* [gentoo-commits] gentoo-x86 commit in sci-biology/wise/files: wise-2.4.0_alpha-glibc-2.10.patch wise-2.4.0_alpha-cflags.patch
@ 2010-06-23 13:10 Justin Lecher (jlec)
0 siblings, 0 replies; only message in thread
From: Justin Lecher (jlec) @ 2010-06-23 13:10 UTC (permalink / raw
To: gentoo-commits
jlec 10/06/23 13:10:09
Added: wise-2.4.0_alpha-glibc-2.10.patch
wise-2.4.0_alpha-cflags.patch
Log:
Version bump, #191982
(Portage version: 2.2_rc67/cvs/Linux x86_64)
Revision Changes Path
1.1 sci-biology/wise/files/wise-2.4.0_alpha-glibc-2.10.patch
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/wise/files/wise-2.4.0_alpha-glibc-2.10.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/wise/files/wise-2.4.0_alpha-glibc-2.10.patch?rev=1.1&content-type=text/plain
Index: wise-2.4.0_alpha-glibc-2.10.patch
===================================================================
diff --git a/src/HMMer2/sqio.c b/src/HMMer2/sqio.c
index 5889e7d..bc95629 100644
--- a/src/HMMer2/sqio.c
+++ b/src/HMMer2/sqio.c
@@ -213,7 +213,7 @@ readline(FILE *f, char *s)
}
}
-/* Function: getline()
+/* Function: get_line()
* 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 @@ readline(FILE *f, char *s)
* Returns: (void)
*/
static void
-getline(struct ReadSeqVars *V)
+get_line(struct ReadSeqVars *V)
{
char *cp;
@@ -299,7 +299,7 @@ readLoop(int addfirst, int (*endTest)(char *,int *), struct ReadSeqVars *V)
V->seqlen = 0;
if (addfirst) addseq(V->sbuffer, V);
do {
- getline(V);
+ get_line(V);
/* feof() alone is a bug; files not necessarily \n terminated */
if (*(V->sbuffer) == '\0' && feof(V->f))
done = TRUE;
@@ -327,7 +327,7 @@ readPIR(struct ReadSeqVars *V)
char *sptr;
/* load first line of entry */
while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
- getline(V);
+ get_line(V);
if (feof(V->f)) return;
if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL)
@@ -336,7 +336,7 @@ readPIR(struct ReadSeqVars *V)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID);
}
do {
- getline(V);
+ get_line(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 @@ readPIR(struct ReadSeqVars *V)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC);
}
} while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0));
- getline(V); /* skip next line, coords */
+ get_line(V); /* skip next line, coords */
readLoop(0, endPIR, V);
@@ -359,7 +359,7 @@ readPIR(struct ReadSeqVars *V)
/* get next line
*/
while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
- getline(V);
+ get_line(V);
}
@@ -377,7 +377,7 @@ readIG(struct ReadSeqVars *V)
char *nm;
/* position past ';' comments */
do {
- getline(V);
+ get_line(V);
} while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) ));
if (!feof(V->f))
@@ -389,7 +389,7 @@ readIG(struct ReadSeqVars *V)
}
while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';'))))
- getline(V);
+ get_line(V);
}
static int
@@ -411,7 +411,7 @@ readStrider(struct ReadSeqVars *V)
if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL)
SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME);
}
- getline(V);
+ get_line(V);
}
if (! feof(V->f))
@@ -420,7 +420,7 @@ readStrider(struct ReadSeqVars *V)
/* load next line
*/
while ((!feof(V->f)) && (*V->sbuffer != ';'))
- getline(V);
+ get_line(V);
}
@@ -438,7 +438,7 @@ readGenBank(struct ReadSeqVars *V)
int in_definition;
while (strncmp(V->sbuffer, "LOCUS", 5) != 0)
- getline(V);
+ get_line(V);
if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL)
{
@@ -449,7 +449,7 @@ readGenBank(struct ReadSeqVars *V)
in_definition = FALSE;
while (! feof(V->f))
{
- getline(V);
+ get_line(V);
if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer)
{
if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL)
@@ -482,11 +482,11 @@ readGenBank(struct ReadSeqVars *V)
while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer))))
- getline(V);
+ get_line(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);
+ get_line(V);
}
static int
@@ -515,7 +515,7 @@ readGCGdata(struct ReadSeqVars *V)
Die("bogus GCGdata format? %s", V->sbuffer);
/* second line contains free text description */
- getline(V);
+ get_line(V);
SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC);
if (binary) {
@@ -535,7 +535,7 @@ readGCGdata(struct ReadSeqVars *V)
else readLoop(0, endGCGdata, V);
while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
- getline(V);
+ get_line(V);
}
static int
@@ -555,12 +555,12 @@ readPearson(struct ReadSeqVars *V)
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)) get_line(V);
readLoop(0, endPearson, V);
while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
- getline(V);
+ get_line(V);
}
@@ -587,7 +587,7 @@ readEMBL(struct ReadSeqVars *V)
/* make sure we have first line */
while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
- getline(V);
+ get_line(V);
if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL)
{
@@ -596,7 +596,7 @@ readEMBL(struct ReadSeqVars *V)
}
do {
- getline(V);
+ get_line(V);
if (!feof(V->f) && strstr(V->sbuffer, "AC ") == V->sbuffer)
{
if ((sptr = strtok(V->sbuffer+5, "; \t\n")) != NULL)
@@ -620,7 +620,7 @@ readEMBL(struct ReadSeqVars *V)
/* load next record's ID line */
while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
- getline(V);
+ get_line(V);
}
@@ -636,7 +636,7 @@ readZuker(struct ReadSeqVars *V)
{
char *sptr;
- getline(V); /*s == "seqLen seqid string..."*/
+ get_line(V); /*s == "seqLen seqid string..."*/
if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
@@ -647,7 +647,7 @@ readZuker(struct ReadSeqVars *V)
readLoop(0, endZuker, V);
while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '('))))
- getline(V);
+ get_line(V);
}
static void
@@ -669,7 +669,7 @@ readUWGCG(struct ReadSeqVars *V)
do {
done = feof(V->f);
- getline(V);
+ get_line(V);
if (! done) addseq(V->sbuffer, V);
} while (!done);
}
@@ -681,7 +681,7 @@ readSquid(struct ReadSeqVars *V)
char *sptr;
int dostruc = FALSE;
- while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V);
+ while (strncmp(V->sbuffer, "NAM ", 4) != 0) get_line(V);
if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
@@ -689,7 +689,7 @@ readSquid(struct ReadSeqVars *V)
/*CONSTCOND*/
while (1)
{
- getline(V);
+ get_line(V);
if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; }
if (strncmp(V->sbuffer, "SRC ", 4) == 0)
@@ -721,14 +721,14 @@ readSquid(struct ReadSeqVars *V)
while (1)
{
/* sequence line */
- getline(V);
+ get_line(V);
if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0)
break;
addseq(V->sbuffer, V);
/* structure line */
if (dostruc)
{
- getline(V);
+ get_line(V);
if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; }
addstruc(V->sbuffer, V);
}
@@ -736,7 +736,7 @@ readSquid(struct ReadSeqVars *V)
while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0)
- getline(V);
+ get_line(V);
}
@@ -816,7 +816,7 @@ SeqfileOpen(char *filename, int format, char *env)
/* Load the first line.
*/
- getline(dbfp);
+ get_line(dbfp);
return dbfp;
}
@@ -833,7 +833,7 @@ SeqfilePosition(SQFILE *sqfp, long offset)
Die("SeqfilePosition() failed: in a nonrewindable data file or stream");
fseek(sqfp->f, offset, SEEK_SET);
- getline(sqfp);
+ get_line(sqfp);
}
@@ -853,7 +853,7 @@ SeqfileRewind(SQFILE *sqfp)
if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0;
else {
rewind(sqfp->f);
- getline(sqfp);
+ get_line(sqfp);
}
}
@@ -949,7 +949,7 @@ ReadSeq(SQFILE *V, int format, char **ret_seq, SQINFO *sqinfo)
do { /* skip leading comments on GCG file */
gotuw = (strstr(V->sbuffer,"..") != NULL);
if (gotuw) readUWGCG(V);
- getline(V);
+ get_line(V);
} while (! feof(V->f));
break;
1.1 sci-biology/wise/files/wise-2.4.0_alpha-cflags.patch
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/wise/files/wise-2.4.0_alpha-cflags.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/wise/files/wise-2.4.0_alpha-cflags.patch?rev=1.1&content-type=text/plain
Index: wise-2.4.0_alpha-cflags.patch
===================================================================
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
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2010-06-23 13:10 [gentoo-commits] gentoo-x86 commit in sci-biology/wise/files: wise-2.4.0_alpha-glibc-2.10.patch wise-2.4.0_alpha-cflags.patch Justin Lecher (jlec)
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