[Bioperl-l] Bundle::BioPerl and Pre-reqs

Chris Fields cjfields at uiuc.edu
Mon Oct 23 11:36:37 EDT 2006


...
> 
> Note we're specifically considering a CPAN install here. If you download
> the tar.gz or use cvs, [option 1] doesn't affect you. Bundle::Bioperl is
> still needed as a convenience if you want to install the optional
> external dependencies.
> 

Agreed.  I don't think the Bundle is dispensable.  For instance, it's very
easy for us to just state to beginners to install Bundle::Bioperl before
installing bioperl itself,  as opposed to having them inundate the mail list
with requests on why x.pl script didn't work, which could be simply from
lack of the required module. 

> I'm pretty sure this isn't a problem, though it would be nice if someone
> could test it on a clean system: does 'make test' pass all ok with none
> of the optional modules installed?

So far on WinXP everything passes; I ran a clean perl installation a while
ago using nmake and tests passed.

> Anyway, to reiterate the question: Do we care if CPAN users get all the
> optional external dependencies installed for them automatically, or do
> we want to force them to install Bundle?
> 
> The current situation is: CPAN users will get all optional external
> dependencies without using Bundle::BioPerl. Manual installers of bioperl
> (from tar.gz, from cvs etc.) must install Bundle::BioPerl manually to
> get full functionality.

I don't think forcing is necessary, so a CPAN installation shouldn't force
someone to install optional modules.  Graph.pm, for instance has a few
optional modules, and the tests which use those get skipped and pass so the
installation proceeds w/o problems.  We could do the same (any tests using
those optional modules display the reason why they are skipped).  

I would strongly state in the INSTALL and INSTALL.WIN docs that (new) users
should install Bundle::Bioperl before installing Bioperl core for full
functionality.  If you are an advanced user and know your way around
CPAN/Perl, then you can install the various independent requirements
depending on your particular requirements. 

Chris




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