[BioC] Oligo error on OS X Leopard

[Tobias Straub]

Hi Dan,

are you running 64bit R?
what's your output of .Machine$sizeof.pointer

Tobias

On Jun 23, 2009, at 12:17 PM, Daniel Brewer 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
> **************************************************************
>
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