=>> Building biology/infernal build started at Sun Mar 31 02:03:42 BST 2024 port directory: /usr/ports/biology/infernal package name: infernal-1.1.4_1 building for: FreeBSD pkg-builder.dan.net.uk 13.2-RELEASE-p10 FreeBSD 13.2-RELEASE-p10 amd64 maintained by: mzaki@e-mail.ne.jp Makefile datestamp: -rw-r--r-- 1 root wheel 1701 Feb 25 10:26 /usr/ports/biology/infernal/Makefile Ports top last git commit: c2c35d895e Ports top unclean checkout: yes Port dir last git commit: 806984bb1b Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.99.20240122_1 Host OSVERSION: 1400097 Jail OSVERSION: 1302001 Job Id: 16 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1302001 UNAME_v=FreeBSD 13.2-RELEASE-p10 UNAME_r=13.2-RELEASE-p10 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=3.4.99.20240122_1 MASTERMNT=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/16/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=13-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.99.20240122_1 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-1.1.4_1: 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=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/python3.9" 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=/ccache/libexec/ccache:/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 CCACHE_DIR="/root/.ccache" 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=/ccache/libexec/ccache:/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=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CCACHE_DIR="/root/.ccache" 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/python3.9 PYTHON_LIBDIR=lib/python3.9 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" OSREL=13.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.36.3 PERL_VER=5.36 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/5.36 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/python3.9 PYTHON_LIBDIR=/usr/local/lib/python3.9 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=/usr/local/lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 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--- 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 #### #### CCACHE_CPP2=1 WITH_SSP_PORTS=yes WITH_SSP=yes #WITH_LTO=yes DISABLE_LICENSES=yes LICENSES_ACCEPTED=AGPLv3 APACHE10 APACHE11 APACHE20 ART10 ARTPERL10 ART20 BSD BSD2CLAUSE BSD3CLAUSE BSD4CLAUSE BSL CC0-1.0 CDDL ClArtistic EPL GFDL GMGPL GPLv1 GPLv2 GPLv3 GPLv3RLE ISCL LGPL20 LGPL21 LGPL3 LPPL10 LPPL11 LPPL12 LPPL13 LPPL13a LPPL13b LPPL13c MIT MPL OpenSSL OFL10 OFL11 OWL PostgreSQL PHP202 PHP30 PHP301 PSFL RUBY ZLIB ZPL21 SVM-Light EULA ALASIR Microsoft-exFAT SIMIAN UDEVGAME unknown MTA COMMERCIAL teamspeak NO_LICENSES_DIALOGS=yes #### #### NO_IGNORE=yes DEFAULT_VERSIONS+=ssl=openssl mysql=8.0 imagemagick=7 samba=4.13 java=18 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache NO_CCACHE_DEPEND=1 CCACHE_WRAPPER_PATH= /ccache/libexec/ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---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-1.1.4_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.9_1.pkg [pkg-builder.dan.net.uk] Installing pkg-1.20.9_1... [pkg-builder.dan.net.uk] Extracting pkg-1.20.9_1: .......... done ===> infernal-1.1.4_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of infernal-1.1.4_1 =========================================================================== =================================================== ===== 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-1.1.4_1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by infernal-1.1.4_1 for building => SHA256 Checksum OK for infernal-1.1.4.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-1.1.4_1 for building ===> Extracting for infernal-1.1.4_1 => SHA256 Checksum OK for infernal-1.1.4.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-1.1.4_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> infernal-1.1.4_1 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [pkg-builder.dan.net.uk] Installing gmake-4.4.1... [pkg-builder.dan.net.uk] `-- Installing gettext-runtime-0.22.3_1... [pkg-builder.dan.net.uk] | `-- Installing indexinfo-0.3.1... [pkg-builder.dan.net.uk] | `-- Extracting indexinfo-0.3.1: . done [pkg-builder.dan.net.uk] `-- Extracting gettext-runtime-0.22.3_1: .......... done [pkg-builder.dan.net.uk] Extracting gmake-4.4.1: .......... done ===> infernal-1.1.4_1 depends on package: gmake>=4.4.1 - found ===> Returning to build of infernal-1.1.4_1 =========================================================================== =================================================== ===== 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-1.1.4_1 configure: loading site script /usr/ports/Templates/config.site configure: Configuring Infernal for your system. checking build system type... amd64-portbld-freebsd13.2 checking host system type... amd64-portbld-freebsd13.2 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 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... 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 Altivec/VMX code... no checking whether cc can compile our SSE code... yes configure: Activating Intel/AMD SSE vector DP implementation checking whether _MM_SET_FLUSH_ZERO_MODE is supported... yes checking compiler support --start-group... yes checking for gzip... /usr/bin/gzip checking for python3... no checking for library containing clock_gettime... none required checking for ANSI C header files... (cached) yes checking for sys/types.h... (cached) yes checking for sys/stat.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for memory.h... (cached) yes checking for strings.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.h... (cached) yes checking endian.h usability... yes checking endian.h presence... yes checking for endian.h... yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/types.h... (cached) yes checking for netinet/in.h... (cached) yes checking for sys/param.h... (cached) yes checking for sys/sysctl.h... (cached) yes checking for uint8_t... (cached) yes checking for uint16_t... (cached) yes checking for uint32_t... (cached) yes checking for uint64_t... (cached) yes checking for off_t... (cached) yes checking whether byte ordering is bigendian... no checking for __attribute__((noreturn))... yes checking for __attribute__((format))... yes checking for mkstemp... (cached) yes checking for popen... yes checking for putenv... (cached) yes checking for strcasecmp... (cached) yes checking for strsep... (cached) yes checking for times... (cached) yes checking for getpid... (cached) yes checking for sysctl... (cached) yes checking for sysconf... (cached) yes checking for getcwd... (cached) yes checking for chmod... yes checking for stat... (cached) yes checking for fstat... (cached) yes checking for erfc... no checking for ntohs... yes checking for ntohl... yes checking for htons... yes checking for htonl... yes checking for library containing socket... none required checking for library containing inet_pton... none required checking for _LARGEFILE_SOURCE value needed for large files... no checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating testsuite/Makefile config.status: creating rmark/Makefile config.status: creating documentation/Makefile config.status: creating documentation/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 linker: -fstack-protector-strong libraries: DP implementation: sse python3: (No python3 found, so 'make check' self tests are disabled.) Now do 'make' to build INFERNAL, and optionally: 'make install' to install programs and man pages. =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for infernal-1.1.4_1 gmake -C easel all gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/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_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_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_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[2]: Entering directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/easel/miniapps' cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L.. -I. -I.. -I. -I./.. -o esl-afetch esl-afetch.c -leasel -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L.. -I. -I.. -I. -I./.. -o esl-alimanip esl-alimanip.c -leasel -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L.. -I. -I.. -I. -I./.. -o esl-alimap esl-alimap.c -leasel -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L.. -I. -I.. -I. -I./.. -o esl-alimask esl-alimask.c -leasel -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L.. -I. -I.. -I. -I./.. -o esl-alimerge esl-alimerge.c -leasel -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L.. -I. -I.. -I. -I./.. -o esl-alipid esl-alipid.c -leasel -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L.. -I. -I.. -I. -I./.. -o esl-alirev esl-alirev.c -leasel -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L.. -I. -I.. -I. -I./.. -o esl-alistat esl-alistat.c -leasel -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L.. -I. -I.. -I. -I./.. -o esl-compalign esl-compalign.c -leasel -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L.. -I. -I.. -I. -I./.. -o esl-compstruct esl-compstruct.c -leasel -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L.. -I. -I.. -I. -I./.. -o esl-construct esl-construct.c -leasel -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L.. -I. -I.. -I. -I./.. -o esl-histplot esl-histplot.c -leasel -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L.. -I. -I.. -I. -I./.. -o esl-mask esl-mask.c -leasel -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L.. -I. -I.. -I. -I./.. -o esl-mixdchlet esl-mixdchlet.c -leasel -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L.. -I. -I.. -I. -I./.. -o esl-reformat esl-reformat.c -leasel -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L.. -I. -I.. -I. -I./.. -o esl-selectn esl-selectn.c -leasel -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L.. -I. -I.. -I. -I./.. -o esl-seqrange esl-seqrange.c -leasel -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L.. -I. -I.. -I. -I./.. -o esl-seqstat esl-seqstat.c -leasel -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L.. -I. -I.. -I. -I./.. -o esl-sfetch esl-sfetch.c -leasel -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L.. -I. -I.. -I. -I./.. -o esl-shuffle esl-shuffle.c -leasel -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L.. -I. -I.. -I. -I./.. -o esl-ssdraw esl-ssdraw.c -leasel -lm esl-ssdraw.c:2323:39: warning: implicit conversion from 'int' to 'float' changes value from 987654321 to 987654336 [-Wimplicit-const-int-float-conversion] if(esl_FCompare(scl->limits[c+1], SSDRAWINFINITY, eslSMALLX1) == eslOK) { /* max value is infinity, special case */ ~~~~~~~~~~~~ ^~~~~~~~~~~~~~ esl-ssdraw.c:34:24: note: expanded from macro 'SSDRAWINFINITY' #define SSDRAWINFINITY 987654321 ^~~~~~~~~ esl-ssdraw.c:3439:17: warning: implicit conversion from 'int' to 'float' changes value from 987654321 to 987654336 [-Wimplicit-const-int-float-conversion] limits_s[5] = SSDRAWINFINITY; ~ ^~~~~~~~~~~~~~ esl-ssdraw.c:34:24: note: expanded from macro 'SSDRAWINFINITY' #define SSDRAWINFINITY 987654321 ^~~~~~~~~ esl-ssdraw.c:4820:15: warning: implicit conversion from 'int' to 'float' changes value from 987654321 to 987654336 [-Wimplicit-const-int-float-conversion] limits[6] = SSDRAWINFINITY; ~ ^~~~~~~~~~~~~~ esl-ssdraw.c:34:24: note: expanded from macro 'SSDRAWINFINITY' #define SSDRAWINFINITY 987654321 ^~~~~~~~~ 3 warnings generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L.. -I. -I.. -I. -I./.. -o esl-translate esl-translate.c -leasel -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L.. -I. -I.. -I. -I./.. -o esl-weight esl-weight.c -leasel -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 -fstack-protector-strong -L.. -I. -I.. -I. -I./.. -o easel easel.c cmd_alistat.o cmd_downsample.o cmd_filter.o cmd_index.o -leasel -lm gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/easel/miniapps' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/easel' gmake -C hmmer/libdivsufsort all gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/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-1.1.4/hmmer/libdivsufsort' gmake -C hmmer all gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/hmmer' gmake -C ../easel all gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/easel' gmake -C miniapps all gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/easel/miniapps' gmake[3]: Nothing to be done for 'all'. gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/easel/miniapps' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/easel' gmake -C libdivsufsort all gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/hmmer/libdivsufsort' gmake[2]: Nothing to be done for 'all'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/hmmer/libdivsufsort' gmake -C src all gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/hmmer/src' cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o alimask.o -c alimask.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o build.o -c build.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o cachedb.o -c cachedb.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o cachedb_shard.o -c cachedb_shard.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o emit.o -c emit.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o errors.o -c errors.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o evalues.o -c evalues.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o eweight.o -c eweight.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o generic_decoding.o -c generic_decoding.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o generic_fwdback.o -c generic_fwdback.c cc -O2 -pipe -fstack-protector-strong -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 -O2 -pipe -fstack-protector-strong -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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o generic_null2.o -c generic_null2.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o generic_msv.o -c generic_msv.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o generic_optacc.o -c generic_optacc.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o generic_stotrace.o -c generic_stotrace.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o generic_viterbi.o -c generic_viterbi.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o generic_vtrace.o -c generic_vtrace.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o h2_io.o -c h2_io.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o heatmap.o -c heatmap.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmlogo.o -c hmmlogo.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmdmstr.o -c hmmdmstr.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmdmstr_shard.o -c hmmdmstr_shard.c cc -O2 -pipe -fstack-protector-strong -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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmdwrkr.o -c hmmdwrkr.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmdwrkr_shard.o -c hmmdwrkr_shard.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmdutils.o -c hmmdutils.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmer.o -c hmmer.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o logsum.o -c logsum.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o modelconfig.o -c modelconfig.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o modelstats.o -c modelstats.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o mpisupport.o -c mpisupport.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o seqmodel.o -c seqmodel.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o tracealign.o -c tracealign.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o p7_alidisplay.o -c p7_alidisplay.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o p7_bg.o -c p7_bg.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o p7_builder.o -c p7_builder.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o p7_domain.o -c p7_domain.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o p7_domaindef.o -c p7_domaindef.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o p7_gbands.o -c p7_gbands.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o p7_gmx.o -c p7_gmx.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o p7_gmxb.o -c p7_gmxb.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o p7_gmxchk.o -c p7_gmxchk.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o p7_hit.o -c p7_hit.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o p7_hmm.o -c p7_hmm.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o p7_hmmcache.o -c p7_hmmcache.c cc -O2 -pipe -fstack-protector-strong -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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o p7_hmmfile.o -c p7_hmmfile.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o p7_hmmwindow.o -c p7_hmmwindow.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o p7_pipeline.o -c p7_pipeline.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o p7_prior.o -c p7_prior.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o p7_profile.o -c p7_profile.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o p7_spensemble.o -c p7_spensemble.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o p7_tophits.o -c p7_tophits.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o p7_trace.o -c p7_trace.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o p7_scoredata.o -c p7_scoredata.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmpgmd2msa.o -c hmmpgmd2msa.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o fm_alphabet.o -c fm_alphabet.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o fm_general.o -c fm_general.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o fm_sse.o -c fm_sse.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o fm_ssv.o -c fm_ssv.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 '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/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-1.1.4/hmmer/src/impl_sse' cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L../../easel -L./impl_sse -L../libdivsufsort -L. -o alimask alimask.o -lhmmer -leasel -ldivsufsort -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmalign.o -c hmmalign.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmalign hmmalign.o -lhmmer -leasel -ldivsufsort -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmbuild.o -c hmmbuild.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmbuild hmmbuild.o -lhmmer -leasel -ldivsufsort -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmconvert.o -c hmmconvert.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmconvert hmmconvert.o -lhmmer -leasel -ldivsufsort -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmemit.o -c hmmemit.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmemit hmmemit.o -lhmmer -leasel -ldivsufsort -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmfetch.o -c hmmfetch.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmfetch hmmfetch.o -lhmmer -leasel -ldivsufsort -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmlogo hmmlogo.o -lhmmer -leasel -ldivsufsort -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmpgmd.o -c hmmpgmd.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmpgmd hmmpgmd.o -lhmmer -leasel -ldivsufsort -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmpgmd_shard.o -c hmmpgmd_shard.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmpgmd_shard hmmpgmd_shard.o -lhmmer -leasel -ldivsufsort -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmpress.o -c hmmpress.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmpress hmmpress.o -lhmmer -leasel -ldivsufsort -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmscan.o -c hmmscan.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmscan hmmscan.o -lhmmer -leasel -ldivsufsort -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmsearch.o -c hmmsearch.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmsearch hmmsearch.o -lhmmer -leasel -ldivsufsort -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmsim.o -c hmmsim.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmsim hmmsim.o -lhmmer -leasel -ldivsufsort -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmstat.o -c hmmstat.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmstat hmmstat.o -lhmmer -leasel -ldivsufsort -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o jackhmmer.o -c jackhmmer.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L../../easel -L./impl_sse -L../libdivsufsort -L. -o jackhmmer jackhmmer.o -lhmmer -leasel -ldivsufsort -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o phmmer.o -c phmmer.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L../../easel -L./impl_sse -L../libdivsufsort -L. -o phmmer phmmer.o -lhmmer -leasel -ldivsufsort -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o nhmmer.o -c nhmmer.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L../../easel -L./impl_sse -L../libdivsufsort -L. -o nhmmer nhmmer.o -lhmmer -leasel -ldivsufsort -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o nhmmscan.o -c nhmmscan.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L../../easel -L./impl_sse -L../libdivsufsort -L. -o nhmmscan nhmmscan.o -lhmmer -leasel -ldivsufsort -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o makehmmerdb.o -c makehmmerdb.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L../../easel -L./impl_sse -L../libdivsufsort -L. -o makehmmerdb makehmmerdb.o -lhmmer -leasel -ldivsufsort -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmc2.o -c hmmc2.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmc2 hmmc2.o -lhmmer -leasel -ldivsufsort -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -I../../easel -I../libdivsufsort -I../../easel -I. -I. -o hmmerfm-exactmatch.o -c hmmerfm-exactmatch.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L../../easel -L./impl_sse -L../libdivsufsort -L. -o hmmerfm-exactmatch hmmerfm-exactmatch.o -lhmmer -leasel -ldivsufsort -lm gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/hmmer/src' gmake -C profmark all gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L../../easel -L../src -o create-profmark create-profmark.o -lhmmer -leasel -lm 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 -fstack-protector-strong -L../../easel -L../src -o rocplot rocplot.o -lhmmer -leasel -lm gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/hmmer/profmark' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/hmmer' gmake -C src all gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/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 cm_p7_band.c:316:30: warning: implicit conversion from 'int' to 'float' changes value from -987654321 to -987654336 [-Wimplicit-const-int-float-conversion] if (P7XMX(i, p7G_N) <= p7_IMPOSSIBLE) ESL_XEXCEPTION(eslFAIL, "impossible N reached at i=%d", i); ~~ ^~~~~~~~~~~~~ cm_p7_band.c:23:24: note: expanded from macro 'p7_IMPOSSIBLE' #define p7_IMPOSSIBLE -987654321 ^~~~~~~~~~ 1 warning generated. 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 cp9.c:151:33: warning: implicit conversion from 'int' to 'float' changes value from -987654321 to -987654336 [-Wimplicit-const-int-float-conversion] hmm->end[0] = hmm->begin[0] = -INFTY; ~ ^~~~~~ 1 warning generated. 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 /usr/bin/ar -r libinfernal.a cm.o cm_alidisplay.o cm_alndata.o cm_dpalign.o cm_dpalign_trunc.o cm_dpsearch.o cm_dpsearch_trunc.o cm_dpsmall.o cm_file.o cm_modelconfig.o cm_modelmaker.o cm_mx.o cm_parsetree.o cm_pipeline.o cm_qdband.o cm_submodel.o cm_tophits.o cm_trunc.o cm_p7_band.o cm_p7_domaindef.o cm_p7_modelconfig_trunc.o cm_p7_modelmaker.o cp9.o cp9_dp.o cp9_modelmaker.o cp9_mx.o cp9_trace.o alphabet.o display.o errors.o eweight.o hmmband.o logsum.o mpisupport.o prior.o rnamat.o stats.o truncyk.o > /dev/null 2>&1 gmake -C impl_sse libinfernal-impl.stamp gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/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-1.1.4/src/impl_sse' cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L../easel -L../hmmer/src -L./impl_sse -L. -o cmalign cmalign.o -linfernal -lhmmer -leasel -lm 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 -fstack-protector-strong -L../easel -L../hmmer/src -L./impl_sse -L. -o cmbuild cmbuild.o -linfernal -lhmmer -leasel -lm 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 -fstack-protector-strong -L../easel -L../hmmer/src -L./impl_sse -L. -o cmcalibrate cmcalibrate.o -linfernal -lhmmer -leasel -lm 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 -fstack-protector-strong -L../easel -L../hmmer/src -L./impl_sse -L. -o cmconvert cmconvert.o -linfernal -lhmmer -leasel -lm 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 -fstack-protector-strong -L../easel -L../hmmer/src -L./impl_sse -L. -o cmemit cmemit.o -linfernal -lhmmer -leasel -lm 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 -fstack-protector-strong -L../easel -L../hmmer/src -L./impl_sse -L. -o cmfetch cmfetch.o -linfernal -lhmmer -leasel -lm 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 -fstack-protector-strong -L../easel -L../hmmer/src -L./impl_sse -L. -o cmpress cmpress.o -linfernal -lhmmer -leasel -lm 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 -fstack-protector-strong -L../easel -L../hmmer/src -L./impl_sse -L. -o cmscan cmscan.o -linfernal -lhmmer -leasel -lm 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 -fstack-protector-strong -L../easel -L../hmmer/src -L./impl_sse -L. -o cmsearch cmsearch.o -linfernal -lhmmer -leasel -lm 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 -fstack-protector-strong -L../easel -L../hmmer/src -L./impl_sse -L. -o cmstat cmstat.o -linfernal -lhmmer -leasel -lm 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 -fstack-protector-strong -L../easel -L../hmmer/src -L./impl_sse -L. -o trcyk trcyk.o -linfernal -lhmmer -leasel -lm 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 -fstack-protector-strong -L../easel -L../hmmer/src -L./impl_sse -L. -o bandcyk-montecarlo-test bandcyk-montecarlo-test.o -linfernal -lhmmer -leasel -lm 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 -fstack-protector-strong -L../easel -L../hmmer/src -L./impl_sse -L. -o bandcyk-truncation-test bandcyk-truncation-test.o -linfernal -lhmmer -leasel -lm 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 -fstack-protector-strong -L../easel -L../hmmer/src -L./impl_sse -L. -o cp9-test cp9-test.o -linfernal -lhmmer -leasel -lm 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 -fstack-protector-strong -L../easel -L../hmmer/src -L./impl_sse -L. -o sub_cm-test sub_cm-test.o -linfernal -lhmmer -leasel -lm 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 cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L../easel -L../hmmer/src -L./impl_sse -L. -o truncyk_check truncyk_check.o -linfernal -lhmmer -leasel -lm gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/src' gmake -C rmark all gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -pthread -DHAVE_CONFIG_H -fstack-protector-strong -L../hmmer/src -L../easel -L../src -o rmark-create rmark-create.o -lhmmer -leasel -lm 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 -fstack-protector-strong -L../hmmer/src -L../easel -L../src -o rmark-rocplot rmark-rocplot.o -lhmmer -leasel -lm gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/rmark' gmake -C src/impl_sse all gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/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 -fstack-protector-strong -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-1.1.4/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-1.1.4_1 ===> 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 gmake -C src install gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/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-1.1.4/src' gmake -C documentation install gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/documentation' gmake -C man install gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/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-1.1.4/documentation/man' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/documentation' install -m 0644 /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/Userguide.pdf /wrkdirs/usr/ports/biology/infernal/work/stage/usr/local/share/doc/infernal install -m 0644 /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/tutorial/5S_rRNA.c.cm /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/tutorial/5S_rRNA.sto /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/tutorial/Cobalamin.c.cm /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/tutorial/Cobalamin.fa /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/tutorial/Cobalamin.sto /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/tutorial/metag-example.fa /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/tutorial/minifam-metag.out /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/tutorial/minifam.cm /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/tutorial/minifam.cm.i1f /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/tutorial/minifam.cm.i1i /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/tutorial/minifam.cm.i1m /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/tutorial/minifam.cm.i1p /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/tutorial/mrum-genome.fa /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/tutorial/mrum-tRNAs10.fa /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/tutorial/mrum-tRNAs10.out /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/tutorial/tRNA5-hand.c.cm /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/tutorial/tRNA5-hand.sto /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/tutorial/tRNA5-mrum.out /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/tutorial/tRNA5-noss.sto /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/tutorial/tRNA5.c.cm /wrkdirs/usr/ports/biology/infernal/work/infernal-1.1.4/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=2024-03-31T01:03:44+0000' 'PKG_NOTE_ports_top_git_hash=c2c35d895e' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=806984bb1b' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.99.20240122_1' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for infernal-1.1.4_1 ===> Building infernal-1.1.4_1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for infernal-1.1.4_1 build of biology/infernal | infernal-1.1.4_1 ended at Sun Mar 31 02:58:43 BST 2024 build time: 00:56:02