Attachment 168716 Details for Bug 208351 – patch file

patch file

bioruby-1.5.0.diff.txt (text/plain), 6.61 KB, created by Wen Heping on 2016-03-28 08:36:03 UTC

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Creator: Wen Heping

Created: 2016-03-28 08:36:03 UTC

Size: 6.61 KB

patch

obsolete

>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

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Attachments on bug 208351: 168716