[med-svn] r18507 - in trunk/packages/discosnp/trunk/debian: . patches

[Olivier Sallou]

Author: osallou
Date: 2014-11-21 17:11:14 +0000 (Fri, 21 Nov 2014)
New Revision: 18507

Added:
   trunk/packages/discosnp/trunk/debian/discosnp.lintian-overrides
Modified:
   trunk/packages/discosnp/trunk/debian/changelog
   trunk/packages/discosnp/trunk/debian/patches/fix_build
Log:
new upstream release 1.2.6

Modified: trunk/packages/discosnp/trunk/debian/changelog
===================================================================
--- trunk/packages/discosnp/trunk/debian/changelog	2014-11-21 12:32:24 UTC (rev 18506)
+++ trunk/packages/discosnp/trunk/debian/changelog	2014-11-21 17:11:14 UTC (rev 18507)
@@ -1,3 +1,9 @@
+discosnp (1.2.6-1) UNRELEASED; urgency=medium
+
+  * New upstream release 
+
+ -- osallou <osallou at debian.org>  Fri, 21 Nov 2014 17:56:37 +0100
+
 discosnp (1.2.5-1) unstable; urgency=medium
 
   * New upstream release

Added: trunk/packages/discosnp/trunk/debian/discosnp.lintian-overrides
===================================================================
--- trunk/packages/discosnp/trunk/debian/discosnp.lintian-overrides	                        (rev 0)
+++ trunk/packages/discosnp/trunk/debian/discosnp.lintian-overrides	2014-11-21 17:11:14 UTC (rev 18507)
@@ -0,0 +1,2 @@
+# Upstream gzip example
+discosnp: package-contains-timestamped-gzip

Modified: trunk/packages/discosnp/trunk/debian/patches/fix_build
===================================================================
--- trunk/packages/discosnp/trunk/debian/patches/fix_build	2014-11-21 12:32:24 UTC (rev 18506)
+++ trunk/packages/discosnp/trunk/debian/patches/fix_build	2014-11-21 17:11:14 UTC (rev 18507)
@@ -4,8 +4,8 @@
 Forwarded: no
 Author: Olivier Sallou <osallou at debian.org>
 Last-Updated: 2014-02-01
---- discoSnp.orig/kissnp2/makefile
-+++ discoSnp/kissnp2/makefile
+--- a/kissnp2/makefile
++++ b/kissnp2/makefile
 @@ -33,7 +33,10 @@
  #knowledge of the CeCILL license and that you accept its terms.
  
@@ -36,35 +36,8 @@
  
  %.o: %.cpp %.h
  	$(CC) -o $@ -c $< $(CFLAGS)
---- discoSnp.orig/kissreads/Makefile
-+++ discoSnp/kissreads/Makefile
-@@ -20,11 +20,13 @@
- # optimized flags
- 
- #CFLAGS=-Wall -O3 -L/../thirdparty/zlib/build/ -lz
--CFLAGS= -O3  -L../thirdparty/zlib/build/ -lz
-+CFLAGS = $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) -Wall -O3 -lz
-+# CFLAGS= -O3  -L../thirdparty/zlib/build/ -lz
- CFLAGS+=$(MYFLAGS)
- 
- #LDFLAGS+=-Wall -lm -O3 -L../thirdparty/zlib/build/ -lz
--LDFLAGS+= -O3 -lm  -L../thirdparty/zlib/build/ -lz
-+#LDFLAGS+= -O3 -lm  -L../thirdparty/zlib/build/ -lz
-+LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS) -Wall -lm -O3 -lz
- 
- ## debug flags
- #CFLAGS		+=-Wall -g -lz -fopenmp
-@@ -54,7 +56,7 @@
- 	@echo "#################"
- 
- kissreads: $(OBJ) 
--	$(CC)  -o $@ $^ $(LDFLAGS)
-+	$(CC)  -o $@ $^  $(CFLAGS) $(LDFLAGS)
- 
- 
- kissReads.o: $(INCLDIR)coherence_algorithm.h  $(INCLDIR)couple.h $(INCLDIR)extension_algorithm.h $(INCLDIR)fragment_info.h  $(INCLDIR)libchash.h  $(INCLDIR)outputs.h $(INCLDIR)commons.h $(INCLDIR)extending_fragment.h $(INCLDIR)fragment_index.h $(INCLDIR)hash.h $(INCLDIR)list.h $(INCLDIR)tree.h
---- discoSnp.orig/minia/makefile
-+++ discoSnp/minia/makefile
+--- a/minia/makefile
++++ b/minia/makefile
 @@ -1,4 +1,7 @@
 -CFLAGS+= -O4 -D_FILE_OFFSET_BITS=64 # needed to handle files > 2 GB on 32 bits systems
 +#CFLAGS+= -O4 -D_FILE_OFFSET_BITS=64 # needed to handle files > 2 GB on 32 bits systems
@@ -83,3 +56,27 @@
  
  %.o: %.cpp %.h
  	$(CXX) -o $@ -c $< $(CFLAGS)
+--- a/kissreads/Makefile
++++ b/kissreads/Makefile
+@@ -20,10 +20,10 @@
+ # optimized flags
+ 
+ #CFLAGS=-Wall -O3 -lz -fopenmp -DOMP #openmp is incompatiblre with clang #@!§
+-CFLAGS= -O3 -lz -fopenmp -DOMP #openmp is incompatiblre with clang #@!
++CFLAGS = $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) -Wall -O3 -lz
+ CFLAGS+=$(MYFLAGS)
+ #LDFLAGS+=-Wall -lm -O3 -lz -DOMP -fopenmp#-fopenmp
+-LDFLAGS+= -lm -O3 -lz -DOMP -fopenmp#-fopenmp
++LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS) -Wall -lm -O3 -lz
+ 
+ ## debug flags
+ 
+@@ -51,7 +51,7 @@
+ 	@echo "#################"
+ 
+ kissreads: $(OBJ) 
+-	$(CC)  -o $@ $^ $(LDFLAGS)
++	$(CC)  -o $@ $^ $(CFLAGS) $(LDFLAGS)
+ 
+ 
+ kissReads.o: $(INCLDIR)coherence_algorithm.h  $(INCLDIR)couple.h $(INCLDIR)extension_algorithm.h $(INCLDIR)fragment_info.h  $(INCLDIR)libchash.h  $(INCLDIR)outputs.h $(INCLDIR)commons.h $(INCLDIR)extending_fragment.h $(INCLDIR)fragment_index.h $(INCLDIR)hash.h $(INCLDIR)list.h