[R-SIG-Mac] R and Valgrind hangs on Snow Leopard
Prof Brian Ripley
ripley at stats.ox.ac.uk
Wed Aug 15 11:02:49 CEST 2012
Erika tracked this down to a known issue with valgrind and (C-level)
system calls. See https://bugs.kde.org/show_bug.cgi?id=301281
I've added a workaround in R-patched/R-devel: set the environment
variable R_OSX_VALGRIND (to anything), preferably before starting the
session but I guess it would also work from the R session. This
circumvents the system call used to remove the session temporary
directory at the end of the session.
On 13/08/2012 13:14, Prof Brian Ripley wrote:
> On Mon, 13 Aug 2012, Cule, Erika wrote:
>> (Reposted in plain text, with apologies)
>> I am having the problem described in this post:
>> In summary, running Valgrind with R hangs.
>> As in the linked case above, if a file test.R contains the single
>> command print(seq(10))
>> Then running the command
>> R -d "valgrind --tool=memcheck --leak-check=full" --vanilla < test.R
>> Produces the following output and hangs
>> ==78868== Memcheck, a memory error detector
>> ==78868== Copyright (C) 2002-2012, and GNU GPL'd, by Julian Seward et al.
>> ==78868== Using Valgrind-3.9.0.SVN and LibVEX; rerun with -h for
>> copyright info
>> ==78868== Command:
>> /Library/Frameworks/R.framework/Resources/bin/exec/x86_64/R --vanilla
>> ==78868== Warning: ignored attempt to set SIGUSR2 handler in sigaction();
>> ==78868== the SIGUSR2 signal is used internally by Valgrind
>> R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
>> Copyright (C) 2012 The R Foundation for Statistical Computing
>> ISBN 3-900051-07-0
>> Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit)
>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>> You are welcome to redistribute it under certain conditions.
>> Type 'license()' or 'licence()' for distribution details.
>> Natural language support but running in an English locale
>> R is a collaborative project with many contributors.
>> Type 'contributors()' for more information and
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>>  1 2 3 4 5 6 7 8 9 10
>> I have followed the advice previously posted by Simon, used the SVN
>> build of valgrind and recompiled R from source with
>> I am running Mac OS X 10.6.8, valgrind-3.9.0.SVN, R version 2.15.1 and
>> Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit).
>> As was the case for the previous poster, a command such as
>> valgrind ls
>> works as expected.
>> I noted that Simon said he had no problem using valgrind from SVN on
>> both Lion and Snow Leopard. Does anyone have any suggestion of what I
>> might be doing differently, or what I could do to fix this problem?
> Not multiple post ... this is a second copy.
> It does not work for me on Lion (I've never tried Snow Leopard). As
> valgrind does not yet (even in the recent 3.8.0) really support Mountain
> Lion and we will be upgraded shortly (and BTW, Snow Leopard is now
> end-of-life for security patches), I've pretty much given up on valgrind
> on OS X.
Brian D. Ripley, ripley at stats.ox.ac.uk
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
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