=>> Building biology/biostar-tools build started at Mon Nov 3 19:08:31 EST 2025 port directory: /usr/ports/biology/biostar-tools package name: biostar-tools-2.0_1 building for: FreeBSD pkg.DaveG.ca 14.3-RELEASE-p1 FreeBSD 14.3-RELEASE-p1 1403000 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 2869 Sep 22 04:12 /usr/ports/biology/biostar-tools/Makefile Ports top last git commit: 9bb805acfc67 Ports top unclean checkout: no Port dir last git commit: b304d8ab18ac Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500066 Jail OSVERSION: 1403000 Job Id: 08 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1403000 UNAME_v=FreeBSD 14.3-RELEASE-p1 1403000 UNAME_r=14.3-RELEASE-p1 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_3_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_3_x64-HEAD-ALL/08/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_14_3_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_14_3_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-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PYTHON="/usr/local/bin/python3.11" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/biostar-tools/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/biostar-tools/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/biostar-tools/work/.cache HOME=/wrkdirs/usr/ports/biology/biostar-tools/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/biostar-tools/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/biostar-tools/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-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/biostar-tools/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/biostar-tools/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/biostar-tools/work/.cache HOME=/wrkdirs/usr/ports/biology/biostar-tools/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/biostar-tools/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/biostar-tools/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-- PYTHON_INCLUDEDIR=include/python3.11 PYTHON_LIBDIR=lib/python3.11 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" OSREL=14.3 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/biostar-tools" EXAMPLESDIR="share/examples/biostar-tools" DATADIR="share/biostar-tools" WWWDIR="www/biostar-tools" ETCDIR="etc/biostar-tools" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.11 PYTHON_LIBDIR=/usr/local/lib/python3.11 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=/usr/local/lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/biostar-tools DOCSDIR=/usr/local/share/doc/biostar-tools EXAMPLESDIR=/usr/local/share/examples/biostar-tools WWWDIR=/usr/local/www/biostar-tools ETCDIR=/usr/local/etc/biostar-tools --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 ===> biostar-tools-2.0_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.3.1_1.pkg [pkg.DaveG.ca] Installing pkg-2.3.1_1... [pkg.DaveG.ca] Extracting pkg-2.3.1_1: .......... done ===> biostar-tools-2.0_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of biostar-tools-2.0_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 biostar-tools-2.0_1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by biostar-tools-2.0_1 for building =========================================================================== =================================================== ===== 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 biostar-tools-2.0_1 for building ===> Extracting for biostar-tools-2.0_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for biostar-tools-2.0_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> biostar-tools-2.0_1 depends on file: /usr/local/bin/python3.11 - not found ===> Installing existing package /packages/All/python311-3.11.14.pkg [pkg.DaveG.ca] Installing python311-3.11.14... [pkg.DaveG.ca] `-- Installing gettext-runtime-0.23.1... [pkg.DaveG.ca] | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] `-- Extracting gettext-runtime-0.23.1: .......... done [pkg.DaveG.ca] `-- 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-8.2.13_2... [pkg.DaveG.ca] `-- Extracting readline-8.2.13_2: .......... done [pkg.DaveG.ca] Extracting python311-3.11.14: .......... done ===== Message from python311-3.11.14: -- 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 ===> biostar-tools-2.0_1 depends on file: /usr/local/bin/python3.11 - found ===> Returning to build of biostar-tools-2.0_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 biostar-tools-2.0_1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> biostar-tools-2.0_1 depends on package: wget>0 - not found ===> Installing existing package /packages/All/wget-1.25.0.pkg [pkg.DaveG.ca] Installing wget-1.25.0... 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[pkg.DaveG.ca] `-- Extracting libssh2-1.11.1,3: .......... done [pkg.DaveG.ca] `-- Installing zstd-1.5.7... [pkg.DaveG.ca] | `-- Installing liblz4-1.10.0,1... [pkg.DaveG.ca] | `-- Extracting liblz4-1.10.0,1: .......... done [pkg.DaveG.ca] `-- Extracting zstd-1.5.7: .......... done [pkg.DaveG.ca] Extracting curl-8.16.0: .......... done ===> biostar-tools-2.0_1 depends on package: curl>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: nano>0 - not found ===> Installing existing package /packages/All/nano-8.6.pkg [pkg.DaveG.ca] Installing nano-8.6... [pkg.DaveG.ca] Extracting nano-8.6: .......... done ===> biostar-tools-2.0_1 depends on package: nano>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: parallel>0 - not found ===> Installing existing package /packages/All/parallel-20250922.pkg [pkg.DaveG.ca] Installing parallel-20250922... [pkg.DaveG.ca] `-- Installing perl5-5.42.0_1... [pkg.DaveG.ca] `-- Extracting perl5-5.42.0_1: .......... done [pkg.DaveG.ca] Extracting parallel-20250922: .......... done ===> biostar-tools-2.0_1 depends on package: parallel>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: seqkit>0 - not found ===> Installing existing package /packages/All/seqkit-2.10.0_8.pkg [pkg.DaveG.ca] Installing seqkit-2.10.0_8... [pkg.DaveG.ca] Extracting seqkit-2.10.0_8: . done ===> biostar-tools-2.0_1 depends on package: seqkit>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: csvtk>0 - not found ===> Installing existing package /packages/All/csvtk-0.34.0_4.pkg [pkg.DaveG.ca] Installing csvtk-0.34.0_4... [pkg.DaveG.ca] Extracting csvtk-0.34.0_4: . done ===> biostar-tools-2.0_1 depends on package: csvtk>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: py311-csvkit>0 - not found ===> Installing existing package /packages/All/py311-csvkit-2.1.0_1.pkg [pkg.DaveG.ca] Installing py311-csvkit-2.1.0_1... [pkg.DaveG.ca] `-- Installing py311-agate-1.13.0_1... [pkg.DaveG.ca] | `-- Installing py311-Babel-2.17.0_1... [pkg.DaveG.ca] | `-- Extracting py311-Babel-2.17.0_1: .......... done [pkg.DaveG.ca] | `-- Installing py311-isodate-0.7.2... [pkg.DaveG.ca] | `-- Extracting py311-isodate-0.7.2: .......... done [pkg.DaveG.ca] | `-- Installing py311-leather-0.4.0_1... [pkg.DaveG.ca] | | `-- Installing py311-six-1.17.0... [pkg.DaveG.ca] | | `-- Extracting py311-six-1.17.0: ........ done [pkg.DaveG.ca] | `-- Extracting py311-leather-0.4.0_1: .......... done [pkg.DaveG.ca] | `-- Installing py311-parsedatetime-2.6_1... 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[pkg.DaveG.ca] | `-- Extracting py311-dbfread-2.0.7_1: .......... done [pkg.DaveG.ca] `-- Extracting py311-agate-dbf-0.2.3_1: .......... done [pkg.DaveG.ca] `-- Installing py311-agate-excel-0.4.1_2... [pkg.DaveG.ca] | `-- Installing py311-olefile-0.46_1... [pkg.DaveG.ca] | `-- Extracting py311-olefile-0.46_1: .......... done [pkg.DaveG.ca] | `-- Installing py311-openpyxl-3.1.1_1... [pkg.DaveG.ca] | | `-- Installing py311-et_xmlfile-1.1.0_1... [pkg.DaveG.ca] | | `-- Extracting py311-et_xmlfile-1.1.0_1: .......... done [pkg.DaveG.ca] | `-- Extracting py311-openpyxl-3.1.1_1: .......... done [pkg.DaveG.ca] | `-- Installing py311-xlrd-2.0.2... [pkg.DaveG.ca] | `-- Extracting py311-xlrd-2.0.2: .......... done [pkg.DaveG.ca] `-- Extracting py311-agate-excel-0.4.1_2: .......... done [pkg.DaveG.ca] `-- Installing py311-agate-sql-0.7.2_1... [pkg.DaveG.ca] | `-- Installing py311-sqlalchemy20-2.0.44... [pkg.DaveG.ca] | | `-- Installing py311-greenlet-3.2.4... [pkg.DaveG.ca] | | `-- Extracting py311-greenlet-3.2.4: .......... done [pkg.DaveG.ca] | | `-- Installing py311-sqlite3-3.11.14_10... [pkg.DaveG.ca] | | `-- Installing sqlite3-3.50.2_1,1... [pkg.DaveG.ca] | | | `-- Installing libedit-3.1.20251016,1... [pkg.DaveG.ca] | | | `-- Extracting libedit-3.1.20251016,1: .......... done [pkg.DaveG.ca] | | `-- Extracting sqlite3-3.50.2_1,1: ......... done [pkg.DaveG.ca] | | `-- Extracting py311-sqlite3-3.11.14_10: ...... done [pkg.DaveG.ca] | | `-- Installing py311-typing-extensions-4.15.0... [pkg.DaveG.ca] | | `-- Extracting py311-typing-extensions-4.15.0: ....... done [pkg.DaveG.ca] | `-- Extracting py311-sqlalchemy20-2.0.44: .......... done [pkg.DaveG.ca] `-- Extracting py311-agate-sql-0.7.2_1: .......... done [pkg.DaveG.ca] Extracting py311-csvkit-2.1.0_1: .......... done ===> biostar-tools-2.0_1 depends on package: py311-csvkit>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: miller>0 - not found ===> Installing existing package /packages/All/miller-6.15.0_2.pkg [pkg.DaveG.ca] Installing miller-6.15.0_2... [pkg.DaveG.ca] Extracting miller-6.15.0_2: . done ===> biostar-tools-2.0_1 depends on package: miller>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: ncbi-entrez-direct>0 - not found ===> Installing existing package /packages/All/ncbi-entrez-direct-14.9.20210423_33.pkg [pkg.DaveG.ca] Installing ncbi-entrez-direct-14.9.20210423_33... 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[pkg.DaveG.ca] | | `-- Installing p5-Authen-NTLM-1.09_1... [pkg.DaveG.ca] | | `-- Installing p5-Digest-HMAC-1.05... [pkg.DaveG.ca] | | `-- Extracting p5-Digest-HMAC-1.05: ....... done [pkg.DaveG.ca] | | `-- Extracting p5-Authen-NTLM-1.09_1: ..... done [pkg.DaveG.ca] | | `-- Installing p5-Encode-Locale-1.05... [pkg.DaveG.ca] | | `-- Extracting p5-Encode-Locale-1.05: ... done [pkg.DaveG.ca] | | `-- Installing p5-File-Listing-6.16... [pkg.DaveG.ca] | | `-- Installing p5-HTTP-Date-6.06... [pkg.DaveG.ca] | | | `-- Installing p5-TimeDate-2.33,1... [pkg.DaveG.ca] | | | `-- Extracting p5-TimeDate-2.33,1: .......... done [pkg.DaveG.ca] | | `-- Extracting p5-HTTP-Date-6.06: ... done [pkg.DaveG.ca] | | `-- Extracting p5-File-Listing-6.16: ... done [pkg.DaveG.ca] | | `-- Installing p5-HTML-Parser-3.83... [pkg.DaveG.ca] | | `-- Installing p5-HTML-Tagset-3.24... [pkg.DaveG.ca] | | `-- Extracting p5-HTML-Tagset-3.24: ... done [pkg.DaveG.ca] | | `-- Installing p5-HTTP-Message-7.01... [pkg.DaveG.ca] | | | `-- Installing p5-Clone-0.47... [pkg.DaveG.ca] | | | `-- Extracting p5-Clone-0.47: ..... done [pkg.DaveG.ca] | | | `-- Installing p5-IO-HTML-1.004... [pkg.DaveG.ca] | | | `-- Extracting p5-IO-HTML-1.004: ... done [pkg.DaveG.ca] | | | `-- Installing p5-LWP-MediaTypes-6.04... [pkg.DaveG.ca] | | | `-- Extracting p5-LWP-MediaTypes-6.04: .... done [pkg.DaveG.ca] | | `-- Extracting p5-HTTP-Message-7.01: .......... done [pkg.DaveG.ca] | | `-- Extracting p5-HTML-Parser-3.83: .......... done [pkg.DaveG.ca] | | `-- Installing p5-HTTP-Cookies-6.11... [pkg.DaveG.ca] | | `-- Extracting p5-HTTP-Cookies-6.11: ....... done [pkg.DaveG.ca] | | `-- Installing p5-HTTP-Negotiate-6.01_1... [pkg.DaveG.ca] | | `-- Extracting p5-HTTP-Negotiate-6.01_1: ... done [pkg.DaveG.ca] | | `-- Installing p5-Try-Tiny-0.32... [pkg.DaveG.ca] | | `-- Extracting p5-Try-Tiny-0.32: ... done [pkg.DaveG.ca] | | `-- Installing p5-WWW-RobotRules-6.02_1... [pkg.DaveG.ca] | | `-- Extracting p5-WWW-RobotRules-6.02_1: ..... done [pkg.DaveG.ca] | `-- Extracting p5-libwww-6.81: .......... done [pkg.DaveG.ca] `-- Extracting p5-LWP-Protocol-https-6.14: ... done [pkg.DaveG.ca] `-- Installing p5-XML-Simple-2.25... [pkg.DaveG.ca] | `-- Installing p5-XML-Parser-2.47... [pkg.DaveG.ca] | | `-- Installing expat-2.7.3... [pkg.DaveG.ca] | | `-- Extracting expat-2.7.3: .......... done [pkg.DaveG.ca] | `-- Extracting p5-XML-Parser-2.47: .......... done [pkg.DaveG.ca] | `-- Installing p5-XML-SAX-1.02... [pkg.DaveG.ca] | | `-- Installing p5-XML-NamespaceSupport-1.12... [pkg.DaveG.ca] | | `-- Extracting p5-XML-NamespaceSupport-1.12: ... done [pkg.DaveG.ca] | | `-- Installing p5-XML-SAX-Base-1.09... [pkg.DaveG.ca] | | `-- Extracting p5-XML-SAX-Base-1.09: ....... done [pkg.DaveG.ca] | `-- Extracting p5-XML-SAX-1.02: .......... done could not find ParserDetails.ini in /usr/local/lib/perl5/site_perl/XML/SAX [pkg.DaveG.ca] | `-- Installing p5-XML-SAX-Expat-0.51_1... [pkg.DaveG.ca] | `-- Extracting p5-XML-SAX-Expat-0.51_1: ... done [pkg.DaveG.ca] `-- Extracting p5-XML-Simple-2.25: ..... done [pkg.DaveG.ca] Extracting ncbi-entrez-direct-14.9.20210423_33: .......... done ===> biostar-tools-2.0_1 depends on package: ncbi-entrez-direct>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: readseq>0 - not found ===> Installing existing package /packages/All/readseq-2.1.19.pkg [pkg.DaveG.ca] Installing readseq-2.1.19... [pkg.DaveG.ca] `-- Installing openjdk8-8.462.08.1... [pkg.DaveG.ca] | `-- Installing alsa-lib-1.2.14... [pkg.DaveG.ca] | `-- Extracting alsa-lib-1.2.14: .......... done [pkg.DaveG.ca] | `-- Installing dejavu-2.37_3... [pkg.DaveG.ca] | | `-- Installing fontconfig-2.15.0_3,1... [pkg.DaveG.ca] | | `-- Installing freetype2-2.14.1... [pkg.DaveG.ca] | | | `-- Installing png-1.6.50... [pkg.DaveG.ca] | | | `-- Extracting png-1.6.50: .......... done [pkg.DaveG.ca] | | `-- Extracting freetype2-2.14.1: .......... done [pkg.DaveG.ca] | | `-- Extracting fontconfig-2.15.0_3,1: .......... done [pkg.DaveG.ca] | | `-- Installing mkfontscale-1.2.3... [pkg.DaveG.ca] | | `-- Installing libfontenc-1.1.8... [pkg.DaveG.ca] | | `-- Extracting libfontenc-1.1.8: ...... done [pkg.DaveG.ca] | | `-- Extracting mkfontscale-1.2.3: .... done [pkg.DaveG.ca] | `-- Extracting dejavu-2.37_3: .......... done [pkg.DaveG.ca] | `-- Installing giflib-5.2.2... [pkg.DaveG.ca] | `-- Extracting giflib-5.2.2: .......... done [pkg.DaveG.ca] | `-- Installing java-zoneinfo-2021.e... [pkg.DaveG.ca] | `-- Extracting java-zoneinfo-2021.e: .......... done [pkg.DaveG.ca] | `-- Installing javavmwrapper-2.7.10... [pkg.DaveG.ca] | `-- Extracting javavmwrapper-2.7.10: .......... done [pkg.DaveG.ca] | `-- Installing libX11-1.8.12,1... [pkg.DaveG.ca] | | `-- Installing libxcb-1.17.0... [pkg.DaveG.ca] | | `-- Installing libXau-1.0.12... [pkg.DaveG.ca] | | `-- Extracting libXau-1.0.12: .......... done [pkg.DaveG.ca] | | `-- Installing libXdmcp-1.1.5... [pkg.DaveG.ca] | | | `-- Installing xorgproto-2024.1... [pkg.DaveG.ca] | | | `-- Extracting xorgproto-2024.1: .......... done [pkg.DaveG.ca] | | `-- Extracting libXdmcp-1.1.5: ...... done [pkg.DaveG.ca] | | `-- Extracting libxcb-1.17.0: .......... done [pkg.DaveG.ca] | `-- Extracting libX11-1.8.12,1: .......... done [pkg.DaveG.ca] | `-- Installing libXext-1.3.6,1... [pkg.DaveG.ca] | `-- Extracting libXext-1.3.6,1: .......... done [pkg.DaveG.ca] | `-- Installing libXi-1.8.2,1... [pkg.DaveG.ca] | | `-- Installing libXfixes-6.0.1... [pkg.DaveG.ca] | | `-- Extracting libXfixes-6.0.1: ....... done [pkg.DaveG.ca] | `-- Extracting libXi-1.8.2,1: .......... done [pkg.DaveG.ca] | `-- Installing libXrender-0.9.12... [pkg.DaveG.ca] | `-- Extracting libXrender-0.9.12: ....... done [pkg.DaveG.ca] | `-- Installing libXt-1.3.0,1... [pkg.DaveG.ca] | | `-- Installing libICE-1.1.2,1... [pkg.DaveG.ca] | | `-- Extracting libICE-1.1.2,1: .......... done [pkg.DaveG.ca] | | `-- Installing libSM-1.2.6,1... [pkg.DaveG.ca] | | `-- Extracting libSM-1.2.6,1: ........ done [pkg.DaveG.ca] | `-- Extracting libXt-1.3.0,1: .......... done [pkg.DaveG.ca] | `-- Installing libXtst-1.2.5... [pkg.DaveG.ca] | `-- Extracting libXtst-1.2.5: .......... done [pkg.DaveG.ca] | `-- Installing libinotify-20240724_3... [pkg.DaveG.ca] | `-- Extracting libinotify-20240724_3: .......... done [pkg.DaveG.ca] `-- Extracting openjdk8-8.462.08.1: .......... done [pkg.DaveG.ca] Extracting readseq-2.1.19: .. done ==> Running trigger: fontconfig.ucl Running fc-cache to build fontconfig cache... ===== Message from freetype2-2.14.1: -- The 2.7.x series now uses the new subpixel hinting mode (V40 port's option) as the default, emulating a modern version of ClearType. This change inevitably leads to different rendering results, and you might change port's options to adapt it to your taste (or use the new "FREETYPE_PROPERTIES" environment variable). The environment variable "FREETYPE_PROPERTIES" can be used to control the driver properties. Example: FREETYPE_PROPERTIES=truetype:interpreter-version=35 \ cff:no-stem-darkening=1 \ autofitter:warping=1 This allows to select, say, the subpixel hinting mode at runtime for a given application. If LONG_PCF_NAMES port's option was enabled, the PCF family names may include the foundry and information whether they contain wide characters. For example, "Sony Fixed" or "Misc Fixed Wide", instead of "Fixed". This can be disabled at run time with using pcf:no-long-family-names property, if needed. Example: FREETYPE_PROPERTIES=pcf:no-long-family-names=1 How to recreate fontconfig cache with using such environment variable, if needed: # env FREETYPE_PROPERTIES=pcf:no-long-family-names=1 fc-cache -fsv The controllable properties are listed in the section "Controlling FreeType Modules" in the reference's table of contents (/usr/local/share/doc/freetype2/reference/index.html, if documentation was installed). ===== Message from dejavu-2.37_3: -- Make sure that the freetype module is loaded. If it is not, add the following line to the "Modules" section of your X Windows configuration file: Load "freetype" Add the following line to the "Files" section of X Windows configuration file: FontPath "/usr/local/share/fonts/dejavu/" Note: your X Windows configuration file is typically /etc/X11/XF86Config if you are using XFree86, and /etc/X11/xorg.conf if you are using X.Org. ===== Message from libinotify-20240724_3: -- You might want to consider increasing the kern.maxfiles tunable if you plan to use this library for applications that need to monitor activity of a lot of files. ===== Message from openjdk8-8.462.08.1: -- This OpenJDK implementation may require procfs(5) mounted on /proc for some applications. If you have not done it yet, please do the following: mount -t procfs proc /proc To make it permanent, you need the following lines in /etc/fstab: proc /proc procfs rw 0 0 ===> biostar-tools-2.0_1 depends on package: readseq>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: snpeff>0 - not found ===> Installing existing package /packages/All/snpeff-5.1.pkg [pkg.DaveG.ca] Installing snpeff-5.1... [pkg.DaveG.ca] `-- Installing bash-5.3.3_2... [pkg.DaveG.ca] `-- Extracting bash-5.3.3_2: .......... done [pkg.DaveG.ca] `-- Installing openjdk17-17.0.16+8.1_4... [pkg.DaveG.ca] | `-- Installing harfbuzz-10.3.0... [pkg.DaveG.ca] | | `-- Installing glib-2.84.1_3,2... [pkg.DaveG.ca] | | `-- Installing libiconv-1.17_1... [pkg.DaveG.ca] | | `-- Extracting libiconv-1.17_1: .......... done [pkg.DaveG.ca] | | `-- Installing pcre2-10.46... [pkg.DaveG.ca] | | `-- Extracting pcre2-10.46: .......... done [pkg.DaveG.ca] | | `-- Installing py311-packaging-25.0... [pkg.DaveG.ca] | | `-- Extracting py311-packaging-25.0: .......... done [pkg.DaveG.ca] | | `-- Extracting glib-2.84.1_3,2: .......... done [pkg.DaveG.ca] | | `-- Installing graphite2-1.3.14... [pkg.DaveG.ca] | | `-- Extracting graphite2-1.3.14: .......... done [pkg.DaveG.ca] | `-- Extracting harfbuzz-10.3.0: .......... done [pkg.DaveG.ca] | `-- Installing jpeg-turbo-3.1.2... [pkg.DaveG.ca] | `-- Extracting jpeg-turbo-3.1.2: .......... done [pkg.DaveG.ca] | `-- Installing lcms2-2.17... [pkg.DaveG.ca] | | `-- Installing tiff-4.7.1... [pkg.DaveG.ca] | | `-- Installing jbigkit-2.1_3... [pkg.DaveG.ca] | | `-- Extracting jbigkit-2.1_3: .......... done [pkg.DaveG.ca] | | `-- Installing lerc-4.0.0... [pkg.DaveG.ca] | | `-- Extracting lerc-4.0.0: ..... done [pkg.DaveG.ca] | | `-- Installing libdeflate-1.24... [pkg.DaveG.ca] | | `-- Extracting libdeflate-1.24: .......... done [pkg.DaveG.ca] | | `-- Extracting tiff-4.7.1: .......... done [pkg.DaveG.ca] | `-- Extracting lcms2-2.17: .......... done [pkg.DaveG.ca] | `-- Installing libXrandr-1.5.4... [pkg.DaveG.ca] | `-- Extracting libXrandr-1.5.4: .......... done [pkg.DaveG.ca] | `-- Installing xorg-fonts-truetype-7.7_1... [pkg.DaveG.ca] | | `-- Installing encodings-1.1.0,1... [pkg.DaveG.ca] | | `-- Extracting encodings-1.1.0,1: .......... done [pkg.DaveG.ca] | | `-- Installing font-bh-ttf-1.0.3_5... [pkg.DaveG.ca] | | `-- Extracting font-bh-ttf-1.0.3_5: .......... done [pkg.DaveG.ca] | | `-- Installing font-misc-ethiopic-1.0.4... [pkg.DaveG.ca] | | `-- Extracting font-misc-ethiopic-1.0.4: ... done [pkg.DaveG.ca] | | `-- Installing font-misc-meltho-1.0.3_5... [pkg.DaveG.ca] | | `-- Extracting font-misc-meltho-1.0.3_5: .......... done [pkg.DaveG.ca] `-- Extracting openjdk17-17.0.16+8.1_4: .......... done [pkg.DaveG.ca] Extracting snpeff-5.1: .......... done ==> Running trigger: fontconfig.ucl Running fc-cache to build fontconfig cache... ==> Running trigger: gio-modules.ucl Generating GIO modules cache ==> Running trigger: glib-schemas.ucl Compiling glib schemas No schema files found: doing nothing. ===== Message from openjdk17-17.0.16+8.1_4: -- This OpenJDK implementation may require procfs(5) mounted on /proc for some applications. If you have not done it yet, please do the following: mount -t procfs proc /proc To make it permanent, you need the following lines in /etc/fstab: proc /proc procfs rw 0 0 ===> biostar-tools-2.0_1 depends on package: snpeff>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: picard-tools>0 - not found ===> Installing existing package /packages/All/picard-tools-2.22.9.pkg [pkg.DaveG.ca] Installing picard-tools-2.22.9... [pkg.DaveG.ca] `-- Installing samtools-1.22... [pkg.DaveG.ca] | `-- Installing htslib-1.22... [pkg.DaveG.ca] | `-- Extracting htslib-1.22: .......... done [pkg.DaveG.ca] `-- Extracting samtools-1.22: .......... done [pkg.DaveG.ca] Extracting picard-tools-2.22.9: .. done ===> biostar-tools-2.0_1 depends on package: picard-tools>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: bbmap>0 - not found ===> Installing existing package /packages/All/bbmap-39.34.pkg [pkg.DaveG.ca] Installing bbmap-39.34... [pkg.DaveG.ca] `-- Installing pbzip2-1.1.13... [pkg.DaveG.ca] `-- Extracting pbzip2-1.1.13: .... done [pkg.DaveG.ca] `-- Installing pigz-2.8... [pkg.DaveG.ca] | `-- Installing zopfli-1.0.3_1... [pkg.DaveG.ca] | `-- Extracting zopfli-1.0.3_1: .......... done [pkg.DaveG.ca] `-- Extracting pigz-2.8: ..... done [pkg.DaveG.ca] Extracting bbmap-39.34: .......... done ===> biostar-tools-2.0_1 depends on package: bbmap>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: minimap2>0 - not found ===> Installing existing package /packages/All/minimap2-2.30.pkg [pkg.DaveG.ca] Installing minimap2-2.30... [pkg.DaveG.ca] Extracting minimap2-2.30: .......... done ===> biostar-tools-2.0_1 depends on package: minimap2>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: bwa>0 - not found ===> Installing existing package /packages/All/bwa-0.7.19.pkg [pkg.DaveG.ca] Installing bwa-0.7.19... [pkg.DaveG.ca] Extracting bwa-0.7.19: .... done ===> biostar-tools-2.0_1 depends on package: bwa>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: bowtie2>0 - not found ===> Installing existing package /packages/All/bowtie2-2.5.4.pkg [pkg.DaveG.ca] Installing bowtie2-2.5.4... [pkg.DaveG.ca] Extracting bowtie2-2.5.4: .......... done ===> biostar-tools-2.0_1 depends on package: bowtie2>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: samtools>0 - found ===> biostar-tools-2.0_1 depends on package: emboss>0 - not found ===> Installing existing package /packages/All/emboss-6.6.0_7.pkg [pkg.DaveG.ca] Installing emboss-6.6.0_7... [pkg.DaveG.ca] `-- Installing libXpm-3.5.17_1... [pkg.DaveG.ca] `-- Extracting libXpm-3.5.17_1: .......... done [pkg.DaveG.ca] `-- Installing libgd-2.3.3_13,1... [pkg.DaveG.ca] | `-- Installing webp-1.6.0... [pkg.DaveG.ca] | `-- Extracting webp-1.6.0: .......... done [pkg.DaveG.ca] `-- Extracting libgd-2.3.3_13,1: .......... done [pkg.DaveG.ca] `-- Installing open-motif-2.3.8_8... [pkg.DaveG.ca] | `-- Installing libXaw-1.0.16,2... [pkg.DaveG.ca] | | `-- Installing libXmu-1.1.4,1... [pkg.DaveG.ca] | | `-- Extracting libXmu-1.1.4,1: .......... done [pkg.DaveG.ca] | `-- Extracting libXaw-1.0.16,2: .......... done [pkg.DaveG.ca] | `-- Installing libXft-2.3.8... [pkg.DaveG.ca] | `-- Extracting libXft-2.3.8: .......... done [pkg.DaveG.ca] | `-- Installing xbitmaps-1.1.3... [pkg.DaveG.ca] | `-- Extracting xbitmaps-1.1.3: .......... done [pkg.DaveG.ca] `-- Extracting open-motif-2.3.8_8: .......... done [pkg.DaveG.ca] `-- Installing postgresql15-client-15.14_1... [pkg.DaveG.ca] `-- Extracting postgresql15-client-15.14_1: .......... done [pkg.DaveG.ca] Extracting emboss-6.6.0_7: .......... done ===== Message from postgresql15-client-15.14_1: -- The PostgreSQL port has a collection of "side orders": postgresql-docs For all of the html documentation p5-Pg A perl5 API for client access to PostgreSQL databases. postgresql-tcltk If you want tcl/tk client support. postgresql-jdbc For Java JDBC support. postgresql-odbc For client access from unix applications using ODBC as access method. Not needed to access unix PostgreSQL servers from Win32 using ODBC. See below. ruby-postgres, py-psycopg For client access to PostgreSQL databases using the ruby & python languages. postgresql-plperl, postgresql-pltcl & postgresql-plruby For using perl5, tcl & ruby as procedural languages. postgresql-contrib Lots of contributed utilities, postgresql functions and datatypes. There you find pg_standby, pgcrypto and many other cool things. etc... ===== Message from emboss-6.6.0_7: -- The EMBOSS suite has been successfully installed under /usr/local/emboss To run EMBOSS programs make sure that /usr/local/emboss/bin is in your PATH. In order to see graphical output from some EMBOSS programs, you will need to set the following environment variable in your shell: set PLPLOT_LIB to: "/usr/local/emboss/share/EMBOSS" A sample configuration file has been installed in /usr/local/emboss/share/EMBOSS/emboss.default.template This must be renamed to emboss.default and edited to suit your site and requirements. A .embossrc file in a user's home directory overrides settings in the system-wide emboss.default. Additional third party applications for EMBOSS can be installed from the biology/embassy port. Remember, though that if you installed EMBOSS in a PREFIX other than the default, you will have to install EMBASSY into this same PREFIX. ===> biostar-tools-2.0_1 depends on package: emboss>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: bedtools>0 - not found ===> Installing existing package /packages/All/bedtools-2.31.1.pkg [pkg.DaveG.ca] Installing bedtools-2.31.1... [pkg.DaveG.ca] Extracting bedtools-2.31.1: .......... done ===> biostar-tools-2.0_1 depends on package: bedtools>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: bamtools>0 - not found ===> Installing existing package /packages/All/bamtools-2.5.3.pkg [pkg.DaveG.ca] Installing bamtools-2.5.3... [pkg.DaveG.ca] `-- Installing jsoncpp-1.9.6_1... [pkg.DaveG.ca] `-- Extracting jsoncpp-1.9.6_1: .......... done [pkg.DaveG.ca] Extracting bamtools-2.5.3: .......... done ===> biostar-tools-2.0_1 depends on package: bamtools>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: py311-cutadapt>0 - not found ===> Installing existing package /packages/All/py311-cutadapt-5.1.pkg [pkg.DaveG.ca] Installing py311-cutadapt-5.1... [pkg.DaveG.ca] `-- Installing py311-dnaio-1.2.4... [pkg.DaveG.ca] `-- Extracting py311-dnaio-1.2.4: .......... done [pkg.DaveG.ca] `-- Installing py311-xopen-2.0.2... [pkg.DaveG.ca] | `-- Installing py311-zstandard-0.23.0_1... [pkg.DaveG.ca] | `-- Extracting py311-zstandard-0.23.0_1: .......... done [pkg.DaveG.ca] `-- Extracting py311-xopen-2.0.2: .......... done [pkg.DaveG.ca] Extracting py311-cutadapt-5.1: .......... done ===> biostar-tools-2.0_1 depends on package: py311-cutadapt>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: seqtk>0 - not found ===> Installing existing package /packages/All/seqtk-1.5.pkg [pkg.DaveG.ca] Installing seqtk-1.5... [pkg.DaveG.ca] Extracting seqtk-1.5: . done ===> biostar-tools-2.0_1 depends on package: seqtk>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: datamash>0 - not found ===> Installing existing package /packages/All/datamash-1.9.pkg [pkg.DaveG.ca] Installing datamash-1.9... [pkg.DaveG.ca] Extracting datamash-1.9: .......... done ===> biostar-tools-2.0_1 depends on package: datamash>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: bcftools>0 - not found ===> Installing existing package /packages/All/bcftools-1.22.pkg [pkg.DaveG.ca] Installing bcftools-1.22... [pkg.DaveG.ca] `-- Installing gsl-2.7.1_1... [pkg.DaveG.ca] `-- Extracting gsl-2.7.1_1: .......... done [pkg.DaveG.ca] Extracting bcftools-1.22: .......... done ===> biostar-tools-2.0_1 depends on package: bcftools>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: subread>0 - not found ===> Installing existing package /packages/All/subread-2.1.0.pkg [pkg.DaveG.ca] Installing subread-2.1.0... [pkg.DaveG.ca] `-- Installing libsysinfo-0.0.3_3... [pkg.DaveG.ca] `-- Extracting libsysinfo-0.0.3_3: ...... done [pkg.DaveG.ca] Extracting subread-2.1.0: .......... done ===> biostar-tools-2.0_1 depends on package: subread>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: hisat2>0 - not found ===> Installing existing package /packages/All/hisat2-2.2.1_2.pkg [pkg.DaveG.ca] Installing hisat2-2.2.1_2... [pkg.DaveG.ca] Extracting hisat2-2.2.1_2: .......... done ===> biostar-tools-2.0_1 depends on package: hisat2>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: trimmomatic>0 - not found ===> Installing existing package /packages/All/trimmomatic-0.39.pkg [pkg.DaveG.ca] Installing trimmomatic-0.39... [pkg.DaveG.ca] Extracting trimmomatic-0.39: ........ done ===== Message from trimmomatic-0.39: -- ===> NOTICE: The trimmomatic port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> biostar-tools-2.0_1 depends on package: trimmomatic>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: fastqc>0 - not found ===> Installing existing package /packages/All/fastqc-0.12.1.pkg [pkg.DaveG.ca] Installing fastqc-0.12.1... [pkg.DaveG.ca] Extracting fastqc-0.12.1: .......... done ===> biostar-tools-2.0_1 depends on package: fastqc>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: picard-tools>0 - found ===> biostar-tools-2.0_1 depends on package: ncbi-blast+>0 - not found ===> Installing existing package /packages/All/ncbi-blast+-2.17.0.pkg [pkg.DaveG.ca] Installing ncbi-blast+-2.17.0... [pkg.DaveG.ca] `-- Installing elfutils-0.187_2... [pkg.DaveG.ca] | `-- Installing argp-standalone-1.5.0_1... [pkg.DaveG.ca] | `-- Extracting argp-standalone-1.5.0_1: ...... done [pkg.DaveG.ca] `-- Extracting elfutils-0.187_2: .......... done [pkg.DaveG.ca] `-- Installing libuv-1.51.0... [pkg.DaveG.ca] `-- Extracting libuv-1.51.0: .......... done [pkg.DaveG.ca] `-- Installing lmdb-0.9.33,1... [pkg.DaveG.ca] `-- Extracting lmdb-0.9.33,1: .......... done [pkg.DaveG.ca] `-- Installing lzo2-2.10_1... [pkg.DaveG.ca] `-- Extracting lzo2-2.10_1: .......... done [pkg.DaveG.ca] `-- Installing p5-JSON-4.10... [pkg.DaveG.ca] `-- Extracting p5-JSON-4.10: .......... done [pkg.DaveG.ca] `-- Installing p5-List-MoreUtils-0.430... [pkg.DaveG.ca] | `-- Installing p5-Exporter-Tiny-1.006002... [pkg.DaveG.ca] | `-- Extracting p5-Exporter-Tiny-1.006002: .......... done [pkg.DaveG.ca] | `-- Installing p5-List-MoreUtils-XS-0.430... [pkg.DaveG.ca] | `-- Extracting p5-List-MoreUtils-XS-0.430: .... done [pkg.DaveG.ca] `-- Extracting p5-List-MoreUtils-0.430: ....... done [pkg.DaveG.ca] Extracting ncbi-blast+-2.17.0: .......... done ===> biostar-tools-2.0_1 depends on package: ncbi-blast+>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: cd-hit>0 - not found ===> Installing existing package /packages/All/cd-hit-4.8.1_3.pkg [pkg.DaveG.ca] Installing cd-hit-4.8.1_3... [pkg.DaveG.ca] Extracting cd-hit-4.8.1_3: .......... done ===> biostar-tools-2.0_1 depends on package: cd-hit>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: py311-biopython>0 - not found ===> Installing existing package /packages/All/py311-biopython-1.85_2.pkg [pkg.DaveG.ca] Installing py311-biopython-1.85_2... [pkg.DaveG.ca] `-- Installing py311-numpy-1.26.4_10,1... [pkg.DaveG.ca] | `-- Installing gcc13-13.3.0_3... [pkg.DaveG.ca] | | `-- Installing binutils-2.44,1... [pkg.DaveG.ca] | | `-- Extracting binutils-2.44,1: .......... done [pkg.DaveG.ca] | | `-- Installing gmp-6.3.0... [pkg.DaveG.ca] | | `-- Extracting gmp-6.3.0: .......... done [pkg.DaveG.ca] | | `-- Installing mpc-1.3.1_1... [pkg.DaveG.ca] | | `-- Installing mpfr-4.2.2,1... 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[pkg.DaveG.ca] | | `-- Installing suitesparse-colamd-3.3.5... [pkg.DaveG.ca] | | `-- Extracting suitesparse-colamd-3.3.5: .......... done [pkg.DaveG.ca] | | `-- Extracting suitesparse-cholmod-5.3.4: .......... done [pkg.DaveG.ca] | `-- Extracting suitesparse-umfpack-6.3.6: .......... done [pkg.DaveG.ca] `-- Extracting py311-numpy-1.26.4_10,1: .......... done [pkg.DaveG.ca] `-- Installing py311-reportlab-4.4.3_1... [pkg.DaveG.ca] | `-- Installing adobe-cmaps-20051217_4... [pkg.DaveG.ca] | `-- Extracting adobe-cmaps-20051217_4: .......... done [pkg.DaveG.ca] | `-- Installing py311-pillow-11.3.0_1... [pkg.DaveG.ca] | | `-- Installing libavif-1.3.0_2... [pkg.DaveG.ca] | | `-- Installing aom-3.13.1... [pkg.DaveG.ca] | | | `-- Installing vmaf-3.0.0... [pkg.DaveG.ca] | | | `-- Extracting vmaf-3.0.0: .......... done [pkg.DaveG.ca] | | `-- Extracting aom-3.13.1: .......... done [pkg.DaveG.ca] | | `-- Installing dav1d-1.5.1_1... [pkg.DaveG.ca] | | `-- Extracting dav1d-1.5.1_1: .......... done [pkg.DaveG.ca] | | `-- Installing gdk-pixbuf2-2.44.1... [pkg.DaveG.ca] | | | `-- Installing libxml2-2.14.6... [pkg.DaveG.ca] | | | `-- Extracting libxml2-2.14.6: .......... done [pkg.DaveG.ca] | | | `-- Installing shared-mime-info-2.4_2... [pkg.DaveG.ca] | | | `-- Extracting shared-mime-info-2.4_2: ......... done [pkg.DaveG.ca] | | `-- Extracting gdk-pixbuf2-2.44.1: .......... done [pkg.DaveG.ca] | | `-- Installing libyuv-0.0.1903... [pkg.DaveG.ca] | | `-- Extracting libyuv-0.0.1903: .......... done [pkg.DaveG.ca] | | `-- Extracting libavif-1.3.0_2: .......... done [pkg.DaveG.ca] | | `-- Installing libimagequant-4.4.0... [pkg.DaveG.ca] | | `-- Extracting libimagequant-4.4.0: ...... done [pkg.DaveG.ca] | | `-- Installing libraqm-0.10.3... [pkg.DaveG.ca] | | `-- Installing fribidi-1.0.16... [pkg.DaveG.ca] | | `-- Extracting fribidi-1.0.16: .......... done [pkg.DaveG.ca] | | `-- Extracting libraqm-0.10.3: .......... done [pkg.DaveG.ca] | | `-- Installing openjpeg-2.5.4... [pkg.DaveG.ca] | | `-- Extracting openjpeg-2.5.4: .......... done [pkg.DaveG.ca] | | `-- Installing py311-tkinter-3.11.14_11... [pkg.DaveG.ca] | | `-- Installing tcl86-8.6.17... [pkg.DaveG.ca] | | `-- Extracting tcl86-8.6.17: .......... done [pkg.DaveG.ca] | | `-- Installing tk86-8.6.17... [pkg.DaveG.ca] | | | `-- Installing libXScrnSaver-1.2.4_1... [pkg.DaveG.ca] | | | `-- Extracting libXScrnSaver-1.2.4_1: .......... done [pkg.DaveG.ca] | | `-- Extracting tk86-8.6.17: .......... done [pkg.DaveG.ca] | | `-- Extracting py311-tkinter-3.11.14_11: ...... done [pkg.DaveG.ca] | `-- Extracting py311-pillow-11.3.0_1: .......... done [pkg.DaveG.ca] `-- Extracting py311-reportlab-4.4.3_1: .......... done [pkg.DaveG.ca] Extracting py311-biopython-1.85_2: .......... done ==> Running trigger: gdk-pixbuf-query-loaders.ucl Generating gdk-pixbuf modules cache ==> Running trigger: shared-mime-info.ucl Building the Shared MIME-Info database cache ===== Message from gcc13-13.3.0_3: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc13 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===== Message from libraqm-0.10.3: -- ===> NOTICE: The libraqm port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> biostar-tools-2.0_1 depends on package: py311-biopython>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: py311-pysam>0 - not found ===> Installing existing package /packages/All/py311-pysam-0.23.0_1.pkg [pkg.DaveG.ca] Installing py311-pysam-0.23.0_1... [pkg.DaveG.ca] `-- Installing py311-cython-0.29.37_2... [pkg.DaveG.ca] `-- Extracting py311-cython-0.29.37_2: .......... done [pkg.DaveG.ca] Extracting py311-pysam-0.23.0_1: .......... done ===> biostar-tools-2.0_1 depends on package: py311-pysam>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: freebayes>0 - not found ===> Installing existing package /packages/All/freebayes-1.3.9.pkg [pkg.DaveG.ca] Installing freebayes-1.3.9... [pkg.DaveG.ca] Extracting freebayes-1.3.9: .. done ===> biostar-tools-2.0_1 depends on package: freebayes>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: p5-Net-SSLeay>0 - found ===> biostar-tools-2.0_1 depends on package: bioawk>0 - not found ===> Installing existing package /packages/All/bioawk-1.0.7.pkg [pkg.DaveG.ca] Installing bioawk-1.0.7... [pkg.DaveG.ca] Extracting bioawk-1.0.7: . done ===> biostar-tools-2.0_1 depends on package: bioawk>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: vt>0 - not found ===> Installing existing package /packages/All/vt-0.57721_3.pkg [pkg.DaveG.ca] Installing vt-0.57721_3... [pkg.DaveG.ca] `-- Installing libsvm-3.24... [pkg.DaveG.ca] `-- Extracting libsvm-3.24: .......... done [pkg.DaveG.ca] Extracting vt-0.57721_3: . done ===== Message from libsvm-3.24: -- Some useful tools are installed to /usr/local/share/libsvm. Most of them are written in Python, please install lang/python before trying them. -- ===> NOTICE: The libsvm port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> biostar-tools-2.0_1 depends on package: vt>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: py311-crossmap>0 - not found ===> Installing existing package /packages/All/py311-crossmap-0.7.3_1.pkg [pkg.DaveG.ca] Installing py311-crossmap-0.7.3_1... [pkg.DaveG.ca] `-- Installing py311-bx-python-0.14.0... [pkg.DaveG.ca] | `-- Installing py311-pyparsing-3.2.5... [pkg.DaveG.ca] | `-- Extracting py311-pyparsing-3.2.5: .......... done [pkg.DaveG.ca] `-- Extracting py311-bx-python-0.14.0: .......... done [pkg.DaveG.ca] `-- Installing py311-pyBigWig-0.3.22_1... [pkg.DaveG.ca] `-- Extracting py311-pyBigWig-0.3.22_1: .......... done [pkg.DaveG.ca] Extracting py311-crossmap-0.7.3_1: .......... done ===> biostar-tools-2.0_1 depends on package: py311-crossmap>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: py311-goatools>0 - not found ===> Installing existing package /packages/All/py311-goatools-1.1.6_2.pkg [pkg.DaveG.ca] Installing py311-goatools-1.1.6_2... [pkg.DaveG.ca] `-- Installing py311-XlsxWriter-3.2.2_1... [pkg.DaveG.ca] `-- Extracting py311-XlsxWriter-3.2.2_1: .......... done [pkg.DaveG.ca] `-- Installing py311-docopt-0.6.2_2... [pkg.DaveG.ca] `-- Extracting py311-docopt-0.6.2_2: .......... done [pkg.DaveG.ca] `-- Installing py311-pandas-2.2.3_3,1... [pkg.DaveG.ca] | `-- Installing py311-bottleneck-1.3.8_1... [pkg.DaveG.ca] | `-- Extracting py311-bottleneck-1.3.8_1: .......... done [pkg.DaveG.ca] | `-- Installing py311-numexpr-2.14.1... 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[pkg.DaveG.ca] | `-- Extracting py311-charset-normalizer-3.4.4: .......... done [pkg.DaveG.ca] | `-- Installing py311-idna-3.11... [pkg.DaveG.ca] | `-- Extracting py311-idna-3.11: .......... done [pkg.DaveG.ca] | `-- Installing py311-pysocks-1.7.1_1... [pkg.DaveG.ca] | `-- Extracting py311-pysocks-1.7.1_1: .......... done [pkg.DaveG.ca] | `-- Installing py311-urllib3-2.5.0,1... [pkg.DaveG.ca] | `-- Extracting py311-urllib3-2.5.0,1: .......... done [pkg.DaveG.ca] `-- Extracting py311-requests-2.32.5: .......... done [pkg.DaveG.ca] `-- Installing py311-scipy-1.11.1_4,1... [pkg.DaveG.ca] | `-- Installing blas-3.12.1... [pkg.DaveG.ca] | `-- Extracting blas-3.12.1: ..... done [pkg.DaveG.ca] `-- Extracting py311-scipy-1.11.1_4,1: .......... done [pkg.DaveG.ca] `-- Installing py311-statsmodels-0.14.5... [pkg.DaveG.ca] | `-- Installing py311-patsy-1.0.2... [pkg.DaveG.ca] | `-- Extracting py311-patsy-1.0.2: .......... done [pkg.DaveG.ca] `-- Extracting py311-statsmodels-0.14.5: .......... done [pkg.DaveG.ca] Extracting py311-goatools-1.1.6_2: .......... done ===== Message from py311-pandas-2.2.3_3,1: -- Install math/py-statsmodels to enable parts of pandas.stats. Install devel/py-xarray to enable the to_xarray() function. ===== Message from py311-urllib3-2.5.0,1: -- Since version 1.25 HTTPS connections are now verified by default which is done via "cert_reqs = 'CERT_REQUIRED'". While certificate verification can be disabled via "cert_reqs = 'CERT_NONE'", it's highly recommended to leave it on. Various consumers of net/py-urllib3 already have implemented routines that either explicitly enable or disable HTTPS certificate verification (e.g. via configuration settings, CLI arguments, etc.). Yet it may happen that there are still some consumers which don't explicitly enable/disable certificate verification for HTTPS connections which could then lead to errors (as is often the case with self-signed certificates). In case of an error one should try first to temporarily disable certificate verification of the problematic urllib3 consumer to see if that approach will remedy the issue. ===> biostar-tools-2.0_1 depends on package: py311-goatools>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: erminej>0 - not found ===> Installing existing package /packages/All/erminej-3.2.pkg [pkg.DaveG.ca] Installing erminej-3.2... [pkg.DaveG.ca] Extracting erminej-3.2: .......... done ===> biostar-tools-2.0_1 depends on package: erminej>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: py311-ont-fast5-api>0 - not found ===> Installing existing package /packages/All/py311-ont-fast5-api-4.0.2_2.pkg [pkg.DaveG.ca] Installing py311-ont-fast5-api-4.0.2_2... [pkg.DaveG.ca] `-- Installing py311-h5py-3.15.1... [pkg.DaveG.ca] | `-- Installing hdf5-1.12.2_2,1... [pkg.DaveG.ca] | | `-- Installing libaec-1.1.4... [pkg.DaveG.ca] | | `-- Extracting libaec-1.1.4: .......... done [pkg.DaveG.ca] | `-- Extracting hdf5-1.12.2_2,1: .......... done [pkg.DaveG.ca] `-- Extracting py311-h5py-3.15.1: .......... done [pkg.DaveG.ca] `-- Installing py311-progressbar-2.5_1... [pkg.DaveG.ca] `-- Extracting py311-progressbar-2.5_1: .......... done [pkg.DaveG.ca] `-- Installing vbz-compression-1.0.13... [pkg.DaveG.ca] `-- Extracting vbz-compression-1.0.13: .. done [pkg.DaveG.ca] Extracting py311-ont-fast5-api-4.0.2_2: .......... done ===> biostar-tools-2.0_1 depends on package: py311-ont-fast5-api>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: py311-multiqc>0 - not found ===> Installing existing package /packages/All/py311-multiqc-1.25.2_3.pkg [pkg.DaveG.ca] Installing py311-multiqc-1.25.2_3... [pkg.DaveG.ca] `-- Installing py311-Jinja2-3.1.6... [pkg.DaveG.ca] | `-- Installing py311-markupsafe-3.0.3... [pkg.DaveG.ca] | `-- Extracting py311-markupsafe-3.0.3: .......... done [pkg.DaveG.ca] `-- Extracting py311-Jinja2-3.1.6: .......... done [pkg.DaveG.ca] `-- Installing py311-coloredlogs-15.0.1_1... [pkg.DaveG.ca] | `-- Installing py311-humanfriendly-10.0_1... 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[pkg.DaveG.ca] | | `-- Extracting py311-scikit-sparse-0.4.16_1: .......... done [pkg.DaveG.ca] | | `-- Extracting py311-networkx-3.5_3,2: .......... done [pkg.DaveG.ca] | `-- Extracting py311-colormath-3.0.0_4: .......... done [pkg.DaveG.ca] `-- Extracting py311-spectra-0.0.11_3: .......... done [pkg.DaveG.ca] `-- Installing py311-tqdm-4.67.1... [pkg.DaveG.ca] `-- Extracting py311-tqdm-4.67.1: .......... done [pkg.DaveG.ca] `-- Installing py311-typeguard-4.4.4... [pkg.DaveG.ca] `-- Extracting py311-typeguard-4.4.4: .......... done [pkg.DaveG.ca] Extracting py311-multiqc-1.25.2_3: .......... done ===== Message from boost-libs-1.89.0: -- You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. ===> biostar-tools-2.0_1 depends on package: py311-multiqc>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: flash>0 - not found ===> Installing existing package /packages/All/flash-1.2.11.pkg [pkg.DaveG.ca] Installing flash-1.2.11... [pkg.DaveG.ca] Extracting flash-1.2.11: . done ===> biostar-tools-2.0_1 depends on package: flash>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on executable: bfc - not found ===> Installing existing package /packages/All/bfc-g20150417.pkg [pkg.DaveG.ca] Installing bfc-g20150417... [pkg.DaveG.ca] Extracting bfc-g20150417: .. done ===> biostar-tools-2.0_1 depends on executable: bfc - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: Jellyfish>0 - not found ===> Installing existing package /packages/All/Jellyfish-2.3.0_4.pkg [pkg.DaveG.ca] Installing Jellyfish-2.3.0_4... [pkg.DaveG.ca] Extracting Jellyfish-2.3.0_4: .......... done ===> biostar-tools-2.0_1 depends on package: Jellyfish>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: mafft>0 - not found ===> Installing existing package /packages/All/mafft-7.267_1.pkg [pkg.DaveG.ca] Installing mafft-7.267_1... [pkg.DaveG.ca] Extracting mafft-7.267_1: .......... done ===> biostar-tools-2.0_1 depends on package: mafft>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: clustal-omega>0 - not found ===> Installing existing package /packages/All/clustal-omega-1.2.4.pkg [pkg.DaveG.ca] Installing clustal-omega-1.2.4... [pkg.DaveG.ca] `-- Installing argtable-2.13_3... [pkg.DaveG.ca] `-- Extracting argtable-2.13_3: .......... done [pkg.DaveG.ca] Extracting clustal-omega-1.2.4: .......... done ===== Message from argtable-2.13_3: -- ===> NOTICE: The argtable port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> biostar-tools-2.0_1 depends on package: clustal-omega>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: sam2pairwise>0 - not found ===> Installing existing package /packages/All/sam2pairwise-1.0.0.pkg [pkg.DaveG.ca] Installing sam2pairwise-1.0.0... [pkg.DaveG.ca] Extracting sam2pairwise-1.0.0: . done ===> biostar-tools-2.0_1 depends on package: sam2pairwise>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: kallisto>0 - not found ===> Installing existing package /packages/All/kallisto-0.51.1_1,1.pkg [pkg.DaveG.ca] Installing kallisto-0.51.1_1,1... 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[pkg.DaveG.ca] | | `-- Extracting py311-sphinxcontrib-applehelp-2.0.0: .......... done [pkg.DaveG.ca] | | `-- Installing py311-sphinxcontrib-devhelp-2.0.0... [pkg.DaveG.ca] | | `-- Extracting py311-sphinxcontrib-devhelp-2.0.0: .......... done [pkg.DaveG.ca] | | `-- Installing py311-sphinxcontrib-htmlhelp-2.1.0... [pkg.DaveG.ca] | | `-- Extracting py311-sphinxcontrib-htmlhelp-2.1.0: .......... done [pkg.DaveG.ca] | | `-- Installing py311-sphinxcontrib-jsmath-1.0.1_1... [pkg.DaveG.ca] | | `-- Extracting py311-sphinxcontrib-jsmath-1.0.1_1: .......... done [pkg.DaveG.ca] | | `-- Installing py311-sphinxcontrib-qthelp-2.0.0... [pkg.DaveG.ca] | | `-- Extracting py311-sphinxcontrib-qthelp-2.0.0: .......... done [pkg.DaveG.ca] | | `-- Installing py311-sphinxcontrib-serializinghtml-2.0.0... [pkg.DaveG.ca] | | `-- Extracting py311-sphinxcontrib-serializinghtml-2.0.0: .......... done [pkg.DaveG.ca] | `-- Extracting py311-sphinx-5.3.0_3,1: .......... done [pkg.DaveG.ca] | `-- Installing py311-tabulate-0.9.0... [pkg.DaveG.ca] | `-- Extracting py311-tabulate-0.9.0: .......... done [pkg.DaveG.ca] `-- Extracting py311-numpydoc-1.6.0_1: .......... done [pkg.DaveG.ca] `-- Installing py311-py2bit-0.3.0_1... [pkg.DaveG.ca] `-- Extracting py311-py2bit-0.3.0_1: .......... done [pkg.DaveG.ca] Extracting py311-deepTools-3.5.2_2: .......... done ===== Message from ca_root_nss-3.117: -- FreeBSD does not, and can not warrant that the certification authorities whose certificates are included in this package have in any way been audited for trustworthiness or RFC 3647 compliance. Assessment and verification of trust is the complete responsibility of the system administrator. This package installs symlinks to support root certificate discovery for software that either uses other cryptographic libraries than OpenSSL, or use OpenSSL but do not follow recommended practice. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem ===> biostar-tools-2.0_1 depends on package: py311-deepTools>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: igv>0 - not found ===> Installing existing package /packages/All/igv-2.16.0_1.pkg [pkg.DaveG.ca] Installing igv-2.16.0_1... [pkg.DaveG.ca] `-- Installing openjdk11-11.0.27+6.1_2... [pkg.DaveG.ca] `-- Extracting openjdk11-11.0.27+6.1_2: .......... done [pkg.DaveG.ca] `-- Installing openjfx14-14.0.2.1+1_17... [pkg.DaveG.ca] | `-- Installing at-spi2-core-2.56.6... [pkg.DaveG.ca] | | `-- Installing dbus-1.16.2_4,1... ===> Creating groups Creating group 'messagebus' with gid '556' ===> Creating users Creating user 'messagebus' with uid '556' [pkg.DaveG.ca] | | `-- Extracting dbus-1.16.2_4,1: ......... done [pkg.DaveG.ca] | | `-- Installing gsettings-desktop-schemas-47.1_2... [pkg.DaveG.ca] | | `-- Extracting gsettings-desktop-schemas-47.1_2: .......... done [pkg.DaveG.ca] | `-- Extracting at-spi2-core-2.56.6: .......... done [pkg.DaveG.ca] | `-- Installing ffmpeg4-4.4.4_25... [pkg.DaveG.ca] | | `-- Installing lame-3.100_5... [pkg.DaveG.ca] | | `-- Extracting lame-3.100_5: .......... done [pkg.DaveG.ca] | | `-- Installing libass-0.17.4... [pkg.DaveG.ca] | | `-- Installing libunibreak-6.1,1... [pkg.DaveG.ca] | | `-- Extracting libunibreak-6.1,1: .......... done [pkg.DaveG.ca] | | `-- Extracting libass-0.17.4: ....... done [pkg.DaveG.ca] | | `-- Installing libdrm-2.4.123,1... [pkg.DaveG.ca] | | `-- Installing libpciaccess-0.18.1_1... [pkg.DaveG.ca] | | | `-- Installing hwdata-0.399,1... [pkg.DaveG.ca] | | | `-- Extracting hwdata-0.399,1: ...... done [pkg.DaveG.ca] | | `-- Extracting libpciaccess-0.18.1_1: ..... done [pkg.DaveG.ca] | | `-- Extracting libdrm-2.4.123,1: .......... done [pkg.DaveG.ca] | | `-- Installing libv4l-1.23.0_5... [pkg.DaveG.ca] | | `-- Installing libudev-devd-0.6.0... [pkg.DaveG.ca] | | `-- Extracting libudev-devd-0.6.0: ..... done [pkg.DaveG.ca] | | `-- Extracting libv4l-1.23.0_5: .......... done [pkg.DaveG.ca] | | `-- Installing libva-2.22.0_1... [pkg.DaveG.ca] | | `-- Installing libglvnd-1.7.0... [pkg.DaveG.ca] | | `-- Extracting libglvnd-1.7.0: .......... done [pkg.DaveG.ca] | | `-- Installing wayland-1.24.0_2... [pkg.DaveG.ca] | | | `-- Installing libepoll-shim-0.0.20240608... [pkg.DaveG.ca] | | | `-- Extracting libepoll-shim-0.0.20240608: .......... done [pkg.DaveG.ca] | | `-- Extracting wayland-1.24.0_2: .......... done [pkg.DaveG.ca] | | `-- Extracting libva-2.22.0_1: .......... done [pkg.DaveG.ca] | | `-- Installing libvdpau-1.5... [pkg.DaveG.ca] | | `-- Extracting libvdpau-1.5: .......... done [pkg.DaveG.ca] | | `-- Installing libvorbis-1.3.7_2,3... [pkg.DaveG.ca] | | `-- Installing libogg-1.3.6,4... [pkg.DaveG.ca] | | `-- Extracting libogg-1.3.6,4: .......... done [pkg.DaveG.ca] | | `-- Extracting libvorbis-1.3.7_2,3: .......... done [pkg.DaveG.ca] | | `-- Installing libvpx-1.15.2... [pkg.DaveG.ca] | | `-- Extracting libvpx-1.15.2: .......... done [pkg.DaveG.ca] | | `-- Installing libx264-0.164.3095... [pkg.DaveG.ca] | | `-- Extracting libx264-0.164.3095: ...... done [pkg.DaveG.ca] | | `-- Installing opus-1.5.2... [pkg.DaveG.ca] | | `-- Extracting opus-1.5.2: .......... done [pkg.DaveG.ca] | | `-- Installing svt-av1-3.1.2... [pkg.DaveG.ca] | | `-- Extracting svt-av1-3.1.2: .......... done [pkg.DaveG.ca] | | `-- Installing x265-3.6_1... [pkg.DaveG.ca] | | `-- Extracting x265-3.6_1: .......... done [pkg.DaveG.ca] | `-- Extracting ffmpeg4-4.4.4_25: .......... done [pkg.DaveG.ca] | `-- Installing gtk2-2.24.33_1... [pkg.DaveG.ca] | | `-- Installing cups-2.4.14... [pkg.DaveG.ca] | | `-- Installing avahi-app-0.8_6... [pkg.DaveG.ca] | | | `-- Installing dbus-glib-0.114... [pkg.DaveG.ca] | | | `-- Extracting dbus-glib-0.114: .......... done [pkg.DaveG.ca] | | | `-- Installing gdbm-1.26... [pkg.DaveG.ca] | | | `-- Extracting gdbm-1.26: .......... done [pkg.DaveG.ca] | | | `-- Installing gnome_subr-1.0... [pkg.DaveG.ca] | | | `-- Extracting gnome_subr-1.0: . done [pkg.DaveG.ca] | | | `-- Installing libdaemon-0.14_1... [pkg.DaveG.ca] | | | `-- Extracting libdaemon-0.14_1: .......... done [pkg.DaveG.ca] | | | `-- Installing libevent-2.1.12... [pkg.DaveG.ca] | | | `-- Extracting libevent-2.1.12: .......... done ===> Creating groups Creating group 'avahi' with gid '558' ===> Creating users Creating user 'avahi' with uid '558' [pkg.DaveG.ca] | | `-- Extracting avahi-app-0.8_6: .......... done [pkg.DaveG.ca] | | `-- Installing libpaper-1.1.28_1... [pkg.DaveG.ca] | | `-- Extracting libpaper-1.1.28_1: .......... done ===> Creating groups Creating group 'cups' with gid '193' ===> Creating users Creating user 'cups' with uid '193' [pkg.DaveG.ca] | | `-- Extracting cups-2.4.14: .......... done [pkg.DaveG.ca] | | `-- Installing gtk-update-icon-cache-3.24.42... [pkg.DaveG.ca] | | `-- Extracting gtk-update-icon-cache-3.24.42: .......... done [pkg.DaveG.ca] | | `-- Installing hicolor-icon-theme-0.18... [pkg.DaveG.ca] | | `-- Extracting hicolor-icon-theme-0.18: . done [pkg.DaveG.ca] | | `-- Installing libXcomposite-0.4.6_1,1... [pkg.DaveG.ca] | | `-- Extracting libXcomposite-0.4.6_1,1: .......... done [pkg.DaveG.ca] | | `-- Installing libXcursor-1.2.3... [pkg.DaveG.ca] | | `-- Extracting libXcursor-1.2.3: .......... done [pkg.DaveG.ca] | | `-- Installing libXdamage-1.1.6... [pkg.DaveG.ca] | | `-- Extracting libXdamage-1.1.6: ...... done [pkg.DaveG.ca] | | `-- Installing libXinerama-1.1.5,1... [pkg.DaveG.ca] | | `-- Extracting libXinerama-1.1.5,1: .......... done [pkg.DaveG.ca] | `-- Extracting gtk2-2.24.33_1: .......... done [pkg.DaveG.ca] | `-- Installing gtk3-3.24.51... [pkg.DaveG.ca] | | `-- Installing adwaita-icon-theme-47.0... [pkg.DaveG.ca] | | `-- Installing adwaita-icon-theme-legacy-46.2... [pkg.DaveG.ca] | | `-- Extracting adwaita-icon-theme-legacy-46.2: .......... done [pkg.DaveG.ca] | | `-- Extracting adwaita-icon-theme-47.0: .......... done [pkg.DaveG.ca] | | `-- Installing colord-1.4.8... [pkg.DaveG.ca] | | `-- Installing libgudev-237... [pkg.DaveG.ca] | | `-- Extracting libgudev-237: .......... done [pkg.DaveG.ca] | | `-- Installing libgusb-0.4.9_1... [pkg.DaveG.ca] | | | `-- Installing json-glib-1.10.8... [pkg.DaveG.ca] | | | `-- Installing gobject-introspection-1.84.0,1... [pkg.DaveG.ca] | | | `-- Extracting gobject-introspection-1.84.0,1: .......... done [pkg.DaveG.ca] | | | `-- Extracting json-glib-1.10.8: .......... done [pkg.DaveG.ca] | | `-- Extracting libgusb-0.4.9_1: .......... done [pkg.DaveG.ca] | | `-- Installing polkit-125_1... [pkg.DaveG.ca] | | | `-- Installing duktape-lib-2.7.0_1... [pkg.DaveG.ca] | | | `-- Extracting duktape-lib-2.7.0_1: ...... done ===> Creating groups Creating group 'polkitd' with gid '565' ===> Creating users Creating user 'polkitd' with uid '565' [pkg.DaveG.ca] | | `-- Extracting polkit-125_1: ......... done ===> Creating groups Creating group 'colord' with gid '970' ===> Creating users Creating user 'colord' with uid '970' [pkg.DaveG.ca] | | `-- Extracting colord-1.4.8: .......... done [pkg.DaveG.ca] | | `-- Installing libepoxy-1.5.10... [pkg.DaveG.ca] | | `-- Extracting libepoxy-1.5.10: .......... done [pkg.DaveG.ca] | | `-- Installing librsvg2-rust-2.60.0_6... [pkg.DaveG.ca] | | `-- Extracting librsvg2-rust-2.60.0_6: .......... done [pkg.DaveG.ca] | | `-- Installing libxkbcommon-1.8.1_3... [pkg.DaveG.ca] | | `-- Installing xkeyboard-config-2.41_4... [pkg.DaveG.ca] | | `-- Extracting xkeyboard-config-2.41_4: .......... done [pkg.DaveG.ca] | | `-- Extracting libxkbcommon-1.8.1_3: .......... done [pkg.DaveG.ca] | `-- Extracting gtk3-3.24.51: .......... done [pkg.DaveG.ca] | `-- Installing libXxf86vm-1.1.6... [pkg.DaveG.ca] | `-- Extracting libXxf86vm-1.1.6: .......... done [pkg.DaveG.ca] | `-- Installing sndio-1.10.0_1... ===> Creating groups Creating group '_sndio' with gid '702' ===> Creating users Creating user '_sndio' with uid '702' [pkg.DaveG.ca] | `-- Extracting sndio-1.10.0_1: .......... done [pkg.DaveG.ca] `-- Extracting openjfx14-14.0.2.1+1_17: .......... done [pkg.DaveG.ca] Extracting igv-2.16.0_1: .......... done ==> Running trigger: gdk-pixbuf-query-loaders.ucl Generating gdk-pixbuf modules cache ==> Running trigger: gtk-update-icon-cache.ucl Generating GTK icon cache for /usr/local/share/icons/hicolor Generating GTK icon cache for /usr/local/share/icons/Adwaita Generating GTK icon cache for /usr/local/share/icons/AdwaitaLegacy ==> Running trigger: glib-schemas.ucl Compiling glib schemas Warning: Schema ?org.gnome.system.locale? has path ?/system/locale/?. Paths starting with ?/apps/?, ?/desktop/? or ?/system/? are deprecated. Warning: Schema ?org.gnome.system.proxy? has path ?/system/proxy/?. Paths starting with ?/apps/?, ?/desktop/? or ?/system/? are deprecated. Warning: Schema ?org.gnome.system.proxy.http? has path ?/system/proxy/http/?. Paths starting with ?/apps/?, ?/desktop/? or ?/system/? are deprecated. Warning: Schema ?org.gnome.system.proxy.https? has path ?/system/proxy/https/?. Paths starting with ?/apps/?, ?/desktop/? or ?/system/? are deprecated. Warning: Schema ?org.gnome.system.proxy.ftp? has path ?/system/proxy/ftp/?. Paths starting with ?/apps/?, ?/desktop/? or ?/system/? are deprecated. Warning: Schema ?org.gnome.system.proxy.socks? has path ?/system/proxy/socks/?. Paths starting with ?/apps/?, ?/desktop/? or ?/system/? are deprecated. ===== Message from openjdk11-11.0.27+6.1_2: -- This OpenJDK implementation may require procfs(5) mounted on /proc for some applications. If you have not done it yet, please do the following: mount -t procfs proc /proc To make it permanent, you need the following lines in /etc/fstab: proc /proc procfs rw 0 0 ===== Message from wayland-1.24.0_2: -- Wayland requires XDG_RUNTIME_DIR to be defined to a path that will contain "wayland-%d" unix(4) sockets. This is usually handled by consolekit2 (via ck-launch-session) or pam_xdg (via login). ===== Message from libxkbcommon-1.8.1_3: -- If arrow keys don't work under X11 switch to legacy rules e.g., For sh/bash/ksh/zsh run and (optionally) add into ~/.profile: export XKB_DEFAULT_RULES=xorg For csh/tcsh run and (optionally) add into ~/.login: setenv XKB_DEFAULT_RULES xorg ===== Message from openjfx14-14.0.2.1+1_17: -- ===> NOTICE: The openjfx14 port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> biostar-tools-2.0_1 depends on package: igv>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: gffread>0 - not found ===> Installing existing package /packages/All/gffread-0.12.7.pkg [pkg.DaveG.ca] Installing gffread-0.12.7... [pkg.DaveG.ca] Extracting gffread-0.12.7: . done ===> biostar-tools-2.0_1 depends on package: gffread>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on package: ucsc-userapps>0 - not found ===> Installing existing package /packages/All/ucsc-userapps-474.pkg [pkg.DaveG.ca] Installing ucsc-userapps-474... [pkg.DaveG.ca] `-- Installing libunwind-20240221_2... [pkg.DaveG.ca] `-- Extracting libunwind-20240221_2: .......... done [pkg.DaveG.ca] `-- Installing mysql80-client-8.0.43... [pkg.DaveG.ca] | `-- Installing cyrus-sasl-2.1.28_5... *** Added group `cyrus' (id 60) *** Added user `cyrus' (id 60) [pkg.DaveG.ca] | `-- Extracting cyrus-sasl-2.1.28_5: .......... done [pkg.DaveG.ca] | `-- Installing groff-1.23.0_5... [pkg.DaveG.ca] | | `-- Installing psutils-1.17_6... [pkg.DaveG.ca] | | `-- Extracting psutils-1.17_6: .......... done [pkg.DaveG.ca] | | `-- Installing uchardet-0.0.8_1... [pkg.DaveG.ca] | | `-- Extracting uchardet-0.0.8_1: .......... done [pkg.DaveG.ca] | `-- Extracting groff-1.23.0_5: .......... done [pkg.DaveG.ca] | `-- Installing hidapi-0.15.0... [pkg.DaveG.ca] | `-- Extracting hidapi-0.15.0: .......... done [pkg.DaveG.ca] | `-- Installing libfido2-1.16.0... [pkg.DaveG.ca] | | `-- Installing libcbor-0.13.0... [pkg.DaveG.ca] | | `-- Extracting libcbor-0.13.0: .......... done [pkg.DaveG.ca] | `-- Extracting libfido2-1.16.0: .......... done [pkg.DaveG.ca] | `-- Installing openldap26-client-2.6.10... [pkg.DaveG.ca] | `-- Extracting openldap26-client-2.6.10: .......... done [pkg.DaveG.ca] `-- Extracting mysql80-client-8.0.43: .......... done [pkg.DaveG.ca] Extracting ucsc-userapps-474: .......... done ===== Message from cyrus-sasl-2.1.28_5: -- You can use sasldb2 for authentication, to add users use: saslpasswd2 -c username If you want to enable SMTP AUTH with the system Sendmail, read Sendmail.README NOTE: This port has been compiled with a default pwcheck_method of auxprop. If you want to authenticate your user by /etc/passwd, PAM or LDAP, install ports/security/cyrus-sasl2-saslauthd and set sasl_pwcheck_method to saslauthd after installing the Cyrus-IMAPd 2.X port. You should also check the /usr/local/lib/sasl2/*.conf files for the correct pwcheck_method. If you want to use GSSAPI mechanism, install ports/security/cyrus-sasl2-gssapi. If you want to use SRP mechanism, install ports/security/cyrus-sasl2-srp. If you want to use LDAP auxprop plugin, install ports/security/cyrus-sasl2-ldapdb. ===== Message from groff-1.23.0_5: -- In order to be able to use the html driver, you need to install the following packages: - ghostscript - netpbm -- ===> NOTICE: The groff port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===== Message from openldap26-client-2.6.10: -- The OpenLDAP client package has been successfully installed. Edit /usr/local/etc/openldap/ldap.conf to change the system-wide client defaults. Try `man ldap.conf' and visit the OpenLDAP FAQ-O-Matic at http://www.OpenLDAP.org/faq/index.cgi?file=3 for more information. ===== Message from mysql80-client-8.0.43: -- This is the mysql CLIENT without the server. for complete server and client, please install databases/mysql80-server ===== Message from ucsc-userapps-474: -- ucsc-kentutils is installed in it's own directory in order to avoid install conflicts with other ports. Run "ucsc-shell" to gain access to ucsc-kentutils commands in your PATH. This port installs only freely available components of the UCSC userApps distribution. See http://genome.ucsc.edu/license/ for more information. ===> biostar-tools-2.0_1 depends on package: ucsc-userapps>0 - found ===> Returning to build of biostar-tools-2.0_1 ===> biostar-tools-2.0_1 depends on file: /usr/local/bin/python3.11 - found ===> biostar-tools-2.0_1 depends on package: sra-tools>0 - not found ===> Installing existing package /packages/All/sra-tools-3.2.1.pkg [pkg.DaveG.ca] Installing sra-tools-3.2.1... [pkg.DaveG.ca] Extracting sra-tools-3.2.1: .......... done ===> biostar-tools-2.0_1 depends on package: sra-tools>0 - found ===> Returning to build of biostar-tools-2.0_1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for biostar-tools-2.0_1 ===> Generating temporary packing list install -m 555 /wrkdirs/usr/ports/biology/biostar-tools/work/biostar-shell /wrkdirs/usr/ports/biology/biostar-tools/work/stage/usr/local/bin ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2025-11-04T00:08:31+0000' 'PKG_NOTE_ports_top_git_hash=9bb805acfc67' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=b304d8ab18ac' '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 biostar-tools-2.0_1 ===> Building biostar-tools-2.0_1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for biostar-tools-2.0_1 build of biology/biostar-tools | biostar-tools-2.0_1 ended at Mon Nov 3 19:19:01 EST 2025 build time: 00:10:32