[BioC] segfault ReadAffy cause 'memory not mapped'
Benilton Carvalho
beniltoncarvalho at gmail.com
Sat Aug 3 20:25:49 CEST 2013
and I would start by checking the integrity of the files.... affyio
(the engine is ReadAffy) throws errors like this when files are
damaged...
2013/8/2 Henrik Bengtsson <hb at biostat.ucsf.edu>:
> Alright, my turn...
>
> http://aroma-project.org/
>
> /Henrik
>
>
> On Fri, Aug 2, 2013 at 2:57 PM, Matthew McCall <mccallm at gmail.com> wrote:
>> Another option if your data comes from one of the more common
>> affymetrix platforms (HGU133a, HGU133plus2, Mouse4302, HuGene, HuEx),
>> you can read in and preprocess your data in subsets using frma and
>> then combine it for further analysis.
>>
>> Best,
>> Matt
>>
>> On Fri, Aug 2, 2013 at 4:59 PM, Adaikalavan Ramasamy
>> <adaikalavan.ramasamy at gmail.com> wrote:
>>> Also worth trying the standalone and free software called affy power tools
>>> if its affy arrays. There is an option to choose sketch normalization.
>>>
>>> On 2 Aug 2013 21:34, "Kasper Daniel Hansen" <kasperdanielhansen at gmail.com>
>>> wrote:
>>>
>>>> ReadAffy constructs a matrix which is probes x samples. If the array is
>>>> big enough, perhaps several thousand samples is enough to push a matrix
>>>> over the internal R limits.
>>>>
>>>> Which array is this?
>>>>
>>>> Kasper
>>>>
>>>>
>>>> On Fri, Aug 2, 2013 at 4:17 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
>>>>
>>>> > 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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>>
>>
>> --
>> Matthew N McCall, PhD
>> 112 Arvine Heights
>> Rochester, NY 14611
>> Cell: 202-222-5880
>>
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