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At 09:07 AM 2/27/2004, you wrote:<br>
<blockquote type=cite class=cite cite>Hi! Chris,<br><br>
The error you get happens because we don't store all the dependent
packages<br>
on Bioperl/DIST...PPM is expected to find them in the repositories you
have<br>
listed in your PPM. So if you add a repository that has the
dependent<br>
modules it will install correctly.<br><br>
Add the repository :
<a href="http://theoryx5.uwinnipeg.ca/ppmpackages/" eudora="autourl">http://theoryx5.uwinnipeg.ca/ppmpackages/</a>
for perl 5.6<br>
Add the repository : <a href="http://theoryx5.uwinnipeg.ca/ppms" eudora="autourl">http://theoryx5.uwinnipeg.ca/ppms</a> for perl 5.8</blockquote><br>
I know that (I already have Kobe's repository and a number of others installed). That's not the problem, though.<br><br>
The problem lies in the redundant requirements of HTML-Parser, HTML-Entities, IO-Parser, and IO-stringy. To give you a better picture of the issue, here is the list of requirements of Bioperl 1.2.3 (for both Perl 5.6 and 5.8), which install fine:<br><br>
<font face="Courier New, Courier"> Name: Bioperl-1.2.3<br>
Version: 1.2.3<br>
Author: Bioperl Team (bioperl-l@bioperl.org)<br>
Title: Bioperl<br>
Abstract: Bioperl 1.2.3 PPM3 Archive<br>
Location: bioperl<br>
Prerequisites:<br>
1. File-Temp 0.12<br>
2. IO-String 1.0.1<br>
3. IO-stringy 2.1<br>
4. XML-Writer 0.4<br>
5. XML-Node 0.11<br>
6. XML-Twig 3.0.4<br>
7. libxml-perl 0.0.7<br>
8. DBD-mysql 2.1025<br>
9. Graph 0.20101<br>
10. GD 2.06<br>
11. Text-Shellwords 1.0<br>
Available Platforms:<br>
1. MSWin32-x86-multi-thread<br>
2. MSWin32-x86-multi-thread-5.8<br><br>
</font>and here are the requirements for Bioperl-1.4, which doesn't install:<br><br>
<font face="Courier New, Courier"> Name: Bioperl-1.4<br>
Version: 1.4<br>
Author: Bioperl Team (bioperl-l@bioperl.org)<br>
Title: Bioperl<br>
Abstract: Bioperl 1.4 PPM3 Archive<br>
Location: bioperl<br>
Prerequisites:<br>
1. File-Temp 0.12<br>
2. IO-String 1.0.1<br>
3. IO-stringy 2.1<br>
4. XML-Writer 0.4<br>
5. XML-Node 0.11<br>
6. XML-Twig 3.0.4<br>
7. libxml-perl 0.0.7<br>
8. DBD-mysql 2.1025<br>
9. Graph 0.20101<br>
10. GD 2.06<br>
11. Text-Shellwords 1.0<br>
12. DB_File 0.0<br>
13. File-Spec 0.0<br>
14. HTML-Entities 0.0 <---------------------<br>
15. IO-Scalar 0.0 <---------------------<br>
Available Platforms:<br>
1. MSWin32-x86-multi-thread<br>
2. MSWin32-x86-multi-thread-5.8<br><br>
</font>The issue that PPM (at least v. 3.1) has with the above is that it will actively look for the packages listed above, including the (nonexistent) packages indicated by the arrows. HTML-Entities is a module, not a package, and is included with the package HTML-Parser in the ActiveState distribution for Perl 5.8 (altough I'm not sure about Perl 5.6), while IO-Scalar is also a module and is part of the IO-stringy package, which can be installed from the ActiveStatae repository. I have Randy Kobe's repository and a number of others (as well as your TEMP repository), and none of them list the two indicated requirements as packages. Notably, also added as a requirement above is File-Spec, but since this is a package and not a module, it is found in the various repositories and installed w/o a problem.<br><br>
This is a problem that I originally thought could be due to a change in PPM (I am working with the newest version). One would think if PPM were able to look for the modules above, it would need to search through all the different package descriptions for the right package that contains the module. If you look at the either the HTML-Parser or IO-stringy PPD files (snagged from the ActiveState web site), there is no listing of the modules included in either package in the description. Hence, there is no way that PPM can possibly know that IO-stringy or HTML-Parser holds the requirements listed above and the reason for the subsequent installation failure. PPM doesn't search for modules, however; it searches for modules bundled together as packages. The PPM documentation also supports this (arrows mine):<br><br>
<br>
The Programmer's Package Manager (PPM), formerly known as the Perl Package Manager, provides a command line interface for managing your modules and extensions (packages). ---> PPM is used to access package repositories (or collections of packages on other machines), install and remove packages from your system, as well as update previously installed packages with the latest versions. <---<br><br>
<br>
I think the best way to handle it, irrespective of the PPM version and their quirks, is to remove the redundant dependencies, add HTML-Parser (the package) and be done with it. In my case, I removed them manually and installed from a local repository.<br><br>
<blockquote type=cite class=cite cite>Hope this helps.<br>
Regards,<br>
Nigam.<br>
</blockquote><br>
Thanks! <br><br>
<blockquote type=cite class=cite cite>Nigam Shah<br>
Graduate Fellow, <br>
Huck Institute for Life Sciences,<br>
Penn State University.<br>
Ph:(814)863-5720<br>
Web: <a href="http://www.personal.psu.edu/nhs109/" eudora="autourl">www.personal.psu.edu/nhs109/</a></blockquote>
<x-sigsep><p></x-sigsep>
__________________________________<br>
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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