[R] cause 'memory not mapped'

[Martin Morgan]

On 06/13/2011 06:23 AM, ascendo 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.

Hi Won -- as suggested, post to the Bioconductor mailing list

https://stat.ethz.ch/mailman/listinfo/bioconductor

Make sure that you've installed and updated your packages following the 
Bioconductor protocol; problems can arise when package versions are not 
matched correctly.

http://bioconductor.org/install/

You include the output of your script, but not the commands. Include the 
commands, and include the output of sessionInfo(). If at all possible 
make the example reproducible, e.g., by using the examples in the 
package or data provided by the sample data sets. For instance after

   source('http://bioconductor.org/biocLite.R')
   biocLite(c("affy", "AffymetrixDataTestFiles"))

Run these commands

   library(affy)
   library(AffymetrixDataTestFiles)
   sessionInfo()
   cel <- system.file("rawData", "FusionSDK_HG-U133A", "HG-U133A",
       "2.Calvin", "ethan1-1.CEL", package="AffymetrixDataTestFiles")
   res <- just.rma(cel)

which produces

 >   library(affy)
 >   library(AffymetrixDataTestFiles)
 >   sessionInfo()
R version 2.12.2 Patched (2011-02-25 r54588)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] AffymetrixDataTestFiles_0.1.2 affy_1.28.0
[3] Biobase_2.10.0

loaded via a namespace (and not attached):
[1] affyio_1.18.0         preprocessCore_1.12.0
 >   cel <- system.file("rawData", "FusionSDK_HG-U133A", "HG-U133A",
+       "2.Calvin", "ethan1-1.CEL", package="AffymetrixDataTestFiles")
 >   res <- just.rma(cel)
Warning message:
In just.rma(cel) : Incompatible phenoData object. Created a new one.

Martin

>
> 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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>
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