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