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

Lincoln Stein lstein at cshl.edu
Fri Feb 27 09:45:17 EST 2004

Hash: SHA1

Hi Chris,

Do you want to try the bioperl-1.4 ppm located on this repository?


I put it together myself and it's the one that seems to work properly 
for me.


On Wednesday 25 February 2004 07:26 pm, Chris Fields wrote:
>  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" />
> <DEPENDENCY NAME="IO-Scalar" 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
>  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

- -- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
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