[Bioperl-l] Misspellings in Bundle::BioPerl

Chris Fields cjfields at uiuc.edu
Mon Oct 23 14:12:16 UTC 2006

> > Right, thanks for that.
> Oh, so this effectively means that our 'optional' dependencies are
> installed for CPAN users, which matches up to my 'force the optional
> ones anyway' desire, leaving Bundle::BioPerl without any use.
> Makefile.PL could be altered again to remove from PREREQ_PM those
> modules the user didn't already have installed, thus CPAN would only
> install Bioperl itself and nothing optional. The user could then install
> Bundle::BioPerl if they wanted a quick way of getting all the optional
> stuff to work.
> I'm happy either way; what do other people think?

I think that we should have it so Bioperl installs as-is (no additional
reqs) and have Bundle::BioPerl used as a convenient way to install all
optional modules for full functionality.  The catch is to make sure that any
optional installations do not crash tests during a CPAN bioperl
installation, otherwise they aren't considered optional by CPAN, and the
install won't work without forcing it.

Frankly, most users will find themselves wanting to install the Bundle
anyway to get full functionality, so we could always 'strongly recommend'
preceding the bioperl installation with a Bundle::Bioperl CPAN installation
to avoid problems, at least for this release. 

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign

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