[R] A question about gc()
wangtong at usc.edu
Wed Sep 6 10:24:46 CEST 2006
Yes, I am using R in windows, sorry for not being specific.
You are right, I have stored too much stuff, and I need to trash some data in the process.
Problem solved for me, Thank you very much.
----- Original Message -----
From: Prof Brian Ripley <ripley at stats.ox.ac.uk>
Date: Tuesday, September 5, 2006 3:42 am
Subject: Re: [R] A question about gc()
To: Tong Wang <wangtong at usc.edu>
Cc: R help <r-help at stat.math.ethz.ch>
> On Tue, 5 Sep 2006, Tong Wang wrote:
> > Hi everyone,
> > I am doing some intensive computation: 50000 regressions of
> > form Y~X with each y of size (1,1000) , even if I break invoke
> gc() for
> > a few time in the loop, it still breaks down at some point with
> > error message:
> gc() does not reclaim memory for you beyond what R has already done.
> > Error in .signalSimpleWarning("Reached total allocation of
> 1024Mb: see help(memory.size)", :
> > recursive default argument reference
> > After getting this, even if I call gc() and resume the
> computation, it
> > won't move at all. May I get some suggestions what should I do to
> > around this problem ?
> Consult the rw-FAQ (since you seem to be using Windows without
> telling us)
> and the help page the message mentions.
> It looks as if you are trying to store too many objects. If you
> have lots
> of RAM you can increase that limit (see the previous para), but you
> getting uncomfortably close to the address space limit of your OS.
> Perhaps you can only save the part of the fit you need, or save()
> objects to separate files and rm() them, and postprocess them in a
> Brian D. Ripley, ripley at stats.ox.ac.uk
> Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
> University of Oxford, Tel: +44 1865 272861 (self)
> 1 South Parks Road, +44 1865 272866 (PA)
> Oxford OX1 3TG, UK Fax: +44 1865 272595
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