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

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