[med-svn] r17781 - in trunk/packages/discosnp/tags: . 1.2.3-1/debian 1.2.3-1/debian/patches
Olivier Sallou
osallou at moszumanska.debian.org
Tue Aug 19 06:52:42 UTC 2014
Author: osallou
Date: 2014-08-19 06:52:42 +0000 (Tue, 19 Aug 2014)
New Revision: 17781
Added:
trunk/packages/discosnp/tags/1.2.3-1/
trunk/packages/discosnp/tags/1.2.3-1/debian/changelog
trunk/packages/discosnp/tags/1.2.3-1/debian/patches/fix_build
Removed:
trunk/packages/discosnp/tags/1.2.3-1/debian/changelog
trunk/packages/discosnp/tags/1.2.3-1/debian/patches/fix_build
Log:
[svn-buildpackage] Tagging discosnp 1.2.3-1
Deleted: trunk/packages/discosnp/tags/1.2.3-1/debian/changelog
===================================================================
--- trunk/packages/discosnp/trunk/debian/changelog 2014-08-18 13:32:39 UTC (rev 17763)
+++ trunk/packages/discosnp/tags/1.2.3-1/debian/changelog 2014-08-19 06:52:42 UTC (rev 17781)
@@ -1,30 +0,0 @@
-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/1.2.3-1/debian/changelog (from rev 17764, trunk/packages/discosnp/trunk/debian/changelog)
===================================================================
--- trunk/packages/discosnp/tags/1.2.3-1/debian/changelog (rev 0)
+++ trunk/packages/discosnp/tags/1.2.3-1/debian/changelog 2014-08-19 06:52:42 UTC (rev 17781)
@@ -0,0 +1,36 @@
+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
+
Deleted: trunk/packages/discosnp/tags/1.2.3-1/debian/patches/fix_build
===================================================================
--- trunk/packages/discosnp/trunk/debian/patches/fix_build 2014-08-18 13:32:39 UTC (rev 17763)
+++ trunk/packages/discosnp/tags/1.2.3-1/debian/patches/fix_build 2014-08-19 06:52:42 UTC (rev 17781)
@@ -1,88 +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
-Index: discoSnp/kissnp2/makefile
-===================================================================
---- 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 @@ OBJ= $(SRC:.cpp=.o)
- 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 @@ endif
- all: $(EXEC)
-
- kissnp2: $(OBJ) kissnp2.cpp
-- $(CC) -o $@ $^ $(CFLAGS)
-+ $(CC) -o $@ $^ $(CFLAGS) $(LDFLAGS)
-
- %.o: %.cpp %.h
- $(CC) -o $@ -c $< $(CFLAGS)
-Index: discoSnp/kissreads/Makefile
-===================================================================
---- discoSnp.orig/kissreads/Makefile
-+++ discoSnp/kissreads/Makefile
-@@ -19,9 +19,10 @@ CC =gcc
-
- # optimized flags
-
--CFLAGS=-Wall -O3 -lz -fopenmp -DOMP #openmp is incompatiblre with clang #@!§
-+CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS)
-+CFLAGS = $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) -Wall -O3 -lz
-+LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS) -Wall -lm -O3 -lz
- CFLAGS+=$(MYFLAGS)
--LDFLAGS+=-Wall -lm -O3 -lz -DOMP -fopenmp#-fopenmp
-
- ## debug flags
-
-@@ -49,7 +50,7 @@ all: $(ALL)
- @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 $(INCLDIR)tree.h
-Index: discoSnp/minia/makefile
-===================================================================
---- discoSnp.orig/minia/makefile
-+++ discoSnp/minia/makefile
-@@ -1,5 +1,7 @@
- CC=g++
--CFLAGS+= -O4 -D_FILE_OFFSET_BITS=64 # needed to handle files > 2 GB on 32 bits systems
-+CPPFLAGS:=$(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)
-@@ -61,7 +63,7 @@ all:
- $(MAKE) $(EXEC)
-
- minia: $(OBJ) Minia.cpp
-- $(CC) -o $@ $(OBJ) Minia.cpp $(CFLAGS) -lz
-+ $(CC) -o $@ $(OBJ) Minia.cpp $(CFLAGS) $(LDFLAGS) -lz
-
- %.o: %.cpp %.h
- $(CC) -o $@ -c $< $(CFLAGS)
Copied: trunk/packages/discosnp/tags/1.2.3-1/debian/patches/fix_build (from rev 17764, trunk/packages/discosnp/trunk/debian/patches/fix_build)
===================================================================
--- trunk/packages/discosnp/tags/1.2.3-1/debian/patches/fix_build (rev 0)
+++ trunk/packages/discosnp/tags/1.2.3-1/debian/patches/fix_build 2014-08-19 06:52:42 UTC (rev 17781)
@@ -0,0 +1,91 @@
+Subject: Add hardening
+Description: makefiles do not import default CFLAGS,...
+this patch add debian cflags for hardening
+Forwarded: no
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 2014-02-01
+Index: discoSnp/kissnp2/makefile
+===================================================================
+--- discoSnp.orig/kissnp2/makefile
++++ discoSnp/kissnp2/makefile
+@@ -33,7 +33,10 @@
+ #knowledge of the CeCILL license and that you accept its terms.
+
+ CC=g++
+-CFLAGS= -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
++CPPFLAGS:=$(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 @@ OBJ= $(SRC:.cpp=.o)
+ 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 @@ endif
+ all: $(EXEC)
+
+ kissnp2: $(OBJ) kissnp2.cpp
+- $(CC) -o $@ $^ $(CFLAGS)
++ $(CC) -o $@ $^ $(CFLAGS) $(LDFLAGS)
+
+ %.o: %.cpp %.h
+ $(CC) -o $@ -c $< $(CFLAGS)
+Index: discoSnp/kissreads/Makefile
+===================================================================
+--- discoSnp.orig/kissreads/Makefile
++++ discoSnp/kissreads/Makefile
+@@ -20,10 +20,13 @@ CC =gcc
+ # optimized flags
+
+ #CFLAGS=-Wall -O3 -lz -fopenmp -DOMP #openmp is incompatiblre with clang #@!§
+-CFLAGS= -O3 -lz -fopenmp -DOMP #openmp is incompatiblre with clang #@!
++#CFLAGS= -O3 -lz -fopenmp -DOMP #openmp is incompatiblre with clang #@!
++CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS)
++CFLAGS = $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) -Wall -O3 -lz
++LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS) -Wall -lm -O3 -lz
+ CFLAGS+=$(MYFLAGS)
+ #LDFLAGS+=-Wall -lm -O3 -lz -DOMP -fopenmp#-fopenmp
+-LDFLAGS+= -lm -O3 -lz -DOMP -fopenmp#-fopenmp
++#LDFLAGS+= -lm -O3 -lz -DOMP -fopenmp#-fopenmp
+
+ ## debug flags
+
+@@ -51,7 +54,7 @@ all: $(ALL)
+ @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 $(INCLDIR)tree.h
+Index: discoSnp/minia/makefile
+===================================================================
+--- discoSnp.orig/minia/makefile
++++ discoSnp/minia/makefile
+@@ -1,4 +1,7 @@
+-CFLAGS+= -O4 -D_FILE_OFFSET_BITS=64 # needed to handle files > 2 GB on 32 bits systems
++#CFLAGS+= -O4 -D_FILE_OFFSET_BITS=64 # needed to handle files > 2 GB on 32 bits systems
++CPPFLAGS:=$(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 @@ all:
+ $(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)
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