[R] cause 'memory not mapped'

Martin Morgan
Mon, 13 Jun 2011 16:19:21 -0000

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
>
> --
> View this message in context:
http://r.789695.n4.nabble.com/cause-memory-not-mapped-tp3593833p3593833.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.


--
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793