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

[Peng Yu]

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.

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