Peng Yu wrote: > On Tue, Dec 29, 2009 at 1:08 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: >> 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. > > I haven't read the source code. Is it a bug in make.cdf.package? If > so, maybe we can reported it to the author. The package maintainer was cc'd on my email message. Martin > >>> On Mon, Dec 28, 2009 at 2:38 AM, Wolfgang Huber <whuber at="" 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 >>>>> 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 >>>> >>>> -- >>>> Wolfgang Huber >>>> EMBL >>>> http://www.embl.de/research/units/genome_biology/huber/contact >>>> >>>> >>>> >>> ______________________________________________ >>> R-help at 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 >> > > _______________________________________________ > 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 -- 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