[Bioperl-l] BioPerl Core 1.6.1 PPM now available

Mark A. Jensen maj at fortinbras.us
Sat Oct 10 17:53:12 EDT 2009

More detail:

The setup:

To install BioPerl via ppm, we require the following in order 
to get a working DB_File for 5.8:

 (possibly required:
 C:> ppm install PPM-Repositories

 C:> ppm repo add http://bioperl.org/DIST
 C:> ppm repo add trouchelle58

 We try

 C:> ppm install BioPerl

 (case is important -- not 'bioperl' eg), but this borks.

When BioPerl is installed, Bundle-BioPerl-Core is subinstalled,
bioperl-1.4 is installed. Pops back up to BioPerl 1.6.1 installation. 
HTML is generated, then "Updating files in site area." Here
ppm borks when it tries to make a ppm backup for the first BioPerl
module it finds, since the file it wants to make already exists.

  * theory: Bio::ASN1::EntrezGene (one of the deps installed by
    Bundle-BioPerl-Core) requires Bio::Index::EntrezGene, so obtains a
    provider that submits bioperl-1.4

The following procedure succeeds:

Install Bundle-BioPerl-Core explicitly first:

 C:> ppm install Bundle-BioPerl-Core

This succeeds, but now

 C:> perl -MBio::Perl -e "print $Bio::Perl::VERSION"

Now install BioPerl

 C:> ppm install BioPerl

and we end up with

 C:> perl -MBio::Perl -e "print $Bio::Perl::VERSION"

----- Original Message ----- 
From: "Chris Fields" <cjfields at illinois.edu>
To: "BioPerl List" <bioperl-l at bioperl.org>
Sent: Saturday, October 10, 2009 1:24 AM
Subject: [Bioperl-l] BioPerl Core 1.6.1 PPM now available

> The first cut at the ActivePerl PPM distribution for BioPerl core  
> 1.6.1 is now available.  Instructions for installing on Windows are  
> here:
> http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows
> I have made this installation architecture-independent, but it has  
> only been testing on WinXP using ActivePerl  A couple of  
> modules may give warnings (specifically SOAP::Lite and  
> XML::SAX::Writer), but the installation should proceed.  We would  
> appreciate feedback on trying to install this with other versions of  
> ActivePerl or on more recent versions of Windows (Vista, Win7).
> Enjoy!
> chris
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

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