[BioRuby] test and bioruby shell questions
Naohisa GOTO
ngoto at gen-info.osaka-u.ac.jp
Sun Aug 31 04:05:52 UTC 2008
Hi,
Thank you for reporting.
On Fri, 29 Aug 2008 16:44:13 +0200
Davide Rambaldi <davide.rambaldi at ifom-ieo-campus.it> wrote:
> Greetings,
> I am a new user of ruby and bioruby and I really like it especially
> for the opportunity to test interactively with irb and BioRuby shell
>
> I have some question please:
>
> - TESTING (bioruby 1.2.1 and ruby 1.8.7 on a Power PC G4 osx)
> during testing
>
> I got 7 errors:
>
> test_gff_exportview(Bio::FuncTestEnsemblHuman) [./functional/bio/
> io/test_ensembl.rb:95]:
> test_gff_exportview_with_named_args(Bio::FuncTestEnsemblHuman) [./
> functional/bio/io/test_ensembl.rb:121]:
> test_tab_exportview_with_named_args(Bio::FuncTestEnsemblHuman) [./
> functional/bio/io/test_ensembl.rb:180]:
Next time, please show all failure message, even if long.
Perhaps they are caused by the change of the Ensembl.
For a reminder, I submitted to the bug tracking system of BioRuby.
http://rubyforge.org/tracker/index.php?func=detail&aid=21744&group_id=769&atid=3037
> test_list_falsenegative(Bio::TestPROSITE) [./unit/bio/db/
> test_prosite.rb:1304]:
> test_list_falsepositive(Bio::TestPROSITE) [./unit/bio/db/
> test_prosite.rb:1356]:
> test_list_potentialhit(Bio::TestPROSITE) [./unit/bio/db/
> test_prosite.rb:1408]:
> test_list_truepositive(Bio::TestPROSITE) [./unit/bio/db/
> test_prosite.rb:1236]:
These are caused by changes of order of data in arrays, due to
the change of hash algorithm in Ruby 1.8.7 (and in Ruby 1.9.0).
I fixed these tests not to affected by order of data.
This is already included in git repository.
http://github.com/bioruby/bioruby/commit/e86f8d757c45805389e154f06ccde5a3d9e8a557
--
Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
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