[med-svn] r4281 - in trunk/packages/wise/trunk/debian: . patches
Philipp Benner
philipp at alioth.debian.org
Sat Oct 31 21:33:35 UTC 2009
Author: philipp
Date: 2009-10-31 21:33:34 +0000 (Sat, 31 Oct 2009)
New Revision: 4281
Added:
trunk/packages/wise/trunk/debian/README.source
trunk/packages/wise/trunk/debian/patches/05_glib2.patch
trunk/packages/wise/trunk/debian/patches/06_getline.patch
Removed:
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/copyright
trunk/packages/wise/trunk/debian/patches/series
Log:
patch for #552821
Added: trunk/packages/wise/trunk/debian/README.source
===================================================================
--- trunk/packages/wise/trunk/debian/README.source (rev 0)
+++ trunk/packages/wise/trunk/debian/README.source 2009-10-31 21:33:34 UTC (rev 4281)
@@ -0,0 +1,19 @@
+01_welcome-csh.patch:
+ Removes dependencies on csh and tcsh.
+
+02_isnumber.patch:
+ Replaces isnumber() with isdigit().
+
+03_doc-nodycache.patch:
+ Bugfix in documentation.
+
+04_wise2-pdflatex-update.patch:
+ Use pdflatex instead of latex.
+
+05_glib2.patch:
+ Use glib2 instead of glib1.
+
+06_getline.patch:
+ Fixes conflicting definitions of getline.
+
+ -- Philipp Benner <philipp at debian.org>, Sat, 31 Oct 2009 21:12:15 +0000
Modified: trunk/packages/wise/trunk/debian/changelog
===================================================================
--- trunk/packages/wise/trunk/debian/changelog 2009-10-30 05:25:25 UTC (rev 4280)
+++ trunk/packages/wise/trunk/debian/changelog 2009-10-31 21:33:34 UTC (rev 4281)
@@ -1,3 +1,12 @@
+wise (2.4.1-8) unstable; urgency=low
+
+ * Fixed conflicting definitions of getline(). (Closes: #552821)
+ * Added README.source.
+ * Standards version 3.8.3.
+ * Fixed spelling error in package description.
+
+ -- Philipp Benner <philipp at debian.org> Sat, 31 Oct 2009 21:25:52 +0000
+
wise (2.4.1-7) unstable; urgency=low
[ Steffen Moeller ]
Modified: trunk/packages/wise/trunk/debian/control
===================================================================
--- trunk/packages/wise/trunk/debian/control 2009-10-30 05:25:25 UTC (rev 4280)
+++ trunk/packages/wise/trunk/debian/control 2009-10-31 21:33:34 UTC (rev 4281)
@@ -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>, Steffen Moeller <moeller at debian.org>, Charles Plessy <plessy at debian.org>
+Uploaders: Philipp Benner <philipp at debian.org>, Steffen Moeller <moeller at debian.org>, Charles Plessy <plessy at debian.org>
DM-Upload-Allowed: yes
Build-Depends: debhelper (>= 7), quilt, texlive-latex-base,
texlive-extra-utils, hevea, docbook-to-man, libglib2.0-dev
-Standards-Version: 3.8.1
+Standards-Version: 3.8.3
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/
@@ -31,7 +31,7 @@
algorithm, or more modern ones such as Stephen Altschul's generalised
gap penalties, or even experimental ones developed in house, such as
dba. The development of these algorithms is due to the ease of developing
- such algorithms in the enviroment used by Wise2.
+ such algorithms in the environment used by Wise2.
.
Wise2 has also been written with an eye for reuse and maintainability.
Although it is a pure C package you can access its functionality
Modified: trunk/packages/wise/trunk/debian/copyright
===================================================================
--- trunk/packages/wise/trunk/debian/copyright 2009-10-30 05:25:25 UTC (rev 4280)
+++ trunk/packages/wise/trunk/debian/copyright 2009-10-31 21:33:34 UTC (rev 4281)
@@ -57,7 +57,7 @@
License: LGPL-any
Files: debian/*
-Copyright: © 2006-2007 Philipp Benner <pbenner at uni-osnabrueck.de>
+Copyright: © 2006-2007 Philipp Benner <philipp at debian.org>
© 2009 Steffen Moeller <moeller at debian.org>
© 2009 Charles Plessy <plessy at debian.org>
© 2009 Barry deFreese <bdefreese at debian.org>
@@ -67,4 +67,4 @@
On Debian GNU/Linux systems, the complete text of the GNU General Public
License version 2 can be found in `/usr/share/common-licenses/GPL-2' and the
complete text of the GNU Lesser General Public License can be found in
-`/usr/share/common-licenses/LGPL'.
+`/usr/share/common-licenses/LGPL-3'.
Copied: trunk/packages/wise/trunk/debian/patches/05_glib2.patch (from rev 4280, trunk/packages/wise/trunk/debian/patches/glib2.patch)
===================================================================
--- trunk/packages/wise/trunk/debian/patches/05_glib2.patch (rev 0)
+++ trunk/packages/wise/trunk/debian/patches/05_glib2.patch 2009-10-31 21:33:34 UTC (rev 4281)
@@ -0,0 +1,256 @@
+Author: Barry deFreese <bdefreese at debian.org>
+Description: To build wise2 with the Glib version 2.0 instead of 1.2.
+Forwarded: birney at sanger.ac.uk
+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
Added: trunk/packages/wise/trunk/debian/patches/06_getline.patch
===================================================================
--- trunk/packages/wise/trunk/debian/patches/06_getline.patch (rev 0)
+++ trunk/packages/wise/trunk/debian/patches/06_getline.patch 2009-10-31 21:33:34 UTC (rev 4281)
@@ -0,0 +1,302 @@
+Index: wise-2.4.1/src/HMMer2/sqio.c
+===================================================================
+--- wise-2.4.1.orig/src/HMMer2/sqio.c 2009-10-31 20:10:25.000000000 +0000
++++ wise-2.4.1/src/HMMer2/sqio.c 2009-10-31 20:11:11.000000000 +0000
+@@ -213,7 +213,7 @@
+ }
+ }
+
+-/* Function: getline()
++/* Function: getline_()
+ * Date: SRE, Tue Mar 3 08:30:01 1998 [St. Louis]
+ *
+ * Purpose: read a line from a sequence file into V->sbuffer.
+@@ -229,7 +229,7 @@
+ * Returns: (void)
+ */
+ static void
+-getline(struct ReadSeqVars *V)
++getline_(struct ReadSeqVars *V)
+ {
+ char *cp;
+
+@@ -299,7 +299,7 @@
+ V->seqlen = 0;
+ if (addfirst) addseq(V->sbuffer, V);
+ do {
+- getline(V);
++ getline_(V);
+ /* feof() alone is a bug; files not necessarily \n terminated */
+ if (*(V->sbuffer) == '\0' && feof(V->f))
+ done = TRUE;
+@@ -327,7 +327,7 @@
+ char *sptr;
+ /* load first line of entry */
+ while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
+- getline(V);
++ getline_(V);
+ if (feof(V->f)) return;
+
+ if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL)
+@@ -336,7 +336,7 @@
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID);
+ }
+ do {
+- getline(V);
++ getline_(V);
+ if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0)
+ SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC);
+ else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0)
+@@ -345,7 +345,7 @@
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC);
+ }
+ } while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0));
+- getline(V); /* skip next line, coords */
++ getline_(V); /* skip next line, coords */
+
+ readLoop(0, endPIR, V);
+
+@@ -359,7 +359,7 @@
+ /* get next line
+ */
+ while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
+- getline(V);
++ getline_(V);
+ }
+
+
+@@ -377,7 +377,7 @@
+ char *nm;
+ /* position past ';' comments */
+ do {
+- getline(V);
++ getline_(V);
+ } while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) ));
+
+ if (!feof(V->f))
+@@ -389,7 +389,7 @@
+ }
+
+ while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';'))))
+- getline(V);
++ getline_(V);
+ }
+
+ static int
+@@ -411,7 +411,7 @@
+ if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL)
+ SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME);
+ }
+- getline(V);
++ getline_(V);
+ }
+
+ if (! feof(V->f))
+@@ -420,7 +420,7 @@
+ /* load next line
+ */
+ while ((!feof(V->f)) && (*V->sbuffer != ';'))
+- getline(V);
++ getline_(V);
+ }
+
+
+@@ -438,7 +438,7 @@
+ int in_definition;
+
+ while (strncmp(V->sbuffer, "LOCUS", 5) != 0)
+- getline(V);
++ getline_(V);
+
+ if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL)
+ {
+@@ -449,7 +449,7 @@
+ in_definition = FALSE;
+ while (! feof(V->f))
+ {
+- getline(V);
++ getline_(V);
+ if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer)
+ {
+ if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL)
+@@ -482,11 +482,11 @@
+
+
+ while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer))))
+- getline(V);
++ getline_(V);
+ /* SRE: V->s now holds "//", so sequential
+ reads are wedged: fixed Tue Jul 13 1993 */
+ while (!feof(V->f) && strstr(V->sbuffer, "LOCUS ") != V->sbuffer)
+- getline(V);
++ getline_(V);
+ }
+
+ static int
+@@ -515,7 +515,7 @@
+ Die("bogus GCGdata format? %s", V->sbuffer);
+
+ /* second line contains free text description */
+- getline(V);
++ getline_(V);
+ SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC);
+
+ if (binary) {
+@@ -535,7 +535,7 @@
+ else readLoop(0, endGCGdata, V);
+
+ while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
+- getline(V);
++ getline_(V);
+ }
+
+ static int
+@@ -555,12 +555,12 @@
+ if ((sptr = strtok(NULL, "\n")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC);
+ /* workaround for long NCBI NR lines */
+- while (V->longline && ! feof(V->f)) getline(V);
++ while (V->longline && ! feof(V->f)) getline_(V);
+
+ readLoop(0, endPearson, V);
+
+ while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
+- getline(V);
++ getline_(V);
+ }
+
+
+@@ -587,7 +587,7 @@
+
+ /* make sure we have first line */
+ while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
+- getline(V);
++ getline_(V);
+
+ if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL)
+ {
+@@ -596,7 +596,7 @@
+ }
+
+ do {
+- getline(V);
++ getline_(V);
+ if (!feof(V->f) && strstr(V->sbuffer, "AC ") == V->sbuffer)
+ {
+ if ((sptr = strtok(V->sbuffer+5, "; \t\n")) != NULL)
+@@ -620,7 +620,7 @@
+
+ /* load next record's ID line */
+ while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
+- getline(V);
++ getline_(V);
+ }
+
+
+@@ -636,7 +636,7 @@
+ {
+ char *sptr;
+
+- getline(V); /*s == "seqLen seqid string..."*/
++ getline_(V); /*s == "seqLen seqid string..."*/
+
+ if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
+@@ -647,7 +647,7 @@
+ readLoop(0, endZuker, V);
+
+ while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '('))))
+- getline(V);
++ getline_(V);
+ }
+
+ static void
+@@ -669,7 +669,7 @@
+
+ do {
+ done = feof(V->f);
+- getline(V);
++ getline_(V);
+ if (! done) addseq(V->sbuffer, V);
+ } while (!done);
+ }
+@@ -681,7 +681,7 @@
+ char *sptr;
+ int dostruc = FALSE;
+
+- while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V);
++ while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline_(V);
+
+ if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
+@@ -689,7 +689,7 @@
+ /*CONSTCOND*/
+ while (1)
+ {
+- getline(V);
++ getline_(V);
+ if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; }
+
+ if (strncmp(V->sbuffer, "SRC ", 4) == 0)
+@@ -721,14 +721,14 @@
+ while (1)
+ {
+ /* sequence line */
+- getline(V);
++ getline_(V);
+ if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0)
+ break;
+ addseq(V->sbuffer, V);
+ /* structure line */
+ if (dostruc)
+ {
+- getline(V);
++ getline_(V);
+ if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; }
+ addstruc(V->sbuffer, V);
+ }
+@@ -736,7 +736,7 @@
+
+
+ while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0)
+- getline(V);
++ getline_(V);
+ }
+
+
+@@ -816,7 +816,7 @@
+
+ /* Load the first line.
+ */
+- getline(dbfp);
++ getline_(dbfp);
+
+ return dbfp;
+ }
+@@ -833,7 +833,7 @@
+ Die("SeqfilePosition() failed: in a nonrewindable data file or stream");
+
+ fseek(sqfp->f, offset, SEEK_SET);
+- getline(sqfp);
++ getline_(sqfp);
+ }
+
+
+@@ -853,7 +853,7 @@
+ if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0;
+ else {
+ rewind(sqfp->f);
+- getline(sqfp);
++ getline_(sqfp);
+ }
+ }
+
+@@ -949,7 +949,7 @@
+ do { /* skip leading comments on GCG file */
+ gotuw = (strstr(V->sbuffer,"..") != NULL);
+ if (gotuw) readUWGCG(V);
+- getline(V);
++ getline_(V);
+ } while (! feof(V->f));
+ break;
+
Deleted: trunk/packages/wise/trunk/debian/patches/glib2.patch
===================================================================
--- trunk/packages/wise/trunk/debian/patches/glib2.patch 2009-10-30 05:25:25 UTC (rev 4280)
+++ trunk/packages/wise/trunk/debian/patches/glib2.patch 2009-10-31 21:33:34 UTC (rev 4281)
@@ -1,256 +0,0 @@
-Author: Barry deFreese <bdefreese at debian.org>
-Description: To build wise2 with the Glib version 2.0 instead of 1.2.
-Forwarded: birney at sanger.ac.uk
-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 2009-10-30 05:25:25 UTC (rev 4280)
+++ trunk/packages/wise/trunk/debian/patches/series 2009-10-31 21:33:34 UTC (rev 4281)
@@ -1,5 +1,6 @@
-glib2.patch
01_welcome-csh.patch
02_isnumber.patch
03_doc-nodycache.patch
04_wise2-pdflatex-update.patch
+05_glib2.patch
+06_getline.patch
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