Hi Marco, I just checked the page I gave you the link to and it appears that the options there are either i386 or amd64. :-( Maybe you'll need to compile from the source (the r-sig-debian folks will have the answer for sure). As you probably noticed, what you want to achieve is .Machine[["sizeof.pointer"]] == 8. b On Fri, Apr 16, 2010 at 8:04 PM, Manca Marco (PATH) <m.manca at="" path.unimaas.nl=""> wrote: > > Dear Benilton, > > thank you for the prompt reply. > > I suspect you are right. R had just been installed from the Canonical repository on this machine and it was a 32bit edition. > > Thank you for your suggestion and for pointing out the 64bit repositories. > > Just for the sake of completeness at this point, since you alread solved the puzzle, I attach the output of the command you suggested: > >> .Machine[["sizeof.pointer"]] > [1] 4 > > > All the best, Marco > > > -- > Marco Manca, MD > University of Maastricht > Faculty of Health, Medicine and Life Sciences (FHML) > Cardiovascular Research Institute (CARIM) > > Mailing address: PO Box 616, 6200 MD Maastricht (The Netherlands) > Visiting address: Experimental Vascular Pathology group, Dept of Pathology - Room5.08, ?Maastricht University Medical Center, P. Debeijelaan 25, 6229 ?HX Maastricht > > E-mail: m.manca at path.unimaas.nl > Office telephone: +31(0)433874633 > Personal mobile: +31(0)626441205 > Twitter: @markomanka > > > ******************************************************************** ************************************************* > > This email and any files transmitted with it are confidential and solely for the use of the intended recipient. > > It may contain material protected by privacy or attorney-client privilege. If you are not the intended recipient or the person responsible for > > delivering to the intended recipient, be advised that you have received this email in error and that any use is STRICTLY PROHIBITED. > > If you have received this email in error please notify us by telephone on +31626441205 Dr Marco MANCA > > ******************************************************************** ************************************************* > ________________________________________ > Da: Benilton Carvalho [beniltoncarvalho at gmail.com] > Inviato: venerd? 16 aprile 2010 18.47 > A: Manca Marco (PATH) > Cc: bioconductor mailing list > Oggetto: Re: [BioC] Memory and vector size management on linux 64bit > > what do you get when you run: > > .Machine[["sizeof.pointer"]] > > ? > > I'm really surprised by the "i486-pc-linux-gnu" bit from your > sessionInfo()... I'd expect something like x86_64, if you were running > a 64 bit version of R. > > Given that you're running Ubuntu, you're expected to follow the steps > as described by the page below: > > http://cran.ma.imperial.ac.uk/bin/linux/ubuntu/ > > b > > On Fri, Apr 16, 2010 at 5:30 PM, Manca Marco (PATH) > <m.manca at="" path.unimaas.nl=""> wrote: >> >> Dear fellow bioconductors, >> >> good afternoon. >> >> I am encountering an error concerning the allocations of vectors bigger than a certain size. My problem is that said size is far below the amount of RAM I have installed on the system. >> >> Following some previous threads on the topic I have at first thought that my RAM could have been temporarily unavailable thus I have monitored the memory usage and the error message appeared when just 2,5Gb were in use out of the about 7 Gb available. >> >> The system is running linux Ubuntu Hardy Heron 64bit, and it sports a Xeon CPU and 8Gb of RAM. >> >> Following I am pasting my code and my sessionInfo() >> >> # Charging my microArray data (44 human whole genome by Illumina) >>>library(lumi) >>>fileName <- "MyExperiment_no_32_no_tech_duplos.csv"; >>>library(lumiHumanAll.db) >>>Data.Immature <- lumiR(fileName, lib="lumiHumanAll.db"); >>>Data <- lumiExpresso(Data.Immature, QC.evaluation=TRUE); >> >> # Extract expression data from lumi object: >>>Expression <- exprs(Data) >>>names(Expression) <- Data at phenoData@data$sampleID >> >> # Calculate distance matrix for cluster analysis >>>distance=dist(Expression, method="euclidean") >> Error: cannot allocate vector of size 1.8 Gb >> >>> sessionInfo() >> R version 2.10.1 (2009-12-14) >> i486-pc-linux-gnu >> >> locale: >> ?[1] LC_CTYPE=en_US.UTF-8 ? ? ? LC_NUMERIC=C >> ?[3] LC_TIME=en_US.UTF-8 ? ? ? ?LC_COLLATE=en_US.UTF-8 >> ?[5] LC_MONETARY=C ? ? ? ? ? ? ?LC_MESSAGES=en_US.UTF-8 >> ?[7] LC_PAPER=en_US.UTF-8 ? ? ? LC_NAME=C >> ?[9] LC_ADDRESS=C ? ? ? ? ? ? ? LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >> >> other attached packages: >> ?[1] lumiHumanAll.db_1.8.1 org.Hs.eg.db_2.3.6 ? ?lumi_1.12.4 >> ?[4] MASS_7.3-5 ? ? ? ? ? ?RSQLite_0.8-3 ? ? ? ? DBI_0.2-5 >> ?[7] preprocessCore_1.8.0 ?mgcv_1.6-1 ? ? ? ? ? ?affy_1.24.2 >> [10] annotate_1.24.1 ? ? ? AnnotationDbi_1.8.1 ? Biobase_2.6.1 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.14.0 ? ? ?grid_2.10.1 ? ? ? ?lattice_0.18-3 ? ? Matrix_0.999375-37 >> [5] nlme_3.1-96 ? ? ? ?tools_2.10.1 ? ? ? xtable_1.5-6 >> >> >> >> Reading this page ( http://stat.ethz.ch/R-manual/R-patched/library/base/html/Memory.html ) I have come to hypothesize that there could be some vector size limit indipendent from the RAM availability, but I wonder whether it is true on a 64bit machine and how ?could I circumvent ?the problem: >> >> 1) any suggestion on how to modify the vector size threshold (if it exists)? >> >> 2) any suggestion on how to force the dist function to strip ?down the matrix into smaller vectors? >> >> >> Thank you in advance for your attention and for any feedback. >> >> All the best, Marco >> >> >> -- >> Marco Manca, MD >> University of Maastricht >> Faculty of Health, Medicine and Life Sciences (FHML) >> Cardiovascular Research Institute (CARIM) >> >> Mailing address: PO Box 616, 6200 MD Maastricht (The Netherlands) >> Visiting address: Experimental Vascular Pathology group, Dept of Pathology - Room5.08, ?Maastricht University Medical Center, P. Debeijelaan 25, 6229 ?HX Maastricht >> >> E-mail: m.manca at path.unimaas.nl >> Office telephone: +31(0)433874633 >> Personal mobile: +31(0)626441205 >> Twitter: @markomanka >> >> >> ******************************************************************* ************************************************** >> >> This email and any files transmitted with it are confide...{{dropped:15}} >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >