Running scripts with R CMD BATCH

Last week, I posted a link to a primer on running R in batch mode, by redirecting the input and output of the R shell command. (By the way, it works the same way in REvolution R too: just replace the command R with Revo). In the comments, Doug Bates reminded me that there's a better way: using R CMD BATCH.

Let's illustrate by example. Suppose I have a script file containing the commands for a statistical analysis. I want to run it in batch mode (perhaps because it will run overnight), and save the output of the commands to a file. Here's my script file, saved as myscript.R:

clotting <- data.frame(
    u = c(5,10,15,20,30,40,60,80,100),
    lot1 = c(118,58,42,35,27,25,21,19,18),
    lot2 = c(69,35,26,21,18,16,13,12,12))
cat("Model data:\n")
print(clotting)
warning("Model starting")
obj <- glm(lot1 ~ log(u), data=clotting, family=Gamma)
cat("\nEstimated parameters:\n")
coef(summary(obj))

I can run it in batch mode from the shell or Windows command line, like this:

$ Revo CMD BATCH myscript.R myscript.Rout
$

(Note: I'm using REvolution R here, so replace Revo with R if you're using CRAN R. $ is the shell prompt, so don't type that.) This has a similar effect to the file redirection method:

Revo < myscript.R > myscript.Rout

with a few differences:

• CMD BATCH automatically captures warnings and errors, which the file redirection method as shown above would lose: they'd be displayed at the shell prompt, not captured in the file. (It is achievable with some tricky shell syntax, but I can never remember how to do it.) 
• CMD BATCH automatically adds a call to proc.time() at the end of the session, to document how long the script took to run. 
• The CMD BATCH syntax is easier to remember (at least for me). 

By default, both methods show both the prompts and input commands and their outputs in the output file myscript.Rout, just as if you'd typed them at the interactive prompt. But if you only want the outputs (you're building a text report using R commands, say), a very handy option is --slave: this suppresses the prompts, commands, and R's startup blurb to leave you only with the output. With the command:

$ Revo CMD BATCH --slave myscript.R myreport.txt

I get the following in the file myreport.txt:

Model data:
    u lot1 lot2
1   5  118   69
2  10   58   35
3  15   42   26
4  20   35   21
5  30   27   18
6  40   25   16
7  60   21   13
8  80   19   12
9 100   18   12
Warning message:
Model starting 

Estimated parameters:
               Estimate   Std. Error   t value     Pr(>|t|)
(Intercept) -0.01655438 0.0009275466 -17.84749 4.279149e-07
log(u)       0.01534311 0.0004149596  36.97496 2.751191e-09
> proc.time()
   user  system elapsed 
  1.153   0.061   1.917 

One last point: you can actually pass your own command-line arguments into R to affect the behaviour of your script. Maybe we'll look at that in detail in some other post, but for now the help for the function commandArgs will get you started. You might also want to use Rscript instead, which we've discussed before.

Comments

[Steve]

Thanks for this! With these instructions I was finally able to get started with R in command line mode!
Steve

[Lu Li]

That's great, really appreciate your help. save me lot of time to investigate how to run R in Java, many thanks.:)

[Benoit Borrel]

Some comments about your list of differences between Revo and R:
* in UNIX world: stdin is 0, stdout is 1, stderr is 2; so, if you are already redirecting command output to a file and would like to append the errors into it, add 2>&1 to your command. Ex: mycmd >outfile 2>&1
BUT, because R CMD BATCH is already appending stderr to stdout in its output, it is not necessary here.
* argument --no-timing will prevent the call to proc.time()

[Tanzy Love]

Does anyone know how to get Revo to pick the 64 bit version of the engine in command mode. When I use Revo CMd BATCH, I see that the Rterm*32 is running.

[Stephen Weller]

I think you will need to specify the path to C:\Revolution\R-Enterprise-4.3\R-2.12.2\bin\x64 on your command line, e.g:

C:\Revolution\R-Enterprise-4.3\R-2.12.2\bin\x64\Rcmd BATCH C:\mybatchtest.R C:\mybatchtest.out

or:

C:\\Revolution\R-Enterprise-4.3\R-2.12.2\bin\x64\Rterm.exe --no-restore --no-save < C:\mybatchtest.R > C:\lmbatchtest.out 2>&1

[Tanzy Love]

Thanks, this did it for me!!

C:\\Revolution\R-Enterprise-4.3\R-2.12.2\bin\x64\Rterm.exe --no-restore --no-save --args "nsim.matrix=37; Nsim=25; which.est=1; which.sim=1" < sim33c.R > sim37.Rout 2>&1

[John]

This is great. Have you ever looked at creating image output? For example, could we do something like this?

Revo < createPlot.R > myplot.png

[David Smith]

Hi John,

If your goal is to be able to specify an output file name from the command line (to customize behavior of a script), one way is like this:

Revo createplot.R --args myplot.png

and in the createplot.R script use commandArgs(trailingOnly=FALSE) to access the specified output file name (here myplot.png).

You might also want to take a look at littler.

[Mohamed]

I have a question, is there anyway i can make php run a R commands file on windows ? it is essential that whenever i run a php script in starts R and processes this R text file..

Thank you very much!

[walkingon2001]

How do you do this if you are working with a remote server? How you "send" your code to the R on the server? Do you run your code on the server, then save it there?

[walkingon2001]

I figured it out. Thanks!

[Nitin]

Dear sir,
I am using PennCNV package for CNV analysis.
Here I am using visualize_cnv .pl for JPG output file. I have installed R in my system, and in Environmental variable I have putted the path C:\Rtools\gcc-4.6.3\bin;C:\Program Files\R\R-2.15.2\bin\x64; and I am running the command
visualize_cnv.pl -format plot -signal offspring.txt ex1.rawcnv
and I am getting the error:cannot execute system command R CMD BATCH.
How can I resolve the error.

[Eduardo Valdes]

Is it possible to customize the prompt (data input) from the actual output in the console?
We would like to have a visual differentiation between what we input and the results (output).