Add v3 r and rstudio images with R 4.5.3 and updated packages

.github/workflows/main.yaml

@@ -19,12 +19,12 @@ jobs:
         run: |
           set -x
           if [[ "${{ github.ref }}" == 'refs/heads/main' ]]; then
-            # build, test and publish both versions on main.
+            # build, test and publish all versions on main.
             # v1 will take ~2 hours
-            echo 'versions=["v1", "v2"]' >> "$GITHUB_OUTPUT"
+            echo 'versions=["v1", "v2", "v3"]' >> "$GITHUB_OUTPUT"
           else
-            # only build v2 in CI as v1 is too slow
-            echo 'versions=["v2"]' >> "$GITHUB_OUTPUT"
+            # only build v2 and v3 in CI as v1 is too slow
+            echo 'versions=["v2", "v3"]' >> "$GITHUB_OUTPUT"
           fi
   tests:
     needs: matrix
@@ -43,7 +43,7 @@ jobs:
       uses: astral-sh/setup-uv@4db96194c378173c656ce18a155ffc14a9fc4355
 
     - name: check
-      run: just check
+      run: just check ${{ matrix.version }}
 
     - name: build
       run: just build ${{ matrix.version }}

README.md

@@ -4,30 +4,32 @@ This repo manages the Docker image for the OpenSAFELY R runtime and rstudio-serv
 images are based on a base Ubuntu LTS version, and come pre-installed with
 a set of standard R packages.
 
-The current latest version is `v2`, and you should use that unless you have
+The current latest version is `v3`, and you should use that unless you have
 a specific reason. You can use it in your `project.yaml` like so:
 
 ```
 actions:
   my_action:
-    run: r:v2 analysis/my_script.R
+    run: r:v3 analysis/my_script.R
 ```
 
 The rstudio images are designed for use with `opensafely launch`. For example, to launch an rstudio-server session (i.e., RStudio running in a browser window) run the following in a Terminal from your research repository.
 
 ```sh
-opensafely launch rstudio:v2
+opensafely launch rstudio:v3
 ```
 
 ## Version List
 
 Current available versions for the r image, in reverse chronological order:
 
+ - v3: Ubuntu 22.04 and R 4.5.3 - [full package list](v3/packages.md)
  - v2: Ubuntu 22.04 and R 4.4.3 - [full package list](v2/packages.md)
- - v1: Ubuntu 20.04 and R 4.0.5 - [full package list](v1/packages.md) - please note that v1 is deprecated, new projects should use r:v2.
+ - v1: Ubuntu 20.04 and R 4.0.5 - [full package list](v1/packages.md) - please note that v1 is deprecated, new projects should use r:v3.
 
 Current available versions for the rstudio image, in reverse chronological order:
 
+ - v3: rstudio-server running r:v3
  - v2: rstudio-server running r:v2
  - v1: rstudio-server running r:v1
 
@@ -46,10 +48,10 @@ use `v1` instead of `latest`.
 
 We do not plan to add anymore packages to the v1 image.
 
-For the v2 image, the versions of R packages from CRAN tied to a CRAN date.
+For the v2 and v3 images, the versions of R packages from CRAN tied to a CRAN date.
 We can easily install any additional package from the same CRAN date.
 Additional packages may be requested by creating an issue in the repo.
-In the v2 image you can request packages that are not on CRAN.
+In the v2 and v3 images you can request packages that are not on CRAN.
 
 Occasionally, we will create a new major version of the image with all packages
 updated to their latest version. We may also possibly remove old and uneeded
@@ -58,8 +60,8 @@ incompatible changes, which is occasionally needed.
 
 ### User installed R packages
 
-Especially when working in say a Codespace using the rstudio:v2 image you may wish to add some packages for your post release analysis.
-The v2 images are configured to allow you to install your own packages, which will be saved to a _.local-packages/r/v2_ directory in your research repository.
+Especially when working in say a Codespace using the rstudio:v2 or rstudio:v3 images you may wish to add some packages for your post release analysis.
+The v2 and v3 images are configured to allow you to install your own packages, which will be saved to a _.local-packages/r/v#_ directory in your research repository.
 If the packages is on CRAN, to do this simply run the following.
 
 ```r

justfile

@@ -23,9 +23,9 @@ build version:
       cp ${MAJOR_VERSION}/renv.lock ${MAJOR_VERSION}/renv.lock.bak
       # cannot use docker compose run as it mangles the output
       docker run --platform linux/amd64 --rm r:{{ version }} cat /renv/renv.lock > ${MAJOR_VERSION}/renv.lock
-    elif [ "{{ version }}" = "v2" ]; then
+    elif [[ "{{ version }}" =~ ^v[23]$ ]]; then
       # update pkg.lock
-      cp ${MAJOR_VERSION}/pkg.lock ${MAJOR_VERSION}/pkg.lock.bak
+      [[ -f ${MAJOR_VERSION}/pkg.lock ]] && cp ${MAJOR_VERSION}/pkg.lock ${MAJOR_VERSION}/pkg.lock.bak || true
       # cannot use docker compose run as it mangles the output
       docker run --platform linux/amd64 --rm r:{{ version }} cat /pkg.lock > ${MAJOR_VERSION}/pkg.lock
     fi
@@ -84,5 +84,8 @@ publish-rstudio version:
       docker push ghcr.io/opensafely-core/rstudio:latest
     fi
 
-check:
-    uvx --python 3.13 toml-validator v2/packages.toml
+check version:
+    #!/usr/bin/env bash
+    if [[ "{{ version }}" =~ ^v[23]$ ]]; then
+      uvx --python 3.13 toml-validator {{ version }}/packages.toml
+    fi

scripts/local-packages-README.md → scripts/local-packages-README.Rmd

@@ -1,10 +1,24 @@
+---
+title: ""
+output:
+  github_document:
+    html_preview: false
+---
+
+```{r setup, include=FALSE}
+v <- Sys.getenv("MAJOR_VERSION")
+r_img <- paste0("`r:", v, "`")
+rstudio_img <- paste0("`rstudio:", v, "`")
+local_dir <- paste0("_.local-packages/r/", v, "_")
+```
+
 # .local-packages a directory for user installed libraries
 
-This directory contains user installed libraries, for say use running OpenSAFELY code in a Codespace or locally.
+This directory contains user installed libraries, for say running OpenSAFELY code in a Codespace or locally.
 
 ## How to add and remove user installed R packages
 
-The _.local-packages/r/v2_ directory contains user installed R packages to work in the `r:v2` and `rstudio:v2` images.
+The `r local_dir` directory contains user installed R packages to work in the `r r_img` and `r rstudio_img` images.
 
 You can install additional packages by running
 
@@ -14,7 +28,7 @@ install.packages("PACKAGENAME")
 
 or by using the RStudio _Package_ pane _Install_ button.
 
-Note that packages are installed from the same date from CRAN as the other packages in the `r:v2` image. This is to ensure user installed packages work with the other packages in the image (at the time of installation).
+Note that packages are installed from the same date from CRAN as the other packages in the `r r_img` image. This is to ensure user installed packages work with the other packages in the image (at the time of installation).
 
 If you no longer require a package you can also remove it as follows.
 

scripts/packages.Rmd

@@ -33,7 +33,7 @@ pkgs <- pkgs %>%
   arrange(Package, .locale = "en")
 knitr::kable(pkgs, row.names = FALSE)
 }
-if (Sys.getenv("MAJOR_VERSION") == "v2") {
+if (Sys.getenv("MAJOR_VERSION") %in% c("v2", "v3")) {
 suppressMessages(library(dplyr))
 pkglock <- jsonlite::fromJSON(paste0("/out/", Sys.getenv("MAJOR_VERSION"), "/pkg.lock"))
 pkgs <- pkglock[["packages"]]
@@ -46,11 +46,12 @@ pkgs <- pkgs %>% mutate(
     .default = metadataremoterepos
   )
 )
+r_minor_version <- if (Sys.getenv("MAJOR_VERSION") == "v3") "4.5" else "4.4"
 pkgs <- pkgs %>%
   mutate(
     url = case_when(
       repotype == "cran" ~ paste0("<https://cran.r-project.org/package=", package, ">"),
-      repotype == "cranlike" ~ paste0("<", sub("/bin/linux/noble/4.4/", "/", metadataremoterepos), package, ">")
+      repotype == "cranlike" ~ paste0("<", sub(paste0("/bin/linux/noble/", r_minor_version, "/"), "/", metadataremoterepos), package, ">")
     )
   )
 pkgs <- pkgs %>%

scripts/rprofile-site-append-2.R

@@ -1,15 +1,17 @@
 # If the local package directory exists set as first entry of R's library path
 # This is so that install.packages() and remove.packages() will use this directory by default.
-if (dir.exists('/workspace/.local-packages/r/v2'))
-  .libPaths(c('/workspace/.local-packages/r/v2', .libPaths()))
+.local_pkg_dir <- paste0('/workspace/.local-packages/r/', Sys.getenv("MAJOR_VERSION"))
+if (dir.exists(.local_pkg_dir))
+  .libPaths(c(.local_pkg_dir, .libPaths()))
 
 # Monkey patch install.packages to create local package directory if it doesn't exist and
 # create a .gitignore file within in and copy in the README.md.
 # In R ... passes function arguments through to a subsequent call.
 install.packages <- function(...) {
-  if (!dir.exists("/workspace/.local-packages/r/v2")) {
-    dir.create("/workspace/.local-packages/r/v2", recursive = TRUE)
-    .libPaths(c("/workspace/.local-packages/r/v2", .libPaths()))
+  local_pkg_dir <- paste0("/workspace/.local-packages/r/", Sys.getenv("MAJOR_VERSION"))
+  if (!dir.exists(local_pkg_dir)) {
+    dir.create(local_pkg_dir, recursive = TRUE)
+    .libPaths(c(local_pkg_dir, .libPaths()))
     # create .gitignore file
     file.create("/workspace/.local-packages/.gitignore")
     fileconn <- file("/workspace/.local-packages/.gitignore")

tests/test-loading-packages.R

@@ -7,12 +7,12 @@ npkgs <- length(pkgs)
 
 for (i in 1:npkgs) {
     package <- pkgs[i]
-    suppressMessages({
-    if (!library(package, logical.return = TRUE, character.only = TRUE)) {
-      stop(paste("Package", package, "failed to load, please investigate"))
-    }
+    tryCatch({
+    suppressMessages(library(package, character.only = TRUE))
     dtch <- paste0("package:", package)
     detach(dtch, force = TRUE, unload = TRUE, character.only = TRUE)
+    }, error = function(e) {
+      stop(paste0("Package ", package, " failed to load: ", conditionMessage(e)))
     })
 }
 

tests/test-preinstalled-user-package-step-1.R

@@ -1,7 +1,8 @@
 # .libPaths() should not have been amended yet
-stopifnot(.libPaths()[1] != "/workspace/.local-packages/r/v2")
+local_pkg_dir <- paste0("/workspace/.local-packages/r/", Sys.getenv("MAJOR_VERSION"))
+stopifnot(.libPaths()[1] != local_pkg_dir)
 # install package to user library in repo
 install.packages("tmsens")
 # .libPaths() should have been amended
-stopifnot(.libPaths()[1] == "/workspace/.local-packages/r/v2")
+stopifnot(.libPaths()[1] == local_pkg_dir)
 print("Step 1: installing user package and amending .libPaths() paths test passed")

tests/test-preinstalled-user-package-step-2.R

@@ -1,5 +1,5 @@
 # User library directory should already exist, hence .libPaths() is amended
-stopifnot(.libPaths()[1] == "/workspace/.local-packages/r/v2")
+stopifnot(.libPaths()[1] == paste0("/workspace/.local-packages/r/", Sys.getenv("MAJOR_VERSION")))
 # Load the pre-installed package from previous R session which is now in repo
 library(tmsens)
 # Delete /workspace/.local-packages

tests/test-user-install-package.R

@@ -34,7 +34,7 @@ library(tmsens)
 print("Loading user installed package test passed.")
 
 print("Library paths")
-stopifnot(.libPaths()[1] == "/workspace/.local-packages/r/v2")
+stopifnot(.libPaths()[1] == paste0("/workspace/.local-packages/r/", Sys.getenv("MAJOR_VERSION")))
 
 # Test adding a second package works
 # (again bpbounds chosen because it also has no hard dependencies)

tests/test.sh

@@ -14,7 +14,7 @@ if [ "${MAJOR_VERSION}" = "v1" ]; then
   # Test all R packages can be loaded
   python3 -c "import json; print('\n'.join(json.load(open(\"./$MAJOR_VERSION/renv.lock\"))['Packages']))" | xargs -I {} echo "if (!library({}, warn.conflicts = FALSE, logical.return = TRUE)) {stop(\"Package {} failed to load, please investigate\")}" > .tests.R
   run_test "${MAJOR_VERSION}" .tests.R
-elif [ "${MAJOR_VERSION}" = "v2" ]; then
+elif [[ "${MAJOR_VERSION}" =~ ^v[23]$ ]]; then
   # Test all R packages can be attached then detached
   run_test "${MAJOR_VERSION}" ./tests/test-loading-packages.R
 fi
@@ -31,8 +31,8 @@ run_test "${MAJOR_VERSION}" ./tests/test-arrow.R
 # Test loading the 14 base packages
 run_test "${MAJOR_VERSION}" ./tests/test-loading-base.R
 
-# Test user installed paackages on v2
-if [ "${MAJOR_VERSION}" = "v2" ]; then
+# Test user installed paackages on v2 and v3
+if [[ "${MAJOR_VERSION}" =~ ^v[23]$ ]]; then
   # Test installing and loading in same R session
   run_test "${MAJOR_VERSION}" ./tests/test-user-install-package.R
 

v2/Dockerfile

@@ -37,6 +37,9 @@ EOF
 # Finally, build the actual image from the base-r image
 FROM base-r AS r
 ARG REPOS="default-arg-to-silence-docker"
+ARG MAJOR_VERSION=v2
+ENV MAJOR_VERSION=${MAJOR_VERSION}
+RUN echo "MAJOR_VERSION=${MAJOR_VERSION}" >> /usr/lib/R/etc/Renviron.site
 
 # Some static metadata for this specific image, as defined by:
 # https://github.com/opencontainers/image-spec/blob/master/annotations.md#pre-defined-annotation-keys
@@ -62,7 +65,9 @@ WORKDIR /workspace
 # Settings to make it easier for users to add packages
 RUN --mount=type=bind,source=scripts/rprofile-site-append-2.R,target=/tmp/rprofile-site-append-2.R \
     cat /tmp/rprofile-site-append-2.R >> /usr/lib/R/etc/Rprofile.site
-COPY scripts/local-packages-README.md /usr/local-packages-README.md
+RUN --mount=type=bind,source=scripts/local-packages-README.Rmd,target=/tmp/local-packages-README.Rmd <<EOF
+    Rscript -e "rmarkdown::render('/tmp/local-packages-README.Rmd', output_file = '/usr/local-packages-README.md')"
+EOF
 
 #################################################
 #

v2/env

@@ -1,6 +1,6 @@
 MAJOR_VERSION=v2
 BASE=22.04
 RSTUDIO_BASE_URL=https://download2.rstudio.org/server/jammy/amd64/
-RSTUDIO_DEB=rstudio-server-2026.01.0-392-amd64.deb
+RSTUDIO_DEB=rstudio-server-2026.01.2-418-amd64.deb
 CRAN_DATE=2025-03-05
 REPOS=https://packagemanager.posit.co/cran/__linux__/jammy/${CRAN_DATE}

v3/Dockerfile

@@ -0,0 +1,105 @@
+# syntax=docker/dockerfile:1.11
+# enable docker linting
+# check=error=true
+#
+#################################################
+ARG BASE=22.04
+FROM ghcr.io/opensafely-core/base-action:$BASE AS base-r
+ARG MAJOR_VERSION=v3
+
+# add cran repo for R packages and install
+RUN --mount=type=cache,target=/var/cache/apt,id=apt-2204,sharing=locked \
+    --mount=type=cache,target=/var/lib/apt,id=apt-2204,sharing=locked \
+    --mount=type=bind,source=${MAJOR_VERSION}/dependencies.txt,target=/tmp/dependencies.txt <<EOF
+    echo "deb https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/" > /etc/apt/sources.list.d/cran.list
+    /usr/lib/apt/apt-helper download-file 'https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc' /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
+    /root/docker-apt-install.sh /tmp/dependencies.txt
+    ln -sf /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 /usr/lib/R/lib/libRblas.so
+    ln -sf /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 /usr/lib/R/lib/libRlapack.so
+EOF
+
+# use pak to install packages
+ENV PKG_CACHE_DIR=/cache/main
+ENV PKG_PACKAGE_CACHE_DIR=/cache/package
+ENV PKG_METADATA_CACHE_DIR=/cache/metadata
+ARG REPOS="default-arg-to-silence-docker"
+ARG CRAN_DATE="default-arg-to-silence-docker"
+RUN --mount=type=cache,target=/cache,id=/cache-2204,sharing=locked \
+    --mount=type=bind,source=scripts/build-toml.R,target=/tmp/scripts/build-toml.R \
+    --mount=type=bind,source=${MAJOR_VERSION}/packages.toml,target=/tmp/packages.toml \
+    --mount=type=bind,source=scripts/rprofile-site-append-1.R,target=/tmp/rprofile-site-append-1.R  <<EOF
+    echo "REPOS=${REPOS}" >> /usr/lib/R/etc/Renviron.site
+    cat /tmp/rprofile-site-append-1.R >> /usr/lib/R/etc/Rprofile.site
+    Rscript /tmp/scripts/build-toml.R
+EOF
+
+
+################################################
+#
+# Finally, build the actual image from the base-r image
+FROM base-r AS r
+ARG REPOS="default-arg-to-silence-docker"
+ARG MAJOR_VERSION=v3
+ENV MAJOR_VERSION=${MAJOR_VERSION}
+RUN echo "MAJOR_VERSION=${MAJOR_VERSION}" >> /usr/lib/R/etc/Renviron.site
+
+# Some static metadata for this specific image, as defined by:
+# https://github.com/opencontainers/image-spec/blob/master/annotations.md#pre-defined-annotation-keys
+# The org.opensafely.action label is used by the jobrunner to indicate this is
+# an approved action image to run.
+LABEL org.opencontainers.image.title="r" \
+      org.opencontainers.image.description="R action for opensafely.org" \
+      org.opencontainers.image.source="https://github.com/opensafely-core/r-docker" \
+      org.opensafely.action="r" \
+      org.opensafely.version="${MAJOR_VERSION}" \
+      org.opensafely.cran-date="${CRAN_DATE}"
+
+# ACTION_EXEC is our default executable
+ENV ACTION_EXEC="/usr/bin/Rscript"
+# INTERACTIVE_EXEC is used when running w/o any args, implying an interactive session.
+# See: https://github.com/opensafely-core/base-docker/blob/main/entrypoint.sh#L5
+ENV INTERACTIVE_EXEC="/usr/bin/R"
+
+# setup /workspace
+RUN mkdir /workspace
+WORKDIR /workspace
+
+# Settings to make it easier for users to add packages
+RUN --mount=type=bind,source=scripts/rprofile-site-append-2.R,target=/tmp/rprofile-site-append-2.R \
+    cat /tmp/rprofile-site-append-2.R >> /usr/lib/R/etc/Rprofile.site
+RUN --mount=type=bind,source=scripts/local-packages-README.Rmd,target=/tmp/local-packages-README.Rmd <<EOF
+    Rscript -e "rmarkdown::render('/tmp/local-packages-README.Rmd', output_file = '/usr/local-packages-README.md')"
+EOF
+
+#################################################
+#
+# Add rstudio-server to r image - creating rstudio image
+ARG RSTUDIO_BASE_URL="default-arg-to-silence-docker"
+ARG RSTUDIO_DEB="default-arg-to-silence-docker"
+FROM r AS rstudio
+
+# Install rstudio-server (and a few dependencies)
+RUN --mount=type=cache,target=/var/cache/apt,id=apt-2204,sharing=locked \
+    --mount=type=cache,target=/var/lib/apt,id=apt-2204,sharing=locked \
+    --mount=type=bind,source=rstudio/rstudio-dependencies.txt,target=/tmp/rstudio-dependencies.txt <<EOF
+    /root/docker-apt-install.sh /tmp/rstudio-dependencies.txt
+    test -f /var/cache/apt/"${RSTUDIO_DEB}" || /usr/lib/apt/apt-helper download-file "${RSTUDIO_BASE_URL}${RSTUDIO_DEB}" /var/cache/apt/"${RSTUDIO_DEB}"
+    apt-get install --no-install-recommends -y /var/cache/apt/"${RSTUDIO_DEB}"
+EOF
+
+# Configuration
+## Start by setting up rstudio user using approach in opensafely-core/research-template-docker
+RUN useradd rstudio -m
+# copy R/rstudio config into user home dir
+COPY rstudio/home/* /home/rstudio/
+COPY rstudio/etc/* /etc/rstudio/
+
+RUN <<EOF
+    chown -R rstudio:rstudio /home/rstudio
+    echo "R_LIBS_SITE=/usr/local/lib/R/site-library" >> /usr/lib/R/etc/Renviron.site
+EOF
+
+COPY rstudio/rstudio-entrypoint.sh /usr/local/bin/rstudio-entrypoint.sh
+
+ENV USER=rstudio
+ENTRYPOINT ["/usr/local/bin/rstudio-entrypoint.sh"]