[Bioperl-l] Problems with installing bioperl using PPM3

Chris Fields cjfields at uiuc.edu
Fri Apr 9 21:53:08 EDT 2004

Not quite sure if this made the Bioperl-l list, so I'll repost the 
general answer here.

On Apr 8, 2004, at 7:58 AM, <omid at rogers.com> wrote:

> Thanks for the reply Chris.. I installed perl 5.6.1 Build 635 and when 
> using PPM3 I encountered a new set of problems.
> it seems that bioperl-1.4 does not work for for PPM3 on build 633 but 
> I was able to install an ealier version of bioperl "Bioinformatics 
> Toolkit".
> with build 635 it seems that ppm3 itself has problems installing some 
> modules. some bioperl dependencies were able to be installed while 
> others that worked with build 633 were not.
> Also, I encountered a problem installing "IO-String"
> with both versions. This module is one of the listed dependencies for 
> bioperl.

This may be due to the perl build failing during ActiveState's 
automated packaging procedures.  If you check the build status of the 
IO-String module at ActiveState's PPM repository site (specifically, 
http://ppm.activestate.com/BuildStatus/5.6-I.html), it lists it as 
failing.  However, the zipped PPM package is available from the same 
You can install this one of two ways:

1)  Create a local repository from a directory ('rep add local_rep 
"C:\Perl\local"' or something similar).  Decompress the zipped archive 
directly into the directory path listed (i.e. the file with the ppd 
extension should not be in a subdirectory under the repository 
directory; other files may be).  Search the local directory and install 
from there.

2)  Decompress the archive into a temp directory.  Run PPM3 ('ppm 
IO-String') from a command prompt within the directory.

I use the first method myself (only have to set up the directory once).

> What I had to do in that case was download the IO-String module from 
> CPAN in a temp directory and run nmake etc on it. Not sure if this is 
> the proper way of doing things??

That works as well, but always make sure to run 'nmake test' to make 
sure the module will work.  Some modules (usually older, less 
maintained ones) tend to fail for various reasons, mainly due to 
included C source code that won't compile in the Windows environment.  
Also, nmake has a tendency to sometimes crash even when it works, so it 
may be hard to tell if you get success!

The main reason to use PPM3 is b/c PPM3 makes it much easier to install 
and upgrade modules (somewhat like a mini version of rpm in Linux, if 
you're familiar with it).  The program keeps track of installed modules 
and is capable of producing nicely formatted HTML from POD; if you add 
modules with nmake, PPM3 will not find them (although you might be able 
to rebuild the PPM3 database).

> Thanks
> Omid
>> From: Chris Fields <cjfields at uiuc.edu>
>> Date: 2004/04/07 Wed PM 05:22:55 EDT
>> To: <omid at rogers.com>,  <bioperl-l at bioperl.org>
>> Subject: Re: [Bioperl-l] Problems with installing bioperl using PPM3
>> Everything works when using ActiveState Perl 5.8.3 Build 809, which 
>> comes
>> with PPM3 as the default package manager.  It may be due to the 
>> earlier PPM
>> version.  I checked the ActiveState web site documentation for 
>> ActivePerl
>> 5.6.1 build 635 (the newest version of the 5.6.1 branch) and there is 
>> a bug
>> fix listed for PPM3.
>> The following link describes a problem very like yours and is from 
>> the PPM
>> bug database 
>> (http://bugs.activestate.com/show_bug.cgi?id=19749&submit=Go)
>> and is likely the bug that is fixed in 5.6.1 build 635, so you might 
>> want
>> to upgrade to that version or to the newest 5.8.3 release for the fix.
>> Chris
>> At 02:08 PM 4/7/2004, omid at rogers.com wrote:
>>> Hello all,
>>> I have ActiveState perl 5.6.1 BUILD 633 installed on a local machine
>>> running windows 2000 and I do the following:
>>> I type "ppm3" at the command prompt
>>> then type "search bioperl" (the repository is set to
>>> http://www.bioperl.org/DIST/).
>>> a listing is displayed with numbers and when I attemp to issue the 
>>> command
>>> "describe 20" or describe "package name" I get an error saying:
>>> Can't call method "name" without a package or object reference at
>>> E:\Perl\bin/ppm3-bin line 4265, <$__ANONIO__> line 9.
>>> I don't know what it means. I searched the bioperl site and looked at
>>> various installation documents but nothing seems to address this 
>>> type of
>>> problem.
>>> Any help you are able to provide is greatly appreciated.
>>> Thanks
>>> Omid
>>> 1
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at portal.open-bio.org
>>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>> __________________________________
>> Chris Fields - Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Address:
>> University of Illinois at Urbana-Champaign
>> Dept. of Biochemistry - 323 RAL
>> 600 S. Mathews Ave.
>> Urbana, IL 61801
>> Phone : (217) 333-7098
>> Fax : (217) 244-5858
> 1
Chris Fields
Postdoctoral Reseacher - Dept. of Biochemistry
Laboratory of Dr. Robert Switzer
University of Illinois at Urbana-Champaign

More information about the Bioperl-l mailing list