[Bioperl-l] regarding DB_File and Data::Stag

[Fields, Christopher J]

Nope, that’s my doing I’m pretty sure :)

https://github.com/bioperl/bioperl-live/blame/master/Bio/SeqIO/swiss.pm#L212
https://github.com/bioperl/bioperl-live/blob/master/Bio/Annotation/TagTree.pm#L123

chris

On Apr 30, 2014, at 9:43 AM, Chris Mungall <cjmungall at lbl.gov> wrote:

> The Data::Stag was possibly my doing. I'm not sure why swissprot parsing would require this. I think you can get rid of this dependency
> 
> On 29 Apr 2014, at 15:22, Francisco J. Ossandón wrote:
> 
>> Hello all,
>> 
>> I’m in the middle of polishing BioPerl to work better with ActivePerl, and a
>> few of the commits have focused on adding DB_File and Data::Stag  as
>> “required_module” to the tests files that depend on them, so they are
>> skipped instead of crashing.
>> 
>> 
>> 
>> So I would like to ask if it would be fine to move DB_File (used in
>> databases-tests) and Data::Stag (used on swiss format-tests) from Required
>> to Recommended on Build.PL. My reasoning is that BioPerl have many features,
>> and users may never need those specific features (and if they need it they
>> will install them). In fact since I started using BioPerl on 2007, I never
>> used those dependencies until I started looking for bugs beyond my work
>> scope. Particularly, DB_File can be tricky to install in Windows for
>> ActivePerl (and I’ve just realized that it behaves differently than in
>> Strawberry Perl), and I don’t think it should be listed as an obligatory
>> installation if it’s beyond the user scope.
>> 
>> 
>> 
>> Right now all tests files are properly skipped or pass for a clean
>> ActivePerl installation (no extra modules installed besides MingGW and
>> Test::Most), so my next step is to check tests after I install all the
>> recommended extra modules.
>> 
>> 
>> 
>> Cheers,
>> 
>> 
>> 
>> Francisco J. Ossandon
>> 
>> 
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