[BioC] Oligo error on OS X Leopard

[Vincent Carey]

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
> **************************************************************
>
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-- 
Vincent Carey, PhD
Biostatistics, Channing Lab
617 525 2265