Passing command line arguments to R CMD BATCH
I have been using R CMD BATCH my_script.R from a terminal to execute an R script. I am now at the point where I would like to pass an argument to the command, but am having some issues getting it working. If I do R CMD BATCH my_script.R blabla then blabla becomes the output file, rather than being interpreted as an argument available to the R script being executed.
I have tried Rscript my_script.R blabla which seems to pass on blabla correctly as an argument, but then I don't get the my_script.Rout output file that I get with R CMD BATCH (I want the .Rout file). While I could redirect the output of a call to Rscript to a file name of my choosing, I would not be getting the R input commands included in the file in the way R CMD BATCH does in the .Rout file.
So, ideally, I'm after a way to pass arguments to an R script being executed via the R CMD BATCH method, though would be happy with an approach using Rscript if there is a way to make it produce a comparable .Rout file.
Answer
My impression is that R CMD BATCH is a bit of a relict. In any case, the more recent Rscript executable (available on all platforms), together with commandArgs() makes processing command line arguments pretty easy.
As an example, here is a little script -- call it "myScript.R":
## myScript.R
args <- commandArgs(trailingOnly = TRUE)
rnorm(n=as.numeric(args[1]), mean=as.numeric(args[2]))
And here is what invoking it from the command line looks like
> Rscript myScript.R 5 100
[1] 98.46435 100.04626 99.44937 98.52910 100.78853
Edit:
Not that I'd recommend it, but ... using a combination of source() and sink(), you could get Rscript to produce an .Rout file like that produced by R CMD BATCH. One way would be to create a little R script -- call it RscriptEcho.R -- which you call directly with Rscript. It might look like this:
## RscriptEcho.R
args <- commandArgs(TRUE)
srcFile <- args[1]
outFile <- paste0(make.names(date()), ".Rout")
args <- args[-1]
sink(outFile, split = TRUE)
source(srcFile, echo = TRUE)
To execute your actual script, you would then do:
Rscript RscriptEcho.R myScript.R 5 100
[1] 98.46435 100.04626 99.44937 98.52910 100.78853
which will execute myScript.R with the supplied arguments and sink interleaved input, output, and messages to a uniquely named .Rout.
Edit2:
You can run Rscript verbosely and place the verbose output in a file.
Rscript --verbose myScript.R 5 100 > myScript.Rout