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

Aaron J. Mackey amackey at pcbi.upenn.edu
Wed Jun 22 09:46:09 EDT 2005

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?



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