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
