[datatable-help] Random segfaults

[Matthew Dowle]

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
> >>>>
> >>>
> >>>
> >>
> >
> >
> > _______________________________________________
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