[datatable-help] Random segfaults

Chris Neff caneff at gmail.com
Fri Dec 16 15:38:28 CET 2011 

On the current latest SVN build, with debugging enabled as listed
below, I get the following when trying to even print the contents of a
data.table:

Error in do.call("cbind", lapply(x, format, justify = justify, ...)) :
  'getCharCE' must be called on a CHARSXP

Never saw this error without debugging.  I tried printing a few times
in a row, got this same error, and then like the 4th time it
segfaulted.

Having a hard time reproducing that, but at least it is something?


On 15 December 2011 15:05, Matthew Dowle <mdowle at mdowle.plus.com> wrote:
>
> One thought ... how about turning on debugging. That way when it crashes
> at least you can report the file and line number. Btw, I've installed
> 2.12.0 on 64bit in case that managed to reproduce, but it still works
> for me ok as does 32bit 2.12.0, and both 32 and 64bit 2.14.0. So we're
> left with you debugging at your end, but should be fairly easy ...
>
> sudo MAKEFLAGS='CFLAGS=-O0\ -g\ -Wall\ -pedantic' R CMD INSTALL
> data.table_1.7.7.tar.gz
>
> R -d gdb
>
> run
>
> Do the stuff that crashes it.  Does it report a C file and line number?
>
> Just to rule out possible svn / R CMD build strangeness, please also use
> the data.table_1.7.7.tar.gz that's on CRAN.  It still hasn't run checks
> for 1.7.7 so on tenterhooks for that.
>
>
>
> On Thu, 2011-12-15 at 12:26 -0500, Chris Neff wrote:
>> Just to come back, it still crashes at seemingly random times.   I'm
>> reverting back to an earlier version (1.7.1) to see if that fixes my
>> problem.
>>
>> On 15 December 2011 11:08, Chris Neff <caneff at gmail.com> wrote:
>> > Internal build of R. Can't upgrade until they do.  I think it is
>> > unlikely to see 2.14 any time soon.
>> >
>> > On 15 December 2011 10:50, Steve Lianoglou
>> > <mailinglist.honeypot at gmail.com> wrote:
>> >> Hi,
>> >>
>> >> Out of curiosity, is it impossible for you to upgrade R to the latest, or?
>> >>
>> >> -steve
>> >>
>> >>
>> >> On Thu, Dec 15, 2011 at 10:42 AM, Chris Neff <caneff at gmail.com> wrote:
>> >>> I always use svn up. I'll reboot and reinstall just to make sure. As
>> >>> for reproducible, it still doesn't seem to crash in any consistent
>> >>> place but I'll give it a stronger try with a test data set.
>> >>>
>> >>> All 480 tests in test.data.table() completed ok in 7.395sec
>> >>> R version 2.12.1 (2010-12-16)
>> >>> Platform: x86_64-pc-linux-gnu (64-bit)
>> >>>
>> >>> locale:
>> >>>  [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
>> >>> LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
>> >>>  [5] LC_MONETARY=C             LC_MESSAGES=en_US.utf8
>> >>> LC_PAPER=en_US.utf8       LC_NAME=C
>> >>>  [9] LC_ADDRESS=C              LC_TELEPHONE=C
>> >>> LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
>> >>>
>> >>> attached base packages:
>> >>> [1] stats     graphics  grDevices utils     datasets  grid
>> >>> methods   base
>> >>>
>> >>> other attached packages:
>> >>> [1] hexbin_1.26.0      lattice_0.19-33    RColorBrewer_1.0-5
>> >>> data.table_1.7.8   ggplot2_0.8.9      reshape_0.8.4
>> >>> [6] plyr_1.6
>> >>>
>> >>> On 15 December 2011 09:52, Matthew Dowle <mdowle at mdowle.plus.com> wrote:
>> >>>>
>> >>>> And you did an 'svn up' (or equivalent)? Grabbing daily tar.gz snapshot
>> >>>> from R-Forge won't include the fix yet. So svn up, then R CMD build, then
>> >>>> R CMD INSTALL, right? (Just checking quick basics first).
>> >>>>
>> >>>>> Result of test.data.table(), sessionInfo() and confirm it's a clean
>> >>>>> install after a reboot to make sure no old .so is still knocking around
>> >>>>> somehow please. Definitely installed to the right library? If it's
>> >>>>> crashing a lot then it should be reproducible?
>> >>>>> Still waiting for CRAN check results for 1.7.7 in old-rel. If it's not
>> >>>>> fixed there either that'll help to know....
>> >>>>>
>> >>>>>> Latest SVN version, no alloccol set, still crashing a lot.  I don't
>> >>>>>> use [<- or $<-, the only times I modify a data.table are with :=  or
>> >>>>>> by doing DT=merge(DT,blah).
>> >>>>>>
>> >>>>>> Any more info I can provide?
>> >>>>>>
>> >>>>>> On 15 December 2011 08:32, Matthew Dowle <mdowle at mdowle.plus.com> wrote:
>> >>>>>>> Great fingers and toes crossed. If you could unset alloccol option just
>> >>>>>>> to
>> >>>>>>> be sure please, that would be great. You're our best hope of confirming
>> >>>>>>> it's fixed since it was biting you several times an hour. If you use
>> >>>>>>> [<-
>> >>>>>>> or $<- syntax then R will copy via *tmp* and at that point the *tmp*
>> >>>>>>> data.table is similar to a data.table loaded from disk in that it isn't
>> >>>>>>> over-allocated anymore, I realised. Also a copy() will lose
>> >>>>>>> over-allocation until the next column addition.  That 'should' all be
>> >>>>>>> fine
>> >>>>>>> now in both <=2.13.2 and >=2.14.0, although the bug was something
>> >>>>>>> simpler.
>> >>>>>>>
>> >>>>>>> 1.7.7 is on CRAN now and been built for windows so if CRAN check
>> >>>>>>> results
>> >>>>>>> tick over from "ERROR" to "OK" later today (for both windows and mac
>> >>>>>>> old-rel), and, you're ok too, then it's fixed.
>> >>>>>>>
>> >>>>>>>
>> >>>>>>>> I've updated to the latest SVN version, and I'll be sure to let you
>> >>>>>>>> know if it still crashes (however I do have the alloccol option set to
>> >>>>>>>> 1000, so I shouldn't be bumping into reallocation very often). Thanks
>> >>>>>>>> for finding the bug so fast!
>> >>>>>>>>
>> >>>>>>>> On 14 December 2011 19:56, Matthew Dowle <mdowle at mdowle.plus.com>
>> >>>>>>>> wrote:
>> >>>>>>>>>
>> >>>>>>>>> Hm. Sounds like it could be a different problem then if it was in R
>> >>>>>>>>> 2.14. There have been quite a few fixes since 1.7.4 so if you can
>> >>>>>>>>> reproduce with 1.7.7 would be great.  Or, we've sometimes seen that
>> >>>>>>>>> just
>> >>>>>>>>> after a package upgrade that a clean re-install can often fix things.
>> >>>>>>>>> Perhaps if the .so was in use by another R process or a zombie, or
>> >>>>>>>>> something. R seems to report data.table v1.7.4 (say) but it hasn't
>> >>>>>>>>> fully
>> >>>>>>>>> installed it properly and is still (perhaps partially) at 1.7.3. So
>> >>>>>>>>> quit
>> >>>>>>>>> all R (reboot to clear zombies too perhaps) and try reinstalling
>> >>>>>>>>> using
>> >>>>>>>>> R
>> >>>>>>>>> CMD INSTALL. Next time it happens I mean. Can also run
>> >>>>>>>>> test.data.table()
>> >>>>>>>>> to check the install.
>> >>>>>>>>>
>> >>>>>>>>> On Wed, 2011-12-14 at 17:40 +0000, Timothée Carayol wrote:
>> >>>>>>>>>> Hi --
>> >>>>>>>>>>
>> >>>>>>>>>> I have been having many unreproducible bugs with R 2.14, data.table
>> >>>>>>>>>> 1.7.4 and ubuntu 64 bits about 10 days ago. Data was getting
>> >>>>>>>>>> corrupted, and then R crashed. I had to go back to data.frame for
>> >>>>>>>>>> the
>> >>>>>>>>>> bits of code affected. I was doing a lot of rather unsafe
>> >>>>>>>>>> manipulations with row names, rbind and cbinds.
>> >>>>>>>>>> I didn't file a report, nor signal it, as it was occurring seemingly
>> >>>>>>>>>> at random, and I was doing operations which aren't really what
>> >>>>>>>>>> data.table was made for (tons of little manipulations on small
>> >>>>>>>>>> data);
>> >>>>>>>>>> still I guess I should now signal that 2.14 didn't fix everything
>> >>>>>>>>>> for
>> >>>>>>>>>> me. I do not know whether bugs subsist on post-1.7.4 versions.
>> >>>>>>>>>>
>> >>>>>>>>>> t
>> >>>>>>>>>>
>> >>>>>>>>>> On Wed, Dec 14, 2011 at 5:31 PM, Matthew Dowle
>> >>>>>>>>>> <mdowle at mdowle.plus.com>
>> >>>>>>>>>> wrote:
>> >>>>>>>>>> >
>> >>>>>>>>>> > Maybe, worth a try. Are you loading any data.table objects from
>> >>>>>>>>>> disk?
>> >>>>>>>>>> >
>> >>>>>>>>>> >> 64 bit 2.12.1 linux.
>> >>>>>>>>>> >>
>> >>>>>>>>>> >> Is there an option I can set in my session in order to work
>> >>>>>>>>>> around
>> >>>>>>>>>> the
>> >>>>>>>>>> >> truelength issue? I don't care if I lose some of the
>> >>>>>>>>>> over-allocation
>> >>>>>>>>>> >> niceties if it stops things from crashing. Looking at the
>> >>>>>>>>>> truelength
>> >>>>>>>>>> >> help, would just doing:
>> >>>>>>>>>> >>
>> >>>>>>>>>> >> options(datatable.alloc=quote(1000))
>> >>>>>>>>>> >>
>> >>>>>>>>>> >> stop this? I never have more than about 50 columns at a time.
>> >>>>>>>>>> >>
>> >>>>>>>>>> >> On 14 December 2011 11:43, Matthew Dowle <mdowle at mdowle.plus.com>
>> >>>>>>>>>> wrote:
>> >>>>>>>>>> >>>
>> >>>>>>>>>> >>> You're R < 2.14.0, right?  I'm really struggling in R < 2.14.0
>> >>>>>>>>>> to
>> >>>>>>>>>> make
>> >>>>>>>>>> >>> over-allocation work because R only started to initialize
>> >>>>>>>>>> truelength to
>> >>>>>>>>>> >>> 0
>> >>>>>>>>>> >>> in R 2.14.0+. Before that it's unitialized (random). Trouble is
>> >>>>>>>>>> my
>> >>>>>>>>>> >>> attempts in R < 2.14.0 to work around that work fine for me in
>> >>>>>>>>>> linux
>> >>>>>>>>>> >>> 32bit
>> >>>>>>>>>> >>> when I test in R 2.13.2, and I even test in 2.12.0 too. I test
>> >>>>>>>>>> on
>> >>>>>>>>>> 64bit
>> >>>>>>>>>> >>> too but just 2.14.0.  CRAN is also showing errors on 2.13.2
>> >>>>>>>>>> (old-rel)
>> >>>>>>>>>> >>> for
>> >>>>>>>>>> >>> both mac and windows.
>> >>>>>>>>>> >>>
>> >>>>>>>>>> >>> So, this is a pre-2.14.0 (only) problem that I'll continue to
>> >>>>>>>>>> try
>> >>>>>>>>>> and
>> >>>>>>>>>> >>> fix.
>> >>>>>>>>>> >>>
>> >>>>>>>>>> >>> Are you 64bit pre-2.14.0? Which OS?  If you are 64bit linux then
>> >>>>>>>>>> it
>> >>>>>>>>>> adds
>> >>>>>>>>>> >>> weight to me installing pre-2.14.0 on my 64bit instance in an
>> >>>>>>>>>> effort to
>> >>>>>>>>>> >>> reproduce.
>> >>>>>>>>>> >>>
>> >>>>>>>>>> >>>
>> >>>>>>>>>> >>>> This will be a crappy help request because I can't seem to
>> >>>>>>>>>> reproduce
>> >>>>>>>>>> >>>> it, but the past few days I've been getting a lot of segfaults.
>> >>>>>>>>>>  The
>> >>>>>>>>>> >>>> only common thing between every crash is that it happens when I
>> >>>>>>>>>> do
>> >>>>>>>>>> >>>>
>> >>>>>>>>>> >>>> DT[, z := x]
>> >>>>>>>>>> >>>>
>> >>>>>>>>>> >>>> where z was not a column that existed in DT before, and x is
>> >>>>>>>>>> either an
>> >>>>>>>>>> >>>> existing column of DT or a separate variable, doesn't matter.
>> >>>>>>>>>>  Beyond
>> >>>>>>>>>> >>>> that I can't reproduce a set of steps that gets R to crash.
>> >>>>>>>>>>  This
>> >>>>>>>>>> is
>> >>>>>>>>>> >>>> with the latest SVN version.
>> >>>>>>>>>> >>>>
>> >>>>>>>>>> >>>> Is there more information I can provide to help track this
>> >>>>>>>>>> down?
>> >>>>>>>>>> >>>> _______________________________________________
>> >>>>>>>>>> >>>> datatable-help mailing list
>> >>>>>>>>>> >>>> datatable-help at lists.r-forge.r-project.org
>> >>>>>>>>>> >>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/datatable-help
>> >>>>>>>>>> >>>>
>> >>>>>>>>>> >>>
>> >>>>>>>>>> >>>
>> >>>>>>>>>> >>
>> >>>>>>>>>> >
>> >>>>>>>>>> >
>> >>>>>>>>>> > _______________________________________________
>> >>>>>>>>>> > datatable-help mailing list
>> >>>>>>>>>> > datatable-help at lists.r-forge.r-project.org
>> >>>>>>>>>> > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/datatable-help
>> >>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>> _______________________________________________
>> >>>>>>>>> datatable-help mailing list
>> >>>>>>>>> datatable-help at lists.r-forge.r-project.org
>> >>>>>>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/datatable-help
>> >>>>>>>>
>> >>>>>>>
>> >>>>>>>
>> >>>>>>
>> >>>>>
>> >>>>>
>> >>>>> _______________________________________________
>> >>>>> datatable-help mailing list
>> >>>>> datatable-help at lists.r-forge.r-project.org
>> >>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/datatable-help
>> >>>>>
>> >>>>
>> >>>>
>> >>> _______________________________________________
>> >>> datatable-help mailing list
>> >>> datatable-help at lists.r-forge.r-project.org
>> >>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/datatable-help
>> >>
>> >>
>> >>
>> >> --
>> >> Steve Lianoglou
>> >> Graduate Student: Computational Systems Biology
>> >>  | Memorial Sloan-Kettering Cancer Center
>> >>  | Weill Medical College of Cornell University
>> >> Contact Info: http://cbio.mskcc.org/~lianos/contact
>
>

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