[BioC] problem with arrayQualityMetrics: cannot allocate vector

[Jarek Bryk]

Hello,
the problem is as in the subject, and here are the details:

> class(RG)
[1] "RGList"
attr(,"package")
[1] "limma"
> library(arrayQualityMetrics)
> library(convert)
> x=as(RG,"NChannelSet")
> class(x)
[1] "NChannelSet"
attr(,"package")
[1] "Biobase"

> arrayQualityMetrics(x,outdir="qc")
The report will be written in directory 'qc'. 
Error: cannot allocate vector of size 74.3 Mb
R(2581,0xa048a500) malloc: *** mmap(size=3899392) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
R(2581,0xa048a500) malloc: *** mmap(size=7794688) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
R(2581,0xa048a500) malloc: *** mmap(size=3899392) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
R(2581,0xa048a500) malloc: *** mmap(size=7794688) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
R(2581,0xa048a500) malloc: *** mmap(size=77922304) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
R(2581,0xa048a500) malloc: *** mmap(size=77922304) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
R(2581,0xa048a500) malloc: *** mmap(size=77922304) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug

> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] convert_1.26.0            marray_1.28.0             limma_3.6.6               arrayQualityMetrics_2.6.0
[5] affyPLM_1.26.0            preprocessCore_1.12.0     gcrma_2.22.0              affy_1.28.0              
[9] Biobase_2.10.0           

loaded via a namespace (and not attached):
 [1] affyio_1.18.0        annotate_1.28.0      AnnotationDbi_1.12.0 beadarray_2.0.1      Biostrings_2.18.0   
 [6] DBI_0.2-5            genefilter_1.32.0    grid_2.12.0          hwriter_1.2          IRanges_1.8.2       
[11] lattice_0.19-13      latticeExtra_0.6-14  RColorBrewer_1.0-2   RSQLite_0.9-2        simpleaffy_2.26.0   
[16] splines_2.12.0       stats4_2.12.0        survival_2.36-1      vsn_3.18.0           xtable_1.5-6 



RG is a result of importing 10 samples into limma from agilent scanner. Each sample is a 1M probe mouse custom CGH array. Is it a memory/performance problem? I have 4Gb of RAM + 2.4GHz Core2 Duo processor. I would be very grateful for any clues as to what is wrong and how to fix it...

Regards,
jarek

-- 
  Jarek Bryk | www.evolbio.mpg.de/~bryk
  Max Planck Institute for Evolutionary Biology 
  August Thienemann Str. 2 | 24306 Plön, Germany 
  tel. +49 4522 763 287 | bryk at evolbio.mpg.de