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/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
\___ /|__| (____ /____/\____ | |__||__|
/_____/ \/ \/
grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
wise-2.4.1/src/snp/makefile-8-#CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ -I.
wise-2.4.1/src/snp/makefile:9:CFLAGS += $(CPPFLAGS) -c -g3 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `$(PKG_CONFIG) --cflags glib-2.0`
wise-2.4.1/src/snp/makefile-10-
wise-2.4.1/src/snp/makefile:11:LDFLAGS += -g -L../base/ -L../dynlibsrc/ -lpthread `$(PKG_CONFIG) --libs glib-2.0` -lpthread -lm
wise-2.4.1/src/snp/makefile-12-AR_OPTIONS = ru
##############################################
wise-2.4.1/src/perl/makelib.pl-63- print STDERR "Updating $dest\n";
wise-2.4.1/src/perl/makelib.pl:64: system("cp $file $dest");
wise-2.4.1/src/perl/makelib.pl-65- } else {
##############################################
wise-2.4.1/src/perl/scripts/blastwise.pl-36-if( !defined $seqfile ) {
wise-2.4.1/src/perl/scripts/blastwise.pl:37: system("pod2text $0");
wise-2.4.1/src/perl/scripts/blastwise.pl-38- exit(1);
##############################################
wise-2.4.1/src/perl/scripts/blastwise.pl-106-if( ! -e $TEMPFILE ) {
wise-2.4.1/src/perl/scripts/blastwise.pl:107: if ( system("$BLASTEXE $db $seqfile > $TEMPFILE") != 0 ) {
wise-2.4.1/src/perl/scripts/blastwise.pl-108- die("Could not run blast [$BLASTEXE $db $seqfile > $TEMPFILE] $! $?");
##############################################
wise-2.4.1/src/perl/scripts/estwise.pl-32-if( !defined $dna_file ) {
wise-2.4.1/src/perl/scripts/estwise.pl:33: system("perldoc $0");
wise-2.4.1/src/perl/scripts/estwise.pl-34- exit(1);
##############################################
wise-2.4.1/src/perl/scripts/halfwise.pl-245-
wise-2.4.1/src/perl/scripts/halfwise.pl:246:if( system("blastx $half_db $filename -V=10000 -B=10000 > $filename.blx.$$") != 0 ) {
wise-2.4.1/src/perl/scripts/halfwise.pl-247- die "There blastx search did not complete correctly\n";
##############################################
wise-2.4.1/src/test/testman.pl-61-
wise-2.4.1/src/test/testman.pl:62: if( ($exit = system($do)) != 0 ) {
wise-2.4.1/src/test/testman.pl-63- print $talk_file ">>> Bad exit status - $exit (system - $!)\n";
##############################################
wise-2.4.1/src/corba/makefile-6-#gCFLAGS = -Wall -g -pedantic -c -DUNIX -I../base/
wise-2.4.1/src/corba/makefile:7:#CFLAGS += -c -DUNIX -I../base/ `$(PKG_CONFIG) --cflags glib-2.0` -I/usr/local/include/orbit-1.0/
wise-2.4.1/src/corba/makefile-8-CFLAGS += $(CPPFLAGS) -pthread -c -DUNIX -I../base/ -I../dynlibsrc `orbit-config --cflags client`
##############################################
wise-2.4.1/src/corba/makefile-17-test_server : test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o
wise-2.4.1/src/corba/makefile:18: cc -g -o test_server test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o ../dynlibsrc/libdyna_glib.a `$(PKG_CONFIG) --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread
wise-2.4.1/src/corba/makefile-19-
wise-2.4.1/src/corba/makefile-20-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
wise-2.4.1/src/corba/makefile:21: 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 `$(PKG_CONFIG) --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread
wise-2.4.1/src/corba/makefile-22-
##############################################
wise-2.4.1/src/corba/makefile-24-test_client : test_client.o hspscan_corba-common.o hspscan_corba-stubs.o
wise-2.4.1/src/corba/makefile:25: cc -g -o test_client test_client.o hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `$(PKG_CONFIG) --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread
wise-2.4.1/src/corba/makefile-26-
##############################################
wise-2.4.1/src/corba/makefile-28-test_wrapper : test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o hspscan_corba_wrapper.o corba_singleton.o
wise-2.4.1/src/corba/makefile:29: 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
wise-2.4.1/src/corba/makefile-30-
##############################################
wise-2.4.1/src/network/makefile-6-INCFLAGS = -I../base/ -I../socket -I../dynlibsrc -I../dnaindex
wise-2.4.1/src/network/makefile:7:CFLAGS += $(CPPFLAGS) -c -pthread -DUNIX -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `$(PKG_CONFIG) --cflags glib-2.0`
wise-2.4.1/src/network/makefile:8:LDFLAGS += -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `$(PKG_CONFIG) --libs glib-2.0`
wise-2.4.1/src/network/makefile-9-AR_OPTIONS = ru
##############################################
wise-2.4.1/src/other_programs/makefile-6-PKG_CONFIG ?= pkg-config
wise-2.4.1/src/other_programs/makefile:7:CFLAGS += $(CPPFLAGS) -g3 -c -pthread -DUNIX -I../base/ -I../dynlibsrc `$(PKG_CONFIG) --cflags glib-2.0`
wise-2.4.1/src/other_programs/makefile:8:LDFLAGS += -g -L../base/ -L../dynlibsrc -lm `$(PKG_CONFIG) --libs glib-2.0`
wise-2.4.1/src/other_programs/makefile-9-AR_OPTIONS = ru
##############################################
wise-2.4.1/src/models/makefile-194-scanwisep.o : scanwisep.c
wise-2.4.1/src/models/makefile:195: $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `$(PKG_CONFIG) --cflags glib-2.0` $?
wise-2.4.1/src/models/makefile-196-
wise-2.4.1/src/models/makefile-197-hsp2aln_sw.o : hsp2aln_sw.c
wise-2.4.1/src/models/makefile:198: $(CC) $(CFLAGS) $(INCFLAGS) `$(PKG_CONFIG) --cflags glib-2.0` $?
wise-2.4.1/src/models/makefile-199-
##############################################
wise-2.4.1/src/models/makefile-228-scanwisep : scanwisep.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o
wise-2.4.1/src/models/makefile:229: $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o $(LDFLAGS) -L../external/mott -lmott -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `$(PKG_CONFIG) --libs glib-2.0` -lpthread
wise-2.4.1/src/models/makefile-230-
wise-2.4.1/src/models/makefile-231-test_gwhsp : test_gwhsp.o genewisehsp.o
wise-2.4.1/src/models/makefile:232: $(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LDFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `$(PKG_CONFIG) --libs glib-2.0` -lpthread
wise-2.4.1/src/models/makefile-233-
wise-2.4.1/src/models/makefile-234-localcishit.o : localcishit.c
wise-2.4.1/src/models/makefile:235: $(CC) $(CFLAGS) $(INCFLAGS) `$(PKG_CONFIG) --cflags glib-2.0` $?
wise-2.4.1/src/models/makefile-236-
wise-2.4.1/src/models/makefile-237-promoterwise.o : promoterwise.c
wise-2.4.1/src/models/makefile:238: $(CC) $(CFLAGS) $(INCFLAGS) `$(PKG_CONFIG) --cflags glib-2.0` $?
wise-2.4.1/src/models/makefile-239-
wise-2.4.1/src/models/makefile-240-promoterwise : promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o
wise-2.4.1/src/models/makefile:241: $(CC) -g -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `$(PKG_CONFIG) --libs glib-2.0` -lpthread
wise-2.4.1/src/models/makefile-242-
wise-2.4.1/src/models/makefile-243-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
wise-2.4.1/src/models/makefile:244: $(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 $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `$(PKG_CONFIG) --libs glib-2.0` -lpthread
wise-2.4.1/src/models/makefile-245-
wise-2.4.1/src/models/makefile-246-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
wise-2.4.1/src/models/makefile:247: $(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 $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `$(PKG_CONFIG) --libs glib-2.0` -lpthread
wise-2.4.1/src/models/makefile-248-
##############################################
wise-2.4.1/src/models/makefile-348-#CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ -I.
wise-2.4.1/src/models/makefile:349:CFLAGS += -c -g3 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `$(PKG_CONFIG) --cflags glib-2.0`
wise-2.4.1/src/models/makefile:350:#CFLAGS += -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `$(PKG_CONFIG) --cflags glib-2.0`
wise-2.4.1/src/models/makefile-351-#LDFLAGS = -L../base/ -L../dynlibsrc/ -L../HMMer2/
wise-2.4.1/src/models/makefile-352-
wise-2.4.1/src/models/makefile:353:LDFLAGS += -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `$(PKG_CONFIG) --libs glib-2.0`
wise-2.4.1/src/models/makefile-354-AR_OPTIONS = ru
##############################################
wise-2.4.1/src/dnaindex/assembly/makefile-29-PKG_CONFIG ?= pkg-config
wise-2.4.1/src/dnaindex/assembly/makefile:30:CFLAGS += $(CPPFLAGS) -Wall -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `$(PKG_CONFIG) --cflags glib-2.0`
wise-2.4.1/src/dnaindex/assembly/makefile-31-
wise-2.4.1/src/dnaindex/assembly/makefile-32-
wise-2.4.1/src/dnaindex/assembly/makefile:33:LDFLAGS += -g -L../../base/ -L../../dynlibsrc/ -lpthread `$(PKG_CONFIG) --libs glib-2.0` -lm
wise-2.4.1/src/dnaindex/assembly/makefile-34-
##############################################
wise-2.4.1/src/dnaindex/makefile-29-kwise : kwise.o $(ASSEMBLY_OBJ)
wise-2.4.1/src/dnaindex/makefile:30: $(CC) -o kwise kwise.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `$(PKG_CONFIG) --libs glib-2.0`
wise-2.4.1/src/dnaindex/makefile-31-
wise-2.4.1/src/dnaindex/makefile-32-arraymatcher : arraymatcher.o $(ASSEMBLY_OBJ)
wise-2.4.1/src/dnaindex/makefile:33: $(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `$(PKG_CONFIG) --libs glib-2.0`
wise-2.4.1/src/dnaindex/makefile-34-
##############################################
wise-2.4.1/src/dnaindex/makefile-36-findbad_kmer : findbad_kmer.o $(ASSEMBLY_OBJ)
wise-2.4.1/src/dnaindex/makefile:37: $(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `$(PKG_CONFIG) --libs glib-2.0`
wise-2.4.1/src/dnaindex/makefile-38-
##############################################
wise-2.4.1/src/dnaindex/makefile-73-PKG_CONFIG ?= pkg-config
wise-2.4.1/src/dnaindex/makefile:74:CFLAGS += $(CPPFLAGS) -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `$(PKG_CONFIG) --cflags glib-2.0`
wise-2.4.1/src/dnaindex/makefile-75-
wise-2.4.1/src/dnaindex/makefile-76-
wise-2.4.1/src/dnaindex/makefile:77:LDFLAGS += -g -L../base/ -L../dynlibsrc/ -lpthread `$(PKG_CONFIG) --libs glib-2.0` -lm
wise-2.4.1/src/dnaindex/makefile-78-
##############################################
wise-2.4.1/src/dynlibsrc/makefile-87-#CFLAGS = -Wall -g -pedantic -c -DUNIX -I../base/
wise-2.4.1/src/dynlibsrc/makefile:88:CFLAGS += $(CPPFLAGS) -Wall -pthread -g3 -DCOMPILE_VERBOSITY -DPTHREAD -c -DUNIX -I../base/ `$(PKG_CONFIG) --cflags glib-2.0`
wise-2.4.1/src/dynlibsrc/makefile:89:#CFLAGS += -Wall -g3 -pg -DPTHREAD -c -DUNIX -I../base/ `$(PKG_CONFIG) --cflags glib-2.0`
wise-2.4.1/src/dynlibsrc/makefile:90:#CFLAGS += -c -pthread -DUNIX -I../base/ `$(PKG_CONFIG) --cflags glib-2.0`
wise-2.4.1/src/dynlibsrc/makefile-91-#CFLAGS = -O -c -DUNIX -DNOERROR -I../base/
##############################################
wise-2.4.1/src/dynlibsrc/makefile-151-test_seqhash : test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a
wise-2.4.1/src/dynlibsrc/makefile:152: $(CC) $(LDFLAGS) -g -o test_seqhash `$(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
wise-2.4.1/src/dynlibsrc/makefile-153-
wise-2.4.1/src/dynlibsrc/makefile-154-test_hsp : test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o
wise-2.4.1/src/dynlibsrc/makefile:155: $(CC) $(LDFLAGS) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `$(PKG_CONFIG) --libs glib-2.0`
wise-2.4.1/src/dynlibsrc/makefile-156-
wise-2.4.1/src/dynlibsrc/makefile-157-test_topscore : test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o
wise-2.4.1/src/dynlibsrc/makefile:158: $(CC) $(LDFLAGS) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `$(PKG_CONFIG) --libs glib-2.0`
wise-2.4.1/src/dynlibsrc/makefile-159-
##############################################
wise-2.4.1/src/makefile-34-# Intel icc flags
wise-2.4.1/src/makefile:35:# CFLAGS += -c -axWK -ipo `$(PKG_CONFIG) --cflags glib-2.0`
wise-2.4.1/src/makefile-36-
wise-2.4.1/src/makefile-37-# alpha flags (-pthread)
wise-2.4.1/src/makefile:38:# CFLAGS += -c -pthread `$(PKG_CONFIG) --cflags glib-2.0`
wise-2.4.1/src/makefile-39-
wise-2.4.1/src/makefile-40-# normal linux/bsd/mac flags
wise-2.4.1/src/makefile:41:CFLAGS += $(CPPFLAGS) -c `$(PKG_CONFIG) --cflags glib-2.0`
wise-2.4.1/src/makefile-42-
##############################################
wise-2.4.1/debian/patches/cross.patch-15--#CFLAGS += -c -DUNIX -I../base/ `pkg-config --cflags glib-2.0` -I/usr/local/include/orbit-1.0/
wise-2.4.1/debian/patches/cross.patch:16:+#CFLAGS += -c -DUNIX -I../base/ `$(PKG_CONFIG) --cflags glib-2.0` -I/usr/local/include/orbit-1.0/
wise-2.4.1/debian/patches/cross.patch-17- CFLAGS += $(CPPFLAGS) -pthread -c -DUNIX -I../base/ -I../dynlibsrc `orbit-config --cflags client`
##############################################
wise-2.4.1/debian/patches/cross.patch-24-- cc -g -o test_server test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o ../dynlibsrc/libdyna_glib.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread
wise-2.4.1/debian/patches/cross.patch:25:+ cc -g -o test_server test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o ../dynlibsrc/libdyna_glib.a `$(PKG_CONFIG) --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread
wise-2.4.1/debian/patches/cross.patch-26-
##############################################
wise-2.4.1/debian/patches/cross.patch-28-- 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
wise-2.4.1/debian/patches/cross.patch:29:+ 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 `$(PKG_CONFIG) --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread
wise-2.4.1/debian/patches/cross.patch-30-
##############################################
wise-2.4.1/debian/patches/cross.patch-33-- cc -g -o test_client test_client.o hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread
wise-2.4.1/debian/patches/cross.patch:34:+ cc -g -o test_client test_client.o hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `$(PKG_CONFIG) --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread
wise-2.4.1/debian/patches/cross.patch-35-
##############################################
wise-2.4.1/debian/patches/cross.patch-38-- 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
wise-2.4.1/debian/patches/cross.patch:39:+ 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
wise-2.4.1/debian/patches/cross.patch-40-
##############################################
wise-2.4.1/debian/patches/cross.patch-50-+PKG_CONFIG ?= pkg-config
wise-2.4.1/debian/patches/cross.patch:51:+CFLAGS += $(CPPFLAGS) -Wall -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `$(PKG_CONFIG) --cflags glib-2.0`
wise-2.4.1/debian/patches/cross.patch-52-
##############################################
wise-2.4.1/debian/patches/cross.patch-54--LDFLAGS += -g -L../../base/ -L../../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lm
wise-2.4.1/debian/patches/cross.patch:55:+LDFLAGS += -g -L../../base/ -L../../dynlibsrc/ -lpthread `$(PKG_CONFIG) --libs glib-2.0` -lm
wise-2.4.1/debian/patches/cross.patch-56-
##############################################
wise-2.4.1/debian/patches/cross.patch-65-- $(CC) -o kwise kwise.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `pkg-config --libs glib-2.0`
wise-2.4.1/debian/patches/cross.patch:66:+ $(CC) -o kwise kwise.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `$(PKG_CONFIG) --libs glib-2.0`
wise-2.4.1/debian/patches/cross.patch-67-
##############################################
wise-2.4.1/debian/patches/cross.patch-69-- $(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `pkg-config --libs glib-2.0`
wise-2.4.1/debian/patches/cross.patch:70:+ $(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `$(PKG_CONFIG) --libs glib-2.0`
wise-2.4.1/debian/patches/cross.patch-71-
##############################################
wise-2.4.1/debian/patches/cross.patch-74-- $(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `pkg-config --libs glib-2.0`
wise-2.4.1/debian/patches/cross.patch:75:+ $(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `$(PKG_CONFIG) --libs glib-2.0`
wise-2.4.1/debian/patches/cross.patch-76-
##############################################
wise-2.4.1/debian/patches/cross.patch-84-+PKG_CONFIG ?= pkg-config
wise-2.4.1/debian/patches/cross.patch:85:+CFLAGS += $(CPPFLAGS) -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `$(PKG_CONFIG) --cflags glib-2.0`
wise-2.4.1/debian/patches/cross.patch-86-
##############################################
wise-2.4.1/debian/patches/cross.patch-88--LDFLAGS += -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lm
wise-2.4.1/debian/patches/cross.patch:89:+LDFLAGS += -g -L../base/ -L../dynlibsrc/ -lpthread `$(PKG_CONFIG) --libs glib-2.0` -lm
wise-2.4.1/debian/patches/cross.patch-90-
##############################################
wise-2.4.1/debian/patches/cross.patch-104--#CFLAGS += -c -pthread -DUNIX -I../base/ `pkg-config --cflags glib-2.0`
wise-2.4.1/debian/patches/cross.patch:105:+CFLAGS += $(CPPFLAGS) -Wall -pthread -g3 -DCOMPILE_VERBOSITY -DPTHREAD -c -DUNIX -I../base/ `$(PKG_CONFIG) --cflags glib-2.0`
wise-2.4.1/debian/patches/cross.patch:106:+#CFLAGS += -Wall -g3 -pg -DPTHREAD -c -DUNIX -I../base/ `$(PKG_CONFIG) --cflags glib-2.0`
wise-2.4.1/debian/patches/cross.patch:107:+#CFLAGS += -c -pthread -DUNIX -I../base/ `$(PKG_CONFIG) --cflags glib-2.0`
wise-2.4.1/debian/patches/cross.patch-108- #CFLAGS = -O -c -DUNIX -DNOERROR -I../base/
##############################################
wise-2.4.1/debian/patches/cross.patch-115-- $(CC) $(LDFLAGS) -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
wise-2.4.1/debian/patches/cross.patch:116:+ $(CC) $(LDFLAGS) -g -o test_seqhash `$(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
wise-2.4.1/debian/patches/cross.patch-117-
##############################################
wise-2.4.1/debian/patches/cross.patch-119-- $(CC) $(LDFLAGS) -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`
wise-2.4.1/debian/patches/cross.patch:120:+ $(CC) $(LDFLAGS) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `$(PKG_CONFIG) --libs glib-2.0`
wise-2.4.1/debian/patches/cross.patch-121-
##############################################
wise-2.4.1/debian/patches/cross.patch-123-- $(CC) $(LDFLAGS) -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`
wise-2.4.1/debian/patches/cross.patch:124:+ $(CC) $(LDFLAGS) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `$(PKG_CONFIG) --libs glib-2.0`
wise-2.4.1/debian/patches/cross.patch-125-
##############################################
wise-2.4.1/debian/patches/cross.patch-142--# CFLAGS += -c -axWK -ipo `pkg-config --cflags glib-2.0`
wise-2.4.1/debian/patches/cross.patch:143:+# CFLAGS += -c -axWK -ipo `$(PKG_CONFIG) --cflags glib-2.0`
wise-2.4.1/debian/patches/cross.patch-144-
##############################################
wise-2.4.1/debian/patches/cross.patch-146--# CFLAGS += -c -pthread `pkg-config --cflags glib-2.0`
wise-2.4.1/debian/patches/cross.patch:147:+# CFLAGS += -c -pthread `$(PKG_CONFIG) --cflags glib-2.0`
wise-2.4.1/debian/patches/cross.patch-148-
##############################################
wise-2.4.1/debian/patches/cross.patch-150--CFLAGS += $(CPPFLAGS) -c `pkg-config --cflags glib-2.0`
wise-2.4.1/debian/patches/cross.patch:151:+CFLAGS += $(CPPFLAGS) -c `$(PKG_CONFIG) --cflags glib-2.0`
wise-2.4.1/debian/patches/cross.patch-152-
##############################################
wise-2.4.1/debian/patches/cross.patch-161-- $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `pkg-config --cflags glib-2.0` $?
wise-2.4.1/debian/patches/cross.patch:162:+ $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `$(PKG_CONFIG) --cflags glib-2.0` $?
wise-2.4.1/debian/patches/cross.patch-163-
##############################################
wise-2.4.1/debian/patches/cross.patch-165-- $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config --cflags glib-2.0` $?
wise-2.4.1/debian/patches/cross.patch:166:+ $(CC) $(CFLAGS) $(INCFLAGS) `$(PKG_CONFIG) --cflags glib-2.0` $?
wise-2.4.1/debian/patches/cross.patch-167-
##############################################
wise-2.4.1/debian/patches/cross.patch-174-- $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o $(LDFLAGS) -L../external/mott -lmott -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread
wise-2.4.1/debian/patches/cross.patch:175:+ $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o $(LDFLAGS) -L../external/mott -lmott -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `$(PKG_CONFIG) --libs glib-2.0` -lpthread
wise-2.4.1/debian/patches/cross.patch-176-
##############################################
wise-2.4.1/debian/patches/cross.patch-178-- $(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LDFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread
wise-2.4.1/debian/patches/cross.patch:179:+ $(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LDFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `$(PKG_CONFIG) --libs glib-2.0` -lpthread
wise-2.4.1/debian/patches/cross.patch-180-
##############################################
wise-2.4.1/debian/patches/cross.patch-182-- $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config --cflags glib-2.0` $?
wise-2.4.1/debian/patches/cross.patch:183:+ $(CC) $(CFLAGS) $(INCFLAGS) `$(PKG_CONFIG) --cflags glib-2.0` $?
wise-2.4.1/debian/patches/cross.patch-184-
##############################################
wise-2.4.1/debian/patches/cross.patch-186-- $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config --cflags glib-2.0` $?
wise-2.4.1/debian/patches/cross.patch:187:+ $(CC) $(CFLAGS) $(INCFLAGS) `$(PKG_CONFIG) --cflags glib-2.0` $?
wise-2.4.1/debian/patches/cross.patch-188-
##############################################
wise-2.4.1/debian/patches/cross.patch-190-- $(CC) -g -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread
wise-2.4.1/debian/patches/cross.patch:191:+ $(CC) -g -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `$(PKG_CONFIG) --libs glib-2.0` -lpthread
wise-2.4.1/debian/patches/cross.patch-192-
##############################################
wise-2.4.1/debian/patches/cross.patch-194-- $(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 $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread
wise-2.4.1/debian/patches/cross.patch:195:+ $(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 $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `$(PKG_CONFIG) --libs glib-2.0` -lpthread
wise-2.4.1/debian/patches/cross.patch-196-
##############################################
wise-2.4.1/debian/patches/cross.patch-198-- $(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 $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread
wise-2.4.1/debian/patches/cross.patch:199:+ $(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 $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `$(PKG_CONFIG) --libs glib-2.0` -lpthread
wise-2.4.1/debian/patches/cross.patch-200-
##############################################
wise-2.4.1/debian/patches/cross.patch-211--#CFLAGS += -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0`
wise-2.4.1/debian/patches/cross.patch:212:+CFLAGS += -c -g3 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `$(PKG_CONFIG) --cflags glib-2.0`
wise-2.4.1/debian/patches/cross.patch:213:+#CFLAGS += -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `$(PKG_CONFIG) --cflags glib-2.0`
wise-2.4.1/debian/patches/cross.patch-214- #LDFLAGS = -L../base/ -L../dynlibsrc/ -L../HMMer2/
##############################################
wise-2.4.1/debian/patches/cross.patch-216--LDFLAGS += -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `pkg-config --libs glib-2.0`
wise-2.4.1/debian/patches/cross.patch:217:+LDFLAGS += -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `$(PKG_CONFIG) --libs glib-2.0`
wise-2.4.1/debian/patches/cross.patch-218- AR_OPTIONS = ru
##############################################
wise-2.4.1/debian/patches/cross.patch-230--LDFLAGS += -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config --libs glib-2.0`
wise-2.4.1/debian/patches/cross.patch:231:+CFLAGS += $(CPPFLAGS) -c -pthread -DUNIX -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `$(PKG_CONFIG) --cflags glib-2.0`
wise-2.4.1/debian/patches/cross.patch:232:+LDFLAGS += -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `$(PKG_CONFIG) --libs glib-2.0`
wise-2.4.1/debian/patches/cross.patch-233- AR_OPTIONS = ru
##############################################
wise-2.4.1/debian/patches/cross.patch-244-+PKG_CONFIG ?= pkg-config
wise-2.4.1/debian/patches/cross.patch:245:+CFLAGS += $(CPPFLAGS) -g3 -c -pthread -DUNIX -I../base/ -I../dynlibsrc `$(PKG_CONFIG) --cflags glib-2.0`
wise-2.4.1/debian/patches/cross.patch:246:+LDFLAGS += -g -L../base/ -L../dynlibsrc -lm `$(PKG_CONFIG) --libs glib-2.0`
wise-2.4.1/debian/patches/cross.patch-247- AR_OPTIONS = ru
##############################################
wise-2.4.1/debian/patches/cross.patch-259--CFLAGS += $(CPPFLAGS) -c -g3 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config --cflags glib-2.0`
wise-2.4.1/debian/patches/cross.patch:260:+CFLAGS += $(CPPFLAGS) -c -g3 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `$(PKG_CONFIG) --cflags glib-2.0`
wise-2.4.1/debian/patches/cross.patch-261-
wise-2.4.1/debian/patches/cross.patch-262--LDFLAGS += -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lpthread -lm
wise-2.4.1/debian/patches/cross.patch:263:+LDFLAGS += -g -L../base/ -L../dynlibsrc/ -lpthread `$(PKG_CONFIG) --libs glib-2.0` -lpthread -lm
wise-2.4.1/debian/patches/cross.patch-264- AR_OPTIONS = ru