Force java to behave?

Author: Susan Vanderplas

.github/workflows/main.yml

@@ -66,6 +66,7 @@ jobs:
             -v "${HOME}/.cache/pip:/root/.cache/pip" \
             -e RENV_PATHS_CACHE=/root/.local/share/renv \
             -e PIP_CACHE_DIR=/root/.cache/pip \
+            -e QUARTO_PYTHON="venv" \
             -e NEWSAPI_KEY="${{ secrets.NEWSAPI_KEY }}" \
             -e GH_APP_ID="${{ secrets.GH_APP_ID }}" \
             -e GH_APP_SECRET="${{ secrets.GH_APP_SECRET }}" \

Dockerfile

@@ -12,13 +12,23 @@ RUN --mount=type=cache,target=/var/cache/apt \
     apt-get update && apt-get install -y --no-install-recommends \
       python3 python3-pip python3-venv python3-dev \
       libcurl4-openssl-dev libssl-dev libxml2-dev \
-      default-jdk \
+      default-jdk default-jre r-cran-rjava unixodbc unixodbc-dev \
       libtesseract-dev libpoppler-cpp-dev tesseract-ocr \
       libleptonica-dev libpng-dev libjpeg-dev libtiff-dev \
       imagemagick gdal-bin libgdal-dev libsecret-1-dev \
       libglpk-dev libudunits2-dev \
       curl gnupg ca-certificates \
-    && rm -rf /var/lib/apt/lists/*
+    && rm -rf /var/lib/apt/lists/* \
+    && install2.r --error --deps TRUE \
+      RJDBC odbc tinytex quarto devtools rmarkdown rstudioapi reticulate yaml digest \\
+    && Rscript -e "tinytex::install_tinytex(force=T)"
+
+ENV JAVA_HOME=/usr/lib/jvm/default-java/
+ENV PATH="${JAVA_HOME}/bin:${PATH}"
+ENV LD_LIBRARY_PATH="${JAVA_HOME}/lib/server:${LD_LIBRARY_PATH}"
+
+# Verify Java install
+RUN java -version && javac -version
 
 # --- Layer 2: GitHub CLI
 RUN curl -fsSL https://cli.github.com/packages/githubcli-archive-keyring.gpg \
@@ -34,12 +44,11 @@ RUN curl -fsSL https://quarto.org/download/latest/quarto-linux-amd64.deb -o /tmp
     apt-get update && apt-get install -y /tmp/quarto.deb && rm -f /tmp/quarto.deb && \
     rm -rf /var/lib/apt/lists/*
 
-# --- Layer 4: TinyTeX
-RUN Rscript -e "install.packages('tinytex', repos='https://cloud.r-project.org'); tinytex::install_tinytex(force=T)"
-
+# --- Layer 4: Check cache dirs
 # Ensure cache dirs exist
 RUN mkdir -p ${RENV_PATHS_CACHE} ${PIP_CACHE_DIR} /root/.virtualenvs
 
+
 WORKDIR /project
 
 # Default command: render and publish