Refactor Images to Multi-Stage Builds

.github/dependabot.yml

@@ -0,0 +1,8 @@
+version: 2
+updates:
+  - package-ecosystem: "docker"
+    directory: "/r-base/"
+    schedule:
+      interval: "monthly"
+    assignees:
+      - "jan-abel-inwt"

Jenkinsfile

@@ -21,7 +21,10 @@ pipeline {
             steps {
                 withDockerRegistry([ credentialsId: "jenkins-docker-hub", url: "" ]) {
                 sh '''
-                docker build -t inwt/r-base:$LABEL r-base
+                docker build \
+                  --label org.opencontainers.image.revision=$(git rev-parse HEAD) \
+                  --label org.opencontainers.image.created=$(date -u +%Y-%m-%dT%H:%M:%SZ) \
+                  -t inwt/r-base:$LABEL r-base
                 docker push inwt/r-base:$LABEL
                 '''
                 }
@@ -31,7 +34,10 @@ pipeline {
             steps {
                 withDockerRegistry([ credentialsId: "jenkins-docker-hub", url: "" ]) {
                 sh '''
-                docker build -t inwt/r-batch:$LABEL r-batch
+                docker build \
+                  --label org.opencontainers.image.revision=$(git rev-parse HEAD) \
+                  --label org.opencontainers.image.created=$(date -u +%Y-%m-%dT%H:%M:%SZ) \
+                  -t inwt/r-batch:$LABEL r-batch
                 docker push inwt/r-batch:$LABEL
                 '''
                 }
@@ -41,7 +47,10 @@ pipeline {
             steps {
                 withDockerRegistry([ credentialsId: "jenkins-docker-hub", url: "" ]) {
                 sh '''
-                docker build -t inwt/r-shiny:$LABEL r-shiny
+                docker build \
+                  --label org.opencontainers.image.revision=$(git rev-parse HEAD) \
+                  --label org.opencontainers.image.created=$(date -u +%Y-%m-%dT%H:%M:%SZ) \
+                  -t inwt/r-shiny:$LABEL r-shiny
                 docker push inwt/r-shiny:$LABEL
                 '''
                 }
@@ -51,7 +60,10 @@ pipeline {
             steps {
                 withDockerRegistry([ credentialsId: "jenkins-docker-hub", url: "" ]) {
                 sh '''
-                docker build -t inwt/r-model:$LABEL r-model
+                docker build \
+                  --label org.opencontainers.image.revision=$(git rev-parse HEAD) \
+                  --label org.opencontainers.image.created=$(date -u +%Y-%m-%dT%H:%M:%SZ) \
+                  -t inwt/r-model:$LABEL r-model
                 docker push inwt/r-model:$LABEL
                 '''
                 }
@@ -61,7 +73,10 @@ pipeline {
             steps {
                 withDockerRegistry([ credentialsId: "jenkins-docker-hub", url: "" ]) {
                 sh '''
-                docker build -t inwt/r-geos:$LABEL r-geos
+                docker build \
+                  --label org.opencontainers.image.revision=$(git rev-parse HEAD) \
+                  --label org.opencontainers.image.created=$(date -u +%Y-%m-%dT%H:%M:%SZ) \
+                  -t inwt/r-geos:$LABEL r-geos
                 docker push inwt/r-geos:$LABEL
                 '''
                 }

Makefile

@@ -0,0 +1,28 @@
+R_VERSION := 4.5.1
+TAG := ${R_VERSION}
+IMAGES := r-base r-batch r-model r-geos r-shiny
+
+.PHONY: update-version
+update-version:
+	@echo "--- Updating R version tags to ${R_VERSION} in Dockerfiles ---"
+	@for image in ${IMAGES}; do \
+		file="$$image/Dockerfile"; \
+		sed -i "s/\(ARG R_VERSION=\)[0-9]\+\.[0-9]\+\.[0-9]\+/\1${R_VERSION}/g" "$$file" \
+		&& echo "Updated $$file"; \
+	done
+	@echo "--- All Dockerfiles updated successfully! ---"
+
+.PHONY: all $(IMAGES) clean
+all: $(IMAGES)
+	@echo "--- Successfully built all Docker images with tag: $(TAG) ---"
+
+$(IMAGES):
+	@echo "Building Docker image: inwt/$@:$(TAG) from folder: $@"
+	docker build -t inwt/$@:$(TAG) $@
+
+.PHONY: clean
+clean:
+	@echo "Removing locally tagged images for version ${TAG}..."
+	@for img in ${ALL_IMAGES}; do \
+		docker rmi inwt/$$img:${TAG} || true; \
+	done

README.md

@@ -1,4 +1,4 @@
-# Container for R Applications
+# Multi Stage Container for R Applications
 
 In this project we keep our configuration for INWT projects. If you are not working with us you can
 see what we think is a good way to bring R applications into production. If you need a clean docker
@@ -13,44 +13,45 @@ The container from this project can be found at:
 
 ## Featured images
 
+All images now use a multi-stage build for minimal size and enforce execution as a non-root user
+
 ### r-base
 
--   Starts from rocker/r-ver:4.1.2
--   Includes basic build tools
+-   Starts from rocker/r-ver
+-   Includes basic build tools and core R packages (`devtools`, `drat`)
+-   Enforces non-root user execution as `user`
+
 -   Adds INWT network settings: certificate and r-repo
 
 ### r-batch
 
 -   Starts from r-base
--   Adds database connectors (MySQL)
+-   Adds database connectors (MySQL, Postgres)
+-   Includes `AWS CLI v2`
 -   Basic packages for modelling (lme4, mgcv, gbm)
--   Packages for data manipulation (data.table, dplyr, tidyr)
--   Home-brewed and open source (dbtools, mctools)
+-   Packages for data manipulation (`data.table`, `dplyr`, `tidyr`)
+-   Home-brewed and open source (`dbtools`, `mctools`)
 
 ### r-geos
 
 -   Starts from r-batch
--   Installs Linux libraries necessary for running geo/gis related operations.
--   Adds geo/gis related r packages (sf, stars, terra, etc.)
+-   Installs Linux libraries for GIS/geo related operations.
+-   Adds geo/gis related r packages (`sf`, `stars`, `terra`, etc.)
 
 ### r-shiny
 
 -   Starts from r-batch
--   Adds shiny related packages (shiny, shinyjs, etc.)
-
-### r-ver-ubuntu (deprecated)
-
--   Based on Ubuntu
--   R in given version with fixed MRAN
--   Based on the rocker r-ver project
+-   Installs `Automake`
+-   Adds shiny related packages (`shiny`, `shinyjs`, `leaflet`  etc.)
+-   Exposes port `3838`
 
 ## Simplest use of an image
 
 Example for `r-base` image:
 
 ```
-docker pull inwt/r-base:3.4.4
-docker run -it inwt/r-base:3.4.4
+docker pull inwt/r-base:4.5.1
+docker run -it inwt/r-base:4.5.1
 ```
 
 ## Why using docker
@@ -88,7 +89,7 @@ make use of the predefined images introduced above. Therefore, a possible Docker
 the following code:
 
 ```
-FROM inwt/r-batch:3.4.4
+FROM inwt/r-batch:4.5.1
 
 ADD . .
 RUN rm -vf .Rprofile && \
@@ -197,5 +198,8 @@ directory of the container. Be aware that with `-v` we are granting write access
 cd /path/to/your/package
 docker run --rm -v $PWD:/app --user `id -u`:`id -g` inwt/r-batch:3.4.4 check
 docker run --rm -v $PWD:/app --user `id -u`:`id -g` inwt/r-batch:3.5.1 check
+
+docker run --rm -v $PWD:/app inwt/r-batch:4.4.3 check
+docker run --rm -v $PWD:/app inwt/r-batch:4.5.1 check
 ```
 

r-base/Dockerfile

@@ -1,20 +1,46 @@
-FROM rocker/r-ver:4.5.1
+# -------------------
+# Setup (Global Args)
+# -------------------
+ARG R_VERSION=4.5.1
+ARG USER_NAME=user
+ARG USER_UID=1000
+ARG USER_GID=1000
+ARG GLOBAL_TZ="Europe/Berlin"
+ARG GLOBAL_LANG="en_US.UTF-8"
+
+# ----------------
+# Stage 1: builder
+# ----------------
+FROM rocker/r-ver:${R_VERSION} AS builder
+
+# 1. User & Environment Setup
+ARG USER_NAME
+ARG USER_UID
+ARG USER_GID
+ARG GLOBAL_TZ
+ARG GLOBAL_LANG
 
-WORKDIR /app
-ENV HOME=/app
 ENV DEBIAN_FRONTEND=noninteractive
 ENV OPENBLAS_NUM_THREADS=1
 ENV _R_CHECK_TESTS_NLINES_=0
-ENV TZ="Europe/Berlin"
-ENV LANG=en_US.UTF-8
+ENV TZ=${GLOBAL_TZ}
+ENV LANG=${GLOBAL_LANG}
 
-ADD . /includes/
+# Create the non-root user (UID 1000:GID 1000)
+RUN groupadd --gid ${USER_GID} ${USER_NAME} \
+    && useradd --uid ${USER_UID} --gid ${USER_GID} -m -G staff ${USER_NAME}
 
+WORKDIR /app
+COPY . /includes/
+
+# 2. System Dependencies, Timezone, and CA Certificates
+    # CA Certificates and Timezone Setup
 RUN mv -v /includes/*.crt /usr/local/share/ca-certificates/ \
     && dpkg-reconfigure ca-certificates \
     && rm /etc/localtime \
     && ln -s /usr/share/zoneinfo/Europe/Berlin /etc/localtime \
     && echo "Europe/Berlin" > /etc/timezone \
+    # Install System Dependencies
     && apt-get -y update \
     && apt-get -y upgrade \
     && apt-get install -y --no-install-recommends \
@@ -42,7 +68,8 @@ RUN mv -v /includes/*.crt /usr/local/share/ca-certificates/ \
     && apt-get autoclean -y \
     && rm -rf /var/lib/apt/lists/*
 
-    # R things
+# 3. R Environment Setup and Package Installation
+    # Link scripts
 RUN chmod +x /includes/*.R \
     && ln -s /usr/local/lib/R/site-library/littler/examples/dratInsert.r /usr/local/bin/dratInsert.r \
     && ln -s /includes/check.R /usr/local/bin/check \
@@ -51,16 +78,76 @@ RUN chmod +x /includes/*.R \
     && ln -s /includes/main.R /usr/local/bin/main \
     && ln -s /includes/installGithub.R /usr/local/bin/installGithub \
     && ln -s /includes/installPackage.R /usr/local/bin/installPackage \
-    && ln -s /includes/installAutomake.sh /usr/local/bin/installAutomake \
+    # Set Posit Package Manager as CRAN Mirror
     && echo "options(repos = c(CRAN = '$(Rscript /includes/get_mirror_date.R)'), download.file.method = 'libcurl')" >> /usr/local/lib/R/etc/Rprofile.site \
-    # temporary fix for stringr & libicu lib
+    # Install R Packages (stringi needs to be recompiled)
     && Rscript -e "options(warn = 2); install.packages('https://github.com/gagolews/stringi/releases/download/v1.8.7/stringi_1.8.7.tar.gz', repos = NULL, type = 'source')" \
     && Rscript -e "options(warn = 2); install.packages(c('devtools', 'docopt', 'drat', 'modules'), Ncpus = parallel::detectCores())" \
     && rm -rf /tmp/downloaded_packages/* \
+    # Setup local repository
     && mkdir -p /r-repo/src/contrib \
     && touch /r-repo/src/contrib/PACKAGES \
     && echo "options(repos = c(getOption('repos'), LOCAL = 'file:////r-repo/'))" >> /usr/local/lib/R/etc/Rprofile.site \
     && echo "options(repos = c(getOption('repos'), INWT = 'https://r-repo.core.cld.htz.int.inwt.de'))" >> /usr/local/lib/R/etc/Rprofile.site \
     && echo "options(repos = c(getOption('repos'), INWTLab = 'https://inwtlab.github.io/drat/'))" >> /usr/local/lib/R/etc/Rprofile.site \
     && echo "options(dratRepo = '/r-repo/')" >> /usr/local/lib/R/etc/Rprofile.site  \
-    && chmod --recursive o+w /usr/local/lib/R/site-library
+    # Set ownership for site-library, local r-repo & R scriüts
+    && chown -R ${USER_NAME}:${USER_NAME} /usr/local/lib/R/site-library/ \
+    && chown -R ${USER_NAME}:${USER_NAME} /r-repo \
+    && chown -R ${USER_NAME}:${USER_NAME} /includes
+
+# --------------
+# Stage 2: final
+# --------------
+FROM rocker/r-ver:${R_VERSION}
+
+LABEL org.opencontainers.image.authors="Sebastian Warnholz, Jan Abel" \
+      org.opencontainers.image.created="BUILD_DATE_TIME_PLACEHOLDER" \
+      org.opencontainers.image.description="Multi-stage R environment based on Rocker" \
+      org.opencontainers.image.licenses="GPL-2.0-or-later" \
+      org.opencontainers.image.revision="GIT_SHA_PLACEHOLDER" \
+      org.opencontainers.image.source="https://github.com/INWTlab/r-docker" \
+      org.opencontainers.image.title="inwt/r-base" \
+      org.opencontainers.image.vendor="INWT Statistics" \
+      org.opencontainers.image.version="${R_VERSION}"
+
+# 1. User Setup
+ARG USER_NAME
+ARG USER_UID
+ARG USER_GID
+ARG GLOBAL_TZ
+ARG GLOBAL_LANG
+
+# Re-create the non-root user in the final stage (since this is a new base layer)
+RUN groupadd --gid ${USER_GID} ${USER_NAME} \
+    && useradd --uid ${USER_UID} --gid ${USER_GID} -m -G staff ${USER_NAME}
+
+# Set runtime environment variables
+ENV HOME=/app
+ENV TZ=${GLOBAL_TZ}
+ENV LANG=${GLOBAL_LANG}
+
+# 2. Copy Artifacts from the builder stage
+COPY --from=builder /usr/local/bin/ /usr/local/bin/
+COPY --from=builder /usr/local/lib/R/site-library/ /usr/local/lib/R/site-library/
+COPY --from=builder /usr/local/lib/R/etc/Rprofile.site /usr/local/lib/R/etc/Rprofile.site
+COPY --from=builder /r-repo/ /r-repo/
+
+# 3. Add utility scripts
+RUN mkdir -p /includes/check-lib
+
+COPY --from=builder /includes/build.R /includes/build.R
+COPY --from=builder /includes/check.R /includes/check.R
+COPY --from=builder /includes/installPackage.R /includes/installPackage.R
+COPY --from=builder /includes/installGithub.R /includes/installGithub.R
+COPY --from=builder /includes/register-dependencies.R /includes/register-dependencies.R
+COPY --from=builder /includes/validate-settings.R /includes/validate-settings.R
+COPY --from=builder /includes/check-lib/ /includes/check-lib/
+
+RUN chown -R ${USER_NAME}:${USER_NAME} /includes
+
+# 3. Set User and Workdir
+USER ${USER_NAME}
+WORKDIR ${HOME}
+
+CMD ["R"]

r-base/installAutomake.sh

@@ -2,27 +2,27 @@
 
 VERSION=${1}
 
-if echo $VERSION | grep -q '\..*\..*'; then 
-    MAJOR_VERSION=${VERSION%.*}
-else 
-    MAJOR_VERSION=${VERSION}
+if echo $VERSION | grep -q '\..*\..*'; then
+  MAJOR_VERSION=${VERSION%.*}
+else
+  MAJOR_VERSION=${VERSION}
 fi
 
 function install_automake() {
-    wget http://ftp.gnu.org/gnu/automake/automake-$VERSION.tar.gz \
-        && tar -xvf automake-$VERSION.tar.gz \
-        && cd automake-$VERSION \
-        && ./configure --prefix=/usr/local/automake-$VERSION \
-        && make \
-        && make install \
-        && cd .. \
-        && rm automake-$VERSION.tar.gz \
-        && rm -rf automake-$VERSION \
-        && rm -f /usr/local/bin/aclocal-$VERSION \
-        && rm -f /usr/local/bin/automake-$VERSION \
-        && ln -s /usr/local/automake-$VERSION/bin/aclocal-$MAJOR_VERSION /usr/local/bin/aclocal-$MAJOR_VERSION \
-        && ln -s /usr/local/automake-$VERSION/bin/automake-$MAJOR_VERSION /usr/local/bin/automake-$MAJOR_VERSION \
-        && echo "Installed automake in version $VERSION"
+  wget https://ftpmirror.gnu.org/gnu/automake/automake-$VERSION.tar.gz &&
+    tar -xvf automake-$VERSION.tar.gz &&
+    cd automake-$VERSION &&
+    ./configure --prefix=/usr/local/automake-$VERSION &&
+    make &&
+    make install &&
+    cd .. &&
+    rm automake-$VERSION.tar.gz &&
+    rm -rf automake-$VERSION &&
+    rm -f /usr/local/bin/aclocal-$VERSION &&
+    rm -f /usr/local/bin/automake-$VERSION &&
+    ln -s /usr/local/automake-$VERSION/bin/aclocal-$MAJOR_VERSION /usr/local/bin/aclocal-$MAJOR_VERSION &&
+    ln -s /usr/local/automake-$VERSION/bin/automake-$MAJOR_VERSION /usr/local/bin/automake-$MAJOR_VERSION &&
+    echo "Installed automake in version $VERSION"
 }
 
-install_automake
+install_automake