check-pak.yml

# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
name: R-CMD-check

on:
  push:
    branches: main
  pull_request:
    branches: main
  workflow_dispatch:
  release:
    types: [published]

concurrency:
  group: ${{ github.workflow }}-${{ github.event_name }}
  cancel-in-progress: true

jobs:
  R-CMD-check:
    runs-on: ${{ matrix.config.os }}

    name: ${{ matrix.config.os }} (${{ matrix.config.r }})

    strategy:
      fail-fast: false
      matrix:
        config:
          - {os: ubuntu-latest,   r: '4.3.2'}

    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      R_KEEP_PKG_SOURCE: yes
      BCFTOOLS_VERSION: 1.16

    steps:
      - uses: actions/checkout@v4

      - uses: r-lib/actions/setup-pandoc@v2

      - name: Install libcurl
        if: runner.os == 'Linux'
        run: |
          sudo apt-get update
          sudo apt-get install libcurl4-openssl-dev

      - uses: r-lib/actions/setup-r@v2
        with:
          r-version: ${{ matrix.config.r }}
          http-user-agent: ${{ matrix.config.http-user-agent }}
          use-public-rspm: true

      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: any::rcmdcheck, local::.

      - name: Install BCFtools
        if: runner.os == 'Linux'
        run: |
          sudo apt-get update && \
          sudo apt-get install -y --no-install-recommends \
            libxt6 \
            ca-certificates \
            bzip2 \
            wget \
            autoconf \
            automake \
            make \
            cmake \
            libbz2-dev \
            liblzma-dev \
            libjpeg-dev \
            libxml2-dev \
            zlib1g-dev \
            libgdal-dev
          wget -q -P /tmp/ https://github.com/samtools/bcftools/releases/download/${BCFTOOLS_VERSION}/bcftools-${BCFTOOLS_VERSION}.tar.bz2 && \
            tar -C /tmp/ -xjf /tmp/bcftools-${BCFTOOLS_VERSION}.tar.bz2 && \
            cd /tmp/bcftools-${BCFTOOLS_VERSION} && \
            sudo autoreconf -i && \
            sudo ./configure --prefix=/usr && \
            sudo make && \
            sudo make install

      - uses: r-lib/actions/check-r-package@v2
        with:
          args: 'c("--no-manual")'
          error-on: '"error"'

      - name: Show testthat output
        if: always()
        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
        shell: bash

      - name: Upload check results
        if: failure()
        uses: actions/upload-artifact@main
        with:
          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
          path: check