Index: Makefile =================================================================== --- Makefile (revision 412024) +++ Makefile (working copy) @@ -2,7 +2,7 @@ # $FreeBSD$ PORTNAME= bio -PORTVERSION= 1.4.1 +PORTVERSION= 1.5.0 CATEGORIES= biology ruby MASTER_SITES= http://bioruby.org/archive/ PKGNAMEPREFIX= ${RUBY_PKGNAMEPREFIX} Index: distinfo =================================================================== --- distinfo (revision 412024) +++ distinfo (working copy) @@ -1,2 +1,2 @@ -SHA256 (ruby/bioruby-1.4.1.tar.gz) = 4610997ef0350b4d17ccd67a76a1712c2d986168523256eb6de395bfc8a3f15d -SIZE (ruby/bioruby-1.4.1.tar.gz) = 1340224 +SHA256 (ruby/bioruby-1.5.0.tar.gz) = b920dd27374d5f9443986f4184bfc34d79a54d927b16a8ce23caf1ce116f7026 +SIZE (ruby/bioruby-1.5.0.tar.gz) = 1475866 Index: pkg-plist =================================================================== --- pkg-plist (revision 412024) +++ pkg-plist (working copy) @@ -1,14 +1,11 @@ %%RUBY_DOCDIR%%/bio/ChangeLog %%RUBY_DOCDIR%%/bio/Changes-0.7.rd -%%RUBY_DOCDIR%%/bio/KEGG_API.rd %%RUBY_DOCDIR%%/bio/README.rdoc %%RUBY_DOCDIR%%/bio/Tutorial.rd -%%RUBY_DOCDIR%%/bio/ja/KEGG_API.rd.ja %%RUBY_DOCDIR%%/bio/ja/Tutorial.rd.ja %%RUBY_EXAMPLESDIR%%/bio/any2fasta.rb %%RUBY_EXAMPLESDIR%%/bio/biofetch.rb %%RUBY_EXAMPLESDIR%%/bio/color_scheme_na.rb -%%RUBY_EXAMPLESDIR%%/bio/dbget %%RUBY_EXAMPLESDIR%%/bio/demo_aaindex.rb %%RUBY_EXAMPLESDIR%%/bio/demo_aminoacid.rb %%RUBY_EXAMPLESDIR%%/bio/demo_bl2seq_report.rb @@ -15,7 +12,6 @@ %%RUBY_EXAMPLESDIR%%/bio/demo_blast_report.rb %%RUBY_EXAMPLESDIR%%/bio/demo_codontable.rb %%RUBY_EXAMPLESDIR%%/bio/demo_das.rb -%%RUBY_EXAMPLESDIR%%/bio/demo_ddbjxml.rb %%RUBY_EXAMPLESDIR%%/bio/demo_fasta_remote.rb %%RUBY_EXAMPLESDIR%%/bio/demo_fastaformat.rb %%RUBY_EXAMPLESDIR%%/bio/demo_genbank.rb @@ -29,8 +25,6 @@ %%RUBY_EXAMPLESDIR%%/bio/demo_kegg_glycan.rb %%RUBY_EXAMPLESDIR%%/bio/demo_kegg_orthology.rb %%RUBY_EXAMPLESDIR%%/bio/demo_kegg_reaction.rb -%%RUBY_EXAMPLESDIR%%/bio/demo_kegg_taxonomy.rb -%%RUBY_EXAMPLESDIR%%/bio/demo_keggapi.rb %%RUBY_EXAMPLESDIR%%/bio/demo_litdb.rb %%RUBY_EXAMPLESDIR%%/bio/demo_locations.rb %%RUBY_EXAMPLESDIR%%/bio/demo_ncbi_rest.rb @@ -63,17 +57,18 @@ %%RUBY_EXAMPLESDIR%%/bio/na2aa.rb %%RUBY_EXAMPLESDIR%%/bio/pmfetch.rb %%RUBY_EXAMPLESDIR%%/bio/pmsearch.rb -%%RUBY_EXAMPLESDIR%%/bio/psortplot_html.rb %%RUBY_EXAMPLESDIR%%/bio/ssearch2tab.rb %%RUBY_EXAMPLESDIR%%/bio/tdiary.rb %%RUBY_EXAMPLESDIR%%/bio/test_phyloxml_big.rb %%RUBY_EXAMPLESDIR%%/bio/tfastx2tab.rb %%RUBY_EXAMPLESDIR%%/bio/vs-genes.rb +%%RUBY_MODEXAMPLESDIR%%/benchmark_clustalw_report.rb +%%RUBY_MODEXAMPLESDIR%%/seqdatabase.ini +%%RUBY_MODEXAMPLESDIR%%/test_restriction_enzyme_long.rb %%RUBY_SITELIBDIR%%/bio.rb %%RUBY_SITELIBDIR%%/bio/alignment.rb %%RUBY_SITELIBDIR%%/bio/appl/bl2seq/report.rb %%RUBY_SITELIBDIR%%/bio/appl/blast.rb -%%RUBY_SITELIBDIR%%/bio/appl/blast/ddbj.rb %%RUBY_SITELIBDIR%%/bio/appl/blast/format0.rb %%RUBY_SITELIBDIR%%/bio/appl/blast/format8.rb %%RUBY_SITELIBDIR%%/bio/appl/blast/genomenet.rb @@ -142,6 +137,7 @@ %%RUBY_SITELIBDIR%%/bio/db/embl/swissprot.rb %%RUBY_SITELIBDIR%%/bio/db/embl/trembl.rb %%RUBY_SITELIBDIR%%/bio/db/embl/uniprot.rb +%%RUBY_SITELIBDIR%%/bio/db/embl/uniprotkb.rb %%RUBY_SITELIBDIR%%/bio/db/fantom.rb %%RUBY_SITELIBDIR%%/bio/db/fasta.rb %%RUBY_SITELIBDIR%%/bio/db/fasta/defline.rb @@ -177,7 +173,6 @@ %%RUBY_SITELIBDIR%%/bio/db/kegg/orthology.rb %%RUBY_SITELIBDIR%%/bio/db/kegg/pathway.rb %%RUBY_SITELIBDIR%%/bio/db/kegg/reaction.rb -%%RUBY_SITELIBDIR%%/bio/db/kegg/taxonomy.rb %%RUBY_SITELIBDIR%%/bio/db/lasergene.rb %%RUBY_SITELIBDIR%%/bio/db/litdb.rb %%RUBY_SITELIBDIR%%/bio/db/medline.rb @@ -209,10 +204,6 @@ %%RUBY_SITELIBDIR%%/bio/io/biosql/biosql.rb %%RUBY_SITELIBDIR%%/bio/io/biosql/config/database.yml %%RUBY_SITELIBDIR%%/bio/io/das.rb -%%RUBY_SITELIBDIR%%/bio/io/dbget.rb -%%RUBY_SITELIBDIR%%/bio/io/ddbjxml.rb -%%RUBY_SITELIBDIR%%/bio/io/ebisoap.rb -%%RUBY_SITELIBDIR%%/bio/io/ensembl.rb %%RUBY_SITELIBDIR%%/bio/io/fastacmd.rb %%RUBY_SITELIBDIR%%/bio/io/fetch.rb %%RUBY_SITELIBDIR%%/bio/io/flatfile.rb @@ -222,14 +213,10 @@ %%RUBY_SITELIBDIR%%/bio/io/flatfile/index.rb %%RUBY_SITELIBDIR%%/bio/io/flatfile/indexer.rb %%RUBY_SITELIBDIR%%/bio/io/flatfile/splitter.rb -%%RUBY_SITELIBDIR%%/bio/io/higet.rb %%RUBY_SITELIBDIR%%/bio/io/hinv.rb -%%RUBY_SITELIBDIR%%/bio/io/keggapi.rb %%RUBY_SITELIBDIR%%/bio/io/ncbirest.rb -%%RUBY_SITELIBDIR%%/bio/io/ncbisoap.rb %%RUBY_SITELIBDIR%%/bio/io/pubmed.rb %%RUBY_SITELIBDIR%%/bio/io/registry.rb -%%RUBY_SITELIBDIR%%/bio/io/soapwsdl.rb %%RUBY_SITELIBDIR%%/bio/io/sql.rb %%RUBY_SITELIBDIR%%/bio/io/togows.rb %%RUBY_SITELIBDIR%%/bio/location.rb @@ -260,13 +247,11 @@ %%RUBY_SITELIBDIR%%/bio/shell/plugin/emboss.rb %%RUBY_SITELIBDIR%%/bio/shell/plugin/entry.rb %%RUBY_SITELIBDIR%%/bio/shell/plugin/flatfile.rb -%%RUBY_SITELIBDIR%%/bio/shell/plugin/keggapi.rb %%RUBY_SITELIBDIR%%/bio/shell/plugin/midi.rb %%RUBY_SITELIBDIR%%/bio/shell/plugin/ncbirest.rb %%RUBY_SITELIBDIR%%/bio/shell/plugin/obda.rb %%RUBY_SITELIBDIR%%/bio/shell/plugin/psort.rb %%RUBY_SITELIBDIR%%/bio/shell/plugin/seq.rb -%%RUBY_SITELIBDIR%%/bio/shell/plugin/soap.rb %%RUBY_SITELIBDIR%%/bio/shell/plugin/togows.rb %%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb %%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml @@ -289,6 +274,7 @@ %%RUBY_SITELIBDIR%%/bio/shell/setup.rb %%RUBY_SITELIBDIR%%/bio/shell/web.rb %%RUBY_SITELIBDIR%%/bio/tree.rb +%%RUBY_SITELIBDIR%%/bio/tree/output.rb %%RUBY_SITELIBDIR%%/bio/util/color_scheme.rb %%RUBY_SITELIBDIR%%/bio/util/color_scheme/buried.rb %%RUBY_SITELIBDIR%%/bio/util/color_scheme/helix.rb @@ -303,6 +289,7 @@ %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/analysis.rb %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/analysis_basic.rb %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/cut_symbol.rb +%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/dense_int_array.rb %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/double_stranded.rb %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb @@ -321,6 +308,7 @@ %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/single_strand.rb %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/single_strand_complement.rb +%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/sorted_num_array.rb %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/string_formatting.rb %%RUBY_SITELIBDIR%%/bio/util/sirna.rb %%RUBY_SITELIBDIR%%/bio/version.rb