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

Chris Fields cjfields at uiuc.edu
Mon Oct 2 10:13:56 EDT 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 ?

I vote for quick deprecation; I had also noticed that these were superfluous
and added them as possible deprecations to the wiki page.  However, we need
to be careful about that 'third-party use' caveat you have for
Bio::Root::Utilities; there's another one with Bio::Root::Storable and
Ensembl:

http://thread.gmane.org/gmane.comp.lang.perl.bio.general/2924/focus=2924

and it seems to have it's users:

http://thread.gmane.org/gmane.comp.lang.perl.bio.general/8242/focus=8242

The others (including Bio::Root::Utilities) haven't had any major threads on
the mail lists in a very long time.

Chris

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign



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