[R] some general advice sought on the use of gctorture()

Martin Morgan mtmorgan at fredhutch.org
Fri Apr 24 16:03:41 CEST 2015

On 04/24/2015 06:49 AM, Franckx Laurent wrote:
> Dear all
> I have bumped into the dreaded 'segfault' error type when running some C++
> code using .Call().

segfaults often involve invalid memory access at the C level that are best 
discovered via valgrind or similar rather than gctorture. A good way to spot 
these is to

(a) come up with a _minimal_ reproducible script test.R that takes just a few 
seconds to run and that tickles, at least some times, the segfault

(b) make sure that your package is compiled without optimizations and with 
debugging symbols, e.g., in  ~/.R/Makevars add the lines

   CFLAGS="-ggdb -O0"
   CXXFLAGS="-ggdb -O0"

(c) run the code under 'valgrind'

   R -d valgrind -f test.r

Look especially for 'invalid read' or 'invalid write' messages, and isolate 
_your_ code in the callback that the message produces.

There is a 'worked example' at


Of course this might lead to nothing, and then you'll be back to your original 
question about using gctorture or other strategies.

Martin Morgan

> I have already undertaken several attempts to debug the C++ code with gdb(),
> but until now I have been unable to pinpoint the origin of the problem. There
> are two elements that I think are puzzling (a) this .Call() has worked fine
> for about three years, for a variety of data (b)  the actual crash occurs at
> random points during the execution of the function (well, random from a human
> eye's point of view).
>> From what I understand in the "R extensions" manual, the actual problem may
>> have been around for a while before the actual call to the C++ code. As
>> recommended in the manual, I am now using  gctorture() to try to pinpoint
>> the origins of the problem. I can, alas, only confirm that gctorture() has
>> an enormous impact on execution time, even for operations that are normally
>> executed within the blink of an eye. From what I have seen until now,
>> executing all the R code before the crash with gctorture(TRUE) could take
>> months.
> I suppose then that the best way to proceed would be to proceed backward from
> the point where the crash occurs when gctorture(FALSE).
> I have tried to find some concrete examples of good practices in the use of
> gctorture() to identify memory problems in R, but most of what I have found
> on the web is simply a copy of the help page. Does anybody know more concrete
> and elaborated examples that could give an indication on how to best proceed
> further?
> Laurent Franckx, PhD Senior researcher sustainable mobility VITO NV |
> Boeretang 200 | 2400 Mol Tel. ++ 32 14 33 58 22| mob. +32 479 25 59 07 |
> Skype: laurent.franckx | laurent.franckx at vito.be | Twitter @LaurentFranckx
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