[Bioperl-l] Misspellings in Bundle::BioPerl

Sendu Bala bix at sendu.me.uk
Mon Oct 23 09:59:52 UTC 2006

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?

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