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I am able to set up a Dockerfile with default ENV variables that I can then configure when running my docker container, e.g. in a Dockerfile I have the lines: 

ENV USERNAME ropensci
ENV EMAIL ropensci@github.com
RUN git config --global user.name $USERNAME
RUN git config --global user.email $EMAIL

Great. When I launch an interactive session:

docker run -it --env USERNAME="Carl" --env EMAIL=cboettig@example.com myimage /bin/bash

I can then issue the command git config --list and see that git is configured to use the values I provided on the command line instead of the defaults.

However, my Dockerfile is also configured to run an RStudio server that I can then log into in the browser when running the image in Daemon mode:

docker run -d -p 8787:8787 --env USERNAME="Carl" --env EMAIL=cboettig@example.com cboettig/ropensci-docker

I go to localhost:8787 and log in to RStudio which all works as expected, start a new "Project" with git enabled, but then RStudio cannot find my git name & email. I can open the shell from the RStudio menu and run git config --list or echo $USERNAME and I just get a blank value. Why does this work for /bin/bash but not from RStudio and how do I fix it?

AlvaroAV
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cboettig
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  • See if this helps http://stackoverflow.com/a/16867818/1205368 – Salem Aug 15 '14 at 23:10
  • @Salem No go. Note this has nothing to do with accessing the environmental variables in R, since they are not available on the shell either. – cboettig Aug 15 '14 at 23:14

1 Answers1

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Your git config is set on /.gitconfig. This config file is for root user. You need to set git config for rstudio user because rstudio run on rstudio user. Below command is a temporary solution.

docker run -it -p 8787:8787 --env USERNAME="Carl" --env EMAIL=cboettig@example.com cboettig/ropensci-docker bash -c "cp /.gitconfig /home/rstudio; /usr/bin/supervisord"

It works!

rstudio

Another solution is writing Dockerfile is based on cboettig/ropensci-docker. Below is sample Dockerfile.

FROM cboettig/ropensci-docker
RUN cp /.gitconfig /home/rstudio
CMD ["/usr/bin/supervisord"]
cboettig
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nacyot
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