[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
>>> 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
> 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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