Merge pull request #257 from nmfs-opensci/test

add R kernel

Author: eeholmes

Dockerfile

@@ -3,9 +3,9 @@ FROM ghcr.io/nmfs-opensci/py-rocket-base/base-image:latest
 LABEL org.opencontainers.image.maintainers="eli.holmes@noaa.gov"
 LABEL org.opencontainers.image.author="eli.holmes@noaa.gov"
 LABEL org.opencontainers.image.source=https://github.com/nmfs-opensci/py-rocket-base
-LABEL org.opencontainers.image.description="Python (3.12), R (4.4.2), Desktop and Publishing tools"
+LABEL org.opencontainers.image.description="Python (3.12), R (4.4.3), Desktop and Publishing tools"
 LABEL org.opencontainers.image.licenses=Apache2.0
-LABEL org.opencontainers.image.version=2025.03.13
+LABEL org.opencontainers.image.version=2025.04.11
 
 USER root
 
@@ -14,7 +14,7 @@ USER root
 # Set QUARTO_VERSION due to Jupyter Lab bug with version 1.6 that won't all qmd to open
 ENV REPO_DIR="/srv/repo" \
     DISPLAY=":1.0" \
-    R_VERSION="4.4.2" \
+    R_VERSION="4.4.3" \
     QUARTO_VERSION="1.5.57" \
     UBUNTU_VERSION="jammy"
 ENV LANG=en_US.UTF-8
@@ -51,6 +51,15 @@ RUN /pyrocket_scripts/install-conda-packages.sh ${REPO_DIR}/environment.yml
 # Be aware that if R_VERSION_PULL is set to the latest release, CRAN repo will use "latest" and date will not be pinned.
 RUN R_VERSION_PULL="master" /pyrocket_scripts/install-rocker.sh "verse_${R_VERSION}"
 
+# Install IRkernel and register it with Jupyter so we can select an R kernel with Jupyter Lab
+# When R is invoked, the PATH is cleaned to remove conda, but need to add conda on temporarily so that
+# installspec can find jupyter (which is in conda dir)
+RUN Rscript - <<EOF
+install.packages('IRkernel')
+Sys.setenv(PATH = paste("/srv/conda/envs/notebook/bin", Sys.getenv("PATH"), sep = ":"))
+IRkernel::installspec(name = "ir443", displayname = "R 4.4.3")
+EOF
+
 # Install Zotero; must be run before apt since zotero apt install requires this is run first
 RUN wget -qO- https://raw.githubusercontent.com/retorquere/zotero-deb/master/install.sh | bash 
 
@@ -85,15 +94,15 @@ RUN mkdir -p ${XDG_CONFIG_HOME} && \
 # Fix home permissions. Not needed in JupyterHub with persistent memory but needed if not used in that context
 RUN /pyrocket_scripts/fix-home-permissions.sh
 
-# Allow user to change the rstudio server conf if needed.
-RUN chown jovyan:users /etc/rstudio/rserver.conf
-
-# Create a symlink for python to python3 and gh-scoped-creds for all users; need for RStudio sinc conda not on path
+# Create a symlink for python to python3 and gh-scoped-creds for all users; need for RStudio since conda not on path
 RUN ln -s /usr/bin/python3 /usr/local/bin/python
 RUN ln -s /srv/conda/envs/notebook/bin/gh-scoped-creds /usr/local/bin/gh-scoped-creds
 RUN ln -s /srv/conda/condabin/conda /usr/local/bin/conda
 RUN ln -s /srv/conda/envs/notebook/bin/pip /usr/local/bin/pip
- 
+
+# Allow user to change the rstudio server conf if needed.
+RUN chown jovyan:users /etc/rstudio/rserver.conf
+
 # Set up the start command 
 USER ${NB_USER}
 RUN chmod +x ${REPO_DIR}/start \

environment.yml

@@ -14,9 +14,7 @@ dependencies:
 
   # R/RStudio Support
   - jupyter-rsession-proxy
-  # Run R in Jupyter Lab
-  - r-irkernel
-  
+
   # VS Code support
   - jupyter-vscode-proxy
   - code-server=4.98.0  # Pin to prevent downgrades when conda env is updated