[Bioperl-l] Misspellings in Bundle::BioPerl

Nathan S. Haigh n.haigh at sheffield.ac.uk
Mon Oct 23 11:22:17 UTC 2006

Sendu Bala wrote:
> Sendu Bala wrote:
>> Nathan S. Haigh wrote:
>>> As far as CPAN discovering dependencies, here is a snip from the
>>> CPAN FAQ's:
>>> --snip--
>>>     I installed a Bundle and had a couple of fails. When I retried,
>>>     everything resolved nicely. Can this be fixed to work on first try?
>>>     The reason for this is that CPAN does not know the dependencies of
>>>     all modules when it starts out. To decide about the additional
>>> items
>>>     to install, it just uses data found in the META.yml file or the
>>>     generated Makefile. An undetected missing piece breaks the process.
>>>     But it may well be that your Bundle installs some prerequisite
>>> later
>>>     than some depending item and thus your second try is able to
>>> resolve
>>>     everything. Please note, CPAN.pm does not know the dependency tree
>>>     in advance and cannot sort the queue of things to install in a
>>>     topologically correct order. It resolves perfectly well IF all
>>>     modules declare the prerequisites correctly with the PREREQ_PM
>>>     attribute to MakeMaker or the |requires| stanza of Module::Build.
>>>     For bundles which fail and you need to install often, it is
>>>     recommended to sort the Bundle definition file manually.
>>> --snip--
>>> Therefore, recent modifications to Makefile.PL should result in a fully
>>> operational Bioperl installation, if installed via CPAN.
>> 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?


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