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