[Bioperl-l] Fwd: Pairwaise_kaks.pl

[dennis prickett (IAH-C)]

Sendu

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? 

Thanks 

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.