On Fri, 2 Feb 2007, Sicotte, Hugues Ph.D. wrote: > Of course, you would know best, so can you tell us if the help pages I > pull using > > help(Memory) > > is wrong? > That help page says (2nd paragraph) > > "(On Windows the --max-mem-size option sets the maximum memory > allocation: it has a minimum allowed value of 16M. This is intended to > catch attempts to allocate excessive amounts of memory which may cause > other processes to run out of resources. The default is the smaller of > the amount of physical RAM in the machine and 1024Mb. See also > memory.limit.) "
It says nothing about 'half' does it? Depending on your version of R and Windows, the default is 1Gb, 1.5Gb or 2.5Gb, and the rw-FAQ gives the whole truth. The current version of that help page is different: https://svn.r-project.org/R/trunk/src/library/base/man/Memory.Rd it looks like in 2.4.1 it had not been updated yet. > > > Hugues > > -----Original Message----- > From: Prof Brian Ripley [mailto:[EMAIL PROTECTED] > Sent: Friday, February 02, 2007 3:05 AM > To: Sicotte, Hugues Ph.D. > Cc: Tristan Coram; R-help@stat.math.ethz.ch > Subject: Re: [R] Affymetrix data analysis > > On Thu, 1 Feb 2007, Sicotte, Hugues Ph.D. wrote: > >> Tristan, >> I have a soft spot for problems analyzing microarrays with R.. >> >> for the memory issue, there have been previous posts to this list.. >> But here is the answer I gave a few weeks ago. >> If you need more memory, you have to move to linux or recompile R for >> windows yourself.. >> .. But you'll still need a computer with more memory. >> The long term solution, which we are implementing, is to rewrite the >> normalization code so it doesn't >> Need to load all those arrays at once. >> >> -- cut previous part of message-- >> The defaults in R is to play nice and limit your allocation to half >> the available RAM. Make sure you have a lot of disk swap space (at > least >> 1G with 2G of RAM) and you can set your memory limit to 2G for R. > > That just isn't true (R uses as much of the RAM as is reasonable, all > for > up to 1.5Gb installed). Please consult the rw-FAQ for the whole truth. > >> See help(memory.size) and use the memory.limit function > > [Please follow the advice you quote.] > >> Hugues >> >> >> P.s. Someone let me use their 16Gig of RAM linux >> And I was able to run R-64 bits with "top" showing 6Gigs of RAM >> allocated (with suitable --max-mem-size command line parameters at >> startup for R). > > There is no such 'command' for R under Linux. > > > -- 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@stat.math.ethz.ch 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.