[datatable-help] Random segfaults

[Matthew Dowle]

I found and fixed one simple error that would definitely explain this in
R <= 2.13.2. Just committed fix. Please grab latest svn and try again. I
also added more checks and warnings in case that's not the only problem.


On Wed, 2011-12-14 at 13:00 -0500, Chris Neff wrote:
> It is crashing several times an hour for me to the point where this is
> unusable. Setting the alloccol option didn't help. Is there a way I
> can go back to the old shallow copy ways of 1.7.3?
> 
> 2011/12/14 Timothée Carayol <timothee.carayol at gmail.com>:
> > 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