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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.<br><br>
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.<br><br>
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!):<br><br>
<pre><DEPENDENCY NAME="HTML-Entities"
VERSION="0,0,0,0" />
<DEPENDENCY NAME="IO-Scalar" VERSION="0,0,0,0"
/>
</pre>I then entered PPM, set up a local ppd repository:<br><br>
<font face="Courier New, Courier">rep add local_bio
"C:/Perl/Bioperl"<br><br>
</font>I then searched for and installed the modifed PPM file and it
worked.<br><br>
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).<br><br>
My two cents...<br>
__________________________________<br><br>
<x-sigsep><p></x-sigsep>
Chris Fields - Postdoctoral Researcher <br>
Lab of Dr. Robert Switzer<br><br>
Address:<br><br>
University of Illinois at Urbana-Champaign<br>
Dept. of Biochemistry - 323 RAL<br>
600 S. Mathews Ave.<br>
Urbana, IL 61801<br><br>
Phone : (217) 333-7098<br>
Fax : (217) 244-5858</body>
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