------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 UNAME_r=6.1 UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=unknown UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 LANG=C HOME=/root USER=root TERM=dumb SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: showconfig ------------------------------------------------------------------------------- ===> The following configuration options are available for hmmer-3.3: 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 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ENV ------------------------------------------------------------------------------- MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 PYTHON="/usr/local/bin/python3.7" 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=gcc80 CONFIG_SITE=/xports/Templates/config.site lt_cv_sys_max_cmd_len=262144 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: MAKE_ENV ------------------------------------------------------------------------------- PERL_USE_UNSAFE_INC=1 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=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" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ARGS ------------------------------------------------------------------------------- V=1 DESTDIR=/construction/biology/hmmer/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: PLIST_SUB ------------------------------------------------------------------------------- PORTDOCS="" PORTEXAMPLES="" PYTHON_INCLUDEDIR=include/python3.7m PYTHON_LIBDIR=lib/python3.7 PYTHON_PLATFORM=dragonfly6 PYTHON_SITELIBDIR=lib/python3.7/site-packages PYTHON_SUFFIX=37 PYTHON_EXT_SUFFIX= PYTHON_VER=3.7 PYTHON_VERSION=python3.7 PYTHON2="@comment " PYTHON3="" OSREL=6.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.32.1 PERL_VER=5.32 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.32 PROFILE="@comment " DOCSDIR="share/doc/hmmer" EXAMPLESDIR="share/examples/hmmer" DATADIR="share/hmmer" WWWDIR="www/hmmer" ETCDIR="etc/hmmer" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: 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 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: /etc/make.conf ------------------------------------------------------------------------------- DPORTS_BUILDER=yes DISABLE_LICENSES=yes DEFAULT_VERSIONS=ssl=openssl FORCE_PACKAGE=yes DEVELOPER=yes USE_PACKAGE_DEPENDS_ONLY=yes PORTSDIR=/xports PORT_DBDIR=/options PKG_DBDIR=/var/db/pkg PKG_CACHEDIR=/var/cache/pkg PKG_SUFX=.txz DEVELOPER=1 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=600100 OSVERSION=9999999 OSREL=6.1 _OSRELEASE=6.1-SYNTH DISTDIR=/distfiles WRKDIRPREFIX=/construction BATCH=yes PACKAGE_BUILDING=yes PKG_CREATE_VERBOSE=yes MAKE_JOBS_NUMBER=10 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gettext-runtime-0.21.txz Installing /packages/All/gmake-4.3_2.txz SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> hmmer-3.3 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> hmmer-3.3 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by hmmer-3.3 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> hmmer-3.3 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by hmmer-3.3 for building => SHA256 Checksum OK for hmmer-3.3.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> hmmer-3.3 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by hmmer-3.3 for building ===> Extracting for hmmer-3.3 => SHA256 Checksum OK for hmmer-3.3.tar.gz. Extracted Memory Use: 34.42M SUCCEEDED 00:00:02 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for hmmer-3.3 ===> Applying ports patches for hmmer-3.3 from /xports/biology/hmmer/files SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> hmmer-3.3 depends on package: gmake>=4.3 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> hmmer-3.3 depends on package: gmake>=4.3 - found ===> Configuring for hmmer-3.3 configure: loading site script /xports/Templates/config.site configure: Configuring HMMER3 for your system. checking build system type... x86_64-portbld-dragonfly6.1 checking host system type... x86_64-portbld-dragonfly6.1 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 cc option to accept ISO C99... none needed checking for cc option to accept ISO Standard C... (cached) none needed checking how to run the C preprocessor... cpp checking for a BSD-compatible install... /usr/bin/install -c checking for ranlib... ranlib checking for ar... /usr/bin/ar checking whether ln -s works... yes checking for a sed that does not truncate output... (cached) /usr/bin/sed checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking whether cc is Clang... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking whether more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking whether cc can compile our Altivec/VMX code... no checking whether cc can compile our SSE code... yes configure: Activating Intel/AMD SSE vector DP implementation checking whether _MM_SET_FLUSH_ZERO_MODE is supported... yes checking compiler support --start-group... yes checking for gzip... /usr/bin/gzip checking for python3... no checking for library containing clock_gettime... none required checking for ANSI C header files... (cached) yes checking for sys/types.h... (cached) yes checking for sys/stat.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for memory.h... (cached) yes checking for strings.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.h... (cached) yes checking endian.h usability... yes checking endian.h presence... yes checking for endian.h... yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/types.h... (cached) yes checking for netinet/in.h... (cached) yes checking for sys/param.h... (cached) yes checking for sys/sysctl.h... (cached) yes checking for uint8_t... (cached) yes checking for uint16_t... (cached) yes checking for uint32_t... (cached) yes checking for uint64_t... (cached) yes checking for off_t... (cached) yes checking whether byte ordering is bigendian... no checking for __attribute__((noreturn))... yes checking for __attribute__((format))... yes checking for mkstemp... (cached) yes checking for popen... yes checking for putenv... (cached) yes checking for strcasecmp... (cached) yes checking for strsep... (cached) yes checking for times... (cached) yes checking for getpid... (cached) yes checking for sysctl... (cached) yes checking for sysconf... (cached) yes checking for getcwd... (cached) yes checking for chmod... yes checking for stat... (cached) yes checking for fstat... (cached) yes checking for erfc... no checking for library containing ntohs... none required checking for library containing ntohl... none required checking for library containing htons... none required checking for library containing htonl... none required checking for library containing socket... none required checking for library containing inet_pton... none required checking for _LARGEFILE_SOURCE value needed for large files... no checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating testsuite/Makefile config.status: creating profmark/Makefile config.status: creating src/impl_sse/Makefile config.status: creating documentation/Makefile config.status: creating documentation/man/Makefile config.status: creating documentation/userguide/Makefile config.status: creating documentation/userguide/inclusions/Makefile config.status: creating libdivsufsort/Makefile config.status: creating easel/Makefile config.status: creating easel/miniapps/Makefile config.status: creating easel/testsuite/Makefile config.status: creating easel/documentation/Makefile config.status: creating documentation/userguide/titlepage.tex config.status: creating documentation/userguide/titlepage_daemon.tex config.status: creating documentation/userguide/copyright.tex config.status: creating documentation/man/alimask.man config.status: creating documentation/man/hmmalign.man config.status: creating documentation/man/hmmbuild.man config.status: creating documentation/man/hmmc2.man config.status: creating documentation/man/hmmconvert.man config.status: creating documentation/man/hmmemit.man config.status: creating documentation/man/hmmer.man config.status: creating documentation/man/hmmfetch.man config.status: creating documentation/man/hmmlogo.man config.status: creating documentation/man/hmmpgmd.man config.status: creating documentation/man/hmmpgmd_shard.man config.status: creating documentation/man/hmmpress.man config.status: creating documentation/man/hmmscan.man config.status: creating documentation/man/hmmsearch.man config.status: creating documentation/man/hmmsim.man config.status: creating documentation/man/hmmstat.man config.status: creating documentation/man/jackhmmer.man config.status: creating documentation/man/makehmmerdb.man config.status: creating documentation/man/nhmmer.man config.status: creating documentation/man/nhmmscan.man config.status: creating documentation/man/phmmer.man config.status: creating easel/miniapps/esl-afetch.man config.status: creating easel/miniapps/esl-alimanip.man config.status: creating easel/miniapps/esl-alimap.man config.status: creating easel/miniapps/esl-alimask.man config.status: creating easel/miniapps/esl-alimerge.man config.status: creating easel/miniapps/esl-alipid.man config.status: creating easel/miniapps/esl-alirev.man config.status: creating easel/miniapps/esl-alistat.man config.status: creating easel/miniapps/esl-compalign.man config.status: creating easel/miniapps/esl-compstruct.man config.status: creating easel/miniapps/esl-construct.man config.status: creating easel/miniapps/esl-histplot.man config.status: creating easel/miniapps/esl-mask.man config.status: creating easel/miniapps/esl-mixdchlet.man config.status: creating easel/miniapps/esl-reformat.man config.status: creating easel/miniapps/esl-selectn.man config.status: creating easel/miniapps/esl-seqrange.man config.status: creating easel/miniapps/esl-seqstat.man config.status: creating easel/miniapps/esl-sfetch.man config.status: creating easel/miniapps/esl-shuffle.man config.status: creating easel/miniapps/esl-ssdraw.man config.status: creating easel/miniapps/esl-translate.man config.status: creating easel/miniapps/esl-weight.man config.status: creating easel/decoy_config.h config.status: creating src/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 -pthread host: x86_64-portbld-dragonfly6.1 linker: libraries: DP implementation: sse (No python3 found, so 'make check' is disabled.) Now do 'make' to build HMMER, and optionally: 'make install' to install programs and man pages, '(cd easel; make install)' to install Easel tools. SUCCEEDED 00:00:07 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for hmmer-3.3 gmake[1]: Entering directory '/construction/biology/hmmer/hmmer-3.3' gmake -C easel all gmake[2]: Entering directory '/construction/biology/hmmer/hmmer-3.3/easel' cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c easel.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_alloc.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_alphabet.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_arr2.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_arr3.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_bitfield.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_buffer.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_cluster.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_composition.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_cpu.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_dirichlet.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_distance.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_dmatrix.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_dsqdata.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_exponential.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_fileparser.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_gamma.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_gencode.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_getopts.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_gev.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_graph.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_gumbel.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_heap.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_histogram.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_hmm.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_huffman.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_hyperexp.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_json.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_keyhash.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_matrixops.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_mem.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_minimizer.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_mixdchlet.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_mixgev.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_mpi.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_msa.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_msacluster.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_msafile.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_msafile2.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_msafile_a2m.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_msafile_afa.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_msafile_clustal.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_msafile_phylip.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_msafile_psiblast.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_msafile_selex.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_msafile_stockholm.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_msashuffle.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_msaweight.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_normal.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_paml.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_quicksort.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_random.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_rand64.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_randomseq.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_ratematrix.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_recorder.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_red_black.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_regexp.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_rootfinder.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_scorematrix.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_sq.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_sqio.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_sqio_ascii.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_sqio_ncbi.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_ssi.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_stack.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_stats.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_stopwatch.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_stretchexp.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_subcmd.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_threads.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_tree.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_varint.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_vectorops.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_weibull.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_workqueue.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_wuss.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_sse.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_avx.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_avx512.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_neon.c cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -c esl_vmx.c /usr/bin/ar -r libeasel.a easel.o esl_alloc.o esl_alphabet.o esl_arr2.o esl_arr3.o esl_bitfield.o esl_buffer.o esl_cluster.o esl_composition.o esl_cpu.o esl_dirichlet.o esl_distance.o esl_dmatrix.o esl_dsqdata.o esl_exponential.o esl_fileparser.o esl_gamma.o esl_gencode.o esl_getopts.o esl_gev.o esl_graph.o esl_gumbel.o esl_heap.o esl_histogram.o esl_hmm.o esl_huffman.o esl_hyperexp.o esl_json.o esl_keyhash.o esl_matrixops.o esl_mem.o esl_minimizer.o esl_mixdchlet.o esl_mixgev.o esl_mpi.o esl_msa.o esl_msacluster.o esl_msafile.o esl_msafile2.o esl_msafile_a2m.o esl_msafile_afa.o esl_msafile_clustal.o esl_msafile_phylip.o esl_msafile_psiblast.o esl_msafile_selex.o esl_msafile_stockholm.o esl_msashuffle.o esl_msaweight.o esl_normal.o esl_paml.o esl_quicksort.o esl_random.o esl_rand64.o esl_randomseq.o esl_ratematrix.o esl_recorder.o esl_red_black.o esl_regexp.o esl_rootfinder.o esl_scorematrix.o esl_sq.o esl_sqio.o esl_sqio_ascii.o esl_sqio_ncbi.o esl_ssi.o esl_stack.o esl_stats.o esl_stopwatch.o esl_stretchexp.o esl_subcmd.o esl_threads.o esl_tree.o esl_varint.o esl_vectorops.o esl_weibull.o esl_workqueue.o esl_wuss.o esl_sse.o esl_avx.o esl_avx512.o esl_neon.o esl_vmx.o > /dev/null 2>&1 gmake -C miniapps all gmake[3]: Entering directory '/construction/biology/hmmer/hmmer-3.3/easel/miniapps' cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-afetch esl-afetch.c -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-alimanip esl-alimanip.c -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-alimap esl-alimap.c -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-alimask esl-alimask.c -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-alimerge esl-alimerge.c -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-alipid esl-alipid.c -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-alirev esl-alirev.c -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-alistat esl-alistat.c -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-compalign esl-compalign.c -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-compstruct esl-compstruct.c -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-construct esl-construct.c -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-histplot esl-histplot.c -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-mask esl-mask.c -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-mixdchlet esl-mixdchlet.c -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-reformat esl-reformat.c -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-selectn esl-selectn.c -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-seqrange esl-seqrange.c -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-seqstat esl-seqstat.c -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-sfetch esl-sfetch.c -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-shuffle esl-shuffle.c -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-ssdraw esl-ssdraw.c -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-translate esl-translate.c -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-weight esl-weight.c -leasel -lm cc -I. -I.. -I. -I./.. -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -c cmd_alistat.c cc -I. -I.. -I. -I./.. -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -c cmd_downsample.c cc -I. -I.. -I. -I./.. -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -c cmd_filter.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o easel easel.c cmd_alistat.o cmd_downsample.o cmd_filter.o -leasel -lm gmake[3]: Leaving directory '/construction/biology/hmmer/hmmer-3.3/easel/miniapps' gmake[2]: Leaving directory '/construction/biology/hmmer/hmmer-3.3/easel' gmake -C libdivsufsort all gmake[2]: Entering directory '/construction/biology/hmmer/hmmer-3.3/libdivsufsort' cc -I. -pipe -O2 -fno-strict-aliasing -pthread -o divsufsort.o -c divsufsort.c /usr/bin/ar rc libdivsufsort.a divsufsort.o gmake[2]: Leaving directory '/construction/biology/hmmer/hmmer-3.3/libdivsufsort' gmake -C src all gmake[2]: Entering directory '/construction/biology/hmmer/hmmer-3.3/src' cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o alimask.o -c alimask.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o build.o -c build.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o cachedb.o -c cachedb.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o cachedb_shard.o -c cachedb_shard.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o emit.o -c emit.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o errors.o -c errors.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o evalues.o -c evalues.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o eweight.o -c eweight.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o generic_decoding.o -c generic_decoding.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o generic_fwdback.o -c generic_fwdback.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o generic_fwdback_chk.o -c generic_fwdback_chk.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o generic_fwdback_banded.o -c generic_fwdback_banded.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o generic_null2.o -c generic_null2.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o generic_msv.o -c generic_msv.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o generic_optacc.o -c generic_optacc.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o generic_stotrace.o -c generic_stotrace.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o generic_viterbi.o -c generic_viterbi.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o generic_vtrace.o -c generic_vtrace.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o h2_io.o -c h2_io.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o heatmap.o -c heatmap.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmlogo.o -c hmmlogo.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmdmstr.o -c hmmdmstr.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmdmstr_shard.o -c hmmdmstr_shard.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmd_search_status.o -c hmmd_search_status.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmdwrkr.o -c hmmdwrkr.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmdwrkr_shard.o -c hmmdwrkr_shard.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmdutils.o -c hmmdutils.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmer.o -c hmmer.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o logsum.o -c logsum.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o modelconfig.o -c modelconfig.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o modelstats.o -c modelstats.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o mpisupport.o -c mpisupport.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o seqmodel.o -c seqmodel.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o tracealign.o -c tracealign.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o p7_alidisplay.o -c p7_alidisplay.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o p7_bg.o -c p7_bg.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o p7_builder.o -c p7_builder.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o p7_domain.o -c p7_domain.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o p7_domaindef.o -c p7_domaindef.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o p7_gbands.o -c p7_gbands.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o p7_gmx.o -c p7_gmx.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o p7_gmxb.o -c p7_gmxb.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o p7_gmxchk.o -c p7_gmxchk.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o p7_hit.o -c p7_hit.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o p7_hmm.o -c p7_hmm.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o p7_hmmcache.o -c p7_hmmcache.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o p7_hmmd_search_stats.o -c p7_hmmd_search_stats.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o p7_hmmfile.o -c p7_hmmfile.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o p7_hmmwindow.o -c p7_hmmwindow.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o p7_pipeline.o -c p7_pipeline.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o p7_prior.o -c p7_prior.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o p7_profile.o -c p7_profile.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o p7_spensemble.o -c p7_spensemble.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o p7_tophits.o -c p7_tophits.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o p7_trace.o -c p7_trace.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o p7_scoredata.o -c p7_scoredata.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmpgmd2msa.o -c hmmpgmd2msa.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o fm_alphabet.o -c fm_alphabet.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o fm_general.o -c fm_general.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o fm_sse.o -c fm_sse.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o fm_ssv.o -c fm_ssv.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmalign.o -c hmmalign.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmbuild.o -c hmmbuild.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmconvert.o -c hmmconvert.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmemit.o -c hmmemit.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmfetch.o -c hmmfetch.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmpgmd.o -c hmmpgmd.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmpgmd_shard.o -c hmmpgmd_shard.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmpress.o -c hmmpress.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmscan.o -c hmmscan.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmsearch.o -c hmmsearch.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmsim.o -c hmmsim.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmstat.o -c hmmstat.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o jackhmmer.o -c jackhmmer.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o phmmer.o -c phmmer.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o nhmmer.o -c nhmmer.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o nhmmscan.o -c nhmmscan.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o makehmmerdb.o -c makehmmerdb.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmc2.o -c hmmc2.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmerfm-exactmatch.o -c hmmerfm-exactmatch.c /usr/bin/ar -r libhmmer.a build.o cachedb.o cachedb_shard.o emit.o errors.o evalues.o eweight.o generic_decoding.o generic_fwdback.o generic_fwdback_chk.o generic_fwdback_banded.o generic_null2.o generic_msv.o generic_optacc.o generic_stotrace.o generic_viterbi.o generic_vtrace.o h2_io.o heatmap.o hmmlogo.o hmmdmstr.o hmmdmstr_shard.o hmmd_search_status.o hmmdwrkr.o hmmdwrkr_shard.o hmmdutils.o hmmer.o logsum.o modelconfig.o modelstats.o mpisupport.o seqmodel.o tracealign.o p7_alidisplay.o p7_bg.o p7_builder.o p7_domain.o p7_domaindef.o p7_gbands.o p7_gmx.o p7_gmxb.o p7_gmxchk.o p7_hit.o p7_hmm.o p7_hmmcache.o p7_hmmd_search_stats.o p7_hmmfile.o p7_hmmwindow.o p7_pipeline.o p7_prior.o p7_profile.o p7_spensemble.o p7_tophits.o p7_trace.o p7_scoredata.o hmmpgmd2msa.o fm_alphabet.o fm_general.o fm_sse.o fm_ssv.o > /dev/null 2>&1 gmake -C impl_sse libhmmer-impl.stamp gmake[3]: Entering directory '/construction/biology/hmmer/hmmer-3.3/src/impl_sse' cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -o decoding.o -c decoding.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -o fwdback.o -c fwdback.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -o io.o -c io.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -o ssvfilter.o -c ssvfilter.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -o msvfilter.o -c msvfilter.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -o null2.o -c null2.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -o optacc.o -c optacc.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -o stotrace.o -c stotrace.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -o vitfilter.o -c vitfilter.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -o p7_omx.o -c p7_omx.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -o p7_oprofile.o -c p7_oprofile.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -o mpi.o -c mpi.c /usr/bin/ar -r ../libhmmer.a decoding.o fwdback.o io.o ssvfilter.o msvfilter.o null2.o optacc.o stotrace.o vitfilter.o p7_omx.o p7_oprofile.o mpi.o > /dev/null 2>&1 gmake[3]: Leaving directory '/construction/biology/hmmer/hmmer-3.3/src/impl_sse' cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L./impl_sse -L../libdivsufsort -L. -o alimask alimask.o -lhmmer -leasel -ldivsufsort -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L./impl_sse -L../libdivsufsort -L. -o hmmalign hmmalign.o -lhmmer -leasel -ldivsufsort -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L./impl_sse -L../libdivsufsort -L. -o hmmbuild hmmbuild.o -lhmmer -leasel -ldivsufsort -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L./impl_sse -L../libdivsufsort -L. -o hmmconvert hmmconvert.o -lhmmer -leasel -ldivsufsort -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L./impl_sse -L../libdivsufsort -L. -o hmmemit hmmemit.o -lhmmer -leasel -ldivsufsort -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L./impl_sse -L../libdivsufsort -L. -o hmmfetch hmmfetch.o -lhmmer -leasel -ldivsufsort -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L./impl_sse -L../libdivsufsort -L. -o hmmlogo hmmlogo.o -lhmmer -leasel -ldivsufsort -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L./impl_sse -L../libdivsufsort -L. -o hmmpgmd hmmpgmd.o -lhmmer -leasel -ldivsufsort -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L./impl_sse -L../libdivsufsort -L. -o hmmpgmd_shard hmmpgmd_shard.o -lhmmer -leasel -ldivsufsort -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L./impl_sse -L../libdivsufsort -L. -o hmmpress hmmpress.o -lhmmer -leasel -ldivsufsort -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L./impl_sse -L../libdivsufsort -L. -o hmmscan hmmscan.o -lhmmer -leasel -ldivsufsort -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L./impl_sse -L../libdivsufsort -L. -o hmmsearch hmmsearch.o -lhmmer -leasel -ldivsufsort -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L./impl_sse -L../libdivsufsort -L. -o hmmsim hmmsim.o -lhmmer -leasel -ldivsufsort -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L./impl_sse -L../libdivsufsort -L. -o hmmstat hmmstat.o -lhmmer -leasel -ldivsufsort -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L./impl_sse -L../libdivsufsort -L. -o jackhmmer jackhmmer.o -lhmmer -leasel -ldivsufsort -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L./impl_sse -L../libdivsufsort -L. -o phmmer phmmer.o -lhmmer -leasel -ldivsufsort -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L./impl_sse -L../libdivsufsort -L. -o nhmmer nhmmer.o -lhmmer -leasel -ldivsufsort -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L./impl_sse -L../libdivsufsort -L. -o nhmmscan nhmmscan.o -lhmmer -leasel -ldivsufsort -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L./impl_sse -L../libdivsufsort -L. -o makehmmerdb makehmmerdb.o -lhmmer -leasel -ldivsufsort -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L./impl_sse -L../libdivsufsort -L. -o hmmc2 hmmc2.o -lhmmer -leasel -ldivsufsort -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L./impl_sse -L../libdivsufsort -L. -o hmmerfm-exactmatch hmmerfm-exactmatch.o -lhmmer -leasel -ldivsufsort -lm gmake[2]: Leaving directory '/construction/biology/hmmer/hmmer-3.3/src' gmake -C profmark all gmake[2]: Entering directory '/construction/biology/hmmer/hmmer-3.3/profmark' cc -I../easel -I../easel -I../src -I../src -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -o create-profmark.o -c create-profmark.c cc -I../easel -I../easel -I../src -I../src -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -o rocplot.o -c rocplot.c cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L../src -o rocplot rocplot.o -lhmmer -leasel -lm cc -pipe -O2 -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L../src -o create-profmark create-profmark.o -lhmmer -leasel -lm gmake[2]: Leaving directory '/construction/biology/hmmer/hmmer-3.3/profmark' gmake[1]: Leaving directory '/construction/biology/hmmer/hmmer-3.3' SUCCEEDED 00:00:35 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for hmmer-3.3 ===> Generating temporary packing list gmake[1]: Entering directory '/construction/biology/hmmer/hmmer-3.3' gmake -C easel all gmake[2]: Entering directory '/construction/biology/hmmer/hmmer-3.3/easel' gmake -C miniapps all gmake[3]: Entering directory '/construction/biology/hmmer/hmmer-3.3/easel/miniapps' gmake[3]: Nothing to be done for 'all'. gmake[3]: Leaving directory '/construction/biology/hmmer/hmmer-3.3/easel/miniapps' gmake[2]: Leaving directory '/construction/biology/hmmer/hmmer-3.3/easel' gmake -C libdivsufsort all gmake[2]: Entering directory '/construction/biology/hmmer/hmmer-3.3/libdivsufsort' gmake[2]: Nothing to be done for 'all'. gmake[2]: Leaving directory '/construction/biology/hmmer/hmmer-3.3/libdivsufsort' gmake -C src all gmake[2]: Entering directory '/construction/biology/hmmer/hmmer-3.3/src' gmake -C impl_sse libhmmer-impl.stamp gmake[3]: Entering directory '/construction/biology/hmmer/hmmer-3.3/src/impl_sse' gmake[3]: 'libhmmer-impl.stamp' is up to date. gmake[3]: Leaving directory '/construction/biology/hmmer/hmmer-3.3/src/impl_sse' gmake[2]: Leaving directory '/construction/biology/hmmer/hmmer-3.3/src' gmake -C profmark all gmake[2]: Entering directory '/construction/biology/hmmer/hmmer-3.3/profmark' gmake[2]: Nothing to be done for 'all'. gmake[2]: Leaving directory '/construction/biology/hmmer/hmmer-3.3/profmark' /usr/bin/install -c -d /construction/biology/hmmer/stage/usr/local/bin /usr/bin/install -c -d /construction/biology/hmmer/stage/usr/local/man/man1 gmake -C src install gmake[2]: Entering directory '/construction/biology/hmmer/hmmer-3.3/src' for file in alimask hmmalign hmmbuild hmmconvert hmmemit hmmfetch hmmlogo hmmpgmd hmmpgmd_shard hmmpress hmmscan hmmsearch hmmsim hmmstat jackhmmer phmmer nhmmer nhmmscan makehmmerdb; do \ /usr/bin/install -c -m 0755 $file /construction/biology/hmmer/stage/usr/local/bin/ ;\ done gmake[2]: Leaving directory '/construction/biology/hmmer/hmmer-3.3/src' gmake -C documentation install gmake[2]: Entering directory '/construction/biology/hmmer/hmmer-3.3/documentation' gmake -C man install gmake[3]: Entering directory '/construction/biology/hmmer/hmmer-3.3/documentation/man' for file in hmmer hmmalign hmmbuild hmmc2 hmmconvert hmmemit hmmfetch hmmlogo hmmpgmd hmmpgmd_shard hmmpress hmmscan hmmsearch hmmsim hmmstat jackhmmer makehmmerdb phmmer nhmmer nhmmscan alimask; do \ /usr/bin/install -c -m 0664 $file.man /construction/biology/hmmer/stage/usr/local/man/man1/${file}.1 ;\ done gmake[3]: Leaving directory '/construction/biology/hmmer/hmmer-3.3/documentation/man' gmake[2]: Leaving directory '/construction/biology/hmmer/hmmer-3.3/documentation' gmake[1]: Leaving directory '/construction/biology/hmmer/hmmer-3.3' install -m 0644 /construction/biology/hmmer/hmmer-3.3/Userguide.pdf /construction/biology/hmmer/stage/usr/local/share/doc/hmmer install -m 0644 /construction/biology/hmmer/hmmer-3.3/tutorial/7LESS_DROME /construction/biology/hmmer/hmmer-3.3/tutorial/HBB_HUMAN /construction/biology/hmmer/hmmer-3.3/tutorial/MADE1.hmm /construction/biology/hmmer/hmmer-3.3/tutorial/MADE1.sto /construction/biology/hmmer/hmmer-3.3/tutorial/Pkinase.hmm /construction/biology/hmmer/hmmer-3.3/tutorial/Pkinase.sto /construction/biology/hmmer/hmmer-3.3/tutorial/dna_target.fa /construction/biology/hmmer/hmmer-3.3/tutorial/fn3.hmm /construction/biology/hmmer/hmmer-3.3/tutorial/fn3.sto /construction/biology/hmmer/hmmer-3.3/tutorial/globins4.hmm /construction/biology/hmmer/hmmer-3.3/tutorial/globins4.sto /construction/biology/hmmer/hmmer-3.3/tutorial/globins45.fa /construction/biology/hmmer/stage/usr/local/share/examples/hmmer ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:02 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for hmmer-3.3 file sizes/checksums [53]: 0% file sizes/checksums [53]: 100% packing files [53]: 0% packing files [53]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:21 TOTAL TIME 00:01:11