BATCH versus pasting commands
On Fri, 8 Feb 2002, David Scott wrote:
I have a problem with trying to run a batch job. I am looping over a number of variables in a dataframe, doing some plots and wilcoxon tests. Then I restrict to a subset of the data, and do the same thing. Because of missing data, some of the wilcoxon tests fall over, so I have used try to get past them. Using R CMD BATCH, the job terminates with a syntax error after the first loop is completed. If I just paste the whole file into R, it runs through without a problem. I can break it up into two command files and use a shell script, but I would welcome and explanation of why I have the problem. Any other workarounds would interest me too.
The setting of error recovery is different under interactive and batch use. R BATCH is batch use (of course) but so is R < infile. To change that under batch use 1) Use options(error==expression(NULL)) to get continuation past errors, or 2) wrap the test that might fail in a try() construct. Option 2) is of course safer and so preferred.
Brian D. Ripley, ripley at stats.ox.ac.uk 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 272860 (secr) Oxford OX1 3TG, UK Fax: +44 1865 272595 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._