On Thu, 2008-12-18 at 10:57 +0100, Peter Dalgaard wrote: > Martyn Plummer wrote: > > This has all the hallmarks of a bug I found and fixed in R-devel > > (r46998). I did not port the patch over to the R release branch because > > I could not reproduce the bug. > > > > In R-devel, I was seeing problems with "make test-Segfault". This would > > occasionally segfault, but most of the time would create the "bad value" > > error, and of course would also run perfectly fine a lot of the time. > > The error came from exactly the same place that Ben found. It was due > > to an invalid SrcRefs being used because SrcFile is not set to zero when > > it should be. > > > > I'll have a look and see if it is the same problem, or a close cousin. > > Yes, this does appear to fix the issue. (Did you forget a NEWS file > entry, though?)
You mean this? * Fixed obscure, poorly reproducible bug that nobody else has reported. Anyway, it's the same bug. There is a call to parse() in plot.mmfit() which generates a parse error. This has been wrapped in a silent call to try, so you never see the error message: Error in parse(text = colnames(z)[seq(1, 2 * np, 2)]) : unexpected numeric constant in "Parameter 1" This error leaves the parser in a bad state. > It's a two-line change fixing a live bug, so it could go in 2.8.1 even > in code freeze. The problem is that it is inside gram.y which will > trigger some maintainer-mode activity, and did trip up my Fedora laptop > slightly. Hmmmm.... > > -p Fedora 10 certainly won't let me do a maintainer mode build. I leave it in your hands. M. > > Martyn > > > > > > On Wed, 2008-12-17 at 22:07 -0500, Duncan Murdoch wrote: > >> On 17/12/2008 9:47 PM, Duncan Murdoch wrote: > >>> On 17/12/2008 8:56 PM, Peter Dalgaard wrote: > >>>> Ben Bolker wrote: > >>>>> I can get the errors to happen on Ubuntu 8.10 with R --vanilla > >>>>> (*without* > >>>>> valgrind) -- but > >>>>> editing momfit.r line 742 so that plot.progress=FALSE seems to make the > >>>>> problem go away. (This was a lucky guess, it looked like there was > >>>>> something > >>>>> odd going on with the plots.) > >>>>> > >>>>> Hope that helps someone ... > >>>> Probably not. The problem is to reproduce the error state in a way so > >>>> that we can understand what is causing it. > >>>> > >>>> I can debug this to > >>>> (gdb) bt > >>>> #0 Rf_error (format=0x8220c65 "bad value") at > >>>> ../../../R/src/main/errors.c:704 > >>>> #1 0x0805a924 in SETCDR (x=0x8f89348, y=0x9b276e8) > >>>> at ../../../R/src/main/memory.c:2728 > >>>> #2 0x0819fa46 in GrowList (l=0x951e8f4, s=<value optimized out>) at > >>>> gram.y:958 > >>>> #3 0x081a2a7b in xxvalue (v=0x8f89348, k=4, lloc=<value optimized out>) > >>>> at gram.y:440 > >>>> > >>>> and the problem in GrowList is that CAR(l) is R_NilValue (==0x8f89348), > >>>> which supposedly "cannot happen", and the thing that calls GrowList is > >>>> something with srcrefs (DuncanM?). > >>>> > >>>> Digging deeper probably has to wait till the weekend for my part. (The > >>>> natural next step is figuring out how the R_NilValue got into that > >>>> location, but I should try to sleep off this cold....) > >>>> > >>>> I'm CCing r-devel on this. Can we move the discussion there? > >>> I can probably take a look tomorrow. I wasn't getting an error, but > >>> maybe I'll see the same corruption if I watch it run. > >> I had time to see if I was getting a NilValue there tonight, and the > >> answer was no, with the Windows RC. I don't get the error in any > >> version I've tried on Windows, though I can see it in 2.8.0 on MacOSX. > >> > >> Duncan > >>> Duncan Murdoch > >>> > >>>> > >>>>> Ben Bolker > >>>>> > >>>>>> sessionInfo() > >>>>> R version 2.8.0 (2008-10-20) > >>>>> i486-pc-linux-gnu > >>>>> > >>>>> locale: > >>>>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C > >>>>> > >>>>> attached base packages: > >>>>> [1] stats graphics grDevices utils datasets methods base > >>> ______________________________________________ > >>> R-devel@r-project.org mailing list > >>> https://stat.ethz.ch/mailman/listinfo/r-devel > >> ______________________________________________ > >> r-h...@r-project.org mailing list > >> https://stat.ethz.ch/mailman/listinfo/r-help > >> PLEASE do read the posting guide > >> http://www.R-project.org/posting-guide.html > >> and provide commented, minimal, self-contained, reproducible code. > > > > ----------------------------------------------------------------------- > > This message and its attachments are strictly confidential. If you are > > not the intended recipient of this message, please immediately notify > > the sender and delete it. Since its integrity cannot be guaranteed, > > its content cannot involve the sender's responsibility. Any misuse, > > any disclosure or publication of its content, either whole or partial, > > is prohibited, exception made of formally approved use > > ----------------------------------------------------------------------- > > ----------------------------------------------------------------------- This message and its attachments are strictly confidenti...{{dropped:8}} ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
