Productionize R Scripts with Batch Mode

Sometimes R is better off without RStudio.

Written on December 22, 2018

Objective: Running R Scripts in Batch Mode

R supports batch mode out of the box. All it takes is to launch R script with rscript.exe in the command-line interface.

set rscript=full-path-to-rscript.exe
start %rscript% cmd_example.R -arg1 job1 -arg2 value1 -arg3 value1
start %rscript% cmd_example.R -arg1 job2 -arg2 value2 -arg3 value2
start %rscript% cmd_example.R -arg1 job3 -arg2 value3 -arg3 value3

Note that Windows’ start command enables each subsequent operation to be executed in a parallel fashion. Without start, sequential execution would be assumed instead.

This is working already, but there are a few more things that would make the experience smoother.

Parsing Arguments

Parsing arguments in R mainly revolves around using the commandArgs function. It does one simple job: converting all (space-delimited) arguments specified in the batch call into a character vector, and it’s up to the users to decide what to do with them.

args <- commandArgs(trailingOnly = TRUE)

For example, suppose all arguments come in the form of “-arg value” pairs, i.e., odd elements stand for argument names and even ones are the values.

# odd elements are the names of the arguments (without the leading "-")
args_names <- gsub("-", "", args[c(TRUE, FALSE)])
# even elements are the values of the arguments
args_values <- args[c(FALSE, TRUE)]

The assign function can then be used for dynamic variable declaration. It’s also important to explicitly assign them in the global environment if you plan to wrap the whole argument processing chunk into a function.

for(i in seq_along(args_names)){
  assign(x = args_names[i], value = args_values[i], envir = .GlobalEnv)

Compatability with RStudio/Interactive Mode

Batch mode is practically useless when it comes to debugging. In order not to lose the compatability with RStudio/interactive mode, a conditional statement can be put in the very beginning to differentiate the two approaches.

# detect whether R script is launched in batch mode or RStudio mode
batch_mode_on <-"RSTUDIO", unset = NA))

  cat("Running in batch mode\r\n")
  # assign args passed from batch call
  # or wrap it into a function
  cat("Running in iteractive mode\r\n")
  # assign args manually
  arg1 <- "some value"
  arg2 <- "some value"
  arg3 <- "some value"

# start your job here

Preventing Auto-Exit

In batch mode, the command-line window automatically closes itself upon completion. If this is undesirable, put a blocking operation at the end of the script.

  cat("Job finished. Press CTRL + C to exit.\r\n")
  readLines(con = "stdin", n = 1)

And the window will remain open indefinitely, until user presses CTRL + C on the keyboard.

Putting It All Together

For non-interactive/production use of R scripts:

  • call rscript from the command-line interface to run them in batch mode, either sequentially (without start) or parallelly (with start)
  • use the commandArgs function in R to parse the arguments into a character vector, and you get to choose how to use it
  • distinguish between batch and interactive mode in the beginning of the script to remain compatible with RStudio
  • put a blocking operation at the end to avoid auto-exit