[Bioperl-l] Test errors in bioperl-run

[Ryan Golhar]

Nevermind - don't check it in yet.  There are still some other problems
not being picked up by the test suite.  I'll work on that and add to the
test suite.  Jason, I'll send you everything once I have it complete.


-----Original Message-----
From: Ryan Golhar [mailto:golharam at umdnj.edu] 
Sent: Tuesday, June 13, 2006 2:34 PM
To: 'Jason Stajich'
Cc: 'bioperl-l at bioperl.org'
Subject: RE: [Bioperl-l] Test errors in bioperl-run


It looks like the output contains two new sections at the bottom and the
comment sections have been changed slightly.  I've modified
bioperl-live/Bio/Tools/PAML.pm to read the new and old format from YN00.
I've attached it to this message.  It passs all the PAML tests from
bioperl-live and bioperl-run using both 3.14 and 3.15 of YN00.  Can you
(or someone) can check it into CVS?

Ryan

-----Original Message-----
From: Jason Stajich [mailto:jason at bioperl.org] 
Sent: Tuesday, June 13, 2006 10:19 AM
To: golharam at umdnj.edu
Cc: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] Test errors in bioperl-run


The latest version of YN00 (3.15) doesn't work with the current code  
as the output has changed substantially as Yang is now provided  
several different method's simple Ka and Ks calculations.  Downgrade  
to PAML 3.14 or roll up your sleeves and figure out what is breaking  
-- which is the regexp in about line 363 that detects when to start  
parsing for the Pairwise data as well as the function  
parse_YN_Pairwise....

I just don't have very much time anymore to follow changes to the  
software packages so I am hopeful that other developers that use our  
software as do molecular evolutionary studies will get involved to  
help this effort.

I may have to run a few batches of analyses myself later in the week  
using PAML so I will try and fix this if I can make the time.

-jason
On Jun 12, 2006, at 4:23 PM, Ryan Golhar wrote:

> I'm trying to install the bioperl-run package and an getting errors 
> from make test regarding PAML:
>
> t/PAML....................ok 2/18Can't call method "get_MLmatrix" on 
> an undefined value at t/PAML.t line 85, <GEN2> line 85.
> t/PAML....................dubious
>         Test returned status 2 (wstat 512, 0x200)
>         after all the subtests completed successfully
>
> Is this a legitimate error or am I missing something?
>
> Ryan
>
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--
Jason Stajich
Duke University
http://www.duke.edu/~jes12