Help with 'memory not mapped'

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.

HTH,

R.
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,n.man)
  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

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Ramon Diaz-Uriarte
Statistical Computing Team
Structural Biology and Biocomputing Programme
Spanish National Cancer Centre (CNIO)
http://ligarto.org/rdiaz

Help with 'memory not mapped'

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