[Bioperl-l] BioPerl Core 1.6.1 PPM now available

[Chris Fields]

Mark,

Definitely suboptimal.  Are you using ActivePerl 5.8? (I used 5.10.1)

I'm wondering if there are a few Bio::ASN1::EntrezGene out there  
floating around in other repos.  The one in the bioperl PPM repo  
doesn't have that requirement.  The only way I can think of to direct  
installation of the BioPerl PPM for Bio::ASN1::EntrezGene is to  
indicate the bioperl repo needs to be first in the repo list.

chris

On Oct 10, 2009, at 4:53 PM, Mark A. Jensen wrote:

> 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
> then...
> )
>
> 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"
> 1.4
>
> Now install BioPerl
>
> C:> ppm install BioPerl
>
> and we end up with
>
> C:> perl -MBio::Perl -e "print $Bio::Perl::VERSION"
> 1.006001
>
> MAJ
> ----- 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 5.10.1.1006.  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
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