[Bioperl-l] bioperl-1.4 ppm package for Windows

Brian Osborne brian_osborne at cognia.com
Fri Feb 27 12:47:42 EST 2004


Nigam Shah has fixed package.lst and Bioperl-1.4.ppd in DIST. Thank you for
telling us about this problem.

Brian O.

-----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: Wednesday, February 25, 2004 12:27 PM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] bioperl-1.4 ppm package for Windows

I was unable to get the PPM package for 1.4 working for Windows from
http:/bioperl.org/DIST and had to perform a workaround.  I decided to post
it in case others were running into problems.

When I first tried installing Bioperl using PPM, it installs bioperl 1.2
first (!?!), then allows upgrading to 1.2.3.  However, it will not install
1.4 b/c of the additional dependencies (HTML-Entities and IO-Scalar).  The
latter dependencies are notably not req'd for 1.2 or 1.2.3.  IMHO, I'm
guessing that PPM can't find these modules b/c it is looking for specific
ppm packages named HTML-Entities and IO-Scalar, not for the modules named
HTML-Entities and IO-Scalar (which are included in the packages HTML-Parser
and IO-stringy).  This problem could be linked to the version of PPM I'm
using (3.1) on ActivePerl 5.8.3-809, both of which are very new, so I have
no idea if this is a problem with older versions of PPM.

The workaround was to remove the dependencies manually.  I downloaded the
relevant ppm tar file and corresponding ppd files (bioperl-1.4-ppm.tar.gz
and Bioperl-1.4.ppd, respectively) to a local directory (C:\Perl\Bioperl).
Using a text editor, I removed all references to the added dependencies and
saved the file.  More specifically, I deleted the following lines, listed
twice under Implementations (so delete both sets!):
VERSION="0,0,0,0" />

I then entered PPM, set up a local ppd repository:

rep add local_bio "C:/Perl/Bioperl"

I then searched for and installed the modifed PPM file and it worked.

Like I said, I don't know if this is a PPM issue or not.  However, I think
it might be a good idea to remove those dependencies just in case, as they
are a bit redundant (both HTML-Parser and IO-stringy are already listed).

My two cents...

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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