[med-svn] r3289 - in trunk/packages/wise/trunk/debian: . patches
Steffen Möller
smoe-guest at alioth.debian.org
Thu Apr 16 12:39:22 UTC 2009
Author: smoe-guest
Date: 2009-04-16 12:39:22 +0000 (Thu, 16 Apr 2009)
New Revision: 3289
Added:
trunk/packages/wise/trunk/debian/patches/glib2.patch
Modified:
trunk/packages/wise/trunk/debian/changelog
trunk/packages/wise/trunk/debian/control
trunk/packages/wise/trunk/debian/patches/series
trunk/packages/wise/trunk/debian/wise-doc.doc-base.api
Log:
Importing Barry's patch for glib-2 compatibility.
Modified: trunk/packages/wise/trunk/debian/changelog
===================================================================
--- trunk/packages/wise/trunk/debian/changelog 2009-04-13 21:28:58 UTC (rev 3288)
+++ trunk/packages/wise/trunk/debian/changelog 2009-04-16 12:39:22 UTC (rev 3289)
@@ -1,3 +1,11 @@
+wise (2.4.1-7) UNRELEASED; urgency=low
+
+ * Now builds with glib-2.0 (Closes: #523715). [ Special thank to Barry deFreese ]
+ * Updated policy to 3.8.1 (no changes required). (Steffen)
+ * fixed api->API lintian warnin. (Steffen)
+
+ -- Steffen Moeller <moeller at debian.org> Thu, 16 Apr 2009 14:16:50 +0200
+
wise (2.4.1-6) unstable; urgency=low
* Updated policy to 3.8.0 (no changes required).
Modified: trunk/packages/wise/trunk/debian/control
===================================================================
--- trunk/packages/wise/trunk/debian/control 2009-04-13 21:28:58 UTC (rev 3288)
+++ trunk/packages/wise/trunk/debian/control 2009-04-16 12:39:22 UTC (rev 3289)
@@ -2,11 +2,11 @@
Section: science
Priority: optional
Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Philipp Benner <pbenner at uni-osnabrueck.de>
+Uploaders: Philipp Benner <pbenner at uni-osnabrueck.de>, Steffen Moeller <moeller at debian.org>
DM-Upload-Allowed: yes
Build-Depends: debhelper (>= 5), quilt, texlive-latex-base,
- texlive-extra-utils, hevea, docbook-to-man, libglib1.2-dev
-Standards-Version: 3.8.0
+ texlive-extra-utils, hevea, docbook-to-man, libglib2.0-dev
+Standards-Version: 3.8.1
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/wise/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/wise/trunk/
Homepage: http://www.ebi.ac.uk/~birney/wise2/
@@ -14,7 +14,7 @@
Package: wise
Architecture: any
Depends: ${shlibs:Depends}
-Recommends: wise-doc (= ${source:Version})
+Suggests: wise-doc (= ${source:Version})
Description: comparison of biopolymers, commonly DNA and protein sequences
Wise2 is a package focused on comparisons of biopolymers, commonly DNA
and protein sequences. There are many other packages which do
Added: trunk/packages/wise/trunk/debian/patches/glib2.patch
===================================================================
--- trunk/packages/wise/trunk/debian/patches/glib2.patch (rev 0)
+++ trunk/packages/wise/trunk/debian/patches/glib2.patch 2009-04-16 12:39:22 UTC (rev 3289)
@@ -0,0 +1,253 @@
+diff -u wise-2.4.1/debian/control wise-2.4.1/debian/control
+--- wise-2.4.1.orig/src/makefile
++++ wise-2.4.1/src/makefile
+@@ -31,13 +31,13 @@
+
+
+ # Intel icc flags
+-# CFLAGS = -c -O3 -axWK -ipo `glib-config --cflags`
++# CFLAGS = -c -O3 -axWK -ipo `pkg-config --cflags glib-2.0`
+
+ # alpha flags (-pthread)
+-# CFLAGS = -c -O3 -pthread `glib-config --cflags`
++# CFLAGS = -c -O3 -pthread `pkg-config --cflags glib-2.0`
+
+ # normal linux/bsd/mac flags
+-CFLAGS = -c -O3 `glib-config --cflags`
++CFLAGS = -c -O3 `pkg-config --cflags glib-2.0`
+
+
+ EXTRALIBS = -lm
+only in patch2:
+unchanged:
+--- wise-2.4.1.orig/src/snp/makefile
++++ wise-2.4.1/src/snp/makefile
+@@ -5,9 +5,9 @@
+ CC = cc
+ #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`
+
+-LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lpthread -lm
++LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lpthread -lm
+ AR_OPTIONS = ru
+
+ RANLIB_NEEDED = 0
+only in patch2:
+unchanged:
+--- wise-2.4.1.orig/src/corba/makefile
++++ wise-2.4.1/src/corba/makefile
+@@ -3,7 +3,7 @@
+ 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 = -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
+ AR_OPTIONS = ru
+@@ -14,18 +14,18 @@
+ orbit-idl hspscan_corba.idl
+
+ test_server : test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o
+- cc -g -o test_server test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o ../dynlibsrc/libdyna_glib.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
++ cc -g -o test_server test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o ../dynlibsrc/libdyna_glib.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread
+
+ scanwise_protein_index : scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o
+- cc -o scanwise_protein_index scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna_glib.a ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
++ cc -o scanwise_protein_index scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna_glib.a ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread
+
+
+ test_client : test_client.o hspscan_corba-common.o hspscan_corba-stubs.o
+- cc -g -o test_client test_client.o hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
++ cc -g -o test_client test_client.o hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread
+
+
+ test_wrapper : test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o hspscan_corba_wrapper.o corba_singleton.o
+- cc -g -o test_wrapper test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o corba_singleton.o hspscan_corba_wrapper.o ../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
++ cc -g -o test_wrapper test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o corba_singleton.o hspscan_corba_wrapper.o ../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread
+
+ .c.o :
+ $(CC) $(CFLAGS) $(INCFLAGS) $?
+only in patch2:
+unchanged:
+--- wise-2.4.1.orig/src/models/makefile
++++ wise-2.4.1/src/models/makefile
+@@ -192,10 +192,10 @@
+ $(CC) -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
+
+ scanwisep.o : scanwisep.c
+- $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `glib-config --cflags` $?
++ $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `pkg-config --cflags glib-2.0` $?
+
+ hsp2aln_sw.o : hsp2aln_sw.c
+- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $?
++ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config --cflags glib-2.0` $?
+
+ scanwisep_mysql.o : scanwisep.c
+ $(CC) $(CFLAGS) -DSCAN_MYSQL -I../corba -I../external/mott -I../mysql/protein_index/ -I/usr/local/mysql/include scanwisep.c
+@@ -226,25 +226,25 @@
+
+
+ scanwisep : scanwisep.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o
+- $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o $(LFLAGS) -L../external/mott -lmott -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `glib-config --libs` -lpthread
++ $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o $(LFLAGS) -L../external/mott -lmott -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread
+
+ test_gwhsp : test_gwhsp.o genewisehsp.o
+- $(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `glib-config --libs` -lpthread
++ $(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread
+
+ localcishit.o : localcishit.c
+- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $?
++ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config --cflags glib-2.0` $?
+
+ promoterwise.o : promoterwise.c
+- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $?
++ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config --cflags glib-2.0` $?
+
+ promoterwise : promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o
+- $(CC) -g -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `glib-config --libs` -lpthread
++ $(CC) -g -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread
+
+ test_deng : test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o
+- $(CC) -o test_deng test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `glib-config --libs` -lpthread
++ $(CC) -o test_deng test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread
+
+ promotercluster : promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o
+- $(CC) -o promotercluster promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `glib-config --libs` -lpthread
++ $(CC) -o promotercluster promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread
+
+ dnawise : dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o
+ $(CC) -o dnawise dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lpthread
+@@ -345,11 +345,11 @@
+ CC = cc
+ #CFLAGS = -c -O2 -pg -I../base/ -I../dynlibsrc/
+ #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ -I.
+-CFLAGS = -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `glib-config --cflags`
+-#CFLAGS = -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `glib-config --cflags`
++CFLAGS = -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config --cflags glib-2.0`
++#CFLAGS = -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0`
+ #LFLAGS = -L../base/ -L../dynlibsrc/ -L../HMMer2/
+
+-LFLAGS = -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `glib-config --libs`
++LFLAGS = -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `pkg-config --libs glib-2.0`
+ AR_OPTIONS = ru
+
+ RANLIB_NEEDED = 0
+only in patch2:
+unchanged:
+--- wise-2.4.1.orig/src/dnaindex/makefile
++++ wise-2.4.1/src/dnaindex/makefile
+@@ -27,14 +27,14 @@
+
+
+ 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`
+
+ 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`
+
+
+ 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`
+
+ 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 = 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`
+
+
+-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
+
+
+ .c.o :
+only in patch2:
+unchanged:
+--- wise-2.4.1.orig/src/dnaindex/assembly/makefile
++++ wise-2.4.1/src/dnaindex/assembly/makefile
+@@ -26,10 +26,10 @@
+
+
+ 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`
+
+
+-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
+
+
+ .c.o :
+only in patch2:
+unchanged:
+--- wise-2.4.1.orig/src/dynlibsrc/makefile
++++ wise-2.4.1/src/dynlibsrc/makefile
+@@ -84,9 +84,9 @@
+ CC = cc
+ INCFLAGS = -I../base/
+ #CFLAGS = -Wall -g -pedantic -c -DUNIX -I../base/
+-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 = -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/
+ LFLAGS = -g -L../base/ -lm
+ AR_OPTIONS = ru
+@@ -148,13 +148,13 @@
+ $(CC) -g -o test_shadowindex test_shadowindex.o shadowseqindex.o shadowseq.o ./libdyna.a ../base/libwisebase.a -lm
+
+ test_seqhash : test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a
+- $(CC) -g -o test_seqhash `glib-config --libs` test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a ../base/libwisebase.a -lm
++ $(CC) -g -o test_seqhash `pkg-config --libs glib-2.0` test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a ../base/libwisebase.a -lm
+
+ test_hsp : test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o
+- $(CC) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `glib-config --libs`
++ $(CC) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `pkg-config --libs glib-2.0`
+
+ test_topscore : test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o
+- $(CC) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `glib-config --libs`
++ $(CC) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `pkg-config --libs glib-2.0`
+
+
+ testgendb : probability.o genomicdb.o genomic.o testgendb.o sequence.o codon.o sequencedb.o complexsequence.o complexevalset.o
+only in patch2:
+unchanged:
+--- wise-2.4.1.orig/src/network/makefile
++++ wise-2.4.1/src/network/makefile
+@@ -3,8 +3,8 @@
+
+ CC = cc
+ 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`
++LFLAGS = -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config --libs glib-2.0`
+ AR_OPTIONS = ru
+
+ RANLIB_NEEDED = 0
+only in patch2:
+unchanged:
+--- wise-2.4.1.orig/src/other_programs/makefile
++++ wise-2.4.1/src/other_programs/makefile
+@@ -3,8 +3,8 @@
+ .SUFFIXES : .dy
+
+ 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`
+ AR_OPTIONS = ru
+
+ RANLIB_NEEDED = 0
Modified: trunk/packages/wise/trunk/debian/patches/series
===================================================================
--- trunk/packages/wise/trunk/debian/patches/series 2009-04-13 21:28:58 UTC (rev 3288)
+++ trunk/packages/wise/trunk/debian/patches/series 2009-04-16 12:39:22 UTC (rev 3289)
@@ -1,3 +1,4 @@
+glib2.patch
01_welcome-csh.patch
02_isnumber.patch
03_doc-nodycache.patch
Modified: trunk/packages/wise/trunk/debian/wise-doc.doc-base.api
===================================================================
--- trunk/packages/wise/trunk/debian/wise-doc.doc-base.api 2009-04-13 21:28:58 UTC (rev 3288)
+++ trunk/packages/wise/trunk/debian/wise-doc.doc-base.api 2009-04-16 12:39:22 UTC (rev 3289)
@@ -1,7 +1,7 @@
Document: wise-api
Title: Wise API Manual
Author: Ewan Birney
-Abstract: This manual describes the wise api.
+Abstract: This manual describes the wise API.
Section: Science/Biology
Format: PDF
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