[R-SIG-Mac] trouble running Bioconductor

[Olga Vitek]

Hi Kasper,

Thanks a lot. I found what it was. The "bus error" apparently occurs when
a program tries to access an invalid memory address, e.g. in case of a
null pointer exception. When I created the eset data stucture, I used a
factor to assign dimnames of exprs(eset), and some <NA> were created. When
I corrected that it worked fine.

Sincerely
Olga


On Fri, 11 Aug 2006, Kasper Daniel Hansen wrote:

> Hmm, in case you installed Bioconductor from source, did you remember
> to install the version of GCC that ships with the CRAN version of R?
> That, or some other installation mishap is all I can think of.
>
> Kasper
>
> On Aug 10, 2006, at 6:33 PM, Olga Vitek wrote:
>
> > Dear All,
> >
> > I am having difficulty running Limma: every time I run the code R
> > crashes, and I can't explain the reason for the problem. Could someone
> > point me out to where to look for trouble? I attach the code and
> > the error
> > messages below.
> >
> > Thanks a lot in advance!
> > Olga
> >
> > ERROR MESSAGE:
> > ---------------
> >  *** caught bus error ***
> > address 0x2c, cause 'invalid alignment'
> >
> > Traceback:
> >  1: sum(out$residuals^2)
> >  2: lm.series(M, design = design, ndups = ndups, spacing = spacing,
> > weights = weights)
> >  3: lmFit(eset, design)
> >  4: NCOL(fit$coefficients)
> >  5: contrasts.fit(lmFit(eset, design), contr.matrix)
> >  6: ebayes(fit = fit, proportion = proportion, stdev.coef.lim =
> > stdev.coef.lim)
> >  7: eBayes(contrasts.fit(lmFit(eset, design), contr.matrix))
> >
> >
> > CODE:
> > ------
> > makeFit <- function(eset) {
> > 	design <- model.matrix(~0+factor(c(eset$stimulation)))
> > 	dimnames(design)[[2]] <- c("Control", "Insulin")
> > 	contr.matrix <- makeContrasts(Insulin-Control, levels=design)
> > 	eBayes( contrasts.fit( lmFit(eset, design), contr.matrix ) )
> > }
> > limmaFit <- makeFit(data$eset)
> > rm(makeFullFit)
> >
> > SPECS:
> > --------
> > Mac OS X V.10.4.7, 1GHz PowerPC G4, 1.25GB memory
> > R Version 2.3.1 (2006-06-01)
> >> package.version("Biobase")
> > [1] "1.10.1"
> >> package.version("limma")
> > [1] "2.7.9"
> >
> > _______________________________________________
> > R-SIG-Mac mailing list
> > R-SIG-Mac at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>