I have been in contact with the team at valgrind. It seems the bug is this one:
https://bugs.kde.org/show_bug.cgi?id=301281 If you add your comment to this bug tracker, this will encourage the valgrind developers to fix it. I will post again to this thread if the bug is fixed in the next release of valgrind. Erika On 13 Aug 2012, at 14:10, peter dalgaard wrote: > > On Aug 13, 2012, at 14:14 , 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. > > I see the hang on Snow Leopard and Lion too. Something seems to be getting > stuck during wrapup. > > For whatever it is worth, I can make it snap out of it by attaching gdb to > the valgrind process in another window (gdb -p 8228), then type c to continue: > > > peter-dalgaards-iMac:tmp pd$ R -d "valgrind --tool=memcheck > --leak-check=full" --vanilla < test.R > ==8228== Memcheck, a memory error detector > ==8228== Copyright (C) 2002-2011, and GNU GPL'd, by Julian Seward et al. > ==8228== Using Valgrind-3.7.0 and LibVEX; rerun with -h for copyright info > ==8228== Command: /Library/Frameworks/R.framework/Resources/bin/exec/x86_64/R > --vanilla > ==8228== > ==8228== Warning: ignored attempt to set SIGUSR2 handler in sigaction(); > ==8228== 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-darwin9.8.0/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 >> > --8228:0:gdbsrv readchar: poll got -1 > ==8228== > ==8228== HEAP SUMMARY: > ==8228== in use at exit: 29,164,319 bytes in 14,301 blocks > ==8228== total heap usage: 30,708 allocs, 16,407 frees, 48,229,523 bytes > allocated > ==8228== > ==8228== LEAK SUMMARY: > ==8228== definitely lost: 0 bytes in 0 blocks > ==8228== indirectly lost: 0 bytes in 0 blocks > ==8228== possibly lost: 0 bytes in 0 blocks > ==8228== still reachable: 29,150,957 bytes in 14,232 blocks > ==8228== suppressed: 13,362 bytes in 69 blocks > ==8228== Reachable blocks (those to which a pointer was found) are not shown. > ==8228== To see them, rerun with: --leak-check=full --show-reachable=yes > ==8228== > ==8228== For counts of detected and suppressed errors, rerun with: -v > ==8228== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 5 from 5) > > > -- > Peter Dalgaard, Professor > Center for Statistics, Copenhagen Business School > Solbjerg Plads 3, 2000 Frederiksberg, Denmark > Phone: (+45)38153501 > Email: [email protected] Priv: [email protected] > _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
