BioRuby 1.4.3 released

We are pleased to announce the release of BioRuby 1.4.3. This new release fixes bugs existed in 1.4.2 and improves portability on JRuby and Rubinius.

Here is a brief summary of changes.

  • Bio::KEGG::KGML bug fixes and new class Bio::KEGG::KGML::Graphics for storing a graphics element.
  • Many failures and errors running on JRuby and Rubinius are resolved.
  • Strange behavior related with “circular require” is fixed.
  • Fixed: Genomenet remote BLAST does not work.
  • Fixed: Bio::NucleicAcid.to_re(“s”) typo.
  • Fixed: Bio::EMBL#os raises RuntimeError.
  • Fixed: bin/bioruby: Failed to save object with error message “can’t convert Symbol into String” on Ruby 1.9.

In addition, many changes have been made, including incompatible changes. For more information, see RELEASE_NOTES.rdoc and ChangeLog.

The archive is available at: http://bioruby.org/archive/bioruby-1.4.3.tar.gz
Gem file is also available at: http://bioruby.org/archive/gems/bio-1.4.3.gem

We also put RubyGems pacakge at RubyGems.org and RubyForge. You can easily install by using RubyGems. First, check the version number by using search command:
% gem search –remote bio
and find “bio (1.4.3)” in the list. Then,
% sudo gem install bio

Acknowledgments: Thanks to all persons reporting issues and/or submitting patches.

Hope you enjoy.

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