[R] "Error: bad value" problem
p.dalgaard at biostat.ku.dk
Thu Dec 18 01:42:32 CET 2008
Peter Dalgaard wrote:
> Rolf Turner wrote:
>> On 18/12/2008, at 11:34 AM, Richard E. Chandler wrote:
>>> Dear R-help,
>>> Like several other subscribers, I have recently encountered a problem
>>> whereby R will execute code apparently correctly and without error,
>>> but any subsequent command will yield "Error: bad value" so that R
>>> has to be killed and restarted. We have checked this out with a few
>>> different operating systems (Windows XP/Vista and Linux) and with
>>> different versions of R. We have established the following:
>>> 1. The error occurs with versions of R from 2.5.0 onwards on all the
>>> OSs we have tried, but not with earlier versions of R.
>>> 2. The error is not reproducable between machines - identical code
>>> will fail at different points on two different machines.
>>> 3. The error is not related to contributed packages, because our code
>>> doesn't use any. The code *does*, however, use repeated calls to
>>> optim() and nlm(), and passes several arguments through a sequence of
>>> functions using "...".
>>> 4. Occasionally, we get an error relating to subset replacement
>>> instead of "Error:bad value". For example:
>>>> x <- rnorm(10)
>>>> x <- 3
>>> Error in x <- 3 : could not find function "[<-"
>>> 5. The error behaviour changes as a result of minor modifications to
>>> print() statements in the code e.g. by inserting a line that prints
>>> the value of a well-defined variable.
>>> I suspect this really *is* a bug (particularly since it only started
>>> happening with version 2.5.0), but I figure it would be worth giving
>>> people a chance to tell me I'm an idiot before reporting it as such.
>>> In case anybody would like to try and see the error for themselves, I
>>> have uploaded some files to
>>> http://www.homepages.ucl.ac.uk/~ucakarc/Rtest/. The file ErrorDemo.r
>>> is the main script - see the file header there for more details.
>>> Files momfit.r and elmstats.dat are also required for this example to
>>> work. I'm sorry that it isn't a very simple example, but I haven't
>>> seen a simple illustration of the problem (and I couldn't find any
>>> examples in the list archives either).
>> I can confirm that the error occurs.
>> I downloaded the files and sourced ``ErrorDemo.R''. Doing x <- rnorm(10)
>> after doing so triggered the error. Subsequently attempting traceback()
>> (or anything else) simply triggered the error again.
>> Good luck to R Core in tracking this down!
> Unfortunately, there's at least on R Core member for which it does NOT
> happen... Fedora 9 i686, R 2.8.0 and 2.8.1 RC (2008-12-15 r47214)
Wrong, actually... It did happen when run with 2.8.0 and valgrind (but
not without it). Unfortunately there were no errors from valgrind....
Error: bad value
Save workspace image? [y/n/c]: n
==29050== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 116 from 1)
==29050== malloc/free: in use at exit: 13,984,907 bytes in 10,061 blocks.
==29050== malloc/free: 117,023 allocs, 106,962 frees, 93,104,003 bytes
==29050== For counts of detected errors, rerun with: -v
==29050== searching for pointers to 10,061 not-freed blocks.
==29050== checked 14,502,208 bytes.
==29050== LEAK SUMMARY:
==29050== definitely lost: 0 bytes in 0 blocks.
==29050== possibly lost: 0 bytes in 0 blocks.
==29050== still reachable: 13,984,907 bytes in 10,061 blocks.
==29050== suppressed: 0 bytes in 0 blocks.
==29050== Rerun with --leak-check=full to see details of leaked memory.
O__ ---- Peter Dalgaard Øster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
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