Merge pull request #206 from nmfs-opensci/eeholmes-patch-1

add a pull version of R

Dockerfile

@@ -14,6 +14,9 @@ USER root
 ENV REPO_DIR="/srv/repo" \
     DISPLAY=":1.0" \
     R_VERSION="4.4.1"
+# The latest rocker will set CRAN to 'latest' but we need a date stamped version for reproducibility
+# So pull the latest and use one earlier
+ARG R_VERSION_PULL="4.4.2"
 
 # Add NB_USER to staff group (required for rocker script)
 # Ensure the staff group exists first
@@ -35,7 +38,7 @@ RUN mkdir -p /pyrocket_scripts && \
 RUN /pyrocket_scripts/install-conda-packages.sh ${REPO_DIR}/environment.yml
 
 # Install R, RStudio via Rocker scripts. Requires the prefix for a rocker Dockerfile
-RUN /pyrocket_scripts/install-rocker.sh "verse_${R_VERSION}"
+RUN R_VERSION_PULL=$R_VERSION_PULL /pyrocket_scripts/install-rocker.sh "verse_${R_VERSION}"
 
 # Install extra apt packages
 # Install linux packages after R installation since the R install scripts get rid of packages

scripts/install-rocker.sh

@@ -17,7 +17,7 @@ fi
 
 # Check if a filename argument is provided
 if [ -z "$1" ]; then
-    echo "Error: install-rocker.sh requires a rocker Dockerfile prefix. Will looke like verse.4.1.1. Exiting." >&2
+    echo "Error: install-rocker.sh requires a rocker Dockerfile prefix. Will look like verse.4.1.1. Exiting." >&2
     echo "Usage: RUN /pyrocket_scripts/install-conda-packages.sh <filename>" >&2
     exit 1
 fi
@@ -34,15 +34,17 @@ R_DOCKERFILE="$1"
 export PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
 
 # Copy in the rocker files. Work in ${REPO_DIR} to make sure I don't clobber anything
+# R_VERSION_PULL may be different than R_VERSION. Specifically pulling latest but using R_VERSION prior to latest
+# So that CRAN repo is pinned to a date.
 cd ${REPO_DIR}
 ROCKER_DOCKERFILE_NAME="${R_DOCKERFILE}.Dockerfile"
 # For degugging use: wget https://github.com/eeholmes/rocker-versioned2/archive/refs/tags/R4.4.1.tar.gz
-wget https://github.com/rocker-org/rocker-versioned2/archive/refs/tags/R${R_VERSION}.tar.gz
-tar zxvf R${R_VERSION}.tar.gz && \
-mv rocker-versioned2-R${R_VERSION}/scripts /rocker_scripts && \
-mv rocker-versioned2-R${R_VERSION}/dockerfiles/${ROCKER_DOCKERFILE_NAME} /rocker_scripts/original.Dockerfile && \
-rm R${R_VERSION}.tar.gz && \
-rm -rf rocker-versioned2-R${R_VERSION}
+wget https://github.com/rocker-org/rocker-versioned2/archive/refs/tags/R${R_VERSION_PULL}.tar.gz
+tar zxvf R${R_VERSION_PULL}.tar.gz && \
+mv rocker-versioned2-R${R_VERSION_PULL}/scripts /rocker_scripts && \
+mv rocker-versioned2-R${R_VERSION_PULL}/dockerfiles/${ROCKER_DOCKERFILE_NAME} /rocker_scripts/original.Dockerfile && \
+rm R${R_VERSION_PULL}.tar.gz && \
+rm -rf rocker-versioned2-R${R_VERSION_PULL}
 
 cd /
 # Read the Dockerfile and process each line