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

Cook, Malcolm MEC at stowers-institute.org
Mon Sep 17 18:14:41 EDT 2007


Chris,

Removing those exceptions makes my application work with current
bioperl-live again.  Hooray!  Thanks.

But!  I have been warned!

Regards,

Malcolm Cook
Stowers Institute for Medical Research - Kansas City, Missouri
  

> -----Original Message-----
> From: Chris Fields [mailto:cjfields at uiuc.edu] 
> Sent: Monday, September 17, 2007 4:53 PM
> To: Cook, Malcolm
> Cc: bioperl list; ensembl-dev at ebi.ac.uk
> Subject: Re: [Bioperl-l] Bioperl -- why so old? ... or ... 
> Feature/Annotation rollback breaks Bioperl/Ensembl compatibility
> 
> 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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