[Bioperl-l] Bioperl 1.5.2 RC5 install onWinXPActivePerl 184.108.40.2069
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
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
> 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.
More information about the Bioperl-l