[Bioperl-l] dependencies in Makefile.PL

Hilmar Lapp hlapp at gmx.net
Mon Sep 25 20:34:27 UTC 2006

Everything that contains compiled code, or depends on stuff that  
contains compiled code.

E.g., GD and friends, all expat-depending XML readers/writers


On Sep 25, 2006, at 2:17 PM, 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?
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :

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