Add rstudio-server to r image as rstudio image

.gitignore

@@ -2,3 +2,10 @@
 renv.lock.bak
 renv/
 .tests.R
+
+# rstudio-server directories
+*.config
+*.local
+
+# R files
+.Rhistory

Dockerfile

@@ -94,3 +94,43 @@ WORKDIR /workspace
 COPY --from=builder /renv /renv
 # this will ensure the renv is activated by default
 RUN echo 'source("/renv/renv/activate.R")' >> /etc/R/Rprofile.site
+
+#################################################
+#
+# Add rstudio-server to r image - creating rstudio image
+FROM r as rstudio
+
+COPY rstudio-dependencies.txt /root/rstudio-dependencies.txt
+COPY rstudio-entrypoint.sh /usr/local/bin/rstudio-entrypoint.sh
+
+# Install rstudio-server (and a few dependencies)
+RUN --mount=type=cache,target=/var/cache/apt /root/docker-apt-install.sh /root/rstudio-dependencies.txt &&\
+    wget -q -O rstudio-server.deb https://download2.rstudio.org/server/focal/amd64/rstudio-server-2024.09.0-375-amd64.deb &&\
+    apt-get install --no-install-recommends -y ./rstudio-server.deb &&\
+    # delete the deb
+    rm rstudio-server.deb &&\
+    # Setup rstudio user using approach in opensafely-core/research-template-docker
+    useradd rstudio &&\
+    # Disable rstudio-server authentication
+    echo "auth-none=1" >> /etc/rstudio/rserver.conf &&\
+    # Run the server under the single user account
+    echo "server-user=rstudio" >> /etc/rstudio/rserver.conf &&\
+    echo "USER=rstudio" >> /etc/environment &&\
+    # Give the rstudio user sudo (aka root) permissions
+    usermod -aG sudo rstudio &&\
+    echo '%sudo ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers &&\
+    # Add a home directory for the rstudio user
+    mkdir /home/rstudio &&\
+    chown -R rstudio:rstudio /home/rstudio/ &&\
+    # Use renv R packages
+    # Remember that the second renv library directory /renv/sandbox/R-4.0/x86_64-pc-linux-gnu/9a444a72
+    # contains 14 symlinks to 14 of the 15 packages in ${R_HOME}/library which is /usr/lib/R/library/
+    # so that is already setup
+    echo "R_LIBS_SITE=/renv/lib/R-4.0/x86_64-pc-linux-gnu" >> /usr/lib/R/etc/Renviron.site &&\
+    # Make entrypoint script executable
+    chmod +x /usr/local/bin/rstudio-entrypoint.sh &&\
+    # open RStudio in /workspace
+    echo "session-default-working-dir=/workspace" >> /etc/rstudio/rsession.conf
+
+ENV USER rstudio
+ENV ACTION_EXEC="/usr/local/bin/rstudio-entrypoint.sh"

README.md

@@ -102,3 +102,17 @@ Find a previous version at `https://cran.r-project.org/src/contrib/Archive/{PACK
 ```sh
 just add-package PACKAGE@VERSION
 ```
+
+## Building and publishing the rstudio image
+
+The rstudio image is based on the r image including rstudio-server. To build run
+
+```sh
+just build-rstudio
+```
+
+And then push the new rstudio image to the GitHub container registry with
+
+```sh
+just publish-rstudio
+```

docker-compose.yaml

@@ -23,4 +23,8 @@ services:
       target: add-package
       args:
        - PACKAGE
-
+  rstudio:
+    extends: r
+    image: rstudio
+    build:
+      target: rstudio

justfile

@@ -22,6 +22,9 @@ build:
 add-package package:
     bash ./add-package.sh {{ package }}
 
+# r image containing rstudio-server
+build-rstudio:
+    docker-compose build --pull rstudio
 
 # test the locally built image
 test image="r": build
@@ -36,3 +39,7 @@ lint:
 publish:
     docker tag r ghcr.io/opensafely-core/r:latest
     docker push ghcr.io/opensafely-core/r:latest
+
+publish-rstudio:
+    docker tag rstudio ghcr.io/opensafely-core/rstudio:latest
+    docker push ghcr.io/opensafely-core/rstudio:latest

rstudio-dependencies.txt

@@ -0,0 +1,6 @@
+git
+libclang-dev
+lsb-release
+psmisc
+sudo
+wget

rstudio-entrypoint.sh

@@ -0,0 +1,33 @@
+#!/bin/bash
+
+# On Linux set rstudio user id to same as id of host if rstudio user id not already the same
+if [ "$HOSTPLATFORM" = "linux" -a "$(id -u rstudio)" != "$HOSTUID" ]; then
+  usermod -u $HOSTUID rstudio
+fi
+
+# Check for 1 .Rproj file
+if [ $(find /workspace -type f -name "*.Rproj" | wc -w) -eq 1 ]; then
+
+  # Copy in Git user.name and user.email from copied local-gitconfig from additionally mounted volume
+  if test -f /home/rstudio/local-gitconfig; then
+    grep -e "\[user\]" -e "name = *" -e "email = *" /home/rstudio/local-gitconfig >> /home/rstudio/.gitconfig
+  fi
+
+  # Avoid Git error: fatal detected dubious ownership of repository if using Git in container
+  # Without this the Git pane fails to open when RStudio project opened
+  echo -e "[safe]\n\tdirectory = \"*\"" >> /home/rstudio/.gitconfig
+
+  # Open RStudio project on opening RStudio Server session
+  echo 'setHook("rstudio.sessionInit", function(newSession) { if (newSession && is.null(rstudioapi::getActiveProject())) rstudioapi::openProject(paste0("/workspace/", list.files(pattern = "Rproj"))) }, action = "append")' >> /home/rstudio/.Rprofile
+fi
+
+# Set file line endings as crlf if docker run from Windows
+if [ "$HOSTPLATFORM" = "win32" ]; then
+  echo -e "{\n\t\"line_ending_conversion\": \"windows\"\n}" >> /etc/rstudio/rstudio-prefs.json
+fi
+
+# Start RStudio Server session in foreground
+# Hence don't use `rstudio-server start` which runs in background
+# and attempt to capture std out and err to a metadata log file
+mkdir -p /workspace/metadata
+exec /usr/lib/rstudio-server/bin/rserver --server-daemonize 0 >> /workspace/metadata/rstudio.log 2>&1