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Question: package "affy" & "simpleaffy"
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gravatar for Cherif Ben Hamda
4.6 years ago by
Tunisia
Cherif Ben Hamda150 wrote:
hello, I need help please, I show you the error mesage : > path = getwd() > celfiles <- read.affy(covdesc="phenodata.txt", path= path) Error: cannot allocate vector of size 310.1 Mb In addition: Warning messages: 1: In readLines(filename) : incomplete final line found on 'C:/Users/benilton/Desktop/gse324451354546/phenodata.txt' 2: In dimnames(elt) <- lapply(dimnames(elt), unname) : Reached total allocation of 1535Mb: see help(memory.size) 3: In dimnames(elt) <- lapply(dimnames(elt), unname) : Reached total allocation of 1535Mb: see help(memory.size) 4: In dimnames(elt) <- lapply(dimnames(elt), unname) : Reached total allocation of 1535Mb: see help(memory.size) 5: In dimnames(elt) <- lapply(dimnames(elt), unname) : Reached total allocation of 1535Mb: see help(memory.size) > sessionInfo() R version 3.0.3 (2014-03-06) Platform: i386-w64-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 LC_MONETARY=French_France.1252 LC_NUMERIC=C LC_TIME=French_France.1252 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] simpleaffy_2.38.0 gcrma_2.34.0 genefilter_1.44.0 BiocInstaller_1.12.0 affy_1.40.0 GEOquery_2.28.0 Biobase_2.22.0 [8] BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] affyio_1.30.0 annotate_1.40.1 AnnotationDbi_1.24.0 Biostrings_2.30.1 DBI_0.2-7 IRanges_1.20.7 preprocessCore_1.24.0 [8] RCurl_1.95-4.1 RSQLite_0.11.4 splines_3.0.3 stats4_3.0.3 survival_2.37-7 tools_3.0.3 XML_3.98-1.1 [15] xtable_1.7-3 XVector_0.2.0 zlibbioc_1.8.0 Thank you very much Best Cherif [[alternative HTML version deleted]]
ADD COMMENTlink modified 4.6 years ago by Vincent J. Carey, Jr.6.2k • written 4.6 years ago by Cherif Ben Hamda150
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gravatar for Vincent J. Carey, Jr.
4.6 years ago by
United States
Vincent J. Carey, Jr.6.2k wrote:
On Sun, Apr 13, 2014 at 7:16 AM, BEN HAMDA Cherif <cherifbenhamda@gmail.com>wrote: > hello, > I need help please, > I show you the error mesage : > > > > > path = getwd() > > celfiles <- read.affy(covdesc="phenodata.txt", path= path) > Error: cannot allocate vector of size 310.1 Mb > In addition: Warning messages: > 1: In readLines(filename) : > incomplete final line found on > 'C:/Users/benilton/Desktop/gse324451354546/phenodata.txt' > 2: In dimnames(elt) <- lapply(dimnames(elt), unname) : > Reached total allocation of 1535Mb: see help(memory.size) > 3: In dimnames(elt) <- lapply(dimnames(elt), unname) : > Reached total allocation of 1535Mb: see help(memory.size) > 4: In dimnames(elt) <- lapply(dimnames(elt), unname) : > Reached total allocation of 1535Mb: see help(memory.size) > 5: In dimnames(elt) <- lapply(dimnames(elt), unname) : > Reached total allocation of 1535Mb: see help(memory.size) > You are attempting to do computations that require more RAM than the computer you are using makes available to R. Have a look at ?memory.size as suggested, and at 8 Choosing between 32- and 64-bit builds in http://cran.r-project.org/doc/manuals/r-release/R-admin.html > > > sessionInfo() > R version 3.0.3 (2014-03-06) > Platform: i386-w64-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 > LC_MONETARY=French_France.1252 LC_NUMERIC=C > LC_TIME=French_France.1252 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] simpleaffy_2.38.0 gcrma_2.34.0 genefilter_1.44.0 > BiocInstaller_1.12.0 affy_1.40.0 GEOquery_2.28.0 > Biobase_2.22.0 > [8] BiocGenerics_0.8.0 > > loaded via a namespace (and not attached): > [1] affyio_1.30.0 annotate_1.40.1 AnnotationDbi_1.24.0 > Biostrings_2.30.1 DBI_0.2-7 IRanges_1.20.7 > preprocessCore_1.24.0 > [8] RCurl_1.95-4.1 RSQLite_0.11.4 splines_3.0.3 > stats4_3.0.3 survival_2.37-7 tools_3.0.3 > XML_3.98-1.1 > [15] xtable_1.7-3 XVector_0.2.0 zlibbioc_1.8.0 > > > > > > > Thank you very much > Best > Cherif > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD COMMENTlink written 4.6 years ago by Vincent J. Carey, Jr.6.2k
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