small base image

images/Dockerfile.R

@@ -1,40 +1,16 @@
-FROM quay.io/jupyter/pytorch-notebook:cuda12-ubuntu-24.04
-COPY jupyter-ai.yml environment.yml
-
-RUN conda update -n base -c conda-forge conda && \
-    conda env update --file environment.yml
+FROM quay.io/jupyter/minimal-notebook
 
 USER root
-RUN curl -fsSL https://code-server.dev/install.sh | sh && rm -rf .cache
-RUN git config --system pull.rebase false && \
-    echo '"\e[5~": history-search-backward' >> /etc/inputrc && \
-    echo '"\e[6~": history-search-forward' >> /etc/inputrc
-
-RUN usermod -a -G staff ${NB_USER} \
-  && echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen \
-  && locale-gen en_US.utf8 \
-  && /usr/sbin/update-locale LANG=en_US.UTF-8
 
-## Set some variables
-ENV LC_ALL en_US.UTF-8
-ENV LANG en_US.UTF-8
-ENV DEBIAN_FRONTEND noninteractive
-ENV TZ UTC
+# Install R
+COPY install_r.sh install_r.sh
+RUN bash install_r.sh
 
-RUN curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/refs/heads/master/inst/scripts/add_cranapt_noble.sh | sh
-RUN apt-get update && \
-  apt-get install -y --no-install-recommends \
-  r-base r-base-dev r-recommended \
-  r-cran-docopt r-cran-littler r-cran-remotes \
-  python3-dbus python3-gi python3-apt sudo \
-  && Rscript -e 'install.packages("bspm")'  \
-  ## Support user-level installation of R packages
-  && chown root:staff /usr/lib/R/site-library \
-  && chmod g+ws /usr/lib/R/site-library \
-  && echo "options(bspm.sudo = TRUE)" >> /usr/lib/R/etc/Rprofile.site
+# Now install any CRAN packages the usual way
+RUN R -e "install.packages(c('terra', 'stars'))"
 
-## add user to sudoers
-RUN echo "${NB_USER} ALL=(ALL) NOPASSWD: ALL" >> /etc/sudoers
+## Or the more concise Rocker way
+RUN install2.r rstan ROracle
 
 ## RStudio
 RUN conda install jupyter-rsession-proxy

images/install_r.sh

@@ -0,0 +1,48 @@
+#!/bin/bash
+
+## First: update apt and get keys
+apt update -qq && apt install --yes --no-install-recommends wget ca-certificates gnupg
+wget -q -O- https://eddelbuettel.github.io/r2u/assets/dirk_eddelbuettel_key.asc \
+    | tee -a /etc/apt/trusted.gpg.d/cranapt_key.asc
+
+## Second: add the repo -- here we use the well-connected mirror
+echo "deb [arch=amd64] https://r2u.stat.illinois.edu/ubuntu noble main" > /etc/apt/sources.list.d/cranapt.list
+apt update
+
+## Third: ensure current R is used
+wget -q -O- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc \
+    | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
+echo "deb [arch=amd64] https://cloud.r-project.org/bin/linux/ubuntu noble-cran40/" > /etc/apt/sources.list.d/cran_r.list
+apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 67C2D66C4B1D4339 51716619E084DAB9
+apt update -qq
+DEBIAN_FRONTEND=noninteractive apt install --yes --no-install-recommends r-base r-base-dev r-recommended 
+
+## Fourth: add pinning to ensure package sorting
+echo "Package: *" > /etc/apt/preferences.d/99cranapt
+echo "Pin: release o=CRAN-Apt Project" >> /etc/apt/preferences.d/99cranapt
+echo "Pin: release l=CRAN-Apt Packages" >> /etc/apt/preferences.d/99cranapt
+echo "Pin-Priority: 700"  >> /etc/apt/preferences.d/99cranapt
+
+## Fifth: install bspm (and its Python requirements) and enable it
+## If needed (in bare container, say) install python tools for bspm and R itself
+apt install --yes --no-install-recommends python3-{dbus,gi,apt} \
+	make sudo r-cran-{docopt,littler,remotes} 
+## Then install bspm (as root) and enable it, and enable a speed optimization
+Rscript -e 'install.packages("bspm")'
+RHOME=$(R RHOME)
+echo "suppressMessages(bspm::enable())" >> ${RHOME}/etc/Rprofile.site
+echo "options(bspm.version.check=FALSE)" >> ${RHOME}/etc/Rprofile.site
+
+chown root:staff ${RHOME}/site-library
+chmod g+ws ${RHOME}/site-library
+echo "options('bspm.sudo' = TRUE)" >> ${RHOME}/etc/Rprofile.site
+
+
+ln -s /usr/lib/R/site-library/littler/examples/install2.r /usr/local/bin/install2.r
+
+
+## add user to sudoers
+usermod -a -G staff ${NB_USER}
+echo "${NB_USER} ALL=(ALL) NOPASSWD: ALL" >> /etc/sudoers
+
+