[R-SIG-Mac] R and Valgrind hangs on Snow Leopard

[Cule, Erika]

A patch for valgrind has fixed this problem. 

The fixed version is currently in the Valgrind source code repository, and will also be in the 3.8.1 release which the Valgrind developers hope can be made available in about a month or so. 

Thanks to Prof Ripley and Peter Dalgaard for their help on this issue, and to Julian Seward and Philippe Waroquiers (Valgrind developers) for the fix. 

Erika

On 15 Aug 2012, at 10:02, Prof Brian Ripley wrote:

> 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:
>>> 
>>> https://stat.ethz.ch/pipermail/r-sig-mac/2011-November/008848.html
>>> 
>>> 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==
>>> ==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
>>> 'citation()' on how to cite R or R packages in publications.
>>> 
>>> Type 'demo()' for some demos, 'help()' for on-line help, or
>>> 'help.start()' for an HTML browser interface to help.
>>> Type 'q()' to quit R.
>>> 
>>>> 
>>>> 
>>>> 
>>>> print(seq(10))
>>> [1]  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
>>> --with-valgrind-instrumentation=2
>>> 
>>> 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