Problem installing Dependencies for R

JupyterHub
1

I am trying to set up an R env and install base packages for all users. The package lives on gitlab and I am using the following to install it. What happens is that during the deployment everything works fine and I can see this package being built and end successfully. Howver, at the end I cannot access any packages either they were installed by mamba or by other commands. They don’t exist in lib folder. What can I improve ?

# Copyright (c) Jupyter Development Team.
# Distributed under the terms of the Modified BSD License.
ARG BASE_CONTAINER=jupyter/r-notebook:hub-4.0.1
FROM $BASE_CONTAINER

ARG IMAGE_R_DEB_PATH=jammy
ARG STUDIO_VERSION=2023.06.1-524
# ============== ENV Variables ==============
ENV RSTUDIO_DEB=rstudio-server-${STUDIO_VERSION}-amd64.deb
ENV JUPYTER_SERVER_PROXY_VERSION=4.0.0
ENV JUPYTER_RSESSION_PROXY=2.2.0
LABEL maintainer="Maintainer <man@test.com>"

SHELL ["/bin/bash", "-o", "pipefail", "-c"]
USER root

RUN python3 -m pip install \
    jupyter-rsession-proxy==${JUPYTER_RSESSION_PROXY} \
    jupyter-server-proxy==${JUPYTER_SERVER_PROXY_VERSION}

RUN apt-get update --yes\
    && apt-get install -yq apt-utils \
    && apt-get install -yq lmodern \
    && apt-get install -yq r-base \
    && apt-get install -y libaio1 libaio-dev

# R pre-requisites
RUN apt-get install --yes --no-install-recommends \
    fonts-dejavu \
    unixodbc \
    unixodbc-dev \
    r-cran-rodbc \
    gfortran \
    gcc && \
    apt-get clean && rm -rf /var/lib/apt/lists/*



# install Java (17) for use w/ rJava
RUN wget https://download.java.net/java/GA/jdk17/0d483333a00540d886896bac774ff48b/35/GPL/openjdk-17_linux-x64_bin.tar.gz
RUN tar xvf openjdk-17_linux-x64_bin.tar.gz
RUN rm openjdk-17_linux-x64_bin.tar.gz
RUN mv jdk-17 /opt/
ENV JAVA_HOME=/opt/jdk-17
RUN echo $JAVA_HOME
RUN echo "JAVA_HOME=$JAVA_HOME" >> /etc/environment
ENV PATH=$JAVA_HOME/bin:$PATH
# The desktop package uses /usr/lib/rstudio/bin
ENV PATH="${PATH}:/usr/lib/rstudio-server/bin"
RUN echo $PATH
RUN echo "PATH=$PATH" >> /etc/environment
# ENV LD_LIBRARY_PATH="/usr/lib/R/lib:/lib:/usr/lib/x86_64-linux-gnu:$JAVA_LD_LIBRARY_PATH:/opt/conda/lib/R/lib"
ENV LD_LIBRARY_PATH="/usr/lib/R/lib:/lib:/usr/lib/x86_64-linux-gnu:${JAVA_HOME}/lib/server:/opt/conda/lib/R/lib"
RUN echo $LD_LIBRARY_PATH
RUN echo "LD_LIBRARY_PATH=$LD_LIBRARY_PATH" >> /etc/environment

USER ${NB_UID}

# i.e. unset
ENV RSTUDIO_DEB=
RUN echo "installing R packages"

# R packages including IRKernel which gets installed globally.
# r-e1071: dependency of the caret R package
RUN mamba install --yes \
    'openjdk' \
    'r-rgbif' \
    'r-raster' \
    'r-readxl' \
    'r-rgeos' \
    'r-sp' \
    'r-rgdal' \
    'r-rjava' \
    'r-svmisc' \
    'r-biomod2' \
    'r-boot' \
    'r-car' \
    'datasets' \
    'r-dismo' \
    'r-earth' \
    'r-gdalUtils' \
    'r-ggdendro' \
    'r-ggmap' \
    'r-sf' \
    'r-spatial' \
    'r-tmap'

RUN mamba install --yes \
    'r-base' \
    'r-caret' \
    'r-crayon' \
    'r-devtools' \
    'r-e1071' \
    'r-forecast' \
    'r-hexbin' \
    'r-htmltools' \
    'r-htmlwidgets' \
    'r-irkernel' \
    'r-nycflights13' \
    'r-randomforest' \
    'r-rcurl' \
    'r-rmarkdown' \
    'r-rodbc' \
    'r-rsqlite' \
    'r-shiny' \
    'r-tidymodels' \
    'r-tidyverse' \
    'r-sass=0.4.7' \
    'r-rcpp=1.0.11' \
    'r-sp=1.6_1' \
    'r-sf=1.0_14' \
    'r-remotes' \
    'unixodbc'

RUN mamba clean --all -f -y && \
    fix-permissions "${CONDA_DIR}" && \
    fix-permissions "/home/${NB_USER}"

RUN R -e "remotes::install_gitlab('my_r_package', dependencies = TRUE)"
                           
RUN echo "installing R packages COMPLETE"

RUN wget -O /opt/conda/lib/R/library/dismo/java/maxent.jar https://github.com/mrmaxent/Maxent/blob/71a46df9a1c054913d73c07a9b9ccd6c5c0dd3b9/ArchivedReleases/3.4.4/maxent.jar?raw=true

RUN R CMD javareconf -e