How to set and use bash variables in R

Question

I have a use case where I need to execute bash commands inside an R program. I can send and verify that bash commands are being executed, but for reasons I do not understand, I can't set and use variables. To begin with, a simple command works fine:

$ R
...
> system("ls")
1a.csv  1b.csv  2.csv  3.csv
[1] 0
>

Now moving on to the problem. I've tried as many approaches as I could find, but none seem to work:

> system("TEST_VAR=\"test_val\"")
[1] 127
Warning message:
In system("TEST_VAR=\"test_val\"") : 'TEST_VAR="test_val"' not found
> system("bash -c 'REPORT_S3=report_s3_test_val'")
[1] 0
> system("echo ${REPORT_S3}")
$REPORT_S3
[1] 0
> system('TEST_VAR=test_var')
[1] 127
Warning message:
In system("TEST_VAR=test_var") : 'TEST_VAR=test_var' not found
> Sys.setenv(TEST_VAR = "test_val")

> system("echo $TEST_VAR")
$TEST_VAR
[1] 0
> system("bash -c 'export TEST_VAR=\"test_val\"'")
[1] 0
> system(" echo ${TEST_VAR}")
$TEST_VAR
[1] 0

None of these attempts succeed.

What I need to do is set variables and subsequently use them to create successively more complex commands. This works fine in in bash. But I can't seem to get it to work in R, apparently for the reasons above.

REPORT_S3="s3://xxxxxxxx-reports/r/html/"$RMD_FILE"_"$EMAIL_ADDRESS"_"$CLOUDWATCH_UUID".html"
PRESIGNED_URL=$(aws s3 presign --expires-in 604800 $REPORT_S3)
JSON_STRING='xxxxx"$CLOUDWATCH_UUID"xxxxxxx"$PRESIGNED_URL".....'
echo $JSON_STRING > message.json
echo '{"ToAddresses":["'$EMAIL_ADDRESS'"],"CcAddresses":[],"BccAddresses":[]}' > destination.json
aws ses send-email --from [email protected] --destination file://destination.json --message file://message.json --region ap-southeast-2

Perhaps there any other options for issuing bash commands other than system that would permit easier reuse of the original source bash code?

that other guy · Accepted Answer · 2022-05-30 22:56:19Z

2

Environment variables are per process, and each system(..) call starts a new process. If you define and reference the variable in the same system call, it works fine:

> system('
  var="foo"
  echo "The variable is: $var"
')
The variable is: foo

If you put your entire script into a single system(..) call, instead of trying to run line by line, it should therefore work.

An alternative method is using Sys.setenv to set the variables in your current R process, so that future system() calls inherit it:

> Sys.setenv(var = "bar")
> system('echo "The variable is: $var"')
The variable is: bar

Obviously, since Sys.setenv is an R function, you must use R code to define your variables, and not rely on shell syntax like $(..)

PS: system() invokes sh and not bash, so all the code you pass it should be sh compatible.

answered May 30, 2022 at 22:56

that other guy

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8 Comments

monkey Over a year ago

Hey. I'm not seeing the behaviour you expect: > Sys.setenv(var = "bar") > system('echo "The variable is: $var"') The variable is: $var [1] 0

monkey Over a year ago

And In system("\n var=\"foo\"\n echo \"The variable is: $var\"\n") : 'var="foo"' not found

that other guy Over a year ago

Weird. Which OS and R version is this? Is Windows involved at all?

monkey Over a year ago

So I'm working on windows machine. I was running this in a linux container, but now testing locally on Windows 10. R version 4.1.2 (2021-11-01) -- "Bird Hippie".

that other guy Over a year ago

git bash has a lot of integration issues with the OS and other programs. Try it in the linux container instead.

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