=>> Building biology/barrnap build started at Fri Mar 13 06:00:04 EDT 2026 port directory: /usr/ports/biology/barrnap package name: barrnap-0.9 building for: FreeBSD pkg.DaveG.ca 14.4-RELEASE FreeBSD 14.4-RELEASE 1404000 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 681 Aug 27 2024 /usr/ports/biology/barrnap/Makefile Ports top last git commit: 26b198eb3ee3 Ports top unclean checkout: no Port dir last git commit: 20cc8e440a21 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1404000 Job Id: 10 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1404000 UNAME_v=FreeBSD 14.4-RELEASE 1404000 UNAME_r=14.4-RELEASE 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_14_4_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_14_4_x64-HEAD-ALL/10/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_14_4_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_14_4_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--- ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --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 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/barrnap/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/barrnap/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/barrnap/work/.cache HOME=/wrkdirs/usr/ports/biology/barrnap/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/barrnap/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/barrnap/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/barrnap/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/barrnap/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/barrnap/work/.cache HOME=/wrkdirs/usr/ports/biology/barrnap/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/barrnap/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/barrnap/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-- OSREL=14.4 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/barrnap" EXAMPLESDIR="share/examples/barrnap" DATADIR="share/barrnap" WWWDIR="www/barrnap" ETCDIR="etc/barrnap" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/barrnap DOCSDIR=/usr/local/share/doc/barrnap EXAMPLESDIR=/usr/local/share/examples/barrnap WWWDIR=/usr/local/www/barrnap ETCDIR=/usr/local/etc/barrnap --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 pipebuf (-y) 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 ===> barrnap-0.9 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.6.2.pkg [pkg.DaveG.ca] Installing pkg-2.6.2... [pkg.DaveG.ca] Extracting pkg-2.6.2: .......... done ===> barrnap-0.9 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of barrnap-0.9 =========================================================================== =================================================== ===== 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 barrnap-0.9 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by barrnap-0.9 for building => SHA256 Checksum OK for tseemann-barrnap-0.9_GH0.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 barrnap-0.9 for building ===> Extracting for barrnap-0.9 => SHA256 Checksum OK for tseemann-barrnap-0.9_GH0.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 barrnap-0.9 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> barrnap-0.9 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-0.26... [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-0.26: .......... done [pkg.DaveG.ca] Extracting gmake-4.4.1: .......... done ===> barrnap-0.9 depends on package: gmake>=4.4.1 - found ===> Returning to build of barrnap-0.9 ===> barrnap-0.9 depends on package: perl5>=5.42.r<5.43 - not found ===> Installing existing package /packages/All/perl5-5.42.0_1.pkg [pkg.DaveG.ca] Installing perl5-5.42.0_1... [pkg.DaveG.ca] Extracting perl5-5.42.0_1: .......... done ===> barrnap-0.9 depends on package: perl5>=5.42.r<5.43 - found ===> Returning to build of barrnap-0.9 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for barrnap-0.9 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> barrnap-0.9 depends on executable: bedtools - not found ===> Installing existing package /packages/All/bedtools-2.31.1.pkg [pkg.DaveG.ca] Installing bedtools-2.31.1... [pkg.DaveG.ca] `-- Installing python311-3.11.15... [pkg.DaveG.ca] | `-- Installing libffi-3.5.1... [pkg.DaveG.ca] | `-- Extracting libffi-3.5.1: .......... done [pkg.DaveG.ca] | `-- Installing mpdecimal-4.0.1... [pkg.DaveG.ca] | `-- Extracting mpdecimal-4.0.1: .......... done [pkg.DaveG.ca] | `-- Installing readline-8.3.3... [pkg.DaveG.ca] | `-- Extracting readline-8.3.3: .......... done [pkg.DaveG.ca] `-- Extracting python311-3.11.15: .......... done [pkg.DaveG.ca] Extracting bedtools-2.31.1: .......... done ===== Message from python311-3.11.15: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py311-gdbm databases/py-gdbm@py311 py311-sqlite3 databases/py-sqlite3@py311 py311-tkinter x11-toolkits/py-tkinter@py311 ===> barrnap-0.9 depends on executable: bedtools - found ===> Returning to build of barrnap-0.9 ===> barrnap-0.9 depends on executable: nhmmer - not found ===> Installing existing package /packages/All/hmmer-3.4.pkg [pkg.DaveG.ca] Installing hmmer-3.4... [pkg.DaveG.ca] Extracting hmmer-3.4: .......... done ===== Message from hmmer-3.4: -- HMMER reads three optional environment variables: HMMERDB - directory location of HMM databases (e.g. PFAM) BLASTDB - directory location of FASTA-formatted sequence databases BLASTMAT - directory location of PAM scoring matrices The BLASTDB and BLASTMAT variables are shared with versions of BLAST such as NCBI BLAST 2.0 (contained in the biology/ncbi-toolkit port). If these variables are set, you do not have to specify the full path to your databases on the command line when using HMMER. Please see the documentation for more information. ===> barrnap-0.9 depends on executable: nhmmer - found ===> Returning to build of barrnap-0.9 ===> barrnap-0.9 depends on package: perl5>=5.42.r<5.43 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for barrnap-0.9 ===> Generating temporary packing list install -m 555 /wrkdirs/usr/ports/biology/barrnap/work/barrnap-0.9/bin/barrnap /wrkdirs/usr/ports/biology/barrnap/work/stage/usr/local/bin cd /wrkdirs/usr/ports/biology/barrnap/work/barrnap-0.9 && /bin/sh -c '(/usr/bin/find -Ed $1 $3 | /usr/bin/cpio -dumpl $2 >/dev/null 2>&1) && /usr/bin/find -Ed $1 $3 \( -type d -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 755 "$@"'\'' . {} + -o -type f -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 0644 "$@"'\'' . {} + \)' COPYTREE_SHARE db /wrkdirs/usr/ports/biology/barrnap/work/stage/usr/local/share/barrnap /usr/bin/sed -i.bak -i '' -e 's|^my $DBDIR = .*|my $DBDIR = "/usr/local/share/barrnap/db";|' /wrkdirs/usr/ports/biology/barrnap/work/stage/usr/local/bin/barrnap ====> 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=2026-03-13T10:00:04+0000' 'PKG_NOTE_ports_top_git_hash=26b198eb3ee3' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=20cc8e440a21' '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 barrnap-0.9 ===> Building barrnap-0.9 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for barrnap-0.9 build of biology/barrnap | barrnap-0.9 ended at Fri Mar 13 06:00:21 EDT 2026 build time: 00:00:19