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

[Martin Morgan]

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.

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
>>>
>>> _______________________________________________
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>>
>>
>> --
>> Wolfgang Huber
>> EMBL
>> http://www.embl.de/research/units/genome_biology/huber/contact
>>
>>
>>
> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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