[Bioperl-l] Do we need Bio::Root::Object anymore?

Torsten Seemann torsten.seemann at infotech.monash.edu.au
Mon Oct 2 06:06:50 UTC 2006

 >>> I have removed all use/@ISA Bio::Root::Object references from
 >>> bioperl-live, except for those in Bio::Root::* itself:

 >> So I'd say they're both relics that can be removed. In fact I was
 >> planning on getting rid off all references to both of these modules
 >> before you did, so thanks! :)

> I think they can go. It's probably a pre-1.0 deprecation that somehow  
> was never followed through on.

Today I did a fresh CVS checkout of bioperl-live, and deleted the 
following modules and tests, and all tests passed with BIOPERLDEBUG=0

     * Bio::Root::Err
     * Bio::Root::Global
     * Bio::Root::IOManager
     * Bio::Root::Object
     * Bio::Root::Storable
     * Bio::Root::Utilities  # may be used by third parties?
     * Bio::Root::Vector
     * Bio::Root::Xref
     * t/Root-Utilities.t    # need to keep if we keep Utilities.pm
     * t/RootStorable.t

Should we schedule for deprecation, or deprecate immediately as Hilmar 
suggested they were meant to be deprecated long ago ?

Dr Torsten Seemann               http://www.vicbioinformatics.com
Victorian Bioinformatics Consortium, Monash University, Australia

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