=> Building biology/infernal Started : Wednesday, 6 MAR 2019 at 05:41:36 UTC Platform: 5.5-DEVELOPMENT DragonFly v5.5.0.192.g15ae7f0-DEVELOPMENT #34: Tue Feb 19 09:07:07 PST 2019 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.5-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.5-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 infernal-1.1.2: 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/infernal XDG_CONFIG_HOME=/construction/biology/infernal HOME=/construction/biology/infernal TMPDIR="/tmp" PATH=/construction/biology/infernal/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 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/infernal XDG_CONFIG_HOME=/construction/biology/infernal HOME=/construction/biology/infernal TMPDIR="/tmp" PATH=/construction/biology/infernal/.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=gcc80 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/infernal/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PORTDOCS="" PORTEXAMPLES="" OSREL=5.5 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/infernal" EXAMPLESDIR="share/examples/infernal" DATADIR="share/infernal" WWWDIR="www/infernal" ETCDIR="etc/infernal" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/infernal DOCSDIR=/usr/local/share/doc/infernal EXAMPLESDIR=/usr/local/share/examples/infernal WWWDIR=/usr/local/www/infernal ETCDIR=/usr/local/etc/infernal -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-BE 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=5 LICENSES_ACCEPTED= NONE HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _PERL5_FROM_BIN=5.26.2 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500500 OSVERSION=9999999 OSREL=5.5 _OSRELEASE=5.5-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License BSD3CLAUSE accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> infernal-1.1.2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_5.txz Installing pkg-1.10.5_5... Extracting pkg-1.10.5_5: .......... done ===> infernal-1.1.2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of infernal-1.1.2 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by infernal-1.1.2 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by infernal-1.1.2 for building => SHA256 Checksum OK for infernal-1.1.2.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by infernal-1.1.2 for building ===> Extracting for infernal-1.1.2 => SHA256 Checksum OK for infernal-1.1.2.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for infernal-1.1.2 ===> Applying ports patches for infernal-1.1.2 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> infernal-1.1.2 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_3.txz Installing gmake-4.2.1_3... `-- Installing gettext-runtime-0.19.8.1_2... | `-- Installing indexinfo-0.3.1... | `-- Extracting indexinfo-0.3.1: .... done `-- Extracting gettext-runtime-0.19.8.1_2: .......... done Extracting gmake-4.2.1_3: .......... done ===> infernal-1.1.2 depends on executable: gmake - found ===> Returning to build of infernal-1.1.2 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for infernal-1.1.2 configure: loading site script /xports/Templates/config.site configure: Configuring Infernal for your system. checking build system type... x86_64-portbld-dragonfly5.5 checking host system type... x86_64-portbld-dragonfly5.5 configure: Full Infernal source distribution - using full configuration checking for gcc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for C compiler vendor... gnu checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... 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 ln -s works... yes checking whether you have a GNU make... yes, you do; and we assume you will use it! ./configure: AX_CC_MAXOPT: not found checking for cc option to produce PIC... -fPIC checking whether C compiler accepts -msse2... yes checking whether C compiler accepts -msse2 -msse3... 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 library containing clock_gettime... none required 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 emmintrin.h usability... yes checking emmintrin.h presence... yes checking for emmintrin.h... yes checking pmmintrin.h usability... yes checking pmmintrin.h presence... yes checking for pmmintrin.h... yes checking xmmintrin.h usability... yes checking xmmintrin.h presence... yes checking for xmmintrin.h... 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 src/Makefile config.status: creating src/impl_sse/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 hmmer/documentation/Makefile config.status: creating hmmer/documentation/man/Makefile config.status: creating hmmer/documentation/userguide/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/libdivsufsort/Makefile config.status: creating hmmer/Makefile config.status: creating easel/miniapps/Makefile config.status: creating easel/testsuite/Makefile config.status: creating easel/Makefile config.status: creating easel/documentation/Makefile config.status: creating Makefile config.status: creating src/config.h config.status: creating hmmer/src/p7_config.h config.status: creating hmmer/libdivsufsort/divsufsort.h config.status: creating easel/esl_config.h config.status: executing hmmer/src/impl commands INFERNAL configuration: compiler: cc -pipe -O2 -fno-strict-aliasing -msse2 -msse3 -pthread -fPIC linker: libraries: DP implementation: sse -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for infernal-1.1.2 gmake[1]: Entering directory '/construction/biology/infernal/infernal-1.1.2' gmake -C easel all gmake[2]: Entering directory '/construction/biology/infernal/infernal-1.1.2/easel' cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o easel.o -c easel.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_alphabet.o -c esl_alphabet.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_avx.o -c esl_avx.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_buffer.o -c esl_buffer.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_cluster.o -c esl_cluster.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_composition.o -c esl_composition.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_dirichlet.o -c esl_dirichlet.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_distance.o -c esl_distance.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_dmatrix.o -c esl_dmatrix.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_dsqdata.o -c esl_dsqdata.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_exponential.o -c esl_exponential.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_fileparser.o -c esl_fileparser.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_gamma.o -c esl_gamma.c esl_fileparser.c: In function 'esl_fileparser_NextLine': esl_fileparser.c:278:21: warning: comparison between pointer and zero character constant [-Wpointer-compare] while (efp->s != '\0' && isspace(*(efp->s))) efp->s++; ^~ esl_fileparser.c:278:14: note: did you mean to dereference the pointer? while (efp->s != '\0' && isspace(*(efp->s))) efp->s++; ^ esl_fileparser.c: In function 'esl_fileparser_NextLinePeeked': esl_fileparser.c:359:17: warning: comparison between pointer and zero character constant [-Wpointer-compare] while (efp->s != '\0' && isspace(*(efp->s))) efp->s++; ^~ esl_fileparser.c:359:10: note: did you mean to dereference the pointer? while (efp->s != '\0' && isspace(*(efp->s))) efp->s++; ^ cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_gencode.o -c esl_gencode.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_getopts.o -c esl_getopts.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_gev.o -c esl_gev.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_gumbel.o -c esl_gumbel.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_heap.o -c esl_heap.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_histogram.o -c esl_histogram.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_hmm.o -c esl_hmm.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_hyperexp.o -c esl_hyperexp.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_keyhash.o -c esl_keyhash.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_mem.o -c esl_mem.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_minimizer.o -c esl_minimizer.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_mixgev.o -c esl_mixgev.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_mpi.o -c esl_mpi.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_msa.o -c esl_msa.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_msacluster.o -c esl_msacluster.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_msafile.o -c esl_msafile.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_msafile2.o -c esl_msafile2.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_msafile_a2m.o -c esl_msafile_a2m.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_msafile_afa.o -c esl_msafile_afa.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_msafile_clustal.o -c esl_msafile_clustal.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_msafile_phylip.o -c esl_msafile_phylip.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_msafile_psiblast.o -c esl_msafile_psiblast.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_msafile_selex.o -c esl_msafile_selex.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_msafile_stockholm.o -c esl_msafile_stockholm.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_msashuffle.o -c esl_msashuffle.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_msaweight.o -c esl_msaweight.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_normal.o -c esl_normal.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_paml.o -c esl_paml.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_random.o -c esl_random.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_randomseq.o -c esl_randomseq.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_ratematrix.o -c esl_ratematrix.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_recorder.o -c esl_recorder.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_regexp.o -c esl_regexp.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_rootfinder.o -c esl_rootfinder.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_scorematrix.o -c esl_scorematrix.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_sq.o -c esl_sq.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_sqio.o -c esl_sqio.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_sqio_ascii.o -c esl_sqio_ascii.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_sqio_ncbi.o -c esl_sqio_ncbi.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_sse.o -c esl_sse.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_ssi.o -c esl_ssi.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_stack.o -c esl_stack.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_stats.o -c esl_stats.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_stopwatch.o -c esl_stopwatch.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_stretchexp.o -c esl_stretchexp.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_threads.o -c esl_threads.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_tree.o -c esl_tree.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_vectorops.o -c esl_vectorops.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_vmx.o -c esl_vmx.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_weibull.o -c esl_weibull.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_workqueue.o -c esl_workqueue.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -o esl_wuss.o -c esl_wuss.c /usr/bin/ar -r libeasel.a easel.o esl_alphabet.o esl_avx.o esl_buffer.o esl_cluster.o esl_composition.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_gumbel.o esl_heap.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_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/infernal/infernal-1.1.2/easel/miniapps' cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-afetch.o -c esl-afetch.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-alimanip.o -c esl-alimanip.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-alimap.o -c esl-alimap.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-alimask.o -c esl-alimask.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-alimerge.o -c esl-alimerge.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-alipid.o -c esl-alipid.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-alirev.o -c esl-alirev.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-alistat.o -c esl-alistat.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-cluster.o -c esl-cluster.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-compalign.o -c esl-compalign.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-compstruct.o -c esl-compstruct.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-construct.o -c esl-construct.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-histplot.o -c esl-histplot.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-mask.o -c esl-mask.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-reformat.o -c esl-reformat.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-selectn.o -c esl-selectn.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-seqrange.o -c esl-seqrange.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-seqstat.o -c esl-seqstat.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-sfetch.o -c esl-sfetch.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-shuffle.o -c esl-shuffle.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-ssdraw.o -c esl-ssdraw.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-translate.o -c esl-translate.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-weight.o -c esl-weight.c cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -L.. -o esl-afetch esl-afetch.o -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -L.. -o esl-alimap esl-alimap.o -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -L.. -o esl-alimask esl-alimask.o -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -L.. -o esl-alimerge esl-alimerge.o -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -L.. -o esl-alipid esl-alipid.o -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -L.. -o esl-alirev esl-alirev.o -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -L.. -o esl-alistat esl-alistat.o -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -L.. -o esl-cluster esl-cluster.o -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -L.. -o esl-compalign esl-compalign.o -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -L.. -o esl-compstruct esl-compstruct.o -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -L.. -o esl-construct esl-construct.o -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -L.. -o esl-histplot esl-histplot.o -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -L.. -o esl-mask esl-mask.o -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -L.. -o esl-reformat esl-reformat.o -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -L.. -o esl-selectn esl-selectn.o -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -L.. -o esl-seqrange esl-seqrange.o -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -L.. -o esl-seqstat esl-seqstat.o -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -L.. -o esl-sfetch esl-sfetch.o -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -L.. -o esl-shuffle esl-shuffle.o -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -L.. -o esl-translate esl-translate.o -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -L.. -o esl-weight esl-weight.o -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -L.. -o esl-alimanip esl-alimanip.o -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -DHAVE_CONFIG_H -L.. -o esl-ssdraw esl-ssdraw.o -leasel -lm gmake[3]: Leaving directory '/construction/biology/infernal/infernal-1.1.2/easel/miniapps' gmake[2]: Leaving directory '/construction/biology/infernal/infernal-1.1.2/easel' gmake -C hmmer/libdivsufsort all gmake[2]: Entering directory '/construction/biology/infernal/infernal-1.1.2/hmmer/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/infernal/infernal-1.1.2/hmmer/libdivsufsort' gmake -C hmmer all gmake[2]: Entering directory '/construction/biology/infernal/infernal-1.1.2/hmmer' gmake -C ../easel all gmake[3]: Entering directory '/construction/biology/infernal/infernal-1.1.2/easel' gmake -C miniapps all gmake[4]: Entering directory '/construction/biology/infernal/infernal-1.1.2/easel/miniapps' gmake[4]: Nothing to be done for 'all'. gmake[4]: Leaving directory '/construction/biology/infernal/infernal-1.1.2/easel/miniapps' gmake[3]: Leaving directory '/construction/biology/infernal/infernal-1.1.2/easel' gmake -C libdivsufsort all gmake[3]: Entering directory '/construction/biology/infernal/infernal-1.1.2/hmmer/libdivsufsort' gmake[3]: Nothing to be done for 'all'. gmake[3]: Leaving directory '/construction/biology/infernal/infernal-1.1.2/hmmer/libdivsufsort' gmake -C src all gmake[3]: Entering directory '/construction/biology/infernal/infernal-1.1.2/hmmer/src' cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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[4]: Entering directory '/construction/biology/infernal/infernal-1.1.2/hmmer/src/impl_sse' cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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-1.1.2/hmmer/src/impl_sse' cc -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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 -msse3 -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-1.1.2/hmmer/src' gmake -C profmark all gmake[3]: Entering directory '/construction/biology/infernal/infernal-1.1.2/hmmer/profmark' cc -I../../easel -I../../easel -I../src -I../../src -pipe -O2 -fno-strict-aliasing -pthread -fPIC -msse2 -msse3 -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 -msse3 -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[3]: Leaving directory '/construction/biology/infernal/infernal-1.1.2/hmmer/profmark' gmake[2]: Leaving directory '/construction/biology/infernal/infernal-1.1.2/hmmer' gmake -C src all gmake[2]: Entering directory '/construction/biology/infernal/infernal-1.1.2/src' cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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-1.1.2/src/impl_sse' cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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-1.1.2/src/impl_sse' cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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 -msse2 -msse3 -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-1.1.2/src' gmake -C rmark all gmake[2]: Entering directory '/construction/biology/infernal/infernal-1.1.2/rmark' cc -I../easel -I../easel -I../src -I../src -pipe -O2 -fno-strict-aliasing -pthread -msse2 -msse3 -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 -msse2 -msse3 -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-1.1.2/rmark' gmake -C src/impl_sse all gmake[2]: Entering directory '/construction/biology/infernal/infernal-1.1.2/src/impl_sse' cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -msse3 -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 -msse2 -msse3 -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-1.1.2/src/impl_sse' gmake[1]: Leaving directory '/construction/biology/infernal/infernal-1.1.2' -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for infernal-1.1.2 ===> Generating temporary packing list gmake[1]: Entering directory '/construction/biology/infernal/infernal-1.1.2' /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-1.1.2/src' for file in cmalign cmbuild cmcalibrate cmconvert cmemit cmfetch cmpress cmscan cmsearch cmstat; do \ /usr/bin/install -c -m 0755 $file /construction/biology/infernal/stage/usr/local/bin/ ;\ done gmake[2]: Leaving directory '/construction/biology/infernal/infernal-1.1.2/src' gmake -C documentation install gmake[2]: Entering directory '/construction/biology/infernal/infernal-1.1.2/documentation' gmake -C manpages install gmake[3]: Entering directory '/construction/biology/infernal/infernal-1.1.2/documentation/manpages' for file in infernal cmalign cmbuild cmcalibrate cmconvert cmemit cmfetch cmpress cmsearch cmscan cmstat; do \ /usr/bin/install -c -m 0755 ./$file.man /construction/biology/infernal/stage/usr/local/man/man1/${file}.1 ;\ done gmake[3]: Leaving directory '/construction/biology/infernal/infernal-1.1.2/documentation/manpages' gmake[2]: Leaving directory '/construction/biology/infernal/infernal-1.1.2/documentation' gmake[1]: Leaving directory '/construction/biology/infernal/infernal-1.1.2' install -m 0644 /construction/biology/infernal/infernal-1.1.2/Userguide.pdf /construction/biology/infernal/stage/usr/local/share/doc/infernal install -m 0644 /construction/biology/infernal/infernal-1.1.2/tutorial/5S_rRNA.c.cm /construction/biology/infernal/infernal-1.1.2/tutorial/5S_rRNA.sto /construction/biology/infernal/infernal-1.1.2/tutorial/Cobalamin.c.cm /construction/biology/infernal/infernal-1.1.2/tutorial/Cobalamin.fa /construction/biology/infernal/infernal-1.1.2/tutorial/Cobalamin.sto /construction/biology/infernal/infernal-1.1.2/tutorial/metag-example.fa /construction/biology/infernal/infernal-1.1.2/tutorial/minifam-metag.out /construction/biology/infernal/infernal-1.1.2/tutorial/minifam.cm /construction/biology/infernal/infernal-1.1.2/tutorial/minifam.cm.i1f /construction/biology/infernal/infernal-1.1.2/tutorial/minifam.cm.i1i /construction/biology/infernal/infernal-1.1.2/tutorial/minifam.cm.i1m /construction/biology/infernal/infernal-1.1.2/tutorial/minifam.cm.i1p /construction/biology/infernal/infernal-1.1.2/tutorial/mrum-genome.fa /construction/biology/infernal/infernal-1.1.2/tutorial/mrum-tRNAs10.fa /construction/biology/infernal/infernal-1.1.2/tutorial/mrum-tRNAs10.out /construction/biology/infernal/infernal-1.1.2/tutorial/tRNA5-hand.c.cm /construction/biology/infernal/infernal-1.1.2/tutorial/tRNA5-hand.sto /construction/biology/infernal/infernal-1.1.2/tutorial/tRNA5-mrum.out /construction/biology/infernal/infernal-1.1.2/tutorial/tRNA5-noss.sto /construction/biology/infernal/infernal-1.1.2/tutorial/tRNA5.c.cm /construction/biology/infernal/infernal-1.1.2/tutorial/tRNA5.sto /construction/biology/infernal/stage/usr/local/share/examples/infernal ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for infernal-1.1.2 file sizes/checksums [46]: . done packing files [46]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Wednesday, 6 MAR 2019 at 05:43:21 UTC Duration: 00:01:44