------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 UNAME_r=6.1 UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=unknown UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 LANG=C HOME=/root USER=root TERM=dumb SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: showconfig ------------------------------------------------------------------------------- ===> The following configuration options are available for ruby27-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 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ENV ------------------------------------------------------------------------------- XDG_DATA_HOME=/construction/biology/ruby-bio XDG_CONFIG_HOME=/construction/biology/ruby-bio HOME=/construction/biology/ruby-bio TMPDIR="/tmp" PATH=/construction/biology/ruby-bio/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: MAKE_ENV ------------------------------------------------------------------------------- XDG_DATA_HOME=/construction/biology/ruby-bio XDG_CONFIG_HOME=/construction/biology/ruby-bio HOME=/construction/biology/ruby-bio TMPDIR="/tmp" PATH=/construction/biology/ruby-bio/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc80 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing " MANPREFIX="/usr/local" 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" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ARGS ------------------------------------------------------------------------------- DESTDIR=/construction/biology/ruby-bio/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: PLIST_SUB ------------------------------------------------------------------------------- PORTDOCS="" RUBY_LIBDIR="lib/ruby/2.7" RUBY_ARCHLIBDIR="lib/ruby/2.7/x86_64-dragonfly6" RUBY_SITELIBDIR="lib/ruby/site_ruby/2.7" RUBY_SITEARCHLIBDIR="lib/ruby/site_ruby/2.7/x86_64-dragonfly6" RUBY_VENDORLIBDIR="lib/ruby/vendor_ruby/2.7" RUBY_VENDORARCHLIBDIR="lib/ruby/vendor_ruby/2.7/x86_64-dragonfly6" RUBY_MODDOCDIR="share/doc/ruby27/bio" RUBY_MODEXAMPLESDIR="share/examples/ruby27/bio" RUBY_DOCDIR="share/doc/ruby27" RUBY_EXAMPLESDIR="share/examples/ruby27" RUBY_RIDIR="share/ri/2.7/system" RUBY_SITERIDIR="share/ri/2.7/site" RUBY_VERSION="2.7.3" RUBY_VER="2.7" RUBY_SHLIBVER="27" RUBY_ARCH="x86_64-dragonfly6" RUBY_SUFFIX="27" RUBY_NAME="ruby27" RUBY_DEFAULT_SUFFIX="27" RUBY26="@comment " RUBY27="" RUBY30="@comment " OSREL=6.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/bio" EXAMPLESDIR="share/examples/bio" DATADIR="share/bio" WWWDIR="www/bio" ETCDIR="etc/bio" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: 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 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: /etc/make.conf ------------------------------------------------------------------------------- DPORTS_BUILDER=yes DISABLE_LICENSES=yes DEFAULT_VERSIONS=ssl=openssl FORCE_PACKAGE=yes DEVELOPER=yes USE_PACKAGE_DEPENDS_ONLY=yes PORTSDIR=/xports PORT_DBDIR=/options PKG_DBDIR=/var/db/pkg PKG_CACHEDIR=/var/cache/pkg PKG_SUFX=.txz DEVELOPER=1 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=600100 OSVERSION=9999999 OSREL=6.1 _OSRELEASE=6.1-SYNTH DISTDIR=/distfiles WRKDIRPREFIX=/construction BATCH=yes PACKAGE_BUILDING=yes PKG_CREATE_VERBOSE=yes MAKE_JOBS_NUMBER=10 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/libyaml-0.2.5.txz Installing /packages/All/ncurses-6.2.20210313_1.txz ===== Message from ncurses-6.2.20210313_1: -- { type: install message: < ruby27-bio-1.5.1 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> ruby27-bio-1.5.1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by ruby27-bio-1.5.1 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> ruby27-bio-1.5.1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by ruby27-bio-1.5.1 for building => SHA256 Checksum OK for ruby/bioruby-1.5.1.tar.gz. SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- ===> ruby27-bio-1.5.1 depends on file: /usr/local/bin/ruby27 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> ruby27-bio-1.5.1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by ruby27-bio-1.5.1 for building ===> Extracting for ruby27-bio-1.5.1 => SHA256 Checksum OK for ruby/bioruby-1.5.1.tar.gz. ===> ruby27-bio-1.5.1 depends on file: /usr/local/bin/ruby27 - found Extracted Memory Use: 6.98M SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- ===> ruby27-bio-1.5.1 depends on file: /usr/local/bin/ruby27 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for ruby27-bio-1.5.1 ===> ruby27-bio-1.5.1 depends on file: /usr/local/bin/ruby27 - found /usr/local/bin/ruby27 -i -pe 'gsub(%r"(/etc/bioinformatics/)") { "/usr/local" + $1 }' /construction/biology/ruby-bio/bioruby-1.5.1/doc/Tutorial.rd /construction/biology/ruby-bio/bioruby-1.5.1/lib/bio/io/registry.rb SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> ruby27-bio-1.5.1 depends on file: /usr/local/bin/ruby27 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> ruby27-bio-1.5.1 depends on file: /usr/local/bin/ruby27 - found ===> Configuring for ruby27-bio-1.5.1 ===> Running setup.rb to configure ---> bin <--- bin ---> lib ---> lib/bio ---> lib/bio/compat <--- lib/bio/compat ---> lib/bio/sequence <--- lib/bio/sequence ---> lib/bio/db ---> lib/bio/db/genbank <--- lib/bio/db/genbank ---> lib/bio/db/pdb <--- lib/bio/db/pdb ---> lib/bio/db/fasta <--- lib/bio/db/fasta ---> lib/bio/db/phyloxml <--- lib/bio/db/phyloxml ---> lib/bio/db/fastq <--- lib/bio/db/fastq ---> lib/bio/db/sanger_chromatogram <--- lib/bio/db/sanger_chromatogram ---> lib/bio/db/biosql <--- lib/bio/db/biosql ---> lib/bio/db/kegg <--- lib/bio/db/kegg ---> lib/bio/db/embl <--- lib/bio/db/embl <--- lib/bio/db ---> lib/bio/util ---> lib/bio/util/color_scheme <--- lib/bio/util/color_scheme ---> 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/double_stranded <--- lib/bio/util/restriction_enzyme/double_stranded ---> lib/bio/util/restriction_enzyme/single_strand <--- lib/bio/util/restriction_enzyme/single_strand <--- lib/bio/util/restriction_enzyme <--- lib/bio/util ---> lib/bio/tree <--- lib/bio/tree ---> lib/bio/appl ---> lib/bio/appl/hmmer <--- lib/bio/appl/hmmer ---> lib/bio/appl/sosui <--- lib/bio/appl/sosui ---> lib/bio/appl/paml ---> lib/bio/appl/paml/baseml <--- lib/bio/appl/paml/baseml ---> lib/bio/appl/paml/codeml <--- lib/bio/appl/paml/codeml ---> lib/bio/appl/paml/yn00 <--- lib/bio/appl/paml/yn00 <--- lib/bio/appl/paml ---> lib/bio/appl/phylip <--- lib/bio/appl/phylip ---> lib/bio/appl/spidey <--- lib/bio/appl/spidey ---> lib/bio/appl/iprscan <--- lib/bio/appl/iprscan ---> lib/bio/appl/fasta <--- lib/bio/appl/fasta ---> lib/bio/appl/blat <--- lib/bio/appl/blat ---> lib/bio/appl/meme ---> lib/bio/appl/meme/mast <--- lib/bio/appl/meme/mast <--- lib/bio/appl/meme ---> lib/bio/appl/tmhmm <--- lib/bio/appl/tmhmm ---> lib/bio/appl/blast <--- lib/bio/appl/blast ---> lib/bio/appl/mafft <--- lib/bio/appl/mafft ---> lib/bio/appl/genscan <--- lib/bio/appl/genscan ---> lib/bio/appl/clustalw <--- lib/bio/appl/clustalw ---> lib/bio/appl/gcg <--- lib/bio/appl/gcg ---> lib/bio/appl/targetp <--- lib/bio/appl/targetp ---> lib/bio/appl/bl2seq <--- lib/bio/appl/bl2seq ---> lib/bio/appl/sim4 <--- lib/bio/appl/sim4 ---> lib/bio/appl/psort <--- lib/bio/appl/psort <--- lib/bio/appl ---> lib/bio/io ---> lib/bio/io/flatfile <--- lib/bio/io/flatfile ---> lib/bio/io/biosql ---> lib/bio/io/biosql/config <--- lib/bio/io/biosql/config <--- lib/bio/io/biosql <--- lib/bio/io ---> 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/data <--- lib/bio/data <--- lib/bio <--- lib SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for ruby27-bio-1.5.1 ===> Running setup.rb to build ---> bin updating shebang: br_bioflat.rb updating shebang: br_biogetseq.rb updating shebang: br_pmfetch.rb updating shebang: bioruby updating shebang: br_biofetch.rb <--- bin ---> lib ---> lib/bio ---> lib/bio/compat <--- lib/bio/compat ---> lib/bio/sequence <--- lib/bio/sequence ---> lib/bio/db ---> lib/bio/db/genbank <--- lib/bio/db/genbank ---> lib/bio/db/pdb <--- lib/bio/db/pdb ---> lib/bio/db/fasta <--- lib/bio/db/fasta ---> lib/bio/db/phyloxml <--- lib/bio/db/phyloxml ---> lib/bio/db/fastq <--- lib/bio/db/fastq ---> lib/bio/db/sanger_chromatogram <--- lib/bio/db/sanger_chromatogram ---> lib/bio/db/biosql <--- lib/bio/db/biosql ---> lib/bio/db/kegg <--- lib/bio/db/kegg ---> lib/bio/db/embl <--- lib/bio/db/embl <--- lib/bio/db ---> lib/bio/util ---> lib/bio/util/color_scheme <--- lib/bio/util/color_scheme ---> 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/double_stranded <--- lib/bio/util/restriction_enzyme/double_stranded ---> lib/bio/util/restriction_enzyme/single_strand <--- lib/bio/util/restriction_enzyme/single_strand <--- lib/bio/util/restriction_enzyme <--- lib/bio/util ---> lib/bio/tree <--- lib/bio/tree ---> lib/bio/appl ---> lib/bio/appl/hmmer <--- lib/bio/appl/hmmer ---> lib/bio/appl/sosui <--- lib/bio/appl/sosui ---> lib/bio/appl/paml ---> lib/bio/appl/paml/baseml <--- lib/bio/appl/paml/baseml ---> lib/bio/appl/paml/codeml <--- lib/bio/appl/paml/codeml ---> lib/bio/appl/paml/yn00 <--- lib/bio/appl/paml/yn00 <--- lib/bio/appl/paml ---> lib/bio/appl/phylip <--- lib/bio/appl/phylip ---> lib/bio/appl/spidey <--- lib/bio/appl/spidey ---> lib/bio/appl/iprscan <--- lib/bio/appl/iprscan ---> lib/bio/appl/fasta <--- lib/bio/appl/fasta ---> lib/bio/appl/blat <--- lib/bio/appl/blat ---> lib/bio/appl/meme ---> lib/bio/appl/meme/mast <--- lib/bio/appl/meme/mast <--- lib/bio/appl/meme ---> lib/bio/appl/tmhmm <--- lib/bio/appl/tmhmm ---> lib/bio/appl/blast <--- lib/bio/appl/blast ---> lib/bio/appl/mafft <--- lib/bio/appl/mafft ---> lib/bio/appl/genscan <--- lib/bio/appl/genscan ---> lib/bio/appl/clustalw <--- lib/bio/appl/clustalw ---> lib/bio/appl/gcg <--- lib/bio/appl/gcg ---> lib/bio/appl/targetp <--- lib/bio/appl/targetp ---> lib/bio/appl/bl2seq <--- lib/bio/appl/bl2seq ---> lib/bio/appl/sim4 <--- lib/bio/appl/sim4 ---> lib/bio/appl/psort <--- lib/bio/appl/psort <--- lib/bio/appl ---> lib/bio/io ---> lib/bio/io/flatfile <--- lib/bio/io/flatfile ---> lib/bio/io/biosql ---> lib/bio/io/biosql/config <--- lib/bio/io/biosql/config <--- lib/bio/io/biosql <--- lib/bio/io ---> 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/data <--- lib/bio/data <--- lib/bio <--- lib SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> ruby27-bio-1.5.1 depends on file: /usr/local/bin/ruby27 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for ruby27-bio-1.5.1 ===> ruby27-bio-1.5.1 depends on file: /usr/local/bin/ruby27 - found ===> Generating temporary packing list ===> Running setup.rb to install rm -f InstalledFiles ---> bin mkdir -p /construction/biology/ruby-bio/stage/usr/local/bin install br_bioflat.rb /usr/local/bin//br_bioflat install br_biogetseq.rb /usr/local/bin//br_biogetseq install br_pmfetch.rb /usr/local/bin//br_pmfetch install bioruby /usr/local/bin//bioruby install br_biofetch.rb /usr/local/bin//br_biofetch <--- bin ---> lib mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7 install bio.rb /usr/local/lib/ruby/site_ruby/2.7/ ---> lib/bio mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio install command.rb /usr/local/lib/ruby/site_ruby/2.7/bio install version.rb /usr/local/lib/ruby/site_ruby/2.7/bio install location.rb /usr/local/lib/ruby/site_ruby/2.7/bio install sequence.rb /usr/local/lib/ruby/site_ruby/2.7/bio install alignment.rb /usr/local/lib/ruby/site_ruby/2.7/bio install reference.rb /usr/local/lib/ruby/site_ruby/2.7/bio install map.rb /usr/local/lib/ruby/site_ruby/2.7/bio install db.rb /usr/local/lib/ruby/site_ruby/2.7/bio install tree.rb /usr/local/lib/ruby/site_ruby/2.7/bio install shell.rb /usr/local/lib/ruby/site_ruby/2.7/bio install feature.rb /usr/local/lib/ruby/site_ruby/2.7/bio install pathway.rb /usr/local/lib/ruby/site_ruby/2.7/bio ---> lib/bio/compat mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/compat install features.rb /usr/local/lib/ruby/site_ruby/2.7/bio/compat install references.rb /usr/local/lib/ruby/site_ruby/2.7/bio/compat <--- lib/bio/compat ---> lib/bio/sequence mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/sequence install generic.rb /usr/local/lib/ruby/site_ruby/2.7/bio/sequence install format.rb /usr/local/lib/ruby/site_ruby/2.7/bio/sequence install na.rb /usr/local/lib/ruby/site_ruby/2.7/bio/sequence install common.rb /usr/local/lib/ruby/site_ruby/2.7/bio/sequence install sequence_masker.rb /usr/local/lib/ruby/site_ruby/2.7/bio/sequence install format_raw.rb /usr/local/lib/ruby/site_ruby/2.7/bio/sequence install dblink.rb /usr/local/lib/ruby/site_ruby/2.7/bio/sequence install aa.rb /usr/local/lib/ruby/site_ruby/2.7/bio/sequence install quality_score.rb /usr/local/lib/ruby/site_ruby/2.7/bio/sequence install adapter.rb /usr/local/lib/ruby/site_ruby/2.7/bio/sequence install compat.rb /usr/local/lib/ruby/site_ruby/2.7/bio/sequence <--- lib/bio/sequence ---> lib/bio/db mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/db install newick.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db install aaindex.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db install fantom.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db install prosite.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db install medline.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db install fastq.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db install nexus.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db install fasta.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db install gff.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db install litdb.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db install rebase.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db install soft.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db install go.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db install pdb.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db install transfac.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db install lasergene.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db install nbrf.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db ---> lib/bio/db/genbank mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/db/genbank install common.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/genbank install format_genbank.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/genbank install genpept.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/genbank install refseq.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/genbank install genbank_to_biosequence.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/genbank install ddbj.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/genbank install genbank.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/genbank <--- lib/bio/db/genbank ---> lib/bio/db/pdb mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/db/pdb install utils.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/pdb install residue.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/pdb install model.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/pdb install chemicalcomponent.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/pdb install atom.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/pdb install pdb.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/pdb install chain.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/pdb <--- lib/bio/db/pdb ---> lib/bio/db/fasta mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/db/fasta install qual_to_biosequence.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/fasta install format_fasta.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/fasta install qual.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/fasta install format_qual.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/fasta install fasta_to_biosequence.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/fasta install defline.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/fasta <--- lib/bio/db/fasta ---> lib/bio/db/phyloxml mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/db/phyloxml install phyloxml_elements.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/phyloxml install phyloxml.xsd /usr/local/lib/ruby/site_ruby/2.7/bio/db/phyloxml install phyloxml_parser.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/phyloxml install phyloxml_writer.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/phyloxml <--- lib/bio/db/phyloxml ---> lib/bio/db/fastq mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/db/fastq install fastq_to_biosequence.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/fastq install format_fastq.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/fastq <--- lib/bio/db/fastq ---> lib/bio/db/sanger_chromatogram mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/db/sanger_chromatogram install scf.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/sanger_chromatogram install chromatogram.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/sanger_chromatogram install chromatogram_to_biosequence.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/sanger_chromatogram install abif.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/sanger_chromatogram <--- lib/bio/db/sanger_chromatogram ---> lib/bio/db/biosql mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/db/biosql install sequence.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/biosql install biosql_to_biosequence.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/biosql <--- lib/bio/db/biosql ---> lib/bio/db/kegg mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/db/kegg install reaction.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/kegg install genes.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/kegg install genome.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/kegg install keggtab.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/kegg install common.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/kegg install kgml.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/kegg install orthology.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/kegg install expression.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/kegg install module.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/kegg install brite.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/kegg install glycan.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/kegg install compound.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/kegg install pathway.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/kegg install enzyme.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/kegg install drug.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/kegg <--- lib/bio/db/kegg ---> lib/bio/db/embl mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/db/embl install uniprot.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/embl install trembl.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/embl install sptr.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/embl install embl_to_biosequence.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/embl install common.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/embl install format_embl.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/embl install uniprotkb.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/embl install embl.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/embl install swissprot.rb /usr/local/lib/ruby/site_ruby/2.7/bio/db/embl <--- lib/bio/db/embl <--- lib/bio/db ---> lib/bio/util mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/util install color_scheme.rb /usr/local/lib/ruby/site_ruby/2.7/bio/util install sirna.rb /usr/local/lib/ruby/site_ruby/2.7/bio/util install contingency_table.rb /usr/local/lib/ruby/site_ruby/2.7/bio/util install restriction_enzyme.rb /usr/local/lib/ruby/site_ruby/2.7/bio/util ---> lib/bio/util/color_scheme mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/util/color_scheme install turn.rb /usr/local/lib/ruby/site_ruby/2.7/bio/util/color_scheme install nucleotide.rb /usr/local/lib/ruby/site_ruby/2.7/bio/util/color_scheme install zappo.rb /usr/local/lib/ruby/site_ruby/2.7/bio/util/color_scheme install helix.rb /usr/local/lib/ruby/site_ruby/2.7/bio/util/color_scheme install strand.rb /usr/local/lib/ruby/site_ruby/2.7/bio/util/color_scheme install taylor.rb /usr/local/lib/ruby/site_ruby/2.7/bio/util/color_scheme install buried.rb /usr/local/lib/ruby/site_ruby/2.7/bio/util/color_scheme install hydropathy.rb /usr/local/lib/ruby/site_ruby/2.7/bio/util/color_scheme <--- lib/bio/util/color_scheme ---> lib/bio/util/restriction_enzyme mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme install sorted_num_array.rb /usr/local/lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme install dense_int_array.rb /usr/local/lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme install string_formatting.rb /usr/local/lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme install analysis.rb /usr/local/lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme install enzymes.yaml /usr/local/lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme install cut_symbol.rb /usr/local/lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme install double_stranded.rb /usr/local/lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme install single_strand.rb /usr/local/lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme install single_strand_complement.rb /usr/local/lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme install analysis_basic.rb /usr/local/lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme ---> lib/bio/util/restriction_enzyme/range mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme/range install cut_ranges.rb /usr/local/lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme/range install cut_range.rb /usr/local/lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme/range install vertical_cut_range.rb /usr/local/lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme/range install sequence_range.rb /usr/local/lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme/range install horizontal_cut_range.rb /usr/local/lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme/range ---> lib/bio/util/restriction_enzyme/range/sequence_range mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme/range/sequence_range install calculated_cuts.rb /usr/local/lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme/range/sequence_range install fragment.rb /usr/local/lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme/range/sequence_range install fragments.rb /usr/local/lib/ruby/site_ruby/2.7/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/double_stranded mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme/double_stranded install cut_locations_in_enzyme_notation.rb /usr/local/lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme/double_stranded install cut_location_pair_in_enzyme_notation.rb /usr/local/lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme/double_stranded install cut_locations.rb /usr/local/lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme/double_stranded install aligned_strands.rb /usr/local/lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme/double_stranded install cut_location_pair.rb /usr/local/lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme/double_stranded <--- lib/bio/util/restriction_enzyme/double_stranded ---> lib/bio/util/restriction_enzyme/single_strand mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme/single_strand install cut_locations_in_enzyme_notation.rb /usr/local/lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme/single_strand <--- lib/bio/util/restriction_enzyme/single_strand <--- lib/bio/util/restriction_enzyme <--- lib/bio/util ---> lib/bio/tree mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/tree install output.rb /usr/local/lib/ruby/site_ruby/2.7/bio/tree <--- lib/bio/tree ---> lib/bio/appl mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/appl install blast.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl install tcoffee.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl install mafft.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl install muscle.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl install sim4.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl install fasta.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl install probcons.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl install psort.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl install emboss.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl install clustalw.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl install hmmer.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl install pts1.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl ---> lib/bio/appl/hmmer mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/appl/hmmer install report.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl/hmmer <--- lib/bio/appl/hmmer ---> lib/bio/appl/sosui mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/appl/sosui install report.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl/sosui <--- lib/bio/appl/sosui ---> lib/bio/appl/paml mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/appl/paml install codeml.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl/paml install common.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl/paml install common_report.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl/paml install baseml.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl/paml install yn00.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl/paml ---> lib/bio/appl/paml/baseml mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/appl/paml/baseml install report.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl/paml/baseml <--- lib/bio/appl/paml/baseml ---> lib/bio/appl/paml/codeml mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/appl/paml/codeml install report.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl/paml/codeml install rates.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl/paml/codeml <--- lib/bio/appl/paml/codeml ---> lib/bio/appl/paml/yn00 mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/appl/paml/yn00 install report.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl/paml/yn00 <--- lib/bio/appl/paml/yn00 <--- lib/bio/appl/paml ---> lib/bio/appl/phylip mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/appl/phylip install alignment.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl/phylip install distance_matrix.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl/phylip <--- lib/bio/appl/phylip ---> lib/bio/appl/spidey mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/appl/spidey install report.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl/spidey <--- lib/bio/appl/spidey ---> lib/bio/appl/iprscan mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/appl/iprscan install report.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl/iprscan <--- lib/bio/appl/iprscan ---> lib/bio/appl/fasta mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/appl/fasta install format10.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl/fasta <--- lib/bio/appl/fasta ---> lib/bio/appl/blat mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/appl/blat install report.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl/blat <--- lib/bio/appl/blat ---> lib/bio/appl/meme mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/appl/meme install motif.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl/meme install mast.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl/meme ---> lib/bio/appl/meme/mast mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/appl/meme/mast install report.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl/meme/mast <--- lib/bio/appl/meme/mast <--- lib/bio/appl/meme ---> lib/bio/appl/tmhmm mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/appl/tmhmm install report.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl/tmhmm <--- lib/bio/appl/tmhmm ---> lib/bio/appl/blast mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/appl/blast install rpsblast.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl/blast install format8.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl/blast install ncbioptions.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl/blast install format0.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl/blast install wublast.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl/blast install remote.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl/blast install report.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl/blast install rexml.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl/blast install xmlparser.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl/blast install genomenet.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl/blast <--- lib/bio/appl/blast ---> lib/bio/appl/mafft mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/appl/mafft install report.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl/mafft <--- lib/bio/appl/mafft ---> lib/bio/appl/genscan mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/appl/genscan install report.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl/genscan <--- lib/bio/appl/genscan ---> lib/bio/appl/clustalw mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/appl/clustalw install report.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl/clustalw <--- lib/bio/appl/clustalw ---> lib/bio/appl/gcg mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/appl/gcg install seq.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl/gcg install msf.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl/gcg <--- lib/bio/appl/gcg ---> lib/bio/appl/targetp mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/appl/targetp install report.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl/targetp <--- lib/bio/appl/targetp ---> lib/bio/appl/bl2seq mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/appl/bl2seq install report.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl/bl2seq <--- lib/bio/appl/bl2seq ---> lib/bio/appl/sim4 mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/appl/sim4 install report.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl/sim4 <--- lib/bio/appl/sim4 ---> lib/bio/appl/psort mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/appl/psort install report.rb /usr/local/lib/ruby/site_ruby/2.7/bio/appl/psort <--- lib/bio/appl/psort <--- lib/bio/appl ---> lib/bio/io mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/io install registry.rb /usr/local/lib/ruby/site_ruby/2.7/bio/io install togows.rb /usr/local/lib/ruby/site_ruby/2.7/bio/io install flatfile.rb /usr/local/lib/ruby/site_ruby/2.7/bio/io install pubmed.rb /usr/local/lib/ruby/site_ruby/2.7/bio/io install ncbirest.rb /usr/local/lib/ruby/site_ruby/2.7/bio/io install fetch.rb /usr/local/lib/ruby/site_ruby/2.7/bio/io install fastacmd.rb /usr/local/lib/ruby/site_ruby/2.7/bio/io install hinv.rb /usr/local/lib/ruby/site_ruby/2.7/bio/io install sql.rb /usr/local/lib/ruby/site_ruby/2.7/bio/io install das.rb /usr/local/lib/ruby/site_ruby/2.7/bio/io ---> lib/bio/io/flatfile mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/io/flatfile install splitter.rb /usr/local/lib/ruby/site_ruby/2.7/bio/io/flatfile install autodetection.rb /usr/local/lib/ruby/site_ruby/2.7/bio/io/flatfile install indexer.rb /usr/local/lib/ruby/site_ruby/2.7/bio/io/flatfile install buffer.rb /usr/local/lib/ruby/site_ruby/2.7/bio/io/flatfile install index.rb /usr/local/lib/ruby/site_ruby/2.7/bio/io/flatfile install bdb.rb /usr/local/lib/ruby/site_ruby/2.7/bio/io/flatfile <--- lib/bio/io/flatfile ---> lib/bio/io/biosql mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/io/biosql install ar-biosql.rb /usr/local/lib/ruby/site_ruby/2.7/bio/io/biosql install biosql.rb /usr/local/lib/ruby/site_ruby/2.7/bio/io/biosql ---> lib/bio/io/biosql/config mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/io/biosql/config install database.yml /usr/local/lib/ruby/site_ruby/2.7/bio/io/biosql/config <--- lib/bio/io/biosql/config <--- lib/bio/io/biosql <--- lib/bio/io ---> lib/bio/shell mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/shell install web.rb /usr/local/lib/ruby/site_ruby/2.7/bio/shell install object.rb /usr/local/lib/ruby/site_ruby/2.7/bio/shell install setup.rb /usr/local/lib/ruby/site_ruby/2.7/bio/shell install core.rb /usr/local/lib/ruby/site_ruby/2.7/bio/shell install script.rb /usr/local/lib/ruby/site_ruby/2.7/bio/shell install demo.rb /usr/local/lib/ruby/site_ruby/2.7/bio/shell install irb.rb /usr/local/lib/ruby/site_ruby/2.7/bio/shell install interface.rb /usr/local/lib/ruby/site_ruby/2.7/bio/shell ---> lib/bio/shell/plugin mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/shell/plugin install togows.rb /usr/local/lib/ruby/site_ruby/2.7/bio/shell/plugin install entry.rb /usr/local/lib/ruby/site_ruby/2.7/bio/shell/plugin install blast.rb /usr/local/lib/ruby/site_ruby/2.7/bio/shell/plugin install flatfile.rb /usr/local/lib/ruby/site_ruby/2.7/bio/shell/plugin install seq.rb /usr/local/lib/ruby/site_ruby/2.7/bio/shell/plugin install ncbirest.rb /usr/local/lib/ruby/site_ruby/2.7/bio/shell/plugin install obda.rb /usr/local/lib/ruby/site_ruby/2.7/bio/shell/plugin install psort.rb /usr/local/lib/ruby/site_ruby/2.7/bio/shell/plugin install emboss.rb /usr/local/lib/ruby/site_ruby/2.7/bio/shell/plugin install midi.rb /usr/local/lib/ruby/site_ruby/2.7/bio/shell/plugin install das.rb /usr/local/lib/ruby/site_ruby/2.7/bio/shell/plugin install codon.rb /usr/local/lib/ruby/site_ruby/2.7/bio/shell/plugin <--- lib/bio/shell/plugin ---> lib/bio/shell/rails mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/shell/rails ---> lib/bio/shell/rails/vendor mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/shell/rails/vendor ---> lib/bio/shell/rails/vendor/plugins mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/shell/rails/vendor/plugins ---> lib/bio/shell/rails/vendor/plugins/bioruby mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/shell/rails/vendor/plugins/bioruby ---> lib/bio/shell/rails/vendor/plugins/bioruby/generators mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/shell/rails/vendor/plugins/bioruby/generators ---> lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby install bioruby_generator.rb /usr/local/lib/ruby/site_ruby/2.7/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby ---> lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install history.rhtml /usr/local/lib/ruby/site_ruby/2.7/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install index.rhtml /usr/local/lib/ruby/site_ruby/2.7/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install bioruby-bg.gif /usr/local/lib/ruby/site_ruby/2.7/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install commands.rhtml /usr/local/lib/ruby/site_ruby/2.7/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install _log.rhtml /usr/local/lib/ruby/site_ruby/2.7/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install _variables.rhtml /usr/local/lib/ruby/site_ruby/2.7/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install bioruby-link.gif /usr/local/lib/ruby/site_ruby/2.7/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install bioruby-gem.png /usr/local/lib/ruby/site_ruby/2.7/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install bioruby.rhtml /usr/local/lib/ruby/site_ruby/2.7/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install bioruby_controller.rb /usr/local/lib/ruby/site_ruby/2.7/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install _classes.rhtml /usr/local/lib/ruby/site_ruby/2.7/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install spinner.gif /usr/local/lib/ruby/site_ruby/2.7/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install _modules.rhtml /usr/local/lib/ruby/site_ruby/2.7/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install _methods.rhtml /usr/local/lib/ruby/site_ruby/2.7/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install bioruby_helper.rb /usr/local/lib/ruby/site_ruby/2.7/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install bioruby.css /usr/local/lib/ruby/site_ruby/2.7/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/data mkdir -p /construction/biology/ruby-bio/stage/usr/local/lib/ruby/site_ruby/2.7/bio/data install na.rb /usr/local/lib/ruby/site_ruby/2.7/bio/data install codontable.rb /usr/local/lib/ruby/site_ruby/2.7/bio/data install aa.rb /usr/local/lib/ruby/site_ruby/2.7/bio/data <--- lib/bio/data <--- lib/bio <--- lib install -m 0644 /construction/biology/ruby-bio/bioruby-1.5.1/etc/bioinformatics/seqdatabase.ini /construction/biology/ruby-bio/stage/usr/local/etc/bioinformatics/seqdatabase.ini.sample /bin/cp -R /construction/biology/ruby-bio/bioruby-1.5.1/sample/ /construction/biology/ruby-bio/stage/usr/local/share/examples/ruby27/bio/ install -m 0644 /construction/biology/ruby-bio/bioruby-1.5.1/ChangeLog /construction/biology/ruby-bio/bioruby-1.5.1/README.rdoc /construction/biology/ruby-bio/stage/usr/local/share/doc/ruby27/bio/ install -m 0644 /construction/biology/ruby-bio/bioruby-1.5.1/doc/*.rd /construction/biology/ruby-bio/stage/usr/local/share/doc/ruby27/bio/ install -m 0644 /construction/biology/ruby-bio/bioruby-1.5.1/doc/*.rd.ja /construction/biology/ruby-bio/stage/usr/local/share/doc/ruby27/bio/ja/ ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Notice: Please install sysutils/rubygem-bundler for additional Gemfile-checks Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:02 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for ruby27-bio-1.5.1 file sizes/checksums [320]: 0% file sizes/checksums [320]: 31% file sizes/checksums [320]: 62% file sizes/checksums [320]: 93% file sizes/checksums [320]: 100% packing files [320]: 0% packing files [320]: 31% packing files [320]: 62% packing files [320]: 93% packing files [320]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:03 TOTAL TIME 00:00:17