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

Dick Beyer
Wed, 26 May 2004 15:52:55 -0000

Thanks very much for your help.  Following your suggestion, I found that the
offending bioconductor package is affy.  I will report that to the bioconductor
folks.

*******************************************************************************
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
*******************************************************************************

On Wed, 26 May 2004, Prof Brian Ripley wrote:

> 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
> >
> > ______________________________________________
> > R-help at stat.math.ethz.ch mailing list
> > https://www.stat.math.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
> >
> >
>
> --
> 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
>
>