[Bioperl-l] Problems with installing bioperl using PPM3

Chris Fields cjfields at uiuc.edu
Wed Apr 14 13:08:41 EDT 2004

At 09:26 PM 4/14/2004, Brian Osborne wrote:
> >Another question I had was can we use the CPAN module to download and
>install packages
> >under a windows environment or are we restricted to using PPM from
>Yes, you can. Lincoln has made this point a couple of times when people
>expressed their frustrations with the ActiveState approach. In the Command
>Prompt, for example, you should be able to do:
> >perl -e shell -MCPAN
>And then things like:
>cpan>install IO::String
>It's been some time since I last used ActiveState, I use Cygwin instead, so
>someone should correct me if this is no longer the case.
>Brian O.

I have tried this before and it works fine.  The only issues that I've seen 
come up are test failures when installing some modules that have C code 
included, upon which nmake crashes and the install fails.

The reason to use PPM can be summed up in one word: simplicity.  I think 
that some Perl users, myself included, have learned Perl and other higher 
level languages w/o experience in the intricacies of the programming 
process that one learns from C or C++ in a basic computer programming 
course (i.e. plan program -> type program -> build (compile and link 
program) -> execute program).  That's fine but becomes a problem when 
trying to install some modules w/o some background knowledge, such as how 
to use 'nmake' or 'make' in a Windows environment.

I personally have a biochemistry and microbiology background and currently 
work as a postdoctoral researcher on RNA-binding proteins.  I have since 
learned C and C++ for various other reasons, one being that I have an avid 
interest in programming.  Learning the basics has helped me tremendously in 
picking out problems that I ran into before, such as how to compile a 
program in a Linux or Windows environment, using the proper header files, 
libraries, etc.  It also has helped in learning a bit more about how Perl 
and how easy it is to use compared to C/C++.  The advantage of using PPM is 
that it allows for easy installation and removal of packages w/o the need 
for building modules, and it also creates nicely HTML-formatted help pages 
from POD (something that pod2html can do as well).  The biggest 
disadvantage with PPM is that it is somewhat like a using a calculator; 
it's quick and easy, but it's a 'black box' in that most people don't know 
how it works, but it does its job (sometimes).  I'm now able to get around 
some of the problems of using PPM through a little detective work (reading 
the man pages!!!, web searches, etc) and learning a bit more about the 
programming process.

I think most problems with PPM arise b/c some modules refuse to compile 
with Windows (for a list of the many failed builds from ActiveState 
automated build process, see http://ppm.activestate.com/).  Randy Kobes has 
many PPM modules not available from ActiveState that have been tweaked for 
Windows, including GD (http://theoryx5.uwinnipeg.ca/), but many 
distributions still have problems.  PDL is one distribution that comes to 
mind, which is required for the Transcription Factor Binding Site modules.

My 2c


>-----Original Message-----
>From: bioperl-l-bounces at portal.open-bio.org
>[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of omid at rogers.com
>Sent: Wednesday, April 14, 2004 10:00 AM
>To: Chris Fields
>Cc: Bioperl-l at bioperl.org
>Subject: Re: Re: [Bioperl-l] Problems with installing bioperl using PPM3
>Thanks for the Reply Chris...
>I managed to get things working for the time being.
>I am reading the the PPM instructions provided by the Activestate and
>getting a feel for how things work.
>I tried the first method you mentioned ie setting up a local repository:
>Here is what I did.
>1) I run PPM3 at command prompt.
>2) rep add my_local "E:/Perl/Local_rep/"
>I got this error message:
>"Can't locate object method "host" via package "URI::_foreign" (perhaps you
>forgot to load "URI::_foreign"?) at E:/Perl/site/lib/PPM/Repository/Local.pm
>line 18, <FIN> line 3."
>I check to see if "URI" is installed (ie query *) and it was. I checked to
>see if there are any upgraded to URI and there was not one available.
>I don't know if you if have come across this type of errors in the past.
>Another question I had was can we use the CPAN module to download and
>install packages under a windows environment or are we restricted to using
>PPM from activestate?
>Many Thanks


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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