Building hmmer-3.0.txz (origin /buildshare/ports/355755/biology/hmmer) for powerpc-10-0 on XXX slot2: created x distfiles/ x distfiles/hmmer-3.0.tar.gz x packages/ x packages/perl5-5.16.3_10.txz x packages/pkg-1.2.7_2.txz ELF ldconfig path: /lib /usr/lib /usr/lib/compat Make depends ===> hmmer-3.0 depends on file: /usr/local/sbin/pkg - not found ===> Verifying install for /usr/local/sbin/pkg in /buildshare/ports/355755/ports-mgmt/pkg ===> Installing existing package /packages/pkg-1.2.7_2.txz Installing pkg-1.2.7_2... done If you are upgrading from the old package format, first run: # pkg2ng ===> Returning to build of hmmer-3.0 ===> hmmer-3.0 depends on file: /usr/local/bin/perl5.16.3 - not found ===> Verifying install for /usr/local/bin/perl5.16.3 in /buildshare/ports/355755/lang/perl5.16 ===> Installing existing package /packages/perl5-5.16.3_10.txz Installing perl5-5.16.3_10... done ===> Returning to build of hmmer-3.0 ===> hmmer-3.0 depends on file: /usr/local/bin/perl5.16.3 - found Make install ===> hmmer-3.0 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by hmmer-3.0 for building ===> Extracting for hmmer-3.0 => SHA256 Checksum OK for hmmer-3.0.tar.gz. ===> Patching for hmmer-3.0 ===> hmmer-3.0 depends on file: /usr/local/bin/perl5.16.3 - found ===> Configuring for hmmer-3.0 ===> FreeBSD 10 autotools fix applied to /obj/buildshare/ports/355755/biology/hmmer/work/hmmer-3.0/easel/aclocal.m4 ===> FreeBSD 10 autotools fix applied to /obj/buildshare/ports/355755/biology/hmmer/work/hmmer-3.0/easel/configure ===> FreeBSD 10 autotools fix applied to /obj/buildshare/ports/355755/biology/hmmer/work/hmmer-3.0/configure configure: WARNING: unrecognized options: --enable-lfs configure: loading site script /buildshare/ports/355755/Templates/config.site configure: Configuring HMMER for your system. checking build system type... powerpc-portbld-freebsd11.0 checking host system type... powerpc-portbld-freebsd11.0 configure: Full HMMER source distribution - using full configuration checking for gcc... cc checking for C compiler default output file name... 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 cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for C compiler vendor... gnu 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... -D_THREAD_SAFE checking for cc_r... cc checking for gcc... (cached) cc checking whether we are using the GNU C compiler... (cached) yes checking whether cc accepts -g... (cached) yes checking for cc option to accept ISO C89... (cached) none needed checking how to run the C preprocessor... cpp checking for C compiler vendor... (cached) gnu checking for cc option to accept ISO C99... -std=gnu99 checking for cc -std=gnu99 option to accept ISO Standard C... (cached) -std=gnu99 checking for ranlib... ranlib checking for ar... /usr/bin/ar checking whether your make is GNU make... nope, assuming sysv make. checking whether C compiler accepts -faltivec... no checking whether C compiler accepts -maltivec -mabi=altivec... yes checking whether Altivec/VMX is supported... yes configure: Activating Altivec/VMX optimized DP implementation checking compiler support --start-group... yes checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for ANSI C header files... (cached) yes checking for sys/types.h... (cached) yes checking for sys/stat.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for memory.h... (cached) yes checking for strings.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/types.h... (cached) yes checking sys/sysctl.h usability... yes checking sys/sysctl.h presence... yes checking for sys/sysctl.h... yes checking for unistd.h... (cached) yes checking for stdint.h... (cached) yes checking for inttypes.h... (cached) yes checking endian.h usability... no checking endian.h presence... no checking for endian.h... no checking altivec.h usability... yes checking altivec.h presence... yes checking for altivec.h... yes checking whether byte ordering is bigendian... yes checking for uint8_t... (cached) yes checking for uint16_t... (cached) yes checking for uint32_t... (cached) yes checking for uint64_t... (cached) yes checking for off_t... (cached) yes checking for mkstemp... (cached) yes checking for popen... yes checking for strcasecmp... (cached) yes checking for times... yes checking for getpid... (cached) yes checking for sysctl... yes checking for sysconf... (cached) yes checking for ntohs... yes checking for ntohl... yes checking for htons... yes checking for htonl... yes checking for _LARGEFILE_SOURCE value needed for large files... no checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no configure: creating ./config.status config.status: creating src/Makefile config.status: creating testsuite/Makefile config.status: creating profmark/Makefile config.status: creating src/impl_vmx/Makefile config.status: creating easel/miniapps/Makefile config.status: creating easel/testsuite/Makefile config.status: creating easel/Makefile config.status: creating Makefile config.status: creating src/p7_config.h config.status: creating easel/esl_config.h config.status: linking src/impl_vmx to src/impl configure: WARNING: unrecognized options: --enable-lfs HMMER configuration: compiler: cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -maltivec -mabi=altivec -D_THREAD_SAFE -pthread linker: libraries: DP implementation: vmx ===> Building for hmmer-3.0 cd easel; /usr/bin/make libeasel.a cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o easel.o -c easel.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_alphabet.o -c esl_alphabet.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_cluster.o -c esl_cluster.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_dirichlet.o -c esl_dirichlet.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_distance.o -c esl_distance.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_dmatrix.o -c esl_dmatrix.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_exponential.o -c esl_exponential.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_fileparser.o -c esl_fileparser.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_gamma.o -c esl_gamma.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_getopts.o -c esl_getopts.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_gev.o -c esl_gev.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_gumbel.o -c esl_gumbel.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_histogram.o -c esl_histogram.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_hmm.o -c esl_hmm.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_hyperexp.o -c esl_hyperexp.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_keyhash.o -c esl_keyhash.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_minimizer.o -c esl_minimizer.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_mixgev.o -c esl_mixgev.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_mpi.o -c esl_mpi.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_msa.o -c esl_msa.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_msacluster.o -c esl_msacluster.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_msashuffle.o -c esl_msashuffle.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_msaweight.o -c esl_msaweight.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_normal.o -c esl_normal.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_paml.o -c esl_paml.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_random.o -c esl_random.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_randomseq.o -c esl_randomseq.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_ratematrix.o -c esl_ratematrix.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_regexp.o -c esl_regexp.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_rootfinder.o -c esl_rootfinder.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_scorematrix.o -c esl_scorematrix.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_sq.o -c esl_sq.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_sqio.o -c esl_sqio.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_sqio_ascii.o -c esl_sqio_ascii.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_sqio_ncbi.o -c esl_sqio_ncbi.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_sse.o -c esl_sse.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_ssi.o -c esl_ssi.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_stack.o -c esl_stack.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_stats.o -c esl_stats.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_stopwatch.o -c esl_stopwatch.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_stretchexp.o -c esl_stretchexp.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_threads.o -c esl_threads.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_tree.o -c esl_tree.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_vectorops.o -c esl_vectorops.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_vmx.o -c esl_vmx.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_weibull.o -c esl_weibull.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_workqueue.o -c esl_workqueue.c cc -std=gnu99 -I. -I. -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -o esl_wuss.o -c esl_wuss.c /usr/bin/ar rcv libeasel.a easel.o esl_alphabet.o esl_cluster.o esl_dirichlet.o esl_distance.o esl_dmatrix.o esl_exponential.o esl_fileparser.o esl_gamma.o esl_getopts.o esl_gev.o esl_gumbel.o esl_histogram.o esl_hmm.o esl_hyperexp.o esl_keyhash.o esl_minimizer.o esl_mixgev.o esl_mpi.o esl_msa.o esl_msacluster.o esl_msashuffle.o esl_msaweight.o esl_normal.o esl_paml.o esl_random.o esl_randomseq.o esl_ratematrix.o esl_regexp.o esl_rootfinder.o esl_scorematrix.o esl_sq.o esl_sqio.o esl_sqio_ascii.o esl_sqio_ncbi.o esl_sse.o esl_ssi.o esl_stack.o esl_stats.o esl_stopwatch.o esl_stretchexp.o esl_threads.o esl_tree.o esl_vectorops.o esl_vmx.o esl_weibull.o esl_workqueue.o esl_wuss.o a - easel.o a - esl_alphabet.o a - esl_cluster.o a - esl_dirichlet.o a - esl_distance.o a - esl_dmatrix.o a - esl_exponential.o a - esl_fileparser.o a - esl_gamma.o a - esl_getopts.o a - esl_gev.o a - esl_gumbel.o a - esl_histogram.o a - esl_hmm.o a - esl_hyperexp.o a - esl_keyhash.o a - esl_minimizer.o a - esl_mixgev.o a - esl_mpi.o a - esl_msa.o a - esl_msacluster.o a - esl_msashuffle.o a - esl_msaweight.o a - esl_normal.o a - esl_paml.o a - esl_random.o a - esl_randomseq.o a - esl_ratematrix.o a - esl_regexp.o a - esl_rootfinder.o a - esl_scorematrix.o a - esl_sq.o a - esl_sqio.o a - esl_sqio_ascii.o a - esl_sqio_ncbi.o a - esl_sse.o a - esl_ssi.o a - esl_stack.o a - esl_stats.o a - esl_stopwatch.o a - esl_stretchexp.o a - esl_threads.o a - esl_tree.o a - esl_vectorops.o a - esl_vmx.o a - esl_weibull.o a - esl_workqueue.o a - esl_wuss.o ranlib libeasel.a chmod 644 libeasel.a cd src/impl_vmx; /usr/bin/make libhmmerimpl.a cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -c decoding.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -c fwdback.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -c io.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -c msvfilter.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -c null2.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -c optacc.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -c stotrace.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -c vitfilter.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -c p7_omx.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -c p7_oprofile.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -c mpi.c /usr/bin/ar rcv libhmmerimpl.a decoding.o fwdback.o io.o msvfilter.o null2.o optacc.o stotrace.o vitfilter.o p7_omx.o p7_oprofile.o mpi.o a - decoding.o a - fwdback.o a - io.o a - msvfilter.o a - null2.o a - optacc.o a - stotrace.o a - vitfilter.o a - p7_omx.o a - p7_oprofile.o a - mpi.o ranlib libhmmerimpl.a chmod 644 libhmmerimpl.a cd src; /usr/bin/make libhmmer.a cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o build.o -c build.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o emit.o -c emit.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o errors.o -c errors.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o evalues.o -c evalues.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o eweight.o -c eweight.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o generic_decoding.o -c generic_decoding.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o generic_fwdback.o -c generic_fwdback.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o generic_null2.o -c generic_null2.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o generic_msv.o -c generic_msv.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o generic_optacc.o -c generic_optacc.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o generic_stotrace.o -c generic_stotrace.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o generic_viterbi.o -c generic_viterbi.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o generic_vtrace.o -c generic_vtrace.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o h2_io.o -c h2_io.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o heatmap.o -c heatmap.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o hmmer.o -c hmmer.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o logsum.o -c logsum.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o modelconfig.o -c modelconfig.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o modelstats.o -c modelstats.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o mpisupport.o -c mpisupport.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o seqmodel.o -c seqmodel.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o tracealign.o -c tracealign.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o p7_alidisplay.o -c p7_alidisplay.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o p7_bg.o -c p7_bg.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o p7_builder.o -c p7_builder.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o p7_domaindef.o -c p7_domaindef.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o p7_gmx.o -c p7_gmx.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o p7_hmm.o -c p7_hmm.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o p7_hmmfile.o -c p7_hmmfile.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o p7_pipeline.o -c p7_pipeline.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o p7_prior.o -c p7_prior.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o p7_profile.o -c p7_profile.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o p7_spensemble.o -c p7_spensemble.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o p7_tophits.o -c p7_tophits.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o p7_trace.o -c p7_trace.c /usr/bin/ar rcv libhmmer.a build.o emit.o errors.o evalues.o eweight.o generic_decoding.o generic_fwdback.o generic_null2.o generic_msv.o generic_optacc.o generic_stotrace.o generic_viterbi.o generic_vtrace.o h2_io.o heatmap.o hmmer.o logsum.o modelconfig.o modelstats.o mpisupport.o seqmodel.o tracealign.o p7_alidisplay.o p7_bg.o p7_builder.o p7_domaindef.o p7_gmx.o p7_hmm.o p7_hmmfile.o p7_pipeline.o p7_prior.o p7_profile.o p7_spensemble.o p7_tophits.o p7_trace.o a - build.o a - emit.o a - errors.o a - evalues.o a - eweight.o a - generic_decoding.o a - generic_fwdback.o a - generic_null2.o a - generic_msv.o a - generic_optacc.o a - generic_stotrace.o a - generic_viterbi.o a - generic_vtrace.o a - h2_io.o a - heatmap.o a - hmmer.o a - logsum.o a - modelconfig.o a - modelstats.o a - mpisupport.o a - seqmodel.o a - tracealign.o a - p7_alidisplay.o a - p7_bg.o a - p7_builder.o a - p7_domaindef.o a - p7_gmx.o a - p7_hmm.o a - p7_hmmfile.o a - p7_pipeline.o a - p7_prior.o a - p7_profile.o a - p7_spensemble.o a - p7_tophits.o a - p7_trace.o ranlib libhmmer.a chmod 644 libhmmer.a cd easel; /usr/bin/make easel_progs cd miniapps; /usr/bin/make easel_progs cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -maltivec -mabi=altivec -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-afetch.o -c esl-afetch.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -maltivec -mabi=altivec -DHAVE_CONFIG_H -L.. -o esl-afetch esl-afetch.o -leasel -lm cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -maltivec -mabi=altivec -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-alimanip.o -c esl-alimanip.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -maltivec -mabi=altivec -DHAVE_CONFIG_H -L.. -o esl-alimanip esl-alimanip.o -leasel -lm cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -maltivec -mabi=altivec -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-alimap.o -c esl-alimap.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -maltivec -mabi=altivec -DHAVE_CONFIG_H -L.. -o esl-alimap esl-alimap.o -leasel -lm cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -maltivec -mabi=altivec -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-alimask.o -c esl-alimask.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -maltivec -mabi=altivec -DHAVE_CONFIG_H -L.. -o esl-alimask esl-alimask.o -leasel -lm cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -maltivec -mabi=altivec -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-alimerge.o -c esl-alimerge.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -maltivec -mabi=altivec -DHAVE_CONFIG_H -L.. -o esl-alimerge esl-alimerge.o -leasel -lm cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -maltivec -mabi=altivec -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-alistat.o -c esl-alistat.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -maltivec -mabi=altivec -DHAVE_CONFIG_H -L.. -o esl-alistat esl-alistat.o -leasel -lm cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -maltivec -mabi=altivec -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-cluster.o -c esl-cluster.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -maltivec -mabi=altivec -DHAVE_CONFIG_H -L.. -o esl-cluster esl-cluster.o -leasel -lm cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -maltivec -mabi=altivec -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-compalign.o -c esl-compalign.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -maltivec -mabi=altivec -DHAVE_CONFIG_H -L.. -o esl-compalign esl-compalign.o -leasel -lm cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -maltivec -mabi=altivec -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-compstruct.o -c esl-compstruct.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -maltivec -mabi=altivec -DHAVE_CONFIG_H -L.. -o esl-compstruct esl-compstruct.o -leasel -lm cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -maltivec -mabi=altivec -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-construct.o -c esl-construct.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -maltivec -mabi=altivec -DHAVE_CONFIG_H -L.. -o esl-construct esl-construct.o -leasel -lm cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -maltivec -mabi=altivec -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-histplot.o -c esl-histplot.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -maltivec -mabi=altivec -DHAVE_CONFIG_H -L.. -o esl-histplot esl-histplot.o -leasel -lm cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -maltivec -mabi=altivec -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-mask.o -c esl-mask.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -maltivec -mabi=altivec -DHAVE_CONFIG_H -L.. -o esl-mask esl-mask.o -leasel -lm cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -maltivec -mabi=altivec -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-reformat.o -c esl-reformat.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -maltivec -mabi=altivec -DHAVE_CONFIG_H -L.. -o esl-reformat esl-reformat.o -leasel -lm cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -maltivec -mabi=altivec -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-selectn.o -c esl-selectn.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -maltivec -mabi=altivec -DHAVE_CONFIG_H -L.. -o esl-selectn esl-selectn.o -leasel -lm cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -maltivec -mabi=altivec -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-seqstat.o -c esl-seqstat.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -maltivec -mabi=altivec -DHAVE_CONFIG_H -L.. -o esl-seqstat esl-seqstat.o -leasel -lm cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -maltivec -mabi=altivec -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-sfetch.o -c esl-sfetch.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -maltivec -mabi=altivec -DHAVE_CONFIG_H -L.. -o esl-sfetch esl-sfetch.o -leasel -lm cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -maltivec -mabi=altivec -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-shuffle.o -c esl-shuffle.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -maltivec -mabi=altivec -DHAVE_CONFIG_H -L.. -o esl-shuffle esl-shuffle.o -leasel -lm cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -maltivec -mabi=altivec -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-ssdraw.o -c esl-ssdraw.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -maltivec -mabi=altivec -DHAVE_CONFIG_H -L.. -o esl-ssdraw esl-ssdraw.o -leasel -lm cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -maltivec -mabi=altivec -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-weight.o -c esl-weight.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -maltivec -mabi=altivec -DHAVE_CONFIG_H -L.. -o esl-weight esl-weight.o -leasel -lm cd src; /usr/bin/make hmmer_progs cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o hmmalign.o -c hmmalign.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -L../easel -L./impl_vmx -L. -o hmmalign hmmalign.o -Wl,--start-group -lhmmer -lhmmerimpl -Wl,--end-group -leasel -lm cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o hmmbuild.o -c hmmbuild.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -L../easel -L./impl_vmx -L. -o hmmbuild hmmbuild.o -Wl,--start-group -lhmmer -lhmmerimpl -Wl,--end-group -leasel -lm cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o hmmconvert.o -c hmmconvert.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -L../easel -L./impl_vmx -L. -o hmmconvert hmmconvert.o -Wl,--start-group -lhmmer -lhmmerimpl -Wl,--end-group -leasel -lm cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o hmmemit.o -c hmmemit.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -L../easel -L./impl_vmx -L. -o hmmemit hmmemit.o -Wl,--start-group -lhmmer -lhmmerimpl -Wl,--end-group -leasel -lm cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o hmmfetch.o -c hmmfetch.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -L../easel -L./impl_vmx -L. -o hmmfetch hmmfetch.o -Wl,--start-group -lhmmer -lhmmerimpl -Wl,--end-group -leasel -lm cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o hmmpress.o -c hmmpress.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -L../easel -L./impl_vmx -L. -o hmmpress hmmpress.o -Wl,--start-group -lhmmer -lhmmerimpl -Wl,--end-group -leasel -lm cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o hmmscan.o -c hmmscan.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -L../easel -L./impl_vmx -L. -o hmmscan hmmscan.o -Wl,--start-group -lhmmer -lhmmerimpl -Wl,--end-group -leasel -lm cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o hmmsearch.o -c hmmsearch.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -L../easel -L./impl_vmx -L. -o hmmsearch hmmsearch.o -Wl,--start-group -lhmmer -lhmmerimpl -Wl,--end-group -leasel -lm cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o hmmsim.o -c hmmsim.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -L../easel -L./impl_vmx -L. -o hmmsim hmmsim.o -Wl,--start-group -lhmmer -lhmmerimpl -Wl,--end-group -leasel -lm cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o hmmstat.o -c hmmstat.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -L../easel -L./impl_vmx -L. -o hmmstat hmmstat.o -Wl,--start-group -lhmmer -lhmmerimpl -Wl,--end-group -leasel -lm cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o jackhmmer.o -c jackhmmer.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -L../easel -L./impl_vmx -L. -o jackhmmer jackhmmer.o -Wl,--start-group -lhmmer -lhmmerimpl -Wl,--end-group -leasel -lm cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o phmmer.o -c phmmer.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -maltivec -mabi=altivec -DHAVE_CONFIG_H -L../easel -L./impl_vmx -L. -o phmmer phmmer.o -Wl,--start-group -lhmmer -lhmmerimpl -Wl,--end-group -leasel -lm cd profmark; /usr/bin/make profmark_progs cc -std=gnu99 -I../easel -I../easel -I../src -I../src -O2 -pipe -fno-strict-aliasing -maltivec -mabi=altivec -DHAVE_CONFIG_H -o create-profmark.o -c create-profmark.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -DHAVE_CONFIG_H -L../easel -L../src -o create-profmark create-profmark.o -lhmmer -leasel -lm cc -std=gnu99 -I../easel -I../easel -I../src -I../src -O2 -pipe -fno-strict-aliasing -maltivec -mabi=altivec -DHAVE_CONFIG_H -o rocplot.o -c rocplot.c cc -std=gnu99 -O2 -pipe -fno-strict-aliasing -DHAVE_CONFIG_H -L../easel -L../src -o rocplot rocplot.o -lhmmer -leasel -lm ===> Staging for hmmer-3.0 ===> hmmer-3.0 depends on file: /usr/local/bin/perl5.16.3 - found ===> Generating temporary packing list cd easel; /usr/bin/make libeasel.a `libeasel.a' is up to date. cd src/impl_vmx; /usr/bin/make libhmmerimpl.a `libhmmerimpl.a' is up to date. cd src; /usr/bin/make libhmmer.a `libhmmer.a' is up to date. cd easel; /usr/bin/make easel_progs cd miniapps; /usr/bin/make easel_progs cd src; /usr/bin/make hmmer_progs cd profmark; /usr/bin/make profmark_progs cd profmark; /usr/bin/make profmark_progs mkdir -p /obj/buildshare/ports/355755/biology/hmmer/work/stage/usr/local/bin for file in hmmalign hmmbuild hmmconvert hmmemit hmmfetch hmmpress hmmscan hmmsearch hmmsim hmmstat jackhmmer phmmer; do cp src/$file /obj/buildshare/ports/355755/biology/hmmer/work/stage/usr/local/bin/; done install -o root -g wheel -m 444 /obj/buildshare/ports/355755/biology/hmmer/work/hmmer-3.0/COPYRIGHT /obj/buildshare/ports/355755/biology/hmmer/work/hmmer-3.0/INSTALL /obj/buildshare/ports/355755/biology/hmmer/work/hmmer-3.0/LICENSE /obj/buildshare/ports/355755/biology/hmmer/work/hmmer-3.0/Userguide.pdf /obj/buildshare/ports/355755/biology/hmmer/work/stage/usr/local/share/doc/hmmer install -o root -g wheel -m 444 /obj/buildshare/ports/355755/biology/hmmer/work/hmmer-3.0/tutorial/7LESS_DROME /obj/buildshare/ports/355755/biology/hmmer/work/hmmer-3.0/tutorial/Pkinase.sto /obj/buildshare/ports/355755/biology/hmmer/work/hmmer-3.0/tutorial/fn3.sto /obj/buildshare/ports/355755/biology/hmmer/work/hmmer-3.0/tutorial/globins4.sto /obj/buildshare/ports/355755/biology/hmmer/work/hmmer-3.0/tutorial/minifam.h3f /obj/buildshare/ports/355755/biology/hmmer/work/hmmer-3.0/tutorial/minifam.h3p /obj/buildshare/ports/355755/biology/hmmer/work/hmmer-3.0/tutorial/HBB_HUMAN /obj/buildshare/ports/355755/biology/hmmer/work/hmmer-3.0/tutorial/fn3.hmm /obj/buildshare/ports/355755/biology/hmmer/work/hmmer-3.0/tutorial/globins4.hmm /obj/buildshare/ports/355755/biology/hmmer/work/hmmer-3.0/tutorial/globins45.fa /obj/buildshare/ports/355755/biology/hmmer/work/hmmer-3.0/tutorial/minifam.h3i /obj/buildshare/ports/355755/biology/hmmer/work/hmmer-3.0/tutorial/Pkinase.hmm /obj/buildshare/ports/355755/biology/hmmer/work/hmmer-3.0/tutorial/fn3.out /obj/buildshare/ports/355755/biology/hmmer/work/hmmer-3.0/tutorial/globins4.out /obj/buildshare/ports/355755/biology/hmmer/work/hmmer-3.0/tutorial/minifam /obj/buildshare/ports/355755/biology/hmmer/work/hmmer-3.0/tutorial/minifam.h3m /obj/buildshare/ports/355755/biology/hmmer/work/stage/usr/local/share/examples/hmmer ====> Compressing man pages (compress-man) ===> Installing for hmmer-3.0 ===> Checking if biology/hmmer already installed ===> Registering installation for hmmer-3.0 Installing hmmer-3.0... done --------------------------------------------------------------------------- HMMER reads three optional environment variables: HMMERDB - directory location of HMM databases (e.g. PFAM) BLASTDB - directory location of FASTA-formatted sequence databases BLASTMAT - directory location of PAM scoring matrices The BLASTDB and BLASTMAT variables are shared with versions of BLAST such as NCBI BLAST 2.0 (contained in the biology/ncbi-toolkit port). If these variables are set, you do not have to specify the full path to your databases on the command line when using HMMER. Please see the documentation for more information. --------------------------------------------------------------------------- Make package ===> Building package for hmmer-3.0 slot2: removed