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

Chris Fields cjfields at uiuc.edu
Mon Oct 2 14:13:56 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 ?

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


and it seems to have it's users:


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


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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