[med-svn] r12862 - in trunk/packages/wise/trunk/debian: . patches
Philipp Benner
philipp at alioth.debian.org
Mon Jan 28 19:39:34 UTC 2013
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 <philipp at debian.org> 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 <philipp at debian.org>, Steffen Moeller <moeller at debian.org>, Charles Plessy <plessy at debian.org>
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
#
More information about the debian-med-commit
mailing list