tags 523715 + patch
thank you
Hi,
Here is a patch that makes wise build with glib-2.0. It seems to build
fine but might need some good testing.
Thank you,
Barry deFreese
Debian QA
diff -u wise-2.4.1/debian/changelog wise-2.4.1/debian/changelog
--- wise-2.4.1/debian/changelog
+++ wise-2.4.1/debian/changelog
@@ -1,3 +1,10 @@
+wise (2.4.1-6.1) unstable; urgency=low
+
+ * Non-maintainer upload.
+ * Build with glib-2.0.
+
+ -- Barry deFreese <bdefre...@debian.org> 13 Apr 2009 11:21:16 -0400
+
wise (2.4.1-6) unstable; urgency=low
* Updated policy to 3.8.0 (no changes required).
diff -u wise-2.4.1/debian/control wise-2.4.1/debian/control
--- wise-2.4.1/debian/control
+++ wise-2.4.1/debian/control
@@ -5,7 +5,7 @@
Uploaders: Philipp Benner <pben...@uni-osnabrueck.de>
DM-Upload-Allowed: yes
Build-Depends: debhelper (>= 5), quilt, texlive-latex-base,
- texlive-extra-utils, hevea, docbook-to-man, libglib1.2-dev
+ texlive-extra-utils, hevea, docbook-to-man, libglib2.0-dev
Standards-Version: 3.8.0
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/
only in patch2:
unchanged:
--- 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
