Wednesday, 22 August 2012

[BioRuby] BioRuby 1.4.3 released

---------- Forwarded message ----------
From: Naohisa GOTO

Hi, all,

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.

Tar.gz file:
Gem file:

We also put RubyGems pacakge at and RubyForge (*).
(* Files on RubyForge will soon be available.)

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

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

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

Hope you enjoy.

P.S. We are having trouble when updating
and webpages now, possibly because
of file/directory permissions in server.

Naohisa Goto
BioRuby Project -
BioRuby mailing list

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