Merge pull request #10 from opensafely-core/Jongmassey/port-R-fixes

Port R and Python fixes from research template "improve devcontainers" branch

Dockerfile

@@ -6,9 +6,6 @@ LABEL org.opencontainers.image.source https://github.com/opensafely/research-tem
 # docker clean up that deletes that cache on every apt install
 RUN rm -f /etc/apt/apt.conf.d/docker-clean
 
-# Install python 3.10. This is the version used by the python-docker 
-# image, used for analyses using the OpenSAFELY pipeline.
-#
 # DL3042: we always want latest package versions when we rebuild
 # DL3013: using an apt cache on the host instead
 # hadolint ignore=DL3042,DL3013
@@ -17,33 +14,38 @@ RUN --mount=type=cache,target=/var/cache/apt \
     echo "deb http://ppa.launchpadcontent.net/deadsnakes/ppa/ubuntu focal main" > /etc/apt/sources.list.d/deadsnakes-ppa.list &&\
     /usr/lib/apt/apt-helper download-file 'https://keyserver.ubuntu.com/pks/lookup?op=get&search=0xf23c5a6cf475977595c89f51ba6932366a755776' /etc/apt/trusted.gpg.d/deadsnakes.asc &&\
     apt-get update &&\
+    # Install python 3.10. This is the version used by the python-docker 
+    # image, used for analyses using the OpenSAFELY pipeline.
     apt-get install -y --no-install-recommends curl python3.10 python3.10-distutils python3.10-venv &&\
     # Pip for Python 3.10 isn't included in deadsnakes, so install separately
     curl https://bootstrap.pypa.io/get-pip.py | python3.10 &&\
     # Set default python, so that the Python virtualenv works as expected
     rm /usr/bin/python3 &&\
-    ln -s /usr/bin/python3.10 /usr/bin/python3
-
-# install renv
-RUN --mount=type=cache,target=/cache,id=/cache-2004 R -e 'install.packages("renv", destdir="/cache"); renv::init(bare = TRUE)'
+    ln -s /usr/bin/python3.10 /usr/bin/python3 &&\
+    # Create a fake system Python pointing at venv python
+    echo 'exec /opt/venv/bin/python3.10 "$@"' > /usr/bin/python &&\
+    # Configure RStudio Server to run without auth
+    echo "auth-none=1" >> /etc/rstudio/rserver.conf &&\
+    echo "USER=rstudio" >> /etc/environment &&\
+    # Remove the packages shipped with the rocker image
+    rm -rf /usr/library/lib/R/site-library/* &&\
+    # Give the local user sudo (aka root) permissions
+    usermod -aG sudo rstudio &&\
+    echo '%sudo ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers
 
-# copy the renv directory from the OpenSAFELY R action image
+# Copy the Python virtualenv from OpenSAFELY Python action image
 #
 # DL3022: hadolint can't access a network and doesn't behave
 # as expected when a reference is made to an external image.
 # hadolint ignore=DL3022
-COPY --from=ghcr.io/opensafely-core/r /renv/ /renv/
+COPY --chown=rstudio:rstudio --from=ghcr.io/opensafely-core/python:v2 /opt/venv /opt/venv
 
-# Copy the Python virtualenv from OpenSAFELY Python action image
+# copy the renv directory into the local site library from the OpenSAFELY R action image
 #
 # DL3022: hadolint can't access a network and doesn't behave
 # as expected when a reference is made to an external image.
 # hadolint ignore=DL3022
-COPY --from=ghcr.io/opensafely-core/python:v2 /opt/venv /opt/venv
-
-# Create a local user and give it sudo (aka root) permissions
-RUN usermod -aG sudo rstudio &&\
-    echo '%sudo ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers
+COPY --chown=rstudio:rstudio --from=ghcr.io/opensafely-core/r:latest /renv/lib/R-4.0/x86_64-pc-linux-gnu/ /usr/local/lib/R/site-library
 
 # Required for installing opensafely cli
 ENV PATH="/home/rstudio/.local/bin:${PATH}"