[R-sig-ME] segfaults from lmer on a 64-bit system

[Ben Hansen]

Thanks for these suggestions.

I updated to the latest versions of the packages, and the segfault persists.

I have isolated an example for reproduction purposes. The data are given in
    http://www.stat.lsa.umich.edu/~bbh/segfault-bh.rda

I get segfaults when I do:
>  library(lme4) ; load("segfault-bh.rda") ; mylme <-lmer(myfmla, data=mydata)

The segfault occurs on a couple of setups:
1.  64-bit Red Hat linux; R version 2.7.1:
> sessionInfo()
R version 2.7.1 (2008-06-23)
x86_64-unknown-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_ADD
RESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] lme4_0.999375-24   Matrix_0.999375-11 lattice_0.17-8

loaded via a namespace (and not attached):
[1] grid_2.7.1  tools_2.7.1

2. Mac OS; R version 2.7.1:
> sessionInfo()
R version 2.7.1 (2008-06-23)
powerpc-apple-darwin8.10.1

locale:
C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] lme4_0.999375-22   Matrix_0.999375-10 lattice_0.17-8

loaded via a namespace (and not attached):
[1] grid_2.7.1

3.  I also got the segfault on the 64-bit linux machine using R version
2.6.1, lme4 version 0.99875-9 (I think), and Matrix version 0.999375-9 (I
think).

4. *On the other hand,* it sort of works (without segfaulting at least)
using older R, lme4 and Matrix on my Mac:
> sessionInfo()
R version 2.6.2 (2008-02-08)
powerpc-apple-darwin8.10.1

locale:
C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] lme4_0.99875-9    Matrix_0.999375-9 lattice_0.17-6

loaded via a namespace (and not attached):
[1] grid_2.6.2

> mylme <- lmer(myfmla, data=mydata)

Warning messages:
1: In .local(x, ..., value) :
  Estimated variance-covariance for factor 'by.var' is singular

2: In .local(x, ..., value) :
  nlminb returned message false convergence (8)

--Perhaps the warnings contain a clue as to what the problem is?

Thanks for your consideration of this.

Ben
On 8/13/08 2:55 AM, "Douglas Bates" <bates at stat.wisc.edu> wrote:

> I would first try later versions of both the Matrix and lme4 packages.
>  Versions currently on CRAN are Matrix_0.999375-11 and
> lme4_0.999375-24
> 
> If you continue to get segfaults then having a reproducible example,
> along with the data - anonymized if you wish, will be important.
> 
> You can determine the versions of the packages that you are using with
> 
> sessionInfo()
> 
> 
> On Wed, Aug 13, 2008 at 12:06 AM, Hansen, Ben <bbh at umich.edu> wrote:
>> Hello all,
>> 
>> 
>> 
>> I am encountering trouble with lme4 on a 64-bit linux system, and I'm
>> wondering if any of you might have advice on how to circumvent it. Using
>> recent versions of lme4 and R, I was able to compile and install the
>> package, and use it with success on relatively small problems.  However,
>> when I tried to scale up to work on a big problem, applying lmer() with
>> thousands of observations and a hundred or so random effects, my R fails
>> reporting a segmentation fault.  I don't see the same problem on a
>> different 32-bit Mac OSX system, which runs the same code without
>> evident difficulty.
>> 
>> 
>> 
>> Some details of the setup where the problem occurs.  We've tried a few
>> combinations of things, so I write what we tried first, with variants
>> noted in parentheses:
>> 
>> 
>> 
>> Red Hat Enterprise Linux 4 (version 5)
>> 
>> R version 2.7.1 (2.6.1)
>> 
>> gcc/g++ compilers for C and C++, Portland Group Fortran compilers
>> (gcc/g++/gfortran, ie full GNU compiler suite)
>> 
>> Matrix package version 0.999375-10  (installed with and without
>> --with-package-versions flag)
>> 
>> lme4 version 0.999375-16 (installed with and without
>> --with-package-versions flag)
>> 
>> 
>> 
>> Any suggestions?  I'd be very appreciative.
>> 
>> 
>> 
>> Ben
>> 
>> 
>> 
>> 
>> 
>> 
>>        [[alternative HTML version deleted]]
>> 
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