[Bioperl-l] More unresolved issues with Bio::AnnotatableI

Hilmar Lapp hlapp at gmx.net
Thu Jun 30 01:00:50 EDT 2005

I fixed this.

I actually turned out that the dependency was more a bug than a real 
dependency, and a rather trivial one: SimpleGOEngine was use'd in 
Bio::Ontology::Ontology.pm even though the code didn't use it - the 
default engine implementation is SimpleOntologyEngine.

Nonetheless I also changed the instantiation of SimpleOntologyEngine to 
be on demand only - so if in the future it acquires a nasty dependency, 
or if the default is changed, the dependency is soft in that it only 
becomes a hard one when you call one of the methods requiring the 


On Jun 22, 2005, at 9:46 AM, Aaron J. Mackey wrote:

> Because AnnotatableI has implementations for add_tag and get_tag that 
> invoke Bio::Annotation::OntologyTerm, and therefore Graph::Directed, 
> which relies on Scalar::Util::weaken(), therefore I cannot even use 
> basic Bio::Seq functionality on any perl that doesn't have weak 
> references (oddly, this cropped up in a 5.8.0 install via an RPM that 
> was evidently compiled without support for weak references, so this 
> isn't just an "ancient perl" problem).
> This is something of a showstopper for any 1.6; in effect, we'd need 
> to disable Annotation::OntologyTerm use for any Perl without weak 
> reference support.
> We've said it before, and we need to say it again: the changes made to 
> the feature/annotation object model are seriously impeding our ability 
> to move forward to a release (and frighteningly, the GBrowse 
> distribution now includes those parts of 1.5 that it relies on, so a 
> user's BioPerl install could be a hodge-podge of 1.4/1.5 code).  This 
> seems important to all GMOD projects, so why hasn't there been any 
> work on it?
> Thanks,
> -Aaron
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757

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