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

[Mark Jensen]

I could look at it, but I agree with Chris that it would be a job to do all at once. If there is interest in starting with a particular module or system, people can let me know. MAJ


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<div>-------- Original message --------</div><div>From: "Fields, Christopher J" <cjfields at illinois.edu> </div><div>Date:04/30/2014  11:40 AM  (GMT-05:00) </div><div>To: "Francisco J. Ossandón" <fossandonc at hotmail.com> </div><div>Cc: BioPerl List <bioperl-l at lists.open-bio.org> </div><div>Subject: Re: [Bioperl-l] regarding DB_File and Data::Stag </div><div>
</div>
On Apr 30, 2014, at 10:34 AM, Francisco J. Ossandón <fossandonc at hotmail.com> wrote:

> I didn't know that ActivePerl changes all "recommends" to "required" for
> ppm, the FAQ page
> (http://docs.activestate.com/activeperl/5.18/faq/ActivePerl-faq2.html#how_to
> _make_ppm_distribution) does not mention it... =/
> 
> BUT I think that is still a good move to demote DB_File status to
> "recommended" meanwhile, because ActivePerl users can still install through
> CPAN after installing MinGW/MinGW64 (which ppm is available up to their Perl
> version 5.16 btw, there is no ppm for their 5.18 yet:
> http://code.activestate.com/ppm/MinGW/), so is still useful for users trying
> to install the latest version (the last BioPerl PPM released was 5 years
> ago). A more ActivePerl-friendly replacement for DB_File could be searched
> later too. =)
> 
> Mark, maybe you want to go further and eradicate DB_File from BioPerl guts
> and replace it with SQLite_File??
> 
> So, can I demote DB_File to recommended?? ;)

I think removal of DB_File (or moving to AnyDBM_File, which is the more flexible solution) would have to be piecemeal.  I tried this with the current code on a branch and it is more complicated than one would think.  Moving these to a demoted ‘Recommends’ status should suffice.

Re: Data::Stag and swissprot that is partly my fault but was the easiest solution in hand for the structured data.  This could be simplified even more to completely remove this dependency, but it would require a likely API change and should wait until 1.7.

chris

> Cheers,
> 
> Francisco J. Ossandon


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