[BioC] gls from nlme package not compatible with methods package

[Douglas Bates]

James Wettenhall <wettenhall@wehi.edu.au> writes:

> Dear Bioconductor,
> 
> I am trying to develop a Bioconductor-style package for fitting 
> linear models to microarray data, to be used with marrayNorm, 
> marrayInput etc.
> 
> I want to use the function gls (generalized least squares) from 
> the nlme package.  But it doesn't seem to be compatible with the 
> methods package.  Any suggestions?

...

> > out <- gls(y~x)
> > library(methods)
> > out <- gls(y~x)
> Error in getClass(Class) : "glsStruct" is not a defined class

What version of R and what version of the nlme package?

Please send the result of R.version and the first few lines of
library(help=nlme).  It should look like

> R.version
         _                
platform i386-pc-linux-gnu
arch     i386             
os       linux-gnu        
system   i386, linux-gnu  
status                    
major    1                
minor    6.2              
year     2003             
month    01               
day      10               
language R                
> library(help=nlme)
nlme            Linear and nonlinear mixed effects models

Description:

Package: nlme
Version: 3.1-36
Date: 2002-12-28
Priority: recommended
Title: Linear and nonlinear mixed effects models

Also, it would help to send the results of running traceback()
immediately after you get the error message.