[BioRuby] test and bioruby shell questions

Naohisa GOTO ngoto at gen-info.osaka-u.ac.jp
Sun Aug 31 04:05:52 UTC 2008


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.

> 	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.

Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org

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