[Bioperl-l] Fwd: Pairwaise_kaks.pl

dennis prickett (IAH-C) dennis.prickett at bbsrc.ac.uk
Wed Oct 31 07:32:35 EDT 2007


Thanks for the quick response.  

Yes I do have the mixed setup as you describe-  bioperl-run from CVS and
the bioperl core package.

But.. to resolve the issue - would installing bioperl 1.5.2_102 work? 


Dennis Prickett

-----Original Message-----
From: Sendu Bala [mailto:bix at sendu.me.uk] 
Sent: 30 October 2007 16:11
To: Jason Stajich
Cc: bioperl-l list; dennis prickett (IAH-C)
Subject: Re: [Bioperl-l] Fwd: Pairwaise_kaks.pl

Jason Stajich wrote:
> Denis -
> Not sure - the list members will know more.
>> From: "dennis prickett \(IAH-C\)" <dennis.prickett at bbsrc.ac.uk>
>> I have installed bioperl-run in /usr/local/bioperl_run-1.5.2
>> And have bioperl             in /usr/local/bioperl-1.5.2_100
>> When I try to run the script I get the following
>> Can't locate object method "_set_from_args" via package 
>> "Bio::Tools::Run::Alignment::Clustalw" at 
>> Bio/Tools/Run/Alignment/Clustalw.pm line 409.
>> I'm not sure how to resolve this so I refer to a higher authority

_set_from_args() first arrived in Jan 2007, after 1.5.2 was released. 
This means you actually have some kind of mixed setup where you probably
have bioperl-run from CVS and bioperl-core 1.5.2.

The solution is to make sure you have core and run packages from the
same place. Ie. 1.5.2 release packages or CVS, not both.

More information about the Bioperl-l mailing list