=>> Building biology/ruby-bio build started at Sat May 3 16:33:01 BST 2025 port directory: /usr/ports/biology/ruby-bio package name: ruby32-bio-1.5.1 building for: FreeBSD pkg-builder.dan.net.uk 14.2-RELEASE FreeBSD 14.2-RELEASE amd64 maintained by: mauricio@arareko.net Makefile datestamp: -rw-r--r-- 1 root wheel 1547 Dec 29 14:16 /usr/ports/biology/ruby-bio/Makefile Ports top last git commit: 5529c5919b Ports top unclean checkout: yes Port dir last git commit: 1a35b19e6d Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1402000 Jail OSVERSION: 1402000 Job Id: 08 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1402000 UNAME_v=FreeBSD 14.2-RELEASE UNAME_r=14.2-RELEASE BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/14-amd64-default-dan/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/14-amd64-default-dan/08/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=14-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/14-amd64-default-dan/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 ruby32-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=" -fstack-protector-strong " 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/3.2" RUBY_ARCHLIBDIR="lib/ruby/3.2/amd64-freebsd14" RUBY_SITELIBDIR="lib/ruby/site_ruby/3.2" RUBY_SITEARCHLIBDIR="lib/ruby/site_ruby/3.2/amd64-freebsd14" RUBY_VENDORLIBDIR="lib/ruby/vendor_ruby/3.2" RUBY_VENDORARCHLIBDIR="lib/ruby/vendor_ruby/3.2/amd64-freebsd14" RUBY_MODDOCDIR="share/doc/ruby32/bio" RUBY_MODEXAMPLESDIR="share/examples/ruby32/bio" RUBY_DOCDIR="share/doc/ruby32" RUBY_EXAMPLESDIR="share/examples/ruby32" RUBY_RIDIR="share/ri/3.2/system" RUBY_SITERIDIR="share/ri/3.2/site" RUBY_VERSION="3.2.8" RUBY_VER="3.2" RUBY_SHLIBVER="32" RUBY_ARCH="amd64-freebsd14" RUBY_SUFFIX="32" RUBY_DEFAULT_SUFFIX="32" OSREL=14.2 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--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### CCACHE_CPP2=1 WITH_SSP_PORTS=yes WITH_SSP=yes #WITH_LTO=yes DISABLE_LICENSES=yes LICENSES_ACCEPTED=AGPLv3 APACHE10 APACHE11 APACHE20 ART10 ARTPERL10 ART20 BSD BSD2CLAUSE BSD3CLAUSE BSD4CLAUSE BSL CC0-1.0 CDDL ClArtistic EPL GFDL GMGPL GPLv1 GPLv2 GPLv3 GPLv3RLE ISCL LGPL20 LGPL21 LGPL3 LPPL10 LPPL11 LPPL12 LPPL13 LPPL13a LPPL13b LPPL13c MIT MPL OpenSSL OFL10 OFL11 OWL PostgreSQL PHP202 PHP30 PHP301 PSFL RUBY ZLIB ZPL21 SVM-Light EULA ALASIR Microsoft-exFAT SIMIAN UDEVGAME unknown MTA COMMERCIAL teamspeak NO_LICENSES_DIALOGS=yes #### #### NO_IGNORE=yes DEFAULT_VERSIONS+=ssl=openssl apache=2.4 imagemagick=7 java=21 linux=c7 mysql=8.0 php=8.3 samba=4.19 varnish=7 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE ALLOW_UNSUPPORTED_SYSTEM=yes WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited 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 ===> ruby32-bio-1.5.1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.1.2.pkg [pkg-builder.dan.net.uk] Installing pkg-2.1.2... [pkg-builder.dan.net.uk] Extracting pkg-2.1.2: .......... done ===> ruby32-bio-1.5.1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of ruby32-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 ruby32-bio-1.5.1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by ruby32-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 ===> ruby32-bio-1.5.1 depends on file: /usr/local/bin/ruby32 - not found ===> Installing existing package /packages/All/ruby-3.2.8,1.pkg [pkg-builder.dan.net.uk] Installing ruby-3.2.8,1... [pkg-builder.dan.net.uk] `-- Installing libedit-3.1.20250104,1... [pkg-builder.dan.net.uk] `-- Extracting libedit-3.1.20250104,1: .......... done [pkg-builder.dan.net.uk] `-- Installing libffi-3.4.8... [pkg-builder.dan.net.uk] | `-- Installing indexinfo-0.3.1_1... [pkg-builder.dan.net.uk] | `-- Extracting indexinfo-0.3.1_1: . done [pkg-builder.dan.net.uk] `-- Extracting libffi-3.4.8: .......... done [pkg-builder.dan.net.uk] `-- Installing libunwind-20240221_2... [pkg-builder.dan.net.uk] `-- Extracting libunwind-20240221_2: .......... done [pkg-builder.dan.net.uk] `-- Installing libyaml-0.2.5... [pkg-builder.dan.net.uk] `-- Extracting libyaml-0.2.5: ...... done [pkg-builder.dan.net.uk] `-- Installing openssl-3.0.16,1... [pkg-builder.dan.net.uk] `-- Extracting openssl-3.0.16,1: .......... done [pkg-builder.dan.net.uk] Extracting ruby-3.2.8,1: .......... done ===== Message from ruby-3.2.8,1: -- 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-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. ===> ruby32-bio-1.5.1 depends on file: /usr/local/bin/ruby32 - found ===> Returning to build of ruby32-bio-1.5.1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by ruby32-bio-1.5.1 for building ===> Extracting for ruby32-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 ===> ruby32-bio-1.5.1 depends on file: /usr/local/bin/ruby32 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for ruby32-bio-1.5.1 /usr/local/bin/ruby32 -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 ===> ruby32-bio-1.5.1 depends on file: /usr/local/bin/ruby32 - found ===> ruby32-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-builder.dan.net.uk] Installing ccache-3.7.12_8... [pkg-builder.dan.net.uk] 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. ===> ruby32-bio-1.5.1 depends on file: /usr/local/bin/ccache - found ===> Returning to build of ruby32-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 ruby32-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 ruby32-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 ===> ruby32-bio-1.5.1 depends on file: /usr/local/bin/ruby32 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for ruby32-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/3.2 install bio.rb /usr/local/lib/ruby/site_ruby/3.2/ ---> lib/bio mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.2/bio install db.rb /usr/local/lib/ruby/site_ruby/3.2/bio install tree.rb /usr/local/lib/ruby/site_ruby/3.2/bio install reference.rb /usr/local/lib/ruby/site_ruby/3.2/bio install shell.rb /usr/local/lib/ruby/site_ruby/3.2/bio install command.rb /usr/local/lib/ruby/site_ruby/3.2/bio install version.rb /usr/local/lib/ruby/site_ruby/3.2/bio install feature.rb /usr/local/lib/ruby/site_ruby/3.2/bio install pathway.rb /usr/local/lib/ruby/site_ruby/3.2/bio install location.rb /usr/local/lib/ruby/site_ruby/3.2/bio install map.rb /usr/local/lib/ruby/site_ruby/3.2/bio install alignment.rb /usr/local/lib/ruby/site_ruby/3.2/bio install sequence.rb /usr/local/lib/ruby/site_ruby/3.2/bio ---> lib/bio/util mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.2/bio/util install color_scheme.rb /usr/local/lib/ruby/site_ruby/3.2/bio/util install contingency_table.rb /usr/local/lib/ruby/site_ruby/3.2/bio/util install sirna.rb /usr/local/lib/ruby/site_ruby/3.2/bio/util install restriction_enzyme.rb /usr/local/lib/ruby/site_ruby/3.2/bio/util ---> lib/bio/util/restriction_enzyme mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.2/bio/util/restriction_enzyme install single_strand.rb /usr/local/lib/ruby/site_ruby/3.2/bio/util/restriction_enzyme install string_formatting.rb /usr/local/lib/ruby/site_ruby/3.2/bio/util/restriction_enzyme install analysis.rb /usr/local/lib/ruby/site_ruby/3.2/bio/util/restriction_enzyme install cut_symbol.rb /usr/local/lib/ruby/site_ruby/3.2/bio/util/restriction_enzyme install dense_int_array.rb /usr/local/lib/ruby/site_ruby/3.2/bio/util/restriction_enzyme install analysis_basic.rb /usr/local/lib/ruby/site_ruby/3.2/bio/util/restriction_enzyme install double_stranded.rb /usr/local/lib/ruby/site_ruby/3.2/bio/util/restriction_enzyme install enzymes.yaml /usr/local/lib/ruby/site_ruby/3.2/bio/util/restriction_enzyme install sorted_num_array.rb /usr/local/lib/ruby/site_ruby/3.2/bio/util/restriction_enzyme install single_strand_complement.rb /usr/local/lib/ruby/site_ruby/3.2/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/3.2/bio/util/restriction_enzyme/range install sequence_range.rb /usr/local/lib/ruby/site_ruby/3.2/bio/util/restriction_enzyme/range install horizontal_cut_range.rb /usr/local/lib/ruby/site_ruby/3.2/bio/util/restriction_enzyme/range install vertical_cut_range.rb /usr/local/lib/ruby/site_ruby/3.2/bio/util/restriction_enzyme/range install cut_ranges.rb /usr/local/lib/ruby/site_ruby/3.2/bio/util/restriction_enzyme/range install cut_range.rb /usr/local/lib/ruby/site_ruby/3.2/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/3.2/bio/util/restriction_enzyme/range/sequence_range install calculated_cuts.rb /usr/local/lib/ruby/site_ruby/3.2/bio/util/restriction_enzyme/range/sequence_range install fragments.rb /usr/local/lib/ruby/site_ruby/3.2/bio/util/restriction_enzyme/range/sequence_range install fragment.rb /usr/local/lib/ruby/site_ruby/3.2/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/3.2/bio/util/restriction_enzyme/single_strand install cut_locations_in_enzyme_notation.rb /usr/local/lib/ruby/site_ruby/3.2/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/3.2/bio/util/restriction_enzyme/double_stranded install cut_location_pair.rb /usr/local/lib/ruby/site_ruby/3.2/bio/util/restriction_enzyme/double_stranded install cut_locations.rb /usr/local/lib/ruby/site_ruby/3.2/bio/util/restriction_enzyme/double_stranded install cut_locations_in_enzyme_notation.rb /usr/local/lib/ruby/site_ruby/3.2/bio/util/restriction_enzyme/double_stranded install aligned_strands.rb /usr/local/lib/ruby/site_ruby/3.2/bio/util/restriction_enzyme/double_stranded install cut_location_pair_in_enzyme_notation.rb /usr/local/lib/ruby/site_ruby/3.2/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/3.2/bio/util/color_scheme install helix.rb /usr/local/lib/ruby/site_ruby/3.2/bio/util/color_scheme install strand.rb /usr/local/lib/ruby/site_ruby/3.2/bio/util/color_scheme install turn.rb /usr/local/lib/ruby/site_ruby/3.2/bio/util/color_scheme install buried.rb /usr/local/lib/ruby/site_ruby/3.2/bio/util/color_scheme install hydropathy.rb /usr/local/lib/ruby/site_ruby/3.2/bio/util/color_scheme install nucleotide.rb /usr/local/lib/ruby/site_ruby/3.2/bio/util/color_scheme install zappo.rb /usr/local/lib/ruby/site_ruby/3.2/bio/util/color_scheme install taylor.rb /usr/local/lib/ruby/site_ruby/3.2/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/3.2/bio/shell install irb.rb /usr/local/lib/ruby/site_ruby/3.2/bio/shell install object.rb /usr/local/lib/ruby/site_ruby/3.2/bio/shell install interface.rb /usr/local/lib/ruby/site_ruby/3.2/bio/shell install setup.rb /usr/local/lib/ruby/site_ruby/3.2/bio/shell install web.rb /usr/local/lib/ruby/site_ruby/3.2/bio/shell install script.rb /usr/local/lib/ruby/site_ruby/3.2/bio/shell install core.rb /usr/local/lib/ruby/site_ruby/3.2/bio/shell install demo.rb /usr/local/lib/ruby/site_ruby/3.2/bio/shell ---> lib/bio/shell/plugin mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.2/bio/shell/plugin install das.rb /usr/local/lib/ruby/site_ruby/3.2/bio/shell/plugin install midi.rb /usr/local/lib/ruby/site_ruby/3.2/bio/shell/plugin install obda.rb /usr/local/lib/ruby/site_ruby/3.2/bio/shell/plugin install codon.rb /usr/local/lib/ruby/site_ruby/3.2/bio/shell/plugin install psort.rb /usr/local/lib/ruby/site_ruby/3.2/bio/shell/plugin install togows.rb /usr/local/lib/ruby/site_ruby/3.2/bio/shell/plugin install blast.rb /usr/local/lib/ruby/site_ruby/3.2/bio/shell/plugin install flatfile.rb /usr/local/lib/ruby/site_ruby/3.2/bio/shell/plugin install entry.rb /usr/local/lib/ruby/site_ruby/3.2/bio/shell/plugin install seq.rb /usr/local/lib/ruby/site_ruby/3.2/bio/shell/plugin install ncbirest.rb /usr/local/lib/ruby/site_ruby/3.2/bio/shell/plugin install emboss.rb /usr/local/lib/ruby/site_ruby/3.2/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/3.2/bio/shell/rails ---> lib/bio/shell/rails/vendor mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.2/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/3.2/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/3.2/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/3.2/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/3.2/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby install bioruby_generator.rb /usr/local/lib/ruby/site_ruby/3.2/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/3.2/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install bioruby_controller.rb /usr/local/lib/ruby/site_ruby/3.2/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install bioruby-bg.gif /usr/local/lib/ruby/site_ruby/3.2/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install _classes.rhtml /usr/local/lib/ruby/site_ruby/3.2/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install _methods.rhtml /usr/local/lib/ruby/site_ruby/3.2/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install commands.rhtml /usr/local/lib/ruby/site_ruby/3.2/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install index.rhtml /usr/local/lib/ruby/site_ruby/3.2/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install bioruby-gem.png /usr/local/lib/ruby/site_ruby/3.2/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install _modules.rhtml /usr/local/lib/ruby/site_ruby/3.2/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install spinner.gif /usr/local/lib/ruby/site_ruby/3.2/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install _variables.rhtml /usr/local/lib/ruby/site_ruby/3.2/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install bioruby.css /usr/local/lib/ruby/site_ruby/3.2/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install _log.rhtml /usr/local/lib/ruby/site_ruby/3.2/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install history.rhtml /usr/local/lib/ruby/site_ruby/3.2/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install bioruby-link.gif /usr/local/lib/ruby/site_ruby/3.2/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install bioruby.rhtml /usr/local/lib/ruby/site_ruby/3.2/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install bioruby_helper.rb /usr/local/lib/ruby/site_ruby/3.2/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/3.2/bio/sequence install na.rb /usr/local/lib/ruby/site_ruby/3.2/bio/sequence install quality_score.rb /usr/local/lib/ruby/site_ruby/3.2/bio/sequence install sequence_masker.rb /usr/local/lib/ruby/site_ruby/3.2/bio/sequence install generic.rb /usr/local/lib/ruby/site_ruby/3.2/bio/sequence install compat.rb /usr/local/lib/ruby/site_ruby/3.2/bio/sequence install common.rb /usr/local/lib/ruby/site_ruby/3.2/bio/sequence install aa.rb /usr/local/lib/ruby/site_ruby/3.2/bio/sequence install dblink.rb /usr/local/lib/ruby/site_ruby/3.2/bio/sequence install format_raw.rb /usr/local/lib/ruby/site_ruby/3.2/bio/sequence install format.rb /usr/local/lib/ruby/site_ruby/3.2/bio/sequence install adapter.rb /usr/local/lib/ruby/site_ruby/3.2/bio/sequence <--- lib/bio/sequence ---> lib/bio/compat mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.2/bio/compat install features.rb /usr/local/lib/ruby/site_ruby/3.2/bio/compat install references.rb /usr/local/lib/ruby/site_ruby/3.2/bio/compat <--- lib/bio/compat ---> lib/bio/io mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.2/bio/io install hinv.rb /usr/local/lib/ruby/site_ruby/3.2/bio/io install fetch.rb /usr/local/lib/ruby/site_ruby/3.2/bio/io install das.rb /usr/local/lib/ruby/site_ruby/3.2/bio/io install registry.rb /usr/local/lib/ruby/site_ruby/3.2/bio/io install fastacmd.rb /usr/local/lib/ruby/site_ruby/3.2/bio/io install togows.rb /usr/local/lib/ruby/site_ruby/3.2/bio/io install sql.rb /usr/local/lib/ruby/site_ruby/3.2/bio/io install flatfile.rb /usr/local/lib/ruby/site_ruby/3.2/bio/io install pubmed.rb /usr/local/lib/ruby/site_ruby/3.2/bio/io install ncbirest.rb /usr/local/lib/ruby/site_ruby/3.2/bio/io ---> lib/bio/io/biosql mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.2/bio/io/biosql install biosql.rb /usr/local/lib/ruby/site_ruby/3.2/bio/io/biosql install ar-biosql.rb /usr/local/lib/ruby/site_ruby/3.2/bio/io/biosql ---> lib/bio/io/biosql/config mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.2/bio/io/biosql/config install database.yml /usr/local/lib/ruby/site_ruby/3.2/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/3.2/bio/io/flatfile install bdb.rb /usr/local/lib/ruby/site_ruby/3.2/bio/io/flatfile install indexer.rb /usr/local/lib/ruby/site_ruby/3.2/bio/io/flatfile install buffer.rb /usr/local/lib/ruby/site_ruby/3.2/bio/io/flatfile install splitter.rb /usr/local/lib/ruby/site_ruby/3.2/bio/io/flatfile install autodetection.rb /usr/local/lib/ruby/site_ruby/3.2/bio/io/flatfile install index.rb /usr/local/lib/ruby/site_ruby/3.2/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/3.2/bio/tree install output.rb /usr/local/lib/ruby/site_ruby/3.2/bio/tree <--- lib/bio/tree ---> lib/bio/db mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.2/bio/db install fastq.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db install aaindex.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db install rebase.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db install lasergene.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db install prosite.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db install litdb.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db install nbrf.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db install medline.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db install transfac.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db install pdb.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db install soft.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db install fasta.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db install fantom.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db install newick.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db install nexus.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db install gff.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db install go.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db ---> lib/bio/db/fasta mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.2/bio/db/fasta install qual_to_biosequence.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/fasta install format_fasta.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/fasta install format_qual.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/fasta install qual.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/fasta install fasta_to_biosequence.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/fasta install defline.rb /usr/local/lib/ruby/site_ruby/3.2/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/3.2/bio/db/fastq install fastq_to_biosequence.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/fastq install format_fastq.rb /usr/local/lib/ruby/site_ruby/3.2/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/3.2/bio/db/kegg install genes.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/kegg install brite.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/kegg install compound.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/kegg install common.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/kegg install genome.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/kegg install drug.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/kegg install orthology.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/kegg install pathway.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/kegg install keggtab.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/kegg install expression.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/kegg install reaction.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/kegg install module.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/kegg install glycan.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/kegg install kgml.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/kegg install enzyme.rb /usr/local/lib/ruby/site_ruby/3.2/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/3.2/bio/db/embl install uniprot.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/embl install common.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/embl install uniprotkb.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/embl install sptr.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/embl install format_embl.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/embl install embl.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/embl install trembl.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/embl install embl_to_biosequence.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/embl install swissprot.rb /usr/local/lib/ruby/site_ruby/3.2/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/3.2/bio/db/phyloxml install phyloxml_elements.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/phyloxml install phyloxml.xsd /usr/local/lib/ruby/site_ruby/3.2/bio/db/phyloxml install phyloxml_writer.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/phyloxml install phyloxml_parser.rb /usr/local/lib/ruby/site_ruby/3.2/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/3.2/bio/db/genbank install ddbj.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/genbank install format_genbank.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/genbank install common.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/genbank install genbank_to_biosequence.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/genbank install refseq.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/genbank install genpept.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/genbank install genbank.rb /usr/local/lib/ruby/site_ruby/3.2/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/3.2/bio/db/pdb install chemicalcomponent.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/pdb install chain.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/pdb install residue.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/pdb install pdb.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/pdb install model.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/pdb install utils.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/pdb install atom.rb /usr/local/lib/ruby/site_ruby/3.2/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/3.2/bio/db/biosql install biosql_to_biosequence.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/biosql install sequence.rb /usr/local/lib/ruby/site_ruby/3.2/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/3.2/bio/db/sanger_chromatogram install scf.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/sanger_chromatogram install chromatogram.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/sanger_chromatogram install chromatogram_to_biosequence.rb /usr/local/lib/ruby/site_ruby/3.2/bio/db/sanger_chromatogram install abif.rb /usr/local/lib/ruby/site_ruby/3.2/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/3.2/bio/data install na.rb /usr/local/lib/ruby/site_ruby/3.2/bio/data install aa.rb /usr/local/lib/ruby/site_ruby/3.2/bio/data install codontable.rb /usr/local/lib/ruby/site_ruby/3.2/bio/data <--- lib/bio/data ---> lib/bio/appl mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.2/bio/appl install clustalw.rb /usr/local/lib/ruby/site_ruby/3.2/bio/appl install pts1.rb /usr/local/lib/ruby/site_ruby/3.2/bio/appl install tcoffee.rb /usr/local/lib/ruby/site_ruby/3.2/bio/appl install muscle.rb /usr/local/lib/ruby/site_ruby/3.2/bio/appl install probcons.rb /usr/local/lib/ruby/site_ruby/3.2/bio/appl install hmmer.rb /usr/local/lib/ruby/site_ruby/3.2/bio/appl install psort.rb /usr/local/lib/ruby/site_ruby/3.2/bio/appl install mafft.rb /usr/local/lib/ruby/site_ruby/3.2/bio/appl install fasta.rb /usr/local/lib/ruby/site_ruby/3.2/bio/appl install blast.rb /usr/local/lib/ruby/site_ruby/3.2/bio/appl install sim4.rb /usr/local/lib/ruby/site_ruby/3.2/bio/appl install emboss.rb /usr/local/lib/ruby/site_ruby/3.2/bio/appl ---> lib/bio/appl/spidey mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.2/bio/appl/spidey install report.rb /usr/local/lib/ruby/site_ruby/3.2/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/3.2/bio/appl/bl2seq install report.rb /usr/local/lib/ruby/site_ruby/3.2/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/3.2/bio/appl/tmhmm install report.rb /usr/local/lib/ruby/site_ruby/3.2/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/3.2/bio/appl/fasta install format10.rb /usr/local/lib/ruby/site_ruby/3.2/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/3.2/bio/appl/mafft install report.rb /usr/local/lib/ruby/site_ruby/3.2/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/3.2/bio/appl/hmmer install report.rb /usr/local/lib/ruby/site_ruby/3.2/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/3.2/bio/appl/psort install report.rb /usr/local/lib/ruby/site_ruby/3.2/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/3.2/bio/appl/phylip install alignment.rb /usr/local/lib/ruby/site_ruby/3.2/bio/appl/phylip install distance_matrix.rb /usr/local/lib/ruby/site_ruby/3.2/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/3.2/bio/appl/meme install motif.rb /usr/local/lib/ruby/site_ruby/3.2/bio/appl/meme install mast.rb /usr/local/lib/ruby/site_ruby/3.2/bio/appl/meme ---> lib/bio/appl/meme/mast mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.2/bio/appl/meme/mast install report.rb /usr/local/lib/ruby/site_ruby/3.2/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/3.2/bio/appl/clustalw install report.rb /usr/local/lib/ruby/site_ruby/3.2/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/3.2/bio/appl/paml install common_report.rb /usr/local/lib/ruby/site_ruby/3.2/bio/appl/paml install common.rb /usr/local/lib/ruby/site_ruby/3.2/bio/appl/paml install codeml.rb /usr/local/lib/ruby/site_ruby/3.2/bio/appl/paml install yn00.rb /usr/local/lib/ruby/site_ruby/3.2/bio/appl/paml install baseml.rb /usr/local/lib/ruby/site_ruby/3.2/bio/appl/paml ---> lib/bio/appl/paml/codeml mkdir -p /wrkdirs/usr/ports/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/3.2/bio/appl/paml/codeml install rates.rb /usr/local/lib/ruby/site_ruby/3.2/bio/appl/paml/codeml install report.rb /usr/local/lib/ruby/site_ruby/3.2/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/3.2/bio/appl/paml/baseml install report.rb /usr/local/lib/ruby/site_ruby/3.2/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/3.2/bio/appl/paml/yn00 install report.rb /usr/local/lib/ruby/site_ruby/3.2/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/3.2/bio/appl/genscan install report.rb /usr/local/lib/ruby/site_ruby/3.2/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/3.2/bio/appl/targetp install report.rb /usr/local/lib/ruby/site_ruby/3.2/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/3.2/bio/appl/iprscan install report.rb /usr/local/lib/ruby/site_ruby/3.2/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/3.2/bio/appl/blast install format8.rb /usr/local/lib/ruby/site_ruby/3.2/bio/appl/blast install rpsblast.rb /usr/local/lib/ruby/site_ruby/3.2/bio/appl/blast install remote.rb /usr/local/lib/ruby/site_ruby/3.2/bio/appl/blast install genomenet.rb /usr/local/lib/ruby/site_ruby/3.2/bio/appl/blast install report.rb /usr/local/lib/ruby/site_ruby/3.2/bio/appl/blast install wublast.rb /usr/local/lib/ruby/site_ruby/3.2/bio/appl/blast install format0.rb /usr/local/lib/ruby/site_ruby/3.2/bio/appl/blast install xmlparser.rb /usr/local/lib/ruby/site_ruby/3.2/bio/appl/blast install rexml.rb /usr/local/lib/ruby/site_ruby/3.2/bio/appl/blast install ncbioptions.rb /usr/local/lib/ruby/site_ruby/3.2/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/3.2/bio/appl/sosui install report.rb /usr/local/lib/ruby/site_ruby/3.2/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/3.2/bio/appl/sim4 install report.rb /usr/local/lib/ruby/site_ruby/3.2/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/3.2/bio/appl/blat install report.rb /usr/local/lib/ruby/site_ruby/3.2/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/3.2/bio/appl/gcg install msf.rb /usr/local/lib/ruby/site_ruby/3.2/bio/appl/gcg install seq.rb /usr/local/lib/ruby/site_ruby/3.2/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/ruby32/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/ruby32/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/ruby32/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/ruby32/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=2025-05-03T15:33:01+0000' 'PKG_NOTE_ports_top_git_hash=5529c5919b' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=1a35b19e6d' '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 ruby32-bio-1.5.1 ===> Building ruby32-bio-1.5.1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for ruby32-bio-1.5.1 build of biology/ruby-bio | ruby32-bio-1.5.1 ended at Sat May 3 16:33:27 BST 2025 build time: 00:00:26