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

[James MacDonald]

This problem may well be due to the repeated R_alloc calls, and might be fixable by refactoring the code, but I am not sure that is the answer here. This package is designed for the 3' biased arrays (and works well enough for them), and isn't intended to be used for the newer random primer arrays. The makecdfenv/affy packages have been supplanted by the pdInfoBuilder/oligo packages for the newer generation of arrays.

Crispin Miller's group was able to get makecdfenv to work by stripping out the background probes first, and have cdf packages available on their website if the end user insists on using affy for this array:

http://xmap.picr.man.ac.uk/download

which by the way appears to be down now.

Anyway, the supported methods of analyzing these chip types are listed in the workflows page

http://www.bioconductor.org/docs/workflows/oligoarrays/

and you will note that makecdfenv/affy is not one of them.

Best,

Jim

>>> Martin Morgan <mtmorgan at fhcrc.org> 12/28/09 2:09 PM >>>
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
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
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