Update Dockerfile

Author: eseiler

.github/dependabot.yml

@@ -0,0 +1,13 @@
+# SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
+# SPDX-License-Identifier: CC-BY-4.0
+
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directories:
+      - "/*"
+    schedule:
+      interval: "weekly"

.github/workflows/build.yml

@@ -0,0 +1,49 @@
+# SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
+# SPDX-License-Identifier: CC-BY-4.0
+
+name: Build
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+  workflow_dispatch:
+  schedule:
+    - cron: "0 3 * * MON"
+
+concurrency:
+  group: build-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: ${{ github.event_name != 'push' }}
+
+env:
+  TZ: Europe/Berlin
+
+defaults:
+  run:
+    shell: bash -Eeuo pipefail {0}
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    if: github.repository_owner == 'OpenMS' || github.event_name == 'workflow_dispatch'
+    timeout-minutes: 60
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v5
+
+      - name: Build image
+        working-directory: ./docker
+        run: docker build . &> ${{ runner.temp }}/build-${{ github.run_id }}.log
+
+      - name: Upload log
+        if: always()
+        uses: actions/upload-artifact@v4
+        with:
+          name: build-${{ github.run_id }}.log
+          path: ${{ runner.temp }}/build-${{ github.run_id }}.log
+
+      - name: Show log
+        if: always()
+        run: cat ${{ runner.temp }}/build-${{ github.run_id }}.log

docker/Dockerfile

@@ -1,13 +1,20 @@
-FROM ubuntu_2204
-RUN echo "Installing apt packages..."
+# syntax=docker/dockerfile:1
 
-RUN sudo apt-get -y update >> packages.log
-RUN sudo apt-get -y install gawk libssl-dev sshpass libpng-dev libudunits2-dev libcairo2-dev libgdal-dev r-base r-base-dev pandoc python3 python-is-python3 >> packages.log
+FROM debian:trixie-slim
 
-RUN export RSTUDIO_PANDOC=/usr/bin/
+ENV DEBIAN_FRONTEND=noninteractive
+ENV GNUMAKEFLAGS="-j2 --no-print-directory --output-sync=target"
+ENV MAKEFLAGS="-j2 --no-print-directory --output-sync=target"
 ENV RSTUDIO_PANDOC=/usr/bin
+ENV TZ=Europe/Berlin
 
-RUN echo "Installing R packages..."
-## mapview not needed anymore
-COPY Rpackages.R Rpackages.R
-RUN sudo Rscript --vanilla Rpackages.R
+SHELL ["/bin/bash", "-Eeuxo", "pipefail", "-c"]
+
+COPY docker_scripts /docker_scripts
+
+# Disable compiler warnings when R compiles packages from source.
+ENV EXTRA_CXXFLAGS=-w
+COPY config/Makevars /root/.R/Makevars
+
+RUN /docker_scripts/install_apt_packages.sh
+RUN /docker_scripts/install_R_packages.R

docker/Rpackages.R

@@ -0,0 +1 @@
+CFLAGS+= -w

docker/config/Makevars

@@ -0,0 +1,4 @@
+#!/usr/bin/env Rscript
+
+install.packages(c('ggplot2','scholar','knitr','rmarkdown','leaflet','rworldmap','lattice','RColorBrewer','sp'), repos='https://cloud.r-project.org/')
+q()

docker/docker_scripts/install_R_packages.R

@@ -0,0 +1,26 @@
+#!/bin/bash -l
+
+set -Eeuxo pipefail
+
+apt-get update 1>/dev/null
+
+# sudo is not needed but still installed for compatibility
+apt-get install --yes --no-install-recommends \
+    ca-certificates \
+    gawk \
+    libabsl-dev \
+    libcairo2-dev \
+    libgdal-dev \
+    libpng-dev \
+    libssl-dev \
+    libudunits2-dev \
+    pandoc \
+    python-is-python3 \
+    python3 \
+    r-base \
+    r-base-dev \
+    sshpass \
+    sudo \
+1>/dev/null
+
+rm -rf /var/lib/apt/lists/*