18:44 +0100
Description: Setting some compile options, fix some gcc errors
---- a/source/Parameters.h
-+++ b/source/Parameters.h
-@@ -60,7 +60,7 @@ class Parameters {
+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;
@@ -13,8 +15,10 @@ Description: Setting some compile options, fix some gcc errors
uint readNmates;
string readMatesLengthsIn;
vector <string> readFilesCommand;
---- a/source/STAR.cpp
-+++ b/source/STAR.cpp
+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++) {
@@ -24,42 +28,4 @@ Description: Setting some compile options, fix some gcc errors
struct stat buffer;
if (stat (bamBinNamesV.back().c_str(), &buffer) != 0) {//check if file exists
bamBinNamesV.pop_back();
---- a/source/Makefile
-+++ b/source/Makefile
-@@ -12,17 +12,17 @@ CXXFLAGSextra ?=
- CXX ?= g++
-
- # pre-defined flags
--LDFLAGS_shared := -pthread -Bstatic -lhts -Bdynamic -lz -lrt
--LDFLAGS_static := -static -static-libgcc -pthread -Lhtslib -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_shared)
-+LDFLAGS_gdb += $(LDFLAGS_shared)
-
- COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE="$(shell echo `date` $(HOSTNAME):`pwd`)"'
-
--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)
-
-@@ -54,10 +54,10 @@ SOURCES := $(wildcard *.cpp) $(wildcard
-
-
- %.o : %.cpp
-- $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $<
-+ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(COMPTIMEPLACE) $<
-
- %.o : %.c
-- $(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 03edc44..f274ea7 100644
--- a/debian/patches/donotuse_own_htslib.patch
+++ b/debian/patches/donotuse_own_htslib.patch
@@ -2,18 +2,48 @@ Author: Steffen Moeller <moeller at debian.org>,
Last-Changed: Thu, 29 Jan 2015 14:18:44 +0100
Description: Use Debian packaged htslib
---- a/source/Makefile
-+++ b/source/Makefile
-@@ -12,7 +12,7 @@ CXXFLAGSextra ?=
+Index: rna-star/source/Makefile
+===================================================================
+--- rna-star.orig/source/Makefile
++++ rna-star/source/Makefile
+@@ -12,17 +12,17 @@ CXXFLAGSextra ?=
CXX ?= g++
# 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_static := -static -static-libgcc -pthread -Lhtslib -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
-@@ -68,20 +68,17 @@ clean:
+-LDFLAGS_gdb := $(LDFLAGS_shared)
++LDFLAGS_gdb += $(LDFLAGS_shared)
+
+ COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE="$(shell echo `date` $(HOSTNAME):`pwd`)"'
+
+-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)
+
+@@ -54,10 +54,10 @@ SOURCES := $(wildcard *.cpp) $(wildcard
+
+
+ %.o : %.cpp
+- $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $<
++ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(COMPTIMEPLACE) $<
+
+ %.o : %.c
+- $(CXX) -c $(CPPFLAGS) $(CFLAGS) $<
++ $(CXX) -c $(CPPFLAGS) $(CFLAGS) $(COMPTIMEPLACE) $<
+
+ all: STAR
+
+@@ -68,12 +68,10 @@ clean:
.PHONY: CLEAN
CLEAN:
rm -f *.o STAR Depend.list
@@ -23,10 +53,10 @@ Description: Use Debian packaged htslib
cleanRelease:
rm -f *.o Depend.list
- $(MAKE) -C htslib clean
--
- ifneq ($(MAKECMDGOALS),clean)
- ifneq ($(MAKECMDGOALS),cleanRelease)
+ .PHONY: install
+ install:
+@@ -84,7 +82,7 @@ ifneq ($(MAKECMDGOALS),cleanRelease)
ifneq ($(MAKECMDGOALS),CLEAN)
ifneq ($(MAKECMDGOALS),STARforMac)
ifneq ($(MAKECMDGOALS),STARforMacGDB)
@@ -35,7 +65,7 @@ Description: Use Debian packaged htslib
echo $(SOURCES)
/bin/rm -f ./Depend.list
$(CXX) $(CXXFLAGS_common) -MM $^ >> Depend.list
-@@ -92,11 +89,6 @@ endif
+@@ -95,11 +93,6 @@ endif
endif
endif
@@ -47,8 +77,10 @@ Description: Use Debian packaged htslib
parametersDefault.xxd: parametersDefault
xxd -i parametersDefault > parametersDefault.xxd
---- a/source/bamRemoveDuplicates.cpp
-+++ b/source/bamRemoveDuplicates.cpp
+Index: rna-star/source/bamRemoveDuplicates.cpp
+===================================================================
+--- rna-star.orig/source/bamRemoveDuplicates.cpp
++++ rna-star/source/bamRemoveDuplicates.cpp
@@ -1,7 +1,7 @@
#include <unordered_map>
#include "bamRemoveDuplicates.h"
@@ -58,8 +90,10 @@ Description: Use Debian packaged htslib
#include "IncludeDefine.h"
#include SAMTOOLS_BGZF_H
#include "ErrorWarning.h"
---- a/source/bam_cat.c
-+++ b/source/bam_cat.c
+Index: rna-star/source/bam_cat.c
+===================================================================
+--- rna-star.orig/source/bam_cat.c
++++ rna-star/source/bam_cat.c
@@ -52,8 +52,8 @@ THE SOFTWARE.
#include <stdlib.h>
#include <unistd.h>
@@ -71,8 +105,10 @@ Description: Use Debian packaged htslib
#include <cstring>
#define BUF_SIZE 0x10000
---- a/source/signalFromBAM.h
-+++ b/source/signalFromBAM.h
+Index: rna-star/source/signalFromBAM.h
+===================================================================
+--- rna-star.orig/source/signalFromBAM.h
++++ rna-star/source/signalFromBAM.h
@@ -1,6 +1,6 @@
#ifndef CODE_signalFromBAM
#define CODE_signalFromBAM
@@ -81,8 +117,10 @@ Description: Use Debian packaged htslib
#include <fstream>
#include <string>
#include "Stats.h"
---- a/source/IncludeDefine.h
-+++ b/source/IncludeDefine.h
+Index: rna-star/source/IncludeDefine.h
+===================================================================
+--- rna-star.orig/source/IncludeDefine.h
++++ rna-star/source/IncludeDefine.h
@@ -28,8 +28,8 @@
#define ERROR_OUT string ( __FILE__ ) +":"+ to_string ( (uint) __LINE__ ) +":"+ string ( __FUNCTION__ )
@@ -94,8 +132,10 @@ Description: Use Debian packaged htslib
using namespace std;
---- a/source/BAMfunctions.cpp
-+++ b/source/BAMfunctions.cpp
+Index: rna-star/source/BAMfunctions.cpp
+===================================================================
+--- rna-star.orig/source/BAMfunctions.cpp
++++ rna-star/source/BAMfunctions.cpp
@@ -1,5 +1,5 @@
#include "BAMfunctions.h"
-#include "htslib/htslib/kstring.h"
@@ -103,8 +143,10 @@ 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
+Index: rna-star/source/STAR.cpp
+===================================================================
+--- rna-star.orig/source/STAR.cpp
++++ rna-star/source/STAR.cpp
@@ -26,7 +26,7 @@
#include "sjdbInsertJunctions.h"
#include "bam_cat.h"
@@ -114,8 +156,10 @@ Description: Use Debian packaged htslib
#include "parametersDefault.xxd"
---- a/source/bam_cat.h
-+++ b/source/bam_cat.h
+Index: rna-star/source/bam_cat.h
+===================================================================
+--- rna-star.orig/source/bam_cat.h
++++ rna-star/source/bam_cat.h
@@ -1,7 +1,7 @@
#ifndef CODE_bam_cat
#define CODE_bam_cat
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/rna-star.git
More information about the debian-med-commit
mailing list