[R] No direct or inherited method for function "update"

[Prof Brian Ripley]

Try doing this without all those Bioconductor packages loaded.  It does 
work in base R, and I suspect that one of your packages has redefined 
update (by adding S4 methods?).  If you track down exactly which package 
causes the problem, you can report it to the appropriate person.

On Tue, 25 May 2004, Dick Beyer wrote:

> I used to be able to call update() for lme objects. Now I get this error:
> 
> >   ge.lme <- update(ge.lme, data=dat)
> Error in update(ge.lme, data = dat) : No direct or inherited method for function "update" for this call
> 
> 
> Here is the relevant portion of my code:
> 
> ge     <- eset[1,]
> dat    <- data.frame(age, gen, fdr, ge)
> ge.lme <- lme(fixed=ge~age+gen+age*gen, data=dat, random=~ 1| fdr)
> for (i in 1:nrow(eset)) {
>   dat$ge <- c(eset[i,])
>   ge.lme <- update(ge.lme, data=dat)
>   .
>   .
>   .
> }
> 
> I am using:
> base 1.9.0 
> utils 1.9.0 
> graphics 1.9.0 
> stats 1.9.0 
> methods 1.9.0 
> Biobase 1.4.14 
> affy 1.4.30 
> gcrma 1.1.0 
> annaffy 1.0.7 
> KEGG 1.4.0 
> GO 1.5.1 
> mgu74av2 1.4.0 
> nlme 3.1-48 
> xtable 1.2-1 
> 
> Any help or suggestions would be most appreciated.
> 
> Thanks much,
> Dick
> *******************************************************************************
> Richard P. Beyer, Ph.D.	University of Washington
> Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
> Fax: (206) 685 4696	4225 Roosevelt Way NE, # 100
> 			Seattle, WA 98105-6099
> http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html
> 
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> 

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595