See ?try ?tryCatch
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: [EMAIL PROTECTED] > Website: www.uea.ac.uk/~e387495 > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@stat.math.ethz.ch 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. > -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595 ______________________________________________ R-help@stat.math.ethz.ch 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.
