Peng Yu wrote: > 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.
For me this tops out at about 13 gigs. The reason is I think in the C-level implementation details. R_alloc is called repeatedly during file parsing, where likely the author intends to Calloc / Free. Martin > > 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. -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 ______________________________________________ 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.
