[BioC] segfault ReadAffy cause 'memory not mapped'

[cstrato]

Dear Ann,

Several thousand CEL-files is quite a lot. Furthermore, you do not 
mention which array type are you using.

In any case you could try to use package 'xps', which should be able to 
handle it. However, you should do your processing stepwise.

Best regards,
Christian
_._._._._._._._._._._._._._._._._._
C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a           A.u.s.t.r.i.a
e.m.a.i.l:        cstrato at aon.at
_._._._._._._._._._._._._._._._._._



On 8/1/13 5:33 PM, Loraine, Ann wrote:
> 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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>
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