[Bioperl-l] dependencies in Makefile.PL

Nathan S. Haigh n.haigh at sheffield.ac.uk
Tue Sep 26 08:01:49 UTC 2006

Sendu Bala wrote:
> Sendu Bala wrote:
>> Nathan Haigh wrote:
>>> File::Spec is mentioned in the PREREQ_PM section of Makefile.PL but is
>>> not mentioned in %packages - which is correct? Is File::Spec no longer
>>> needed?
>>> IO::Scalar is now commented out of %packages, but is still included in
>>> PREREQ_PM - again, which is correct?
>> I'm not sure how Makefile.PL is supposed to work, but I can say that 
>> File::Spec and IO::Scaler are certainly required for Bioperl. Of 
>> course, they're in Bundle::BioPerl which presumably is (must be!) 
>> itself a requirement, so maybe that's why there's confusion in the 
>> Makefile.PL.
> Oh, woops, Bundle::BioPerl is supposed to be optional. So its more 
> correct to say that certain things in Bioperl require Bundle::BioPerl 
> (because they require the modules it contains), but those certain 
> things can themselves be considered optional.
> Even Bundle::BioPerl doesn't install some modules which it considers 
> even 'more' optional...
> Yes, it gets kind of muddy and needs to be fully clarified/simplified 
> I think. Is there a real burden to installing a couple of extra 
> modules? If not, I'd say that we just stop considering things as 
> optional. If its in Bioperl, it should work after you complete an 
> installation process (eg. make, make install for linux, whatever the 
> equivalent is under Windows). If there is something in Bioperl core 
> that seems like a burden for most users to have to install, move it 
> out to a different package.
> So what are the burdensome things that don't easily work out of the box?
I'm with you Sendu, I think after an installation of Bioperl users would 
expect to have a fully functional installation (almost certainly with 
Windows, where users may be less likely to have sys admin experience). 
Where this is not the case with specific setups/OS's, it could be moved 
out to an optional package that is said to extent Bioperl functionality 
and have the caveat that it is difficult to install/run on certain setups.

Under Windows, the dependencies could be included in Bioperls PPD 
directly, or have them in Bundle::BioPerl PPD, and have Bioperl depend 
on Bundle::BioPerl - either is straight forward to do. Which to do, I 
suppose, depends on whether there are any benefits to maintaining a 
separate Bundle::BioPerl or not. If there is a benefit to keeping 
Bundle::BioPerl, then the only decision would be if any dependencies 
should definitely be with Bioperl rather than Bundle::BioPerl. Otherwise 
Bundle::BioPerl would become obsolete.


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