Docker with renv using rocker/rstudio

[gclarkjr5]

Hi, I was following the best practices for docker with renv from here. I am not sure what I'm doing wrong but it does not seem that I am able to use the rocker/rstudio image in order to use this best practice for running containers. Here is some supporting information:

• Docker version 19.03.8, build afacb8b
• Dockerfile for building an image using renv

FROM rocker/rstudio:3.6.3-ubuntu18.04
RUN apt-get upgrade -y && \
apt-get update -y && \
apt-get install -y tzdata
RUN R -e 'install.packages("remotes")'
RUN R -e "remotes::install_github('rstudio/[email protected]')"

• Docker run command

docker run -d --rm -it --name renv `
-e ROOT=TRUE `
-e DISABLE_AUTH=TRUE `
-e RENV_PATHS_CACHE=/renv/cache `
-p 8787:8787 `
-v C:\Users\other\docker\renv\cache:/renv/cache `
renv:latest

Some issues I tried to work through with no luck

1. The environment variable RENV_PATHS_CACHE does not pass through to Rstudio

• In a shell outside of RStudio I am able to run printenv and view the env var, but using Sys.getenv() in Rstudio console the variable does not get picked up. Additionally, if I use the Terminal within Rstudio and run printenv I am unable to see the variable as rstudio user or as root.
• Manually executing Sys.setenv(RENV_PATHS_CACHE = /renv/cache) has worked, but again, its manual

2. I'm unable to run renv::restore() as a post-command for the run command above

• I think this is because of how the base image of rocker/rstudio is designed
• I was able to begin running post-commands once I added ENTRYPOINT ['R'] as the last command to Dockerfile, but then I have to manually run /init which kickstarts Rstudio

Thanks for your help.

[kevinushey]

I suspect this is just due to how RStudio Server is launched within Docker containers. I'm not aware of a better fix than just setting RENV_PATHS_CACHE manually. (Maybe you could set it in ~/.Renviron, so it's visible to all new R sessions?)

I'm unable to run renv::restore() as a post-command for the run command above

What do you see when you try to call renv::restore()?

[gclarkjr5]

What do you see when you try to call renv::restore()?

Error response from daemon: OCI runtime create failed: container_linux.go:349: starting container process caused "exec: \"renv::restore()\": executable file not found in $PATH": unknown.

or even if i try kicking off R to run renv::restore() as a sub command, i.e calling R -e "renv::restore()" instead, i get...
Error response from daemon: OCI runtime create failed: container_linux.go:349: starting container process caused "exec: \"R -e renv::restore()\": executable file not found in $PATH": unknown

I believe it has to do with the CMD ["/init"] as the last line to the Dockerfile for the image.

Currently, my workaround is to run this:

docker run -d --rm -it
-e ROOT=TRUE
-e DISABLE_AUTH=TRUE
-e RENV_PATHS_CACHE=/renv/cache
-p 8787:8787
-v C:\Users\other\docker\renv\cache:/renv/cache
-v C:\Users\other\docker\myproject:/home/rstudio/myproject
renv:latest

As you can see I've added an extra volume, and at the location locally, i have an Rscript containing this:

Sys.setenv(RENV_PATHS_CACHE = '/renv/cache')
setwd("~/myproject")
renv::restore(prompt = FALSE)

once I'm in Rstudio, i just run this and I'm good.

A bit manual, but it works in the meantime i guess.

[KasperSkytte]

Having the same problem. It's related to this issue rocker-org/rocker#376.

I solved it by also setting RENV_PATHS_CACHE in /usr/local/lib/R/etc/Renviron when building the container, for example adding the line echo "RENV_PATHS_CACHE=/usr/local/lib/R/renv-cache/" >> /usr/local/lib/R/etc/Renviron to the Dockerfile and then making sure the folder is mounted when starting the container.

[KasperSkytte]

I made a script to generate a Dockerfile and run here https://gist.github.com/KasperSkytte/270ceb8bc19af7f3bd24c8f9f08f259a. Added a few extra system packages I needed for some R packages, fx Cairo, XML

[KasperSkytte]

I guess it would be nice to set RENV_PATHS_SOURCE as well?

[hadley]

Tracking docker recommendation improvements in #599