How can I suppress the line numbers output using R CMD BATCH? - r

Question

If I have an R script:
print("hi")
commandArgs()
And I run it using:
r CMD BATCH --slave --no-timing test.r output.txt
The output will contain:
[1] "hi"
[1] "/Library/Frameworks/R.framework/Resources/bin/exec/x86_64/R"
[2] "-f"
[3] "test.r"
[4] "--restore"
[5] "--save"
[6] "--no-readline"
[7] "--slave"
How can i suppress the line numbers[1]..[7] in the output so only the output of the script appears?

Answer 1

Use cat instead of print if you want to suppress the line numbers ([1], [2], ...) in the output.
I think you are also going to want to pass command line arguments. I think the easiest way to do that is to create a file with the RScript shebang:
For example, create a file called args.r:
#!/usr/bin/env Rscript
args <- commandArgs(TRUE)
cat(args, sep = "\n")
Make it executable with chmod +x args.r and then you can run it with ./args.r ARG1 ARG2
FWIW, passing command line parameters with the R CMD BATCH ... syntax is a pain. Here is how you do it: R CMD BATCH "--args ARG1 ARG2" args.r Note the quotes. More discussion here
UPDATE: changed shebang line above from #!/usr/bin/Rscript to #!/usr/bin/env Rscript in response to #mbq's comment (thanks!)

Answer 2

Yes, mbq is right -- use Rscript, or, if it floats your boat, littler:
$ cat /tmp/tommy.r
#!/usr/bin/r
cat("hello world\n")
print(argv[])
$ /tmp/tommy.r a b c
hello world
[1] "a" "b" "c"
$
You probably want to look at CRAN packages getopt and optparse for argument-parsing as you'd do in other scripting languages/

Answer 3

Use commandArgs(TRUE) and run your script with Rscript.
EDIT: Ok, I've misread your question. David has it right.

Answer 4

Stop Rscript from command-numbering the output from print
By default, R makes print(...) pre-pend command numbering to stdout like this:
print("we get signal")
Produces:
[1] "we get signal"
Rscript lets the user change the definition of functions like print, so it serves our purpose by default:
print = cat
print("we get signal")
Produces:
we get signal
Notice the command numbering and double quoting is gone.
Get more control of print by using R first class functions:
my_print <- function(x, ...){
#extra shenanigans for when the wind blows from the east on tuesdays, go here.
cat(x)
}
print = my_print
print("we get signal")
Prints:
we get signal
If you're using print as a poor mans debugger... We're not laughing at you, we're laughing with you.