Fix the user and the rserver settings.

Dockerfile

@@ -9,6 +9,7 @@ LABEL org.d4science.image.licenses="EUPL-1.2" \
 ARG NB_USER="jovyan"
 ARG NB_UID="1000"
 ARG NB_GID="100"
+ARG HOME="/home/${NB_USER}"
 ENV S6_VERSION=v2.1.0.2
 ENV RSTUDIO_VERSION=2022.02.1+461
 ENV DEFAULT_USER="jovyan"
@@ -37,14 +38,35 @@ RUN /rocker_scripts/install_rstudio.sh
 RUN echo "www-frame-origin=same" >> /etc/rstudio/disable_auth_rserver.conf
 RUN echo "www-verify-user-agent=0" >> /etc/rstudio/disable_auth_rserver.conf
 
-ADD 01_set_env.sh /etc/cont-init.d/01_set_env
-ADD 02_userconf.sh /etc/cont-init.d/02_userconf
-ADD 03_setup_root_path.sh /etc/cont-init.d/03_setup_root_path
+ARG EXCLUDE_VARS="HOME PASSWORD RSTUDIO_VERSION BATCH_USER_CREATION"
+ARG R_HOME="/usr/local"
+# The 0*_ scripts cannot be used anymore
+# ADD 01_set_env.sh /etc/cont-init.d/01_set_env
+RUN for file in /var/run/s6/container_environment/* ; do sed -i "/^${file##*/}=/d" ${R_HOME}/etc/Renviron.site ; regex="(^| )${file##*/}($| )" ;
+  [[ ! $exclude_vars =~ $regex ]] && echo "${file##*/}=$(cat $file)" >> ${R_HOME}/etc/Renviron.site ; done
+
+# ADD 02_userconf.sh /etc/cont-init.d/02_userconf
+RUN mv -f /etc/rstudio/disable_auth_rserver.conf /etc/rstudio/rserver.conf
+RUN echo "USER=$NB_USER" >> /etc/environment
+
+# ADD 03_setup_root_path.sh /etc/cont-init.d/03_setup_root_path
 
 # By default RStudio does not give access to all enviornment variables defined in the container (e.g. using ShinyProxy).
 # Uncomment the next line, to change this behavior.
-ADD 04_copy_env.sh /etc/cont-init.d/04_copy_env
-ADD 05_setup_rsession_parameters.sh /etc/cont-init.d/05_setup_rsession_parameters
+# ADD 04_copy_env.sh /etc/cont-init.d/04_copy_env
+# ADD 05_setup_rsession_parameters.sh /etc/cont-init.d/05_setup_rsession_parameters
+RUN echo "session-timeout-minutes=7200" >> /etc/rstudio/rsession.conf
+RUN echo "session-disconnected-timeout-minutes=1440" >> /etc/rstudio/rsession.conf
+RUN echo "session-quit-child-processes-on-exit=0" >> /etc/rstudio/rsession.conf
+RUN echo "session-default-working-dir=~" >> /etc/rstudio/rsession.conf
+RUN echo "session-default-new-project-dir=~" >> /etc/rstudio/rsession.conf
+RUN #echo "session-save-action-default=yes" >> /etc/rstudio/rsession.conf
+RUN echo "allow-shell=1" >> /etc/rstudio/rsession.conf
+RUN #echo "allow-terminal-websockets=1" >> /etc/rstudio/rsession.conf
+RUN echo "limit-cpu-time-minutes=0" >> /etc/rstudio/rsession.conf
+RUN echo "limit-file-upload-size-mb=0" >> /etc/rstudio/rsession.conf
+RUN #echo "limit-xfs-disk-quota=no" >> /etc/rstudio/rsession.conf
+RUN curl -o /etc/R/Rprofile.site "https://code-repo.d4science.org/gCubeSystem/rstudio-rprofile/raw/branch/master/jupyter-Rprofile.site"
 
 # Copy a script that we will use to correct permissions after running certain commands
 COPY fix-permissions /usr/local/bin/fix-permissions
@@ -55,6 +77,8 @@ RUN chmod a+rx /usr/local/bin/fix-permissions
 RUN echo "auth requisite pam_deny.so" >> /etc/pam.d/su && \
     sed -i.bak -e 's/^%admin/#%admin/' /etc/sudoers && \
     sed -i.bak -e 's/^%sudo/#%sudo/' /etc/sudoers && \
+    userdel -r rstudio && \
+    useradd -l -m -s /bin/bash -N -u "${NB_UID}" "${NB_USER}" && \
     chmod g+w /etc/passwd && \
     fix-permissions "${HOME}"
 
@@ -71,11 +95,12 @@ RUN apt-get clean && rm -rf /var/lib/apt/lists/* && \
     echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \
     locale-gen
 
-
 # Enable prompt color in the skeleton .bashrc before creating the default NB_USER
 # hadolint ignore=SC2016
 RUN sed -i 's/^#force_color_prompt=yes/force_color_prompt=yes/' /etc/skel/.bashrc
 
+WORKDIR ${HOME}
+
 # Prepare the workspace environment
 # RUN mkdir -p /opt/workspace-lib
 # RUN mkdir /var/log/workspace-lib
@@ -84,5 +109,4 @@ RUN sed -i 's/^#force_color_prompt=yes/force_color_prompt=yes/' /etc/skel/.bashr
 # ADD 06-fuse-logback.xml /opt/workspace-lib/logback.xml
 
 # EXPOSE 8787
-
-CMD ["/init"]
+# CMD ["/init"]