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

Sendu Bala bix at sendu.me.uk
Mon Oct 23 14:51:25 UTC 2006

Chris Fields wrote:

[option 1]
>> 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.

[option 2]
>> 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.

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.

> 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.

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?

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.

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