[Bioperl-l] Misspellings in Bundle::BioPerl

Chris Fields cjfields at uiuc.edu
Mon Oct 23 14:23:04 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?
> >From my point of view, removing them from PREREQ_PM means building the
> Bundle::BioPerl a bit of a pain :o(
> I prefer the way it is currently set up - most people have fast internet
> connections and GB of harddrive space. Other than the reason "why
> install something I won't ever need" I don't see much point maintaining
> Bundle::BioPerl and having "optional" dependencies. I think if there are
> any modules which are not going to be used by the majority of users,
> then this could be used as the rationale for removing them from
> bioperl-core into another package?
> Nath

I think you'll likely find it much easier to maintain a Bundle package
long-term and indicate that it should be installed along with bioperl, than
to have users complain about a particular Bioperl module failing b/c a
particular dependency wasn't installed.  

If we have the Bundle around in CPAN and in PPM for Win32 users, and
indicate in the INSTALL docs and the wiki our preference that it be
installed prior to or along with a Bioperl installation for beginners, we
can mitigate most of those problems.  Nip it in the bud, to quote a Mr.
Barney Fife.

My 2c


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

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