Entering edit mode
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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> PLEASE do read the posting guide http://www.R-project.org/posting-
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> and provide commented, minimal, self-contained, reproducible code.
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
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