BioRuby 1.4.3 released

Posted on August 21, 2012 by Naohisa Goto

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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