[Bioperl-l] BioPerl Core 1.6.1 PPM now available

[Mark A. Jensen]

Yeah-- It is 5.8-- I'll try with 5.10. The Bio::ASN1::EntrezGene package
contains the  Bio::ASN1::EntrezGene::Indexer module, which has the bioperl
dependency-- What I'm going for (for a class I'm teaching) is a ppm installation
that will transparently include B::A::E, since we'll be doing some DB and EUtils
stuff that I believe needs NCBIHelper. (Agggh...). I'm trying to make the 
install
as painless as possible for the participants....
cheers
----- Original Message ----- 
From: "Chris Fields" <cjfields at illinois.edu>
To: "Mark A. Jensen" <maj at fortinbras.us>
Cc: "BioPerl List" <bioperl-l at bioperl.org>
Sent: Saturday, October 10, 2009 6:45 PM
Subject: Re: [Bioperl-l] BioPerl Core 1.6.1 PPM now available

> 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
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
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>
>
>