=>> Building biology/ruby-bio build started at Tue Mar 17 10:11:19 EDT 2026 port directory: /usr/ports/biology/ruby-bio package name: ruby33-bio-1.5.1 building for: FreeBSD pkg.DaveG.ca 15.0-RELEASE-p3 FreeBSD 15.0-RELEASE-p3 1500068 amd64 maintained by: mauricio@arareko.net Makefile datestamp: -rw-r--r-- 1 root wheel 1547 Aug 27 2024 /usr/ports/biology/ruby-bio/Makefile Ports top last git commit: 8c988f802ea2 Ports top unclean checkout: no Port dir last git commit: 18c6e1827669 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1500068 Job Id: 13 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1500068 UNAME_v=FreeBSD 15.0-RELEASE-p3 1500068 UNAME_r=15.0-RELEASE-p3 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_15_0_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_15_0_x64-HEAD-ALL/13/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_15_0_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_15_0_x64-HEAD-ALL/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for ruby33-bio-1.5.1: BDB4=off: bdb4 support for faster flat file indexing DOCS=on: Build and/or install documentation MYSQL=off: MySQL database support PGSQL=off: PostgreSQL database support ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- mauricio@arareko.net --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/ruby-bio/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/ruby-bio/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/ruby-bio/work/.cache HOME=/wrkdirs/usr/ports/biology/ruby-bio/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/ruby-bio/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/ruby-bio/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/ruby-bio/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/ruby-bio/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/ruby-bio/work/.cache HOME=/wrkdirs/usr/ports/biology/ruby-bio/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/ruby-bio/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/ruby-bio/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- PORTDOCS="" RUBY_LIBDIR="lib/ruby/3.3" RUBY_ARCHLIBDIR="lib/ruby/3.3/amd64-freebsd15" RUBY_SITELIBDIR="lib/ruby/site_ruby/3.3" RUBY_SITEARCHLIBDIR="lib/ruby/site_ruby/3.3/amd64-freebsd15" RUBY_VENDORLIBDIR="lib/ruby/vendor_ruby/3.3" RUBY_VENDORARCHLIBDIR="lib/ruby/vendor_ruby/3.3/amd64-freebsd15" RUBY_MODDOCDIR="share/doc/ruby33/bio" RUBY_MODEXAMPLESDIR="share/examples/ruby33/bio" RUBY_DOCDIR="share/doc/ruby33" RUBY_EXAMPLESDIR="share/examples/ruby33" RUBY_RIDIR="share/ri/3.3/system" RUBY_SITERIDIR="share/ri/3.3/site" RUBY_VERSION="3.3.10" RUBY_VER="3.3" RUBY_SHLIBVER="33" RUBY_ARCH="amd64-freebsd15" RUBY_SUFFIX="33" RUBY_DEFAULT_SUFFIX="33" OSREL=15.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/bio" EXAMPLESDIR="share/examples/bio" DATADIR="share/bio" WWWDIR="www/bio" ETCDIR="etc/bio" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/bio DOCSDIR=/usr/local/share/doc/bio EXAMPLESDIR=/usr/local/share/examples/bio WWWDIR=/usr/local/www/bio ETCDIR=/usr/local/etc/bio --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 ===> ruby33-bio-1.5.1 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 ===> ruby33-bio-1.5.1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of ruby33-bio-1.5.1 =========================================================================== =================================================== ===== 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 ruby33-bio-1.5.1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by ruby33-bio-1.5.1 for building => SHA256 Checksum OK for ruby/bioruby-1.5.1.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> ruby33-bio-1.5.1 depends on file: /usr/local/bin/ruby33 - not found ===> Installing existing package /packages/All/ruby-3.3.10,1.pkg [pkg.DaveG.ca] Installing ruby-3.3.10,1... [pkg.DaveG.ca] `-- Installing libffi-3.5.1... [pkg.DaveG.ca] | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] `-- Extracting libffi-3.5.1: .......... done [pkg.DaveG.ca] `-- Installing libunwind-20250904... [pkg.DaveG.ca] `-- Extracting libunwind-20250904: .......... done [pkg.DaveG.ca] `-- Installing libyaml-0.2.5... [pkg.DaveG.ca] `-- Extracting libyaml-0.2.5: ...... done [pkg.DaveG.ca] Extracting ruby-3.3.10,1: .......... done ===== Message from ruby-3.3.10,1: -- Some of the standard commands and libraries are provided as separate ports for ease of upgrading: devel/ruby-gems: gem - RubyGems package manager devel/rubygem-debug: debug - Debugging functionality for Ruby devel/rubygem-erb: erb - Templating system for Ruby devel/rubygem-irb: irb - Interactive Ruby devel/rubygem-minitest: minitest - Complete suite of testing facilities devel/rubygem-power_assert: power_assert - Power Assert for Ruby devel/rubygem-racc: racc - LALR(1) parser generator for Ruby devel/rubygem-rake: rake - Ruby Make devel/rubygem-rbs: rbs - Language for type signatures for Ruby and standard library definitions devel/rubygem-rdoc: rdoc - Ruby Documentation System devel/rubygem-test-unit: test-unit - Unit testing framework for Ruby devel/rubygem-typeprof: typeprof - Type analysis tool for Ruby code ftp/rubygem-net-ftp: net-ftp - Support for the File Transfer Protocol mail/rubygem-net-imap: net-imap - Ruby client api for Internet Message Access Protocol mail/rubygem-net-pop: net-pop - Ruby client library for POP3 mail/rubygem-net-smtp: net-smtp - Simple Mail Transfer Protocol client library for Ruby math/rubygem-matrix: matrix - Implementation of Matrix and Vector classes math/rubygem-prime: prime - Prime numbers and factorization library sysutils/rubygem-bundler: bundler - Tool that manages gem dependencies for ruby applications textproc/rubygem-rexml: rexml - XML toolkit for Ruby www/rubygem-rss: rss - Family of libraries that support various formats of XML "feeds" Install them as occasion demands. ===> ruby33-bio-1.5.1 depends on file: /usr/local/bin/ruby33 - found ===> Returning to build of ruby33-bio-1.5.1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by ruby33-bio-1.5.1 for building ===> Extracting for ruby33-bio-1.5.1 => SHA256 Checksum OK for ruby/bioruby-1.5.1.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> ruby33-bio-1.5.1 depends on file: /usr/local/bin/ruby33 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for ruby33-bio-1.5.1 /usr/local/bin/ruby33 -i -pe 'gsub(%r"(/etc/bioinformatics/)") { "/usr/local" + $1 }' /wrkdirs/usr/ports/biology/ruby-bio/work/bioruby-1.5.1/doc/Tutorial.rd /wrkdirs/usr/ports/biology/ruby-bio/work/bioruby-1.5.1/lib/bio/io/registry.rb =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> ruby33-bio-1.5.1 depends on file: /usr/local/bin/ruby33 - found ===> ruby33-bio-1.5.1 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg.DaveG.ca] Installing ccache-3.7.12_8... [pkg.DaveG.ca] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> ruby33-bio-1.5.1 depends on file: /usr/local/bin/ccache - found ===> Returning to build of ruby33-bio-1.5.1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for ruby33-bio-1.5.1 ===> Running setup.rb to configure ---> bin <--- bin ---> lib ---> lib/bio ---> lib/bio/util ---> lib/bio/util/restriction_enzyme ---> lib/bio/util/restriction_enzyme/range ---> lib/bio/util/restriction_enzyme/range/sequence_range <--- lib/bio/util/restriction_enzyme/range/sequence_range <--- lib/bio/util/restriction_enzyme/range ---> lib/bio/util/restriction_enzyme/single_strand <--- lib/bio/util/restriction_enzyme/single_strand ---> lib/bio/util/restriction_enzyme/double_stranded <--- lib/bio/util/restriction_enzyme/double_stranded <--- lib/bio/util/restriction_enzyme ---> lib/bio/util/color_scheme <--- lib/bio/util/color_scheme <--- lib/bio/util ---> lib/bio/shell ---> lib/bio/shell/plugin <--- lib/bio/shell/plugin ---> lib/bio/shell/rails ---> lib/bio/shell/rails/vendor ---> lib/bio/shell/rails/vendor/plugins ---> lib/bio/shell/rails/vendor/plugins/bioruby ---> lib/bio/shell/rails/vendor/plugins/bioruby/generators ---> lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby ---> lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates <--- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates <--- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby <--- lib/bio/shell/rails/vendor/plugins/bioruby/generators <--- lib/bio/shell/rails/vendor/plugins/bioruby <--- lib/bio/shell/rails/vendor/plugins <--- lib/bio/shell/rails/vendor <--- lib/bio/shell/rails <--- lib/bio/shell ---> lib/bio/sequence <--- lib/bio/sequence ---> lib/bio/compat <--- lib/bio/compat ---> lib/bio/io ---> lib/bio/io/biosql ---> lib/bio/io/biosql/config <--- lib/bio/io/biosql/config <--- lib/bio/io/biosql ---> lib/bio/io/flatfile <--- lib/bio/io/flatfile <--- lib/bio/io ---> lib/bio/tree <--- lib/bio/tree ---> lib/bio/db ---> lib/bio/db/fasta <--- lib/bio/db/fasta ---> lib/bio/db/fastq <--- lib/bio/db/fastq ---> lib/bio/db/kegg <--- lib/bio/db/kegg ---> lib/bio/db/embl <--- lib/bio/db/embl ---> lib/bio/db/phyloxml <--- lib/bio/db/phyloxml ---> lib/bio/db/genbank <--- lib/bio/db/genbank ---> lib/bio/db/pdb <--- lib/bio/db/pdb ---> lib/bio/db/biosql <--- lib/bio/db/biosql ---> lib/bio/db/sanger_chromatogram <--- lib/bio/db/sanger_chromatogram <--- lib/bio/db ---> lib/bio/data <--- lib/bio/data ---> lib/bio/appl ---> lib/bio/appl/spidey <--- lib/bio/appl/spidey ---> lib/bio/appl/bl2seq <--- lib/bio/appl/bl2seq ---> lib/bio/appl/tmhmm <--- lib/bio/appl/tmhmm ---> lib/bio/appl/fasta <--- lib/bio/appl/fasta ---> lib/bio/appl/mafft <--- lib/bio/appl/mafft ---> lib/bio/appl/hmmer <--- lib/bio/appl/hmmer ---> lib/bio/appl/psort <--- lib/bio/appl/psort ---> lib/bio/appl/phylip <--- lib/bio/appl/phylip ---> lib/bio/appl/meme ---> lib/bio/appl/meme/mast <--- lib/bio/appl/meme/mast <--- lib/bio/appl/meme ---> lib/bio/appl/clustalw <--- lib/bio/appl/clustalw ---> lib/bio/appl/paml ---> lib/bio/appl/paml/codeml <--- lib/bio/appl/paml/codeml ---> lib/bio/appl/paml/baseml <--- lib/bio/appl/paml/baseml ---> lib/bio/appl/paml/yn00 <--- lib/bio/appl/paml/yn00 <--- lib/bio/appl/paml ---> lib/bio/appl/genscan <--- lib/bio/appl/genscan ---> lib/bio/appl/targetp <--- lib/bio/appl/targetp ---> lib/bio/appl/iprscan <--- lib/bio/appl/iprscan ---> lib/bio/appl/blast <--- lib/bio/appl/blast ---> lib/bio/appl/sosui <--- lib/bio/appl/sosui ---> lib/bio/appl/sim4 <--- lib/bio/appl/sim4 ---> lib/bio/appl/blat <--- lib/bio/appl/blat ---> lib/bio/appl/gcg <--- lib/bio/appl/gcg <--- lib/bio/appl <--- lib/bio <--- lib =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for ruby33-bio-1.5.1 ===> Running setup.rb to build ---> bin updating shebang: br_biogetseq.rb updating shebang: br_biofetch.rb updating shebang: br_pmfetch.rb updating shebang: br_bioflat.rb updating shebang: bioruby <--- bin ---> lib ---> lib/bio ---> lib/bio/util ---> lib/bio/util/restriction_enzyme ---> lib/bio/util/restriction_enzyme/range ---> lib/bio/util/restriction_enzyme/range/sequence_range <--- lib/bio/util/restriction_enzyme/range/sequence_range <--- lib/bio/util/restriction_enzyme/range ---> lib/bio/util/restriction_enzyme/single_strand <--- lib/bio/util/restriction_enzyme/single_strand ---> lib/bio/util/restriction_enzyme/double_stranded <--- lib/bio/util/restriction_enzyme/double_stranded <--- lib/bio/util/restriction_enzyme ---> lib/bio/util/color_scheme <--- lib/bio/util/color_scheme <--- lib/bio/util ---> lib/bio/shell ---> lib/bio/shell/plugin <--- lib/bio/shell/plugin ---> lib/bio/shell/rails ---> lib/bio/shell/rails/vendor ---> lib/bio/shell/rails/vendor/plugins ---> lib/bio/shell/rails/vendor/plugins/bioruby ---> lib/bio/shell/rails/vendor/plugins/bioruby/generators ---> lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby ---> lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates <--- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates <--- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby <--- lib/bio/shell/rails/vendor/plugins/bioruby/generators <--- lib/bio/shell/rails/vendor/plugins/bioruby <--- lib/bio/shell/rails/vendor/plugins <--- lib/bio/shell/rails/vendor <--- lib/bio/shell/rails <--- lib/bio/shell ---> lib/bio/sequence <--- lib/bio/sequence ---> lib/bio/compat <--- lib/bio/compat ---> lib/bio/io ---> lib/bio/io/biosql ---> lib/bio/io/biosql/config <--- lib/bio/io/biosql/config <--- lib/bio/io/biosql ---> lib/bio/io/flatfile <--- lib/bio/io/flatfile <--- lib/bio/io ---> lib/bio/tree <--- lib/bio/tree ---> lib/bio/db ---> lib/bio/db/fasta <--- lib/bio/db/fasta ---> lib/bio/db/fastq <--- lib/bio/db/fastq ---> lib/bio/db/kegg <--- lib/bio/db/kegg ---> lib/bio/db/embl <--- lib/bio/db/embl ---> lib/bio/db/phyloxml <--- lib/bio/db/phyloxml ---> lib/bio/db/genbank <--- lib/bio/db/genbank ---> lib/bio/db/pdb <--- lib/bio/db/pdb ---> lib/bio/db/biosql <--- lib/bio/db/biosql ---> lib/bio/db/sanger_chromatogram <--- lib/bio/db/sanger_chromatogram <--- lib/bio/db ---> lib/bio/data <--- lib/bio/data ---> lib/bio/appl ---> lib/bio/appl/spidey <--- lib/bio/appl/spidey ---> lib/bio/appl/bl2seq <--- lib/bio/appl/bl2seq ---> lib/bio/appl/tmhmm <--- lib/bio/appl/tmhmm ---> lib/bio/appl/fasta <--- lib/bio/appl/fasta ---> lib/bio/appl/mafft <--- lib/bio/appl/mafft ---> lib/bio/appl/hmmer <--- lib/bio/appl/hmmer ---> lib/bio/appl/psort <--- lib/bio/appl/psort ---> lib/bio/appl/phylip <--- lib/bio/appl/phylip ---> lib/bio/appl/meme ---> lib/bio/appl/meme/mast <--- lib/bio/appl/meme/mast <--- lib/bio/appl/meme ---> lib/bio/appl/clustalw <--- lib/bio/appl/clustalw ---> lib/bio/appl/paml ---> lib/bio/appl/paml/codeml <--- lib/bio/appl/paml/codeml ---> lib/bio/appl/paml/baseml <--- lib/bio/appl/paml/baseml ---> lib/bio/appl/paml/yn00 <--- lib/bio/appl/paml/yn00 <--- lib/bio/appl/paml ---> lib/bio/appl/genscan <--- lib/bio/appl/genscan ---> lib/bio/appl/targetp <--- lib/bio/appl/targetp ---> lib/bio/appl/iprscan <--- lib/bio/appl/iprscan ---> lib/bio/appl/blast <--- lib/bio/appl/blast ---> lib/bio/appl/sosui <--- lib/bio/appl/sosui ---> lib/bio/appl/sim4 <--- lib/bio/appl/sim4 ---> lib/bio/appl/blat <--- lib/bio/appl/blat ---> lib/bio/appl/gcg <--- lib/bio/appl/gcg <--- lib/bio/appl <--- lib/bio <--- lib =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> ruby33-bio-1.5.1 depends on file: /usr/local/bin/ruby33 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for ruby33-bio-1.5.1 ===> Generating temporary packing list ===> Running setup.rb to install rm -f InstalledFiles ---> bin mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/bin install br_biogetseq.rb /usr/local/bin//br_biogetseq install br_biofetch.rb /usr/local/bin//br_biofetch install br_pmfetch.rb /usr/local/bin//br_pmfetch install br_bioflat.rb /usr/local/bin//br_bioflat install bioruby /usr/local/bin//bioruby <--- bin ---> lib mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3 install bio.rb /usr/local/lib/ruby/site_ruby/3.3/ ---> lib/bio mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio install db.rb /usr/local/lib/ruby/site_ruby/3.3/bio install tree.rb /usr/local/lib/ruby/site_ruby/3.3/bio install reference.rb /usr/local/lib/ruby/site_ruby/3.3/bio install shell.rb /usr/local/lib/ruby/site_ruby/3.3/bio install command.rb /usr/local/lib/ruby/site_ruby/3.3/bio install version.rb /usr/local/lib/ruby/site_ruby/3.3/bio install feature.rb /usr/local/lib/ruby/site_ruby/3.3/bio install pathway.rb /usr/local/lib/ruby/site_ruby/3.3/bio install location.rb /usr/local/lib/ruby/site_ruby/3.3/bio install map.rb /usr/local/lib/ruby/site_ruby/3.3/bio install alignment.rb /usr/local/lib/ruby/site_ruby/3.3/bio install sequence.rb /usr/local/lib/ruby/site_ruby/3.3/bio ---> lib/bio/util mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/util install color_scheme.rb /usr/local/lib/ruby/site_ruby/3.3/bio/util install contingency_table.rb /usr/local/lib/ruby/site_ruby/3.3/bio/util install sirna.rb /usr/local/lib/ruby/site_ruby/3.3/bio/util install restriction_enzyme.rb /usr/local/lib/ruby/site_ruby/3.3/bio/util ---> lib/bio/util/restriction_enzyme mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/util/restriction_enzyme install single_strand.rb /usr/local/lib/ruby/site_ruby/3.3/bio/util/restriction_enzyme install string_formatting.rb /usr/local/lib/ruby/site_ruby/3.3/bio/util/restriction_enzyme install analysis.rb /usr/local/lib/ruby/site_ruby/3.3/bio/util/restriction_enzyme install cut_symbol.rb /usr/local/lib/ruby/site_ruby/3.3/bio/util/restriction_enzyme install dense_int_array.rb /usr/local/lib/ruby/site_ruby/3.3/bio/util/restriction_enzyme install analysis_basic.rb /usr/local/lib/ruby/site_ruby/3.3/bio/util/restriction_enzyme install double_stranded.rb /usr/local/lib/ruby/site_ruby/3.3/bio/util/restriction_enzyme install enzymes.yaml /usr/local/lib/ruby/site_ruby/3.3/bio/util/restriction_enzyme install sorted_num_array.rb /usr/local/lib/ruby/site_ruby/3.3/bio/util/restriction_enzyme install single_strand_complement.rb /usr/local/lib/ruby/site_ruby/3.3/bio/util/restriction_enzyme ---> lib/bio/util/restriction_enzyme/range mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/util/restriction_enzyme/range install sequence_range.rb /usr/local/lib/ruby/site_ruby/3.3/bio/util/restriction_enzyme/range install horizontal_cut_range.rb /usr/local/lib/ruby/site_ruby/3.3/bio/util/restriction_enzyme/range install vertical_cut_range.rb /usr/local/lib/ruby/site_ruby/3.3/bio/util/restriction_enzyme/range install cut_ranges.rb /usr/local/lib/ruby/site_ruby/3.3/bio/util/restriction_enzyme/range install cut_range.rb /usr/local/lib/ruby/site_ruby/3.3/bio/util/restriction_enzyme/range ---> lib/bio/util/restriction_enzyme/range/sequence_range mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/util/restriction_enzyme/range/sequence_range install calculated_cuts.rb /usr/local/lib/ruby/site_ruby/3.3/bio/util/restriction_enzyme/range/sequence_range install fragments.rb /usr/local/lib/ruby/site_ruby/3.3/bio/util/restriction_enzyme/range/sequence_range install fragment.rb /usr/local/lib/ruby/site_ruby/3.3/bio/util/restriction_enzyme/range/sequence_range <--- lib/bio/util/restriction_enzyme/range/sequence_range <--- lib/bio/util/restriction_enzyme/range ---> lib/bio/util/restriction_enzyme/single_strand mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/util/restriction_enzyme/single_strand install cut_locations_in_enzyme_notation.rb /usr/local/lib/ruby/site_ruby/3.3/bio/util/restriction_enzyme/single_strand <--- lib/bio/util/restriction_enzyme/single_strand ---> lib/bio/util/restriction_enzyme/double_stranded mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/util/restriction_enzyme/double_stranded install cut_location_pair.rb /usr/local/lib/ruby/site_ruby/3.3/bio/util/restriction_enzyme/double_stranded install cut_locations.rb /usr/local/lib/ruby/site_ruby/3.3/bio/util/restriction_enzyme/double_stranded install cut_locations_in_enzyme_notation.rb /usr/local/lib/ruby/site_ruby/3.3/bio/util/restriction_enzyme/double_stranded install aligned_strands.rb /usr/local/lib/ruby/site_ruby/3.3/bio/util/restriction_enzyme/double_stranded install cut_location_pair_in_enzyme_notation.rb /usr/local/lib/ruby/site_ruby/3.3/bio/util/restriction_enzyme/double_stranded <--- lib/bio/util/restriction_enzyme/double_stranded <--- lib/bio/util/restriction_enzyme ---> lib/bio/util/color_scheme mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/util/color_scheme install helix.rb /usr/local/lib/ruby/site_ruby/3.3/bio/util/color_scheme install strand.rb /usr/local/lib/ruby/site_ruby/3.3/bio/util/color_scheme install turn.rb /usr/local/lib/ruby/site_ruby/3.3/bio/util/color_scheme install buried.rb /usr/local/lib/ruby/site_ruby/3.3/bio/util/color_scheme install hydropathy.rb /usr/local/lib/ruby/site_ruby/3.3/bio/util/color_scheme install nucleotide.rb /usr/local/lib/ruby/site_ruby/3.3/bio/util/color_scheme install zappo.rb /usr/local/lib/ruby/site_ruby/3.3/bio/util/color_scheme install taylor.rb /usr/local/lib/ruby/site_ruby/3.3/bio/util/color_scheme <--- lib/bio/util/color_scheme <--- lib/bio/util ---> lib/bio/shell mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/shell install irb.rb /usr/local/lib/ruby/site_ruby/3.3/bio/shell install object.rb /usr/local/lib/ruby/site_ruby/3.3/bio/shell install interface.rb /usr/local/lib/ruby/site_ruby/3.3/bio/shell install setup.rb /usr/local/lib/ruby/site_ruby/3.3/bio/shell install web.rb /usr/local/lib/ruby/site_ruby/3.3/bio/shell install script.rb /usr/local/lib/ruby/site_ruby/3.3/bio/shell install core.rb /usr/local/lib/ruby/site_ruby/3.3/bio/shell install demo.rb /usr/local/lib/ruby/site_ruby/3.3/bio/shell ---> lib/bio/shell/plugin mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/shell/plugin install das.rb /usr/local/lib/ruby/site_ruby/3.3/bio/shell/plugin install midi.rb /usr/local/lib/ruby/site_ruby/3.3/bio/shell/plugin install obda.rb /usr/local/lib/ruby/site_ruby/3.3/bio/shell/plugin install codon.rb /usr/local/lib/ruby/site_ruby/3.3/bio/shell/plugin install psort.rb /usr/local/lib/ruby/site_ruby/3.3/bio/shell/plugin install togows.rb /usr/local/lib/ruby/site_ruby/3.3/bio/shell/plugin install blast.rb /usr/local/lib/ruby/site_ruby/3.3/bio/shell/plugin install flatfile.rb /usr/local/lib/ruby/site_ruby/3.3/bio/shell/plugin install entry.rb /usr/local/lib/ruby/site_ruby/3.3/bio/shell/plugin install seq.rb /usr/local/lib/ruby/site_ruby/3.3/bio/shell/plugin install ncbirest.rb /usr/local/lib/ruby/site_ruby/3.3/bio/shell/plugin install emboss.rb /usr/local/lib/ruby/site_ruby/3.3/bio/shell/plugin <--- lib/bio/shell/plugin ---> lib/bio/shell/rails mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/shell/rails ---> lib/bio/shell/rails/vendor mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/shell/rails/vendor ---> lib/bio/shell/rails/vendor/plugins mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/shell/rails/vendor/plugins ---> lib/bio/shell/rails/vendor/plugins/bioruby mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/shell/rails/vendor/plugins/bioruby ---> lib/bio/shell/rails/vendor/plugins/bioruby/generators mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/shell/rails/vendor/plugins/bioruby/generators ---> lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby install bioruby_generator.rb /usr/local/lib/ruby/site_ruby/3.3/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby ---> lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install bioruby_controller.rb /usr/local/lib/ruby/site_ruby/3.3/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install bioruby-bg.gif /usr/local/lib/ruby/site_ruby/3.3/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install _classes.rhtml /usr/local/lib/ruby/site_ruby/3.3/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install _methods.rhtml /usr/local/lib/ruby/site_ruby/3.3/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install commands.rhtml /usr/local/lib/ruby/site_ruby/3.3/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install index.rhtml /usr/local/lib/ruby/site_ruby/3.3/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install bioruby-gem.png /usr/local/lib/ruby/site_ruby/3.3/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install _modules.rhtml /usr/local/lib/ruby/site_ruby/3.3/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install spinner.gif /usr/local/lib/ruby/site_ruby/3.3/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install _variables.rhtml /usr/local/lib/ruby/site_ruby/3.3/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install bioruby.css /usr/local/lib/ruby/site_ruby/3.3/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install _log.rhtml /usr/local/lib/ruby/site_ruby/3.3/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install history.rhtml /usr/local/lib/ruby/site_ruby/3.3/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install bioruby-link.gif /usr/local/lib/ruby/site_ruby/3.3/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install bioruby.rhtml /usr/local/lib/ruby/site_ruby/3.3/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install bioruby_helper.rb /usr/local/lib/ruby/site_ruby/3.3/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates <--- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates <--- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby <--- lib/bio/shell/rails/vendor/plugins/bioruby/generators <--- lib/bio/shell/rails/vendor/plugins/bioruby <--- lib/bio/shell/rails/vendor/plugins <--- lib/bio/shell/rails/vendor <--- lib/bio/shell/rails <--- lib/bio/shell ---> lib/bio/sequence mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/sequence install na.rb /usr/local/lib/ruby/site_ruby/3.3/bio/sequence install quality_score.rb /usr/local/lib/ruby/site_ruby/3.3/bio/sequence install sequence_masker.rb /usr/local/lib/ruby/site_ruby/3.3/bio/sequence install generic.rb /usr/local/lib/ruby/site_ruby/3.3/bio/sequence install compat.rb /usr/local/lib/ruby/site_ruby/3.3/bio/sequence install common.rb /usr/local/lib/ruby/site_ruby/3.3/bio/sequence install aa.rb /usr/local/lib/ruby/site_ruby/3.3/bio/sequence install dblink.rb /usr/local/lib/ruby/site_ruby/3.3/bio/sequence install format_raw.rb /usr/local/lib/ruby/site_ruby/3.3/bio/sequence install format.rb /usr/local/lib/ruby/site_ruby/3.3/bio/sequence install adapter.rb /usr/local/lib/ruby/site_ruby/3.3/bio/sequence <--- lib/bio/sequence ---> lib/bio/compat mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/compat install features.rb /usr/local/lib/ruby/site_ruby/3.3/bio/compat install references.rb /usr/local/lib/ruby/site_ruby/3.3/bio/compat <--- lib/bio/compat ---> lib/bio/io mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/io install hinv.rb /usr/local/lib/ruby/site_ruby/3.3/bio/io install fetch.rb /usr/local/lib/ruby/site_ruby/3.3/bio/io install das.rb /usr/local/lib/ruby/site_ruby/3.3/bio/io install registry.rb /usr/local/lib/ruby/site_ruby/3.3/bio/io install fastacmd.rb /usr/local/lib/ruby/site_ruby/3.3/bio/io install togows.rb /usr/local/lib/ruby/site_ruby/3.3/bio/io install sql.rb /usr/local/lib/ruby/site_ruby/3.3/bio/io install flatfile.rb /usr/local/lib/ruby/site_ruby/3.3/bio/io install pubmed.rb /usr/local/lib/ruby/site_ruby/3.3/bio/io install ncbirest.rb /usr/local/lib/ruby/site_ruby/3.3/bio/io ---> lib/bio/io/biosql mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/io/biosql install biosql.rb /usr/local/lib/ruby/site_ruby/3.3/bio/io/biosql install ar-biosql.rb /usr/local/lib/ruby/site_ruby/3.3/bio/io/biosql ---> lib/bio/io/biosql/config mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/io/biosql/config install database.yml /usr/local/lib/ruby/site_ruby/3.3/bio/io/biosql/config <--- lib/bio/io/biosql/config <--- lib/bio/io/biosql ---> lib/bio/io/flatfile mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/io/flatfile install bdb.rb /usr/local/lib/ruby/site_ruby/3.3/bio/io/flatfile install indexer.rb /usr/local/lib/ruby/site_ruby/3.3/bio/io/flatfile install buffer.rb /usr/local/lib/ruby/site_ruby/3.3/bio/io/flatfile install splitter.rb /usr/local/lib/ruby/site_ruby/3.3/bio/io/flatfile install autodetection.rb /usr/local/lib/ruby/site_ruby/3.3/bio/io/flatfile install index.rb /usr/local/lib/ruby/site_ruby/3.3/bio/io/flatfile <--- lib/bio/io/flatfile <--- lib/bio/io ---> lib/bio/tree mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/tree install output.rb /usr/local/lib/ruby/site_ruby/3.3/bio/tree <--- lib/bio/tree ---> lib/bio/db mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/db install fastq.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db install aaindex.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db install rebase.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db install lasergene.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db install prosite.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db install litdb.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db install nbrf.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db install medline.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db install transfac.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db install pdb.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db install soft.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db install fasta.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db install fantom.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db install newick.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db install nexus.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db install gff.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db install go.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db ---> lib/bio/db/fasta mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/db/fasta install qual_to_biosequence.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/fasta install format_fasta.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/fasta install format_qual.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/fasta install qual.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/fasta install fasta_to_biosequence.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/fasta install defline.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/fasta <--- lib/bio/db/fasta ---> lib/bio/db/fastq mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/db/fastq install fastq_to_biosequence.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/fastq install format_fastq.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/fastq <--- lib/bio/db/fastq ---> lib/bio/db/kegg mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/db/kegg install genes.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/kegg install brite.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/kegg install compound.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/kegg install common.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/kegg install genome.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/kegg install drug.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/kegg install orthology.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/kegg install pathway.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/kegg install keggtab.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/kegg install expression.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/kegg install reaction.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/kegg install module.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/kegg install glycan.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/kegg install kgml.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/kegg install enzyme.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/kegg <--- lib/bio/db/kegg ---> lib/bio/db/embl mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/db/embl install uniprot.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/embl install common.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/embl install uniprotkb.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/embl install sptr.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/embl install format_embl.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/embl install embl.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/embl install trembl.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/embl install embl_to_biosequence.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/embl install swissprot.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/embl <--- lib/bio/db/embl ---> lib/bio/db/phyloxml mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/db/phyloxml install phyloxml_elements.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/phyloxml install phyloxml.xsd /usr/local/lib/ruby/site_ruby/3.3/bio/db/phyloxml install phyloxml_writer.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/phyloxml install phyloxml_parser.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/phyloxml <--- lib/bio/db/phyloxml ---> lib/bio/db/genbank mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/db/genbank install ddbj.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/genbank install format_genbank.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/genbank install common.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/genbank install genbank_to_biosequence.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/genbank install refseq.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/genbank install genpept.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/genbank install genbank.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/genbank <--- lib/bio/db/genbank ---> lib/bio/db/pdb mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/db/pdb install chemicalcomponent.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/pdb install chain.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/pdb install residue.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/pdb install pdb.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/pdb install model.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/pdb install utils.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/pdb install atom.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/pdb <--- lib/bio/db/pdb ---> lib/bio/db/biosql mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/db/biosql install biosql_to_biosequence.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/biosql install sequence.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/biosql <--- lib/bio/db/biosql ---> lib/bio/db/sanger_chromatogram mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/db/sanger_chromatogram install scf.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/sanger_chromatogram install chromatogram.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/sanger_chromatogram install chromatogram_to_biosequence.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/sanger_chromatogram install abif.rb /usr/local/lib/ruby/site_ruby/3.3/bio/db/sanger_chromatogram <--- lib/bio/db/sanger_chromatogram <--- lib/bio/db ---> lib/bio/data mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/data install na.rb /usr/local/lib/ruby/site_ruby/3.3/bio/data install aa.rb /usr/local/lib/ruby/site_ruby/3.3/bio/data install codontable.rb /usr/local/lib/ruby/site_ruby/3.3/bio/data <--- lib/bio/data ---> lib/bio/appl mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/appl install clustalw.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl install pts1.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl install tcoffee.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl install muscle.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl install probcons.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl install hmmer.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl install psort.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl install mafft.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl install fasta.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl install blast.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl install sim4.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl install emboss.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl ---> lib/bio/appl/spidey mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/appl/spidey install report.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl/spidey <--- lib/bio/appl/spidey ---> lib/bio/appl/bl2seq mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/appl/bl2seq install report.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl/bl2seq <--- lib/bio/appl/bl2seq ---> lib/bio/appl/tmhmm mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/appl/tmhmm install report.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl/tmhmm <--- lib/bio/appl/tmhmm ---> lib/bio/appl/fasta mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/appl/fasta install format10.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl/fasta <--- lib/bio/appl/fasta ---> lib/bio/appl/mafft mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/appl/mafft install report.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl/mafft <--- lib/bio/appl/mafft ---> lib/bio/appl/hmmer mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/appl/hmmer install report.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl/hmmer <--- lib/bio/appl/hmmer ---> lib/bio/appl/psort mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/appl/psort install report.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl/psort <--- lib/bio/appl/psort ---> lib/bio/appl/phylip mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/appl/phylip install alignment.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl/phylip install distance_matrix.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl/phylip <--- lib/bio/appl/phylip ---> lib/bio/appl/meme mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/appl/meme install motif.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl/meme install mast.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl/meme ---> lib/bio/appl/meme/mast mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/appl/meme/mast install report.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl/meme/mast <--- lib/bio/appl/meme/mast <--- lib/bio/appl/meme ---> lib/bio/appl/clustalw mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/appl/clustalw install report.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl/clustalw <--- lib/bio/appl/clustalw ---> lib/bio/appl/paml mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/appl/paml install common_report.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl/paml install common.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl/paml install codeml.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl/paml install yn00.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl/paml install baseml.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl/paml ---> lib/bio/appl/paml/codeml mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/appl/paml/codeml install rates.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl/paml/codeml install report.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl/paml/codeml <--- lib/bio/appl/paml/codeml ---> lib/bio/appl/paml/baseml mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/appl/paml/baseml install report.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl/paml/baseml <--- lib/bio/appl/paml/baseml ---> lib/bio/appl/paml/yn00 mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/appl/paml/yn00 install report.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl/paml/yn00 <--- lib/bio/appl/paml/yn00 <--- lib/bio/appl/paml ---> lib/bio/appl/genscan mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/appl/genscan install report.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl/genscan <--- lib/bio/appl/genscan ---> lib/bio/appl/targetp mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/appl/targetp install report.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl/targetp <--- lib/bio/appl/targetp ---> lib/bio/appl/iprscan mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/appl/iprscan install report.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl/iprscan <--- lib/bio/appl/iprscan ---> lib/bio/appl/blast mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/appl/blast install format8.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl/blast install rpsblast.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl/blast install remote.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl/blast install genomenet.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl/blast install report.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl/blast install wublast.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl/blast install format0.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl/blast install xmlparser.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl/blast install rexml.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl/blast install ncbioptions.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl/blast <--- lib/bio/appl/blast ---> lib/bio/appl/sosui mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/appl/sosui install report.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl/sosui <--- lib/bio/appl/sosui ---> lib/bio/appl/sim4 mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/appl/sim4 install report.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl/sim4 <--- lib/bio/appl/sim4 ---> lib/bio/appl/blat mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/appl/blat install report.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl/blat <--- lib/bio/appl/blat ---> lib/bio/appl/gcg mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.3/bio/appl/gcg install msf.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl/gcg install seq.rb /usr/local/lib/ruby/site_ruby/3.3/bio/appl/gcg <--- lib/bio/appl/gcg <--- lib/bio/appl <--- lib/bio <--- lib install -m 0644 /wrkdirs/usr/ports/biology/ruby-bio/work/bioruby-1.5.1/etc/bioinformatics/seqdatabase.ini /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/etc/bioinformatics/seqdatabase.ini.sample cp -f -R /wrkdirs/usr/ports/biology/ruby-bio/work/bioruby-1.5.1/sample/ /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/share/examples/ruby33/bio/ install -m 0644 /wrkdirs/usr/ports/biology/ruby-bio/work/bioruby-1.5.1/ChangeLog /wrkdirs/usr/ports/biology/ruby-bio/work/bioruby-1.5.1/README.rdoc /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/share/doc/ruby33/bio/ install -m 0644 /wrkdirs/usr/ports/biology/ruby-bio/work/bioruby-1.5.1/doc/*.rd /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/share/doc/ruby33/bio/ install -m 0644 /wrkdirs/usr/ports/biology/ruby-bio/work/bioruby-1.5.1/doc/*.rd.ja /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/share/doc/ruby33/bio/ja/ ====> 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=2026-03-17T14:11:19+0000' 'PKG_NOTE_ports_top_git_hash=8c988f802ea2' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=18c6e1827669' '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 ruby33-bio-1.5.1 ===> Building ruby33-bio-1.5.1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for ruby33-bio-1.5.1 build of biology/ruby-bio | ruby33-bio-1.5.1 ended at Tue Mar 17 10:12:14 EDT 2026 build time: 00:00:59