[Bioperl-l] Bioperl -- why so old? ... or ... Feature/Annotation rollback breaks Bioperl/Ensembl compatibility

Chris Fields cjfields at uiuc.edu
Mon Sep 17 17:52:55 EDT 2007


Malcolm,

I have removed the Bio::Annotation overloading exceptions from  
bioperl-live; they're just more trouble than they're worth right  
now.  Could you try it out and see if that suffices, and drop us a  
note if it doesn't or if you run into other odd issues?  I'll be busy  
until the end of the month but I'll do the best I can to help out.

The rollbacks were fairly simple and essentially reversed, corrected,  
or simplified many changes made prior to the 1.5 release (most of  
which were undocumented and not completely implemented).  They pass  
all current tests and should make BioPerl classes (particularly  
Annotations and SeqFeatures) behave more like 1.4.  Beyond the now- 
removed exceptions it should be fine unless it is in an area of  
already-known incompatibility between BioPerl and Ensembl, some of  
which you've already outlined.

chris

On Sep 17, 2007, at 3:15 PM, Cook, Malcolm wrote:

> ...
> FWIW, I have just discovered that the round of bioperl changes in
> service of http://www.bioperl.org/wiki/Feature_Annotation_rollback
> introduce (additional?) incompatibilities between current bioperl and
> the Ensembl Core API.  The changes bring me to obtain and use Bioperl
> version 1.2.3 for use in conjunction with Ensemble API application (as
> is recommended by Ensembl).
>
> Until now, the ways I have used the Ensembl API appear not to have
> been effected by changes in Bioperl; I have successfully used it
> in conjunction with the bioperl's leading edge.  Of course there  
> may be
> other incompatibilities that I have just not noticed yet.
>
> Evidence of the new incompatibility is present in this back trace,
> which bridges between code in current bioperl-live and current
> ensembl/modules/Bio:
>
> -------------------- EXCEPTION --------------------
> MSG: Operator overloading of AnnotationI is deprecated
> STACK Bio::Annotation::DBLink::__ANON__
> /home/mec/cvs/bioperl-live/Bio/Annotation/DBLink.pm:59
> STACK Bio::EnsEMBL::DBSQL::DBEntryAdaptor::_fetch_by_object_type
> /home/mec/cvs/foo/ensembl/modules/Bio/EnsEMBL/DBSQL/ 
> DBEntryAdaptor.pm:77
> 8
>
>
> Obtaining version 1.2.3 fixes the issue for me.
>
> This is just a warning to others....
>
> Your milage may vary....
>
> --
>
> Malcolm Cook
> Stowers Institute for Medical Research - Kansas City, Missouri




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