[med-svn] r18509 - in trunk/packages/discosnp/tags: . 1.2.6-1/debian 1.2.6-1/debian/patches

Olivier Sallou osallou at moszumanska.debian.org
Fri Nov 21 17:17:40 UTC 2014


Author: osallou
Date: 2014-11-21 17:17:39 +0000 (Fri, 21 Nov 2014)
New Revision: 18509

Added:
   trunk/packages/discosnp/tags/1.2.6-1/
   trunk/packages/discosnp/tags/1.2.6-1/debian/changelog
   trunk/packages/discosnp/tags/1.2.6-1/debian/discosnp.lintian-overrides
   trunk/packages/discosnp/tags/1.2.6-1/debian/patches/fix_build
Removed:
   trunk/packages/discosnp/tags/1.2.6-1/debian/changelog
   trunk/packages/discosnp/tags/1.2.6-1/debian/patches/fix_build
Log:
[svn-buildpackage] Tagging discosnp 1.2.6-1

Deleted: trunk/packages/discosnp/tags/1.2.6-1/debian/changelog
===================================================================
--- trunk/packages/discosnp/trunk/debian/changelog	2014-11-21 12:32:24 UTC (rev 18506)
+++ trunk/packages/discosnp/tags/1.2.6-1/debian/changelog	2014-11-21 17:17:39 UTC (rev 18509)
@@ -1,44 +0,0 @@
-discosnp (1.2.5-1) unstable; urgency=medium
-
-  * New upstream release
-  * cme fix dpkg-control
-  * Fix some DEP3 lintian issues
-
- -- Andreas Tille <tille at debian.org>  Sat, 11 Oct 2014 10:41:32 +0200
-
-discosnp (1.2.3-1) unstable; urgency=medium
-
-  * New upstream release
-
- -- Olivier Sallou <osallou at debian.org>  Mon, 18 Aug 2014 16:42:33 +0200
-
-discosnp (1.2.2-1) unstable; urgency=medium
-
-  * New upstream release 
-
- -- Olivier Sallou <osallou at debian.org>  Thu, 29 May 2014 14:09:41 +0200
-
-discosnp (1.2.1-1) unstable; urgency=low
-
-  * New upstream release 
-
- -- Olivier Sallou <osallou at debian.org>  Wed, 09 Apr 2014 14:41:03 +0200
-
-discosnp (1.0.1-3) unstable; urgency=low
-
-  * d/rules: FTBS fix help2man command
-
- -- Olivier Sallou <osallou at debian.org>  Thu, 06 Feb 2014 09:10:12 +0100
-
-discosnp (1.0.1-2) unstable; urgency=low
-
-  * d/control: FTBS due to missing deps
-
- -- Olivier Sallou <osallou at debian.org>  Thu, 06 Feb 2014 08:04:38 +0100
-
-discosnp (1.0.1-1) unstable; urgency=low
-
-  * First debian package (Closes: #737098).
-
- -- Olivier Sallou <osallou at debian.org>  Sat, 01 Feb 2014 16:55:29 +0100
-

Copied: trunk/packages/discosnp/tags/1.2.6-1/debian/changelog (from rev 18508, trunk/packages/discosnp/trunk/debian/changelog)
===================================================================
--- trunk/packages/discosnp/tags/1.2.6-1/debian/changelog	                        (rev 0)
+++ trunk/packages/discosnp/tags/1.2.6-1/debian/changelog	2014-11-21 17:17:39 UTC (rev 18509)
@@ -0,0 +1,50 @@
+discosnp (1.2.6-1) unstable; urgency=medium
+
+  * New upstream release 
+
+ -- Olivier Sallou <osallou at debian.org>  Fri, 21 Nov 2014 17:56:37 +0100
+
+discosnp (1.2.5-1) unstable; urgency=medium
+
+  * New upstream release
+  * cme fix dpkg-control
+  * Fix some DEP3 lintian issues
+
+ -- Andreas Tille <tille at debian.org>  Sat, 11 Oct 2014 10:41:32 +0200
+
+discosnp (1.2.3-1) unstable; urgency=medium
+
+  * New upstream release
+
+ -- Olivier Sallou <osallou at debian.org>  Mon, 18 Aug 2014 16:42:33 +0200
+
+discosnp (1.2.2-1) unstable; urgency=medium
+
+  * New upstream release 
+
+ -- Olivier Sallou <osallou at debian.org>  Thu, 29 May 2014 14:09:41 +0200
+
+discosnp (1.2.1-1) unstable; urgency=low
+
+  * New upstream release 
+
+ -- Olivier Sallou <osallou at debian.org>  Wed, 09 Apr 2014 14:41:03 +0200
+
+discosnp (1.0.1-3) unstable; urgency=low
+
+  * d/rules: FTBS fix help2man command
+
+ -- Olivier Sallou <osallou at debian.org>  Thu, 06 Feb 2014 09:10:12 +0100
+
+discosnp (1.0.1-2) unstable; urgency=low
+
+  * d/control: FTBS due to missing deps
+
+ -- Olivier Sallou <osallou at debian.org>  Thu, 06 Feb 2014 08:04:38 +0100
+
+discosnp (1.0.1-1) unstable; urgency=low
+
+  * First debian package (Closes: #737098).
+
+ -- Olivier Sallou <osallou at debian.org>  Sat, 01 Feb 2014 16:55:29 +0100
+

Copied: trunk/packages/discosnp/tags/1.2.6-1/debian/discosnp.lintian-overrides (from rev 18507, trunk/packages/discosnp/trunk/debian/discosnp.lintian-overrides)
===================================================================
--- trunk/packages/discosnp/tags/1.2.6-1/debian/discosnp.lintian-overrides	                        (rev 0)
+++ trunk/packages/discosnp/tags/1.2.6-1/debian/discosnp.lintian-overrides	2014-11-21 17:17:39 UTC (rev 18509)
@@ -0,0 +1,2 @@
+# Upstream gzip example
+discosnp: package-contains-timestamped-gzip

Deleted: trunk/packages/discosnp/tags/1.2.6-1/debian/patches/fix_build
===================================================================
--- trunk/packages/discosnp/trunk/debian/patches/fix_build	2014-11-21 12:32:24 UTC (rev 18506)
+++ trunk/packages/discosnp/tags/1.2.6-1/debian/patches/fix_build	2014-11-21 17:17:39 UTC (rev 18509)
@@ -1,85 +0,0 @@
-Subject: Add hardening
-Description: makefiles do not import default CFLAGS,...
-this patch add debian cflags for hardening
-Forwarded: no
-Author: Olivier Sallou <osallou at debian.org>
-Last-Updated: 2014-02-01
---- discoSnp.orig/kissnp2/makefile
-+++ discoSnp/kissnp2/makefile
-@@ -33,7 +33,10 @@
- #knowledge of the CeCILL license and that you accept its terms.
- 
- CC=g++
--CFLAGS=  -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
-+CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS)
-+CFLAGS = $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
-+LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS)
-+
- #CFLAGS=  -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER -DDONTMARK
- SRC=../minia/Pool.cpp ../minia/Bank.cpp ../minia/Bloom.cpp ../minia/Hash16.cpp ../minia/Terminator.cpp ../minia/Kmer.cpp ../minia/Traversal.cpp ../minia/LinearCounter.cpp ../minia/Set.cpp ../minia/Utils.cpp ../minia/SortingCount.cpp ../minia/Debloom.cpp ../minia/OAHash.cpp Kmer_for_kissnp2.cpp SNP.cpp filter.cpp IterativeExtensions.cpp commons.cpp
- EXEC=kissnp2
-@@ -41,7 +44,7 @@
- all: $(EXEC)
- 
- ifeq ($(prof),1)
-- CFLAGS=-O3 -pg -lz
-+ CFLAGS= $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) -O3 -pg -lz
- endif
- ifeq ($(deb),1)
-  CFLAGS+=-O0 -DASSERTS -g -lz 
-@@ -79,7 +82,7 @@
- all: $(EXEC)
- 
- kissnp2:  $(OBJ) kissnp2.cpp
--	$(CC) -o $@ $^ $(CFLAGS) 
-+	$(CC) -o $@ $^ $(CFLAGS) $(LDFLAGS)
- 
- %.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 $(INCLDIR)tree.h
---- discoSnp.orig/minia/makefile
-+++ discoSnp/minia/makefile
-@@ -1,4 +1,7 @@
--CFLAGS+= -O4 -D_FILE_OFFSET_BITS=64 # needed to handle files > 2 GB on 32 bits systems
-+#CFLAGS+= -O4 -D_FILE_OFFSET_BITS=64 # needed to handle files > 2 GB on 32 bits systems
-+CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS)
-+CFLAGS = $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) -O4 -D_FILE_OFFSET_BITS=64
-+LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS)
- SRC=Pool.cpp Bank.cpp Bloom.cpp Hash16.cpp LargeInt.cpp Kmer.cpp Terminator.cpp Traversal.cpp LinearCounter.cpp Set.cpp Utils.cpp SortingCount.cpp Debloom.cpp OAHash.cpp
- EXEC=minia
- OBJ= $(SRC:.cpp=.o)
-@@ -60,7 +63,7 @@
- 	$(MAKE) $(EXEC)
- 
- minia: $(OBJ) Minia.cpp
--	$(CXX) -o $@ $(OBJ) Minia.cpp $(CFLAGS) -lz
-+	$(CXX) -o $@ $(OBJ) Minia.cpp $(CFLAGS) $(LDFLAGS) -lz
- 
- %.o: %.cpp %.h
- 	$(CXX) -o $@ -c $< $(CFLAGS)

Copied: trunk/packages/discosnp/tags/1.2.6-1/debian/patches/fix_build (from rev 18507, trunk/packages/discosnp/trunk/debian/patches/fix_build)
===================================================================
--- trunk/packages/discosnp/tags/1.2.6-1/debian/patches/fix_build	                        (rev 0)
+++ trunk/packages/discosnp/tags/1.2.6-1/debian/patches/fix_build	2014-11-21 17:17:39 UTC (rev 18509)
@@ -0,0 +1,82 @@
+Subject: Add hardening
+Description: makefiles do not import default CFLAGS,...
+this patch add debian cflags for hardening
+Forwarded: no
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 2014-02-01
+--- a/kissnp2/makefile
++++ b/kissnp2/makefile
+@@ -33,7 +33,10 @@
+ #knowledge of the CeCILL license and that you accept its terms.
+ 
+ CC=g++
+-CFLAGS=  -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
++CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS)
++CFLAGS = $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
++LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS)
++
+ #CFLAGS=  -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER -DDONTMARK
+ SRC=../minia/Pool.cpp ../minia/Bank.cpp ../minia/Bloom.cpp ../minia/Hash16.cpp ../minia/Terminator.cpp ../minia/Kmer.cpp ../minia/Traversal.cpp ../minia/LinearCounter.cpp ../minia/Set.cpp ../minia/Utils.cpp ../minia/SortingCount.cpp ../minia/Debloom.cpp ../minia/OAHash.cpp Kmer_for_kissnp2.cpp SNP.cpp filter.cpp IterativeExtensions.cpp commons.cpp
+ EXEC=kissnp2
+@@ -41,7 +44,7 @@
+ all: $(EXEC)
+ 
+ ifeq ($(prof),1)
+- CFLAGS=-O3 -pg -lz
++ CFLAGS= $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) -O3 -pg -lz
+ endif
+ ifeq ($(deb),1)
+  CFLAGS+=-O0 -DASSERTS -g -lz 
+@@ -79,7 +82,7 @@
+ all: $(EXEC)
+ 
+ kissnp2:  $(OBJ) kissnp2.cpp
+-	$(CC) -o $@ $^ $(CFLAGS) 
++	$(CC) -o $@ $^ $(CFLAGS) $(LDFLAGS)
+ 
+ %.o: %.cpp %.h
+ 	$(CC) -o $@ -c $< $(CFLAGS)
+--- a/minia/makefile
++++ b/minia/makefile
+@@ -1,4 +1,7 @@
+-CFLAGS+= -O4 -D_FILE_OFFSET_BITS=64 # needed to handle files > 2 GB on 32 bits systems
++#CFLAGS+= -O4 -D_FILE_OFFSET_BITS=64 # needed to handle files > 2 GB on 32 bits systems
++CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS)
++CFLAGS = $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) -O4 -D_FILE_OFFSET_BITS=64
++LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS)
+ SRC=Pool.cpp Bank.cpp Bloom.cpp Hash16.cpp LargeInt.cpp Kmer.cpp Terminator.cpp Traversal.cpp LinearCounter.cpp Set.cpp Utils.cpp SortingCount.cpp Debloom.cpp OAHash.cpp
+ EXEC=minia
+ OBJ= $(SRC:.cpp=.o)
+@@ -60,7 +63,7 @@
+ 	$(MAKE) $(EXEC)
+ 
+ minia: $(OBJ) Minia.cpp
+-	$(CXX) -o $@ $(OBJ) Minia.cpp $(CFLAGS) -lz
++	$(CXX) -o $@ $(OBJ) Minia.cpp $(CFLAGS) $(LDFLAGS) -lz
+ 
+ %.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 




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