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Running R in Batch mode

Learning Objectives:

  • Invoking and running R in match mode
  • Understand the command R CMD BATCH
  • Execute some scripts

R CMD

R provides an special kind of command called R CMD which should be executed from the command line. This command is an interface or wrapper to various R tools such as processing files in R documentation format, or manipulating add-on packages. These tools are useful in conjunction with R, but not intended to be called “directly”. The main source of reference to know more about R CMD is the R manual An Introduction to R

The general form is:

R CMD command options args

  • command is the name of the tool

  • options are the command line options of R

  • args refers to the arguments passed on to the command

Some of the relevant options for this tutorial are:

  • --save saves data sets at the end of the R session.

  • --no-save does not save data sets at the end of the R session.

  • --no-environ don’t read any user file to set environment variables.

  • --restore restores .RData file in the directory where R was started

  • --vanilla combines --no-save, --no-environ, --no-site-file, --no-init-file and --no-restore

  • --quiet, --silent, and -q don’t print out the initial copyright and welcome messages

  • --slave makes R run as quietly as possible.

R CMD BATCH

Among the several available R tools, the one that we are interested in is the BATCH tool, which is designed to run R in batch mode, that is, batch execution of R.

When you run R CMD BATCH, the default options are --restore --save

To see more information, check the manual documentation by typing ?BATCH (or help(BATCH)) from within an R interactive session. Or by typing R CMD BATCH --help from the command line.

The usage is as follows:

R CMD BATCH options infile outfile

  • options are optional options from the command R

  • infile is the required input file with the code to be executed

  • outfile is the name of an optional output file. If no output file is provided, the name of infile is taken as default, appending the extension .Rout to it.

Running a script

Consider the file myscript1.R (inside the folder scripts/). If you take a look at its contents, this script generates two vectors x and y of length 20. It fits a regression line (regressing y on x). Then it produces two plots: 1) a scatterplot with the fitted regression line, and 2) a residual plot. Both plots are saved as png images.

To run the code inside myscript1.R in batch mode, you have type the following commands from the command line:

R CMD BATCH myscript1.R

The file myscript1.R is the input file.

R CMD BATCH generates an output file. By default, this file has the same name as the input file, but its extension will be .Rout. In other words, the output of R CMD BATCH always goes to a file that is built with name of the input filename and appending out. For this particular example, the output file will be myscript1.Rout. However, you can provide a different name if you want so.

# specifying the name of the output file
R CMD BATCH myscript1.R myscript1-output.R

If you run the command R CMD BATCH myscript1.R, you should be able to see a file called myscript1.Rout. If you open this file, you will see the welcome message that appears every time you open a new session in R, followed by the R commands (i.e. R code) that were executed, and finally an additional command at the end of the file with information about the execution time:


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # Regression analysis of two random vectors
> 
> # random data
> x <- rnorm(20)
> y <- x + rnorm(20)
> 
> # regression line
> reg <- lm(y ~ x)
> 
> # scatter diagram with fitted regression line
> png('scatterplot.png')
> plot(x, y, las = 1, pch = 19, col = "#555555")
> abline(reg, col = "#0000DD59", lwd = 2)
> dev.off()
null device 
          1 
> 
> # residuals plot
> png('residuals_plot.png')
> plot(x, reg$residuals, las = 1, pch = 19, col = "#606060")
> abline(h = 0)
> dev.off()
null device 
          1 
> 
> proc.time()
   user  system elapsed 
  0.179   0.036   0.210

Notice that the R code inside the output file is displayed with the prompt character >.

R CMD BATCH has default options --restore --save --no-readline

  • --save saves all the objects in the workspace (i.e. all the objects created while the script was executed) into a hidden file .RData which is a file in R’s binary format. When you save the available objects, this is known as saving the image (see help(save) for more information).

  • --restore will load the saved images, that is, will load() the content of the file .RData in the directory where R was started.

  • --no-readline turns off command-line editing via readline. This option is not that important.

If you don’t want R CMD BATCH to save the image, use the option --no-save. Likewise, if you don’t want R CMD BATCH to load the objects in .RData use --no-restore.

You can further modify the contents of the output file with a couple of additional options:

  • R CMD BATCH --silent won’t print out the initial copyright and welcome messages.

  • R CMD BATCH --no-save won’t save the workspace image (i.e. no .RData will be saved).

  • R CMD BATCH --vanilla combines --no-save, --no-environ, --no-site-file, --no-init-file and --no-restore.

Passing arguments to a script

In script1.R, the number of random values used to create vectors x and y was fixed. However, it would be nice if the user could specify a a value of n to control the length of the random numbers. In other words, it would be nice if we could specify a value for an argument n that we could pass it to the script file.

When running R scripts, often you will want to provide values for certain arguments. Luckily, R CMD BATCH allows you specify arguments and pass them to the script.

How to run an R script in batch mode and passing argument? You can pass parameters to scripts via additional arguments on the command line. This is done by quoting the arguments using the --args option:

R CMD BATCH "--args arg1 arg2" myscript.R

To see an example, take a look at the file myscript2.R which is almost identical to myscript1.R. The difference is that myscript2.R reads in a parameter for n which is the number of values to generate the x-y coordinates for the scatterplot.

Let’s say we want to generate 50 values. Here’s how to pass this number:

R CMD BATCH "--args 50" myscript2.R