[Bioperl-l] ActiveState Perl problems

Chris Fields cjfields at uiuc.edu
Tue Feb 5 20:32:52 EST 2008


Kobes keeps two separate repos because there are several binary-only  
modules (DBD::mysql, GD, etc) which are incompatible with older major  
perl releases (5.6, 5.8, 5.10).  If the modules are pure perl then  
there shouldn't be a problem.

Saying that, there is one issue which tanks Bio::SeqIO::entrezgene  
parsing (which mistakenly made pseudohashes) which Stefan and I fixed  
recently; that'll tank in perl 5.10.

chris

On Feb 5, 2008, at 6:25 PM, Kevin Brown wrote:

> Well, Kobes seems to have two different ppm repos.  One for 8xx builds
> of activestate perl and one for 10xx builds.  So, Bioperl probably  
> needs
> to be rebuilt for 5.10 to get it to show in the 5.10 repos.  I just
> opened up Activestate perl 5.8 and I see 1.5.2_100 listed in it from  
> the
> Regular Release site.
>
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of
>> Lincoln Stein
>> Sent: Tuesday, February 05, 2008 4:43 PM
>> To: Scott Cain
>> Cc: bioperl-l
>> Subject: [Bioperl-l] ActiveState Perl problems
>>
>> Hi Scott, Bioperl folk,
>>
>> I'm afraid that the ActiveState ppm install of BioPerl no
>> longer works.
>> Using the current ActiveState (perl version 5.10), I added the  
>> Bribes,
>> Kobes, BioPerl-Regular Releases, and BioPerl-Release Candidates
>> repositories. However, when I synched up, all but the Bribes
>> reps showed up
>> empty in the ppm tool.
>>
>> In addition, there's nothing in the release candidate rep any
>> longer. I used
>> to use this to get at Bioperl 1.5.
>>
>> Perhaps the architecture needs to be changed?
>>
>> Lincoln
>>
>>
>>
>> -- 
>> Lincoln D. Stein
>> Cold Spring Harbor Laboratory
>> 1 Bungtown Road
>> Cold Spring Harbor, NY 11724
>> (516) 367-8380 (voice)
>> (516) 367-8389 (fax)
>> FOR URGENT MESSAGES & SCHEDULING,
>> PLEASE CONTACT MY ASSISTANT,
>> SANDRA MICHELSEN, AT michelse at cshl.edu
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>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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