How to set and use bash variables in R-CodePudding

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?

CodePudding user response：

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.