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

[Peng Yu]

On Tue, Dec 29, 2009 at 1:08 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> 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.

I haven't read the source code. Is it a bug in make.cdf.package? If
so, maybe we can reported it to the author.

>> 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.
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>
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>