[Bioperl-l] Test errors in bioperl-run

Jason Stajich jason at bioperl.org
Tue Jun 13 11:45:27 EDT 2006


And just to say - codeml 3.15 parsing does work - yn00 parsing just  
hasn't been updated.   I agree that it is bad the test is failing but  
it is dependent on the version that is installed and we should put  
some sort of detect version-skip test code in there so it doesn't  
cause the tests to fail.  Just need more hands on deck tracking these  
sort of things....

-jason
On Jun 13, 2006, at 10:19 AM, Jason Stajich wrote:

> 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
>
>
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--
Jason Stajich
Duke University
http://www.duke.edu/~jes12




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