Docker image for running R code in OpenSAFELY, both locally and in production.
- docker
- docker-compose
- just
just build
Under the hood, this builds ./Dockerfile
using docker-compose and buildkit.
We currently build a lot of packages, so an initial build on a fresh checkout can take a long time (e.g. an hour). However, to alleviate this, the Dockerfile is carefully designed to use local buildkit cache, so subequent rebuilds should be very fast.
- Enough bandwidth to comfortably push potentionally gigabytes worth of Docker layers.
- Several hours worth of CPU time to re-compile all the packages (if this is the first time you've done this and don't have them cached locally).
- Push access to ghcr.io.
If you don't have all these things then please don't start.
Before adding a package, check with an OpenSAFELY team member with R experience to approve the package.
To add a package, by default it will be installed from CRAN.
just add-package PACKAGE
If you need to install a package from another CRAN-like repository, specify its URL as the REPOS argument.
just add-package PACKAGE REPOS
This will attempt to install and build the package and its dependencies, and
update the renv.lock
. It will then rebuild the R image with the new lock file
and test it.
Note that the first time you do this it will need to compile every included R package (because you won't have the R package builds cached locally). This can take several hours. (When we solve the caching problem here we'll be able to do this all in CI.)
You will need to configure authentication to GitHub's container registry first. See GitHub's documentation.
When you have authentication configured, run:
just publish
Commit and push the small resulting change (should only be a few extra
lines in packages.csv
and renv.lock
) to a branch, then get the changes
merged via pull request.
The review is a trivial exercise because the Docker image has already been pushed to GitHub.
The updated image will need pulling into production. This is covered
separately in the tech team manual. If you don't have access, ask in
#tech
.
If the package requires any system build dependencies (e.g. -dev packages with
headers), they should be added to build-dependencies.txt
. If it requires
runtime dependencies, they should be added to dependencies.txt
. Packages
don't advertise their system dependencies, so you may need to figure them out
by trying to add the package and reading any error output on failure.
If the package still fails to build, you may be able to install an older version.
Find a previous version at https://cran.r-project.org/src/contrib/Archive/{PACKAGE}/
, and attempt to install it specifically with
just add-package PACKAGE@VERSION
The rstudio image is based on the r image including rstudio-server. To build run
just build-rstudio
To test that rstudio-server appears at http://localhost:8787
run
just test-rstudio
And then push the new rstudio image to the GitHub container registry with
just publish-rstudio