[Bioperl-l] bioperl-1.4 ppm package for Windows
brian_osborne at cognia.com
Fri Feb 27 10:57:14 EST 2004
I'd always intended to have a double-boot Windows/Linux machine but I
thought I'd check out Cygwin, just for fun. I was so impressed with it
running Bioperl that I decided not to install Linux.
I must use Windows at work so pure Unix is not an option for me. Someone
recently showed me Windows on a Linux machine running VMWare, that was
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Chris Fields
Sent: Friday, February 27, 2004 10:47 AM
To: bioperl-l at bioperl.org; Lincoln Stein
Cc: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] bioperl-1.4 ppm package for Windows
I already have it installed an it seems to be fine.
I have just one question (and I don't want to start a flame war): what OS
do you find that Bioperl works best for? I'm using a duel-boot system with
Windows XP and Fedora Core 1, and I've had fewer problems with Fedora (esp.
when using GBrowse), but I don't know if this is due to the configuration
of Bioperl, GBrowse, or Perl on either OS. I'm considering going pure
Linux within the year (although Mac OS X is looking very appealing).
At 08:45 AM 2/27/2004, Lincoln Stein wrote:
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>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
>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!):
> > <DEPENDENCY NAME="HTML-Entities"
> > 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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>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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