🐳

Author: cboettig

Dockerfile

@@ -18,6 +18,9 @@ RUN adduser "$NB_USER" sudo && echo '%sudo ALL=(ALL) NOPASSWD:ALL' >>/etc/sudoer
 RUN curl -s https://raw.githubusercontent.com/rocker-org/ml/refs/heads/master/install_r.sh | bash
 RUN curl -s https://raw.githubusercontent.com/rocker-org/ml/refs/heads/master/install_rstudio.sh | bash
 
+# Configure Runiverse
+COPY Rprofile $/usr/lib/R/etc/Rprofile.site
+
 ## Add rstudio's binaries to path for quarto
 ENV PATH=$PATH:/usr/lib/rstudio-server/bin/quarto/bin
 

install_bspm.sh

@@ -0,0 +1,17 @@
+## 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-get 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")'
+
+R_HOME=$(R RHOME)
+# must go first.  Only configure for ROOT user
+echo "options(bspm.sudo = TRUE)" >> ${HOME}/.Rprofile
+echo "options(bspm.version.check=FALSE)" >> ${HOME}/.Rprofile
+echo "suppressMessages(bspm::enable())" >> ${HOME}/.Rprofile
+
+chown root:users ${R_HOME}/site-library
+chmod g+ws ${R_HOME}/site-library
+
+

install_r.sh

@@ -0,0 +1,38 @@
+#!/bin/bash
+
+# determine Ubuntu release
+source /etc/os-release
+
+## First: update apt and get keys
+apt-get update -qq && apt-get 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 ${UBUNTU_CODENAME} main" > /etc/apt/sources.list.d/cranapt.list
+apt-get 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 ${UBUNTU_CODENAME}-cran40/" > /etc/apt/sources.list.d/cran_r.list
+apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 67C2D66C4B1D4339 51716619E084DAB9
+apt-get update -qq
+DEBIAN_FRONTEND=noninteractive apt-get 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
+
+chown root:users ${R_HOME}/site-library
+chmod g+ws ${R_HOME}/site-library
+
+ln -s /usr/lib/R/site-library/littler/examples/install2.r /usr/local/bin/install2.r
+
+## add user to sudoers -- not jupyterhub compatible
+# usermod -a -G staff ${NB_USER}
+# echo "${NB_USER} ALL=(ALL) NOPASSWD: ALL" >> /etc/sudoers
+
+