configure: configuring HMMER for your system. configure: This is a full source distribution - using full config checking for gcc... gcc checking for C compiler default output... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking for ranlib... ranlib checking for ar... /usr/bin/ar checking build system type... i386-unknown-openbsd3.2 checking host system type... i386-unknown-openbsd3.2 checking whether your make is GNU make... nope, assuming sysv make. configure: configured for optional LFS, large file support configure: enabled POSIX multithreading support checking for pthread_setconcurrency... no checking for pthread_attr_setscope... no checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... gcc checking for ntohs... yes checking for ntohl... yes checking for htons... yes checking for htonl... yes configure: creating ./config.status config.status: creating src/Makefile config.status: creating testsuite/Makefile config.status: creating Makefile config.status: creating src/config.h configure: configuring in squid configure: running /bin/sh './configure' --prefix=/usr/local '--enable-threads' '--enable-lfs' 'CFLAGS=-O2 -static' --cache-file=/dev/null --srcdir=. configure: configuring the SQUID library for your system. checking for gcc... gcc checking for C compiler default output... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking for ranlib... ranlib checking for ar... /usr/bin/ar checking whether your make is GNU make... nope, assuming sysv make. checking whether byte ordering is bigendian... no checking for ntohs... yes checking for ntohl... yes checking for htons... yes checking for htonl... yes checking how to run the C preprocessor... gcc -E checking for egrep... grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... no checking for unistd.h... yes checking for unsigned short... yes checking size of unsigned short... 2 checking for unsigned int... yes checking size of unsigned int... 4 checking for unsigned long... yes checking size of unsigned long... 4 checking for unsigned long long... yes checking size of unsigned long long... 8 checking for strtoul... yes checking for strtoull... yes checking whether fpos_t is an arithmetic datatype... yes. checking for strtoull... (cached) yes checking for ftello... yes checking for fseeko... yes checking for ftello64... no checking for fseeko64... no checking for ftell64... no checking for fseek64... no checking for stat64... no checking for off_t... yes checking size of off_t... 8 checking for off64_t... no checking size of off64_t... 0 checking for fpos_t... yes checking size of fpos_t... 8 configure: configured for optional LFS, large file support configure: creating ./config.status config.status: creating Makefile config.status: creating Testsuite/Makefile config.status: creating squid.h config.status: creating squidconf.h gcc -O2 -static -DHAVE_CONFIG_H -c afetch_main.c gcc -O2 -static -DHAVE_CONFIG_H -c a2m.c gcc -O2 -static -DHAVE_CONFIG_H -c aligneval.c gcc -O2 -static -DHAVE_CONFIG_H -c alignio.c gcc -O2 -static -DHAVE_CONFIG_H -c clustal.c gcc -O2 -static -DHAVE_CONFIG_H -c cluster.c gcc -O2 -static -DHAVE_CONFIG_H -c dayhoff.c gcc -O2 -static -DHAVE_CONFIG_H -c eps.c gcc -O2 -static -DHAVE_CONFIG_H -c file.c gcc -O2 -static -DHAVE_CONFIG_H -c getopt.c gcc -O2 -static -DHAVE_CONFIG_H -c gki.c gcc -O2 -static -DHAVE_CONFIG_H -c gsi.c gcc -O2 -static -DHAVE_CONFIG_H -c hsregex.c gcc -O2 -static -DHAVE_CONFIG_H -c iupac.c gcc -O2 -static -DHAVE_CONFIG_H -c msa.c gcc -O2 -static -DHAVE_CONFIG_H -c msf.c gcc -O2 -static -DHAVE_CONFIG_H -c phylip.c gcc -O2 -static -DHAVE_CONFIG_H -c revcomp.c gcc -O2 -static -DHAVE_CONFIG_H -c rk.c gcc -O2 -static -DHAVE_CONFIG_H -c selex.c gcc -O2 -static -DHAVE_CONFIG_H -c seqencode.c gcc -O2 -static -DHAVE_CONFIG_H -c shuffle.c gcc -O2 -static -DHAVE_CONFIG_H -c sqerror.c gcc -O2 -static -DHAVE_CONFIG_H -c sqio.c gcc -O2 -static -DHAVE_CONFIG_H -c squidcore.c gcc -O2 -static -DHAVE_CONFIG_H -c sre_ctype.c gcc -O2 -static -DHAVE_CONFIG_H -c sre_math.c gcc -O2 -static -DHAVE_CONFIG_H -c sre_random.c gcc -O2 -static -DHAVE_CONFIG_H -c sre_string.c gcc -O2 -static -DHAVE_CONFIG_H -c ssi.c gcc -O2 -static -DHAVE_CONFIG_H -c stack.c gcc -O2 -static -DHAVE_CONFIG_H -c stockholm.c gcc -O2 -static -DHAVE_CONFIG_H -c stopwatch.c gcc -O2 -static -DHAVE_CONFIG_H -c translate.c gcc -O2 -static -DHAVE_CONFIG_H -c types.c gcc -O2 -static -DHAVE_CONFIG_H -c vectorops.c gcc -O2 -static -DHAVE_CONFIG_H -c weight.c gcc -O2 -static -DHAVE_CONFIG_H -o afetch afetch_main.o a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o -lm gcc -O2 -static -DHAVE_CONFIG_H -c alistat_main.c gcc -O2 -static -DHAVE_CONFIG_H -o alistat alistat_main.o a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o -lm gcc -O2 -static -DHAVE_CONFIG_H -c compalign_main.c gcc -O2 -static -DHAVE_CONFIG_H -o compalign compalign_main.o a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o -lm gcc -O2 -static -DHAVE_CONFIG_H -c compstruct_main.c gcc -O2 -static -DHAVE_CONFIG_H -o compstruct compstruct_main.o a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o -lm gcc -O2 -static -DHAVE_CONFIG_H -c revcomp_main.c gcc -O2 -static -DHAVE_CONFIG_H -o revcomp revcomp_main.o a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o -lm gcc -O2 -static -DHAVE_CONFIG_H -c seqsplit_main.c gcc -O2 -static -DHAVE_CONFIG_H -o seqsplit seqsplit_main.o a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o -lm gcc -O2 -static -DHAVE_CONFIG_H -c seqstat_main.c gcc -O2 -static -DHAVE_CONFIG_H -o seqstat seqstat_main.o a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o -lm gcc -O2 -static -DHAVE_CONFIG_H -c sfetch_main.c gcc -O2 -static -DHAVE_CONFIG_H -o sfetch sfetch_main.o a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o -lm gcc -O2 -static -DHAVE_CONFIG_H -c shuffle_main.c gcc -O2 -static -DHAVE_CONFIG_H -o shuffle shuffle_main.o a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o -lm gcc -O2 -static -DHAVE_CONFIG_H -c sindex_main.c gcc -O2 -static -DHAVE_CONFIG_H -o sindex sindex_main.o a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o -lm gcc -O2 -static -DHAVE_CONFIG_H -c sreformat_main.c gcc -O2 -static -DHAVE_CONFIG_H -o sreformat sreformat_main.o a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o -lm gcc -O2 -static -DHAVE_CONFIG_H -c translate_main.c gcc -O2 -static -DHAVE_CONFIG_H -o translate translate_main.o a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o -lm gcc -O2 -static -DHAVE_CONFIG_H -c weight_main.c gcc -O2 -static -DHAVE_CONFIG_H -o weight weight_main.o a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o -lm /usr/bin/ar rcv libsquid.a a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o a - a2m.o a - aligneval.o a - alignio.o a - clustal.o a - cluster.o a - dayhoff.o a - eps.o a - file.o a - getopt.o a - gki.o a - gsi.o a - hsregex.o a - iupac.o a - msa.o a - msf.o a - phylip.o a - revcomp.o a - rk.o a - selex.o a - seqencode.o a - shuffle.o a - sqerror.o a - sqio.o a - squidcore.o a - sre_ctype.o a - sre_math.o a - sre_random.o a - sre_string.o a - ssi.o a - stack.o a - stockholm.o a - stopwatch.o a - translate.o a - types.o a - vectorops.o a - weight.o ranlib libsquid.a chmod 644 libsquid.a gcc -O2 -static -DHAVE_CONFIG_H -c a2m.c gcc -O2 -static -DHAVE_CONFIG_H -c aligneval.c gcc -O2 -static -DHAVE_CONFIG_H -c alignio.c gcc -O2 -static -DHAVE_CONFIG_H -c clustal.c gcc -O2 -static -DHAVE_CONFIG_H -c cluster.c gcc -O2 -static -DHAVE_CONFIG_H -c dayhoff.c gcc -O2 -static -DHAVE_CONFIG_H -c eps.c gcc -O2 -static -DHAVE_CONFIG_H -c file.c gcc -O2 -static -DHAVE_CONFIG_H -c getopt.c gcc -O2 -static -DHAVE_CONFIG_H -c gki.c gcc -O2 -static -DHAVE_CONFIG_H -c gsi.c gcc -O2 -static -DHAVE_CONFIG_H -c hsregex.c gcc -O2 -static -DHAVE_CONFIG_H -c iupac.c gcc -O2 -static -DHAVE_CONFIG_H -c msa.c gcc -O2 -static -DHAVE_CONFIG_H -c msf.c gcc -O2 -static -DHAVE_CONFIG_H -c phylip.c gcc -O2 -static -DHAVE_CONFIG_H -c revcomp.c gcc -O2 -static -DHAVE_CONFIG_H -c rk.c gcc -O2 -static -DHAVE_CONFIG_H -c selex.c gcc -O2 -static -DHAVE_CONFIG_H -c seqencode.c gcc -O2 -static -DHAVE_CONFIG_H -c shuffle.c gcc -O2 -static -DHAVE_CONFIG_H -c sqerror.c gcc -O2 -static -DHAVE_CONFIG_H -c sqio.c gcc -O2 -static -DHAVE_CONFIG_H -c squidcore.c gcc -O2 -static -DHAVE_CONFIG_H -c sre_ctype.c gcc -O2 -static -DHAVE_CONFIG_H -c sre_math.c gcc -O2 -static -DHAVE_CONFIG_H -c sre_random.c gcc -O2 -static -DHAVE_CONFIG_H -c sre_string.c gcc -O2 -static -DHAVE_CONFIG_H -c ssi.c gcc -O2 -static -DHAVE_CONFIG_H -c stack.c gcc -O2 -static -DHAVE_CONFIG_H -c stockholm.c gcc -O2 -static -DHAVE_CONFIG_H -c stopwatch.c gcc -O2 -static -DHAVE_CONFIG_H -c translate.c gcc -O2 -static -DHAVE_CONFIG_H -c types.c gcc -O2 -static -DHAVE_CONFIG_H -c vectorops.c gcc -O2 -static -DHAVE_CONFIG_H -c weight.c /usr/bin/ar rcv libsquid.a a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o r - a2m.o r - aligneval.o r - alignio.o r - clustal.o r - cluster.o r - dayhoff.o r - eps.o r - file.o r - getopt.o r - gki.o r - gsi.o r - hsregex.o r - iupac.o r - msa.o r - msf.o r - phylip.o r - revcomp.o r - rk.o r - selex.o r - seqencode.o r - shuffle.o r - sqerror.o r - sqio.o r - squidcore.o r - sre_ctype.o r - sre_math.o r - sre_random.o r - sre_string.o r - ssi.o r - stack.o r - stockholm.o r - stopwatch.o r - translate.o r - types.o r - vectorops.o r - weight.o ranlib libsquid.a chmod 644 libsquid.a gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c hmmalign.c gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c alphabet.c gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c core_algorithms.c gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c debug.c gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c display.c gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c emit.c gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c emulation.c gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c fast_algorithms.c gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c histogram.c gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c hmmio.c gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c mathsupport.c gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c masks.c gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c misc.c gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c modelmakers.c gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c plan7.c gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c plan9.c gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c postprob.c gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c prior.c gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c pvm.c gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c threads.c gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c tophits.c gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c trace.c gcc -O2 -static -pthread -DHAVE_CONFIG_H -L../squid -o hmmalign hmmalign.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o -lsquid -lm gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c hmmbuild.c gcc -O2 -static -pthread -DHAVE_CONFIG_H -L../squid -o hmmbuild hmmbuild.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o -lsquid -lm gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c hmmcalibrate.c gcc -O2 -static -pthread -DHAVE_CONFIG_H -L../squid -o hmmcalibrate hmmcalibrate.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o -lsquid -lm gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c hmmconvert.c gcc -O2 -static -pthread -DHAVE_CONFIG_H -L../squid -o hmmconvert hmmconvert.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o -lsquid -lm gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c hmmemit.c gcc -O2 -static -pthread -DHAVE_CONFIG_H -L../squid -o hmmemit hmmemit.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o -lsquid -lm gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c hmmfetch.c gcc -O2 -static -pthread -DHAVE_CONFIG_H -L../squid -o hmmfetch hmmfetch.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o -lsquid -lm gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c hmmindex.c gcc -O2 -static -pthread -DHAVE_CONFIG_H -L../squid -o hmmindex hmmindex.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o -lsquid -lm gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c hmmpfam.c gcc -O2 -static -pthread -DHAVE_CONFIG_H -L../squid -o hmmpfam hmmpfam.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o -lsquid -lm gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c hmmsearch.c gcc -O2 -static -pthread -DHAVE_CONFIG_H -L../squid -o hmmsearch hmmsearch.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o -lsquid -lm gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c alphabet.c gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c core_algorithms.c gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c debug.c gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c display.c gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c emit.c gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c emulation.c gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c fast_algorithms.c gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c histogram.c gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c hmmio.c gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c mathsupport.c gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c masks.c gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c misc.c gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c modelmakers.c gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c plan7.c gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c plan9.c gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c postprob.c gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c prior.c gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c pvm.c gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c threads.c gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c tophits.c gcc -O2 -static -DHAVE_CONFIG_H -pthread -I../squid -c trace.c /usr/bin/ar rcv libhmmer.a alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o a - alphabet.o a - core_algorithms.o a - debug.o a - display.o a - emit.o a - emulation.o a - fast_algorithms.o a - histogram.o a - hmmio.o a - mathsupport.o a - masks.o a - misc.o a - modelmakers.o a - plan7.o a - plan9.o a - postprob.o a - prior.o a - pvm.o a - threads.o a - tophits.o a - trace.o ranlib libhmmer.a chmod 644 libhmmer.a gcc -O2 -static -pthread -DHAVE_CONFIG_H -I../squid -I../src -c alignalign_test.c gcc -O2 -static -pthread -DHAVE_CONFIG_H -o alignalign_test -L../squid -L../src alignalign_test.o -lhmmer -lsquid -lm gcc -O2 -static -pthread -DHAVE_CONFIG_H -I../squid -I../src -c evd_test.c gcc -O2 -static -pthread -DHAVE_CONFIG_H -o evd_test -L../squid -L../src evd_test.o -lhmmer -lsquid -lm gcc -O2 -static -pthread -DHAVE_CONFIG_H -I../squid -I../src -c masks_test.c gcc -O2 -static -pthread -DHAVE_CONFIG_H -o masks_test -L../squid -L../src masks_test.o -lhmmer -lsquid -lm gcc -O2 -static -pthread -DHAVE_CONFIG_H -I../squid -I../src -c parsingviterbi_test.c gcc -O2 -static -pthread -DHAVE_CONFIG_H -o parsingviterbi_test -L../squid -L../src parsingviterbi_test.o -lhmmer -lsquid -lm gcc -O2 -static -pthread -DHAVE_CONFIG_H -I../squid -I../src -c tophits_test.c gcc -O2 -static -pthread -DHAVE_CONFIG_H -o tophits_test -L../squid -L../src tophits_test.o -lhmmer -lsquid -lm gcc -O2 -static -pthread -DHAVE_CONFIG_H -I../squid -I../src -c trace_test.c gcc -O2 -static -pthread -DHAVE_CONFIG_H -o trace_test -L../squid -L../src trace_test.o -lhmmer -lsquid -lm gcc -O2 -static -pthread -DHAVE_CONFIG_H -I../squid -I../src -c viterbi_exercise.c gcc -O2 -static -pthread -DHAVE_CONFIG_H -o viterbi_exercise -L../squid -L../src viterbi_exercise.o -lhmmer -lsquid -lm gcc -O2 -static -pthread -DHAVE_CONFIG_H -I../squid -I../src -c weeviterbi_test.c gcc -O2 -static -pthread -DHAVE_CONFIG_H -o weeviterbi_test -L../squid -L../src weeviterbi_test.o -lhmmer -lsquid -lm (cd testsuite; make check) Running test suite exercises. Warning: some tests may take several minutes to complete. ./sqc 2 exercises.sqc . ../src exercise 1 [ hmmalign] ... ok. exercise 2 [ hmmalign/h] ... ok. exercise 3 [ hmmalign/m] ... ok. exercise 4 [ hmmalign/o] ... ok. exercise 5 [ hmmalign/q] ... ok. exercise 6 [ hmmalign/informat] ... ok. exercise 7 [ hmmalign/selex] ... ok. exercise 8 [ hmmalign/a2m] ... ok. exercise 9 [ hmmalign/clustal] ... ok. exercise 10 [ hmmalign/msf] ... ok. exercise 11 [ hmmalign/phylip] ... ok. exercise 12 [ hmmalign/oneline] ... ok. exercise 13 [ hmmalign/withali] ... ok. exercise 14 [ hmmalign/mapali] ... ok. exercise 15 [ hmmbuild] ... ok. exercise 16 [ hmmbuild/h] ... ok. exercise 17 [ hmmbuild/F] ... ok. exercise 18 [ hmmbuild/n] ... ok. exercise 19 [ hmmbuild/o] ... ok. exercise 20 [ hmmbuild/A] ... ok. exercise 21 [ hmmbuild/f] ... ok. exercise 22 [ hmmbuild/g] ... ok. exercise 23 [ hmmbuild/s] ... ok. exercise 24 [ hmmbuild/fast] ... ok. exercise 25 [ hmmbuild/hand] ... ok. exercise 26 [ hmmbuild/null] ... ok. exercise 27 [ hmmbuild/pam] ... ok. exercise 28 [ hmmbuild/prior] ... ok. exercise 29 [ hmmbuild/wblosum] ... ok. exercise 30 [ hmmbuild/wgsc] ... ok. exercise 31 [ hmmbuild/wme] ... ok. exercise 32 [ hmmbuild/wpb] ... ok. exercise 33 [ hmmbuild/wvoronoi] ... ok. exercise 34 [ hmmbuild/wnone] ... ok. exercise 35 [ hmmbuild/noeff] ... ok. exercise 36 [ hmmbuild/pbswitch] ... ok. exercise 37 [ hmmbuild/amino] ... ok. exercise 38 [ hmmbuild/nucleic] ... ok. exercise 39 [ hmmbuild/archpri] ... ok. exercise 40 [ hmmbuild/binary] ... ok. exercise 41 [ hmmbuild/cfile] ... ok. exercise 42 [ hmmbuild/gapmax] ... ok. exercise 43 [ hmmbuild/idlevel] ... ok. exercise 44 [ hmmbuild/informat] ... ok. exercise 45 [ hmmbuild/pamwgt] ... ok. exercise 46 [ hmmbuild/swentry] ... ok. exercise 47 [ hmmbuild/swexit] ... ok. exercise 48 [ hmmbuild/verbose] ... ok. exercise 49 [ hmmcalibrate] ... ok. exercise 50 [ hmmcalibrate/h] ... ok. exercise 51 [ hmmcalibrate/fixed] ... ok. exercise 52 [ hmmcalibrate/mean] ... ok. exercise 53 [ hmmcalibrate/hist] ... ok. exercise 54 [ hmmcalibrate/num] ... ok. exercise 55 [ hmmcalibrate/sd] ... ok. exercise 56 [ hmmcalibrate/seed] ... ok. exercise 57 [ hmmconvert] ... ok. exercise 58 [ hmmconvert/h] ... ok. exercise 59 [ hmmconvert/F] ... ok. exercise 60 [ hmmconvert/a] ... ok. exercise 61 [ hmmconvert/A] ... ok. exercise 62 [ hmmconvert/b] ... ok. exercise 63 [ hmmconvert/p] ... ok. exercise 64 [ hmmconvert/P] ... ok. exercise 65 [ hmmemit] ... ok. exercise 66 [ hmmemit/a] ... ok. exercise 67 [ hmmemit/c] ... ok. exercise 68 [ hmmemit/h] ... ok. exercise 69 [ hmmemit/n] ... ok. exercise 70 [ hmmemit/o] ... ok. exercise 71 [ hmmemit/q] ... ok. exercise 72 [ hmmemit/seed] ... ok. exercise 73 [ hmmindex] ... ok. exercise 74 [ hmmindex/h] ... ok. exercise 75 [ hmmfetch] ... ok. exercise 76 [ hmmfetch/h] ... ok. exercise 77 [ hmmfetch/n] ... ok. exercise 78 [ hmmpfam] ... ok. exercise 79 [ hmmpfam/h] ... ok. exercise 80 [ hmmpfam/n] ... ok. exercise 81 [ hmmpfam/A] ... ok. exercise 82 [ hmmpfam/E] ... ok. exercise 83 [ hmmpfam/T] ... ok. exercise 84 [ hmmpfam/Z] ... ok. exercise 85 [ hmmpfam/acc] ... ok. exercise 86 [ hmmpfam/compat] ... ok. exercise 87 [ hmmpfam/cut_ga] ... ok. exercise 88 [ hmmpfam/cut_nc] ... ok. exercise 89 [ hmmpfam/cut_tc] ... ok. exercise 90 [ hmmpfam/domE] ... ok. exercise 91 [ hmmpfam/domT] ... ok. exercise 92 [ hmmpfam/forward] ... ok. exercise 93 [ hmmpfam/informat] ... ok. exercise 94 [ hmmpfam/null2] ... ok. exercise 95 [ hmmpfam/xnu] ... ok. exercise 96 [ hmmsearch] ... ok. exercise 97 [ hmmsearch/h] ... ok. exercise 98 [ hmmsearch/A] ... ok. exercise 99 [ hmmsearch/E] ... ok. exercise 100 [ hmmsearch/T] ... ok. exercise 101 [ hmmsearch/Z] ... ok. exercise 102 [ hmmsearch/compat] ... ok. exercise 103 [ hmmsearch/cut_ga] ... ok. exercise 104 [ hmmsearch/cut_nc] ... ok. exercise 105 [ hmmsearch/cut_tc] ... ok. exercise 106 [ hmmsearch/domE] ... ok. exercise 107 [ hmmsearch/domT] ... ok. exercise 108 [ hmmsearch/forward] ... ok. exercise 109 [ hmmsearch/informat] ... ok. exercise 110 [ hmmsearch/null2] ... ok. exercise 111 [ hmmsearch/xnu] ... ok. exercise 112 [ align_align] ... ok. exercise 113 [ evd] ... ok. exercise 114 [ masks] ... ok. exercise 115 [ parsingv] ... ok. exercise 116 [ tophits] ... ok. exercise 117 [ trace] ... ok. exercise 118 [ viterbi] ... ok. exercise 119 [ weeviterbi] ... ok. exercise 120 [ test1/conversion] ... ok. All 120 exercises at level <= 2 passed. System information: Sat Oct 4 05:30:06 CDT 2003 OpenBSD wonderboy 3.2 GENERIC#25 i386 mkdir binaries for prog in hmmalign hmmbuild hmmcalibrate hmmconvert hmmemit hmmfetch hmmindex hmmpfam hmmsearch; do (cd binaries; ln -s ../src/$prog .); done make binclean (cd src; make binclean) rm -f *.o *~ Makefile.bak core TAGS gmon.out libhmmer.a (cd squid; make binclean) (cd Testsuite; make binclean) rm -f *.o *~ Makefile.bak core TAGS gmon.out sqdconfig rm -f *.o *~ core TAGS llib-lsquid.ln ccmalloc.log rm -f libsquid.a squid.h squidconf.h rm -f config.log config.status rm -rf autom4te.cache (cd testsuite; make binclean) rm -f *.o *~ Makefile.bak core TAGS gmon.out rm -f *.o *~ Makefile.bak core TAGS gmon.out rm config.log config.status rm -rf autom4te.cache