[Bioperl-l] Cleanup of BioPerl distribution website

Nathan S. Haigh n.haigh at sheffield.ac.uk
Sun Sep 17 22:10:46 UTC 2006

Chris Fields wrote:
> On Sep 17, 2006, at 1:46 PM, Mauricio Herrera Cuadra wrote:
>> Nathan S. Haigh wrote:
>>> I don't have any immediate problems about the changes either. I've
>>> seen a few posts recently about installing Bioperl on Windows - how
>>> soon will 1.5.2 been released? It's not too difficult to generate a
>>> new ppd file etc so I could make a barebones ppd for 1.5.1?
>> Go ahead if you want, I'll gladly upload it to the DIST directory.
> If so, we'll need to update package.lst to include it as well.
>>> I know when I made the ppd file for 1.5 I included a lot of prereqs
>>> to ensure that most of bioperl would work without the need to
>>> manually install the modules later once the user found out that
>>> something didn't work. Personally, despite the need to download and
>>> install a lot more packages in one sitting, I thought this was
>>> important since Windows users that install bioperl are probably (or
>>> more likely) not from a programming background (no offence intended
>>> if your a whiz programmer working in Windows! :o) ). Therefore, their
>>> first experience of bioperl would get off to a better start if
>>> everything worked out of the hat after its installation, despite
>>> having a longer/bigger install. What do you think?
>> Definitely this would be better, not only for Windows installations :)
> Make sure that the required packages and versions are available for 
> Windows as well.  As for other systems, we could always ask Chris D. 
> to add any extra dependencies to Bundle::Bioperl on CPAN in 
> anticipation for this release.
>>> What is the state of play with regards to tracking dependencies? I've
>>>  just noticed that Makefile.PL has a lot more packages in %packages,
>>> is this a complete list of prereqs? If so, could they be added to
>>> PREREQ_PM in the WriteMakefile sub in order to make it easier for
>>> generating a ppd with a complete prereqs list?
>>> Nath
>> Supposedly it's complete, so they should be the same ones to add into 
>> the ppd file. Take a look into Bioperl-1.5.ppd in the 'old_releases' 
>> directory, since it's for the 1.5.0 release, the list should be very 
>> similar to the one you'll have to create.
>> Mauricio.
>> -- 
>> arareko at campus.iztacala.unam.mx <mailto:arareko at campus.iztacala.unam.mx>
>> Laboratorio de Genética
>> Unidad de Morfofisiología y Función
>> Facultad de Estudios Superiores Iztacala, UNAM
> There may be a few more; I need to add XML::Simple myself.
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
OK, I'll have a look into this sometime this week. Shall I go for a 
prereqs of Perl 5.6.1? That way I'll ensure I do tests on a virtual 
machine with a fresh install of Perl in order to check that dependencies 
are satisfied. Should the test suite should show up any dependencies 
that aren't satisfied or would the be silently skipped? I'll also try to 
check multiple Perl versions from whatever minimal version you suggest.

What exactly should/needs to go into Bundle::Bioperl and why is it needed?


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