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

Chris Fields cjfields at uiuc.edu
Mon Aug 7 09:04:25 EDT 2006


Brian already knows about the 'pseudohash' issue with protgraph.  I  
think it's a weird ref call or construct that tripping the perl  
warnings.  I don't think perl 5.6 does this; the pseudohash warning  
was added in perl 5.8.

I really wouldn't worry about the other tests throwing warnings.  You  
have your hands full with Taxonomy now; focus on getting that up and  
running before you move on to other ventures.

Chris

On Aug 7, 2006, at 4:31 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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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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