=>> Building biology/infernal build started at Wed Dec 10 14:35:45 EST 2025 port directory: /usr/ports/biology/infernal package name: infernal-1.1.5 building for: FreeBSD pkg.DaveG.ca 13.5-RELEASE-p7 FreeBSD 13.5-RELEASE-p7 1305000 amd64 maintained by: mzaki@e-mail.ne.jp Makefile datestamp: -rw-r--r-- 1 root wheel 1754 Jan 31 2025 /usr/ports/biology/infernal/Makefile Ports top last git commit: 62d8b1999233 Ports top unclean checkout: no Port dir last git commit: 8e8bb4267860 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1305000 Job Id: 08 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1305000 UNAME_v=FreeBSD 13.5-RELEASE-p7 1305000 UNAME_r=13.5-RELEASE-p7 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/freebsd_13_5_x64-HEAD-ALL/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/freebsd_13_5_x64-HEAD-ALL/08/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_13_5_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_13_5_x64-HEAD-ALL/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for infernal-1.1.5: 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 ---End OPTIONS List--- --MAINTAINER-- mzaki@e-mail.ne.jp --End MAINTAINER-- --CONFIGURE_ARGS-- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=/usr/local/bin/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/python3.11" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/infernal/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/infernal/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/infernal/work/.cache HOME=/wrkdirs/usr/ports/biology/infernal/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/infernal/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/infernal/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/infernal/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/infernal/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/infernal/work/.cache HOME=/wrkdirs/usr/ports/biology/infernal/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/infernal/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/infernal/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " 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" --End MAKE_ENV-- --PLIST_SUB-- PORTDOCS="" PORTEXAMPLES="" PYTHON_INCLUDEDIR=include/python3.11 PYTHON_LIBDIR=lib/python3.11 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" OSREL=13.5 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.42.0 PERL_VER=5.42 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/5.42 DOCSDIR="share/doc/infernal" EXAMPLESDIR="share/examples/infernal" DATADIR="share/infernal" WWWDIR="www/infernal" ETCDIR="etc/infernal" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.11 PYTHON_LIBDIR=/usr/local/lib/python3.11 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=/usr/local/lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" 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 --End SUB_LIST-- ---Begin make.conf--- DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> infernal-1.1.5 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.4.2_1.pkg [pkg.DaveG.ca] Installing pkg-2.4.2_1... [pkg.DaveG.ca] Extracting pkg-2.4.2_1: .......... done ===> infernal-1.1.5 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of infernal-1.1.5 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by infernal-1.1.5 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by infernal-1.1.5 for building => SHA256 Checksum OK for infernal-1.1.5.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by infernal-1.1.5 for building ===> Extracting for infernal-1.1.5 => SHA256 Checksum OK for infernal-1.1.5.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for infernal-1.1.5 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> infernal-1.1.5 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [pkg.DaveG.ca] Installing gmake-4.4.1... [pkg.DaveG.ca] `-- Installing gettext-runtime-0.23.1... [pkg.DaveG.ca] | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] `-- Extracting gettext-runtime-0.23.1: .......... done [pkg.DaveG.ca] Extracting gmake-4.4.1: .......... done ===> infernal-1.1.5 depends on package: gmake>=4.4.1 - found ===> Returning to build of infernal-1.1.5 ===> infernal-1.1.5 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg.DaveG.ca] Installing ccache-3.7.12_8... [pkg.DaveG.ca] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> infernal-1.1.5 depends on file: /usr/local/bin/ccache - found ===> Returning to build of infernal-1.1.5 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for infernal-1.1.5 configure: loading site script /usr/ports/Templates/config.site configure: Configuring Infernal for your system. checking build system type... amd64-portbld-freebsd13.5 checking host system type... amd64-portbld-freebsd13.5 checking whether to compile using MPI... no 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 the compiler supports GNU C... yes checking whether cc accepts -g... yes checking for cc option to enable C11 features... none needed checking for gcc... (cached) cc checking whether the compiler supports GNU C... (cached) yes checking whether cc accepts -g... (cached) yes checking for cc option to enable C11 features... (cached) none needed checking how to run the C preprocessor... cpp checking for a BSD-compatible install... /usr/bin/install -c checking for strip... strip 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... yes checking whether pthreads work with "-pthread" and "-lpthread"... yes checking whether Clang needs flag to prevent "argument unused" warning when linking with -pthread... no 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 NEON code... no 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 stdio.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for strings.h... (cached) yes checking for sys/stat.h... (cached) yes checking for sys/types.h... (cached) yes checking for unistd.h... (cached) 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 rmark/Makefile config.status: creating documentation/Makefile config.status: creating documentation/man/Makefile config.status: creating documentation/userguide/Makefile config.status: creating src/impl_sse/Makefile config.status: creating documentation/userguide/titlepage.tex config.status: creating documentation/userguide/copyright.tex config.status: creating documentation/man/cmalign.man config.status: creating documentation/man/cmbuild.man config.status: creating documentation/man/cmcalibrate.man config.status: creating documentation/man/cmconvert.man config.status: creating documentation/man/cmemit.man config.status: creating documentation/man/cmfetch.man config.status: creating documentation/man/cmpress.man config.status: creating documentation/man/cmscan.man config.status: creating documentation/man/cmsearch.man config.status: creating documentation/man/cmsearch_dual.man config.status: creating documentation/man/cmstat.man config.status: creating documentation/man/infernal.man config.status: creating documentation/man/sse_cmsearch.man config.status: creating hmmer/Makefile config.status: creating hmmer/src/Makefile config.status: creating hmmer/testsuite/Makefile config.status: creating hmmer/profmark/Makefile config.status: creating hmmer/src/impl_sse/Makefile config.status: creating hmmer/documentation/Makefile config.status: creating hmmer/documentation/man/Makefile config.status: creating hmmer/documentation/userguide/Makefile config.status: creating hmmer/documentation/userguide/inclusions/Makefile config.status: creating hmmer/libdivsufsort/Makefile config.status: creating easel/Makefile config.status: creating easel/miniapps/Makefile config.status: creating easel/testsuite/Makefile config.status: creating easel/documentation/Makefile config.status: creating hmmer/documentation/userguide/titlepage.tex config.status: creating hmmer/documentation/userguide/titlepage_daemon.tex config.status: creating hmmer/documentation/userguide/copyright.tex config.status: creating hmmer/documentation/man/alimask.man config.status: creating hmmer/documentation/man/hmmalign.man config.status: creating hmmer/documentation/man/hmmbuild.man config.status: creating hmmer/documentation/man/hmmc2.man config.status: creating hmmer/documentation/man/hmmconvert.man config.status: creating hmmer/documentation/man/hmmemit.man config.status: creating hmmer/documentation/man/hmmer.man config.status: creating hmmer/documentation/man/hmmfetch.man config.status: creating hmmer/documentation/man/hmmlogo.man config.status: creating hmmer/documentation/man/hmmpgmd.man config.status: creating hmmer/documentation/man/hmmpgmd_shard.man config.status: creating hmmer/documentation/man/hmmpress.man config.status: creating hmmer/documentation/man/hmmscan.man config.status: creating hmmer/documentation/man/hmmsearch.man config.status: creating hmmer/documentation/man/hmmsim.man config.status: creating hmmer/documentation/man/hmmstat.man config.status: creating hmmer/documentation/man/jackhmmer.man config.status: creating hmmer/documentation/man/makehmmerdb.man config.status: creating hmmer/documentation/man/nhmmer.man config.status: creating hmmer/documentation/man/nhmmscan.man config.status: creating hmmer/documentation/man/phmmer.man config.status: creating easel/miniapps/esl-afetch.man config.status: creating easel/miniapps/esl-alimanip.man config.status: creating easel/miniapps/esl-alimap.man config.status: creating easel/miniapps/esl-alimask.man config.status: creating easel/miniapps/esl-alimerge.man config.status: creating easel/miniapps/esl-alipid.man config.status: creating easel/miniapps/esl-alirev.man config.status: creating easel/miniapps/esl-alistat.man config.status: creating easel/miniapps/esl-compalign.man config.status: creating easel/miniapps/esl-compstruct.man config.status: creating easel/miniapps/esl-construct.man config.status: creating easel/miniapps/esl-histplot.man config.status: creating easel/miniapps/esl-mask.man config.status: creating easel/miniapps/esl-mixdchlet.man config.status: creating easel/miniapps/esl-reformat.man config.status: creating easel/miniapps/esl-selectn.man config.status: creating easel/miniapps/esl-seqrange.man config.status: creating easel/miniapps/esl-seqstat.man config.status: creating easel/miniapps/esl-sfetch.man config.status: creating easel/miniapps/esl-shuffle.man config.status: creating easel/miniapps/esl-ssdraw.man config.status: creating easel/miniapps/esl-translate.man config.status: creating easel/miniapps/esl-weight.man config.status: creating easel/decoy_config.h config.status: creating src/config.h config.status: creating hmmer/src/p7_config.h config.status: creating easel/esl_config.h config.status: creating hmmer/libdivsufsort/divsufsort.h INFERNAL configuration: compiler: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread host: amd64-portbld-freebsd13.5 linker: libraries: -lpthread DP implementation: sse (No python3 found, so 'make check' is disabled.) Now do 'make' to build INFERNAL, and optionally: 'make install' to install programs and man pages. '(cd hmmer; make install)' to install HMMER tools. '(cd easel; make install)' to install Easel tools. =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for infernal-1.1.5 /usr/local/bin/gmake -C easel all gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/easel' cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c easel.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_alloc.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_alphabet.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_arr2.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_arr3.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_bitfield.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_buffer.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_cluster.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_composition.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_cpu.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_dirichlet.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_distance.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_dmatrix.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_dsqdata.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_exponential.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_fileparser.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_gamma.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_gencode.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_getopts.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_gev.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_graph.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_gumbel.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_heap.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_histogram.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_hmm.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_huffman.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_hyperexp.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_iset.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_json.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_keyhash.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_lognormal.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_matrixops.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_mem.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_minimizer.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_mixdchlet.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_mixgev.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_mpi.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_msa.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_msacluster.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_msafile.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_msafile2.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_msafile_a2m.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_msafile_afa.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_msafile_clustal.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_msafile_phylip.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_msafile_psiblast.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_msafile_selex.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_msafile_stockholm.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_msashuffle.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_msaweight.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_normal.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_paml.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_quicksort.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_random.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_rand64.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_randomseq.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_ratematrix.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_recorder.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_red_black.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_regexp.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_rootfinder.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_scorematrix.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_sq.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_sqio.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_sqio_ascii.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_sqio_ncbi.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_ssi.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_stack.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_stats.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_stopwatch.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_stretchexp.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_subcmd.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_threads.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_tree.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_varint.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_vectorops.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_weibull.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_workqueue.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_wuss.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_sse.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_avx.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_avx512.c cc -I. -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -c esl_neon.c cc -I. -I. -O2 -pipe -fstack-protector-strong -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_iset.o esl_json.o esl_keyhash.o esl_lognormal.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 /usr/local/bin/gmake -C miniapps all gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/easel/miniapps' cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-afetch esl-afetch.c -leasel -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-alimanip esl-alimanip.c -leasel -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-alimap esl-alimap.c -leasel -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-alimask esl-alimask.c -leasel -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-alimerge esl-alimerge.c -leasel -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-alipid esl-alipid.c -leasel -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-alirev esl-alirev.c -leasel -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-alistat esl-alistat.c -leasel -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-compalign esl-compalign.c -leasel -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-compstruct esl-compstruct.c -leasel -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-construct esl-construct.c -leasel -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-histplot esl-histplot.c -leasel -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-mask esl-mask.c -leasel -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-mixdchlet esl-mixdchlet.c -leasel -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-reformat esl-reformat.c -leasel -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-selectn esl-selectn.c -leasel -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-seqrange esl-seqrange.c -leasel -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-seqstat esl-seqstat.c -leasel -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-sfetch esl-sfetch.c -leasel -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-shuffle esl-shuffle.c -leasel -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-ssdraw esl-ssdraw.c -leasel -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-translate esl-translate.c -leasel -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L.. -I. -I.. -I. -I./.. -o esl-weight esl-weight.c -leasel -lpthread -lm cc -I. -I.. -I. -I./.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -c cmd_alistat.c cc -I. -I.. -I. -I./.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -c cmd_downsample.c cc -I. -I.. -I. -I./.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -c cmd_filter.c cc -I. -I.. -I. -I./.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -c cmd_index.c cc -O2 -pipe -fstack-protector-strong -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 cmd_index.o -leasel -lpthread -lm gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/easel/miniapps' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/easel' /usr/local/bin/gmake -C hmmer/libdivsufsort all gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/hmmer/libdivsufsort' cc -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -o divsufsort.o -c divsufsort.c /usr/bin/ar rc libdivsufsort.a divsufsort.o gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/hmmer/libdivsufsort' /usr/local/bin/gmake -C hmmer all gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/hmmer' /usr/local/bin/gmake -C ../easel all gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/easel' /usr/local/bin/gmake -C miniapps all gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/easel/miniapps' gmake[3]: Nothing to be done for 'all'. gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/easel/miniapps' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/easel' /usr/local/bin/gmake -C libdivsufsort all gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/hmmer/libdivsufsort' gmake[2]: Nothing to be done for 'all'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/hmmer/libdivsufsort' /usr/local/bin/gmake -C src all gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/hmmer/src' cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o alimask.o -c alimask.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o build.o -c build.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o cachedb.o -c cachedb.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o cachedb_shard.o -c cachedb_shard.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o emit.o -c emit.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o errors.o -c errors.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o evalues.o -c evalues.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o eweight.o -c eweight.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o generic_decoding.o -c generic_decoding.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o generic_fwdback.o -c generic_fwdback.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o generic_fwdback_chk.o -c generic_fwdback_chk.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o generic_fwdback_banded.o -c generic_fwdback_banded.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o generic_null2.o -c generic_null2.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o generic_msv.o -c generic_msv.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o generic_optacc.o -c generic_optacc.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o generic_stotrace.o -c generic_stotrace.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o generic_viterbi.o -c generic_viterbi.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o generic_vtrace.o -c generic_vtrace.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o h2_io.o -c h2_io.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o heatmap.o -c heatmap.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o hmmlogo.o -c hmmlogo.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o hmmdmstr.o -c hmmdmstr.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o hmmdmstr_shard.o -c hmmdmstr_shard.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o hmmd_search_status.o -c hmmd_search_status.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o hmmdwrkr.o -c hmmdwrkr.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o hmmdwrkr_shard.o -c hmmdwrkr_shard.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o hmmdutils.o -c hmmdutils.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o hmmer.o -c hmmer.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o logsum.o -c logsum.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o modelconfig.o -c modelconfig.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o modelstats.o -c modelstats.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o mpisupport.o -c mpisupport.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o seqmodel.o -c seqmodel.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o tracealign.o -c tracealign.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o p7_alidisplay.o -c p7_alidisplay.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o p7_bg.o -c p7_bg.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o p7_builder.o -c p7_builder.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o p7_domain.o -c p7_domain.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o p7_domaindef.o -c p7_domaindef.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o p7_gbands.o -c p7_gbands.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o p7_gmx.o -c p7_gmx.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o p7_gmxb.o -c p7_gmxb.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o p7_gmxchk.o -c p7_gmxchk.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o p7_hit.o -c p7_hit.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o p7_hmm.o -c p7_hmm.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o p7_hmmcache.o -c p7_hmmcache.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o p7_hmmd_search_stats.o -c p7_hmmd_search_stats.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o p7_hmmfile.o -c p7_hmmfile.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o p7_hmmwindow.o -c p7_hmmwindow.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o p7_pipeline.o -c p7_pipeline.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o p7_prior.o -c p7_prior.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o p7_profile.o -c p7_profile.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o p7_spensemble.o -c p7_spensemble.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o p7_tophits.o -c p7_tophits.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o p7_trace.o -c p7_trace.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o p7_scoredata.o -c p7_scoredata.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o hmmpgmd2msa.o -c hmmpgmd2msa.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o fm_alphabet.o -c fm_alphabet.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o fm_general.o -c fm_general.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o fm_sse.o -c fm_sse.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o fm_ssv.o -c fm_ssv.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o hmmalign.o -c hmmalign.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o hmmbuild.o -c hmmbuild.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o hmmconvert.o -c hmmconvert.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o hmmemit.o -c hmmemit.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o hmmfetch.o -c hmmfetch.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o hmmpgmd.o -c hmmpgmd.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o hmmpgmd_shard.o -c hmmpgmd_shard.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o hmmpress.o -c hmmpress.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o hmmscan.o -c hmmscan.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o hmmsearch.o -c hmmsearch.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o hmmsim.o -c hmmsim.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o hmmstat.o -c hmmstat.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o jackhmmer.o -c jackhmmer.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o phmmer.o -c phmmer.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o nhmmer.o -c nhmmer.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o nhmmscan.o -c nhmmscan.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o makehmmerdb.o -c makehmmerdb.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -o hmmc2.o -c hmmc2.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I. -I../libdivsufsort -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 /usr/local/bin/gmake -C impl_sse libhmmer-impl.stamp gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/hmmer/src/impl_sse' cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../../easel -I../../../easel -I. -I.. -I. -I../../../src -I./.. -o decoding.o -c decoding.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../../easel -I../../../easel -I. -I.. -I. -I../../../src -I./.. -o fwdback.o -c fwdback.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../../easel -I../../../easel -I. -I.. -I. -I../../../src -I./.. -o io.o -c io.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../../easel -I../../../easel -I. -I.. -I. -I../../../src -I./.. -o ssvfilter.o -c ssvfilter.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../../easel -I../../../easel -I. -I.. -I. -I../../../src -I./.. -o msvfilter.o -c msvfilter.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../../easel -I../../../easel -I. -I.. -I. -I../../../src -I./.. -o null2.o -c null2.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../../easel -I../../../easel -I. -I.. -I. -I../../../src -I./.. -o optacc.o -c optacc.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../../easel -I../../../easel -I. -I.. -I. -I../../../src -I./.. -o stotrace.o -c stotrace.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../../easel -I../../../easel -I. -I.. -I. -I../../../src -I./.. -o vitfilter.o -c vitfilter.c cc -O2 -pipe -fstack-protector-strong -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 -O2 -pipe -fstack-protector-strong -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 -O2 -pipe -fstack-protector-strong -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 '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/hmmer/src/impl_sse' cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L./impl_sse -L../libdivsufsort -L. -o alimask alimask.o -lhmmer -leasel -ldivsufsort -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmalign hmmalign.o -lhmmer -leasel -ldivsufsort -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmbuild hmmbuild.o -lhmmer -leasel -ldivsufsort -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmconvert hmmconvert.o -lhmmer -leasel -ldivsufsort -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmemit hmmemit.o -lhmmer -leasel -ldivsufsort -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmfetch hmmfetch.o -lhmmer -leasel -ldivsufsort -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmlogo hmmlogo.o -lhmmer -leasel -ldivsufsort -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmpgmd hmmpgmd.o -lhmmer -leasel -ldivsufsort -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmpgmd_shard hmmpgmd_shard.o -lhmmer -leasel -ldivsufsort -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmpress hmmpress.o -lhmmer -leasel -ldivsufsort -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmscan hmmscan.o -lhmmer -leasel -ldivsufsort -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmsearch hmmsearch.o -lhmmer -leasel -ldivsufsort -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmsim hmmsim.o -lhmmer -leasel -ldivsufsort -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmstat hmmstat.o -lhmmer -leasel -ldivsufsort -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L./impl_sse -L../libdivsufsort -L. -o jackhmmer jackhmmer.o -lhmmer -leasel -ldivsufsort -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L./impl_sse -L../libdivsufsort -L. -o phmmer phmmer.o -lhmmer -leasel -ldivsufsort -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L./impl_sse -L../libdivsufsort -L. -o nhmmer nhmmer.o -lhmmer -leasel -ldivsufsort -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L./impl_sse -L../libdivsufsort -L. -o nhmmscan nhmmscan.o -lhmmer -leasel -ldivsufsort -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L./impl_sse -L../libdivsufsort -L. -o makehmmerdb makehmmerdb.o -lhmmer -leasel -ldivsufsort -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmc2 hmmc2.o -lhmmer -leasel -ldivsufsort -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmerfm-exactmatch hmmerfm-exactmatch.o -lhmmer -leasel -ldivsufsort -lpthread -lm gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/hmmer/src' /usr/local/bin/gmake -C profmark all gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/hmmer/profmark' cc -I../../easel -I../../easel -I../src -I../../src -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -o create-profmark.o -c create-profmark.c cc -I../../easel -I../../easel -I../src -I../../src -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -o rocplot.o -c rocplot.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L../src -o rocplot rocplot.o -lhmmer -leasel -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L../src -o create-profmark create-profmark.o -lhmmer -leasel -lpthread -lm gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/hmmer/profmark' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/hmmer' /usr/local/bin/gmake -C src all gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/src' cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cmalign.o -c cmalign.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cm.o -c cm.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cm_alidisplay.o -c cm_alidisplay.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cm_alndata.o -c cm_alndata.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cm_dpalign.o -c cm_dpalign.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cm_dpalign_trunc.o -c cm_dpalign_trunc.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cm_dpsearch.o -c cm_dpsearch.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cm_dpsearch_trunc.o -c cm_dpsearch_trunc.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cm_dpsmall.o -c cm_dpsmall.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cm_file.o -c cm_file.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cm_modelconfig.o -c cm_modelconfig.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cm_modelmaker.o -c cm_modelmaker.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cm_mx.o -c cm_mx.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cm_parsetree.o -c cm_parsetree.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cm_pipeline.o -c cm_pipeline.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cm_qdband.o -c cm_qdband.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cm_submodel.o -c cm_submodel.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cm_tophits.o -c cm_tophits.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cm_trunc.o -c cm_trunc.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cm_p7_band.o -c cm_p7_band.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cm_p7_domaindef.o -c cm_p7_domaindef.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cm_p7_modelconfig_trunc.o -c cm_p7_modelconfig_trunc.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cm_p7_modelmaker.o -c cm_p7_modelmaker.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cp9.o -c cp9.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cp9_dp.o -c cp9_dp.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cp9_modelmaker.o -c cp9_modelmaker.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cp9_mx.o -c cp9_mx.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cp9_trace.o -c cp9_trace.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o alphabet.o -c alphabet.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o display.o -c display.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o errors.o -c errors.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o eweight.o -c eweight.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o hmmband.o -c hmmband.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o logsum.o -c logsum.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o mpisupport.o -c mpisupport.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o prior.o -c prior.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o rnamat.o -c rnamat.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o stats.o -c stats.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o truncyk.o -c truncyk.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cmbuild.o -c cmbuild.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cmcalibrate.o -c cmcalibrate.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cmconvert.o -c cmconvert.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cmemit.o -c cmemit.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cmfetch.o -c cmfetch.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cmpress.o -c cmpress.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cmscan.o -c cmscan.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cmsearch.o -c cmsearch.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cmstat.o -c cmstat.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o trcyk.o -c trcyk.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o bandcyk-montecarlo-test.o -c bandcyk-montecarlo-test.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o bandcyk-truncation-test.o -c bandcyk-truncation-test.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o cp9-test.o -c cp9-test.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o sub_cm-test.o -c sub_cm-test.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../easel -I../hmmer/src -I../easel -I../hmmer/src -I. -I. -o truncyk_check.o -c truncyk_check.c /usr/bin/ar -r libinfernal.a cm.o cm_alidisplay.o cm_alndata.o cm_dpalign.o cm_dpalign_trunc.o cm_dpsearch.o cm_dpsearch_trunc.o cm_dpsmall.o cm_file.o cm_modelconfig.o cm_modelmaker.o cm_mx.o cm_parsetree.o cm_pipeline.o cm_qdband.o cm_submodel.o cm_tophits.o cm_trunc.o cm_p7_band.o cm_p7_domaindef.o cm_p7_modelconfig_trunc.o cm_p7_modelmaker.o cp9.o cp9_dp.o cp9_modelmaker.o cp9_mx.o cp9_trace.o alphabet.o display.o errors.o eweight.o hmmband.o logsum.o mpisupport.o prior.o rnamat.o stats.o truncyk.o > /dev/null 2>&1 /usr/local/bin/gmake -C impl_sse libinfernal-impl.stamp gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/src/impl_sse' cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I../../hmmer/src -I../../hmmer/src -I. -I.. -I. -I../../src -o cm_optimized.o -c cm_optimized.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I../../hmmer/src -I../../hmmer/src -I. -I.. -I. -I../../src -o sse_cm_dpsearch.o -c sse_cm_dpsearch.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I../../hmmer/src -I../../hmmer/src -I. -I.. -I. -I../../src -o sse_cm_dpsmall.o -c sse_cm_dpsmall.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I../../hmmer/src -I../../hmmer/src -I. -I.. -I. -I../../src -o sse_cmcons_hitmx.o -c sse_cmcons_hitmx.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I../../hmmer/src -I../../hmmer/src -I. -I.. -I. -I../../src -o sse_cmcons_mscyk.o -c sse_cmcons_mscyk.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I../../hmmer/src -I../../hmmer/src -I. -I.. -I. -I../../src -o sse_util.o -c sse_util.c /usr/bin/ar -r ../libinfernal.a cm_optimized.o sse_cm_dpsearch.o sse_cm_dpsmall.o sse_cmcons_hitmx.o sse_cmcons_mscyk.o sse_util.o > /dev/null 2>&1 gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/src/impl_sse' cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L../hmmer/src -L./impl_sse -L. -o cmalign cmalign.o -linfernal -lhmmer -leasel -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L../hmmer/src -L./impl_sse -L. -o cmbuild cmbuild.o -linfernal -lhmmer -leasel -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L../hmmer/src -L./impl_sse -L. -o cmcalibrate cmcalibrate.o -linfernal -lhmmer -leasel -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L../hmmer/src -L./impl_sse -L. -o cmconvert cmconvert.o -linfernal -lhmmer -leasel -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L../hmmer/src -L./impl_sse -L. -o cmemit cmemit.o -linfernal -lhmmer -leasel -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L../hmmer/src -L./impl_sse -L. -o cmfetch cmfetch.o -linfernal -lhmmer -leasel -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L../hmmer/src -L./impl_sse -L. -o cmpress cmpress.o -linfernal -lhmmer -leasel -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L../hmmer/src -L./impl_sse -L. -o cmscan cmscan.o -linfernal -lhmmer -leasel -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L../hmmer/src -L./impl_sse -L. -o cmsearch cmsearch.o -linfernal -lhmmer -leasel -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L../hmmer/src -L./impl_sse -L. -o cmstat cmstat.o -linfernal -lhmmer -leasel -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L../hmmer/src -L./impl_sse -L. -o trcyk trcyk.o -linfernal -lhmmer -leasel -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L../hmmer/src -L./impl_sse -L. -o bandcyk-montecarlo-test bandcyk-montecarlo-test.o -linfernal -lhmmer -leasel -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L../hmmer/src -L./impl_sse -L. -o bandcyk-truncation-test bandcyk-truncation-test.o -linfernal -lhmmer -leasel -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L../hmmer/src -L./impl_sse -L. -o cp9-test cp9-test.o -linfernal -lhmmer -leasel -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L../hmmer/src -L./impl_sse -L. -o sub_cm-test sub_cm-test.o -linfernal -lhmmer -leasel -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../easel -L../hmmer/src -L./impl_sse -L. -o truncyk_check truncyk_check.o -linfernal -lhmmer -leasel -lpthread -lm gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/src' /usr/local/bin/gmake -C rmark all gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/rmark' cc -I../easel -I../easel -I../src -I../src -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -o rmark-create.o -c rmark-create.c cc -I../easel -I../easel -I../src -I../src -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -o rmark-rocplot.o -c rmark-rocplot.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -pthread -DHAVE_CONFIG_H -L../hmmer/src -L../easel -L../src -o rmark-rocplot rmark-rocplot.o -lhmmer -leasel -lpthread -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -pthread -DHAVE_CONFIG_H -L../hmmer/src -L../easel -L../src -o rmark-create rmark-create.o -lhmmer -leasel -lpthread -lm gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/rmark' /usr/local/bin/gmake -C src/impl_sse all gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/src/impl_sse' cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../../easel -I../../hmmer/src -I../../hmmer/src -I. -I.. -I. -I../../src -o sse_cmsearch.o -c sse_cmsearch.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -L../../easel -L../../hmmer/src -L.. -I../../easel -I../../easel -I../../hmmer/src -I../../hmmer/src -I. -I.. -I. -I../../src -o sse_cmsearch sse_cmsearch.o -linfernal -lhmmer -leasel -lm gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/src/impl_sse' =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for infernal-1.1.5 ===> Generating temporary packing list /usr/bin/install -c -d /wrkdirs/usr/ports/biology/infernal/work/stage/usr/local/bin /usr/bin/install -c -d /wrkdirs/usr/ports/biology/infernal/work/stage/usr/local/share/man/man1 /usr/bin/install -c -d /wrkdirs/usr/ports/biology/infernal/work/stage/usr/local/share/doc/infernal /usr/local/bin/gmake -C src install gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/src' for file in cmalign cmbuild cmcalibrate cmconvert cmemit cmfetch cmpress cmscan cmsearch cmstat; do \ /usr/bin/install -c -m 0755 $file /wrkdirs/usr/ports/biology/infernal/work/stage/usr/local/bin/ ;\ done gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/src' /usr/local/bin/gmake -C documentation install gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/documentation' /usr/local/bin/gmake -C man install gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/documentation/man' for file in infernal cmalign cmbuild cmcalibrate cmconvert cmemit cmfetch cmpress cmsearch cmscan cmstat; do \ /usr/bin/install -c -m 0664 $file.man /wrkdirs/usr/ports/biology/infernal/work/stage/usr/local/share/man/man1/${file}.1 ;\ done gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/documentation/man' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/documentation' install -m 0644 /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/Userguide.pdf /wrkdirs/usr/ports/biology/infernal/work/stage/usr/local/share/doc/infernal install -m 0644 /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/tutorial/5S_rRNA.c.cm /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/tutorial/5S_rRNA.sto /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/tutorial/Cobalamin.c.cm /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/tutorial/Cobalamin.fa /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/tutorial/Cobalamin.sto /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/tutorial/Rfam.14.9.clanin /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/tutorial/metag-example.fa /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/tutorial/minifam-metag.out /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/tutorial/minifam.cm /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/tutorial/minifam.cm.i1f /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/tutorial/minifam.cm.i1i /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/tutorial/minifam.cm.i1m /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/tutorial/minifam.cm.i1p /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/tutorial/mrum-genome.fa /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/tutorial/mrum-tRNAs10.fa /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/tutorial/mrum-tRNAs10.out /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/tutorial/tRNA5-hand.c.cm /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/tutorial/tRNA5-hand.frag.sto /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/tutorial/tRNA5-hand.fraggiven.sto /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/tutorial/tRNA5-hand.sto /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/tutorial/tRNA5-mrum.out /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/tutorial/tRNA5-noss.sto /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/tutorial/tRNA5.c.cm /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.5/tutorial/tRNA5.sto /wrkdirs/usr/ports/biology/infernal/work/stage/usr/local/share/examples/infernal ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2025-12-10T19:35:45+0000' 'PKG_NOTE_ports_top_git_hash=62d8b1999233' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=8e8bb4267860' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for infernal-1.1.5 ===> Building infernal-1.1.5 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for infernal-1.1.5 build of biology/infernal | infernal-1.1.5 ended at Wed Dec 10 14:36:29 EST 2025 build time: 00:00:45