=> Building biology/hmmer Started : Thursday, 30 AUG 2018 at 13:03:14 UTC Platform: 5.3-DEVELOPMENT DragonFly 5.3-DEVELOPMENT #140: Wed Aug 29 22:06:30 PDT 2018 root@test.backplane.com:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.3-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.3-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- ===> The following configuration options are available for hmmer-3.1b2: DOCS=on: Build and/or install documentation EXAMPLES=on: Build and/or install examples TEST=off: Build and/or run tests ===> Use 'make config' to modify these settings -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- MAKE=gmake XDG_DATA_HOME=/construction/biology/hmmer XDG_CONFIG_HOME=/construction/biology/hmmer HOME=/construction/biology/hmmer TMPDIR="/tmp" PATH=/construction/biology/hmmer/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 CONFIG_SITE=/xports/Templates/config.site lt_cv_sys_max_cmd_len=262144 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/biology/hmmer XDG_CONFIG_HOME=/construction/biology/hmmer HOME=/construction/biology/hmmer TMPDIR="/tmp" PATH=/construction/biology/hmmer/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc50 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS="" LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing" MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- V=1 DESTDIR=/construction/biology/hmmer/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PORTDOCS="" PORTEXAMPLES="" OSREL=5.3 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/hmmer" EXAMPLESDIR="share/examples/hmmer" DATADIR="share/hmmer" WWWDIR="www/hmmer" ETCDIR="etc/hmmer" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/hmmer DOCSDIR=/usr/local/share/doc/hmmer EXAMPLESDIR=/usr/local/share/examples/hmmer WWWDIR=/usr/local/www/hmmer ETCDIR=/usr/local/etc/hmmer -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=LiveSystem USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=12 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=32 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500316 OSVERSION=9999999 OSREL=5.3 _OSRELEASE=5.3-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> hmmer-3.1b2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_1.txz Installing pkg-1.10.5_1... Extracting pkg-1.10.5_1: .......... done ===> hmmer-3.1b2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of hmmer-3.1b2 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by hmmer-3.1b2 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by hmmer-3.1b2 for building => SHA256 Checksum OK for hmmer-3.1b2.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by hmmer-3.1b2 for building ===> Extracting for hmmer-3.1b2 => SHA256 Checksum OK for hmmer-3.1b2.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for hmmer-3.1b2 ===> Applying ports patches for hmmer-3.1b2 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> hmmer-3.1b2 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_2.txz Installing gmake-4.2.1_2... `-- Installing gettext-runtime-0.19.8.1_1... | `-- Installing indexinfo-0.3.1... | `-- Extracting indexinfo-0.3.1: .... done `-- Extracting gettext-runtime-0.19.8.1_1: .......... done Extracting gmake-4.2.1_2: .......... done ===> hmmer-3.1b2 depends on executable: gmake - found ===> Returning to build of hmmer-3.1b2 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for hmmer-3.1b2 configure: loading site script /xports/Templates/config.site configure: Configuring HMMER for your system. checking build system type... x86_64-portbld-dragonfly5.3 checking host system type... x86_64-portbld-dragonfly5.3 configure: Full HMMER source distribution - using full configuration 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 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... no 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 for a BSD-compatible install... /usr/bin/install -c checking how to run the C preprocessor... cpp checking for C compiler vendor... (cached) gnu checking for cc option to accept ISO C99... none needed checking for cc option to accept ISO Standard C... (cached) none needed checking for ranlib... ranlib checking for ar... /usr/bin/ar checking whether you have a GNU make... yes, you do; and we assume you will use it! checking for a sed that does not truncate output... (cached) /usr/bin/sed checking for cc option to produce PIC... -fPIC checking whether C compiler accepts -msse2... yes checking compiler support for sse2 cast functions... yes checking whether SSE2 is supported... yes checking whether _MM_SET_FLUSH_ZERO_MODE is supported... yes configure: Activating Intel/AMD SSE optimized DP implementation checking compiler support --start-group... yes checking for gzip... /usr/bin/gzip 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 endian.h usability... no checking endian.h presence... no checking for endian.h... no 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 whether byte ordering is bigendian... no 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... (cached) yes checking for getpid... (cached) yes checking for sysctl... (cached) yes checking for sysconf... (cached) yes checking for getcwd... (cached) yes checking for stat... (cached) yes checking for fstat... (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 documentation/Makefile config.status: creating documentation/man/Makefile config.status: creating src/Makefile config.status: creating testsuite/Makefile config.status: creating profmark/Makefile config.status: creating src/impl_sse/Makefile config.status: creating easel/miniapps/Makefile config.status: creating easel/testsuite/Makefile config.status: creating easel/Makefile config.status: creating libdivsufsort/Makefile config.status: creating Makefile config.status: creating src/p7_config.h config.status: creating easel/esl_config.h config.status: creating libdivsufsort/divsufsort.h config.status: linking src/impl_sse to src/impl HMMER configuration: compiler: cc -pipe -O2 -fno-strict-aliasing -msse2 -pthread -fPIC host: x86_64-portbld-dragonfly5.3 linker: libraries: DP implementation: sse -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for hmmer-3.1b2 gmake[1]: Entering directory '/construction/biology/hmmer/hmmer-3.1b2' gmake -C easel all gmake[2]: Entering directory '/construction/biology/hmmer/hmmer-3.1b2/easel' cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o easel.o -c easel.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_alphabet.o -c esl_alphabet.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_buffer.o -c esl_buffer.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_cluster.o -c esl_cluster.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_composition.o -c esl_composition.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_dirichlet.o -c esl_dirichlet.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_distance.o -c esl_distance.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_dmatrix.o -c esl_dmatrix.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_exponential.o -c esl_exponential.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_fileparser.o -c esl_fileparser.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_gamma.o -c esl_gamma.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_getopts.o -c esl_getopts.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_gev.o -c esl_gev.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_gumbel.o -c esl_gumbel.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_histogram.o -c esl_histogram.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_hmm.o -c esl_hmm.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_hyperexp.o -c esl_hyperexp.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_keyhash.o -c esl_keyhash.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_mem.o -c esl_mem.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_minimizer.o -c esl_minimizer.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_mixgev.o -c esl_mixgev.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_mpi.o -c esl_mpi.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_msa.o -c esl_msa.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_msacluster.o -c esl_msacluster.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_msafile.o -c esl_msafile.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_msafile2.o -c esl_msafile2.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_msafile_a2m.o -c esl_msafile_a2m.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_msafile_afa.o -c esl_msafile_afa.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_msafile_clustal.o -c esl_msafile_clustal.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_msafile_phylip.o -c esl_msafile_phylip.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_msafile_psiblast.o -c esl_msafile_psiblast.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_msafile_selex.o -c esl_msafile_selex.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_msafile_stockholm.o -c esl_msafile_stockholm.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_msashuffle.o -c esl_msashuffle.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_msaweight.o -c esl_msaweight.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_normal.o -c esl_normal.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_paml.o -c esl_paml.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_random.o -c esl_random.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_randomseq.o -c esl_randomseq.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_ratematrix.o -c esl_ratematrix.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_recorder.o -c esl_recorder.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_regexp.o -c esl_regexp.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_rootfinder.o -c esl_rootfinder.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_scorematrix.o -c esl_scorematrix.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_sq.o -c esl_sq.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_sqio.o -c esl_sqio.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_sqio_ascii.o -c esl_sqio_ascii.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_sqio_ncbi.o -c esl_sqio_ncbi.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_sse.o -c esl_sse.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_ssi.o -c esl_ssi.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_stack.o -c esl_stack.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_stats.o -c esl_stats.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_stopwatch.o -c esl_stopwatch.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_stretchexp.o -c esl_stretchexp.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_threads.o -c esl_threads.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_translate.o -c esl_translate.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_tree.o -c esl_tree.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_vectorops.o -c esl_vectorops.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_vmx.o -c esl_vmx.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_weibull.o -c esl_weibull.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_workqueue.o -c esl_workqueue.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -o esl_wuss.o -c esl_wuss.c /usr/bin/ar -r libeasel.a easel.o esl_alphabet.o esl_buffer.o esl_cluster.o esl_composition.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_mem.o esl_minimizer.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_random.o esl_randomseq.o esl_ratematrix.o esl_recorder.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_translate.o esl_tree.o esl_vectorops.o esl_vmx.o esl_weibull.o esl_workqueue.o esl_wuss.o > /dev/null 2>&1 gmake -C miniapps all gmake[3]: Entering directory '/construction/biology/hmmer/hmmer-3.1b2/easel/miniapps' cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-afetch.o -c esl-afetch.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-alimanip.o -c esl-alimanip.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-alimap.o -c esl-alimap.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-alimask.o -c esl-alimask.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-alimerge.o -c esl-alimerge.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-alipid.o -c esl-alipid.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-alistat.o -c esl-alistat.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-cluster.o -c esl-cluster.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-compalign.o -c esl-compalign.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-compstruct.o -c esl-compstruct.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-construct.o -c esl-construct.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-histplot.o -c esl-histplot.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-mask.o -c esl-mask.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-reformat.o -c esl-reformat.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-selectn.o -c esl-selectn.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-seqrange.o -c esl-seqrange.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-seqstat.o -c esl-seqstat.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-sfetch.o -c esl-sfetch.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-shuffle.o -c esl-shuffle.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-ssdraw.o -c esl-ssdraw.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-stranslate.o -c esl-stranslate.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-weight.o -c esl-weight.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L.. -o esl-afetch esl-afetch.o -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L.. -o esl-alimap esl-alimap.o -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L.. -o esl-alipid esl-alipid.o -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L.. -o esl-cluster esl-cluster.o -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L.. -o esl-compstruct esl-compstruct.o -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L.. -o esl-histplot esl-histplot.o -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L.. -o esl-mask esl-mask.o -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L.. -o esl-selectn esl-selectn.o -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L.. -o esl-seqrange esl-seqrange.o -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L.. -o esl-seqstat esl-seqstat.o -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L.. -o esl-shuffle esl-shuffle.o -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L.. -o esl-stranslate esl-stranslate.o -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L.. -o esl-weight esl-weight.o -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L.. -o esl-reformat esl-reformat.o -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L.. -o esl-compalign esl-compalign.o -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L.. -o esl-alistat esl-alistat.o -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L.. -o esl-sfetch esl-sfetch.o -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L.. -o esl-construct esl-construct.o -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L.. -o esl-alimask esl-alimask.o -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L.. -o esl-alimerge esl-alimerge.o -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L.. -o esl-alimanip esl-alimanip.o -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L.. -o esl-ssdraw esl-ssdraw.o -leasel -lm gmake[3]: Leaving directory '/construction/biology/hmmer/hmmer-3.1b2/easel/miniapps' gmake[2]: Leaving directory '/construction/biology/hmmer/hmmer-3.1b2/easel' gmake -C libdivsufsort all gmake[2]: Entering directory '/construction/biology/hmmer/hmmer-3.1b2/libdivsufsort' cc -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -o divsufsort.o -c divsufsort.c /usr/bin/ar rc libdivsufsort.a divsufsort.o gmake[2]: Leaving directory '/construction/biology/hmmer/hmmer-3.1b2/libdivsufsort' gmake -C src all gmake[2]: Entering directory '/construction/biology/hmmer/hmmer-3.1b2/src' cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o alimask.o -c alimask.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o build.o -c build.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o cachedb.o -c cachedb.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o emit.o -c emit.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o errors.o -c errors.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o evalues.o -c evalues.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o eweight.o -c eweight.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o heatmap.o -c heatmap.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmlogo.o -c hmmlogo.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmdmstr.o -c hmmdmstr.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmdwrkr.o -c hmmdwrkr.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmdutils.o -c hmmdutils.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmer.o -c hmmer.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o logsum.o -c logsum.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o modelconfig.o -c modelconfig.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o modelstats.o -c modelstats.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o mpisupport.o -c mpisupport.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o seqmodel.o -c seqmodel.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o tracealign.o -c tracealign.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o p7_null3.o -c p7_null3.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmpgmd2msa.o -c hmmpgmd2msa.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmalign.o -c hmmalign.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmbuild.o -c hmmbuild.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmconvert.o -c hmmconvert.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmemit.o -c hmmemit.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmfetch.o -c hmmfetch.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmpress.o -c hmmpress.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmscan.o -c hmmscan.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmsearch.o -c hmmsearch.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmsim.o -c hmmsim.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmstat.o -c hmmstat.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o jackhmmer.o -c jackhmmer.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o phmmer.o -c phmmer.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o nhmmer.o -c nhmmer.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o nhmmscan.o -c nhmmscan.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmpgmd.o -c hmmpgmd.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmc2.o -c hmmc2.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o makehmmerdb.o -c makehmmerdb.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -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 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 hmmdwrkr.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_domaindef.o p7_gbands.o p7_gmx.o p7_gmxb.o p7_gmxchk.o p7_hmm.o p7_hmmcache.o p7_hmmfile.o p7_hmmwindow.o p7_null3.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[3]: Entering directory '/construction/biology/hmmer/hmmer-3.1b2/src/impl_sse' cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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[3]: Leaving directory '/construction/biology/hmmer/hmmer-3.1b2/src/impl_sse' cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -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 -fPIC -msse2 -DHAVE_CONFIG_H -L../easel -L./impl_sse -L../libdivsufsort -L. -o hmmerfm-exactmatch hmmerfm-exactmatch.o -lhmmer -leasel -ldivsufsort -lm gmake[2]: Leaving directory '/construction/biology/hmmer/hmmer-3.1b2/src' gmake -C profmark all gmake[2]: Entering directory '/construction/biology/hmmer/hmmer-3.1b2/profmark' cc -I../easel -I../easel -I../src -I../src -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -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 -fPIC -msse2 -DHAVE_CONFIG_H -o rocplot.o -c rocplot.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -DHAVE_CONFIG_H -L../easel -L../src -o rocplot rocplot.o -lhmmer -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -DHAVE_CONFIG_H -L../easel -L../src -o create-profmark create-profmark.o -lhmmer -leasel -lm gmake[2]: Leaving directory '/construction/biology/hmmer/hmmer-3.1b2/profmark' gmake[1]: Leaving directory '/construction/biology/hmmer/hmmer-3.1b2' -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for hmmer-3.1b2 ===> Generating temporary packing list gmake[1]: Entering directory '/construction/biology/hmmer/hmmer-3.1b2' /usr/bin/install -c -d /construction/biology/hmmer/stage/usr/local/bin /usr/bin/install -c -d /construction/biology/hmmer/stage/usr/local/lib /usr/bin/install -c -d /construction/biology/hmmer/stage/usr/local/include /usr/bin/install -c -d /construction/biology/hmmer/stage/usr/local/man/man1 /usr/bin/install -c -d /construction/biology/hmmer/stage/usr/local/share/doc/hmmer gmake -C src install gmake[2]: Entering directory '/construction/biology/hmmer/hmmer-3.1b2/src' gmake -C impl_sse install gmake[3]: Entering directory '/construction/biology/hmmer/hmmer-3.1b2/src/impl_sse' for file in impl_sse.h; do \ /usr/bin/install -c -m 0644 ./$file /construction/biology/hmmer/stage/usr/local/include/ ;\ done gmake[3]: Leaving directory '/construction/biology/hmmer/hmmer-3.1b2/src/impl_sse' for file in alimask hmmalign hmmbuild hmmconvert hmmemit hmmfetch hmmlogo hmmpress hmmscan hmmsearch hmmsim hmmstat jackhmmer phmmer nhmmer nhmmscan hmmpgmd hmmc2 makehmmerdb hmmerfm-exactmatch; do \ /usr/bin/install -c -m 0755 $file /construction/biology/hmmer/stage/usr/local/bin/ ;\ done /usr/bin/install -c -m 0755 libhmmer.a /construction/biology/hmmer/stage/usr/local/lib/ for file in hmmer.h cachedb.h p7_gbands.h p7_gmxb.h p7_gmxchk.h p7_hmmcache.h; do \ /usr/bin/install -c -m 0644 ./$file /construction/biology/hmmer/stage/usr/local/include/ ;\ done /usr/bin/install -c -m 0644 p7_config.h /construction/biology/hmmer/stage/usr/local/include/ ;\ gmake[2]: Leaving directory '/construction/biology/hmmer/hmmer-3.1b2/src' gmake -C documentation install gmake[2]: Entering directory '/construction/biology/hmmer/hmmer-3.1b2/documentation' gmake -C man install gmake[3]: Entering directory '/construction/biology/hmmer/hmmer-3.1b2/documentation/man' for file in hmmer hmmalign hmmbuild hmmconvert hmmemit hmmfetch hmmlogo hmmpgmd hmmpress hmmscan hmmsearch hmmsim hmmstat jackhmmer makehmmerdb phmmer nhmmer nhmmscan alimask; do \ /usr/bin/install -c -m 0755 ./$file.man /construction/biology/hmmer/stage/usr/local/man/man1/${file}.1 ;\ done gmake[3]: Leaving directory '/construction/biology/hmmer/hmmer-3.1b2/documentation/man' gmake[2]: Leaving directory '/construction/biology/hmmer/hmmer-3.1b2/documentation' gmake[1]: Leaving directory '/construction/biology/hmmer/hmmer-3.1b2' install -m 0644 /construction/biology/hmmer/hmmer-3.1b2/COPYRIGHT /construction/biology/hmmer/hmmer-3.1b2/Userguide.pdf /construction/biology/hmmer/stage/usr/local/share/doc/hmmer install -m 0644 /construction/biology/hmmer/hmmer-3.1b2/tutorial/7LESS_DROME /construction/biology/hmmer/hmmer-3.1b2/tutorial/HBB_HUMAN /construction/biology/hmmer/hmmer-3.1b2/tutorial/MADE1.hmm /construction/biology/hmmer/hmmer-3.1b2/tutorial/MADE1.out /construction/biology/hmmer/hmmer-3.1b2/tutorial/MADE1.sto /construction/biology/hmmer/hmmer-3.1b2/tutorial/Pkinase.hmm /construction/biology/hmmer/hmmer-3.1b2/tutorial/Pkinase.sto /construction/biology/hmmer/hmmer-3.1b2/tutorial/dna_target.fa /construction/biology/hmmer/hmmer-3.1b2/tutorial/fn3.hmm /construction/biology/hmmer/hmmer-3.1b2/tutorial/fn3.out /construction/biology/hmmer/hmmer-3.1b2/tutorial/fn3.sto /construction/biology/hmmer/hmmer-3.1b2/tutorial/globins4.hmm /construction/biology/hmmer/hmmer-3.1b2/tutorial/globins4.out /construction/biology/hmmer/hmmer-3.1b2/tutorial/globins4.sto /construction/biology/hmmer/hmmer-3.1b2/tutorial/globins45.fa /construction/biology/hmmer/hmmer-3.1b2/tutorial/minifam /construction/biology/hmmer/hmmer-3.1b2/tutorial/minifam.h3f /construction/biology/hmmer/hmmer-3.1b2/tutorial/minifam.h3i /construction/biology/hmmer/hmmer-3.1b2/tutorial/minifam.h3m /construction/biology/hmmer/hmmer-3.1b2/tutorial/minifam.h3p /construction/biology/hmmer/stage/usr/local/share/examples/hmmer ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for hmmer-3.1b2 file sizes/checksums [73]: . done packing files [73]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Thursday, 30 AUG 2018 at 13:04:22 UTC Duration: 00:01:07