On Fri, 21 Mar 2008, Georgios Marentakis wrote: > Dear all, > I am having a memory problem when analyzing a rather large data set with > nested factors in R. > The model is of the form X~A*B*(C/D/F) A,B,C,D,F being the independent > variables some of which are nested. > The problem occurs when using aov but also when using glm or lme. > In particular I get the following response, > > Error: cannot allocate vector of size 1.6 Gb > R(311,0xa000d000) malloc: *** vm_allocate(size=1733365760) failed (error > code=3) > R(311,0xa000d000) malloc: *** error: can't allocate region > R(311,0xa000d000) malloc: *** set a breakpoint in szone_error to debug > R(311,0xa000d000) malloc: *** vm_allocate(size=1733365760) failed (error > code=3) > R(311,0xa000d000) malloc: *** error: can't allocate region > R(311,0xa000d000) malloc: *** set a breakpoint in szone_error to debug > > This is on an Intel Mac with 2 GBytes of RAM running MacOS X vs. 10.4.11 > The very same result appears on an 8 core Intel Mac with 6 Gbytes of RAM and > on a Linux Box with 2 GBytes of RAM. > Is there a way to bypass this and let R allocate the necessary memory? Is > this a system problem? Would it be resolved in a mainframe for example?
It is not R which is failing to allocate the memory, but the OS. Most likely it is a 32-bit address space issue (1.6Gb is a large hole to find in a (probably) 3Gb address space), so you need a 64-bit OS (e.g. Mac OS 10.5) and a 64-bit version of R. > > thank you very much for your time, > georgios > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > -- Brian D. Ripley, [EMAIL PROTECTED] 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 ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
