[Bioperl-l] Test errors in bioperl-run

Ryan Golhar golharam at umdnj.edu
Tue Jun 13 21:55:49 EDT 2006


Okay, that's fine.  It does pass the bioperl-live tests.  When I ran the
bp_pairwise_kaks script, it didn't work, the script doesn't work with
3.15.  It looks like the current test suite is not exhaustive.  

When I looked into the code more so, I see that codeml 3.15 generates
some files slightly different than 3.14 which needs to be accounted for.
I'll work on that and post it here...shouldn't be too long.

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
Sent: Tuesday, June 13, 2006 9:42 PM
To: golharam at umdnj.edu; 'Jason Stajich'
Cc: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] Test errors in bioperl-run


I committed it.  Passes PAML.t for bioperl-live.

Chris

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- 
> bounces at lists.open-bio.org] On Behalf Of Ryan Golhar
> Sent: Tuesday, June 13, 2006 1:34 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
> >
> > _______________________________________________
> > 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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