[Bioperl-l] t/entrezgene, t/protgraph and t/FeatureIO

Hilmar Lapp hlapp at gmx.net
Mon Aug 7 08:47:09 EDT 2006


Don't worry too much about the warnings. They are annoying and  
contribute to screen clutter, and especially the entrezgene one  
raises concerns. The FeatureIO warnings just point out what they say  
I believe, and yes those things are implementable I suppose.

	-hilmar

On Aug 7, 2006, at 5:31 AM, Sendu Bala wrote:

> Hi,
> I was previously trying to tidy up the test suite to remove all
> failures, skips and warnings. I managed to reduce it quite a bit,  
> but am
> left with 3 main problem scripts.
>
>
> Failed Test   Total Fail  Failed  List of Failed
> ------------------------------------------------
> t/protgraph.t 66    23    34.85%  11 13 20-21 26 33 36-37 45 48-56
>                                    59-61 65-66
>
> I don't know enough about it to know why its failing or what the  
> answers
> are really supposed to be. Does it fail for other people? Has it ever
> worked in the past?
>
>
> t/entrezgene.................ok 3/1003Pseudo-hashes are deprecated at
> /.../Bio/SeqIO/entrezgene.pm line 469.
> t/entrezgene.................ok 509/1003Pseudo-hashes are  
> deprecated at
> /.../Bio/SeqIO/entrezgene.pm line 469.
> Pseudo-hashes are deprecated at /.../Bio/SeqIO/entrezgene.pm line 469.
> t/entrezgene.................ok 824/1003Pseudo-hashes are  
> deprecated at
> /.../Bio/SeqIO/entrezgene.pm line 469.
>
> Does anyone have the time to re-implement entrezgene.pm to not use
> pseudo-hashes?
>
>
> t/FeatureIO..................ok 2/22
>
> -------------------- WARNING ---------------------
> MSG: '##feature-ontology' directive handling not yet implemented
> ---------------------------------------------------
>
> -------------------- WARNING ---------------------
> MSG: '##attribute-ontology' directive handling not yet implemented
> ---------------------------------------------------
>
> -------------------- WARNING ---------------------
> MSG: '##source-ontology' directive handling not yet implemented
> ---------------------------------------------------
>
> Is anyone planning to implement those things? Is it at least  
> possible to
> do so?
>
> Cheers,
> Sendu.
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>

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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