[BioC] make.cdf.package: Error: cannot allocate vector of size 1 Kb
Wolfgang Huber
whuber at embl.de
Mon Dec 28 09:38:47 CET 2009
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
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