Re: [R] Help with 'memory not mapped'

From: Ramon Diaz-Uriarte <>
Date: Fri, 07 Mar 2008 10:43:22 +0100

Dear Javier,

>From your description, it seems you are not the author of the C
function rrfunc, which is where the problem is probably located (the segmentation fault is most likely a pointer related problem where the C code is trying to do something with memory it should not be trying to do). Depending on the exact settings of your simulation, the state of your machine, etc
the problem will show up at one point or another. I'd get in touch with the author of the C code and let her/him know that there is a problem in it. Most of these are very quickly located using valgrind. Search on the archives and the manual (Writing R extensions) but a call such as

R -d "valgrind --tool=memcheck --leak-check=full --log-file=marian.valgrind.log" --vanilla < mariam1_2.R > mariam1_2.with.valgrind.Rout

after compiling the C code with the "-O1" (not -O2, as per default) flag.


On Fri, Mar 7, 2008 at 10:26 AM, <> wrote:
> Hi,
> I'm no expert programmer at all;
> I'm running an R script ("mariam1_2.R"). This scripts calls another
> script, which contains an R function, which .Call some C code.
> It runs several times without any problem, but sometimes I get the error:
> -------
> *** caught segfault ***
> address 0x1c404ec8, cause 'memory not mapped'
> Traceback:
> 1: .Call("rrfunc", as.double(dx), as.integer(nrows), as.integer(ncols),
> as.double(deltadt), as.character(binmaps), as.integer(ldd),
> as.double(downst),as.integer(outl), as.double(maxinte), as.double(nmn))
> 2: rrfuncR(dx, nrows, ncols, delta.t,binmaps.pathed,ldd,downst,
> out.index,interc,
> 3: eval.with.vis(expr, envir, enclos)
> 4: eval.with.vis(ei, envir)
> 5: source("rrprogv1_2.R")
> 6: eval.with.vis(expr, envir, enclos)
> 7: eval.with.vis(ei, envir)
> 8: source("mariam1_2.R")
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
> Selection:
> ---------------
> I've seen something related in the documentation, but it is not easy to
> understand it for me. I'm trying to perform a Monte Carlo analysis that
> calls the function iteratively. My question is why sometimes I can call
> forty or fifty times the function without any problem, and other times it
> crashes at the first, second or 6th time. Can you give me any advice?
> Thanks and best regards,
> Javier
> ______________________________________________
> mailing list
> PLEASE do read the posting guide
> and provide commented, minimal, self-contained, reproducible code.

Ramon Diaz-Uriarte
Statistical Computing Team
Structural Biology and Biocomputing Programme
Spanish National Cancer Centre (CNIO)

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Received on Fri 07 Mar 2008 - 09:46:31 GMT

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