gcc -O2 -fPIC  -DUNIX=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_STRINGS_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STDINT_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LSEEK64=1 -DUSE_TCL_STUBS=1 -Wall -DSTDC_HEADERS=1 -DTCL_THREADS=1 -DTCL_WIDE_INT_TYPE=long\ long -pipe -fomit-frame-pointer -Wno-implicit-int -I/usr/local/ActiveTcl/include -c main.c
main.c: In function ‘Fastme_ObjCmd’:
main.c:457:5: warning: implicit declaration of function ‘ReplaceForbiddenChars’ [-Wimplicit-function-declaration]
main.c:360:15: warning: unused variable ‘tmpbuf’ [-Wunused-variable]
main.c:359:11: warning: unused variable ‘input’ [-Wunused-variable]
main.c:358:21: warning: variable ‘wtype’ set but not used [-Wunused-but-set-variable]
main.c:358:7: warning: variable ‘ntype’ set but not used [-Wunused-but-set-variable]
main.c:356:14: warning: unused variable ‘count’ [-Wunused-variable]
main.c:355:7: warning: unused variable ‘numSets’ [-Wunused-variable]
main.c:345:7: warning: unused variable ‘setCounter’ [-Wunused-variable]
gcc -O2 -fPIC  -DUNIX=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_STRINGS_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STDINT_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LSEEK64=1 -DUSE_TCL_STUBS=1 -Wall -DSTDC_HEADERS=1 -DTCL_THREADS=1 -DTCL_WIDE_INT_TYPE=long\ long -pipe -fomit-frame-pointer -Wno-implicit-int -I/usr/local/ActiveTcl/include -c graph.c
graph.c: In function ‘detrifurcate’:
graph.c:176:11: warning: ‘w’ may be used uninitialized in this function [-Wuninitialized]
gcc -O2 -fPIC  -DUNIX=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_STRINGS_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STDINT_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LSEEK64=1 -DUSE_TCL_STUBS=1 -Wall -DSTDC_HEADERS=1 -DTCL_THREADS=1 -DTCL_WIDE_INT_TYPE=long\ long -pipe -fomit-frame-pointer -Wno-implicit-int -I/usr/local/ActiveTcl/include -c inputs.c
gcc -O2 -fPIC  -DUNIX=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_STRINGS_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STDINT_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LSEEK64=1 -DUSE_TCL_STUBS=1 -Wall -DSTDC_HEADERS=1 -DTCL_THREADS=1 -DTCL_WIDE_INT_TYPE=long\ long -pipe -fomit-frame-pointer -Wno-implicit-int -I/usr/local/ActiveTcl/include -c gme.c
gme.c: In function ‘GMEsplitEdge’:
gme.c:418:3: warning: zero-length gnu_printf format string [-Wformat-zero-length]
gme.c:418:3: warning: zero-length gnu_printf format string [-Wformat-zero-length]
gcc -O2 -fPIC  -DUNIX=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_STRINGS_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STDINT_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LSEEK64=1 -DUSE_TCL_STUBS=1 -Wall -DSTDC_HEADERS=1 -DTCL_THREADS=1 -DTCL_WIDE_INT_TYPE=long\ long -pipe -fomit-frame-pointer -Wno-implicit-int -I/usr/local/ActiveTcl/include -c bme.c	
bme.c: In function ‘BMEsplitEdge’:
bme.c:265:3: warning: zero-length gnu_printf format string [-Wformat-zero-length]
bme.c:265:3: warning: zero-length gnu_printf format string [-Wformat-zero-length]
gcc -O2 -fPIC  -DUNIX=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_STRINGS_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STDINT_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LSEEK64=1 -DUSE_TCL_STUBS=1 -Wall -DSTDC_HEADERS=1 -DTCL_THREADS=1 -DTCL_WIDE_INT_TYPE=long\ long -pipe -fomit-frame-pointer -Wno-implicit-int -I/usr/local/ActiveTcl/include -c newick.c
newick.c: In function ‘readNewickString’:
newick.c:216:3: warning: format not a string literal and no format arguments [-Wformat-security]
newick.c:216:3: warning: format not a string literal and no format arguments [-Wformat-security]
newick.c: In function ‘loadNewickTree’:
newick.c:295:3: warning: format not a string literal and no format arguments [-Wformat-security]
newick.c:295:3: warning: format not a string literal and no format arguments [-Wformat-security]
newick.c: In function ‘NewickPrintSubtree’:
newick.c:318:11: warning: unused variable ‘NeedComma’ [-Wunused-variable]
newick.c: In function ‘NewickPrintTrinaryTree’:
newick.c:422:8: warning: unused variable ‘stmp’ [-Wunused-variable]
newick.c: In function ‘decodeNewickSubtree’:
newick.c:140:13: warning: ‘thisWeight’ may be used uninitialized in this function [-Wuninitialized]
newick.c:141:25: warning: ‘thisNode’ may be used uninitialized in this function [-Wuninitialized]
gcc -O2 -fPIC  -DUNIX=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_STRINGS_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STDINT_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LSEEK64=1 -DUSE_TCL_STUBS=1 -Wall -DSTDC_HEADERS=1 -DTCL_THREADS=1 -DTCL_WIDE_INT_TYPE=long\ long -pipe -fomit-frame-pointer -Wno-implicit-int -I/usr/local/ActiveTcl/include -c heap.c
gcc -O2 -fPIC  -DUNIX=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_STRINGS_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STDINT_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LSEEK64=1 -DUSE_TCL_STUBS=1 -Wall -DSTDC_HEADERS=1 -DTCL_THREADS=1 -DTCL_WIDE_INT_TYPE=long\ long -pipe -fomit-frame-pointer -Wno-implicit-int -I/usr/local/ActiveTcl/include -c traverse.c
gcc -O2 -fPIC  -DUNIX=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_STRINGS_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STDINT_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LSEEK64=1 -DUSE_TCL_STUBS=1 -Wall -DSTDC_HEADERS=1 -DTCL_THREADS=1 -DTCL_WIDE_INT_TYPE=long\ long -pipe -fomit-frame-pointer -Wno-implicit-int -I/usr/local/ActiveTcl/include -c NNI.c
gcc -O2 -fPIC  -DUNIX=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_STRINGS_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STDINT_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LSEEK64=1 -DUSE_TCL_STUBS=1 -Wall -DSTDC_HEADERS=1 -DTCL_THREADS=1 -DTCL_WIDE_INT_TYPE=long\ long -pipe -fomit-frame-pointer -Wno-implicit-int -I/usr/local/ActiveTcl/include -c bNNI.c
bNNI.c: In function ‘bNNI’:
bNNI.c:64:13: warning: variable ‘centerEdge’ set but not used [-Wunused-but-set-variable]
gcc -O2 -fPIC  -DUNIX=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_STRINGS_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STDINT_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LSEEK64=1 -DUSE_TCL_STUBS=1 -Wall -DSTDC_HEADERS=1 -DTCL_THREADS=1 -DTCL_WIDE_INT_TYPE=long\ long -pipe -fomit-frame-pointer -Wno-implicit-int -I/usr/local/ActiveTcl/include -c interface_utilities.c
interface_utilities.c: In function ‘askOption’:
interface_utilities.c:103:2: warning: format not a string literal and no format arguments [-Wformat-security]
interface_utilities.c: In function ‘Getstring_Stdin’:
interface_utilities.c:30:8: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
gcc -O2 -fPIC  -DUNIX=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_STRINGS_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STDINT_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LSEEK64=1 -DUSE_TCL_STUBS=1 -Wall -DSTDC_HEADERS=1 -DTCL_THREADS=1 -DTCL_WIDE_INT_TYPE=long\ long -pipe -fomit-frame-pointer -Wno-implicit-int -I/usr/local/ActiveTcl/include -c interface_free.c
gcc -O2 -fPIC  -DUNIX=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_STRINGS_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STDINT_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LSEEK64=1 -DUSE_TCL_STUBS=1 -Wall -DSTDC_HEADERS=1 -DTCL_THREADS=1 -DTCL_WIDE_INT_TYPE=long\ long -pipe -fomit-frame-pointer -Wno-implicit-int -I/usr/local/ActiveTcl/include -c interface_options.c
interface_options.c: In function ‘Get_Input_Interactive’:
interface_options.c:149:7: warning: format not a string literal and no format arguments [-Wformat-security]
interface_options.c:303:5: warning: format not a string literal and no format arguments [-Wformat-security]
interface_options.c:131:15: warning: unused variable ‘choix_T’ [-Wunused-variable]
interface_options.c:168:10: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result]
interface_options.c:241:13: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result]
gcc -O2 -fPIC  -DUNIX=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_STRINGS_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STDINT_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LSEEK64=1 -DUSE_TCL_STUBS=1 -Wall -DSTDC_HEADERS=1 -DTCL_THREADS=1 -DTCL_WIDE_INT_TYPE=long\ long -pipe -fomit-frame-pointer -Wno-implicit-int -I/usr/local/ActiveTcl/include -c BIONJ.c
BIONJ.c: In function ‘bionj’:
BIONJ.c:247:10: warning: unused variable ‘t’ [-Wunused-variable]
BIONJ.c:234:9: warning: variable ‘chain2’ set but not used [-Wunused-but-set-variable]
BIONJ.c:257:9: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
BIONJ.c: In function ‘Initialize’:
BIONJ.c:153:14: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
BIONJ.c:168:14: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
BIONJ.c: In function ‘Compute_sums_Sx’:
BIONJ.c:560:18: warning: ‘sum’ may be used uninitialized in this function [-Wuninitialized]
gcc -shared -o libtclfastme0.1.so main.o graph.o inputs.o gme.o bme.o newick.o heap.o traverse.o NNI.o bNNI.o interface_utilities.o interface_free.o interface_options.o BIONJ.o -L/usr/local/ActiveTcl/lib/ -ltclstub8.6 -lm -O2 -fPIC 
