Hello,

I am trying to process several thousand CEL files using the ReadAffy command.

The machine has 96 Gb RAM.

However I get this error:

> expr=ReadAffy(filenames=d.uniq$cel,celfile.path='CEL',sampleNames=d.uniq$gsm,compress=T)

 *** caught segfault ***
address 0x7fc79b4b1048, cause 'memory not mapped'

Traceback:
 1: .Call("read_abatch", filenames, rm.mask, rm.outliers, rm.extra,     ref.cdfName, dim.intensity[c(1, 2)], verbose, PACKAGE = "affyio")
 2: read.affybatch(filenames = l$filenames, phenoData = l$phenoData,     description = l$description, notes = notes, compress = compress,     rm.mask = rm.mask, rm.outliers = rm.outliers, rm.extra = rm.extra,     verbose = verbose, sd = sd, cdfname = cdfname)
 3: ReadAffy(filenames = d.uniq$cel, celfile.path = "CEL", sampleNames = d.uniq$gsm,     compress = T)

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:

R and session info:

R version 3.0.1 (2013-05-16) -- "Good Sport"
Copyright (C) 2013 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)

> sessionInfo()
R version 3.0.1 (2013-05-16)
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=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] affy_1.38.1        Biobase_2.20.1     BiocGenerics_0.6.0

loaded via a namespace (and not attached):
[1] affyio_1.28.0         BiocInstaller_1.10.3  preprocessCore_1.22.0
[4] zlibbioc_1.6.0

Can you help?

Best,

Ann


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