[Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network

Chris Fields cjfields at illinois.edu
Sun Feb 8 17:41:23 EST 2009


Yes, saw that.  It is a 'feature' of Module::Build that snuck by us,  
at least by me.  We can take advantage of that at some future point,  
but at this time I think we should attempt turning off installing  
Bio::ConfigData completely, at least until we do the following:

(1) determine whether we want to call it 'Bio::ConfigData'
(I vote 'no'; I don't like anything installed by default to our core  
namespace when it should probably be in Bio::Root, such as  

(2) determine whether we want bioperl core and the subdistributions to  
use the same or different ConfigData modules
(I vote 'same', no need to get overly complicated at this point)

(3) describe exactly what does and does not belong in any permanent  
BioPerl config file
(I think they should only be relevant to the local build/test/ 
installation and shouldn't include possibly volatile DB configuration  

Right now it just houses the feature-related settings used within all  
the Build.PL.  Based on their current naming ('BioDBSeqFeature_mysql',  
'BioDBSeqFeature_BDB') I don't trust those to always contain the same  
key/value pairing, so we need to probably standardize these for the  
next bioperl minor release (they're potentially too volatile and could  
be consolidated in a meaningful way).

Anyway, until then I wouldn't rely on ConfigData's existence or the  
specific namespace Bio::ConfigData; I'll probably add it to  


On Feb 8, 2009, at 1:12 PM, Mark A. Jensen wrote:

> As I understand it, Foo::Bar::ConfigData is generated by M:B to  
> provide persistent access to
> the configuration parameters after (perhaps long after)  
> installation, via a script
> config_data that comes with M:B. Is there a collision between  
> Bio::ConfigData created by
> the main distribution and Bio::ConfigData created by bioperl-run?
> See the docs at
> http://search.cpan.org/~ewilhelm/Module-Build-0.31012/lib/Module/Build/Authoring.pod#SAVING_CONFIGURATION_INFORMATION
> ----- Original Message ----- From: "Chris Fields" <cjfields at illinois.edu 
> >
> To: "Alex Lancaster" <alexl at users.sourceforge.net>
> Cc: <bioperl-l at lists.open-bio.org>
> Sent: Sunday, February 08, 2009 1:13 PM
> Subject: Re: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of  
> BioPerl-run,BioPerl-db, BioPerl-network
>> Alex,
>> Odd.  From what I'm reading that file shouldn't be added to the   
>> distribution or installed.  It's generated on the fly by  
>> Module::Build  for build and configuration only (triggered when  
>> using the 'features'  option).  Makes me wonder if this is an issue  
>> with Module::Build or  our derived Bio::Root::Build,  It does  
>> appear this is also popping up  as a possible issue with  
>> Module::Build itself (included along with  perl 5.10.0):
>> http://www.nntp.perl.org/group/perl.module.build/2009/01/msg1809.html
>> The obvious fix is to have it ignored upon installation.  I'll try  
>> to  get a fix up for the next alphas of BioPerl-run/db/network and  
>> the  next point release of BioPerl.
>> chris
>> On Feb 8, 2009, at 10:41 AM, Alex Lancaster wrote:
>>>>>>>> "CF" == Chris Fields  writes:
>>> CF> Alex,
>>> CF> I don't see Bio::ConfigData with the last BioPerl core  
>>> release  on CPAN
>>> CF> (1.6.0) or any of the BioPerl-*.  Could you send me the  
>>> actual  file in
>>> CF> question?
>>> You are right that it doesn't appear to be contained in the source,
>>> but looking at the build log it appears to be dynamically  
>>> generated in
>>> both packages.
>>> 1) In the case of bioperl:
>>> Writing config notes to blib/lib/Bio/ConfigData.pm
>>> and later:
>>> Manifying blib/lib/Bio/ConfigData.pm ->blib/libdoc/Bio::ConfigData. 
>>> 3pm
>>> later still:
>>> Installing /builddir/build/BUILDROOT/perl-  
>>> bioperl-1.6.0-1.fc11.noarch/usr/lib/perl5/vendor_perl/5.10.0/Bio/  
>>> ConfigData.pm
>>> See full log here:
>>> http://kojipkgs.fedoraproject.org/packages/perl-bioperl/1.6.0/1.fc11/data/logs/noarch/build.log
>>> 2) Similar generation of the ConfigData is done in bioperl-run:
>>> http://kojipkgs.fedoraproject.org/packages/perl-bioperl-run/1.5.9/0.1.1.fc11/data/logs/noarch/build.log
>>> Alex
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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