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

Fri May 2 01:53:42 UTC 2014

[I believe the tests that call ncbi web services needed the valid email]

Sent from my T-Mobile 4G LTE Device

<div>-------- Original message --------</div><div>From: "Fields, Christopher J" <cjfields at illinois.edu> </div><div>Date:05/01/2014  9:29 PM  (GMT-05:00) </div><div>To: "Francisco J. Ossandón" <fossandonc at hotmail.com> </div><div>Cc: Mark Jensen <maj at fortinbras.us>,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 May 1, 2014, at 7:12 PM, Francisco J. Ossandón <fossandonc at hotmail.com> wrote:

I’ve finished working on ActivePerl!! I’ve also updated the wiki section on Windows installation to use MinGW instead of nmake for ActivePerl.

After testing I found that there are 4 modules that can’t be installed straightforward for ActivePerl using CPAN, but 2 of them can be still installed using the PPM, so that only leaves ‘DB_File’ and ‘GraphViz’ without an easy CPAN/PPM install. Is kind of funny because PPM shows a weird message if you tell it to install DB_File (it says “No missing packages to install”) instead of “not found” or something like that. The ActiveState pages related to those modules shows that they have never been able to compile them in Windows (http://code.activestate.com/ppm/DB_File/, http://code.activestate.com/ppm/GraphViz/). Problems with DB_File for ActivePerl have been there for a while, in a 2010 post they mention to have dropped it because of problems compiling it in most platforms (https://community.activestate.com/forum/510-and-dbfile).
The fixes are already pushed on the Git repo and all tests pass (or are skipped correctly) in ActivePerl. I proceeded to demote DB_File to recommended and kept Data::Stag where it is (which is not a problem because it can be installed fine), and added a few missing modules needed for some tests.

I have 1 question for Chris though… Is about the tests that usually print “skipped: Network tests have not been requested”. I just can’t make them run through Build, only independently through my debugger (I have the extra environment variables “AUTHOR_TESTING” and “BIOPERLDEBUG” set there). When I run “perl Build.PL”, it ask me if I want to “run tests that require connection to servers” and I say yes, then it ask me I want to “run tests requiring a valid email address” and say yes again and put an email address, but the test  are skipped anyway with the above message. And if I use the “--network” argument (saw that inside the script), it asks the “connection to servers” question but not the “valid email” question (which tests use the email??)… In summary, I explicitly request the network tests but Build is ignoring me, maybe some parameter is not being passed to the test files??

They should work, but something has apparently broken them lately.  The culprit would be Bio::Root::Build.

The plan for those eventually is to make them ‘author tests’ under dzil and remove the ‘magic’ that makes that work.

Oh, and a last question (related to the change in dependecies), how the “DEPENDENCIES” files is updated?? Has not been updated in 4 years. =)

We had updated this at one point via a maintenance script, but the migration of dependency-based code and the intended move to dzil would make keeping this up-to-date unnecessary.  

-c

 Cheers,

Francisco J. Ossandon

De: Mark Jensen [mailto:maj at fortinbras.us] 
Enviado el: miércoles, 30 de abril de 2014 12:31
Para: Fields, Christopher J; Francisco J. Ossandón
CC: BioPerl List
Asunto: Re: [Bioperl-l] regarding DB_File and Data::Stag

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

Sent from my T-Mobile 4G LTE Device

-------- Original message --------
From: "Fields, Christopher J"
Date:04/30/2014 11:40 AM (GMT-05:00)
To: "Francisco J. Ossandón"
Cc: BioPerl List
Subject: Re: [Bioperl-l] regarding DB_File and Data::Stag

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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