[Bioperl-l] About Bioperl - patch - installation Windows

Mark A. Jensen maj at fortinbras.us
Sat Oct 31 11:47:44 EDT 2009

Re: PPM issues--
If you are experiencing a problem with  "Apache ... SOAP::Lite", or
other module gaps, see the workaround recently posted under

> In general, I understand that mixing perl versions on Windows is NOT 
> recommended unless you know what you are doing.

Even if you do, I wouldn't recommend it (except that you can learn a lot!)


----- Original Message ----- 
From: "Chris Fields" <cjfields at illinois.edu>
To: "djibrilo" <djibrilo at yahoo.fr>
Cc: <cjfields at bioperl.org>; <bioperl-l at bioperl.org>
Sent: Saturday, October 31, 2009 11:11 AM
Subject: Re: [Bioperl-l] About Bioperl - patch - installation Windows

> Djibril,
> (Comments interspersed)
> On Oct 30, 2009, at 8:00 AM, djibrilo wrote:
>> Dear,
>> There are some problems about bioperl installation on Windows.
>> I am using bioperl on Windows XP, Vista, ... and I  use activeperl  5.8 and 
>> some times 5.10. for module installation
>> , I use ppm on Windows system and sometimes I use cpan or build via 
>> compilation.
>> The problem now is about ppm.
> In general, I understand that mixing perl versions on Windows is NOT 
> recommended unless you know what you are doing.  Not sure about  upgrading, 
> but this is problematic through PPM for many reasons, first  being PPMs are 
> missing (DB_File is a dummy PPM on ActivePerl) and  others are problematic 
> (SOAP::Lite is apparently an issue).
>> There are 2 repositories to install bioperl :
>> 1- trouchelle, there are :
>> - bioperl 1.4, 1.5.2_100
>> - bioperl-db 0.01, 1.5.2_100
>> - bioperl-run 1.2.2
>> ...
>> 2- BioPerl ( http://bioperl.org/DIST), there are :
>> - BioPerl 1.6.1
>> - bioperl-db 1.5.2_100
>> - bioperl-network 1.5.2_100
>> - bioperl-run 1.5.2_100
>> - Bundle-BioPerl-Core 1.6.1
>> ....
>> I have seen the package.XML of BioPerl repository :
>> ...
>> <SOFTPKG NAME="SVG-Graph" VERSION="0.01">
>> <SOFTPKG NAME="Bio-ASN1-EntrezGene" VERSION="1.09">
>> <SOFTPKG NAME="Class-AutoClass" VERSION="1.01">
>> <SOFTPKG NAME="Graph" VERSION="0.80">
>> <SOFTPKG NAME="GraphViz" VERSION="2.04">
>> <SOFTPKG NAME="bioperl-db" VERSION="1.5.2_100" DATE="2006-12-6">
>> <SOFTPKG NAME="Bundle-BioPerl-Db" VERSION="1.5.2_100"  DATE="2006-12-6">
>> <SOFTPKG NAME="bioperl-network" VERSION="1.5.2_100" DATE="2006-12-6">
>> <SOFTPKG NAME="Bundle-BioPerl-Network" VERSION="1.5.2_100"  DATE="2006-12-6">
>> <SOFTPKG NAME="bioperl-run" VERSION="1.5.2_100" DATE="2006-12-6">
>> <SOFTPKG NAME="Bundle-BioPerl-Run" VERSION="1.5.2_100"  DATE="2006-12-6">
>> <SOFTPKG NAME="BioPerl" VERSION="1.6.1" DATE="2009-9-29">
>> <SOFTPKG NAME="Bundle-BioPerl-Core" VERSION="1.6.1" DATE="2009-9-29">
>> ...
>> The file have been updated at 10 October 2009 but some files are  old. Then, 
>> it is impossible to many people using bioperl on Windows to
>> update correctly bioperl. And, it is difficult to me to send you a  patch 
>> about clustalw and primer3 modules because I can not install 
>> BioPerl-run-1.6.1 on my Windows PC.
> I'll remove the older ones.  Just to note, I haven't uploaded the  final CPAN 
> releases and the PPMs for BioPerl-DB, BioPerl-Run, and  BioPerl-Network to the 
> repo yet, for many various reasons (I haven't  had a chance to test them on 
> Win being one of them).
> To acknowledge something Robert said in another post, Perl is  generally 
> configured to work best with UNIX'y flavors, but support for  a UNIX-like Perl 
> on Windows is growing, particularly with Strawberry  Perl.
>> I have seen another BioPerl repository ( http://bioperl.org/DIST/RC)  and 
>> there are the same problems.
> Those are release candidates, and should be removed (they haven't been  tested 
> yet).  The package.xml In the meantime, you can try out code  very easily by 
> setting your local PERL5LIB, or having a 'use lib'  directive (this also works 
> for bioperl-live).
>> Nevertheless there are PPM-BioPerl-Run-1.6.1_001.tar.gz,  PPM- 
>> BioPerl-DB-1.6.0_001.tar.gz, PPM-BioPerl-Network-1.6.0_001.tar.gz
>> files.
>> Can you try to update all your ppd files on your repositories  because it is 
>> a real problem
>> to many lab and user wich try to updated bioperl and use it on  Windows 
>> server.
>> Best Regards,
>> Djibril Ousmanou
> We appreciate pointing these things out, I'll file them as a bug for 
> tracking.  This is probably the best way to address problems in the  future.
> Also, realize this is a completely volunteer project.  It takes an  inordinate 
> amount of our (not so free) time to work on BioPerl and  related projects, so 
> any help towards this end would be greatly  appreciated, including 
> contributing back.  Personally, I am a Linux/OS  X user and generally avoid 
> anything Win-related (my preference) unless  needed.  I believe a large number 
> of users here fall in the same  category; we only have a couple of active Win 
> users who have time to  work on portability issues.
> I myself managed to get PPM and CPAN installation working by testing  via 
> Remote Desktop and (soonish) VM, but that's hardly optimal and is  based on my 
> schedule, which has been very busy as of late.  To that  end, we would really 
> appreciate anyone volunteering and dedicating  some time towards getting the 
> Windows bits to work, otherwise Windows  support will always be determined on 
> how much time we dedicate to it  (at the moment, that being very little).
> chris
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