R-CMD-check.yaml

# 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
on:
  push:
    branches: [main, master]
  pull_request:
    branches: [main, master]

name: R-CMD-check

concurrency:
  group: ${{ github.workflow }}-${{ github.ref }}
  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:
          # vignette rendering is switched off though because of:
          #  - https://github.com/tidyverse/ggplot2/issues/2252#issuecomment-1006713187
          #  - https://github.com/lcolladotor/biocthis/issues/27
          - {os: macOS-latest,   r: 'release'}
          - {os: windows-latest, r: 'release'}
          - {os: ubuntu-latest,  r: 'devel'}
          - {os: ubuntu-latest,  r: 'release'}
          - {os: ubuntu-latest,  r: 'oldrel-1'}

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

    steps:
      - uses: actions/checkout@v4

      # - name: Set NOT_CRAN=false on Windows
      #   if: runner.os == 'Windows'
      #   run: |
      #     echo "NOT_CRAN=false" >> $GITHUB_ENV
      #   shell: bash

      - name: Install rgdal dependencies (macOS)
        if: runner.os == 'macOS'
        run: brew install gdal

      - name: Install ADMIXTOOLS dependencies (Linux)
        if: runner.os == 'Linux'
        run: sudo apt-get install libopenblas-dev libgsl-dev liblapack-dev

      - name: Install ADMIXTOOLS dependencies (macOS)
        if: runner.os == 'macOS'
        run: brew install openblas gsl lapack bedtools

      - name: Compile and install ADMIXTOOLS (Linux) # + macOS)
        # if: runner.os != 'Windows'
        if: runner.os == 'Linux'
        run: |
          # create a single directory for all external software
          mkdir -p ~/deps
          cd ~/deps

          # download and unpack the ADMIXTOOLS source code
          curl -LO https://github.com/DReichLab/AdmixTools/archive/v7.0.2.tar.gz
          tar xf v7.0.2.tar.gz
          cd AdmixTools-7.0.2

          # set compiler flags (compilation on macOS was failing unable to find
          # openblas library files)
          export LDFLAGS="-L/usr/local/opt/openblas/lib"
          export CPPFLAGS="-I/usr/local/opt/openblas/include"

          # compile ADMIXTOOLS and move binaries under bin/
          cd src
          make clobber
          make LDLIBS="-llapack" all
          make install

          # # download testing data for unit tests
          # cd ../
          # curl -LO https://reich.hms.harvard.edu/sites/reich.hms.harvard.edu/files/inline-files/AdmixTools_Example_Data.tar_.gz
          # tar xf AdmixTools_Example_Data.tar_.gz
          #
          # # run the Perl script with tests for the compiled binaries
          # cd examples
          # # fix unportable Perl shebang
          # if [[ "$OSTYPE" == "darwin"* ]]; then
          #   sed -i '' "1s/.*/\#\!\/usr\/bin\/env perl -w/" mklog
          # else
          #   sed -i "1s/.*/\#\!\/usr\/bin\/env perl/" mklog
          # fi
          # ./mklog
          # cd ../

          # we need to do this in bash because of $OSTYPE above
        shell: bash

      - name: Compile and install SLiM on Unix
        if: runner.os != 'Windows'
        run: |
          # download SLiM into a separate directory to avoid CRAN errors
          mkdir -p ~/deps
          cd ~/deps

          # installation instructions copied from the SLiM manual:
          wget https://github.com/MesserLab/SLiM/releases/download/v4.2/SLiM.zip
          unzip SLiM.zip
          cd SLiM
          cmake .
          make slim

      - name: Populate PATH with compiled binaries on Unix
        if: runner.os != 'Windows'
        run: |
          export PATH="$HOME/deps/SLiM:$HOME/deps/AdmixTools-7.0.2/bin:$PATH"
          echo "PATH=$PATH" >> ~/.Renviron

      - name: Install SLiM on Windows
        if: runner.os == 'Windows'
        uses: msys2/setup-msys2@v2
        with:
          update: true
          install: >-
            mingw-w64-x86_64-slim-simulator
            bash

      - name: Install pandoc on Windows
        if: runner.os == 'Windows'
        run: |
          install.packages("gh", repos = "http://cran.rstudio.com")
          install.packages("pandoc", repos = "http://cran.rstudio.com")
          pandoc::pandoc_install()
        shell: Rscript {0}

      #- name: Check ming64/bin contents
      #  if: runner.os == 'Windows'
      #  run: |
      #    dir ${{ runner.temp }}\msys64\mingw64\bin
      #  shell: cmd

      #- name: Check usr/bin contents
      #  if: runner.os == 'Windows'
      #  run: dir ${{ runner.temp }}\msys64\usr\bin
      #  shell: cmd

      - name: Populate PATH with compiled binaries on Windows
        if: runner.os == 'Windows'
        run: |
          writeLines(
            paste0(
              "PATH=D:/a/_temp/msys64/mingw64/bin",
              "\n",
              "RSTUDIO_PANDOC=", normalizePath(dirname(pandoc::pandoc_bin()), winslash = "/"),
              "\n",
              "GTIFF_SRS_SOURCE=EPSG # silence GDAL warning"
            ),
            con = paste0(normalizePath(path.expand("~"), winslash = "/"), "/.Renviron"))
        shell: Rscript {0}

        # The Windows GDAL GitHub Actions warning solved by setting 'GTIFF_SRS_SOURCE' above
        # is actually not the first time this happened, interesting:
        # https://github.com/bodkan/slendr/blob/3e02fa2ad7fb085ccbcc23df518bca6b72e782b1/R/compilation.R#L730

      # - name: Check PATHs
      #   if: runner.os == 'Windows'
      #   run: |
      #     cat(Sys.getenv("PATH"), "\n")
      #     cat(Sys.getenv("RSTUDIO_PANDOC"), "\n")
      #   shell: Rscript {0}

      - name: Set R_LIBS path on unix
        if: runner.os == 'Windows'
        run: |
          mkdir ~/R_LIBS
          echo "GTIFF_SRS_SOURCE='EPSG'" >> ~/.Renviron

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

      - 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

      - name: Setup dedicated Python environment for slendr
        run: |
          install.packages("reticulate", repos = "http://cran.rstudio.com")
          reticulate::install_miniconda()
          deps <- c("msprime==1.3.3", "tskit==0.5.8", "pyslim==1.0.4")
          PYTHON_ENV <- paste0("Python-3.12_", paste(gsub("==", "-", c(deps, "tspop==0.0.2")), collapse = "_"))
          reticulate::conda_create(envname = PYTHON_ENV, python_version = '3.12')
          reticulate::use_condaenv(PYTHON_ENV, required = TRUE)
          reticulate::conda_install(envname = PYTHON_ENV, packages = c("msprime==1.3.1", "tskit==0.5.6"), pip = FALSE)
          reticulate::conda_install(envname = PYTHON_ENV, packages = c("tspop==0.0.2", "pyslim==1.0.4", "pyarrow"), pip = TRUE)
        shell: Rscript {0}

      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: any::rcmdcheck
          needs: check

      - uses: r-lib/actions/check-r-package@v2