chore: update Rstudio and R version

.github/workflows/build_and_push_to_docker.yml

@@ -322,8 +322,7 @@ jobs:
           - 4.0.3
           - 4.0.4
           - 4.0.5
-          # TODO: enable once compatibility issues are fixed  - see #154 and #160
-          # - 4.1.0
+          - 4.1.0
     steps:
     - name: Docker Login
       uses: Azure/docker-login@v1
@@ -375,11 +374,10 @@ jobs:
       fail-fast: false
       matrix:
         RELEASE:
-        # - devel --> commented out until issues with RStudio versions are resolved
+          - devel
           - RELEASE_3_11
           - RELEASE_3_12
-          # TODO: enable once compatibility issues are fixed - see #154 and #160
-          # - RELEASE_3_13
+          - RELEASE_3_13
     steps:
     - name: Docker Login
       uses: Azure/docker-login@v1

docker/py/requirements.txt

@@ -1,4 +1,4 @@
-jupyter-server-proxy~=3.1.0
+jupyter-server-proxy~=3.2.1
 jupyterlab-git==0.30.1
 jupyterlab-system-monitor~=0.8.0
 jupyterlab~=3.0.0

docker/r/Dockerfile

@@ -17,12 +17,16 @@ ENV VENV_DIR /srv/venv
 ENV HOME /home/${NB_USER}
 ENV SHELL bash
 ENV CONDA_PATH /opt/conda
+# Do not change the line below, by default the shell is /bin/sh -c
+# and /bin/sh -c does not work when you do source venv/bin/activate
+# in the reknu project template Dockerfile
+SHELL ["/bin/bash", "-c"]
 
 # prepend conda and local/bin to PATH
 ENV PATH ${HOME}/.local/bin:${CONDA_PATH}/bin:$PATH
 
 # And set PATH for R! It doesn't read from the environment...
-RUN echo "PATH=${PATH}" >> /usr/local/lib/R/etc/Renviron && \
+RUN echo "PATH=${PATH}" >> /usr/local/lib/R/etc/Renviron.site && \
     echo "PATH=${PATH}" >> /etc/profile.d/set_path.sh && \
     echo "RENKU_DISABLE_VERSION_CHECK=1" >> /usr/local/lib/R/etc/Renviron
 
@@ -31,9 +35,9 @@ RUN echo "PATH=${PATH}" >> /usr/local/lib/R/etc/Renviron && \
 ENV LD_LIBRARY_PATH /usr/local/lib/R/lib
 
 # pin the version of RStudio
-# ENV RSTUDIO_VERSION 2021.09.2+382
-# RUN /rocker_scripts/install_rstudio.sh
-# This version of rocker should already have RStudio installed!
+ARG RSTUDIO_VERSION="2021.09.2-382"
+ENV RSTUDIO_VERSION="$RSTUDIO_VERSION"
+RUN /rocker_scripts/install_rstudio.sh
 
 # Add Tini
 ENV TINI_VERSION v0.18.0
@@ -82,7 +86,9 @@ RUN fix-permissions.sh /usr/local/lib/R && \
     # this hack lets some of the setup from the base renku image work here
     ln -s /home/${NB_USER} /home/jovyan && \
     # this allows rstudio to run in an iframe in the UI
-    echo "\nwww-frame-origin=same\n" >> /etc/rstudio/rserver.conf
+    echo "" >> /etc/rstudio/rserver.conf && \
+    echo "www-frame-origin=same" >> /etc/rstudio/rserver.conf && \
+    echo "" >> /etc/rstudio/rserver.conf
 
 USER ${NB_USER}