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"
>
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