🙊

Dockerfile

@@ -17,5 +17,7 @@ RUN conda env update -f environment.yml
 COPY install.r install.r
 RUN Rscript install.r
 
+# regular user shouldn't default to bspm
+RUN sed -i 's/^suppressMessages(bspm::enable())//' /usr/lib/R/etc/Rprofile.site
 USER ${NB_USER}
 

install_r.sh

@@ -1,21 +1,21 @@
 #!/bin/bash
 
 ## First: update apt and get keys
-apt update -qq && apt install --yes --no-install-recommends wget ca-certificates gnupg
+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 noble main" > /etc/apt/sources.list.d/cranapt.list
-apt update
+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 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 
+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
@@ -25,7 +25,7 @@ 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} \
+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")'
@@ -35,7 +35,7 @@ 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
+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