[Bioperl-l] Bioperl 1.5.2 RC5 install onWinXPActivePerl

Chris Fields cjfields at uiuc.edu
Fri Dec 1 09:08:55 EST 2006

On Dec 1, 2006, at 3:13 AM, Sendu Bala wrote:

> Chris Fields wrote:
>> I know that setting up the PPM is a pain, but I have to say it is  
>> much faster, and all required PPMs are available.  Which makes me  
>> curious: why bother with trying out a CPAN installation process at  
>> this point, especially when you have to use PPM to install some of  
>> the prereqs properly anyway?
> Firstly, problems discovered and resulting fixes will help all  
> platforms, not just Windows. So thanks for trying it out and  
> reporting back. Secondly, the PPM method, like Bundle::BioPerl, is  
> all-or-nothing. The CPAN installation method allows an interactive  
> choice of which optional things to install.

Yes, I understand that.  My point is, you are generally forced to use  
PPM anyway due to several modules not installing properly (all the  
'trouble' distributions, like DB_File, are available via PPM).  I can  
see using CPAN as an alternative way of installing Bioperl for a  
distribution, or as the primary method via CVS or manually, but not  
for distributions.  At least not until the kinks are worked out for  
Windows users.

What are the significant issues for a bioperl PPM installation, based  
on the last PPM Nathan set up?  If there is a redirection problem,  
could we just modify the installation docs to address that ('due to  
problem X, you must install the following modules prior to installing  
BioPerl 1.5.2...').

> If what you say about DB_File is true, then that's a great shame!

We need to go through the various prereqs to see which ones need PPM  
vs CPAN.  In general, anything that requires C code compilation (and  
thus needs a recent VC++) will likely be an issue.

> So I can do further trouble-shooting of my own, what is the sure- 
> fire way to completely clean-out an ActivePerl install, including  
> any modules you might have installed with PPMs or CPAN?

Not sure, beyond uninstalling and cleaning out the Perl directory (I  
think you might be able to delete the site/ directory, but I haven't  
tried it).  ActivePerl comes preloaded with a number of non-core  
modules which makes it tricky to uninstall them one-by-one.


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