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Question: problems with "cannot allocate vector of size.."
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gravatar for Manuela Di Russo
6.6 years ago by
Manuela Di Russo70 wrote:
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,a s.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@for.unipi.it tel: +39050993538 [[alternative HTML version deleted]]
ADD COMMENTlink modified 6.6 years ago by Wolfgang Huber13k • written 6.6 years ago by Manuela Di Russo70
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gravatar for Wolfgang Huber
6.6 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:
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,a s.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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Best wishes Wolfgang Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
ADD COMMENTlink written 6.6 years ago by Wolfgang Huber13k
Or (iii) a computer under UNIX or LINUX? Simon No?l 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 f?vrier 2012 15:57 ? : 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,a s.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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Best wishes Wolfgang Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 6.6 years ago by SimonNoël450
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