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Diffstat (limited to 'sci-biology/wise/files/wise-2.4.0_alpha-cflags.patch')
-rw-r--r--sci-biology/wise/files/wise-2.4.0_alpha-cflags.patch407
1 files changed, 0 insertions, 407 deletions
diff --git a/sci-biology/wise/files/wise-2.4.0_alpha-cflags.patch b/sci-biology/wise/files/wise-2.4.0_alpha-cflags.patch
deleted file mode 100644
index d3c17098105..00000000000
--- a/sci-biology/wise/files/wise-2.4.0_alpha-cflags.patch
+++ /dev/null
@@ -1,407 +0,0 @@
-diff --git a/src/base/makefile b/src/base/makefile
-index 4620f19..a84e2c7 100644
---- a/src/base/makefile
-+++ b/src/base/makefile
-@@ -20,8 +20,8 @@ NBASEOBJ = wiseconfig.o \
-
-
- #CFLAGS = -c -g -DUNIX -DWISE_MEMORY_WATCH
--CFLAGS = -c -O2 -DUNIX -pthread
--LFLAGS = -g -lm
-+CFLAGS += -c -DUNIX -pthread
-+LFLAGS = -lm
- DFLAGS = -n Wise2_ -a _api.h -b _api.t -l -D
- AR_OPTIONS = ru
-
-diff --git a/src/corba/makefile b/src/corba/makefile
-index df3dd78..237a1ba 100644
---- a/src/corba/makefile
-+++ b/src/corba/makefile
-@@ -1,10 +1,10 @@
-
-
--CC = cc
-+CC += gcc
- INCFLAGS = -I../base/ -I../dynlibsrc
- #gCFLAGS = -Wall -g -pedantic -c -DUNIX -I../base/
--#CFLAGS = -O2 -c -DUNIX -I../base/ `glib-config --cflags` -I/usr/local/include/orbit-1.0/
--CFLAGS = -pthread -c -DUNIX -I../base/ -I../dynlibsrc `orbit-config --cflags client`
-+#CFLAGS = -O2 -c -DUNIX -I../base/ `pkg-config glib-2.0 --cflags` -I/usr/local/include/orbit-1.0/
-+CFLAGS += -pthread -c -DUNIX -I../base/ -I../dynlibsrc `pkg-config ORBit-2.0 --cflags`
- LFLAGS = -L../base/ -lm -lpthread
- AR_OPTIONS = ru
-
-@@ -14,18 +14,18 @@ hspscan_corba.c : hspscan_corba.idl
- 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) $(CFLAGS) $(LDFLAGS) -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 glib-2.0 --libs` -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) $(CFLAGS) $(LDFLAGS) -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 glib-2.0 --libs` -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) $(CFLAGS) $(LDFLAGS) -o test_client test_client.o hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config glib-2.0 --libs` -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) $(CFLAGS) $(LDFLAGS) -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 glib-2.0 --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
-
- .c.o :
- $(CC) $(CFLAGS) $(INCFLAGS) $?
-diff --git a/src/dnaindex/assembly/makefile b/src/dnaindex/assembly/makefile
-index ef3334a..3a0bc2a 100644
---- a/src/dnaindex/assembly/makefile
-+++ b/src/dnaindex/assembly/makefile
-@@ -26,10 +26,10 @@ arraymatcher : arraymatcher.o assemblygraph.o assemblystats.o basegraph.o
-
-
- 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 glib-2.0 --cflags`
-
-
--LFLAGS = -g -L../../base/ -L../../dynlibsrc/ -lpthread `glib-config --libs` -lm
-+LFLAGS = -g -L../../base/ -L../../dynlibsrc/ -lpthread `pkg-config glib-2.0 --libs` -lm
-
-
- .c.o :
-diff --git a/src/dnaindex/makefile b/src/dnaindex/makefile
-index 285e6a0..8c6a0dc 100644
---- a/src/dnaindex/makefile
-+++ b/src/dnaindex/makefile
-@@ -27,14 +27,14 @@ all: $(ASSEMBLY_OBJ)
-
-
- 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 glib-2.0 --libs`
-
- 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 glib-2.0 --libs`
-
-
- 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 glib-2.0 --libs`
-
- make_shotgun : make_shotgun.o shotgun.o
- $(CC) -o make_shotgun make_shotgun.o shotgun.o -ldyna -lwisebase $(LFLAGS)
-@@ -70,10 +70,10 @@ show_euler : show_euler.o eulerindex.o singleseqspace.o
- $(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 glib-2.0 --cflags`
-
-
--LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lm
-+LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config glib-2.0 --libs` -lm
-
-
- .c.o :
-diff --git a/src/dynlibsrc/makefile b/src/dynlibsrc/makefile
-index d1d77af..cad8900 100644
---- a/src/dynlibsrc/makefile
-+++ b/src/dynlibsrc/makefile
-@@ -78,11 +78,11 @@ DYNHELPEROBJ = packaln.o \
-
-
-
--CC = cc
-+CC ?= gcc
- INCFLAGS = -I../base/
- #CFLAGS = -Wall -g -pedantic -c -DUNIX -I../base/
--CFLAGS = -Wall -g3 -DPTHREAD -O2 -c -DUNIX -I../base/ `glib-config --cflags`
--#CFLAGS = -O2 -c -pthread -DUNIX -I../base/ `glib-config --cflags`
-+CFLAGS += -DPTHREAD -c -DUNIX -I../base/ `pkg-config glib-2.0 --cflags`
-+#CFLAGS = -O2 -c -pthread -DUNIX -I../base/ `pkg-config glib-2.0 --cflags`
- #CFLAGS = -O -c -DUNIX -DNOERROR -I../base/
- LFLAGS = -g -L../base/ -lm
- AR_OPTIONS = ru
-@@ -144,13 +144,13 @@ test_shadowindex : test_shadowindex.o shadowseqindex.o shadowseq.o libdyna.a
- $(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 glib-2.0 --libs` 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 glib-2.0 --libs`
-
- 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 glib-2.0 --libs`
-
-
- testgendb : probability.o genomicdb.o genomic.o testgendb.o sequence.o codon.o sequencedb.o complexsequence.o complexevalset.o
-diff --git a/src/external/mott/makefile b/src/external/mott/makefile
-index 8d7c1d4..940c438 100644
---- a/src/external/mott/makefile
-+++ b/src/external/mott/makefile
-@@ -14,10 +14,10 @@ libmott.a : mott_api.o gaplib.o wise2_mott_bridge.o
- wise2_mott_bridge.o : wise2_mott_bridge.c
- $(CC) $(CFLAGS) -I../../dynlibsrc -I../../base wise2_mott_bridge.c
-
--CC = cc
-+CC ?= gcc
-
--CFLAGS = -Wall -g3 -DPTHREAD -O2 -c
--LFLAGS = -g -L../base/ -lm
-+CFLAGS += -DPTHREAD -c
-+LFLAGS = -L../base/ -lm
- AR_OPTIONS = ru
-
-
-diff --git a/src/makefile b/src/makefile
-index bdff4ff..0d7c871 100644
---- a/src/makefile
-+++ b/src/makefile
-@@ -26,12 +26,12 @@
-
- # Change the cc line to gcc if you get compiler errors
- # Most likely you have a non ANSI C compiler
--CC ?= cc
-+CC ?= gcc
-
- # These are the CFLAGS to use. These days Wise2 is inherently
- # pthreaded, and everything is compiled with threads. More
- # info on running threads can be found in the documentation
--CFLAGS = -c -pthread -O2 `glib-config --cflags`
-+CFLAGS += -c -pthread `pkg-config glib-2.0 --cflags`
-
-
-
-diff --git a/src/models/makefile b/src/models/makefile
-index f518d0c..a297eff 100644
---- a/src/models/makefile
-+++ b/src/models/makefile
-@@ -50,6 +50,8 @@ NEWG = geneparser21.o \
- proteinsw.o \
- estquick3.o
-
-+EXTRALIBS += `pkg-config glib-2.0 --libs`
-+
- all : dnal psw pswdb dba estwise genewise genewisedb estwisedb genomewise sywise pseudowise promoterwise scanwisep scanwisep_wiseserver libmodel.a
-
- libmodel.a : $(NEWG)
-@@ -180,7 +182,7 @@ fivestarscan.o : fivestarscan.c
- $(CC) $(CFLAGS) fivestarscan.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I.
-
- oldpostwise : oldpostwise.o $(NEWG)
-- $(CC) -g -o oldpostwise oldpostwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm
-+ $(CC) $(LDFLAGS) -o oldpostwise oldpostwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm
-
- testdna : testdna.o dnaalign.o seqaligndisplay.o
- $(CC) -o testdna testdna.o dnaalign.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-@@ -192,10 +194,10 @@ psw : psw.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o
- $(CC) -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-
- scanwisep.o : scanwisep.c
-- $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `glib-config --cflags` $?
-+ $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `pkg-config glib-2.0 --cflags` $?
-
- hsp2aln_sw.o : hsp2aln_sw.c
-- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $?
-+ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config glib-2.0 --cflags` $?
-
- 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
-@@ -212,10 +214,10 @@ scanwisep_corba : scanwisep_corba.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.
-
-
- scanwisep_wiseserver.o : scanwisep.c
-- $(CC) $(CFLAGS) $(INCFLAGS) -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c
-+ $(CC) $(LDFLAGS) $(CFLAGS) $(INCFLAGS) -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c `pkg-config glib-2.0 --libs`
-
- scanwisep_wiseserver : scanwisep_wiseserver.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o
-- $(CC) -o scanwisep_wiseserver scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o $(LFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase -lm $(EXTRALIBS) -lpthread
-+ $(CC) -o scanwisep_wiseserver scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o $(LFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase -lm $(EXTRALIBS) -lpthread `pkg-config glib-2.0 --libs`
-
- scanwisep_compress.o : scanwisep.c
- $(CC) $(CFLAGS) -DSCAN_COMPRESS -I../dnaindex -I../network -I../socket -I../external/mott scanwisep.c
-@@ -226,25 +228,25 @@ scanwisep_compress : scanwisep_compress.o seqaligndisplay.o proteinsw.o sw_wrap.
-
-
- 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 -lm $(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 -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -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 -lm $(EXTRALIBS) `glib-config --libs` -lpthread
-+ $(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread
-
- localcishit.o : localcishit.c
-- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $?
-+ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config glib-2.0 --cflags` $?
-
- promoterwise.o : promoterwise.c
-- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $?
-+ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config glib-2.0 --cflags` $?
-
- 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 -lm $(EXTRALIBS) `glib-config --libs` -lpthread
-+ $(CC) $(LDFLAGS) -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 -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -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 -lm $(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 -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -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 -lm $(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 -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -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 -lm -lpthread
-@@ -275,66 +277,66 @@ makerandomdb : makerandomdb.o
- $(CC) -o makerandomdb makerandomdb.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-
- genewise : genewise.o $(NEWG)
-- $(CC) -g -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-+ $(CC) $(LDFLAGS) -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs`
-
- cdnawise : cdnawise.o $(NEWG) cdnawise10.o
-- $(CC) -g -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-+ $(CC) $(LDFLAGS) -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-
- fivestar : fivestar.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o
-- $(CC) -g -o fivestar fivestar.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-+ $(CC) $(LDFLAGS) -o fivestar fivestar.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-
-
- fivestarsearch : fivestarsearch.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o
-- $(CC) -g -o fivestarsearch fivestarsearch.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-+ $(CC) $(LDFLAGS) -o fivestarsearch fivestarsearch.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-
- fivestarscan : fivestarscan.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o
-- $(CC) -g -o fivestarscan fivestarscan.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-+ $(CC) $(LDFLAGS) -o fivestarscan fivestarscan.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-
-
- editdist : editdist.o editdistdp.o standardout.o seqaligndisplay.o
-- $(CC) -g -o editdist editdist.o editdistdp.o standardout.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm
-+ $(CC) $(LDFLAGS) -o editdist editdist.o editdistdp.o standardout.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm
-
-
- efgw : genewise.o $(NEWG)
-- $(CC) -g -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -lefence
-+ $(CC) $(LDFLAGS) -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -lefence
-
-
- genewisedb : genewisedb.o $(NEWG)
-- $(CC) -g -o genewisedb genewisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-+ $(CC) $(LDFLAGS) -o genewisedb genewisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs`
-
- estwisedb : estwisedb.o $(NEWG)
-- $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-+ $(CC) $(LDFLAGS) -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs`
-
- edb : estwisedb.o $(NEWG)
-- $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -lefence
-+ $(CC) $(LDFLAGS) -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -lefence
-
- estwise : estwise.o $(NEWG)
-- $(CC) -g -o estwise estwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-+ $(CC) $(LDFLAGS) -o estwise estwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs`
-
-
- amplimer_resolver : amplimer_resolver.o dnaalign.o dnamatcher.o
-- $(CC) -g -o amplimer_resolver amplimer_resolver.o dnamatcher.o dnaalign.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-+ $(CC) $(LDFLAGS) -o amplimer_resolver amplimer_resolver.o dnamatcher.o dnaalign.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-
- genomewise : genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneutil.o geneoutput.o
-- $(CC) -g -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-+ $(CC) $(LDFLAGS) -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-
- sywise : sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o geneutil.o standardout.o
-- $(CC) -g -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-+ $(CC) $(LDFLAGS) -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-
- alignwise : alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o
-- $(CC) -g -o alignwise alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-+ $(CC) $(LDFLAGS) -o alignwise alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-
- test_splice : test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o
-- $(CC) -g -o test_splice test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-+ $(CC) $(LDFLAGS) -o test_splice test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-
- statwise : statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o
-- $(CC) -g -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-+ $(CC) $(LDFLAGS) -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-
- pseudowise : pseudowise.o pseudowise7.o $(NEWG)
-- $(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-+ $(CC) $(LDFLAGS) -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs`
-
- clonewise : clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o
-- $(CC) -g -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-+ $(CC) $(LDFLAGS) -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-
-
- HMMER_LIBS = ../HMMer2/
-@@ -345,11 +347,11 @@ HMMER_DEFINE =
- CC = cc
- #CFLAGS = -c -O2 -pg -I../base/ -I../dynlibsrc/
- #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ -I.
--CFLAGS = -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `glib-config --cflags`
--#CFLAGS = -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `glib-config --cflags`
-+CFLAGS = -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config glib-2.0 --cflags`
-+#CFLAGS = -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config glib-2.0 --cflags`
- #LFLAGS = -L../base/ -L../dynlibsrc/ -L../HMMer2/
-
--LFLAGS = -g -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `glib-config --libs`
-+LFLAGS = -g -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `pkg-config glib-2.0 --libs`
- AR_OPTIONS = ru
-
- RANLIB_NEEDED = 0
-diff --git a/src/network/makefile b/src/network/makefile
-index 303c2da..e607310 100644
---- a/src/network/makefile
-+++ b/src/network/makefile
-@@ -3,8 +3,8 @@
-
- CC = cc
- INCFLAGS = -I../base/ -I../socket -I../dynlibsrc -I../dnaindex
--CFLAGS = -O2 -g3 -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 -g3 -c -pthread -DUNIX -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `pkg-config glib-2.0 --cflags`
-+LFLAGS = -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config glib-2.0 --libs`
- AR_OPTIONS = ru
-
- RANLIB_NEEDED = 0
-diff --git a/src/snp/makefile b/src/snp/makefile
-index ccf750a..2b83c43 100644
---- a/src/snp/makefile
-+++ b/src/snp/makefile
-@@ -2,12 +2,12 @@
- .SUFFIXES : .dy
-
-
--CC = cc
-+CC ?= gcc
- #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 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config glib-2.0 --cflags`
-
--LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lpthread -lm
-+LFLAGS = -L../base/ -L../dynlibsrc/ -lpthread `pkg-config glib-2.0 --libs` -lpthread -lm
- AR_OPTIONS = ru
-
- RANLIB_NEEDED = 0
-@@ -16,7 +16,7 @@ RANLIB_NEEDED = 0
- $(CC) $(CFLAGS) $(INCFLAGS) $?
-
- test_est : test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o
-- $(CC) -o test_est test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o ../dynlibsrc/libdyna.a ../base/libwisebase.a $(LFLAGS)
-+ $(CC) $(LDFLAGS) -o test_est test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o ../dynlibsrc/libdyna.a ../base/libwisebase.a $(LFLAGS)
-
- INCFLAGS = -I../base/ -I../dynlibsrc/
- DFLAGS = -l -D -n Wise2_ -a _api.h -b _api.t -pthreads -dbtrace 5 -nocwarn