diff --git a/.github/workflows/build_and_push_to_docker.yml b/.github/workflows/build_and_push_to_docker.yml index 52490c91..43d143cd 100644 --- a/.github/workflows/build_and_push_to_docker.yml +++ b/.github/workflows/build_and_push_to_docker.yml @@ -319,11 +319,10 @@ jobs: fail-fast: true matrix: RVERSION: - - 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 + - 4.1.1 + - 4.1.2 + - devel steps: - name: Docker Login uses: Azure/docker-login@v1 @@ -375,11 +374,9 @@ jobs: fail-fast: false matrix: RELEASE: - # - devel --> commented out until issues with RStudio versions are resolved - - RELEASE_3_11 - - RELEASE_3_12 - # TODO: enable once compatibility issues are fixed - see #154 and #160 - # - RELEASE_3_13 + - RELEASE_3_13 + - RELEASE_3_14 + - devel steps: - name: Docker Login uses: Azure/docker-login@v1 diff --git a/docker/py/requirements.txt b/docker/py/requirements.txt index 7575333f..499d3c77 100644 --- a/docker/py/requirements.txt +++ b/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 diff --git a/docker/r/Dockerfile b/docker/r/Dockerfile index 8a079d3a..d333fb93 100644 --- a/docker/r/Dockerfile +++ b/docker/r/Dockerfile @@ -1,6 +1,6 @@ # define build arguments ARG RENKU_BASE=renku/renkulab-py:latest -ARG BASE_IMAGE=rocker/verse:4.0.5 +ARG BASE_IMAGE=rocker/verse:4.1.2 # define base images FROM $RENKU_BASE as renku_base @@ -17,12 +17,13 @@ ENV VENV_DIR /srv/venv ENV HOME /home/${NB_USER} ENV SHELL bash ENV CONDA_PATH /opt/conda +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 @@ -31,8 +32,13 @@ RUN echo "PATH=${PATH}" >> /usr/local/lib/R/etc/Renviron && \ ENV LD_LIBRARY_PATH /usr/local/lib/R/lib # pin the version of RStudio -ENV RSTUDIO_VERSION 1.3.959 -RUN /rocker_scripts/install_rstudio.sh +ARG RSTUDIO_VERSION_OVERRIDE="2021.09.2-382" +ENV RSTUDIO_VERSION=${RSTUDIO_VERSION_OVERRIDE} +# if rstudio and rstudio-server users are not deleted below, the installation +# script fails when it installs rstudio and tries to add them back in +RUN userdel rstudio-server && \ + userdel rstudio && \ + /rocker_scripts/install_rstudio.sh $RSTUDIO_VERSION # Add Tini ENV TINI_VERSION v0.18.0 @@ -81,7 +87,9 @@ RUN fix-permissions.sh /usr/local/lib/R && \ # this hack lets some of the setup from the base renku image work here ln -s /home/${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} @@ -89,7 +97,7 @@ USER ${NB_USER} RUN echo ". ${CONDA_PATH}/etc/profile.d/conda.sh" >> ~/.bashrc && \ echo "conda activate base" >> ~/.bashrc -RUN pip install "jupyter-rsession-proxy==1.1" +RUN pip install "jupyter-rsession-proxy==2.0.1" # install IRKernel RUN R --quiet -e "install.packages('IRkernel')" && \