[R] cannot allocate vector

[Prof Brian Ripley]

On Wed, 17 Mar 2004, Matt Loveland wrote:

> I'm having trouble with glmmPQL.

I think you are having trouble with memory limits, actually.  As the 
author of glmmPQL, I don't appreciate my code being blamed for something 
else.

> I'm fitting a 2 level random intercept model, with 90,000 cases and about 330 groups.  I'm unable to get any results on the full data set.  I can get it to work if I sample down to about 30,000 cases.  But for models with N's much larger than that I get the following warning message:
> 
>  m3=glmmPQL(prepfood~iage+iemployed+iwhite+ieduclevl+imarried+servcomm+leadgrup+leadsty4, family=binomial, random=~1|congrega1,data=data)
> Error: cannot allocate vector of size 4135 Kb
> In addition: Warning message: 
> Reached total allocation of 253Mb: see help(memory.size) 
> 
> I've tried increasing my virtual memory size, and also defragmenting my
> hard drive.  It hasn't helped.  I've seen other people asking similar
> questions on the archive, but it seems that this problem should have
> gone away after earlier versions of R, is that right?

Do read the page it asks you too.  You are on Windows, and you need to use 
the --max-mem-size flag when starting R to increase the memory available 
to R.  However, if you do swapping may make your machine nigh unusable.

What did you not understand about help(memory.size)?
This is also in the rw-FAQ: what in that did you not understand?

> Is this a data problem, am I fitting a bad model, or is it a memory size
> problem.  I'm hoping the last one, and any help is appreciated.

Yes, so try a machine with 2Gb RAM.

-- 
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