CODEWITHSUNDEEP
renvironment-variablesubuntu-14.04rstudiorevolution-r
cryo111
cryo111

Reputation: 4474

RStudio Server together with Microsoft R open: environment variables missing

I am running RStudio Server (0.99.879) on Amazon EC2 and have recently updated to Microsoft R Open 3.2.3 (formerly Revolution R). All software runs on Ubuntu 14.04.

Since I wanted to have my Amazon access keys available in all shell sessions for all users, I have put them in /etc/environment like AWS_ACCESS_KEY=123.

RStudio runs under user rstudio which I have checked via executing system("whoami") in RStudio. Before switching to Microsoft R Open [MRO], system("echo $AWS_ACCESS_KEY") (executed from RStudio) gave the correct result 123. But now it returns an empty string.

However, if I switch to user rstudio in the console via su - rstudio and start MRO from the shell, system("echo $AWS_ACCESS_KEY") gives the correct result, which really puzzles me.

It seems as if only RStudio together with MRO makes R forget the environment variables defined in etc/environment.

Do you guys know what could be the reason for this strange behavior? Any pointers to possible fixes?

I would really like to keep the keys in just one place (which is /etc/environment) and definitely not hard coded in my R code. One fix that I could think of is to read /etc/environment from R, extract the AWS_ACCESS_KEY and set it via Sys.setenv(). But this is mostly just a hack and I would like to understand what the real problem is...

BTW: Maybe I should mention that I had to change the R_HOME_DIR variable in the R start script /usr/bin/R to R_HOME_DIR=/usr/lib64/MRO-3.2.3/R-3.2.3/lib/R because the code that was determining the home directory before did not work with MRO.

Upvotes: 2

Views: 1057

Answers (1)

Jonathan
Jonathan

Reputation: 8832

It's important to keep in mind that RStudio Server (the open source edition) does not run user sessions under a login shell. So when you su - rstudio, you're getting the shell variables that are initialized when bash starts.

Thankfully there's a pretty easy way around this: symlink R_HOME/etc/Renviron.site (see R initialization) to /etc/environment. R's environment files have the same format as Linux's (i.e. KEY=VALUE), so you can supply the same list of environment initializers to both R and bash.

Upvotes: 2

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