About Bioperl - patch - installation Windows

[djibrilo]

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.

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="GD-SVG" VERSION="0.25">
<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 have seen another BioPerl repository ( http://bioperl.org/DIST/RC) and there are the same problems.

BioPerl-Run.ppd

<SOFTPKG NAME="BioPerl-Run" VERSION="1,006000_001,0,0">

    <TITLE>BioPerl-Run</TITLE>
    <ABSTRACT>BioPerl-Run - wrapper toolkit</ABSTRACT>
    <AUTHOR>BioPerl Team <bioperl-l@...></AUTHOR>
    <IMPLEMENTATION>
        <DEPENDENCY NAME="Bio-Root-Version" VERSION="1,006001,0,0" />
        <CODEBASE HREF="PPM-BioPerl-Run-1.006000_001.tar.gz" />
    </IMPLEMENTATION>
</SOFTPKG>
BioPerl-DB.ppd    

<SOFTPKG NAME="BioPerl-DB" VERSION="1,006000_001,0,0">
    <TITLE>BioPerl-DB</TITLE>
    <ABSTRACT>BioPerl-DB - package for biological databases</ABSTRACT>
    <AUTHOR>BioPerl Team <bioperl-l@...></AUTHOR>
    <IMPLEMENTATION>
        <DEPENDENCY NAME="Bio-Root-Version" VERSION="1,006001,0,0" />
        <DEPENDENCY NAME="DBI" VERSION="0,0,0,0" />
        <CODEBASE HREF="PPM-BioPerl-DB-1.006000_001.tar.gz" />
    </IMPLEMENTATION>
</SOFTPKG>


BioPerl-Network.ppd  

<SOFTPKG NAME="BioPerl-Network" VERSION="1,006000_001,0,0">
    <TITLE>BioPerl-Network</TITLE>
    <ABSTRACT>BioPerl-Network - package for biological networks</ABSTRACT>
    <AUTHOR>BioPerl Team <bioperl-l@...></AUTHOR>
    <IMPLEMENTATION>
        <DEPENDENCY NAME="Bio-Root-Version" VERSION="1,006001,0,0" />
        <DEPENDENCY NAME="Graph" VERSION="0,86,0,0" />
        <CODEBASE HREF="PPM-BioPerl-Network-1.006000_001.tar.gz" />
    </IMPLEMENTATION>
</SOFTPKG>

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


     
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Bioperl-l@...
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[Chris Fields-5]

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="GD-SVG" VERSION="0.25">
> <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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Bioperl-l mailing list
Bioperl-l@...
http://lists.open-bio.org/mailman/listinfo/bioperl-l

[Mark A. Jensen]

Re: PPM issues--
If you are experiencing a problem with  "Apache ... SOAP::Lite", or
other module gaps, see the workaround recently posted under
http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows#Comand-line_Installation


> 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!)

MAJ

----- Original Message -----
From: "Chris Fields" <cjfields@...>
To: "djibrilo" <djibrilo@...>
Cc: <cjfields@...>; <bioperl-l@...>
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="GD-SVG" VERSION="0.25">
>> <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
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@...
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>

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