Pass shell environment variable to Rscript

Question

Is there a way to pass a shell environment variable to Rscript. For example:

Rscript -e 'devtools::install_github("private/repo",auth_token = "$GITHUB_CRED")'

I've tried this and it just passes the literal character. I'm wondering if there's another way?

I'm going to give it a shot. I have a hacky solution right now where I'm pushing it to a file and then readLines() — Brandon Bertelsen
– Brandon Bertelsen, Commented Oct 24, 2016 at 20:52
How about args? Rscript -e 'args <- commandArgs(trailingOnly = TRUE); paste("bla", args[1])' myPassword — zx8754
– zx8754, Commented Oct 24, 2016 at 21:18
@RichScriven I tried both shell and system, neither worked. — Brandon Bertelsen
– Brandon Bertelsen, Commented Oct 24, 2016 at 21:18

Hong Ooi · Accepted Answer · 2016-10-24 23:18:43Z

1

Have you tried using Sys.getenv?

Rscript -e 'devtools::install_github("private/repo", auth_token=Sys.getenv("GITHUB_CRED"))'

answered Oct 24, 2016 at 23:18

Hong Ooi

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2 Comments

Hong Ooi Over a year ago

Does Sys.getenv retrieve the correct value? You can check by printing it out.

ristonj Over a year ago

It worked for me as long as I exported the environment variable.

Dirk is no longer here · Accepted Answer · 2016-10-25 13:38:03Z

1

In the narrow sense of the question: "yes, Rscript can":

edd@max:~$ SOME_VAR="some value" Rscript -e 'print(Sys.getenv("SOME_VAR"))'
[1] "some value"
edd@max:~$

As for dealing with GitHub credentials, there are probably better solutions available via the proper GitHub clients. Did you try the (excellent and recommended) git2r package?

answered Oct 25, 2016 at 13:38

Dirk is no longer here

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3 Comments

Brandon Bertelsen Over a year ago

No, I haven't tried git2r. I think the main problem, unstated, is that I'm passing it as an environment variable to a Dockerfile that's being built by a CI system. So none of the more conventional approaches are working.

Dirk is no longer here Over a year ago

I am no security expert but some people have worked in that space. Don't reinvent the wheel -- do some google search around Docker, git, credentials, ...

Brandon Bertelsen Over a year ago

Even Docker doesn't have a well-defined strategy for sharing secrets. Everything right now is just a hack with security issues. For your reading pleasure github.com/docker/docker/issues/13490

Brandon Bertelsen · Accepted Answer · 2016-10-24 23:54:11Z

0

Seems a bit ridiculous, but:

echo $GITHUB_CRED > file.txt
Rscript -e 'devtools::install_github("private/repo",auth_token = readLines("file.txt"))'

I'm using this in jenkins build(s) with docker-slaves-plugin so that I can store all my configuration in Dockerfiles associated with my package repositories (clean builds)

edited Oct 24, 2016 at 23:54

answered Oct 24, 2016 at 23:12

Brandon Bertelsen

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