[BioC] Oligo error on OS X Leopard

[cstrato]

Dear Daniel

As Vincent already mentioned, one alternative is package xps, which can 
easily handle many exon CEL-files on computers with 1 GB RAM only 
(another alternative would be package aroma.affymetrix).

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
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Vincent Carey wrote:
> it looks like 10GB is simply not enough.  on a fairly large machine i just read
> 33 _mouse_ exon 1.0 st arrays using oligo::read.celfiles and noted that the
> memory consumption did rise above 10GB (but not by much) after parsing.
>
> you didn't include your sessionInfo() output but that could be useful.
>
> it remains to be seen whether one could profitably chop up the parsing
> with oligo
> into blocks and then combine the results into something useful given this
> RAM limitation.  other approaches for these arrays include exonmap and xps
> but illustration of a complete oligo-based workflow for these arrays
> should be forthcoming
> soon
>
> On Tue, Jun 23, 2009 at 6:17 AM, Daniel Brewer<daniel.brewer at icr.ac.uk> wrote:
>   
>> Just trying out the oligo package on some Human Exon 1.0 ST microarrays
>> and I get an error while doing a read.celfiles.  I am running OS X
>> Leopard on a macpro with 10GB memory.
>>
>>     
>>> yoda <- read.celfiles(list.celfiles("CEL",full.names=T))
>>>       
>> Platform design info loaded.
>> Reading in : CEL/1208_CoC(3)25_ExH_PRC125.CEL
>> Reading in : CEL/1208_CoC(3)26_ExH_PRC126.CEL
>> Reading in : CEL/1208_CoC(3)27_ExH_PRC127.CEL
>> Reading in : CEL/1208_CoC(3)28_ExH_PRC128.CEL
>> Reading in : CEL/1208_CoC(3)29_ExH_PRC129.CEL
>> Reading in : CEL/1208_CoC(3)30_ExH_PRC130.CEL
>> Reading in : CEL/1208_CoC(3)31_ExH_NP1.CEL
>> Reading in : CEL/1208_CoC(3)32_ExH_NP2.CEL
>> Reading in : CEL/1208_CoC(3)33_ExH_NP3.CEL
>> Reading in : CEL/1208_CoC(3)34_ExH_NP4.CEL
>> Reading in : CEL/1208_CoC(3)35_ExH_NP5.CEL
>> Reading in : CEL/1208_CoC(3)36_ExH_NP6.CEL
>> Reading in : CEL/1208_CoC(3)37_ExH_NP7.CEL
>> Reading in : CEL/1208_CoC(3)38_ExH_ST1.CEL
>> R(2640) malloc: *** mmap(size=734007296) failed (error code=12)
>> *** error: can't allocate region
>> *** set a breakpoint in malloc_error_break to debug
>> R(2640) malloc: *** mmap(size=734007296) failed (error code=12)
>> *** error: can't allocate region
>> *** set a breakpoint in malloc_error_break to debug
>> Error: cannot allocate vector of size 700.0 Mb
>>
>>
>> Any ideas whats going on?
>>
>> Dan
>>
>> --
>> **************************************************************
>> Daniel Brewer, Ph.D.
>>
>> Institute of Cancer Research
>> Molecular Carcinogenesis
>> Email: daniel.brewer at icr.ac.uk
>> **************************************************************
>>
>> The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.
>>
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>>
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>>     
>
>
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