[BioC] problem with arrayQualityMetrics: cannot allocate vector

[Wolfgang Huber]

Hi Jarek

this is weird, and ugly. Thank you for reporting. Can you:

- make the object 'RG' available on a public fileserver for me & others 
to try to reproduce the error?

- can you set
     options(error=recover)
and then send us the output (error message and call stack) that you get? 
This will help localise where the problem happens.

- try on a different machine (with more RAM, or different OS)

- also try with arrayQualityMetrics_3.2.0 *and* SVGannotation_0.7-2 [1] 
(which fixes the problem with libcairo 1.10 that I reported earlier, 
https://stat.ethz.ch/pipermail/bioconductor/2010-October/035958.html - I 
planned to announce this fix as soon as SVGannotation_0.7-2 is on the 
build system in Seattle.)

[1] http://www.omegahat.org/SVGAnnotation

	Best wishes
	Wolfgang

Il Nov/8/10 2:07 PM, Jarek Bryk ha scritto:
> 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
>