printf ' ' | fink --no-use-binary-dist --yes --build-as-nobody rebuild bioruby-rb20 2>&1 The package 'bioruby-rb20' will be built without being installed. Reading build dependency for bioruby-rb20-1.4.3.0001-2... Reading dependency for bioruby-rb20-1.4.3.0001-2... Reading build conflict for bioruby-rb20-1.4.3.0001-2... The package 'ruby20-dev' will be installed. Reading dependency for ruby20-dev-2.0.0-p481-1... Reading runtime dependency for ruby20-dev-2.0.0-p481-1... The package 'ruby20' will be installed. Reading dependency for ruby20-2.0.0-p481-1... Reading runtime dependency for ruby20-2.0.0-p481-1... The package 'ruby20-shlibs' will be installed. Reading dependency for ruby20-shlibs-2.0.0-p481-1... Reading runtime dependency for ruby20-shlibs-2.0.0-p481-1... The package 'gdbm3-shlibs' will be installed. Reading dependency for gdbm3-shlibs-1.8.3-4... Reading runtime dependency for gdbm3-shlibs-1.8.3-4... The package 'libncursesw5-shlibs' will be installed. Reading dependency for libncursesw5-shlibs-5.9-20110507-1... Reading runtime dependency for libncursesw5-shlibs-5.9-20110507-1... The package 'readline6-shlibs' will be installed. Reading dependency for readline6-shlibs-6.3.6-1... Reading runtime dependency for readline6-shlibs-6.3.6-1... The package 'openssl100-shlibs' will be installed. Reading dependency for openssl100-shlibs-1.0.1h-1... Reading runtime dependency for openssl100-shlibs-1.0.1h-1... The package 'libyaml-shlibs' will be installed. Reading dependency for libyaml-shlibs-0.1.6-1... Reading runtime dependency for libyaml-shlibs-0.1.6-1... The following package will be rebuilt: bioruby-rb20 The following 8 additional packages will be installed: gdbm3-shlibs libncursesw5-shlibs libyaml-shlibs openssl100-shlibs readline6-shlibs ruby20 ruby20-dev ruby20-shlibs Do you want to continue? [Y/n] (assuming default) curl --connect-timeout 30 -f -L -A 'fink/0.37.0' -O http://distfiles.master.finkmirrors.net/distfiles/bioruby-1.4.3.0001.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 2 1465k 2 41748 0 0 83267 0 0:00:18 --:--:-- 0:00:18 83163 21 1465k 21 316k 0 0 212k 0 0:00:06 0:00:01 0:00:05 212k 42 1465k 42 629k 0 0 238k 0 0:00:06 0:00:02 0:00:04 237k 42 1465k 42 629k 0 0 172k 0 0:00:08 0:00:03 0:00:05 172k 44 1465k 44 653k 0 0 146k 0 0:00:09 0:00:04 0:00:05 146k 63 1465k 63 937k 0 0 169k 0 0:00:08 0:00:05 0:00:03 177k 70 1465k 70 1036k 0 0 159k 0 0:00:09 0:00:06 0:00:03 143k 82 1465k 82 1205k 0 0 161k 0 0:00:09 0:00:07 0:00:02 119k 100 1465k 100 1465k 0 0 175k 0 0:00:08 0:00:08 --:--:-- 178k Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/gdbm3-shlibs_1.8.3-4_darwin-x86_64.deb Selecting previously deselected package gdbm3-shlibs. (Reading database ... 4296 files and directories currently installed.) Unpacking gdbm3-shlibs (from .../gdbm3-shlibs_1.8.3-4_darwin-x86_64.deb) ... Setting up gdbm3-shlibs (1.8.3-4) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/base/libncursesw5-shlibs_5.9-20110507-1_darwin-x86_64.deb Selecting previously deselected package libncursesw5-shlibs. (Reading database ... 4304 files and directories currently installed.) Unpacking libncursesw5-shlibs (from .../libncursesw5-shlibs_5.9-20110507-1_darwin-x86_64.deb) ... Setting up libncursesw5-shlibs (5.9-20110507-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/languages/libyaml-shlibs_0.1.6-1_darwin-x86_64.deb Selecting previously deselected package libyaml-shlibs. (Reading database ... 4315 files and directories currently installed.) Unpacking libyaml-shlibs (from .../libyaml-shlibs_0.1.6-1_darwin-x86_64.deb) ... Setting up libyaml-shlibs (0.1.6-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/base/openssl100-shlibs_1.0.1h-1_darwin-x86_64.deb Selecting previously deselected package openssl100-shlibs. (Reading database ... 4318 files and directories currently installed.) Unpacking openssl100-shlibs (from .../openssl100-shlibs_1.0.1h-1_darwin-x86_64.deb) ... Setting up openssl100-shlibs (1.0.1h-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/readline6-shlibs_6.3.6-1_darwin-x86_64.deb Selecting previously deselected package readline6-shlibs. (Reading database ... 4339 files and directories currently installed.) Unpacking readline6-shlibs (from .../readline6-shlibs_6.3.6-1_darwin-x86_64.deb) ... Setting up readline6-shlibs (6.3.6-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/languages/ruby20-dev_2.0.0-p481-1_darwin-x86_64.deb /sw/fink/debs/ruby20_2.0.0-p481-1_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/languages/ruby20-shlibs_2.0.0-p481-1_darwin-x86_64.deb Selecting previously deselected package ruby20-dev. (Reading database ... 4350 files and directories currently installed.) Unpacking ruby20-dev (from .../ruby20-dev_2.0.0-p481-1_darwin-x86_64.deb) ... Selecting previously deselected package ruby20. Unpacking ruby20 (from .../ruby20_2.0.0-p481-1_darwin-x86_64.deb) ... Selecting previously deselected package ruby20-shlibs. Unpacking ruby20-shlibs (from .../ruby20-shlibs_2.0.0-p481-1_darwin-x86_64.deb) ... Setting up ruby20-shlibs (2.0.0-p481-1) ... Setting up ruby20 (2.0.0-p481-1) ... Setting up ruby20-dev (2.0.0-p481-1) ... Setting runtime build-lock... dpkg-deb -b /sw/build.build/root-fink-buildlock-bioruby-rb20-1.4.3.0001-2 /sw/build.build dpkg-deb: building package `fink-buildlock-bioruby-rb20-1.4.3.0001-2' in `/sw/build.build/fink-buildlock-bioruby-rb20-1.4.3.0001-2_2014.07.26-04.13.53_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-bioruby-rb20-1.4.3.0001-2_2014.07.26-04.13.53_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-bioruby-rb20-1.4.3.0001-2. (Reading database ... 5535 files and directories currently installed.) Unpacking fink-buildlock-bioruby-rb20-1.4.3.0001-2 (from .../fink-buildlock-bioruby-rb20-1.4.3.0001-2_2014.07.26-04.13.53_darwin-x86_64.deb) ... Setting up fink-buildlock-bioruby-rb20-1.4.3.0001-2 (2014.07.26-04.13.53) ... sudo -u fink-bld [ENV] sh -c /tmp/fink.8PX74 env LANG=C LC_ALL=C /sw/bin/tar --no-same-owner --no-same-permissions -xvf /sw/src/bioruby-1.4.3.0001.tar.gz bioruby-1.4.3.0001/ bioruby-1.4.3.0001/gemfiles/ bioruby-1.4.3.0001/gemfiles/Gemfile.travis-jruby1.9 bioruby-1.4.3.0001/gemfiles/Gemfile.travis-ruby1.9 bioruby-1.4.3.0001/gemfiles/Gemfile.travis-ruby1.8 bioruby-1.4.3.0001/gemfiles/Gemfile.travis-jruby1.8 bioruby-1.4.3.0001/gemfiles/prepare-gemspec.rb bioruby-1.4.3.0001/gemfiles/modify-Gemfile.rb bioruby-1.4.3.0001/lib/ bioruby-1.4.3.0001/lib/bio.rb bioruby-1.4.3.0001/lib/bio/ bioruby-1.4.3.0001/lib/bio/command.rb bioruby-1.4.3.0001/lib/bio/version.rb bioruby-1.4.3.0001/lib/bio/location.rb bioruby-1.4.3.0001/lib/bio/compat/ bioruby-1.4.3.0001/lib/bio/compat/features.rb bioruby-1.4.3.0001/lib/bio/compat/references.rb bioruby-1.4.3.0001/lib/bio/sequence.rb bioruby-1.4.3.0001/lib/bio/sequence/ bioruby-1.4.3.0001/lib/bio/sequence/generic.rb bioruby-1.4.3.0001/lib/bio/sequence/format.rb bioruby-1.4.3.0001/lib/bio/sequence/na.rb bioruby-1.4.3.0001/lib/bio/sequence/common.rb bioruby-1.4.3.0001/lib/bio/sequence/sequence_masker.rb bioruby-1.4.3.0001/lib/bio/sequence/format_raw.rb bioruby-1.4.3.0001/lib/bio/sequence/dblink.rb bioruby-1.4.3.0001/lib/bio/sequence/aa.rb bioruby-1.4.3.0001/lib/bio/sequence/quality_score.rb bioruby-1.4.3.0001/lib/bio/sequence/adapter.rb bioruby-1.4.3.0001/lib/bio/sequence/compat.rb bioruby-1.4.3.0001/lib/bio/db/ bioruby-1.4.3.0001/lib/bio/db/newick.rb bioruby-1.4.3.0001/lib/bio/db/aaindex.rb bioruby-1.4.3.0001/lib/bio/db/fantom.rb bioruby-1.4.3.0001/lib/bio/db/genbank/ bioruby-1.4.3.0001/lib/bio/db/genbank/common.rb bioruby-1.4.3.0001/lib/bio/db/genbank/format_genbank.rb bioruby-1.4.3.0001/lib/bio/db/genbank/genpept.rb bioruby-1.4.3.0001/lib/bio/db/genbank/refseq.rb bioruby-1.4.3.0001/lib/bio/db/genbank/genbank_to_biosequence.rb bioruby-1.4.3.0001/lib/bio/db/genbank/ddbj.rb bioruby-1.4.3.0001/lib/bio/db/genbank/genbank.rb bioruby-1.4.3.0001/lib/bio/db/pdb/ bioruby-1.4.3.0001/lib/bio/db/pdb/utils.rb bioruby-1.4.3.0001/lib/bio/db/pdb/residue.rb bioruby-1.4.3.0001/lib/bio/db/pdb/model.rb bioruby-1.4.3.0001/lib/bio/db/pdb/chemicalcomponent.rb bioruby-1.4.3.0001/lib/bio/db/pdb/atom.rb bioruby-1.4.3.0001/lib/bio/db/pdb/pdb.rb bioruby-1.4.3.0001/lib/bio/db/pdb/chain.rb bioruby-1.4.3.0001/lib/bio/db/prosite.rb bioruby-1.4.3.0001/lib/bio/db/fasta/ bioruby-1.4.3.0001/lib/bio/db/fasta/qual_to_biosequence.rb bioruby-1.4.3.0001/lib/bio/db/fasta/format_fasta.rb bioruby-1.4.3.0001/lib/bio/db/fasta/qual.rb bioruby-1.4.3.0001/lib/bio/db/fasta/format_qual.rb bioruby-1.4.3.0001/lib/bio/db/fasta/fasta_to_biosequence.rb bioruby-1.4.3.0001/lib/bio/db/fasta/defline.rb bioruby-1.4.3.0001/lib/bio/db/medline.rb bioruby-1.4.3.0001/lib/bio/db/fastq.rb bioruby-1.4.3.0001/lib/bio/db/nexus.rb bioruby-1.4.3.0001/lib/bio/db/fasta.rb bioruby-1.4.3.0001/lib/bio/db/phyloxml/ bioruby-1.4.3.0001/lib/bio/db/phyloxml/phyloxml_elements.rb bioruby-1.4.3.0001/lib/bio/db/phyloxml/phyloxml.xsd bioruby-1.4.3.0001/lib/bio/db/phyloxml/phyloxml_parser.rb bioruby-1.4.3.0001/lib/bio/db/phyloxml/phyloxml_writer.rb bioruby-1.4.3.0001/lib/bio/db/fastq/ bioruby-1.4.3.0001/lib/bio/db/fastq/fastq_to_biosequence.rb bioruby-1.4.3.0001/lib/bio/db/fastq/format_fastq.rb bioruby-1.4.3.0001/lib/bio/db/gff.rb bioruby-1.4.3.0001/lib/bio/db/sanger_chromatogram/ bioruby-1.4.3.0001/lib/bio/db/sanger_chromatogram/scf.rb bioruby-1.4.3.0001/lib/bio/db/sanger_chromatogram/chromatogram.rb bioruby-1.4.3.0001/lib/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb bioruby-1.4.3.0001/lib/bio/db/sanger_chromatogram/abif.rb bioruby-1.4.3.0001/lib/bio/db/litdb.rb bioruby-1.4.3.0001/lib/bio/db/rebase.rb bioruby-1.4.3.0001/lib/bio/db/biosql/ bioruby-1.4.3.0001/lib/bio/db/biosql/sequence.rb bioruby-1.4.3.0001/lib/bio/db/biosql/biosql_to_biosequence.rb bioruby-1.4.3.0001/lib/bio/db/kegg/ bioruby-1.4.3.0001/lib/bio/db/kegg/reaction.rb bioruby-1.4.3.0001/lib/bio/db/kegg/genes.rb bioruby-1.4.3.0001/lib/bio/db/kegg/taxonomy.rb bioruby-1.4.3.0001/lib/bio/db/kegg/genome.rb bioruby-1.4.3.0001/lib/bio/db/kegg/keggtab.rb bioruby-1.4.3.0001/lib/bio/db/kegg/common.rb bioruby-1.4.3.0001/lib/bio/db/kegg/kgml.rb bioruby-1.4.3.0001/lib/bio/db/kegg/orthology.rb bioruby-1.4.3.0001/lib/bio/db/kegg/expression.rb bioruby-1.4.3.0001/lib/bio/db/kegg/module.rb bioruby-1.4.3.0001/lib/bio/db/kegg/brite.rb bioruby-1.4.3.0001/lib/bio/db/kegg/glycan.rb bioruby-1.4.3.0001/lib/bio/db/kegg/compound.rb bioruby-1.4.3.0001/lib/bio/db/kegg/pathway.rb bioruby-1.4.3.0001/lib/bio/db/kegg/enzyme.rb bioruby-1.4.3.0001/lib/bio/db/kegg/drug.rb bioruby-1.4.3.0001/lib/bio/db/soft.rb bioruby-1.4.3.0001/lib/bio/db/go.rb bioruby-1.4.3.0001/lib/bio/db/embl/ bioruby-1.4.3.0001/lib/bio/db/embl/uniprot.rb bioruby-1.4.3.0001/lib/bio/db/embl/trembl.rb bioruby-1.4.3.0001/lib/bio/db/embl/sptr.rb bioruby-1.4.3.0001/lib/bio/db/embl/embl_to_biosequence.rb bioruby-1.4.3.0001/lib/bio/db/embl/common.rb bioruby-1.4.3.0001/lib/bio/db/embl/format_embl.rb bioruby-1.4.3.0001/lib/bio/db/embl/embl.rb bioruby-1.4.3.0001/lib/bio/db/embl/swissprot.rb bioruby-1.4.3.0001/lib/bio/db/pdb.rb bioruby-1.4.3.0001/lib/bio/db/transfac.rb bioruby-1.4.3.0001/lib/bio/db/lasergene.rb bioruby-1.4.3.0001/lib/bio/db/nbrf.rb bioruby-1.4.3.0001/lib/bio/alignment.rb bioruby-1.4.3.0001/lib/bio/util/ bioruby-1.4.3.0001/lib/bio/util/color_scheme.rb bioruby-1.4.3.0001/lib/bio/util/sirna.rb bioruby-1.4.3.0001/lib/bio/util/contingency_table.rb bioruby-1.4.3.0001/lib/bio/util/color_scheme/ bioruby-1.4.3.0001/lib/bio/util/color_scheme/turn.rb bioruby-1.4.3.0001/lib/bio/util/color_scheme/nucleotide.rb bioruby-1.4.3.0001/lib/bio/util/color_scheme/zappo.rb bioruby-1.4.3.0001/lib/bio/util/color_scheme/helix.rb bioruby-1.4.3.0001/lib/bio/util/color_scheme/strand.rb bioruby-1.4.3.0001/lib/bio/util/color_scheme/taylor.rb bioruby-1.4.3.0001/lib/bio/util/color_scheme/buried.rb bioruby-1.4.3.0001/lib/bio/util/color_scheme/hydropathy.rb bioruby-1.4.3.0001/lib/bio/util/restriction_enzyme.rb bioruby-1.4.3.0001/lib/bio/util/restriction_enzyme/ bioruby-1.4.3.0001/lib/bio/util/restriction_enzyme/sorted_num_array.rb bioruby-1.4.3.0001/lib/bio/util/restriction_enzyme/dense_int_array.rb bioruby-1.4.3.0001/lib/bio/util/restriction_enzyme/range/ bioruby-1.4.3.0001/lib/bio/util/restriction_enzyme/range/cut_ranges.rb bioruby-1.4.3.0001/lib/bio/util/restriction_enzyme/range/cut_range.rb bioruby-1.4.3.0001/lib/bio/util/restriction_enzyme/range/sequence_range/ bioruby-1.4.3.0001/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb bioruby-1.4.3.0001/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb bioruby-1.4.3.0001/lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb bioruby-1.4.3.0001/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb bioruby-1.4.3.0001/lib/bio/util/restriction_enzyme/range/sequence_range.rb bioruby-1.4.3.0001/lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb bioruby-1.4.3.0001/lib/bio/util/restriction_enzyme/double_stranded/ bioruby-1.4.3.0001/lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb bioruby-1.4.3.0001/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb bioruby-1.4.3.0001/lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb bioruby-1.4.3.0001/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb bioruby-1.4.3.0001/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb bioruby-1.4.3.0001/lib/bio/util/restriction_enzyme/string_formatting.rb bioruby-1.4.3.0001/lib/bio/util/restriction_enzyme/analysis.rb bioruby-1.4.3.0001/lib/bio/util/restriction_enzyme/enzymes.yaml bioruby-1.4.3.0001/lib/bio/util/restriction_enzyme/cut_symbol.rb bioruby-1.4.3.0001/lib/bio/util/restriction_enzyme/double_stranded.rb bioruby-1.4.3.0001/lib/bio/util/restriction_enzyme/single_strand.rb bioruby-1.4.3.0001/lib/bio/util/restriction_enzyme/single_strand_complement.rb bioruby-1.4.3.0001/lib/bio/util/restriction_enzyme/single_strand/ bioruby-1.4.3.0001/lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb bioruby-1.4.3.0001/lib/bio/util/restriction_enzyme/analysis_basic.rb bioruby-1.4.3.0001/lib/bio/tree/ bioruby-1.4.3.0001/lib/bio/tree/output.rb bioruby-1.4.3.0001/lib/bio/reference.rb bioruby-1.4.3.0001/lib/bio/map.rb bioruby-1.4.3.0001/lib/bio/db.rb bioruby-1.4.3.0001/lib/bio/tree.rb bioruby-1.4.3.0001/lib/bio/shell.rb bioruby-1.4.3.0001/lib/bio/appl/ bioruby-1.4.3.0001/lib/bio/appl/hmmer/ bioruby-1.4.3.0001/lib/bio/appl/hmmer/report.rb bioruby-1.4.3.0001/lib/bio/appl/blast.rb bioruby-1.4.3.0001/lib/bio/appl/sosui/ 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bioruby-1.4.3.0001/test/data/KEGG/ko00312.pathway bioruby-1.4.3.0001/test/data/KEGG/D00063.drug bioruby-1.4.3.0001/test/data/gcg/ bioruby-1.4.3.0001/test/data/gcg/pileup-aa.msf bioruby-1.4.3.0001/test/data/go/ bioruby-1.4.3.0001/test/data/go/selected_component.ontology bioruby-1.4.3.0001/test/data/go/selected_wikipedia2go bioruby-1.4.3.0001/test/data/go/selected_gene_association.sgd bioruby-1.4.3.0001/test/data/command/ bioruby-1.4.3.0001/test/data/command/echoarg2.sh bioruby-1.4.3.0001/test/data/command/echoarg2.bat bioruby-1.4.3.0001/test/data/bl2seq/ bioruby-1.4.3.0001/test/data/bl2seq/cd8a_p53_e-5blastp.bl2seq bioruby-1.4.3.0001/test/data/bl2seq/cd8a_cd8b_blastp.bl2seq bioruby-1.4.3.0001/test/data/sim4/ bioruby-1.4.3.0001/test/data/sim4/complement-A4.sim4 bioruby-1.4.3.0001/test/data/sim4/simple-A4.sim4 bioruby-1.4.3.0001/test/data/sim4/simple2-A4.sim4 bioruby-1.4.3.0001/test/data/soft/ bioruby-1.4.3.0001/test/data/soft/GDS100_partial.soft bioruby-1.4.3.0001/test/data/soft/GSE3457_family_partial.soft bioruby-1.4.3.0001/test/data/embl/ bioruby-1.4.3.0001/test/data/embl/AB090716.embl.rel89 bioruby-1.4.3.0001/test/data/embl/AB090716.embl bioruby-1.4.3.0001/bin/ bioruby-1.4.3.0001/bin/br_bioflat.rb bioruby-1.4.3.0001/bin/br_biogetseq.rb bioruby-1.4.3.0001/bin/br_pmfetch.rb bioruby-1.4.3.0001/bin/bioruby bioruby-1.4.3.0001/bin/br_biofetch.rb bioruby-1.4.3.0001/COPYING.ja bioruby-1.4.3.0001/sample/ bioruby-1.4.3.0001/sample/any2fasta.rb bioruby-1.4.3.0001/sample/demo_aminoacid.rb bioruby-1.4.3.0001/sample/seqdatabase.ini bioruby-1.4.3.0001/sample/demo_pathway.rb bioruby-1.4.3.0001/sample/test_phyloxml_big.rb bioruby-1.4.3.0001/sample/tdiary.rb bioruby-1.4.3.0001/sample/demo_fastaformat.rb bioruby-1.4.3.0001/sample/demo_codontable.rb bioruby-1.4.3.0001/sample/demo_genscan_report.rb bioruby-1.4.3.0001/sample/demo_keggapi.rb bioruby-1.4.3.0001/sample/biofetch.rb bioruby-1.4.3.0001/sample/demo_psort.rb bioruby-1.4.3.0001/sample/enzymes.rb bioruby-1.4.3.0001/sample/ssearch2tab.rb bioruby-1.4.3.0001/sample/demo_fasta_remote.rb bioruby-1.4.3.0001/sample/pmfetch.rb bioruby-1.4.3.0001/sample/demo_genbank.rb bioruby-1.4.3.0001/sample/goslim.rb bioruby-1.4.3.0001/sample/gbtab2mysql.rb bioruby-1.4.3.0001/sample/color_scheme_na.rb bioruby-1.4.3.0001/sample/demo_bl2seq_report.rb bioruby-1.4.3.0001/sample/vs-genes.rb bioruby-1.4.3.0001/sample/demo_sosui_report.rb bioruby-1.4.3.0001/sample/demo_prosite.rb bioruby-1.4.3.0001/sample/demo_pubmed.rb bioruby-1.4.3.0001/sample/fasta2tab.rb bioruby-1.4.3.0001/sample/demo_sirna.rb bioruby-1.4.3.0001/sample/psortplot_html.rb bioruby-1.4.3.0001/sample/demo_aaindex.rb bioruby-1.4.3.0001/sample/demo_nucleicacid.rb bioruby-1.4.3.0001/sample/demo_locations.rb bioruby-1.4.3.0001/sample/demo_litdb.rb bioruby-1.4.3.0001/sample/demo_kegg_compound.rb bioruby-1.4.3.0001/sample/test_restriction_enzyme_long.rb bioruby-1.4.3.0001/sample/genome2tab.rb bioruby-1.4.3.0001/sample/demo_blast_report.rb bioruby-1.4.3.0001/sample/demo_kegg_drug.rb bioruby-1.4.3.0001/sample/demo_kegg_glycan.rb bioruby-1.4.3.0001/sample/demo_gff1.rb bioruby-1.4.3.0001/sample/tfastx2tab.rb bioruby-1.4.3.0001/sample/demo_sequence.rb bioruby-1.4.3.0001/sample/demo_kegg_taxonomy.rb bioruby-1.4.3.0001/sample/demo_ncbi_rest.rb bioruby-1.4.3.0001/sample/fastagrep.rb bioruby-1.4.3.0001/sample/genome2rb.rb bioruby-1.4.3.0001/sample/demo_psort_report.rb bioruby-1.4.3.0001/sample/genes2nuc.rb bioruby-1.4.3.0001/sample/gb2fasta.rb bioruby-1.4.3.0001/sample/demo_kegg_orthology.rb bioruby-1.4.3.0001/sample/demo_hmmer_report.rb bioruby-1.4.3.0001/sample/genes2tab.rb bioruby-1.4.3.0001/sample/demo_das.rb bioruby-1.4.3.0001/sample/genes2pep.rb bioruby-1.4.3.0001/sample/demo_kegg_reaction.rb bioruby-1.4.3.0001/sample/demo_ddbjxml.rb bioruby-1.4.3.0001/sample/demo_go.rb bioruby-1.4.3.0001/sample/demo_kegg_genome.rb bioruby-1.4.3.0001/sample/na2aa.rb bioruby-1.4.3.0001/sample/demo_tmhmm_report.rb bioruby-1.4.3.0001/sample/dbget bioruby-1.4.3.0001/sample/gb2tab.rb bioruby-1.4.3.0001/sample/demo_targetp_report.rb bioruby-1.4.3.0001/sample/fsplit.rb bioruby-1.4.3.0001/sample/fastasort.rb bioruby-1.4.3.0001/sample/pmsearch.rb bioruby-1.4.3.0001/sample/gt2fasta.rb bioruby-1.4.3.0001/LGPL bioruby-1.4.3.0001/RELEASE_NOTES.rdoc bioruby-1.4.3.0001/README_DEV.rdoc sudo -u fink-bld [ENV] sh -c /tmp/fink.LleXf [ -r /sw/fink/dists/stable/main/finkinfo/libs/rubymods/bioruby-rb.patch ] sudo -u fink-bld [ENV] sh -c /tmp/fink.nJO3R patch -p1 < /sw/fink/dists/stable/main/finkinfo/libs/rubymods/bioruby-rb.patch patching file test/unit/bio/db/test_phyloxml.rb perl -pi -e 's|!/usr/bin/env ruby|!/sw/bin/ruby2.0|g' sample/*.rb perl -pi -e 's|!/usr/proj/bioruby/bin/ruby|!/sw/bin/ruby2.0|g' sample/biofetch.rb sudo -u fink-bld [ENV] sh -c /tmp/fink.GqDRu /sw/bin/ruby2.0 setup.rb config setup.rb:789:in `load_rbconfig': Use RbConfig instead of obsolete and deprecated Config. setup.rb:789:in `load_rbconfig': Use RbConfig instead of obsolete and deprecated Config. ---> bin <--- bin ---> lib ---> lib/bio ---> lib/bio/appl ---> lib/bio/appl/bl2seq <--- lib/bio/appl/bl2seq ---> lib/bio/appl/blast <--- lib/bio/appl/blast ---> lib/bio/appl/blat <--- lib/bio/appl/blat ---> lib/bio/appl/clustalw <--- lib/bio/appl/clustalw ---> lib/bio/appl/fasta <--- lib/bio/appl/fasta ---> lib/bio/appl/gcg <--- lib/bio/appl/gcg ---> lib/bio/appl/genscan <--- lib/bio/appl/genscan ---> lib/bio/appl/hmmer <--- lib/bio/appl/hmmer ---> lib/bio/appl/iprscan <--- lib/bio/appl/iprscan ---> lib/bio/appl/mafft <--- lib/bio/appl/mafft ---> lib/bio/appl/meme ---> lib/bio/appl/meme/mast <--- lib/bio/appl/meme/mast <--- lib/bio/appl/meme ---> 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/psort <--- lib/bio/appl/psort ---> lib/bio/appl/sim4 <--- lib/bio/appl/sim4 ---> lib/bio/appl/sosui <--- lib/bio/appl/sosui ---> lib/bio/appl/spidey <--- lib/bio/appl/spidey ---> lib/bio/appl/targetp <--- lib/bio/appl/targetp ---> lib/bio/appl/tmhmm <--- lib/bio/appl/tmhmm <--- lib/bio/appl ---> lib/bio/compat <--- lib/bio/compat ---> lib/bio/data <--- lib/bio/data ---> lib/bio/db ---> lib/bio/db/biosql <--- lib/bio/db/biosql ---> lib/bio/db/embl <--- lib/bio/db/embl ---> lib/bio/db/fasta <--- lib/bio/db/fasta ---> lib/bio/db/fastq <--- lib/bio/db/fastq ---> lib/bio/db/genbank <--- lib/bio/db/genbank ---> lib/bio/db/kegg <--- lib/bio/db/kegg ---> lib/bio/db/pdb <--- lib/bio/db/pdb ---> lib/bio/db/phyloxml <--- lib/bio/db/phyloxml ---> lib/bio/db/sanger_chromatogram <--- lib/bio/db/sanger_chromatogram <--- lib/bio/db ---> 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/sequence <--- lib/bio/sequence ---> 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/tree <--- lib/bio/tree ---> lib/bio/util ---> lib/bio/util/color_scheme <--- lib/bio/util/color_scheme ---> lib/bio/util/restriction_enzyme ---> lib/bio/util/restriction_enzyme/double_stranded <--- lib/bio/util/restriction_enzyme/double_stranded ---> 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 <--- lib/bio/util <--- lib/bio <--- lib /sw/bin/ruby2.0 setup.rb setup setup.rb:789:in `load_rbconfig': Use RbConfig instead of obsolete and deprecated Config. setup.rb:789:in `load_rbconfig': Use RbConfig instead of obsolete and deprecated Config. ---> bin updating shebang: bioruby updating shebang: br_biofetch.rb updating shebang: br_bioflat.rb updating shebang: br_biogetseq.rb updating shebang: br_pmfetch.rb <--- bin ---> lib ---> lib/bio ---> lib/bio/appl ---> lib/bio/appl/bl2seq <--- lib/bio/appl/bl2seq ---> lib/bio/appl/blast <--- lib/bio/appl/blast ---> lib/bio/appl/blat <--- lib/bio/appl/blat ---> lib/bio/appl/clustalw <--- lib/bio/appl/clustalw ---> lib/bio/appl/fasta <--- lib/bio/appl/fasta ---> lib/bio/appl/gcg <--- lib/bio/appl/gcg ---> lib/bio/appl/genscan <--- lib/bio/appl/genscan ---> lib/bio/appl/hmmer <--- lib/bio/appl/hmmer ---> lib/bio/appl/iprscan <--- lib/bio/appl/iprscan ---> lib/bio/appl/mafft <--- lib/bio/appl/mafft ---> lib/bio/appl/meme ---> lib/bio/appl/meme/mast <--- lib/bio/appl/meme/mast <--- lib/bio/appl/meme ---> 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/psort <--- lib/bio/appl/psort ---> lib/bio/appl/sim4 <--- lib/bio/appl/sim4 ---> lib/bio/appl/sosui <--- lib/bio/appl/sosui ---> lib/bio/appl/spidey <--- lib/bio/appl/spidey ---> lib/bio/appl/targetp <--- lib/bio/appl/targetp ---> lib/bio/appl/tmhmm <--- lib/bio/appl/tmhmm <--- lib/bio/appl ---> lib/bio/compat <--- lib/bio/compat ---> lib/bio/data <--- lib/bio/data ---> lib/bio/db ---> lib/bio/db/biosql <--- lib/bio/db/biosql ---> lib/bio/db/embl <--- lib/bio/db/embl ---> lib/bio/db/fasta <--- lib/bio/db/fasta ---> lib/bio/db/fastq <--- lib/bio/db/fastq ---> lib/bio/db/genbank <--- lib/bio/db/genbank ---> lib/bio/db/kegg <--- lib/bio/db/kegg ---> lib/bio/db/pdb <--- lib/bio/db/pdb ---> lib/bio/db/phyloxml <--- lib/bio/db/phyloxml ---> lib/bio/db/sanger_chromatogram <--- lib/bio/db/sanger_chromatogram <--- lib/bio/db ---> 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/sequence <--- lib/bio/sequence ---> 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/tree <--- lib/bio/tree ---> lib/bio/util ---> lib/bio/util/color_scheme <--- lib/bio/util/color_scheme ---> lib/bio/util/restriction_enzyme ---> lib/bio/util/restriction_enzyme/double_stranded <--- lib/bio/util/restriction_enzyme/double_stranded ---> 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 <--- lib/bio/util <--- lib/bio <--- lib /bin/rm -rf /sw/build.build/root-bioruby-rb20-1.4.3.0001-2 /bin/mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw /bin/mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-bioruby-rb20-1.4.3.0001-2 sudo -u fink-bld [ENV] sh -c /tmp/fink.qJuwY /tmp/fink.2FGet #!/bin/sh -ev /sw/bin/ruby2.0 setup.rb install --prefix=/sw/build.build/root-bioruby-rb20-1.4.3.0001-2 setup.rb:789:in `load_rbconfig': Use RbConfig instead of obsolete and deprecated Config. setup.rb:789:in `load_rbconfig': Use RbConfig instead of obsolete and deprecated Config. rm -f InstalledFiles ---> bin mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/bin install bioruby /sw/bin//bioruby install br_biofetch.rb /sw/bin//br_biofetch install br_bioflat.rb /sw/bin//br_bioflat install br_biogetseq.rb /sw/bin//br_biogetseq install br_pmfetch.rb /sw/bin//br_pmfetch <--- bin ---> lib mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0 install bio.rb /sw/lib/ruby/site_ruby/2.0/ ---> lib/bio mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio install alignment.rb /sw/lib/ruby/site_ruby/2.0/bio install command.rb /sw/lib/ruby/site_ruby/2.0/bio install db.rb /sw/lib/ruby/site_ruby/2.0/bio install feature.rb /sw/lib/ruby/site_ruby/2.0/bio install location.rb /sw/lib/ruby/site_ruby/2.0/bio install map.rb /sw/lib/ruby/site_ruby/2.0/bio install pathway.rb /sw/lib/ruby/site_ruby/2.0/bio install reference.rb /sw/lib/ruby/site_ruby/2.0/bio install sequence.rb /sw/lib/ruby/site_ruby/2.0/bio install shell.rb /sw/lib/ruby/site_ruby/2.0/bio install tree.rb /sw/lib/ruby/site_ruby/2.0/bio install version.rb /sw/lib/ruby/site_ruby/2.0/bio ---> lib/bio/appl mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/appl install blast.rb /sw/lib/ruby/site_ruby/2.0/bio/appl install clustalw.rb /sw/lib/ruby/site_ruby/2.0/bio/appl install emboss.rb /sw/lib/ruby/site_ruby/2.0/bio/appl install fasta.rb /sw/lib/ruby/site_ruby/2.0/bio/appl install hmmer.rb /sw/lib/ruby/site_ruby/2.0/bio/appl install mafft.rb /sw/lib/ruby/site_ruby/2.0/bio/appl install muscle.rb /sw/lib/ruby/site_ruby/2.0/bio/appl install probcons.rb /sw/lib/ruby/site_ruby/2.0/bio/appl install psort.rb /sw/lib/ruby/site_ruby/2.0/bio/appl install pts1.rb /sw/lib/ruby/site_ruby/2.0/bio/appl install sim4.rb /sw/lib/ruby/site_ruby/2.0/bio/appl install tcoffee.rb /sw/lib/ruby/site_ruby/2.0/bio/appl ---> lib/bio/appl/bl2seq mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/appl/bl2seq install report.rb /sw/lib/ruby/site_ruby/2.0/bio/appl/bl2seq <--- lib/bio/appl/bl2seq ---> lib/bio/appl/blast mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/appl/blast install ddbj.rb /sw/lib/ruby/site_ruby/2.0/bio/appl/blast install format0.rb /sw/lib/ruby/site_ruby/2.0/bio/appl/blast install format8.rb /sw/lib/ruby/site_ruby/2.0/bio/appl/blast install genomenet.rb /sw/lib/ruby/site_ruby/2.0/bio/appl/blast install ncbioptions.rb /sw/lib/ruby/site_ruby/2.0/bio/appl/blast install remote.rb /sw/lib/ruby/site_ruby/2.0/bio/appl/blast install report.rb /sw/lib/ruby/site_ruby/2.0/bio/appl/blast install rexml.rb /sw/lib/ruby/site_ruby/2.0/bio/appl/blast install rpsblast.rb /sw/lib/ruby/site_ruby/2.0/bio/appl/blast install wublast.rb /sw/lib/ruby/site_ruby/2.0/bio/appl/blast install xmlparser.rb /sw/lib/ruby/site_ruby/2.0/bio/appl/blast <--- lib/bio/appl/blast ---> lib/bio/appl/blat mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/appl/blat install report.rb /sw/lib/ruby/site_ruby/2.0/bio/appl/blat <--- lib/bio/appl/blat ---> lib/bio/appl/clustalw mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/appl/clustalw install report.rb /sw/lib/ruby/site_ruby/2.0/bio/appl/clustalw <--- lib/bio/appl/clustalw ---> lib/bio/appl/fasta mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/appl/fasta install format10.rb /sw/lib/ruby/site_ruby/2.0/bio/appl/fasta <--- lib/bio/appl/fasta ---> lib/bio/appl/gcg mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/appl/gcg install msf.rb /sw/lib/ruby/site_ruby/2.0/bio/appl/gcg install seq.rb /sw/lib/ruby/site_ruby/2.0/bio/appl/gcg <--- lib/bio/appl/gcg ---> lib/bio/appl/genscan mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/appl/genscan install report.rb /sw/lib/ruby/site_ruby/2.0/bio/appl/genscan <--- lib/bio/appl/genscan ---> lib/bio/appl/hmmer mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/appl/hmmer install report.rb /sw/lib/ruby/site_ruby/2.0/bio/appl/hmmer <--- lib/bio/appl/hmmer ---> lib/bio/appl/iprscan mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/appl/iprscan install report.rb /sw/lib/ruby/site_ruby/2.0/bio/appl/iprscan <--- lib/bio/appl/iprscan ---> lib/bio/appl/mafft mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/appl/mafft install report.rb /sw/lib/ruby/site_ruby/2.0/bio/appl/mafft <--- lib/bio/appl/mafft ---> lib/bio/appl/meme mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/appl/meme install mast.rb /sw/lib/ruby/site_ruby/2.0/bio/appl/meme install motif.rb /sw/lib/ruby/site_ruby/2.0/bio/appl/meme ---> lib/bio/appl/meme/mast mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/appl/meme/mast install report.rb /sw/lib/ruby/site_ruby/2.0/bio/appl/meme/mast <--- lib/bio/appl/meme/mast <--- lib/bio/appl/meme ---> lib/bio/appl/paml mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/appl/paml install baseml.rb /sw/lib/ruby/site_ruby/2.0/bio/appl/paml install codeml.rb /sw/lib/ruby/site_ruby/2.0/bio/appl/paml install common.rb /sw/lib/ruby/site_ruby/2.0/bio/appl/paml install common_report.rb /sw/lib/ruby/site_ruby/2.0/bio/appl/paml install yn00.rb /sw/lib/ruby/site_ruby/2.0/bio/appl/paml ---> lib/bio/appl/paml/baseml mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/appl/paml/baseml install report.rb /sw/lib/ruby/site_ruby/2.0/bio/appl/paml/baseml <--- lib/bio/appl/paml/baseml ---> lib/bio/appl/paml/codeml mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/appl/paml/codeml install rates.rb /sw/lib/ruby/site_ruby/2.0/bio/appl/paml/codeml install report.rb /sw/lib/ruby/site_ruby/2.0/bio/appl/paml/codeml <--- lib/bio/appl/paml/codeml ---> lib/bio/appl/paml/yn00 mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/appl/paml/yn00 install report.rb /sw/lib/ruby/site_ruby/2.0/bio/appl/paml/yn00 <--- lib/bio/appl/paml/yn00 <--- lib/bio/appl/paml ---> lib/bio/appl/phylip mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/appl/phylip install alignment.rb /sw/lib/ruby/site_ruby/2.0/bio/appl/phylip install distance_matrix.rb /sw/lib/ruby/site_ruby/2.0/bio/appl/phylip <--- lib/bio/appl/phylip ---> lib/bio/appl/psort mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/appl/psort install report.rb /sw/lib/ruby/site_ruby/2.0/bio/appl/psort <--- lib/bio/appl/psort ---> lib/bio/appl/sim4 mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/appl/sim4 install report.rb /sw/lib/ruby/site_ruby/2.0/bio/appl/sim4 <--- lib/bio/appl/sim4 ---> lib/bio/appl/sosui mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/appl/sosui install report.rb /sw/lib/ruby/site_ruby/2.0/bio/appl/sosui <--- lib/bio/appl/sosui ---> lib/bio/appl/spidey mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/appl/spidey install report.rb /sw/lib/ruby/site_ruby/2.0/bio/appl/spidey <--- lib/bio/appl/spidey ---> lib/bio/appl/targetp mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/appl/targetp install report.rb /sw/lib/ruby/site_ruby/2.0/bio/appl/targetp <--- lib/bio/appl/targetp ---> lib/bio/appl/tmhmm mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/appl/tmhmm install report.rb /sw/lib/ruby/site_ruby/2.0/bio/appl/tmhmm <--- lib/bio/appl/tmhmm <--- lib/bio/appl ---> lib/bio/compat mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/compat install features.rb /sw/lib/ruby/site_ruby/2.0/bio/compat install references.rb /sw/lib/ruby/site_ruby/2.0/bio/compat <--- lib/bio/compat ---> lib/bio/data mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/data install aa.rb /sw/lib/ruby/site_ruby/2.0/bio/data install codontable.rb /sw/lib/ruby/site_ruby/2.0/bio/data install na.rb /sw/lib/ruby/site_ruby/2.0/bio/data <--- lib/bio/data ---> lib/bio/db mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/db install aaindex.rb /sw/lib/ruby/site_ruby/2.0/bio/db install fantom.rb /sw/lib/ruby/site_ruby/2.0/bio/db install fasta.rb /sw/lib/ruby/site_ruby/2.0/bio/db install fastq.rb /sw/lib/ruby/site_ruby/2.0/bio/db install gff.rb /sw/lib/ruby/site_ruby/2.0/bio/db install go.rb /sw/lib/ruby/site_ruby/2.0/bio/db install lasergene.rb /sw/lib/ruby/site_ruby/2.0/bio/db install litdb.rb /sw/lib/ruby/site_ruby/2.0/bio/db install medline.rb /sw/lib/ruby/site_ruby/2.0/bio/db install nbrf.rb /sw/lib/ruby/site_ruby/2.0/bio/db install newick.rb /sw/lib/ruby/site_ruby/2.0/bio/db install nexus.rb /sw/lib/ruby/site_ruby/2.0/bio/db install pdb.rb /sw/lib/ruby/site_ruby/2.0/bio/db install prosite.rb /sw/lib/ruby/site_ruby/2.0/bio/db install rebase.rb /sw/lib/ruby/site_ruby/2.0/bio/db install soft.rb /sw/lib/ruby/site_ruby/2.0/bio/db install transfac.rb /sw/lib/ruby/site_ruby/2.0/bio/db ---> lib/bio/db/biosql mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/db/biosql install biosql_to_biosequence.rb /sw/lib/ruby/site_ruby/2.0/bio/db/biosql install sequence.rb /sw/lib/ruby/site_ruby/2.0/bio/db/biosql <--- lib/bio/db/biosql ---> lib/bio/db/embl mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/db/embl install common.rb /sw/lib/ruby/site_ruby/2.0/bio/db/embl install embl.rb /sw/lib/ruby/site_ruby/2.0/bio/db/embl install embl_to_biosequence.rb /sw/lib/ruby/site_ruby/2.0/bio/db/embl install format_embl.rb /sw/lib/ruby/site_ruby/2.0/bio/db/embl install sptr.rb /sw/lib/ruby/site_ruby/2.0/bio/db/embl install swissprot.rb /sw/lib/ruby/site_ruby/2.0/bio/db/embl install trembl.rb /sw/lib/ruby/site_ruby/2.0/bio/db/embl install uniprot.rb /sw/lib/ruby/site_ruby/2.0/bio/db/embl <--- lib/bio/db/embl ---> lib/bio/db/fasta mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/db/fasta install defline.rb /sw/lib/ruby/site_ruby/2.0/bio/db/fasta install fasta_to_biosequence.rb /sw/lib/ruby/site_ruby/2.0/bio/db/fasta install format_fasta.rb /sw/lib/ruby/site_ruby/2.0/bio/db/fasta install format_qual.rb /sw/lib/ruby/site_ruby/2.0/bio/db/fasta install qual.rb /sw/lib/ruby/site_ruby/2.0/bio/db/fasta install qual_to_biosequence.rb /sw/lib/ruby/site_ruby/2.0/bio/db/fasta <--- lib/bio/db/fasta ---> lib/bio/db/fastq mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/db/fastq install fastq_to_biosequence.rb /sw/lib/ruby/site_ruby/2.0/bio/db/fastq install format_fastq.rb /sw/lib/ruby/site_ruby/2.0/bio/db/fastq <--- lib/bio/db/fastq ---> lib/bio/db/genbank mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/db/genbank install common.rb /sw/lib/ruby/site_ruby/2.0/bio/db/genbank install ddbj.rb /sw/lib/ruby/site_ruby/2.0/bio/db/genbank install format_genbank.rb /sw/lib/ruby/site_ruby/2.0/bio/db/genbank install genbank.rb /sw/lib/ruby/site_ruby/2.0/bio/db/genbank install genbank_to_biosequence.rb /sw/lib/ruby/site_ruby/2.0/bio/db/genbank install genpept.rb /sw/lib/ruby/site_ruby/2.0/bio/db/genbank install refseq.rb /sw/lib/ruby/site_ruby/2.0/bio/db/genbank <--- lib/bio/db/genbank ---> lib/bio/db/kegg mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/db/kegg install brite.rb /sw/lib/ruby/site_ruby/2.0/bio/db/kegg install common.rb /sw/lib/ruby/site_ruby/2.0/bio/db/kegg install compound.rb /sw/lib/ruby/site_ruby/2.0/bio/db/kegg install drug.rb /sw/lib/ruby/site_ruby/2.0/bio/db/kegg install enzyme.rb /sw/lib/ruby/site_ruby/2.0/bio/db/kegg install expression.rb /sw/lib/ruby/site_ruby/2.0/bio/db/kegg install genes.rb /sw/lib/ruby/site_ruby/2.0/bio/db/kegg install genome.rb /sw/lib/ruby/site_ruby/2.0/bio/db/kegg install glycan.rb /sw/lib/ruby/site_ruby/2.0/bio/db/kegg install keggtab.rb /sw/lib/ruby/site_ruby/2.0/bio/db/kegg install kgml.rb /sw/lib/ruby/site_ruby/2.0/bio/db/kegg install module.rb /sw/lib/ruby/site_ruby/2.0/bio/db/kegg install orthology.rb /sw/lib/ruby/site_ruby/2.0/bio/db/kegg install pathway.rb /sw/lib/ruby/site_ruby/2.0/bio/db/kegg install reaction.rb /sw/lib/ruby/site_ruby/2.0/bio/db/kegg install taxonomy.rb /sw/lib/ruby/site_ruby/2.0/bio/db/kegg <--- lib/bio/db/kegg ---> lib/bio/db/pdb mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/db/pdb install atom.rb /sw/lib/ruby/site_ruby/2.0/bio/db/pdb install chain.rb /sw/lib/ruby/site_ruby/2.0/bio/db/pdb install chemicalcomponent.rb /sw/lib/ruby/site_ruby/2.0/bio/db/pdb install model.rb /sw/lib/ruby/site_ruby/2.0/bio/db/pdb install pdb.rb /sw/lib/ruby/site_ruby/2.0/bio/db/pdb install residue.rb /sw/lib/ruby/site_ruby/2.0/bio/db/pdb install utils.rb /sw/lib/ruby/site_ruby/2.0/bio/db/pdb <--- lib/bio/db/pdb ---> lib/bio/db/phyloxml mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/db/phyloxml install phyloxml.xsd /sw/lib/ruby/site_ruby/2.0/bio/db/phyloxml install phyloxml_elements.rb /sw/lib/ruby/site_ruby/2.0/bio/db/phyloxml install phyloxml_parser.rb /sw/lib/ruby/site_ruby/2.0/bio/db/phyloxml install phyloxml_writer.rb /sw/lib/ruby/site_ruby/2.0/bio/db/phyloxml <--- lib/bio/db/phyloxml ---> lib/bio/db/sanger_chromatogram mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/db/sanger_chromatogram install abif.rb /sw/lib/ruby/site_ruby/2.0/bio/db/sanger_chromatogram install chromatogram.rb /sw/lib/ruby/site_ruby/2.0/bio/db/sanger_chromatogram install chromatogram_to_biosequence.rb /sw/lib/ruby/site_ruby/2.0/bio/db/sanger_chromatogram install scf.rb /sw/lib/ruby/site_ruby/2.0/bio/db/sanger_chromatogram <--- lib/bio/db/sanger_chromatogram <--- lib/bio/db ---> lib/bio/io mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/io install das.rb /sw/lib/ruby/site_ruby/2.0/bio/io install dbget.rb /sw/lib/ruby/site_ruby/2.0/bio/io install ddbjrest.rb /sw/lib/ruby/site_ruby/2.0/bio/io install ddbjxml.rb /sw/lib/ruby/site_ruby/2.0/bio/io install ebisoap.rb /sw/lib/ruby/site_ruby/2.0/bio/io install ensembl.rb /sw/lib/ruby/site_ruby/2.0/bio/io install fastacmd.rb /sw/lib/ruby/site_ruby/2.0/bio/io install fetch.rb /sw/lib/ruby/site_ruby/2.0/bio/io install flatfile.rb /sw/lib/ruby/site_ruby/2.0/bio/io install higet.rb /sw/lib/ruby/site_ruby/2.0/bio/io install hinv.rb /sw/lib/ruby/site_ruby/2.0/bio/io install keggapi.rb /sw/lib/ruby/site_ruby/2.0/bio/io install ncbirest.rb /sw/lib/ruby/site_ruby/2.0/bio/io install ncbisoap.rb /sw/lib/ruby/site_ruby/2.0/bio/io install pubmed.rb /sw/lib/ruby/site_ruby/2.0/bio/io install registry.rb /sw/lib/ruby/site_ruby/2.0/bio/io install soapwsdl.rb /sw/lib/ruby/site_ruby/2.0/bio/io install sql.rb /sw/lib/ruby/site_ruby/2.0/bio/io install togows.rb /sw/lib/ruby/site_ruby/2.0/bio/io ---> lib/bio/io/biosql mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/io/biosql install ar-biosql.rb /sw/lib/ruby/site_ruby/2.0/bio/io/biosql install biosql.rb /sw/lib/ruby/site_ruby/2.0/bio/io/biosql ---> lib/bio/io/biosql/config mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/io/biosql/config install database.yml /sw/lib/ruby/site_ruby/2.0/bio/io/biosql/config <--- lib/bio/io/biosql/config <--- lib/bio/io/biosql ---> lib/bio/io/flatfile mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/io/flatfile install autodetection.rb /sw/lib/ruby/site_ruby/2.0/bio/io/flatfile install bdb.rb /sw/lib/ruby/site_ruby/2.0/bio/io/flatfile install buffer.rb /sw/lib/ruby/site_ruby/2.0/bio/io/flatfile install index.rb /sw/lib/ruby/site_ruby/2.0/bio/io/flatfile install indexer.rb /sw/lib/ruby/site_ruby/2.0/bio/io/flatfile install splitter.rb /sw/lib/ruby/site_ruby/2.0/bio/io/flatfile <--- lib/bio/io/flatfile <--- lib/bio/io ---> lib/bio/sequence mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/sequence install aa.rb /sw/lib/ruby/site_ruby/2.0/bio/sequence install adapter.rb /sw/lib/ruby/site_ruby/2.0/bio/sequence install common.rb /sw/lib/ruby/site_ruby/2.0/bio/sequence install compat.rb /sw/lib/ruby/site_ruby/2.0/bio/sequence install dblink.rb /sw/lib/ruby/site_ruby/2.0/bio/sequence install format.rb /sw/lib/ruby/site_ruby/2.0/bio/sequence install format_raw.rb /sw/lib/ruby/site_ruby/2.0/bio/sequence install generic.rb /sw/lib/ruby/site_ruby/2.0/bio/sequence install na.rb /sw/lib/ruby/site_ruby/2.0/bio/sequence install quality_score.rb /sw/lib/ruby/site_ruby/2.0/bio/sequence install sequence_masker.rb /sw/lib/ruby/site_ruby/2.0/bio/sequence <--- lib/bio/sequence ---> lib/bio/shell mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/shell install core.rb /sw/lib/ruby/site_ruby/2.0/bio/shell install demo.rb /sw/lib/ruby/site_ruby/2.0/bio/shell install interface.rb /sw/lib/ruby/site_ruby/2.0/bio/shell install irb.rb /sw/lib/ruby/site_ruby/2.0/bio/shell install object.rb /sw/lib/ruby/site_ruby/2.0/bio/shell install script.rb /sw/lib/ruby/site_ruby/2.0/bio/shell install setup.rb /sw/lib/ruby/site_ruby/2.0/bio/shell install web.rb /sw/lib/ruby/site_ruby/2.0/bio/shell ---> lib/bio/shell/plugin mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/shell/plugin install blast.rb /sw/lib/ruby/site_ruby/2.0/bio/shell/plugin install codon.rb /sw/lib/ruby/site_ruby/2.0/bio/shell/plugin install das.rb /sw/lib/ruby/site_ruby/2.0/bio/shell/plugin install emboss.rb /sw/lib/ruby/site_ruby/2.0/bio/shell/plugin install entry.rb /sw/lib/ruby/site_ruby/2.0/bio/shell/plugin install flatfile.rb /sw/lib/ruby/site_ruby/2.0/bio/shell/plugin install keggapi.rb /sw/lib/ruby/site_ruby/2.0/bio/shell/plugin install midi.rb /sw/lib/ruby/site_ruby/2.0/bio/shell/plugin install ncbirest.rb /sw/lib/ruby/site_ruby/2.0/bio/shell/plugin install obda.rb /sw/lib/ruby/site_ruby/2.0/bio/shell/plugin install psort.rb /sw/lib/ruby/site_ruby/2.0/bio/shell/plugin install seq.rb /sw/lib/ruby/site_ruby/2.0/bio/shell/plugin install soap.rb /sw/lib/ruby/site_ruby/2.0/bio/shell/plugin install togows.rb /sw/lib/ruby/site_ruby/2.0/bio/shell/plugin <--- lib/bio/shell/plugin ---> lib/bio/shell/rails mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/shell/rails ---> lib/bio/shell/rails/vendor mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/shell/rails/vendor ---> lib/bio/shell/rails/vendor/plugins mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/shell/rails/vendor/plugins ---> lib/bio/shell/rails/vendor/plugins/bioruby mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/shell/rails/vendor/plugins/bioruby ---> lib/bio/shell/rails/vendor/plugins/bioruby/generators mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/shell/rails/vendor/plugins/bioruby/generators ---> lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby install bioruby_generator.rb /sw/lib/ruby/site_ruby/2.0/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby ---> lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install _classes.rhtml /sw/lib/ruby/site_ruby/2.0/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install _log.rhtml /sw/lib/ruby/site_ruby/2.0/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install _methods.rhtml /sw/lib/ruby/site_ruby/2.0/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install _modules.rhtml /sw/lib/ruby/site_ruby/2.0/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install _variables.rhtml /sw/lib/ruby/site_ruby/2.0/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install bioruby-bg.gif /sw/lib/ruby/site_ruby/2.0/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install bioruby-gem.png /sw/lib/ruby/site_ruby/2.0/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install bioruby-link.gif /sw/lib/ruby/site_ruby/2.0/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install bioruby.css /sw/lib/ruby/site_ruby/2.0/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install bioruby.rhtml /sw/lib/ruby/site_ruby/2.0/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install bioruby_controller.rb /sw/lib/ruby/site_ruby/2.0/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install bioruby_helper.rb /sw/lib/ruby/site_ruby/2.0/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install commands.rhtml /sw/lib/ruby/site_ruby/2.0/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install history.rhtml /sw/lib/ruby/site_ruby/2.0/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install index.rhtml /sw/lib/ruby/site_ruby/2.0/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates install spinner.gif /sw/lib/ruby/site_ruby/2.0/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/tree mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/tree install output.rb /sw/lib/ruby/site_ruby/2.0/bio/tree <--- lib/bio/tree ---> lib/bio/util mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/util install color_scheme.rb /sw/lib/ruby/site_ruby/2.0/bio/util install contingency_table.rb /sw/lib/ruby/site_ruby/2.0/bio/util install restriction_enzyme.rb /sw/lib/ruby/site_ruby/2.0/bio/util install sirna.rb /sw/lib/ruby/site_ruby/2.0/bio/util ---> lib/bio/util/color_scheme mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/util/color_scheme install buried.rb /sw/lib/ruby/site_ruby/2.0/bio/util/color_scheme install helix.rb /sw/lib/ruby/site_ruby/2.0/bio/util/color_scheme install hydropathy.rb /sw/lib/ruby/site_ruby/2.0/bio/util/color_scheme install nucleotide.rb /sw/lib/ruby/site_ruby/2.0/bio/util/color_scheme install strand.rb /sw/lib/ruby/site_ruby/2.0/bio/util/color_scheme install taylor.rb /sw/lib/ruby/site_ruby/2.0/bio/util/color_scheme install turn.rb /sw/lib/ruby/site_ruby/2.0/bio/util/color_scheme install zappo.rb /sw/lib/ruby/site_ruby/2.0/bio/util/color_scheme <--- lib/bio/util/color_scheme ---> lib/bio/util/restriction_enzyme mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/util/restriction_enzyme install analysis.rb /sw/lib/ruby/site_ruby/2.0/bio/util/restriction_enzyme install analysis_basic.rb /sw/lib/ruby/site_ruby/2.0/bio/util/restriction_enzyme install cut_symbol.rb /sw/lib/ruby/site_ruby/2.0/bio/util/restriction_enzyme install dense_int_array.rb /sw/lib/ruby/site_ruby/2.0/bio/util/restriction_enzyme install double_stranded.rb /sw/lib/ruby/site_ruby/2.0/bio/util/restriction_enzyme install enzymes.yaml /sw/lib/ruby/site_ruby/2.0/bio/util/restriction_enzyme install single_strand.rb /sw/lib/ruby/site_ruby/2.0/bio/util/restriction_enzyme install single_strand_complement.rb /sw/lib/ruby/site_ruby/2.0/bio/util/restriction_enzyme install sorted_num_array.rb /sw/lib/ruby/site_ruby/2.0/bio/util/restriction_enzyme install string_formatting.rb /sw/lib/ruby/site_ruby/2.0/bio/util/restriction_enzyme ---> lib/bio/util/restriction_enzyme/double_stranded mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/util/restriction_enzyme/double_stranded install aligned_strands.rb /sw/lib/ruby/site_ruby/2.0/bio/util/restriction_enzyme/double_stranded install cut_location_pair.rb /sw/lib/ruby/site_ruby/2.0/bio/util/restriction_enzyme/double_stranded install cut_location_pair_in_enzyme_notation.rb /sw/lib/ruby/site_ruby/2.0/bio/util/restriction_enzyme/double_stranded install cut_locations.rb /sw/lib/ruby/site_ruby/2.0/bio/util/restriction_enzyme/double_stranded install cut_locations_in_enzyme_notation.rb /sw/lib/ruby/site_ruby/2.0/bio/util/restriction_enzyme/double_stranded <--- lib/bio/util/restriction_enzyme/double_stranded ---> lib/bio/util/restriction_enzyme/range mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/util/restriction_enzyme/range install cut_range.rb /sw/lib/ruby/site_ruby/2.0/bio/util/restriction_enzyme/range install cut_ranges.rb /sw/lib/ruby/site_ruby/2.0/bio/util/restriction_enzyme/range install horizontal_cut_range.rb /sw/lib/ruby/site_ruby/2.0/bio/util/restriction_enzyme/range install sequence_range.rb /sw/lib/ruby/site_ruby/2.0/bio/util/restriction_enzyme/range install vertical_cut_range.rb /sw/lib/ruby/site_ruby/2.0/bio/util/restriction_enzyme/range ---> lib/bio/util/restriction_enzyme/range/sequence_range mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/util/restriction_enzyme/range/sequence_range install calculated_cuts.rb /sw/lib/ruby/site_ruby/2.0/bio/util/restriction_enzyme/range/sequence_range install fragment.rb /sw/lib/ruby/site_ruby/2.0/bio/util/restriction_enzyme/range/sequence_range install fragments.rb /sw/lib/ruby/site_ruby/2.0/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 /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/lib/ruby/site_ruby/2.0/bio/util/restriction_enzyme/single_strand install cut_locations_in_enzyme_notation.rb /sw/lib/ruby/site_ruby/2.0/bio/util/restriction_enzyme/single_strand <--- lib/bio/util/restriction_enzyme/single_strand <--- lib/bio/util/restriction_enzyme <--- lib/bio/util <--- lib/bio <--- lib mkdir -p /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/share/bioruby-rb20/sample cp -R sample/ /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/share/bioruby-rb20/sample ### prepare for u-a for file in /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/bin/*; do mv $file $file-rb20 done sudo -u fink-bld [ENV] sh -c /tmp/fink.TCCPc /usr/bin/install -d -m 700 /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/share/doc/bioruby-rb20 /bin/cp -r COPYING /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/share/doc/bioruby-rb20/ /bin/cp -r KNOWN_ISSUES.rdoc /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/share/doc/bioruby-rb20/ /bin/cp -r README.rdoc /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/share/doc/bioruby-rb20/ /bin/cp -r RELEASE_NOTES.rdoc /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/share/doc/bioruby-rb20/ /bin/cp -r ChangeLog /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/share/doc/bioruby-rb20/ /bin/cp -r doc/* /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/share/doc/bioruby-rb20/ /bin/chmod -R go=u-w /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/share/doc/bioruby-rb20 /bin/rm -f /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/info/dir /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/info/dir.old /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/share/info/dir /sw/build.build/root-bioruby-rb20-1.4.3.0001-2/sw/share/info/dir.old Reverting ownership of install dir to root Writing control file... Writing package script postinst... Writing package script prerm... Writing md5sums file... env LANG=C LC_ALL=C dpkg-deb -b root-bioruby-rb20-1.4.3.0001-2 /sw/fink/10.9/stable/main/binary-darwin-x86_64/libs/rubymods dpkg-deb: building package `bioruby-rb20' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/libs/rubymods/bioruby-rb20_1.4.3.0001-2_darwin-x86_64.deb'. Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-bioruby-rb20-1.4.3.0001-2 (Reading database ... 5536 files and directories currently installed.) Removing fink-buildlock-bioruby-rb20-1.4.3.0001-2 ...