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

Cook, Malcolm MEC at stowers-institute.org
Mon Sep 17 16:15:39 EDT 2007


Sometime ago, in the ensembl-dev mailing list, mdr wrote:

> > I'm always running into bugs in bioperl that have been fixed in more
recent
> > versions than the version 1-2-3 that the installation document
specifies.  
> > 
> > Just wondering, are there plans to try to move to 1-5 any time soon,
or is that
> > not possible for some reason?  Or, by any chance, is Ensembl
actually compatible
> > with 1-5 and it's just a documentation issue?
> 
> "Ewan Birney" replied
> Ensembl doesn't make heavy use of Bioperl anymore - most of the
critical things
> we re-wrote, mainly due to speed/memory issues. I think the short
answer is that
> it _probably_ works with 1.5, but we don't have a strong desire to
move up
> as certainly there are no problems with the 1.2.3 release we are
using.

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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