[Bioperl-l] What's to depend on for BioPerl-run version check

Chris Fields cjfields at illinois.edu
Wed Mar 17 11:13:20 EDT 2010

What is probably the best thing to do is set up a stub module for each of the subdistributions that contains a proper version to match against.  So, for BioPerl-Run, use Bio::Run or Bio::Tools::Run, BioPerl-DB use Bio::DB, etc.  Distribution-specific general documentation would go in those stub modules.  I sort of started this, with the first alphas but didn't get around to finishing it up.  

Just as a footnote, the universal $VERSION thingy was set up quite a while ago, prior to perl 5.8 I believe, and doesn't play very well with $VERSION (and version.pm) on newer perl versions.  Once we move beyond 1.6.x towards breaking things up we'll have to assign new VERSIONs to anything released independently on CPAN, anyway, so this may eventually be a moot point.


The inherited $VERSION thingy was set up a while back, basically as a way of assigning a common version across BioPerl. 
On Mar 17, 2010, at 9:41 AM, Mark A. Jensen wrote:

> I'd say the RTTD would be to submit a bugzilla report; this sounds pretty fishy
> to me--(esp since the Pise stuff is deprecated, IIRC) cheers MAJ
> ----- Original Message ----- From: "George Hartzell" <hartzell at alerce.com>
> To: "bioperl-l List" <bioperl-l at bioperl.org>
> Sent: Tuesday, March 16, 2010 7:35 PM
> Subject: [Bioperl-l] What's to depend on for BioPerl-run version check
>> Apologies if this is as silly of a question as it seems, I think that
>> I must just be decaffeinated this morning....
>> I'm cleaning up some modules and would like to express a dependency on
>> BioPerl-run version 1.6.1.
>> For the main bioperl I use Bio::Root::Version and 1.006001.  That
>> works, although the course of investigating below I found that
>> Bio::Root::RootI (which uses BR::Version) doesn't.
>> A couple of the modules in -run (e.g. Bio::Tools::Run::PiseWorkflow)
>> use Bio::Root::Version and thereby acquire a reasonable version number
>> but:
>> a) it's funny to list Bio::Tools::Run::PiseWorkflow as a dependency
>>    when I want bioperl-run
>> c) it's funny that PiseWorkflow uses Bio::Root::Version (which
>>    imports a $VERSION into it's package) then goes on to set one
>>    itself.
>> b) there's something hinky going on, when I do 'perl Build.PL' on my
>>    Task it doesn't think that PiseWorkflow is up to date (it thinks
>>    I have version (0) if I understand correctly), but when I
>>    './Build installdeps' everything appears up to date.
>>    It looks like the trickiness of assigning
>>    $Bio::Root::Version::VERSION to $VERSION confuses
>>    Module::Build::ModuleInfo::_evaluate_version_line and the result
>>    is that VERSION appears to be 0.
>> What's The Right Thing to do?
>> Thanks,
>> g.
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