[Bioperl-l] PPM for bioperl-1.5?

Chris Fields cjfields at uiuc.edu
Fri Jul 22 11:11:25 EDT 2005

I found the links for both the PPD and PPM in your older response from the 
bioperl emails (I think from Jan 2005), downloaded the files to a local 
directory, and installed everything through a local repository (although I 
had a few slight hitches, see below).  I also installed GBrowse directly 
from the GMOD site and it works as well.  I also found GD-SVG and installed 
it, and I get SVG images with GBrowse just fine!

A few notes:  I had to change the location of the tar archive in the PPD 
file for Bioperl and GD-SVG.  For some reason PPM kept looking for them in 
the Bioperl website (where they are still MIA); I found the link in the PPD 
files for both Bioperl and GD-SVG and changed them by removing the path to 
the file on the site to the local file, reflecting their location in the 
local repository (this is done for every link in each file), so for GD-SVG:

         <ARCHITECTURE NAME="MSWin32-x86-multi-thread-5.8" />
         <CODEBASE HREF="http://bioperl.org/DIST/GD-SVG-0.25-ppm.tar.gz" />


         <ARCHITECTURE NAME="MSWin32-x86-multi-thread-5.8" />
         <CODEBASE HREF="GD-SVG-0.25-ppm.tar.gz" />


Also, the repository for Kobes (http://theoryx5.uwinnipeg.ca/ppms) didn't 
work and stopped installation of Bioperl; it is very likely due a problem 
with the latest XML-SAX module (and not Bioperl), which leaves out or 
doesn't initialize the file ParserDetails.ini, which may be causing some 
problems when parsing repositories (although I can't see why); I kep 
getting messages that ParserDetails.ini couldn't be found.  I got around it 
by using the PPM repository for Randy Kobes that ActiveState lists 
(http://theoryx5.uwinnipeg.ca/cgi-bin/ppmserver?urn:/PPMServer58 for Perl 
5.8, http://theoryx5.uwinnipeg.ca/cgi-bin/ppmserver?urn:/PPMServer for 
5.6).  Installation worked fine after that.  I also reinstalled XML-SAX 
from the Kobes repository and everything now loads from the original 
repository listed under the INSTALL.WIN file for Bioperl.  This may be 
something we want to remember if someone comes up with a similar issue; 
since your PPM package has XML-SAX listed as a dependency, it may install 
the ActiveState version (the bad one) vs. the Kobes version (the good one).



At 03:51 AM 7/22/2005, you wrote:
>Would you be confident enough to install these locally from your own
>computer if I give you the relevant files? It would involve saving the files
>to a dir on your computer adding that directory to your PPM repository list
>and then installing as usual through PPM. Let me know and I can send you the
>files (just over 2Mb), or make them available from a web server.
>-----Original Message-----
>From: bioperl-l-bounces at portal.open-bio.org
>[mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of Chris Fields
>Sent: 21 July 2005 19:29
>To: bioperl-l at bioperl.org
>Subject: [Bioperl-l] PPM for bioperl-1.5?
>I noticed the PPM for the latest developer bioperl (v 1.5) isn't found in
>http://bioperl.org/DIST.  I saw that Nathan created one a while back; did
>anyone transfer it over to the above directory?
>Chris Fields - Postdoctoral Researcher
>Lab of Dr. Robert Switzer
>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
>Bioperl-l mailing list
>Bioperl-l at portal.open-bio.org


Chris Fields - Postdoctoral Researcher
Lab of Dr. Robert Switzer


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 

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