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, Oct 24 '16 at 20:52
How about args? `Rscript -e 'args <- commandArgs(trailingOnly = TRUE); paste("bla", args[1])' myPassword` — zx8754, Oct 24 '16 at 21:18
@RichScriven I tried both `shell` and `system`, neither worked. — Brandon Bertelsen, Oct 24 '16 at 21:18
If args option worked then this is a possible duplicate of http://stackoverflow.com/questions/2151212 ? — zx8754, Oct 25 '16 at 05:52

score 2 · Answer 1 · answered Oct 24 '16 at 23:18

2

Have you tried using Sys.getenv?

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

answered Oct 24 '16 at 23:18

Hong Ooi

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Does `Sys.getenv` retrieve the correct value? You can check by printing it out. – Hong Ooi Oct 25 '16 at 00:03
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It worked for me as long as I `export`ed the environment variable. – ristonj Aug 05 '19 at 15:39

score 1 · Answer 2 · answered Oct 25 '16 at 13:38

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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 '16 at 13:38

Dirk Eddelbuettel

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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. – Brandon Bertelsen Oct 25 '16 at 14:11
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, ... – Dirk Eddelbuettel Oct 25 '16 at 14:12
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 https://github.com/docker/docker/issues/13490 – Brandon Bertelsen Oct 25 '16 at 18:05

Brandon Bertelsen · Accepted Answer · 2016-10-24T23:54:11.833

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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 '16 at 23:54

answered Oct 24 '16 at 23:12

Brandon Bertelsen

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Pass shell environment variable to Rscript

3 Answers3