[BioRuby] Fwd: BioRuby 1.2.0 is released

[Toshiaki Katayama]

Hi all,

Does anybody has the same problem on Linux/Windows?

Toshiaki

Begin forwarded message:

> From: "jan aerts (RI)" <jan.aerts at bbsrc.ac.uk>
> Date: 2007年12月15日 5:50:42:JST
> To: "Toshiaki Katayama" <ktym at hgc.jp>
> Cc: <n at bioruby.org>
> Subject: RE: [BioRuby] BioRuby 1.2.0 is released
>
> Ubuntu 7.10 (Gutsy Gibbon).
> ruby 1.8.6
> soap4r 1.5.5-1 (apt-get package)
>
> j.
>
>
> -----Original Message-----
> From: Toshiaki Katayama [mailto:ktym at hgc.jp]
> Sent: Fri 14/12/2007 18:42
> To: jan aerts (RI)
> Cc: n at bioruby.org
> Subject: Re: [BioRuby] BioRuby 1.2.0 is released
>
> Jan,
>
> In my environment (OS X Leopard), I have no errors on all tests in BioRuby 1.2.0 with Ruby 1.8.6
> What kind of environment do you use?
>
> Regards,
> Toshiaki
>
> On 2007/12/15, at 3:28, jan aerts (RI) wrote:
>
>> Thanks T.
>>
>> Good to see a new release is out.
>>
>> I noticed that the test/functional/bio/io/test_soapwsdl.rb test returned errors. All 4 tests in that testfile give the following error:
>>
>> NoMethodError: undefined method `location=' for nil:NilClass
>>   /usr/lib/ruby/1.8/wsdl/xmlSchema/importer.rb:31:in `import'
>>   /usr/lib/ruby/1.8/wsdl/importer.rb:18:in `import'
>>   /usr/lib/ruby/1.8/soap/wsdlDriver.rb:124:in `import'
>>   /usr/lib/ruby/1.8/soap/wsdlDriver.rb:28:in `initialize'
>>   ../../../../lib/bio/io/soapwsdl.rb:63:in `new'
>>   ../../../../lib/bio/io/soapwsdl.rb:63:in `create_driver'
>>   ../../../../lib/bio/io/soapwsdl.rb:57:in `initialize'
>>   ./test_soapwsdl.rb:25:in `new'
>>   ./test_soapwsdl.rb:25:in `setup'
>>
>> jan.
>>
>>
>> -----Original Message-----
>> From: bioruby-bounces at lists.open-bio.org on behalf of Toshiaki Katayama
>> Sent: Fri 14/12/2007 17:20
>> To: BioRuby; bioruby-ja at lists.open-bio.org
>> Subject: [BioRuby] BioRuby 1.2.0 is released
>>
>> Hi all,
>>
>> I just released the BioRuby 1.2.0 at http://bioruby.org/archive/bioruby-1.2.0.tar.gz
>>
>> http://bioruby.org/
>> http://bioruby.org/rdoc/
>> http://rubyforge.org/projects/bioruby/
>> http://raa.ruby-lang.org/project/bioruby/
>>
>> I also put RubyGems pacakge at RubyForge as always.
>>
>> % sudo gem update bio
>>
>> Here is a brief summary of updates snipped from the ChangeLog file.
>>
>>       * BioRuby 1.2.0 released
>>
>>         * BioRuby shell is improved
>>           * file save functionality is fixed
>>           * deprecated require_gem is changed to gem to suppress warnings
>>           * deprecated end_form_tag is rewrited to suppress warnings
>>           * images for Rails shell are separated to the bioruby directory
>>           * spinner is shown during the evaluation
>>           * background image in the textarea is removed for the visibility
>>         * Bio::Blast is fixed to parse -m 8 formatted result correctly
>>         * Bio::PubMed is rewrited to enhance its functionality
>>           * e.g. 'rettype' => 'count' and 'retmode' => 'xml' are available
>>         * Bio::FlatFile is improved to accept recent MEDLINE format
>>         * Bio::KEGG::COMPOUND is enhanced to utilize REMARK field
>>         * Bio::KEGG::API is fixed to skip filter when the value is Fixnum
>>         * A number of minor bug fixes
>>
>> Hope you enjoy.
>>
>> Regards,
>> Toshiaki Katayama
>> --
>> Human Genome Center, Institute of Medical Science, University of Tokyo
>> 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-0071, Japan
>> tel://+81-3-5449-5614
>> fax://+81-3-5449-5434
>> http://www.hgc.jp/ (Human Genome Center)
>> http://bioruby.org/ (BioRuby project)
>> http://das.hgc.jp/ (KEGG DAS)
>> http://www.genome.jp/kegg/soap/ (KEGG API)
>>
>>
>>
>> _______________________________________________
>> BioRuby mailing list
>> BioRuby at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioruby
>>
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