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

Brian Osborne osborne1 at optonline.net
Mon Oct 2 10:14:13 EDT 2006


Sendu,

No objection but someone should check the scripts in examples/root to make
sure that they are not used there.

Brian O.


On 10/2/06 5:55 AM, "Sendu Bala" <bix at sendu.me.uk> wrote:

> Torsten Seemann wrote:
>>>>> 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'm happy to get rid of them all straight away. Does anyone object?
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