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 <[email protected]> Thu, 29 May 2014 14:09:41 +0200 - -discosnp (1.2.1-1) unstable; urgency=low - - * New upstream release - - -- Olivier Sallou <[email protected]> Wed, 09 Apr 2014 14:41:03 +0200 - -discosnp (1.0.1-3) unstable; urgency=low - - * d/rules: FTBS fix help2man command - - -- Olivier Sallou <[email protected]> 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 <[email protected]> Thu, 06 Feb 2014 08:04:38 +0100 - -discosnp (1.0.1-1) unstable; urgency=low - - * First debian package (Closes: #737098). - - -- Olivier Sallou <[email protected]> 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 <[email protected]> Mon, 18 Aug 2014 16:42:33 +0200 + +discosnp (1.2.2-1) unstable; urgency=medium + + * New upstream release + + -- Olivier Sallou <[email protected]> Thu, 29 May 2014 14:09:41 +0200 + +discosnp (1.2.1-1) unstable; urgency=low + + * New upstream release + + -- Olivier Sallou <[email protected]> Wed, 09 Apr 2014 14:41:03 +0200 + +discosnp (1.0.1-3) unstable; urgency=low + + * d/rules: FTBS fix help2man command + + -- Olivier Sallou <[email protected]> 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 <[email protected]> Thu, 06 Feb 2014 08:04:38 +0100 + +discosnp (1.0.1-1) unstable; urgency=low + + * First debian package (Closes: #737098). + + -- Olivier Sallou <[email protected]> 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 <[email protected]> -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 $< $(CFLAGS) Copied: trunk/packages/discosnp/tags/1.2.3-1/debian/patches/fix_build (from rev 17764, trunk/packages/discosnp/trunk/debian/patches/fix_build) =================================================================== --- trunk/packages/discosnp/tags/1.2.3-1/debian/patches/fix_build (rev 0) +++ trunk/packages/discosnp/tags/1.2.3-1/debian/patches/fix_build 2014-08-19 06:52:42 UTC (rev 17781) @@ -0,0 +1,91 @@ +Subject: Add hardening +Description: makefiles do not import default CFLAGS,... +this patch add debian cflags for hardening +Forwarded: no +Author: Olivier Sallou <[email protected]> +Last-Updated: 2014-02-01 +Index: discoSnp/kissnp2/makefile +=================================================================== +--- discoSnp.orig/kissnp2/makefile ++++ discoSnp/kissnp2/makefile +@@ -33,7 +33,10 @@ + #knowledge of the CeCILL license and that you accept its terms. + + CC=g++ +-CFLAGS= -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER ++CPPFLAGS:=$(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) _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
