[BioC] segfault ReadAffy cause 'memory not mapped'

[Martin Morgan]

On 08/02/2013 11:00 AM, cstrato wrote:
> 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.

also, perhaps justRMA is a more memory-efficient way to do standard 
normalization. Probably there is a bug in ReadAffy, but it would be difficult to 
track down without a more reproducible example. Martin

>
> 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
>>
>>
>>     [[alternative HTML version deleted]]
>>
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>
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