Update Dockerfile (revert back to last working version)

Dockerfile

@@ -3,11 +3,11 @@
 # For finding rocker images see
 # https://github.com/rocker-org/rocker-versioned2
 
-# Define build arguments
+# define build arguments
 ARG RENKU_BASE=renku/renkulab-py:3.8-0.8.0
 ARG BASE_IMAGE=rocker/geospatial:4.0.5
 
-# Define base images
+# define base images
 FROM $RENKU_BASE as renku_base
 FROM $BASE_IMAGE
 
@@ -23,19 +23,28 @@ ENV HOME /home/${NB_USER}
 ENV SHELL bash
 ENV CONDA_PATH /opt/conda
 
-# Prepend conda and local/bin to PATH
+# prepend conda and local/bin to PATH
 ENV PATH ${HOME}/.local/bin:${CONDA_PATH}/bin:$PATH
 
 # The `rsession` binary that is called by nbrsessionproxy to start R
 # doesn't seem to start without this being explicitly set
 ENV LD_LIBRARY_PATH /usr/local/lib/R/lib
 
+# pin the version of RStudio
+ENV RSTUDIO_VERSION 1.3.959
+#ENV RSESSION_PROXY_RSTUDIO_1_4 yes # Required if RStudio version is >= 1.4
+# Set PATH for R! It doesn't read from the environment...
+# and install pinned RStudio version
+RUN echo "PATH=${PATH}" >> /usr/local/lib/R/etc/Renviron && \
+echo "PATH=${PATH}" >> /etc/profile.d/set_path.sh && \
+/rocker_scripts/install_rstudio.sh
+
 # Add Tini
 ENV TINI_VERSION v0.18.0
 ADD https://github.com/krallin/tini/releases/download/${TINI_VERSION}/tini /tini
 RUN chmod +x /tini && ln -s /tini /usr/bin/
 
-# Install system dependencies
+# install dependencies
 RUN apt-get update --fix-missing && \
     apt-get install -yq --no-install-recommends \
     bzip2 \
@@ -58,47 +67,26 @@ RUN apt-get update --fix-missing && \
     wget \
     vim \
     # for mongolite
-    #libssl-dev \
-    libsasl2-dev \
-    # for sys
-    #libapparmor-dev \
-    # for nloptr
-    #libnlopt-dev \
+    #libsasl2-dev \
     # for keyring
-    libsecret-1-dev \
-    # for sodium
-    #libsodium-dev \
-    # for ssh
-    #libssh-dev \
-    # suggested by magick and gganimate
-    #libavfilter-dev \
+    #libsecret-1-dev \
     # added for SciViews Box/BioDataScience
     hunspell-en-us \
     hunspell-en-gb \
     hunspell-fr-classical \
-    #xclip \
     nano && \
     apt-get purge && \
     apt-get clean && \
     apt autoremove --yes && \
     rm -rf /var/lib/apt/lists/*
 
-# Inject the renku-jupyter stack
+# inject the renku-jupyter stack
 COPY --from=renku_base /opt/conda /opt/conda
 COPY --from=renku_base --chown=rstudio:rstudio  /usr/local/bin/ /usr/local/bin/
 COPY --from=renku_base --chown=rstudio:rstudio  /home/jovyan/ /home/rstudio/
 COPY --from=renku_base /entrypoint.sh /entrypoint.sh
 
-# Pin the version of RStudio
-ENV RSTUDIO_VERSION 1.3.959
-#ENV RSESSION_PROXY_RSTUDIO_1_4 yes # Required if RStudio version is >= 1.4
-# Set PATH for R! It doesn't read from the environment...
-# and install pinned RStudio version
-RUN echo "PATH=${PATH}" >> /usr/local/lib/R/etc/Renviron && \
-    echo "PATH=${PATH}" >> /etc/profile.d/set_path.sh && \
-    /rocker_scripts/install_rstudio.sh
-
-# Set permissions of the R library directory to be editable by NB_USER
+# set permissions of the R library directory to be editable by NB_USER
 # This is done in the original image, but we don't want this: we want users to
 # install packages in the ~/R folder instead
 #ADD fix-permissions.sh /usr/local/bin
@@ -108,7 +96,7 @@ RUN chown 1000:1000 /opt/conda && \
     # this hack lets some of the setup from the base renku image work here
     ln -s /home/${NB_USER} /home/jovyan
 
-# Customize RStudio
+# customize RStudio
 COPY config/dictionaries/* /usr/share/hunspell/
 RUN mkdir -p /home/rstudio/.config/rstudio/dictionaries && \
     chown 1000:1000 /home/rstudio/.config/rstudio/dictionaries && \
@@ -134,7 +122,7 @@ COPY config/rstudio-prefs.json /etc/rstudio
 
 USER ${NB_USER}
 
-# Set up conda in the NB_USER environment
+# set up conda in the NB_USER environment
 RUN echo ". ${CONDA_PATH}/etc/profile.d/conda.sh" >> ~/.bashrc && \
     echo "conda activate base" >> ~/.bashrc && \
     pip install "jupyter-rsession-proxy==1.1" && \
@@ -143,11 +131,11 @@ RUN echo ". ${CONDA_PATH}/etc/profile.d/conda.sh" >> ~/.bashrc && \
     R --quiet -e "IRkernel::installspec(prefix='${CONDA_PATH}')" && \
     echo "source ~/.bashrc" >> ~/.bash_profile
 
-# Install R and python dependencies (plus a JS dependency for webshot)
+# install R and python dependencies
 COPY install.R /tmp/
 COPY requirements.txt /tmp/
 RUN R -f /tmp/install.R && \
-    R --quiet -e "install.packages('webshot'); webshot::install_phantomjs()" && \
+    #R --quiet -e "install.packages('webshot'); webshot::install_phantomjs()" && \
     pip3 install -r /tmp/requirements.txt
 
 COPY post-init.sh /post-init.sh