[Bioperl-l] 1.1 core and run released

[Catherine Letondal]

Jason Stajich wrote:
> I have put bioperl-1.1 and bioperl-run-1.1 releases in the usual place
> ftp://bioperl.org/pub/DIST
> http://bioperl.org/DIST
> 
> Download, test, debug, etc.  We'll try and do 1.1.1 in a month or so
> depending on how much new code and activity there is.  The usual caveats
> that this code may not represent the final API in a stable release,
> modules/methods etc may come and go on the odd-numbered (developer)
> releases.  But please give it some use in non-production environments and
> report and bugs or missing features to the list.
> 

I have corrected (in CVS) some warnings and bugs in the Pise part, such as unused 
variables in PiseJob.pm, updated some programs in PiseApplication, and added a 
program (http://bioweb.pasteur.fr/seqanal/interfaces/pdbsearch.html).

Also, the Makefile.PL now ask for an email without suggesting any default value for it.
(I think Jason has changed the ftp version to display an example after
RFC 2606 - which recommands using the example.{com,net,org} domains).
(a valid email is important in the sense that the server accepts very long 
computations, or very repetitive automated tasks, and we need to be able to contact
people submitting such jobs or just having troubles with input formats etc...).

Apart from this, I had a problem with the neighbor test, which seemed to run forever?
Which versions of Phylip is used? Latest version of Phylip (3.6a2) behaves very 
differently I believe.

--
Catherine Letondal -- Pasteur Institute Computing Center