FROM d4science/rstudio-base:2023-03-R4-2

LABEL org.d4science.image.licenses="EUPL-1.2" \
      org.d4science.image.source="https://code-repo.d4science.org/gCubeSystem/rstudio-d4science" \
      org.d4science.image.vendor="D4Science <https://www.d4science.org>" \
      org.d4science.image.authors="Andrea Dell'Amico <andrea.dellamico@isti.cnr.it>"

# R required by vlab5 VRE https://support.d4science.org/issues/23536

ENV DEBIAN_FRONTEND noninteractive
# Upgrade, install some R dependencies and base python3
# Add libcurl4-gnutls-dev and remove libcurl4-openssl-dev because
# 
# libraptor2-dev : Depends: libcurl4-gnutls-dev but it is not installable
RUN apt-get update --yes && \
    apt-get install --yes --no-install-recommends \
    libgdal-dev \
    pandoc \
    pandoc-citeproc \
    texlive-xetex \
    texlive-latex-base \
    texlive-latex-recommended \
    texlive-fonts-recommended \
    texlive-fonts-extra \
    texlive-formats-extra \
    libssl-dev \
    libxml2-dev \
    libv8-dev \
    libsecret-1-dev \
    librdf0-dev \
    libgit2-dev \
    libxslt-dev \
    librdf0 \
    redland-utils \
    rasqal-utils \
    raptor2-utils \
    libcairo2-dev \
    libpoppler-cpp-dev \
    libmagick++-dev \
    cmake \
    cargo \
    libavfilter-dev \
    libjq-dev \
    libprotobuf-dev \
    protobuf-compiler \
    libproj-dev \
    libcurl4-gnutls-dev \
    libsodium-dev \
    libudunits2-dev \
    libglpk40

RUN mkdir -p /opt/workspace-lib
RUN mkdir /var/log/workspace-lib
ADD https://maven.d4science.org/nexus/content/repositories/gcube-snapshots/org/gcube/data-access/sh-fuse-integration/2.0.0-SNAPSHOT/sh-fuse-integration-2.0.0-20211005.090627-1-jar-with-dependencies.jar /opt/workspace-lib/fuse-workspace.jar
RUN chmod 0644 /opt/workspace-lib/fuse-workspace.jar

COPY install2r-packages.txt /rocker_scripts
RUN for f in `cat /rocker_scripts/install2r-packages.txt` ; do install2.r --error --skipinstalled --ncpus -1 $f || exit 1 ; done

RUN installGithub.r -d TRUE -u FALSE -r https://packagemanager.rstudio.com/all/__linux__/jammy/latest r-geoflow/geoflow
RUN installGithub.r -d TRUE -u FALSE -r https://packagemanager.rstudio.com/all/__linux__/jammy/latest hrbrmstr/streamgraph

# Rstudio settings
COPY rsession.conf /etc/rstudio/rsession.conf
RUN chmod 0644 /etc/rstudio/rsession.conf
RUN curl -o "${R_HOME}/etc/Rprofile.site" "https://code-repo.d4science.org/gCubeSystem/rstudio-rprofile/raw/branch/master/jupyter-Rprofile.site"

RUN rm -fr /tmp/downloaded_packages/*

RUN rm -fr /tmp/downloaded_packages/* && \
    apt-get clean && rm -rf /var/lib/apt/lists/* && \
    rm -f /tmp/R*