[BioC] RE : problems with "cannot allocate vector of size.."

[Simon Noël]

Or (iii) a computer under UNIX or LINUX?

Simon Noël
CdeC
________________________________________
De : bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] de la part de Wolfgang Huber [whuber at embl.de]
Date d'envoi : 28 février 2012 15:57
À : bioconductor at r-project.org
Objet : Re: [BioC] problems with "cannot allocate vector of size.."

Ciao Manuela,

did you try using (i) a smaller dataset or (ii) a computer with more RAM?

        Best wishes
        Wolfgang

Feb/28/12 12:33 PM, Manuela Di Russo scripsit::
> Dear all,
> I have some problems with the error "cannot allocate vector of size..."
> I am using the Bioc package "arrayQualityMetrics" to assess the quality of a microarray experiment saved in an Affybatch object (rawData) but I encountered the same problem with oneChannelGUI package, when I apply the gcrma function.
> My pc has 3.37 GB RAM.
> I read several posts in the mailing list and I changed some parameters to increase the memory limit. For example I used the command  memory.limit (4095), I set paging file dimensions to 4092 MB (it was 2046 MB) and I used the 3 GB switch in the Boot.ini file in order to increase the virtual address space of processes and applications.
> Moreover I reduced the code lines in a single session to the strictly necessary commands.
>
> R version 2.14.1 (2011-12-22)
> Copyright (C) 2011 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> Platform: i386-pc-mingw32/i386 (32-bit)
>
>> memory.limit(4095)
> [1] 4095
>> setwd("C:/BACKUP/Dati/Progetti/Landi/meta-analisi MPM/GSE12345_RAW")
>> library(affy)
> Carico il pacchetto richiesto: Biobase
>
> Welcome to Bioconductor
>
>    Vignettes contain introductory material. To view, type
>    'browseVignettes()'. To cite Bioconductor, see
>    'citation("Biobase")' and for packages 'citation("pkgname")'.
>
>> pd<- read.AnnotatedDataFrame("target.txt",header=TRUE,row.names=1,as.is=TRUE)
>> rawData<- read.affybatch(filenames=pData(pd)$FileName,phenoData=pd)
>> library(arrayQualityMetrics)
>> a<-arrayQualityMetrics(rawData, outdir = "RawData QualityMetrics Report",force = TRUE, do.logtransform = TRUE)
> The report will be written into directory 'RawData QualityMetrics Report'.
> Loading required package: AnnotationDbi
>
> Errore: cannot allocate vector of size 30.0 Mb
>> sessionInfo()
> R version 2.14.1 (2011-12-22)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=Italian_Italy.1252  LC_CTYPE=Italian_Italy.1252
> [3] LC_MONETARY=Italian_Italy.1252 LC_NUMERIC=C
> [5] LC_TIME=Italian_Italy.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] hgu133plus2cdf_2.9.1       AnnotationDbi_1.16.17
> [3] arrayQualityMetrics_3.10.0 affy_1.32.1
> [5] Biobase_2.14.0
>
> loaded via a namespace (and not attached):
>   [1] affyio_1.22.0         affyPLM_1.30.0        annotate_1.32.1
>   [4] beadarray_2.4.1       BiocInstaller_1.2.1   Biostrings_2.22.0
>   [7] Cairo_1.5-1           cluster_1.14.2        DBI_0.2-5
> [10] genefilter_1.36.0     grid_2.14.1           Hmisc_3.9-2
> [13] hwriter_1.3           IRanges_1.12.6        lattice_0.20-0
> [16] latticeExtra_0.6-19   limma_3.10.2          preprocessCore_1.16.0
> [19] RColorBrewer_1.0-5    RSQLite_0.11.1        setRNG_2009.11-1
> [22] splines_2.14.1        survival_2.36-12      SVGAnnotation_0.9-0
> [25] tools_2.14.1          vsn_3.22.0            XML_3.9-4.1
> [28] xtable_1.7-0          zlibbioc_1.0.0
>> traceback()
> 4: density.default(as.matrix(log2(x$pm)))
> 3: density(as.matrix(log2(x$pm)))
> 2: aqm.pmmm(x)
> 1: arrayQualityMetrics(rawData, outdir = "RawData QualityMetrics Report",
>         force = TRUE, do.logtransform = TRUE)
>
> Can anyone suggest anything?
> Thank you!
> Have a nice day!
> Manuela
>
>
> ----------------------------------------------------------------------------------------
> Manuela Di Russo, Ph.D. Student
> Department of Experimental Pathology, MBIE
> University of Pisa
> Pisa, Italy
> e-mail: manuela.dirusso at for.unipi.it
> tel: +39050993538
>       [[alternative HTML version deleted]]
>
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--
Best wishes
        Wolfgang

Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber

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