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

[Hilmar Lapp]

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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>

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