CODEWITHSUNDEEP
rbashmacosrscript
Ben Carlson
Ben Carlson

Reputation: 1265

Exit code when calling R script from bash

I have an R script that I call from an interactive bash shell (MacOS Catalina). This is one of a series of scripts that I call from the interactive shell, so I need to know if the initial script failed. It seems that no matter how the script fails (assert_that, stop, stopfinot, quit), R always returns an exit status of 0. How can I return a non-zero exist status from a failed R script?

Here is an example R script (fail.r).

#!/usr/bin/env Rscript

#library(assertthat)

message("Starting script")

#assert_that(FALSE)

#stop('Fail')

#stopifnot(FALSE)

q(save="no", status=10, runLast=FALSE)

message("Should not reach here")

And here is how I might call it from a bash prompt

src/poc/fail.r

echo $?

Regardless of the method I use to exit the R script $? always returns 0.

A couple other posts address this issue, but do not seem to apply to my situation (How to get an Rscript to return a status code in non-interactive bash mode) and (Make R exit with non-zero status code)

Upvotes: 4

Views: 1702

Answers (1)

Timur Shtatland
Timur Shtatland

Reputation: 12377

I can get the status from Rscript back to the calling shell (R version 4.0.2, bash version 3.2.57 or zsh version 5.8 running on a MacBook Pro, macOS Mohave 10.14.6) using q(status = N). To get non-zero exit status from a failed R script, use q(status = 2) or higher, see quit:

$ Rscript -e 'q(status = 0);'
$ echo $?
0

$ Rscript -e 'q(status = 2);'
$ echo $?
2

$ Rscript -e 'q(status = 10);'
$ echo $?
10

$ R --version
R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (64-bit)

$ bash --version
GNU bash, version 3.2.57(1)-release (x86_64-apple-darwin18)

$ zsh --version
zsh 5.8 (x86_64-apple-darwin17.7.0)

Using a script essentially identical to the one you posted, I get the expected results (the status from quit is passed successfully to the enclosing shell):

Script:

#!/usr/bin/env Rscript

message("Starting script")
## Use status = 0, 2 or 10:
q(save = "no", status = 2, runLast = FALSE)
message("Should not reach here")

Output (tested with zsh and bash versions shown above):

$ ~/test/test1.r
Starting script
$ echo $?       
0
$ ~/test/test1.r
Starting script
$ echo $?       
2
$ ~/test/test1.r
Starting script
$ echo $?       
10

SEE ALSO:

Some error status values are used by R itself. The default error handler for non-interactive use effectively calls q("no", 1, FALSE) and returns error status 1. Error status 2 is used for R ‘suicide’, that is a catastrophic failure, and other small numbers are used by specific ports for initialization failures. It is recommended that users choose statuses of 10 or more.

Valid values of status are system-dependent, but 0:255 are normally valid.

(From quit docs)

Upvotes: 5

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