[Bioperl-l] ActiveState Perl problems

Chris Fields cjfields at uiuc.edu
Wed Feb 6 12:54:16 EST 2008


Just an update: I have installed ActivePerl 5.10 on my WinXP box and  
added the following repos to PPM4 (in the following order, just in  
case it matters):

Kobes:
http://cpan.uwinnipeg.ca/PPMPackages/10xx/

Bribes:
http://www.bribes.org/perl/ppm

BioPerl:
http://bioperl.org/DIST

Note that the above Kobes repo is 5.10-specific.  SOAP::Lite is in  
both Kobes and Bribes for perl 5.10.

I then ran into issues with XML::SAX::ExpatXS and XML::SAX::Writer  
(the former is a binary-only, so likely failed with the ActiveState  
autobuild process; the latter should work though, so it might be worth  
hosting a version in BioPerl).  I removed both dependencies from  
package.xml on the server and everything appears to install fine now  
using PPM4.

I'll see if Randy Kobes can get an XML::SAX::ExpatXS version up.  It  
is only required for 1.5.2; bioperl-live no longer requires it (just  
XML::SAX).

chris

On Feb 6, 2008, at 10:36 AM, Nathan S Haigh wrote:

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> Last time I was playing with Windows PPM packages, I seem to  
> remember having to build some packages for inclusion in the BioPerl  
> repo so that all
> dependencies were satisfied. Unfortunately, I don't have time to do  
> this myself, but it's a work around if someone has time to do it?  
> Alternatively,
> contact one of the other repo's and see if they can do something  
> about it as it will/should be available for at least an older  
> version of ActivePerl.
>
> Sorry I can't be more help.
> Nath
>
>
> Lincoln Stein wrote:
>> Sadly, bioperl still won't install under ActiveState 5.10 because  
>> it can't
>> find a repository with the SOAP::Lite prerequisite.
>>
>> Lincoln
>>
>> On Feb 5, 2008 10:06 PM, Chris Fields <cjfields at uiuc.edu> wrote:
>>
>>> According to this page you can remove the <ARCHITECTURE> tags and it
>>> will assume the files are for any OS:
>>>
>>>
>>> http://aspn.activestate.com/ASPN/docs/ActivePerl/5.10/lib/ActivePerl/PPM/PPD.html#ppd_xml_format
>>>
>>> I have moved the old package.xml to package.bak and replaced it with
>>> one w/o those tags; I can now pick it up on Mac OS X using  
>>> ActiveState
>>> perl 5.10:
>>>
>>> ppm> search *
>>> Downloading bioperl.org packlist...not modified
>>> 1: Bio-ASN1-EntrezGene v1.09
>>> 2: Bundle-BioPerl-Core v1.5.2_100
>>> 3: Bundle-BioPerl-Db v1.5.2_100
>>> 4: Bundle-BioPerl-Network v1.5.2_100
>>> 5: Bundle-BioPerl-Run v1.5.2_100
>>> 6: Class-AutoClass v1.01
>>> 7: GD-SVG v0.25
>>> 8: Graph v0.80
>>> 9: SVG-Graph v0.01
>>> 10: bioperl v1.5.2_100
>>> 11: bioperl-db v1.5.2_100
>>> 12: bioperl-network v1.5.2_100
>>> 13: bioperl-run v1.5.2_100
>>>
>>> I'll add ARCHITECTURE versioning tags back when we know it's working
>>> (maybe tomorrow, when I can get on to WinXP to test it).
>>>
>>> chris
>>>
>>> On Feb 5, 2008, at 5:43 PM, Lincoln Stein wrote:
>>>
>>>> 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
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> Christopher Fields
>>> Postdoctoral Researcher
>>> Lab of Dr. Robert Switzer
>>> Dept of Biochemistry
>>> University of Illinois Urbana-Champaign
>>>
>>>
>>>
>>>
>>
>>
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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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