[R] Why would something work in R but not Rscript?

Ben Tupper ben.bighair at gmail.com
Wed Nov 19 19:03:57 CET 2014


On Nov 19, 2014, at 11:48 AM, Jeff Hansen <dscheffy at gmail.com> wrote:

> I have a script that uses RWeka (and consequently rJava).  When I run
> it in Rstudio everything works fine. When I run it with `R CMD BATCH`,
> everything also works fine. However, when I run it with Rscript, I get
> the following error:
> Error in FUN(X[[1L]], ...) :
>  object is not a Java object reference (jobjRef/jarrayRef).
> Calls: evaluate_Weka_classifier -> t -> sapply -> lapply -> FUN
> Execution halted
> The following is a very simple toy script that you can run to produce
> the results:
> library("RWeka")
> observation <- c(TRUE,FALSE,TRUE,FALSE,TRUE)
> df <- data.frame(result,observation)
> j48 <- J48(result ~ .,data=df)
> evaluate_Weka_classifier(j48)
> Save that to a file called help.R and run
> R CMD BATCH help.R
> Check the output file help.Rout and you should see no errors. Now try
> running it from:
> Rscript help.R

You might try using the the --vanilla option for each.  At least then you can rule out that something is being restored in the session of one but not the other. 

R --vanilla CMD BATCH help.R
Rscript --vanilla help.R


> And you should see the error I've pasted above.
> I have consulted (and will continue to consult) the literature, but
> the manuals tend to answer how usage differs between the two commands
> rather than going into implementation details. I imagine there's a
> difference in how environments get loaded and I just need to adjust
> something on the Rscript side.
> I'm working on a Mac (OSX) running R 3.1.0, but I get the same results
> when I run everything from a Centos 6.4 virtual machine (headless)
> with R 3.1.1 installed.
> Thanks for any help!
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