Building ruby19-bio-1.4.1.txz (origin /buildshare/ports/355755/biology/ruby-bio) for powerpc-10-0 on XXX
slot2: created
x distfiles/
x distfiles/ruby/
x distfiles/ruby/bioruby-1.4.1.tar.gz
x packages/
x packages/perl5-5.16.3_10.txz
x packages/pkg-1.2.7_2.txz
x packages/autoconf-wrapper-20131203.txz
x packages/p5-Locale-gettext-1.05_3.txz
x packages/libffi-3.0.13_1.txz
x packages/gettext-0.18.3.1_1.txz
x packages/m4-1.4.17_1,1.txz
x packages/autoconf-2.69.txz
x packages/ruby-1.9.3.484_2,1.txz
x packages/gmake-3.82_1.txz
x packages/libexecinfo-1.1_3.txz
x packages/libyaml-0.1.6.txz
x packages/help2man-1.43.3_1.txz
ELF ldconfig path: /lib /usr/lib /usr/lib/compat
Make depends
===>   ruby19-bio-1.4.1 depends on file: /usr/local/sbin/pkg - not found
===>    Verifying install for /usr/local/sbin/pkg in /buildshare/ports/355755/ports-mgmt/pkg
===>   Installing existing package /packages/pkg-1.2.7_2.txz
Installing pkg-1.2.7_2... done
If you are upgrading from the old package format, first run:

  # pkg2ng
===>   Returning to build of ruby19-bio-1.4.1
===>   ruby19-bio-1.4.1 depends on file: /usr/local/bin/ruby19 - not found
===>    Verifying install for /usr/local/bin/ruby19 in /buildshare/ports/355755/lang/ruby19
===>   Installing existing package /packages/ruby-1.9.3.484_2,1.txz
Installing ruby-1.9.3.484_2,1...Installing libffi-3.0.13_1... done
Installing libyaml-0.1.6... done
 done
====
Some of the standard commands are provided as separate ports for ease
of upgrading:

	devel/ruby-gems:	gem - RubyGems package manager
	devel/rubygem-rake:	rake - Ruby Make

And some of the standard libraries are provided as separate ports
since they require extra dependencies:

	converters/ruby-iconv:	iconv module
	databases/ruby-gdbm:	GDBM module
	x11-toolkits/ruby-tk:	Tcl/Tk modules
	japanese/ruby-tk:	Tcl/Tk modules for Japanized Tcl/Tk

Install them as occasion demands.
====
===>   Returning to build of ruby19-bio-1.4.1
===>   ruby19-bio-1.4.1 depends on file: /usr/local/bin/ruby19 - found
===>   ruby19-bio-1.4.1 depends on file: /usr/local/bin/ruby19 - found
===>   ruby19-bio-1.4.1 depends on file: /usr/local/bin/ruby19 - found
Make install
===>   ruby19-bio-1.4.1 depends on file: /usr/local/sbin/pkg - found
===> Fetching all distfiles required by ruby19-bio-1.4.1 for building
===>  Extracting for ruby19-bio-1.4.1
=> SHA256 Checksum OK for ruby/bioruby-1.4.1.tar.gz.
===>   ruby19-bio-1.4.1 depends on file: /usr/local/bin/ruby19 - found
===>  Patching for ruby19-bio-1.4.1
===>   ruby19-bio-1.4.1 depends on file: /usr/local/bin/ruby19 - found
/usr/local/bin/ruby19 -i -pe 'gsub(%r"(/etc/bioinformatics/)") { "/usr/local" + $1 }'  /obj/buildshare/ports/355755/biology/ruby-bio/work/bioruby-1.4.1/doc/Tutorial.rd  /obj/buildshare/ports/355755/biology/ruby-bio/work/bioruby-1.4.1/lib/bio/io/registry.rb
===>   ruby19-bio-1.4.1 depends on file: /usr/local/bin/ruby19 - found
===>  Configuring for ruby19-bio-1.4.1
===>  Running setup.rb to configure
setup.rb:789: Use RbConfig instead of obsolete and deprecated Config.
---> 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/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
===>  Building for ruby19-bio-1.4.1
===>  Running setup.rb to build
setup.rb:789: Use RbConfig instead of obsolete and deprecated Config.
---> 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/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
===>  Staging for ruby19-bio-1.4.1
===>   ruby19-bio-1.4.1 depends on file: /usr/local/bin/ruby19 - found
===>   Generating temporary packing list
===>  Running setup.rb to install
setup.rb:789: Use RbConfig instead of obsolete and deprecated Config.
rm -f InstalledFiles
---> bin
mkdir -p /obj/buildshare/ports/355755/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 /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9
install bio.rb /usr/local/lib/ruby/site_ruby/1.9/
---> lib/bio
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio
install db.rb /usr/local/lib/ruby/site_ruby/1.9/bio
install tree.rb /usr/local/lib/ruby/site_ruby/1.9/bio
install reference.rb /usr/local/lib/ruby/site_ruby/1.9/bio
install shell.rb /usr/local/lib/ruby/site_ruby/1.9/bio
install command.rb /usr/local/lib/ruby/site_ruby/1.9/bio
install version.rb /usr/local/lib/ruby/site_ruby/1.9/bio
install feature.rb /usr/local/lib/ruby/site_ruby/1.9/bio
install pathway.rb /usr/local/lib/ruby/site_ruby/1.9/bio
install location.rb /usr/local/lib/ruby/site_ruby/1.9/bio
install map.rb /usr/local/lib/ruby/site_ruby/1.9/bio
install alignment.rb /usr/local/lib/ruby/site_ruby/1.9/bio
install sequence.rb /usr/local/lib/ruby/site_ruby/1.9/bio
---> lib/bio/util
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/util
install color_scheme.rb /usr/local/lib/ruby/site_ruby/1.9/bio/util
install contingency_table.rb /usr/local/lib/ruby/site_ruby/1.9/bio/util
install sirna.rb /usr/local/lib/ruby/site_ruby/1.9/bio/util
install restriction_enzyme.rb /usr/local/lib/ruby/site_ruby/1.9/bio/util
---> lib/bio/util/restriction_enzyme
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/util/restriction_enzyme
install single_strand.rb /usr/local/lib/ruby/site_ruby/1.9/bio/util/restriction_enzyme
install string_formatting.rb /usr/local/lib/ruby/site_ruby/1.9/bio/util/restriction_enzyme
install analysis.rb /usr/local/lib/ruby/site_ruby/1.9/bio/util/restriction_enzyme
install cut_symbol.rb /usr/local/lib/ruby/site_ruby/1.9/bio/util/restriction_enzyme
install analysis_basic.rb /usr/local/lib/ruby/site_ruby/1.9/bio/util/restriction_enzyme
install double_stranded.rb /usr/local/lib/ruby/site_ruby/1.9/bio/util/restriction_enzyme
install enzymes.yaml /usr/local/lib/ruby/site_ruby/1.9/bio/util/restriction_enzyme
install single_strand_complement.rb /usr/local/lib/ruby/site_ruby/1.9/bio/util/restriction_enzyme
---> lib/bio/util/restriction_enzyme/range
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/util/restriction_enzyme/range
install sequence_range.rb /usr/local/lib/ruby/site_ruby/1.9/bio/util/restriction_enzyme/range
install horizontal_cut_range.rb /usr/local/lib/ruby/site_ruby/1.9/bio/util/restriction_enzyme/range
install vertical_cut_range.rb /usr/local/lib/ruby/site_ruby/1.9/bio/util/restriction_enzyme/range
install cut_ranges.rb /usr/local/lib/ruby/site_ruby/1.9/bio/util/restriction_enzyme/range
install cut_range.rb /usr/local/lib/ruby/site_ruby/1.9/bio/util/restriction_enzyme/range
---> lib/bio/util/restriction_enzyme/range/sequence_range
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/util/restriction_enzyme/range/sequence_range
install calculated_cuts.rb /usr/local/lib/ruby/site_ruby/1.9/bio/util/restriction_enzyme/range/sequence_range
install fragments.rb /usr/local/lib/ruby/site_ruby/1.9/bio/util/restriction_enzyme/range/sequence_range
install fragment.rb /usr/local/lib/ruby/site_ruby/1.9/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 /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/util/restriction_enzyme/single_strand
install cut_locations_in_enzyme_notation.rb /usr/local/lib/ruby/site_ruby/1.9/bio/util/restriction_enzyme/single_strand
<--- lib/bio/util/restriction_enzyme/single_strand
---> lib/bio/util/restriction_enzyme/double_stranded
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/util/restriction_enzyme/double_stranded
install cut_location_pair.rb /usr/local/lib/ruby/site_ruby/1.9/bio/util/restriction_enzyme/double_stranded
install cut_locations.rb /usr/local/lib/ruby/site_ruby/1.9/bio/util/restriction_enzyme/double_stranded
install cut_locations_in_enzyme_notation.rb /usr/local/lib/ruby/site_ruby/1.9/bio/util/restriction_enzyme/double_stranded
install aligned_strands.rb /usr/local/lib/ruby/site_ruby/1.9/bio/util/restriction_enzyme/double_stranded
install cut_location_pair_in_enzyme_notation.rb /usr/local/lib/ruby/site_ruby/1.9/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 /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/util/color_scheme
install helix.rb /usr/local/lib/ruby/site_ruby/1.9/bio/util/color_scheme
install strand.rb /usr/local/lib/ruby/site_ruby/1.9/bio/util/color_scheme
install turn.rb /usr/local/lib/ruby/site_ruby/1.9/bio/util/color_scheme
install buried.rb /usr/local/lib/ruby/site_ruby/1.9/bio/util/color_scheme
install hydropathy.rb /usr/local/lib/ruby/site_ruby/1.9/bio/util/color_scheme
install nucleotide.rb /usr/local/lib/ruby/site_ruby/1.9/bio/util/color_scheme
install zappo.rb /usr/local/lib/ruby/site_ruby/1.9/bio/util/color_scheme
install taylor.rb /usr/local/lib/ruby/site_ruby/1.9/bio/util/color_scheme
<--- lib/bio/util/color_scheme
<--- lib/bio/util
---> lib/bio/shell
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/shell
install irb.rb /usr/local/lib/ruby/site_ruby/1.9/bio/shell
install object.rb /usr/local/lib/ruby/site_ruby/1.9/bio/shell
install interface.rb /usr/local/lib/ruby/site_ruby/1.9/bio/shell
install setup.rb /usr/local/lib/ruby/site_ruby/1.9/bio/shell
install web.rb /usr/local/lib/ruby/site_ruby/1.9/bio/shell
install script.rb /usr/local/lib/ruby/site_ruby/1.9/bio/shell
install core.rb /usr/local/lib/ruby/site_ruby/1.9/bio/shell
install demo.rb /usr/local/lib/ruby/site_ruby/1.9/bio/shell
---> lib/bio/shell/plugin
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/shell/plugin
install das.rb /usr/local/lib/ruby/site_ruby/1.9/bio/shell/plugin
install midi.rb /usr/local/lib/ruby/site_ruby/1.9/bio/shell/plugin
install obda.rb /usr/local/lib/ruby/site_ruby/1.9/bio/shell/plugin
install codon.rb /usr/local/lib/ruby/site_ruby/1.9/bio/shell/plugin
install soap.rb /usr/local/lib/ruby/site_ruby/1.9/bio/shell/plugin
install psort.rb /usr/local/lib/ruby/site_ruby/1.9/bio/shell/plugin
install togows.rb /usr/local/lib/ruby/site_ruby/1.9/bio/shell/plugin
install keggapi.rb /usr/local/lib/ruby/site_ruby/1.9/bio/shell/plugin
install blast.rb /usr/local/lib/ruby/site_ruby/1.9/bio/shell/plugin
install flatfile.rb /usr/local/lib/ruby/site_ruby/1.9/bio/shell/plugin
install entry.rb /usr/local/lib/ruby/site_ruby/1.9/bio/shell/plugin
install seq.rb /usr/local/lib/ruby/site_ruby/1.9/bio/shell/plugin
install ncbirest.rb /usr/local/lib/ruby/site_ruby/1.9/bio/shell/plugin
install emboss.rb /usr/local/lib/ruby/site_ruby/1.9/bio/shell/plugin
<--- lib/bio/shell/plugin
---> lib/bio/shell/rails
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/shell/rails
---> lib/bio/shell/rails/vendor
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/shell/rails/vendor
---> lib/bio/shell/rails/vendor/plugins
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/shell/rails/vendor/plugins
---> lib/bio/shell/rails/vendor/plugins/bioruby
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/shell/rails/vendor/plugins/bioruby
---> lib/bio/shell/rails/vendor/plugins/bioruby/generators
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/shell/rails/vendor/plugins/bioruby/generators
---> lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby
install bioruby_generator.rb /usr/local/lib/ruby/site_ruby/1.9/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby
---> lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates
install bioruby_controller.rb /usr/local/lib/ruby/site_ruby/1.9/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates
install bioruby-bg.gif /usr/local/lib/ruby/site_ruby/1.9/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates
install _classes.rhtml /usr/local/lib/ruby/site_ruby/1.9/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates
install _methods.rhtml /usr/local/lib/ruby/site_ruby/1.9/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates
install commands.rhtml /usr/local/lib/ruby/site_ruby/1.9/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates
install index.rhtml /usr/local/lib/ruby/site_ruby/1.9/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates
install bioruby-gem.png /usr/local/lib/ruby/site_ruby/1.9/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates
install _modules.rhtml /usr/local/lib/ruby/site_ruby/1.9/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates
install spinner.gif /usr/local/lib/ruby/site_ruby/1.9/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates
install _variables.rhtml /usr/local/lib/ruby/site_ruby/1.9/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates
install bioruby.css /usr/local/lib/ruby/site_ruby/1.9/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates
install _log.rhtml /usr/local/lib/ruby/site_ruby/1.9/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates
install history.rhtml /usr/local/lib/ruby/site_ruby/1.9/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates
install bioruby-link.gif /usr/local/lib/ruby/site_ruby/1.9/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates
install bioruby.rhtml /usr/local/lib/ruby/site_ruby/1.9/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates
install bioruby_helper.rb /usr/local/lib/ruby/site_ruby/1.9/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 /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/sequence
install na.rb /usr/local/lib/ruby/site_ruby/1.9/bio/sequence
install quality_score.rb /usr/local/lib/ruby/site_ruby/1.9/bio/sequence
install sequence_masker.rb /usr/local/lib/ruby/site_ruby/1.9/bio/sequence
install generic.rb /usr/local/lib/ruby/site_ruby/1.9/bio/sequence
install compat.rb /usr/local/lib/ruby/site_ruby/1.9/bio/sequence
install common.rb /usr/local/lib/ruby/site_ruby/1.9/bio/sequence
install aa.rb /usr/local/lib/ruby/site_ruby/1.9/bio/sequence
install dblink.rb /usr/local/lib/ruby/site_ruby/1.9/bio/sequence
install format_raw.rb /usr/local/lib/ruby/site_ruby/1.9/bio/sequence
install format.rb /usr/local/lib/ruby/site_ruby/1.9/bio/sequence
install adapter.rb /usr/local/lib/ruby/site_ruby/1.9/bio/sequence
<--- lib/bio/sequence
---> lib/bio/compat
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/compat
install features.rb /usr/local/lib/ruby/site_ruby/1.9/bio/compat
install references.rb /usr/local/lib/ruby/site_ruby/1.9/bio/compat
<--- lib/bio/compat
---> lib/bio/io
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/io
install ebisoap.rb /usr/local/lib/ruby/site_ruby/1.9/bio/io
install hinv.rb /usr/local/lib/ruby/site_ruby/1.9/bio/io
install fetch.rb /usr/local/lib/ruby/site_ruby/1.9/bio/io
install das.rb /usr/local/lib/ruby/site_ruby/1.9/bio/io
install ensembl.rb /usr/local/lib/ruby/site_ruby/1.9/bio/io
install dbget.rb /usr/local/lib/ruby/site_ruby/1.9/bio/io
install registry.rb /usr/local/lib/ruby/site_ruby/1.9/bio/io
install ddbjxml.rb /usr/local/lib/ruby/site_ruby/1.9/bio/io
install higet.rb /usr/local/lib/ruby/site_ruby/1.9/bio/io
install ncbisoap.rb /usr/local/lib/ruby/site_ruby/1.9/bio/io
install fastacmd.rb /usr/local/lib/ruby/site_ruby/1.9/bio/io
install togows.rb /usr/local/lib/ruby/site_ruby/1.9/bio/io
install soapwsdl.rb /usr/local/lib/ruby/site_ruby/1.9/bio/io
install sql.rb /usr/local/lib/ruby/site_ruby/1.9/bio/io
install keggapi.rb /usr/local/lib/ruby/site_ruby/1.9/bio/io
install flatfile.rb /usr/local/lib/ruby/site_ruby/1.9/bio/io
install pubmed.rb /usr/local/lib/ruby/site_ruby/1.9/bio/io
install ncbirest.rb /usr/local/lib/ruby/site_ruby/1.9/bio/io
---> lib/bio/io/biosql
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/io/biosql
install biosql.rb /usr/local/lib/ruby/site_ruby/1.9/bio/io/biosql
install ar-biosql.rb /usr/local/lib/ruby/site_ruby/1.9/bio/io/biosql
---> lib/bio/io/biosql/config
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/io/biosql/config
install database.yml /usr/local/lib/ruby/site_ruby/1.9/bio/io/biosql/config
<--- lib/bio/io/biosql/config
<--- lib/bio/io/biosql
---> lib/bio/io/flatfile
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/io/flatfile
install bdb.rb /usr/local/lib/ruby/site_ruby/1.9/bio/io/flatfile
install indexer.rb /usr/local/lib/ruby/site_ruby/1.9/bio/io/flatfile
install buffer.rb /usr/local/lib/ruby/site_ruby/1.9/bio/io/flatfile
install splitter.rb /usr/local/lib/ruby/site_ruby/1.9/bio/io/flatfile
install autodetection.rb /usr/local/lib/ruby/site_ruby/1.9/bio/io/flatfile
install index.rb /usr/local/lib/ruby/site_ruby/1.9/bio/io/flatfile
<--- lib/bio/io/flatfile
<--- lib/bio/io
---> lib/bio/db
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/db
install fastq.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db
install aaindex.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db
install rebase.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db
install lasergene.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db
install prosite.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db
install litdb.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db
install nbrf.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db
install medline.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db
install transfac.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db
install pdb.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db
install soft.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db
install fasta.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db
install fantom.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db
install newick.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db
install nexus.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db
install gff.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db
install go.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db
---> lib/bio/db/fasta
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/db/fasta
install qual_to_biosequence.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/fasta
install format_fasta.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/fasta
install format_qual.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/fasta
install qual.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/fasta
install fasta_to_biosequence.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/fasta
install defline.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/fasta
<--- lib/bio/db/fasta
---> lib/bio/db/fastq
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/db/fastq
install fastq_to_biosequence.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/fastq
install format_fastq.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/fastq
<--- lib/bio/db/fastq
---> lib/bio/db/kegg
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/db/kegg
install genes.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/kegg
install taxonomy.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/kegg
install brite.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/kegg
install compound.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/kegg
install common.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/kegg
install genome.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/kegg
install drug.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/kegg
install orthology.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/kegg
install pathway.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/kegg
install keggtab.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/kegg
install expression.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/kegg
install reaction.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/kegg
install module.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/kegg
install glycan.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/kegg
install kgml.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/kegg
install enzyme.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/kegg
<--- lib/bio/db/kegg
---> lib/bio/db/embl
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/db/embl
install uniprot.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/embl
install common.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/embl
install sptr.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/embl
install format_embl.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/embl
install embl.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/embl
install trembl.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/embl
install embl_to_biosequence.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/embl
install swissprot.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/embl
<--- lib/bio/db/embl
---> lib/bio/db/phyloxml
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/db/phyloxml
install phyloxml_elements.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/phyloxml
install phyloxml.xsd /usr/local/lib/ruby/site_ruby/1.9/bio/db/phyloxml
install phyloxml_writer.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/phyloxml
install phyloxml_parser.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/phyloxml
<--- lib/bio/db/phyloxml
---> lib/bio/db/genbank
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/db/genbank
install ddbj.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/genbank
install format_genbank.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/genbank
install common.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/genbank
install genbank_to_biosequence.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/genbank
install refseq.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/genbank
install genpept.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/genbank
install genbank.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/genbank
<--- lib/bio/db/genbank
---> lib/bio/db/pdb
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/db/pdb
install chemicalcomponent.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/pdb
install chain.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/pdb
install residue.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/pdb
install pdb.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/pdb
install model.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/pdb
install utils.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/pdb
install atom.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/pdb
<--- lib/bio/db/pdb
---> lib/bio/db/biosql
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/db/biosql
install biosql_to_biosequence.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/biosql
install sequence.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/biosql
<--- lib/bio/db/biosql
---> lib/bio/db/sanger_chromatogram
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/db/sanger_chromatogram
install scf.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/sanger_chromatogram
install chromatogram.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/sanger_chromatogram
install chromatogram_to_biosequence.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/sanger_chromatogram
install abif.rb /usr/local/lib/ruby/site_ruby/1.9/bio/db/sanger_chromatogram
<--- lib/bio/db/sanger_chromatogram
<--- lib/bio/db
---> lib/bio/data
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/data
install na.rb /usr/local/lib/ruby/site_ruby/1.9/bio/data
install aa.rb /usr/local/lib/ruby/site_ruby/1.9/bio/data
install codontable.rb /usr/local/lib/ruby/site_ruby/1.9/bio/data
<--- lib/bio/data
---> lib/bio/appl
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/appl
install clustalw.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl
install pts1.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl
install tcoffee.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl
install muscle.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl
install probcons.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl
install hmmer.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl
install psort.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl
install mafft.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl
install fasta.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl
install blast.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl
install sim4.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl
install emboss.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl
---> lib/bio/appl/spidey
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/appl/spidey
install report.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl/spidey
<--- lib/bio/appl/spidey
---> lib/bio/appl/bl2seq
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/appl/bl2seq
install report.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl/bl2seq
<--- lib/bio/appl/bl2seq
---> lib/bio/appl/tmhmm
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/appl/tmhmm
install report.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl/tmhmm
<--- lib/bio/appl/tmhmm
---> lib/bio/appl/fasta
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/appl/fasta
install format10.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl/fasta
<--- lib/bio/appl/fasta
---> lib/bio/appl/mafft
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/appl/mafft
install report.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl/mafft
<--- lib/bio/appl/mafft
---> lib/bio/appl/hmmer
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/appl/hmmer
install report.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl/hmmer
<--- lib/bio/appl/hmmer
---> lib/bio/appl/psort
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/appl/psort
install report.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl/psort
<--- lib/bio/appl/psort
---> lib/bio/appl/phylip
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/appl/phylip
install alignment.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl/phylip
install distance_matrix.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl/phylip
<--- lib/bio/appl/phylip
---> lib/bio/appl/meme
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/appl/meme
install motif.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl/meme
install mast.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl/meme
---> lib/bio/appl/meme/mast
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/appl/meme/mast
install report.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl/meme/mast
<--- lib/bio/appl/meme/mast
<--- lib/bio/appl/meme
---> lib/bio/appl/clustalw
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/appl/clustalw
install report.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl/clustalw
<--- lib/bio/appl/clustalw
---> lib/bio/appl/paml
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/appl/paml
install common_report.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl/paml
install common.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl/paml
install codeml.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl/paml
install yn00.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl/paml
install baseml.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl/paml
---> lib/bio/appl/paml/codeml
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/appl/paml/codeml
install rates.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl/paml/codeml
install report.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl/paml/codeml
<--- lib/bio/appl/paml/codeml
---> lib/bio/appl/paml/baseml
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/appl/paml/baseml
install report.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl/paml/baseml
<--- lib/bio/appl/paml/baseml
---> lib/bio/appl/paml/yn00
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/appl/paml/yn00
install report.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl/paml/yn00
<--- lib/bio/appl/paml/yn00
<--- lib/bio/appl/paml
---> lib/bio/appl/genscan
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/appl/genscan
install report.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl/genscan
<--- lib/bio/appl/genscan
---> lib/bio/appl/targetp
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/appl/targetp
install report.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl/targetp
<--- lib/bio/appl/targetp
---> lib/bio/appl/iprscan
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/appl/iprscan
install report.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl/iprscan
<--- lib/bio/appl/iprscan
---> lib/bio/appl/blast
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/appl/blast
install ddbj.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl/blast
install format8.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl/blast
install rpsblast.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl/blast
install remote.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl/blast
install genomenet.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl/blast
install report.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl/blast
install wublast.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl/blast
install format0.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl/blast
install xmlparser.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl/blast
install rexml.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl/blast
install ncbioptions.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl/blast
<--- lib/bio/appl/blast
---> lib/bio/appl/sosui
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/appl/sosui
install report.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl/sosui
<--- lib/bio/appl/sosui
---> lib/bio/appl/sim4
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/appl/sim4
install report.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl/sim4
<--- lib/bio/appl/sim4
---> lib/bio/appl/blat
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/appl/blat
install report.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl/blat
<--- lib/bio/appl/blat
---> lib/bio/appl/gcg
mkdir -p /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/lib/ruby/site_ruby/1.9/bio/appl/gcg
install msf.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl/gcg
install seq.rb /usr/local/lib/ruby/site_ruby/1.9/bio/appl/gcg
<--- lib/bio/appl/gcg
<--- lib/bio/appl
<--- lib/bio
<--- lib
install  -o root -g wheel -m 444 /obj/buildshare/ports/355755/biology/ruby-bio/work/bioruby-1.4.1/etc/bioinformatics/seqdatabase.ini /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/etc/bioinformatics/seqdatabase.ini.sample
/bin/cp -R /obj/buildshare/ports/355755/biology/ruby-bio/work/bioruby-1.4.1/sample/ /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/share/examples/ruby19/bio/
install  -o root -g wheel -m 444 /obj/buildshare/ports/355755/biology/ruby-bio/work/bioruby-1.4.1/ChangeLog /obj/buildshare/ports/355755/biology/ruby-bio/work/bioruby-1.4.1/README.rdoc /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/share/doc/ruby19/bio/
install  -o root -g wheel -m 444 /obj/buildshare/ports/355755/biology/ruby-bio/work/bioruby-1.4.1/doc/*.rd /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/share/doc/ruby19/bio/
install  -o root -g wheel -m 444 /obj/buildshare/ports/355755/biology/ruby-bio/work/bioruby-1.4.1/doc/*.rd.ja /obj/buildshare/ports/355755/biology/ruby-bio/work/stage/usr/local/share/doc/ruby19/bio/ja/
====> Compressing man pages (compress-man)
===>  Installing for ruby19-bio-1.4.1
===>  Checking if biology/ruby-bio already installed
===>   Registering installation for ruby19-bio-1.4.1
Installing ruby19-bio-1.4.1... done
Make package
===>  Building package for ruby19-bio-1.4.1
slot2: removed