[Bioperl-l] Bioperl 1.5.2 RC5 installonWinXPActivePerl

Nathan S. Haigh n.haigh at sheffield.ac.uk
Fri Dec 1 14:05:38 EST 2006

Chris Fields wrote:
>> Chris Fields wrote:
>> 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.
>> CPAN isn't being suggested as the primary or preferred 
>> installation method for Windows. That will still be PPM. I'm 
>> mentioning CPAN / manual installation in the Windows INSTALL 
>> docs for the benefit of anyone who wants a simple install and 
>> test environment when checking out from CVS.
> That's fine by me.  I think the focus is making sure the PPM works, but that
> shouldn't hold up the final 1.5.2 release.  The PPM for previous releases
> was never released concurrently with the distribution (if at all); it
> generally followed by a few weeks to a few months past a final release.

Forgot to say, one really annoying thing about PPM is that it seems to 
display all the versions of Bioperl defined in the XML file. An 
addition, I think a bug in PPM4 means that if a package is available in 
ActiveStates repo PPM4 always want to install it rather than a more 
recent version in a different repo (this includes upgrades). This 
results in this annoying behaviour:
1) If activestate and bioperl repos are active, searching for bioperl 
lists several versions
2) If you are using PPM4 GUI, and have installed a non activestate 
version, then it says you can upgrade to the version in activestates 
repo (even if it's actually a downgrade).
3) Using ppm-shell, if you choose "install bioperl" or "upgrade bioperl" 
it will always install the version in the activestate repo.
4) I'm sure there are also some other annoyances.

In the end, it means the best way to install and upgrade bioperl, is to 
search for bioperl packages and install the latest version by eye rather 
than relying in the "upgrade feature" (at least for the time being). You 
may also need to remove an old version of bioperl before installing a 
more recent version. NOTE: using "upgrade" runs the risk of installing 
bioperl 1.2.3 from activestate and not the latest version in any other repo!

I'll update the wiki when I have time.

>>> What are the significant issues for a bioperl PPM installation
>> None that I'm aware of - I just need to find the time to 
>> start looking into generating an appropriate PPD. Hopefully 
>> Nathan's wiki page on the subject will be all I need.
> I'll try testing it out today and next week (the more people we have looking
> into the issue the better).  I'm sure that Module::Build hasn't updated to
> using PPM4 XML formatting, but the tags are similar enough.  I can always
> create a local PPM database using a similar directory structure to
> bioperl.org/DIST and test an installation from it.
> chris
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