stack overflow using step()

Please note the message is about the protect stack, and not the `stack'. 
The message you quote did not come from a current version of R (and you 
have not told us what version you are using, as asked in the posting 
guide).

Hi,
I'm using step() for forward regression with 680 main effects and the
correspomding 230860 interactions.

Hmm.  How many data points?  step() only tries 1000 steps by default.

However, the calculation is stopped with the message:
Error: protect(): stack overflow

How can I specify the maximum size of the pointer protection stack when running
R not from command line but in an emacs-subwindow?

Ask ESS questions on the ESS list please, as the FAQ does ask you.

How can I perform these calculations when the maximum value accepted is 
100000?

which is a lot larger than the default value (which depends on your 
unstated R version).

Without a lot more information it is unclear why the protection stack is 
being used up.  Please show us the last few lines of the output.

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