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

Sendu Bala bix at sendu.me.uk
Mon Aug 7 05:31:50 EDT 2006


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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