[R] cause 'memory not mapped'

Jeff Newmiller
Mon, 13 Jun 2011 14:18:13 -0000

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ascendo <ascendo@dongguk.edu> wrote:

Dear R-help

Hi,

I'm Won.

I try to do microarray normalization by R.

I use justRMA function within affy package, got error about segment fault.

I don't know why it happen.

I attached error below.

Please help me.

Thank you.

Cheers,

Won

======================OS : Redhat linux
Cpu : intel xeon X5570
Memory : 26Gb

&

OS : Ubuntu
Cpu : intel q6600
Memory : 8Gb

======================Loading required package: Biobase
Loading required package: methods

Welcome to Bioconductor

Vignettes contain introductory material. To view, type
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")' and for packages
'citation("pkgname")'.

Loading required package: gcrma
Loading required package: preprocessCore

Attaching package: 'affyPLM'

The following object(s) are masked from 'package:stats':

resid, residuals, weights


*** caught segfault ***
address 0xc609000, cause 'memory not mapped'

Traceback:
1: .Call("rma_c_complete", probeintensities$pm, pNList, ngenes,
normalize, background, bgversion, verbose, PACKAGE = "affy")
2: just.rma(filenames = l$filenames, phenoData = l$phenoData, description
l$description, notes = notes, compress = compress, rm.mask = rm.mask,
rm.outliers = rm.outliers, rm.extra = rm.extra, verbose = verbose,
normalize = normalize, background = background, bgversion = bgversion,
destructive = destructive, cdfname = cdfname)
3: justRMA()
aborting ...
/var/spool/sge/tachyon1145/job_scripts/477103: line 21: 22829 Segmentation
fault /home01/e133ywc/R/R-2.13.0/bin/Rscript
/scratch/e133ywc/big/198/198.R

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