[FIXED] How can I make R read my environmental variables?

Issue

I am running R on EC2 spot instances and I need R to terminate the instance and cancel the spot request once the script has run.

For that I have set the "Request ID" into an environmental variable in /.bashrc and my plan was to simply call the following code into R once the script is ready

system("ec2-cancel-spot-instance-requests $SIR")

The issue I am having is that R is not "seeing" the same environmental variables I seen when I type env from outside R thus the command is not working.

I have checked and if I set my environmental variables at /etc/environment R is able to see those variables, but here is the other problem. As those variables are dynamic (the instance ID and the request ID is different each time a spot instance is created), I am running a script to create them in the form of:

export SIR=`cat /etc/ec2_instance_spot_id.txt`

Where that file contains the dynamic ID

So, how can I insert "dynamic" environmental variables into /etc/environment ? Or, how can I make R read the environmental variables at /.bashrc?

Solution

You want Sys.getenv() as in Sys.getenv("PATH"), say.

Or for your example, try

SIR <- Sys.getenv("SIR")   
system(paste("ec2-cancel-spot-instance-requests",  SIR))

As for setting variables at startup, see help(Startup) to learn about ~/.Renvironment etc

Answered By - Dirk Eddelbuettel

Answer Checked By - Marilyn (PHPFixing Volunteer)