Author: philipp Date: 2013-01-28 19:39:34 +0000 (Mon, 28 Jan 2013) New Revision: 12862
Modified: trunk/packages/wise/trunk/debian/changelog trunk/packages/wise/trunk/debian/control trunk/packages/wise/trunk/debian/patches/05_glib2.patch Log: release 2.4.1-12 Modified: trunk/packages/wise/trunk/debian/changelog =================================================================== --- trunk/packages/wise/trunk/debian/changelog 2013-01-28 14:35:35 UTC (rev 12861) +++ trunk/packages/wise/trunk/debian/changelog 2013-01-28 19:39:34 UTC (rev 12862) @@ -1,3 +1,10 @@ +wise (2.4.1-12) unstable; urgency=low + + * Added missing -D_FORTIFY_SOURCE=2 for hardening support + * Standards version 3.9.4 + + -- Philipp Benner <[email protected]> Mon, 28 Jan 2013 20:33:16 +0100 + wise (2.4.1-11) unstable; urgency=low [ Andreas Tille ] Modified: trunk/packages/wise/trunk/debian/control =================================================================== --- trunk/packages/wise/trunk/debian/control 2013-01-28 14:35:35 UTC (rev 12861) +++ trunk/packages/wise/trunk/debian/control 2013-01-28 19:39:34 UTC (rev 12862) @@ -5,7 +5,7 @@ Uploaders: Philipp Benner <[email protected]>, Steffen Moeller <[email protected]>, Charles Plessy <[email protected]> Build-Depends: debhelper (>= 8), dpkg-dev (>= 1.16.1~), quilt, texlive-latex-base, texlive-extra-utils, hevea, docbook-to-man, libglib2.0-dev -Standards-Version: 3.9.3 +Standards-Version: 3.9.4 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/wise/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/wise/trunk/ Homepage: http://www.ebi.ac.uk/~birney/wise2/ Modified: trunk/packages/wise/trunk/debian/patches/05_glib2.patch =================================================================== --- trunk/packages/wise/trunk/debian/patches/05_glib2.patch 2013-01-28 14:35:35 UTC (rev 12861) +++ trunk/packages/wise/trunk/debian/patches/05_glib2.patch 2013-01-28 19:39:34 UTC (rev 12862) @@ -16,7 +16,7 @@ # normal linux/bsd/mac flags -CFLAGS = -c -O3 `glib-config --cflags` -+CFLAGS += -c -O3 `pkg-config --cflags glib-2.0` ++CFLAGS += $(CPPFLAGS) -c -O3 `pkg-config --cflags glib-2.0` EXTRALIBS = -lm @@ -27,7 +27,7 @@ #CFLAGS = -c -O2 -pg -I../base/ -I../dynlibsrc/ #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ -I. -CFLAGS = -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `glib-config --cflags` -+CFLAGS += -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config --cflags glib-2.0` ++CFLAGS += $(CPPFLAGS) -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config --cflags glib-2.0` -LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lpthread -lm +LDFLAGS += -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lpthread -lm @@ -45,15 +45,19 @@ DFLAGS = -l -D -n Wise2_ -a _api.h -b _api.t -pthreads -dbtrace 5 -nocwarn --- a/src/corba/makefile +++ b/src/corba/makefile -@@ -3,7 +3,7 @@ +@@ -3,9 +3,9 @@ CC = cc INCFLAGS = -I../base/ -I../dynlibsrc #gCFLAGS = -Wall -g -pedantic -c -DUNIX -I../base/ -#CFLAGS = -O2 -c -DUNIX -I../base/ `glib-config --cflags` -I/usr/local/include/orbit-1.0/ +-CFLAGS = -pthread -c -DUNIX -I../base/ -I../dynlibsrc `orbit-config --cflags client` +-LFLAGS = -L../base/ -lm -lpthread +#CFLAGS += -O2 -c -DUNIX -I../base/ `pkg-config --cflags glib-2.0` -I/usr/local/include/orbit-1.0/ - CFLAGS = -pthread -c -DUNIX -I../base/ -I../dynlibsrc `orbit-config --cflags client` - LFLAGS = -L../base/ -lm -lpthread ++CFLAGS += $(CPPFLAGS) -pthread -c -DUNIX -I../base/ -I../dynlibsrc `orbit-config --cflags client` ++LDFLAGS += -L../base/ -lm -lpthread AR_OPTIONS = ru + + @@ -14,18 +14,18 @@ orbit-idl hspscan_corba.idl @@ -410,49 +414,116 @@ # --- a/src/dnaindex/makefile +++ b/src/dnaindex/makefile -@@ -27,14 +27,14 @@ +@@ -27,53 +27,53 @@ kwise : kwise.o $(ASSEMBLY_OBJ) - $(CC) -o kwise kwise.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs` -+ $(CC) -o kwise kwise.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `pkg-config --libs glib-2.0` ++ $(CC) -o kwise kwise.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `pkg-config --libs glib-2.0` arraymatcher : arraymatcher.o $(ASSEMBLY_OBJ) - $(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs` -+ $(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `pkg-config --libs glib-2.0` ++ $(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `pkg-config --libs glib-2.0` findbad_kmer : findbad_kmer.o $(ASSEMBLY_OBJ) - $(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs` -+ $(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `pkg-config --libs glib-2.0` ++ $(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `pkg-config --libs glib-2.0` make_shotgun : make_shotgun.o shotgun.o - $(CC) -o make_shotgun make_shotgun.o shotgun.o -ldyna -lwisebase $(LFLAGS) -@@ -70,10 +70,10 @@ - $(CC) -o show_euler show_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LFLAGS) +- $(CC) -o make_shotgun make_shotgun.o shotgun.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o make_shotgun make_shotgun.o shotgun.o -ldyna -lwisebase $(LDFLAGS) + test_dnanumber : test_dnanumber.o dnanumber.o +- $(CC) -o test_dnanumber test_dnanumber.o dnanumber.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o test_dnanumber test_dnanumber.o dnanumber.o -ldyna -lwisebase $(LDFLAGS) + + test_linkindex : test_linkindex.o linkindex.o dnanumber.o +- $(CC) -o test_linkindex test_linkindex.o linkindex.o dnanumber.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o test_linkindex test_linkindex.o linkindex.o dnanumber.o -ldyna -lwisebase $(LDFLAGS) + + test_forwardindex : test_forwardindex.o forwardindex.o +- $(CC) -o test_forwardindex test_forwardindex.o forwardindex.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o test_forwardindex test_forwardindex.o forwardindex.o -ldyna -lwisebase $(LDFLAGS) + + test_euler : test_euler.o eulerindex.o singleseqspace.o +- $(CC) -o test_euler test_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o test_euler test_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LDFLAGS) + + test_kmer : test_kmer.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o kmer_assembly_untangler.o kmer_assembly_contig.o kmer_assembly_error.o assembly.o +- $(CC) -o test_kmer test_kmer.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o kmer_assembly_untangler.o kmer_assembly_error.o kmer_assembly_contig.o assembly.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o test_kmer test_kmer.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o kmer_assembly_untangler.o kmer_assembly_error.o kmer_assembly_contig.o assembly.o -ldyna -lwisebase $(LDFLAGS) + + kmer_stat : kmer_stat.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o +- $(CC) -o kmer_stat kmer_stat.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o kmer_stat kmer_stat.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o -ldyna -lwisebase $(LDFLAGS) + + test_compara : test_compara.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o +- $(CC) -o test_compara test_compara.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o test_compara test_compara.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o -ldyna -lwisebase $(LDFLAGS) + + bigseqwise : bigseqwise.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o +- $(CC) -o bigseqwise bigseqwise.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o bigseqwise bigseqwise.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o -ldyna -lwisebase $(LDFLAGS) + + + + + show_euler : show_euler.o eulerindex.o singleseqspace.o +- $(CC) -o show_euler show_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o show_euler show_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LDFLAGS) + CC = cc -CFLAGS = -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `glib-config --cflags` -+CFLAGS += -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` ++CFLAGS += $(CPPFLAGS) -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` -LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lm -+LFLAGS += -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lm ++LDFLAGS += -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lm .c.o : --- a/src/dnaindex/assembly/makefile +++ b/src/dnaindex/assembly/makefile -@@ -26,10 +26,10 @@ +@@ -3,33 +3,33 @@ + .SUFFIXES : .dy + test_basegraph : test_basegraph.o basegraph.o +- $(CC) -o test_basegraph test_basegraph.o basegraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o test_basegraph test_basegraph.o basegraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o $(LDFLAGS) -ldyna -lwisebase + test_assemblygraph : test_assemblygraph.o assemblygraph.o assemblystats.o basegraph.o +- $(CC) -o test_assemblygraph test_assemblygraph.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o test_assemblygraph test_assemblygraph.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LDFLAGS) -ldyna -lwisebase + + + test_graphtangle : test_graphtangle.o assemblygraph.o assemblystats.o basegraph.o graphtangle.o assemblypath.o +- $(CC) -o test_graphtangle test_graphtangle.o assemblystats.o basegraph.o assemblygraph.o graphtangle.o assemblypath.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o ../kmer_hash.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o test_graphtangle test_graphtangle.o assemblystats.o basegraph.o assemblygraph.o graphtangle.o assemblypath.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o ../kmer_hash.o $(LDFLAGS) -ldyna -lwisebase + + + pathwise : pathwise.o supertangle.o assemblygraph.o assemblystats.o basegraph.o graphtangle.o assemblypath.o grapherror.o graphmanager.o depthmanager.o +- $(CC) -o pathwise pathwise.o supertangle.o depthmanager.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o graphtangle.o assemblypath.o grapherror.o graphmanager.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o ../assembly_sanger_project.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o pathwise pathwise.o supertangle.o depthmanager.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o graphtangle.o assemblypath.o grapherror.o graphmanager.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o ../assembly_sanger_project.o $(LDFLAGS) -ldyna -lwisebase + + + badkmer : badkmer.o assemblygraph.o assemblystats.o basegraph.o +- $(CC) -o badkmer badkmer.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o badkmer badkmer.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LDFLAGS) -ldyna -lwisebase + + arraymatcher : arraymatcher.o assemblygraph.o assemblystats.o basegraph.o +- $(CC) -o arraymatcher arraymatcher.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o arraymatcher arraymatcher.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LDFLAGS) -ldyna -lwisebase + + + CC = cc -CFLAGS = -Wall -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `glib-config --cflags` -+CFLAGS += -Wall -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `pkg-config --cflags glib-2.0` ++CFLAGS += $(CPPFLAGS) -Wall -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `pkg-config --cflags glib-2.0` -LFLAGS = -g -L../../base/ -L../../dynlibsrc/ -lpthread `glib-config --libs` -lm -+LFLAGS += -g -L../../base/ -L../../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lm ++LDFLAGS += -g -L../../base/ -L../../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lm .c.o : @@ -465,7 +536,7 @@ -CFLAGS = -Wall -pthread -g3 -DCOMPILE_VERBOSITY -DPTHREAD -O2 -c -DUNIX -I../base/ `glib-config --cflags` -#CFLAGS = -Wall -g3 -pg -DPTHREAD -O2 -c -DUNIX -I../base/ `glib-config --cflags` -#CFLAGS = -O2 -c -pthread -DUNIX -I../base/ `glib-config --cflags` -+CFLAGS += -Wall -pthread -g3 -DCOMPILE_VERBOSITY -DPTHREAD -O2 -c -DUNIX -I../base/ `pkg-config --cflags glib-2.0` ++CFLAGS += $(CPPFLAGS) -Wall -pthread -g3 -DCOMPILE_VERBOSITY -DPTHREAD -O2 -c -DUNIX -I../base/ `pkg-config --cflags glib-2.0` +#CFLAGS += -Wall -g3 -pg -DPTHREAD -O2 -c -DUNIX -I../base/ `pkg-config --cflags glib-2.0` +#CFLAGS += -O2 -c -pthread -DUNIX -I../base/ `pkg-config --cflags glib-2.0` #CFLAGS = -O -c -DUNIX -DNOERROR -I../base/ @@ -544,7 +615,7 @@ INCFLAGS = -I../base/ -I../socket -I../dynlibsrc -I../dnaindex -CFLAGS = -O2 -c -pthread -DUNIX -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `glib-config --cflags` -LFLAGS = -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `glib-config --libs` -+CFLAGS += -O2 -c -pthread -DUNIX -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `pkg-config --cflags glib-2.0` ++CFLAGS += $(CPPFLAGS) -O2 -c -pthread -DUNIX -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `pkg-config --cflags glib-2.0` +LDFLAGS += -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config --libs glib-2.0` AR_OPTIONS = ru @@ -566,8 +637,8 @@ CC = cc -CFLAGS = -O2 -g3 -c -pthread -DUNIX -I../base/ -I../dynlibsrc `glib-config --cflags` -LFLAGS = -g -L../base/ -L../dynlibsrc -lm `glib-config --libs` -+CFLAGS += -O2 -g3 -c -pthread -DUNIX -I../base/ -I../dynlibsrc `pkg-config --cflags glib-2.0` -+LFLAGS += -g -L../base/ -L../dynlibsrc -lm `pkg-config --libs glib-2.0` ++CFLAGS += $(CPPFLAGS) -O2 -g3 -c -pthread -DUNIX -I../base/ -I../dynlibsrc `pkg-config --cflags glib-2.0` ++LDFLAGS += -g -L../base/ -L../dynlibsrc -lm `pkg-config --libs glib-2.0` AR_OPTIONS = ru RANLIB_NEEDED = 0 @@ -581,8 +652,8 @@ -CFLAGS = -c -O2 -DUNIX -pthread -LFLAGS = -g -lm +#CFLAGS += -c -g -DUNIX -DWISE_MEMORY_WATCH -+CFLAGS += -c -O2 -DUNIX -pthread -+LDFLAGS += -g -lm ++CFLAGS += $(CPPFLAGS) -c -O2 -DUNIX -pthread ++LDFLAGS += -g -lm DFLAGS = -n Wise2_ -a _api.h -b _api.t -l -D AR_OPTIONS = ru @@ -593,7 +664,7 @@ # CC = cc -CFLAGS = -g -+CFLAGS += -g ++CFLAGS += $(CPPFLAGS) -g ## machine specific definitions # _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
