[Bioperl-l] Test errors in bioperl-run

Brian Osborne osborne1 at optonline.net
Tue Jun 13 21:38:09 EDT 2006


Checked in.


On 6/13/06 2:34 PM, "Ryan Golhar" <golharam at umdnj.edu> wrote:

> 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
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> --
> Jason Stajich
> Duke University
> http://www.duke.edu/~jes12
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