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 <[email protected]> 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 <[email protected]> >>> 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 >>>>> <[email protected]> >>>>> 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 <[email protected]> >>>>> 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 >>>>> >>>> [email protected] >>>>> >>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/datatable-help >>>>> >>>> >>>>> >>> >>>>> >>> >>>>> >> >>>>> > >>>>> > >>>>> > _______________________________________________ >>>>> > datatable-help mailing list >>>>> > [email protected] >>>>> > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/datatable-help >>>> >>>> >>>> _______________________________________________ >>>> datatable-help mailing list >>>> [email protected] >>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/datatable-help >>> >> >> > _______________________________________________ datatable-help mailing list [email protected] https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/datatable-help
