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

[Martin Morgan]

Peng Yu wrote:
> 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.

The package maintainer was cc'd on my email message. 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
>>>>>
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
>>>>> Bioconductor at stat.math.ethz.ch
>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>> Search the archives:
>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>
>>>> --
>>>> Wolfgang Huber
>>>> EMBL
>>>> http://www.embl.de/research/units/genome_biology/huber/contact
>>>>
>>>>
>>>>
>>> ______________________________________________
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>>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>
>> --
>> Martin Morgan
>> Computational Biology / Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N.
>> PO Box 19024 Seattle, WA 98109
>>
>> Location: Arnold Building M1 B861
>> Phone: (206) 667-2793
>>
> 
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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
Phone: (206) 667-2793