fix container failing to install required R packages.

.github/workflows/create-publish-docker.yml

@@ -57,6 +57,8 @@ jobs:
             r-version: 'release'
           - target-os: 'fedora'
             r-version: 'patched'
+          - target-os: 'fedora'
+            compiler: 'clang' # no clang on fedora (see build map to r-hub images)
           - compiler: 'clang'
             r-version: 'patched'
           - compiler: 'clang'
@@ -90,6 +92,49 @@ jobs:
       #   run: |
       #     echo "${{  secrets.DEVEL_ABN_DEPLOY }}" >> ssh_key
       #   shell: bash
+      - name: Map to R-hub container names
+        id: rhub-mapping
+        run: |
+          # Map CRAN-style naming to R-hub container names
+          # Based on https://r-hub.github.io/containers/ and https://cran.r-project.org/web/checks/check_flavors.html#r-devel-linux-x86_64-fedora-clang 
+
+          TARGET_OS="${{ matrix.target-os }}"
+          COMPILER="${{ matrix.compiler }}"
+          R_VERSION="${{ matrix.r-version }}"
+
+          echo "Input: ${TARGET_OS}/${COMPILER}/${R_VERSION}"
+
+          # Default fallback
+          RHUB_IMAGE="ubuntu-clang"
+
+          # Map debian combinations
+          if [[ "$TARGET_OS" == "debian" ]]; then
+            if [[ "$COMPILER" == "clang" && "$R_VERSION" == "devel" ]]; then
+              RHUB_IMAGE="ubuntu-clang"
+            elif [[ "$COMPILER" == "gcc" && "$R_VERSION" == "devel" ]]; then
+              RHUB_IMAGE="ubuntu-gcc12"
+            elif [[ "$R_VERSION" == "release" ]]; then
+              RHUB_IMAGE="ubuntu-release"
+            elif [[ "$R_VERSION" == "patched" ]]; then
+              RHUB_IMAGE="ubuntu-next"
+            fi
+          # Map fedora combinations  
+          elif [[ "$TARGET_OS" == "fedora" ]]; then
+            # Note: R-hub doesn't have direct fedora equivalents for primary CRAN containers
+            # Map to closest Ubuntu equivalents or specific Fedora containers
+            if [[ "$COMPILER" == "gcc" && "$R_VERSION" == "devel" ]]; then
+              RHUB_IMAGE="gcc15"  # Use Fedora-based gcc15 container
+            elif [[ "$COMPILER" == "clang" && "$R_VERSION" == "devel" ]]; then
+              RHUB_IMAGE="gcc15"  # No Fedora clang equivalent, use Fedora gcc15
+              echo "Warning: No direct Fedora clang equivalent on r-hub, using gcc15"
+            fi
+          # Map valgrind
+          elif [[ "$TARGET_OS" == "valgrind" ]]; then
+            RHUB_IMAGE="valgrind"
+          fi
+
+          echo "Mapped to R-hub image: rhub/${RHUB_IMAGE}"
+          echo "rhub-image=${RHUB_IMAGE}" >> $GITHUB_OUTPUT
       - name: Build and push
         uses: docker/build-push-action@f2a1d5e99d037542a71f64918e516c093c6f3fc4
         with:
@@ -101,6 +146,7 @@ jobs:
             TARGET_OS=${{ matrix.target-os }}
             COMPILER=${{ matrix.compiler }}
             R_VERSION=${{ matrix.r-version }}
+            RHUB_IMAGE=${{ steps.rhub-mapping.outputs.rhub-image }}
             PACKAGE_PATH=${{ env.PACKAGE_PATH}}
             REPO_PATH=${{ env.REPO_PATH }}
             JAGS=${{ env.JAGS }}
@@ -130,6 +176,8 @@ jobs:
             r-version: 'release'
           - target-os: 'fedora'
             r-version: 'patched'
+          - target-os: 'fedora'
+            compiler: 'clang' # no clang on fedora (see build map to r-hub images))
           - compiler: 'clang'
             r-version: 'patched'
           - compiler: 'clang'

.github/workflows/onlabel_check_build.yml

@@ -44,6 +44,8 @@ jobs:
             r-version: 'release'
           - target-os: 'fedora'
             r-version: 'patched'
+          - target-os: 'fedora'
+            compiler: 'clang' # no clang on fedora (see build map to r-hub images)
           - compiler: 'clang'
             r-version: 'patched'
           - compiler: 'clang'
@@ -77,6 +79,49 @@ jobs:
       #   run: |
       #     echo "${{  secrets.DEVEL_ABN_DEPLOY }}" >> ssh_key
       #   shell: bash
+      - name: Map to R-hub container names
+        id: rhub-mapping
+        run: |
+          # Map CRAN-style naming to R-hub container names
+          # Based on https://r-hub.github.io/containers/ and https://cran.r-project.org/web/checks/check_flavors.html#r-devel-linux-x86_64-fedora-clang
+
+          TARGET_OS="${{ matrix.target-os }}"
+          COMPILER="${{ matrix.compiler }}"
+          R_VERSION="${{ matrix.r-version }}"
+
+          echo "Input: ${TARGET_OS}/${COMPILER}/${R_VERSION}"
+
+          # Default fallback
+          RHUB_IMAGE="ubuntu-clang"
+
+          # Map debian combinations
+          if [[ "$TARGET_OS" == "debian" ]]; then
+            if [[ "$COMPILER" == "clang" && "$R_VERSION" == "devel" ]]; then
+              RHUB_IMAGE="ubuntu-clang"
+            elif [[ "$COMPILER" == "gcc" && "$R_VERSION" == "devel" ]]; then
+              RHUB_IMAGE="ubuntu-gcc12"
+            elif [[ "$R_VERSION" == "release" ]]; then
+              RHUB_IMAGE="ubuntu-release"
+            elif [[ "$R_VERSION" == "patched" ]]; then
+              RHUB_IMAGE="ubuntu-next"
+            fi
+          # Map fedora combinations  
+          elif [[ "$TARGET_OS" == "fedora" ]]; then
+            # Note: R-hub doesn't have direct fedora equivalents for primary CRAN containers
+            # Map to closest Ubuntu equivalents or specific Fedora containers
+            if [[ "$COMPILER" == "gcc" && "$R_VERSION" == "devel" ]]; then
+              RHUB_IMAGE="gcc15"  # Use Fedora-based gcc15 container
+            elif [[ "$COMPILER" == "clang" && "$R_VERSION" == "devel" ]]; then
+              RHUB_IMAGE="gcc15"  # No Fedora clang equivalent, use Fedora gcc15
+              echo "Warning: No direct Fedora clang equivalent on r-hub, using gcc15"
+            fi
+          # Map valgrind
+          elif [[ "$TARGET_OS" == "valgrind" ]]; then
+            RHUB_IMAGE="valgrind"
+          fi
+
+          echo "Mapped to R-hub image: rhub/${RHUB_IMAGE}"
+          echo "rhub-image=${RHUB_IMAGE}" >> $GITHUB_OUTPUT
       - name: Build and push
         uses: docker/build-push-action@f2a1d5e99d037542a71f64918e516c093c6f3fc4
         with:
@@ -88,6 +133,7 @@ jobs:
             TARGET_OS=${{ matrix.target-os }}
             COMPILER=${{ matrix.compiler }}
             R_VERSION=${{ matrix.r-version }}
+            RHUB_IMAGE=${{ steps.rhub-mapping.outputs.rhub-image }}
             PACKAGE_PATH=${{ env.PACKAGE_PATH}}
             REPO_PATH=${{ env.REPO_PATH }}
             JAGS=${{ env.JAGS }}
@@ -119,6 +165,8 @@ jobs:
             r-version: 'release'
           - target-os: 'fedora'
             r-version: 'patched'
+          - target-os: 'fedora'
+            compiler: 'clang' # no clang on fedora (see build map to r-hub images))
           - compiler: 'clang'
             r-version: 'patched'
           - compiler: 'clang'

containers/debian/Dockerfile

@@ -2,8 +2,10 @@
 ARG TARGET_OS
 ARG COMPILER
 ARG R_VERSION
+ARG RHUB_IMAGE=ubuntu-clang
 
-FROM rhub/${TARGET_OS}-${COMPILER}-${R_VERSION}
+# Use the mapped R-hub image name from the workflow
+FROM rhub/${RHUB_IMAGE}
 
 # Build stage: ARGs need to be redeclared
 ARG TARGET_OS
@@ -19,16 +21,36 @@ ARG REPO_PATH
 RUN apt-get update --allow-releaseinfo-change && apt-get install -y --no-install-recommends \
   libssl-dev \
   libcurl4-openssl-dev \
-  gfortran
+  gfortran \
+  libfontconfig1-dev \
+  libxml2-dev \
+  libharfbuzz-dev \
+  libfribidi-dev \
+  libfreetype6-dev \
+  libpng-dev \
+  libtiff5-dev \
+  libjpeg-dev \
+  libwebp-dev
 
 # add R to PATH
 # NOTE: For R-release this is not needed
 ENV PATH="/opt/R-$R_VERSION/bin:${PATH}"
 
+# Configure clang C++ compilation environment
+ENV CPLUS_INCLUDE_PATH="/usr/include/c++/13:/usr/include/x86_64-linux-gnu/c++/13"
+ENV C_INCLUDE_PATH="/usr/include"
+
 # ENV PATH "$PATH:/opt/R-devel/bin/"
 # Set a mirror for CRAN
-RUN if [ "$R_VERSION" = "release" ]; then RPATH=""; else RPATH=/opt/R-$R_VERSION; fi \
-    && echo 'options(repos =c(CRAN = "https://cran.rstudio.com"))' >> ${RPATH}/lib/R/library/base/R/Rprofile
+# Find where R is installed and set the CRAN repository
+RUN R_HOME=$(R RHOME) && \
+    if [ -d "${R_HOME}/library/base/R" ]; then \
+      echo 'options(repos =c(CRAN = "https://cran.rstudio.com"))' >> ${R_HOME}/library/base/R/Rprofile; \
+    elif [ -d "${R_HOME}/etc" ]; then \
+      echo 'options(repos =c(CRAN = "https://cran.rstudio.com"))' >> ${R_HOME}/etc/Rprofile.site; \
+    else \
+      echo "Warning: Could not find R profile location, skipping CRAN mirror setup"; \
+    fi
 
 # Get and install packages for local debugging
 RUN R -e "install.packages('devtools')" \
@@ -81,9 +103,6 @@ RUN R -e "install.packages('INLA',repos=c(getOption('repos'),INLA='https://inla.
 # - Magick++
 RUN apt-get update --allow-releaseinfo-change && apt-get install -y --no-install-recommends \
       libmagick++-dev
-# - libxml-2.0
-RUN apt-get update --allow-releaseinfo-change && apt-get install -y --no-install-recommends \
-      libxml2-dev
 # glmmTMB:
 RUN R -e "install.packages('glmmTMB')" # Workaround for glmmTMB installation issue. Should be installed automatically below in the future.
 ###
@@ -100,3 +119,7 @@ WORKDIR target/
 # Install all dependencies of PACKAGE_NAME but not the package it self
 RUN R -e "renv::deactivate()"
 RUN R -e "package<-desc::desc()\$get_field('Package');pckgs<-unique(renv::dependencies('$PACKAGE_PATH')[,'Package']);pres_pckgs<-installed.packages()[,'Package'];install.packages(pckgs[!(pckgs %in% pres_pckgs) & !(pckgs == package)])"
+
+# Check if the dependencies were installed correctly
+RUN R -e "renv::deactivate()"
+RUN R -e "package<-desc::desc()\$get_field('Package');pckgs<-unique(renv::dependencies('$PACKAGE_PATH')[,'Package']);pres_pckgs<-installed.packages()[,'Package'];if(any(!(pckgs %in% pres_pckgs) & !(pckgs == package))) { stop(paste0('Some dependencies were not installed correctly. Missing: ', paste(pckgs[!(pckgs %in% pres_pckgs) & !(pckgs == package)], collapse=', '))) } else { cat('All dependencies were installed correctly.\n') }"

containers/fedora/Dockerfile

@@ -2,8 +2,10 @@
 ARG TARGET_OS
 ARG COMPILER
 ARG R_VERSION
+ARG RHUB_IMAGE=ubuntu-gcc12
 
-FROM rhub/${TARGET_OS}-${COMPILER}-${R_VERSION}
+# Use the mapped R-hub image name from the workflow
+FROM rhub/${RHUB_IMAGE}
 
 # Build stage: ARGs need to be redeclared
 ARG TARGET_OS
@@ -19,16 +21,31 @@ ARG JAGS
 # Update package repositories
 RUN dnf check-update && dnf -y install \
   openssl-devel \
-  libcurl-devel
+  libcurl-devel \
+  fontconfig-devel \
+  libxml2-devel \
+  harfbuzz-devel \
+  fribidi-devel \
+  freetype-devel \
+  libpng-devel \
+  libtiff-devel \
+  libjpeg-devel \
+  libwebp-devel
 
 # add R to PATH
 ENV PATH="/opt/R-$R_VERSION/bin:${PATH}"
 
 # diff to debian: /lib/ > /lib64/
 # ENV PATH "$PATH:/opt/R-devel/bin/"
-# Set a mirror for CRAN
-RUN if [ "$R_VERSION" = "release" ]; then RPATH=""; else RPATH=/opt/R-$R_VERSION; fi \
-    && echo 'options(repos =c(CRAN = "https://cran.rstudio.com"))' >> ${RPATH}/lib64/R/library/base/R/Rprofile
+# Find where R is installed and set the CRAN repository
+RUN R_HOME=$(R RHOME) && \
+    if [ -d "${R_HOME}/library/base/R" ]; then \
+      echo 'options(repos =c(CRAN = "https://cran.rstudio.com"))' >> ${R_HOME}/library/base/R/Rprofile; \
+    elif [ -d "${R_HOME}/etc" ]; then \
+      echo 'options(repos =c(CRAN = "https://cran.rstudio.com"))' >> ${R_HOME}/etc/Rprofile.site; \
+    else \
+      echo "Warning: Could not find R profile location, skipping CRAN mirror setup"; \
+    fi
 
 # rjags:
 RUN dnf -y install \
@@ -95,9 +112,6 @@ RUN R -e "install.packages('INLA',repos=c(getOption('repos'),INLA='https://inla.
 # - Magick++
 RUN dnf -y install \
       ImageMagick-c++-devel
-# - libxml-2.0
-RUN dnf -y install \
-      libxml2-devel
 
 ###
 # install all package dependencies

containers/valgrind/Dockerfile

@@ -2,12 +2,12 @@
 ARG TARGET_OS
 ARG COMPILER
 ARG R_VERSION
+ARG RHUB_IMAGE=valgrind
 
-# For the valgrind container, target_os, compiler and r_vresion are not specified
-# Hovever, the valgrind container is fedora, gcc, devel
+# For the valgrind container, target_os, compiler and r_version are not specified
+# However, the valgrind container is fedora, gcc, devel
 # see https://r-hub.github.io/containers/containers.html#valgrind
-# FROM rhub/${TARGET_OS}
-FROM ghcr.io/r-hub/containers/valgrind:latest
+FROM rhub/${RHUB_IMAGE}
 
 # Build stage: ARGs need to be redeclared
 ARG TARGET_OS