[Bioperl-l] dependencies in Makefile.PL

[Sendu Bala]

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?