Author: osallou Date: 2014-05-29 13:01:27 +0000 (Thu, 29 May 2014) New Revision: 17015
Modified: trunk/packages/discosnp/trunk/debian/patches/fix_build Log: update patch for new release Modified: trunk/packages/discosnp/trunk/debian/patches/fix_build =================================================================== --- trunk/packages/discosnp/trunk/debian/patches/fix_build 2014-05-29 12:51:19 UTC (rev 17014) +++ trunk/packages/discosnp/trunk/debian/patches/fix_build 2014-05-29 13:01:27 UTC (rev 17015) @@ -4,8 +4,10 @@ Forwarded: no Author: Olivier Sallou <[email protected]> Last-Updated: 2014-02-01 ---- a/kissnp2/makefile -+++ b/kissnp2/makefile +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. @@ -18,7 +20,7 @@ #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 @@ +@@ -41,7 +44,7 @@ OBJ= $(SRC:.cpp=.o) all: $(EXEC) ifeq ($(prof),1) @@ -27,7 +29,7 @@ endif ifeq ($(deb),1) CFLAGS+=-O0 -DASSERTS -g -lz -@@ -79,7 +82,7 @@ +@@ -79,7 +82,7 @@ endif all: $(EXEC) kissnp2: $(OBJ) kissnp2.cpp @@ -36,9 +38,11 @@ %.o: %.cpp %.h $(CC) -o $@ -c $< $(CFLAGS) ---- a/kissreads/Makefile -+++ b/kissreads/Makefile -@@ -19,9 +19,10 @@ +Index: discoSnp/kissreads/Makefile +=================================================================== +--- discoSnp.orig/kissreads/Makefile ++++ discoSnp/kissreads/Makefile +@@ -19,9 +19,10 @@ CC =gcc # optimized flags @@ -51,7 +55,7 @@ ## debug flags -@@ -49,7 +50,7 @@ +@@ -49,7 +50,7 @@ all: $(ALL) @echo "#################" kissreads: $(OBJ) @@ -60,21 +64,23 @@ 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 $(INCLDIR)tree.h ---- a/minia/makefile -+++ b/minia/makefile +Index: discoSnp/minia/makefile +=================================================================== +--- discoSnp.orig/minia/makefile ++++ discoSnp/minia/makefile @@ -1,5 +1,7 @@ CC=g++ --CFLAGS = -O4 -D_FILE_OFFSET_BITS=64 # needed to handle files > 2 GB on 32 bits systems +-CFLAGS+= -O4 -D_FILE_OFFSET_BITS=64 # needed to handle files > 2 GB on 32 bits systems +CPPFLAGS:=$(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 +62,7 @@ - all: $(EXEC) +@@ -61,7 +63,7 @@ all: + $(MAKE) $(EXEC) - minia: clean $(OBJ) Minia.cpp + minia: $(OBJ) Minia.cpp - $(CC) -o $@ $(OBJ) Minia.cpp $(CFLAGS) -lz + $(CC) -o $@ $(OBJ) Minia.cpp $(CFLAGS) $(LDFLAGS) -lz _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
