My machine has 8GB memory. I had quit all other programs that might take a lot of memory when I try the script (before I post the first message in this thread). The cdf file is of only 741 MB. It is strange to me to see the error.
On Mon, Dec 28, 2009 at 2:38 AM, Wolfgang Huber <whu...@embl.de> wrote: > Dear Peng Yu > > how big is the RAM of your computer? You could try with closing all other > applications before running this script. You could try on a server with more > RAM. > > I tried downloading the file whose URL who give below, but gave up after > some failed rounds with the extraordinarily annoying and intrusive > registration procedure that Affymetrix has set up for this. Let us know how > it goes with the suggestions above, if they don't help, I'd try again with > that. > > Best wishes > Wolfgang > > >> I run the following example. The cdf file is downloaded from the >> following link. I'm wondering what the problem is with >> make.cdf.package. >> >> >> http://www.affymetrix.com/Auth/support/downloads/library_files/MoEx-1_0-st-v1.text.cdf.zip >> >> $ Rscript MoEx-1_0-st-v1.cdf.R >>> >>> library(makecdfenv) >> >> Loading required package: Biobase >> >> Welcome to Bioconductor >> >> Vignettes contain introductory material. To view, type >> 'openVignette()'. To cite Bioconductor, see >> 'citation("Biobase")' and for packages 'citation(pkgname)'. >> >> Loading required package: affy >> Loading required package: affyio >>> >>> sessionInfo() >> >> R version 2.10.0 (2009-10-26) >> x86_64-unknown-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] makecdfenv_1.24.0 affyio_1.14.0 affy_1.24.2 Biobase_2.6.1 >> >> loaded via a namespace (and not attached): >> [1] preprocessCore_1.8.0 >>> >>> make.cdf.package('MoEx-1_0-st-v1.text.cdf', species='Mus_musculus') >> >> Reading CDF file. >> Error: cannot allocate vector of size 1 Kb >> Execution halted >> >> _______________________________________________ >> Bioconductor mailing list >> bioconduc...@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > -- > Wolfgang Huber > EMBL > http://www.embl.de/research/units/genome_biology/huber/contact > > > ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
