------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gettext-runtime-0.21.txz Installing /packages/All/gmake-4.3_2.txz SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> infernal-1.1.3 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> infernal-1.1.3 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by infernal-1.1.3 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> infernal-1.1.3 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by infernal-1.1.3 for building => SHA256 Checksum OK for infernal-1.1.3.tar.gz. SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> infernal-1.1.3 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by infernal-1.1.3 for building ===> Extracting for infernal-1.1.3 => SHA256 Checksum OK for infernal-1.1.3.tar.gz. Extracted Memory Use: 68.11M SUCCEEDED 00:00:02 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for infernal-1.1.3 ===> Applying ports patches for infernal-1.1.3 from /xports/biology/infernal/files SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> infernal-1.1.3 depends on package: gmake>=4.3 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> infernal-1.1.3 depends on package: gmake>=4.3 - found ===> Configuring for infernal-1.1.3 configure: loading site script /xports/Templates/config.site configure: Configuring Infernal for your system. checking build system type... x86_64-portbld-dragonfly5.9 checking host system type... x86_64-portbld-dragonfly5.9 checking for gcc... cc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no 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 how to run the C preprocessor... cpp checking for a BSD-compatible install... /usr/bin/install -c checking for ranlib... ranlib checking for ar... /usr/bin/ar checking whether ln -s works... yes checking for cc option to accept ISO C99... none needed checking for cc option to accept ISO Standard C... (cached) none needed checking for a sed that does not truncate output... (cached) /usr/bin/sed checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking whether cc is Clang... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking whether more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking whether cc can compile our Altivec/VMX code... no checking whether cc can compile our SSE code... yes configure: Activating Intel/AMD SSE vector DP implementation checking whether _MM_SET_FLUSH_ZERO_MODE is supported... yes checking compiler support --start-group... yes checking for gzip... /usr/bin/gzip checking for python3... no checking for library containing clock_gettime... none required 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 endian.h usability... yes checking endian.h presence... yes checking for endian.h... 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 for netinet/in.h... (cached) yes checking for sys/param.h... (cached) yes checking for sys/sysctl.h... (cached) 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 whether byte ordering is bigendian... no checking for __attribute__((noreturn))... yes checking for __attribute__((format))... yes checking for mkstemp... (cached) yes checking for popen... yes checking for putenv... (cached) yes checking for strcasecmp... (cached) yes checking for strsep... (cached) yes checking for times... (cached) yes checking for getpid... (cached) yes checking for sysctl... (cached) yes checking for sysconf... (cached) yes checking for getcwd... (cached) yes checking for chmod... yes checking for stat... (cached) yes checking for fstat... (cached) yes checking for erfc... no checking for ntohs... yes checking for ntohl... yes checking for htons... yes checking for htonl... yes checking for library containing socket... none required checking for library containing inet_pton... none required 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 Makefile config.status: creating src/Makefile config.status: creating testsuite/Makefile config.status: creating rmark/Makefile config.status: creating documentation/Makefile config.status: creating documentation/manpages/Makefile config.status: creating documentation/userguide/Makefile config.status: creating src/impl_sse/Makefile config.status: creating hmmer/Makefile config.status: creating hmmer/src/Makefile config.status: creating hmmer/testsuite/Makefile config.status: creating hmmer/profmark/Makefile config.status: creating hmmer/src/impl_sse/Makefile config.status: creating hmmer/documentation/Makefile config.status: creating hmmer/documentation/man/Makefile config.status: creating hmmer/documentation/userguide/Makefile config.status: creating hmmer/documentation/userguide/inclusions/Makefile config.status: creating hmmer/libdivsufsort/Makefile config.status: creating easel/Makefile config.status: creating easel/miniapps/Makefile config.status: creating easel/testsuite/Makefile config.status: creating easel/documentation/Makefile config.status: creating hmmer/documentation/userguide/titlepage.tex config.status: creating hmmer/documentation/userguide/titlepage_daemon.tex config.status: creating hmmer/documentation/userguide/copyright.tex config.status: creating hmmer/documentation/man/alimask.man config.status: creating hmmer/documentation/man/hmmalign.man config.status: creating hmmer/documentation/man/hmmbuild.man config.status: creating hmmer/documentation/man/hmmc2.man config.status: creating hmmer/documentation/man/hmmconvert.man config.status: creating hmmer/documentation/man/hmmemit.man config.status: creating hmmer/documentation/man/hmmer.man config.status: creating hmmer/documentation/man/hmmfetch.man config.status: creating hmmer/documentation/man/hmmlogo.man config.status: creating hmmer/documentation/man/hmmpgmd.man config.status: creating hmmer/documentation/man/hmmpgmd_shard.man config.status: creating hmmer/documentation/man/hmmpress.man config.status: creating hmmer/documentation/man/hmmscan.man config.status: creating hmmer/documentation/man/hmmsearch.man config.status: creating hmmer/documentation/man/hmmsim.man config.status: creating hmmer/documentation/man/hmmstat.man config.status: creating hmmer/documentation/man/jackhmmer.man config.status: creating hmmer/documentation/man/makehmmerdb.man config.status: creating hmmer/documentation/man/nhmmer.man config.status: creating hmmer/documentation/man/nhmmscan.man config.status: creating hmmer/documentation/man/phmmer.man config.status: creating easel/miniapps/esl-afetch.man config.status: creating easel/miniapps/esl-alimanip.man config.status: creating easel/miniapps/esl-alimap.man config.status: creating easel/miniapps/esl-alimask.man config.status: creating easel/miniapps/esl-alimerge.man config.status: creating easel/miniapps/esl-alipid.man config.status: creating easel/miniapps/esl-alirev.man config.status: creating easel/miniapps/esl-alistat.man config.status: creating easel/miniapps/esl-compalign.man config.status: creating easel/miniapps/esl-compstruct.man config.status: creating easel/miniapps/esl-construct.man config.status: creating easel/miniapps/esl-histplot.man config.status: creating easel/miniapps/esl-mask.man config.status: creating easel/miniapps/esl-mixdchlet.man config.status: creating easel/miniapps/esl-reformat.man config.status: creating easel/miniapps/esl-selectn.man config.status: creating easel/miniapps/esl-seqrange.man config.status: creating easel/miniapps/esl-seqstat.man config.status: creating easel/miniapps/esl-sfetch.man config.status: creating easel/miniapps/esl-shuffle.man config.status: creating easel/miniapps/esl-ssdraw.man config.status: creating easel/miniapps/esl-translate.man config.status: creating easel/miniapps/esl-weight.man config.status: creating easel/decoy_config.h config.status: creating src/config.h config.status: creating hmmer/src/p7_config.h config.status: creating easel/esl_config.h config.status: creating hmmer/libdivsufsort/divsufsort.h INFERNAL configuration: compiler: cc -pipe -O2 -fno-strict-aliasing -pthread linker: libraries: DP implementation: sse python3: (No python3 found, so 'make check' self tests are disabled.) Now do 'make' to build INFERNAL, and optionally: 'make install' to install programs and man pages. SUCCEEDED 00:00:08 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for infernal-1.1.3 gmake[1]: Entering directory '/construction/biology/infernal/infernal-1.1.3' gmake -C easel all gmake[2]: Entering directory '/construction/biology/infernal/infernal-1.1.3/easel' cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c easel.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_alloc.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_alphabet.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_arr2.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_arr3.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_bitfield.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_buffer.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_cluster.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_composition.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_cpu.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_dirichlet.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_distance.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_dmatrix.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_dsqdata.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_exponential.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_fileparser.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_gamma.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_gencode.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_getopts.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_gev.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_graph.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_gumbel.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_heap.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_histogram.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_hmm.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_huffman.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_hyperexp.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_json.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_keyhash.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_matrixops.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_mem.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_minimizer.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_mixdchlet.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_mixgev.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_mpi.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_msa.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_msacluster.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_msafile.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_msafile2.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_msafile_a2m.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_msafile_afa.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_msafile_clustal.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_msafile_phylip.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_msafile_psiblast.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_msafile_selex.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_msafile_stockholm.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_msashuffle.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_msaweight.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_normal.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_paml.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_quicksort.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_random.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_rand64.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_randomseq.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_ratematrix.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_recorder.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_red_black.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_regexp.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_rootfinder.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_scorematrix.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_sq.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_sqio.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_sqio_ascii.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_sqio_ncbi.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_ssi.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_stack.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_stats.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_stopwatch.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_stretchexp.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_subcmd.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_threads.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_tree.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_varint.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_vectorops.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_weibull.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_workqueue.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_wuss.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_sse.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_avx.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_avx512.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_neon.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_vmx.c /usr/bin/ar -r libeasel.a easel.o esl_alloc.o esl_alphabet.o esl_arr2.o esl_arr3.o esl_bitfield.o esl_buffer.o esl_cluster.o esl_composition.o esl_cpu.o esl_dirichlet.o esl_distance.o esl_dmatrix.o esl_dsqdata.o esl_exponential.o esl_fileparser.o esl_gamma.o esl_gencode.o esl_getopts.o esl_gev.o esl_graph.o esl_gumbel.o esl_heap.o esl_histogram.o esl_hmm.o esl_huffman.o esl_hyperexp.o esl_json.o esl_keyhash.o esl_matrixops.o esl_mem.o esl_minimizer.o esl_mixdchlet.o esl_mixgev.o esl_mpi.o esl_msa.o esl_msacluster.o esl_msafile.o esl_msafile2.o esl_msafile_a2m.o esl_msafile_afa.o esl_msafile_clustal.o esl_msafile_phylip.o esl_msafile_psiblast.o esl_msafile_selex.o esl_msafile_stockholm.o esl_msashuffle.o esl_msaweight.o esl_normal.o esl_paml.o esl_quicksort.o esl_random.o esl_rand64.o esl_randomseq.o esl_ratematrix.o esl_recorder.o esl_red_black.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_ssi.o esl_stack.o esl_stats.o esl_stopwatch.o esl_stretchexp.o esl_subcmd.o esl_threads.o esl_tree.o esl_varint.o esl_vectorops.o esl_weibull.o esl_workqueue.o esl_wuss.o esl_sse.o esl_avx.o esl_avx512.o esl_neon.o esl_vmx.o > /dev/null 2>&1 gmake -C miniapps all gmake[3]: Entering directory '/construction/biology/infernal/infernal-1.1.3/easel/miniapps' cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-afetch esl-afetch.c -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-alimanip esl-alimanip.c -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-alimap esl-alimap.c -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-alimask esl-alimask.c -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-alimerge esl-alimerge.c -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-alipid esl-alipid.c -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-alirev esl-alirev.c -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-alistat esl-alistat.c -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-compalign esl-compalign.c -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-compstruct esl-compstruct.c -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-construct esl-construct.c -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-histplot esl-histplot.c -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-mask esl-mask.c -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-mixdchlet esl-mixdchlet.c -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-reformat esl-reformat.c -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-selectn esl-selectn.c -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-seqrange esl-seqrange.c -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-seqstat esl-seqstat.c -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-sfetch esl-sfetch.c -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-shuffle esl-shuffle.c -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-ssdraw esl-ssdraw.c -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-translate esl-translate.c -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-weight esl-weight.c -leasel -lm cc -I. -I.. -I. -I./.. -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -c cmd_alistat.c cc -I. -I.. -I. -I./.. -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -c cmd_downsample.c cc -I. -I.. -I. -I./.. -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -c cmd_filter.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o easel easel.c cmd_alistat.o cmd_downsample.o cmd_filter.o -leasel -lm gmake[3]: Leaving directory '/construction/biology/infernal/infernal-1.1.3/easel/miniapps' gmake[2]: Leaving directory '/construction/biology/infernal/infernal-1.1.3/easel' gmake -C hmmer/libdivsufsort all gmake[2]: Entering directory '/construction/biology/infernal/infernal-1.1.3/hmmer/libdivsufsort' cc -I. -pipe -O2 -fno-strict-aliasing -pthread -o divsufsort.o -c divsufsort.c /usr/bin/ar rc libdivsufsort.a divsufsort.o gmake[2]: Leaving directory '/construction/biology/infernal/infernal-1.1.3/hmmer/libdivsufsort' gmake -C hmmer all gmake[2]: Entering directory '/construction/biology/infernal/infernal-1.1.3/hmmer' gmake -C ../easel all gmake[3]: Entering directory '/construction/biology/infernal/infernal-1.1.3/easel' gmake -C miniapps all gmake[4]: Entering directory '/construction/biology/infernal/infernal-1.1.3/easel/miniapps' gmake[4]: Nothing to be done for 'all'. gmake[4]: Leaving directory '/construction/biology/infernal/infernal-1.1.3/easel/miniapps' gmake[3]: Leaving directory '/construction/biology/infernal/infernal-1.1.3/easel' gmake -C libdivsufsort all gmake[3]: Entering directory '/construction/biology/infernal/infernal-1.1.3/hmmer/libdivsufsort' gmake[3]: Nothing to be done for 'all'. gmake[3]: Leaving directory '/construction/biology/infernal/infernal-1.1.3/hmmer/libdivsufsort' gmake -C src all gmake[3]: Entering directory '/construction/biology/infernal/infernal-1.1.3/hmmer/src' cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o alimask.o -c alimask.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o build.o -c build.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o cachedb.o -c cachedb.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o cachedb_shard.o -c cachedb_shard.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o emit.o -c emit.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o errors.o -c errors.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o evalues.o -c evalues.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o eweight.o -c eweight.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o generic_decoding.o -c generic_decoding.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o generic_fwdback.o -c generic_fwdback.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o generic_fwdback_chk.o -c generic_fwdback_chk.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o generic_fwdback_banded.o -c generic_fwdback_banded.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o generic_null2.o -c generic_null2.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o generic_msv.o -c generic_msv.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o generic_optacc.o -c generic_optacc.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o generic_stotrace.o -c generic_stotrace.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o generic_viterbi.o -c generic_viterbi.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o generic_vtrace.o -c generic_vtrace.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o h2_io.o -c h2_io.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o heatmap.o -c heatmap.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmlogo.o -c hmmlogo.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmdmstr.o -c hmmdmstr.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmdmstr_shard.o -c hmmdmstr_shard.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmd_search_status.o -c hmmd_search_status.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmdwrkr.o -c hmmdwrkr.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmdwrkr_shard.o -c hmmdwrkr_shard.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmdutils.o -c hmmdutils.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmer.o -c hmmer.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o logsum.o -c logsum.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o modelconfig.o -c modelconfig.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o modelstats.o -c modelstats.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o mpisupport.o -c mpisupport.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o seqmodel.o -c seqmodel.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o tracealign.o -c tracealign.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o p7_alidisplay.o -c p7_alidisplay.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o p7_bg.o -c p7_bg.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o p7_builder.o -c p7_builder.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o p7_domain.o -c p7_domain.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o p7_domaindef.o -c p7_domaindef.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o p7_gbands.o -c p7_gbands.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o p7_gmx.o -c p7_gmx.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o p7_gmxb.o -c p7_gmxb.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o p7_gmxchk.o -c p7_gmxchk.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o p7_hit.o -c p7_hit.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o p7_hmm.o -c p7_hmm.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o p7_hmmcache.o -c p7_hmmcache.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o p7_hmmd_search_stats.o -c p7_hmmd_search_stats.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o p7_hmmfile.o -c p7_hmmfile.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o p7_hmmwindow.o -c p7_hmmwindow.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o p7_pipeline.o -c p7_pipeline.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o p7_prior.o -c p7_prior.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o p7_profile.o -c p7_profile.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o p7_spensemble.o -c p7_spensemble.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o p7_tophits.o -c p7_tophits.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o p7_trace.o -c p7_trace.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o p7_scoredata.o -c p7_scoredata.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmpgmd2msa.o -c hmmpgmd2msa.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o fm_alphabet.o -c fm_alphabet.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o fm_general.o -c fm_general.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o fm_sse.o -c fm_sse.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o fm_ssv.o -c fm_ssv.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmalign.o -c hmmalign.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmbuild.o -c hmmbuild.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmconvert.o -c hmmconvert.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmemit.o -c hmmemit.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmfetch.o -c hmmfetch.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmpgmd.o -c hmmpgmd.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmpgmd_shard.o -c hmmpgmd_shard.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmpress.o -c hmmpress.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmscan.o -c hmmscan.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmsearch.o -c hmmsearch.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmsim.o -c hmmsim.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmstat.o -c hmmstat.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o jackhmmer.o -c jackhmmer.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o phmmer.o -c phmmer.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o nhmmer.o -c nhmmer.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o nhmmscan.o -c nhmmscan.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o makehmmerdb.o -c makehmmerdb.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmc2.o -c hmmc2.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmerfm-exactmatch.o -c hmmerfm-exactmatch.c /usr/bin/ar -r libhmmer.a build.o cachedb.o cachedb_shard.o emit.o errors.o evalues.o eweight.o generic_decoding.o generic_fwdback.o generic_fwdback_chk.o generic_fwdback_banded.o generic_null2.o generic_msv.o generic_optacc.o generic_stotrace.o generic_viterbi.o generic_vtrace.o h2_io.o heatmap.o hmmlogo.o hmmdmstr.o hmmdmstr_shard.o hmmd_search_status.o hmmdwrkr.o hmmdwrkr_shard.o hmmdutils.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_domain.o p7_domaindef.o p7_gbands.o p7_gmx.o p7_gmxb.o p7_gmxchk.o p7_hit.o p7_hmm.o p7_hmmcache.o p7_hmmd_search_stats.o p7_hmmfile.o p7_hmmwindow.o p7_pipeline.o p7_prior.o p7_profile.o p7_spensemble.o p7_tophits.o p7_trace.o p7_scoredata.o hmmpgmd2msa.o fm_alphabet.o fm_general.o fm_sse.o fm_ssv.o > /dev/null 2>&1 gmake -C impl_sse libhmmer-impl.stamp gmake[4]: Entering directory '/construction/biology/infernal/infernal-1.1.3/hmmer/src/impl_sse' cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../../easel -I../../../easel -I. -I.. -I. -I../../../src -I./.. -o decoding.o -c decoding.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../../easel -I../../../easel -I. -I.. -I. -I../../../src -I./.. -o fwdback.o -c fwdback.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../../easel -I../../../easel -I. -I.. -I. -I../../../src -I./.. -o io.o -c io.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../../easel -I../../../easel -I. -I.. -I. -I../../../src -I./.. -o ssvfilter.o -c ssvfilter.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../../easel -I../../../easel -I. -I.. -I. -I../../../src -I./.. -o msvfilter.o -c msvfilter.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../../easel -I../../../easel -I. -I.. -I. -I../../../src -I./.. -o null2.o -c null2.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../../easel -I../../../easel -I. -I.. -I. -I../../../src -I./.. -o optacc.o -c optacc.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../../easel -I../../../easel -I. -I.. -I. -I../../../src -I./.. -o stotrace.o -c stotrace.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../../easel -I../../../easel -I. -I.. -I. -I../../../src -I./.. -o vitfilter.o -c vitfilter.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../../easel -I../../../easel -I. -I.. -I. -I../../../src -I./.. -o p7_omx.o -c p7_omx.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../../easel -I../../../easel -I. -I.. -I. -I../../../src -I./.. -o p7_oprofile.o -c p7_oprofile.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../../easel -I../../../easel -I. -I.. -I. -I../../../src -I./.. -o mpi.o -c mpi.c /usr/bin/ar -r ../libhmmer.a decoding.o fwdback.o io.o ssvfilter.o msvfilter.o null2.o optacc.o stotrace.o vitfilter.o p7_omx.o p7_oprofile.o mpi.o > /dev/null 2>&1 gmake[4]: Leaving directory '/construction/biology/infernal/infernal-1.1.3/hmmer/src/impl_sse' cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L./impl_sse -L../libdivsufsort -L. -o alimask alimask.o -lhmmer -leasel -ldivsufsort -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmalign hmmalign.o -lhmmer -leasel -ldivsufsort -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmbuild hmmbuild.o -lhmmer -leasel -ldivsufsort -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmconvert hmmconvert.o -lhmmer -leasel -ldivsufsort -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmemit hmmemit.o -lhmmer -leasel -ldivsufsort -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmfetch hmmfetch.o -lhmmer -leasel -ldivsufsort -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmlogo hmmlogo.o -lhmmer -leasel -ldivsufsort -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmpgmd hmmpgmd.o -lhmmer -leasel -ldivsufsort -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmpgmd_shard hmmpgmd_shard.o -lhmmer -leasel -ldivsufsort -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmpress hmmpress.o -lhmmer -leasel -ldivsufsort -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmscan hmmscan.o -lhmmer -leasel -ldivsufsort -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmsearch hmmsearch.o -lhmmer -leasel -ldivsufsort -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmsim hmmsim.o -lhmmer -leasel -ldivsufsort -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmstat hmmstat.o -lhmmer -leasel -ldivsufsort -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L./impl_sse -L../libdivsufsort -L. -o jackhmmer jackhmmer.o -lhmmer -leasel -ldivsufsort -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L./impl_sse -L../libdivsufsort -L. -o phmmer phmmer.o -lhmmer -leasel -ldivsufsort -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L./impl_sse -L../libdivsufsort -L. -o nhmmer nhmmer.o -lhmmer -leasel -ldivsufsort -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L./impl_sse -L../libdivsufsort -L. -o nhmmscan nhmmscan.o -lhmmer -leasel -ldivsufsort -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L./impl_sse -L../libdivsufsort -L. -o makehmmerdb makehmmerdb.o -lhmmer -leasel -ldivsufsort -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmc2 hmmc2.o -lhmmer -leasel -ldivsufsort -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmerfm-exactmatch hmmerfm-exactmatch.o -lhmmer -leasel -ldivsufsort -lm gmake[3]: Leaving directory '/construction/biology/infernal/infernal-1.1.3/hmmer/src' gmake -C profmark all gmake[3]: Entering directory '/construction/biology/infernal/infernal-1.1.3/hmmer/profmark' cc -I../../easel -I../../easel -I../src -I../../src -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -o create-profmark.o -c create-profmark.c cc -I../../easel -I../../easel -I../src -I../../src -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -o rocplot.o -c rocplot.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L../src -o rocplot rocplot.o -lhmmer -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L../src -o create-profmark create-profmark.o -lhmmer -leasel -lm gmake[3]: Leaving directory '/construction/biology/infernal/infernal-1.1.3/hmmer/profmark' gmake[2]: Leaving directory '/construction/biology/infernal/infernal-1.1.3/hmmer' gmake -C src all gmake[2]: Entering directory '/construction/biology/infernal/infernal-1.1.3/src' cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cmalign.o -c cmalign.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cm.o -c cm.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cm_alidisplay.o -c cm_alidisplay.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cm_alndata.o -c cm_alndata.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cm_dpalign.o -c cm_dpalign.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cm_dpalign_trunc.o -c cm_dpalign_trunc.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cm_dpsearch.o -c cm_dpsearch.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cm_dpsearch_trunc.o -c cm_dpsearch_trunc.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cm_dpsmall.o -c cm_dpsmall.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cm_file.o -c cm_file.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cm_modelconfig.o -c cm_modelconfig.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cm_modelmaker.o -c cm_modelmaker.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cm_mx.o -c cm_mx.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cm_parsetree.o -c cm_parsetree.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cm_pipeline.o -c cm_pipeline.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cm_qdband.o -c cm_qdband.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cm_submodel.o -c cm_submodel.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cm_tophits.o -c cm_tophits.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cm_trunc.o -c cm_trunc.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cm_p7_band.o -c cm_p7_band.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cm_p7_domaindef.o -c cm_p7_domaindef.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cm_p7_modelconfig_trunc.o -c cm_p7_modelconfig_trunc.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cm_p7_modelmaker.o -c cm_p7_modelmaker.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cp9.o -c cp9.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cp9_dp.o -c cp9_dp.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cp9_modelmaker.o -c cp9_modelmaker.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cp9_mx.o -c cp9_mx.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cp9_trace.o -c cp9_trace.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o alphabet.o -c alphabet.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o display.o -c display.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o errors.o -c errors.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o eweight.o -c eweight.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o hmmband.o -c hmmband.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o logsum.o -c logsum.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o mpisupport.o -c mpisupport.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o prior.o -c prior.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o rnamat.o -c rnamat.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o stats.o -c stats.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o truncyk.o -c truncyk.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cmbuild.o -c cmbuild.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cmcalibrate.o -c cmcalibrate.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cmconvert.o -c cmconvert.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cmemit.o -c cmemit.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cmfetch.o -c cmfetch.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cmpress.o -c cmpress.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cmscan.o -c cmscan.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cmsearch.o -c cmsearch.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cmstat.o -c cmstat.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o trcyk.o -c trcyk.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o bandcyk-montecarlo-test.o -c bandcyk-montecarlo-test.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o bandcyk-truncation-test.o -c bandcyk-truncation-test.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cp9-test.o -c cp9-test.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o sub_cm-test.o -c sub_cm-test.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o truncyk_check.o -c truncyk_check.c /usr/bin/ar -r libinfernal.a cm.o cm_alidisplay.o cm_alndata.o cm_dpalign.o cm_dpalign_trunc.o cm_dpsearch.o cm_dpsearch_trunc.o cm_dpsmall.o cm_file.o cm_modelconfig.o cm_modelmaker.o cm_mx.o cm_parsetree.o cm_pipeline.o cm_qdband.o cm_submodel.o cm_tophits.o cm_trunc.o cm_p7_band.o cm_p7_domaindef.o cm_p7_modelconfig_trunc.o cm_p7_modelmaker.o cp9.o cp9_dp.o cp9_modelmaker.o cp9_mx.o cp9_trace.o alphabet.o display.o errors.o eweight.o hmmband.o logsum.o mpisupport.o prior.o rnamat.o stats.o truncyk.o > /dev/null 2>&1 gmake -C impl_sse libinfernal-impl.stamp gmake[3]: Entering directory '/construction/biology/infernal/infernal-1.1.3/src/impl_sse' cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I../../hmmer/src -I../../hmmer/src -I. -I.. -I. -I../../src -o cm_optimized.o -c cm_optimized.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I../../hmmer/src -I../../hmmer/src -I. -I.. -I. -I../../src -o sse_cm_dpsearch.o -c sse_cm_dpsearch.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I../../hmmer/src -I../../hmmer/src -I. -I.. -I. -I../../src -o sse_cm_dpsmall.o -c sse_cm_dpsmall.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I../../hmmer/src -I../../hmmer/src -I. -I.. -I. -I../../src -o sse_cmcons_hitmx.o -c sse_cmcons_hitmx.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I../../hmmer/src -I../../hmmer/src -I. -I.. -I. -I../../src -o sse_cmcons_mscyk.o -c sse_cmcons_mscyk.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I../../hmmer/src -I../../hmmer/src -I. -I.. -I. -I../../src -o sse_util.o -c sse_util.c /usr/bin/ar -r ../libinfernal.a cm_optimized.o sse_cm_dpsearch.o sse_cm_dpsmall.o sse_cmcons_hitmx.o sse_cmcons_mscyk.o sse_util.o > /dev/null 2>&1 gmake[3]: Leaving directory '/construction/biology/infernal/infernal-1.1.3/src/impl_sse' cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L../hmmer/src -L./impl_sse -L. -o cmalign cmalign.o -linfernal -lhmmer -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L../hmmer/src -L./impl_sse -L. -o cmbuild cmbuild.o -linfernal -lhmmer -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L../hmmer/src -L./impl_sse -L. -o cmcalibrate cmcalibrate.o -linfernal -lhmmer -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L../hmmer/src -L./impl_sse -L. -o cmconvert cmconvert.o -linfernal -lhmmer -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L../hmmer/src -L./impl_sse -L. -o cmemit cmemit.o -linfernal -lhmmer -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L../hmmer/src -L./impl_sse -L. -o cmfetch cmfetch.o -linfernal -lhmmer -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L../hmmer/src -L./impl_sse -L. -o cmpress cmpress.o -linfernal -lhmmer -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L../hmmer/src -L./impl_sse -L. -o cmscan cmscan.o -linfernal -lhmmer -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L../hmmer/src -L./impl_sse -L. -o cmsearch cmsearch.o -linfernal -lhmmer -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L../hmmer/src -L./impl_sse -L. -o cmstat cmstat.o -linfernal -lhmmer -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L../hmmer/src -L./impl_sse -L. -o trcyk trcyk.o -linfernal -lhmmer -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L../hmmer/src -L./impl_sse -L. -o bandcyk-montecarlo-test bandcyk-montecarlo-test.o -linfernal -lhmmer -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L../hmmer/src -L./impl_sse -L. -o bandcyk-truncation-test bandcyk-truncation-test.o -linfernal -lhmmer -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L../hmmer/src -L./impl_sse -L. -o cp9-test cp9-test.o -linfernal -lhmmer -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L../hmmer/src -L./impl_sse -L. -o sub_cm-test sub_cm-test.o -linfernal -lhmmer -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L../hmmer/src -L./impl_sse -L. -o truncyk_check truncyk_check.o -linfernal -lhmmer -leasel -lm gmake[2]: Leaving directory '/construction/biology/infernal/infernal-1.1.3/src' gmake -C rmark all gmake[2]: Entering directory '/construction/biology/infernal/infernal-1.1.3/rmark' cc -I../easel -I../easel -I../src -I../src -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -o rmark-create.o -c rmark-create.c cc -I../easel -I../easel -I../src -I../src -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -o rmark-rocplot.o -c rmark-rocplot.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../hmmer/src -L../easel -L../src -o rmark-rocplot rmark-rocplot.o -lhmmer -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../hmmer/src -L../easel -L../src -o rmark-create rmark-create.o -lhmmer -leasel -lm gmake[2]: Leaving directory '/construction/biology/infernal/infernal-1.1.3/rmark' gmake -C src/impl_sse all gmake[2]: Entering directory '/construction/biology/infernal/infernal-1.1.3/src/impl_sse' cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I../../hmmer/src -I../../hmmer/src -I. -I.. -I. -I../../src -o sse_cmsearch.o -c sse_cmsearch.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L../../hmmer/src -L.. -o sse_cmsearch sse_cmsearch.o -linfernal -lhmmer -leasel -lm gmake[2]: Leaving directory '/construction/biology/infernal/infernal-1.1.3/src/impl_sse' gmake[1]: Leaving directory '/construction/biology/infernal/infernal-1.1.3' SUCCEEDED 00:01:32 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for infernal-1.1.3 ===> Generating temporary packing list gmake[1]: Entering directory '/construction/biology/infernal/infernal-1.1.3' /usr/bin/install -c -d /construction/biology/infernal/stage/usr/local/bin /usr/bin/install -c -d /construction/biology/infernal/stage/usr/local/man/man1 /usr/bin/install -c -d /construction/biology/infernal/stage/usr/local/share/doc/infernal gmake -C src install gmake[2]: Entering directory '/construction/biology/infernal/infernal-1.1.3/src' for file in cmalign cmbuild cmcalibrate cmconvert cmemit cmfetch cmpress cmscan cmsearch cmstat; do \ /usr/bin/install -c -m 0755 $file /construction/biology/infernal/stage/usr/local/bin/ ;\ done gmake[2]: Leaving directory '/construction/biology/infernal/infernal-1.1.3/src' gmake -C documentation install gmake[2]: Entering directory '/construction/biology/infernal/infernal-1.1.3/documentation' gmake -C manpages install gmake[3]: Entering directory '/construction/biology/infernal/infernal-1.1.3/documentation/manpages' for file in infernal cmalign cmbuild cmcalibrate cmconvert cmemit cmfetch cmpress cmsearch cmscan cmstat; do \ /usr/bin/install -c -m 0755 ./$file.man /construction/biology/infernal/stage/usr/local/man/man1/${file}.1 ;\ done gmake[3]: Leaving directory '/construction/biology/infernal/infernal-1.1.3/documentation/manpages' gmake[2]: Leaving directory '/construction/biology/infernal/infernal-1.1.3/documentation' gmake[1]: Leaving directory '/construction/biology/infernal/infernal-1.1.3' install -m 0644 /construction/biology/infernal/infernal-1.1.3/Userguide.pdf /construction/biology/infernal/stage/usr/local/share/doc/infernal install -m 0644 /construction/biology/infernal/infernal-1.1.3/tutorial/5S_rRNA.c.cm /construction/biology/infernal/infernal-1.1.3/tutorial/5S_rRNA.sto /construction/biology/infernal/infernal-1.1.3/tutorial/Cobalamin.c.cm /construction/biology/infernal/infernal-1.1.3/tutorial/Cobalamin.fa /construction/biology/infernal/infernal-1.1.3/tutorial/Cobalamin.sto /construction/biology/infernal/infernal-1.1.3/tutorial/metag-example.fa /construction/biology/infernal/infernal-1.1.3/tutorial/minifam-metag.out /construction/biology/infernal/infernal-1.1.3/tutorial/minifam.cm /construction/biology/infernal/infernal-1.1.3/tutorial/minifam.cm.i1f /construction/biology/infernal/infernal-1.1.3/tutorial/minifam.cm.i1i /construction/biology/infernal/infernal-1.1.3/tutorial/minifam.cm.i1m /construction/biology/infernal/infernal-1.1.3/tutorial/minifam.cm.i1p /construction/biology/infernal/infernal-1.1.3/tutorial/mrum-genome.fa /construction/biology/infernal/infernal-1.1.3/tutorial/mrum-tRNAs10.fa /construction/biology/infernal/infernal-1.1.3/tutorial/mrum-tRNAs10.out /construction/biology/infernal/infernal-1.1.3/tutorial/tRNA5-hand.c.cm /construction/biology/infernal/infernal-1.1.3/tutorial/tRNA5-hand.sto /construction/biology/infernal/infernal-1.1.3/tutorial/tRNA5-mrum.out /construction/biology/infernal/infernal-1.1.3/tutorial/tRNA5-noss.sto /construction/biology/infernal/infernal-1.1.3/tutorial/tRNA5.c.cm /construction/biology/infernal/infernal-1.1.3/tutorial/tRNA5.sto /construction/biology/infernal/stage/usr/local/share/examples/infernal ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for infernal-1.1.3 file sizes/checksums [43]: 0% file sizes/checksums [43]: 100% packing files [43]: 0% packing files [43]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:43 TOTAL TIME 00:02:30