[BioC] make.cdf.package: Error: cannot allocate vector of size 1 Kb

[Wolfgang Huber]

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
> 
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--
Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber/contact