[med-svn] r18629 - in trunk/packages/rna-star/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2015-01-30 04:53:16 +0000 (Fri, 30 Jan 2015)
New Revision: 18629

Modified:
   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/rules
Log:
Package now at least debuild's


Modified: trunk/packages/rna-star/trunk/debian/patches/compilationstuff.patch
===================================================================
--- trunk/packages/rna-star/trunk/debian/patches/compilationstuff.patch	2015-01-29 22:26:45 UTC (rev 18628)
+++ trunk/packages/rna-star/trunk/debian/patches/compilationstuff.patch	2015-01-30 04:53:16 UTC (rev 18629)
@@ -1,3 +1,7 @@
+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
 @@ -54,7 +54,7 @@ class Parameters {
@@ -33,7 +37,7 @@
 -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 := -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)
  

Modified: trunk/packages/rna-star/trunk/debian/patches/donotuse_own_htslib.patch
===================================================================
--- trunk/packages/rna-star/trunk/debian/patches/donotuse_own_htslib.patch	2015-01-29 22:26:45 UTC (rev 18628)
+++ trunk/packages/rna-star/trunk/debian/patches/donotuse_own_htslib.patch	2015-01-30 04:53:16 UTC (rev 18629)
@@ -1,3 +1,7 @@
+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
 @@ -17,7 +17,7 @@ OBJECTS = PackedArray.o SuffixArrayFuns.
@@ -88,3 +92,14 @@
  #include  <fstream>
  #include <string>
  #include "Stats.h"
+--- a/source/IncludeDefine.h
++++ b/source/IncludeDefine.h
+@@ -24,7 +24,7 @@
+ #include "VERSION"
+ 
+ //external libs
+-#define SAMTOOLS_BGZF_H "htslib/htslib/bgzf.h"
++#define SAMTOOLS_BGZF_H <htslib/bgzf.h>
+ 
+ using namespace std;
+ 

Modified: trunk/packages/rna-star/trunk/debian/rules
===================================================================
--- trunk/packages/rna-star/trunk/debian/rules	2015-01-29 22:26:45 UTC (rev 18628)
+++ trunk/packages/rna-star/trunk/debian/rules	2015-01-30 04:53:16 UTC (rev 18629)
@@ -14,8 +14,7 @@
 	dh $@ 
 
 override_dh_auto_build:
-	mkdir -p source/htslib && ln -s /usr/include/htslib source/htslib
-	cd source && $(MAKE) CCFLAGS_common=-flto CCFLAGS="$(CCFLAGS)" LDFLAGS="$(LDFLAGS)"
+	cd source && $(MAKE) CCFLAGS_common_add=-flto CCFLAGS="$(CCFLAGS)" LDFLAGS="$(LDFLAGS)"
 
 override_dh_auto_clean:
 	cd source && $(MAKE) clean