Re: [R] Execution halting of lmer on UNIX when no problem on windows

From: Prof Brian Ripley <>
Date: Mon 16 Oct 2006 - 07:00:10 GMT



FAQ 7.32 This is not a Windows/UNIX difference as you suppose, but an interactive/batch difference. You could also look into using options(error=).

On Sun, 15 Oct 2006, Toby Gardner wrote:

> Dear R-users,
> I have a frustrating problem that I am hoping has a simple fix. I am
> running a series of lmer models from the lme4 package of the general
> form:
> model<-lmer(y~x1 + x2 ..... + xn + (1|site),data=dataframe,family=poisson,method="Laplace",control=list(usePQL=FALSE,msVerbose=TRUE))
> where the same model is executed multiple times on a bootstrapped
> dataframe. For each bootstrapped model run the resulting model object
> is used to return the AIC (and models are then compared using a
> bootstrapped weight - frequency of runs a given model had the lowest
> AIC).
> This works just fine when running interactively on my windows machine
> (so there is nothing the matter with the code, hence I have not bored
> you with the details here).... however when I submit the job as a batch
> to a UNIX system it usually (but not always) fails and the execution is
> halted after an error message is produced:
> Error in objective (.par,...): Leading minor of order 1 in downdated X'X is not positive definite
> In addition: There were 12 warnings (use warnings() to see them)
> Error in logLik(model) : no applicable method for "logLik"
> Execution halted
> On windows when the execution of a single model run fails to estimate
> the logLik (an unstable model...) R just continues past the error and
> still runs to the end of the script (i.e. runs through all the
> bootstraps), and I can then inspect the output and any errors at the
> end.
> My question, then is when using UNIX on batch mode, how can I get the
> job to NOT halt it's execution on the production of an unstable model
> (not positive definite) and continue running? If the models are not
> bootstrapped then the script is executed without any problem in UNIX (so
> the script is successfuly submitted as a batch job), so it seems that
> some of the bootstrap runs are producing unstable models in rare
> instances, but just one is sufficient to halt the execution of the
> script.
> I am running R.2.3.1 on both Windows and UNIX,
> Many thanks in advance,
> Toby Gardner
> School of Environmental Sciences
> University of East Anglia
> Norwich, NR4 7TJ
> United Kingdom
> Email:
> Website:
> [[alternative HTML version deleted]]
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Brian D. Ripley,        
Professor of Applied Statistics,
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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Received on Mon Oct 16 17:06:53 2006

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