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

[James Wettenhall]

Douglas,

I just tried R 1.6.1 in Windows with methods 1.6.1 and 
nlme 3.1-33 and there was no problem :)

But when running on Linux with R 1.5.0 and methods 1.5.0 and 
nlme 3.1-23 I got the error described previously.

Maybe I'll have to tell my sysadmin to upgrade R !

Regards,
James

> R.version
         _
platform i686-pc-linux-gnu
arch     i686
os       linux-gnu
system   i686, linux-gnu
status
major    1
minor    5.0
year     2002
month    04
day      29
language R

> library(help=nlme)
nlme            Linear and nonlinear mixed effects models

Description:

Package: nlme
Version: 3.1-23
Date: 2001/01/28

> out<-gls(y~x)
Error in getClass(Class) : "glsStruct" is not a defined class
> traceback()
4: stop(paste("\"", Class, "\" is not a defined class", sep = 
""))
3: getClass(Class)
2: initialize(glsSt, dataMod, glsEstControl)
1: gls(y ~ x)




On 13 Jan 2003, Douglas Bates wrote:

> 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.
> 
> 

-- 
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James Wettenhall                                  Tel: (+61 3) 9345 2629
Division of Genetics and Bioinformatics           Fax: (+61 3) 9347 0852
The Walter & Eliza Hall Institute         E-mail: wettenhall@wehi.edu.au
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