[BioC] [R-SIG-Mac] trouble running Bioconductor

[stefano iacus]

I'm forwarding this to the BioC mailing list with a reproducible  
example to see if this is also happening in other platforms, if it is  
specific to limma, or whatever.
thanks
stefano

On 11/ago/06, at 09:09, Olga Vitek wrote:

> 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"
>>>
>>> _______________________________________________
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>>> R-SIG-Mac at stat.math.ethz.ch
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>>
>
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