test.yml

on:
  push:
    branches: [ master ]
  pull_request:
    branches: [ master ]
name: CI
jobs:
  build:
    runs-on: ubuntu-latest
    env:
       AUTHOR_TESTING: 1
       AUTOMATED_TESTING: 1
       RELEASE_TESTING: 1
       R_MAX_NUM_DLLS: 256
       R_LIBS_SITE: /home/runner/R
       R_LIBS: /home/runner/R
       R_LIBS_USER: /home/runner/R
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
       TMPDIR: /home/runner/tmp
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
    steps:
    - uses: actions/checkout@v2
    - uses: r-lib/actions/setup-pandoc@v2
    - uses: r-lib/actions/setup-r@v2
    - uses: r-lib/actions/setup-renv@v2

    - name: Install packages
      run: |
        sudo apt-get update
        sudo apt-get install libcurl4-openssl-dev libcurl4 curl libnetcdf-dev
        sudo apt-get install circos libsvg-perl default-jdk texlive texlive-fonts-extra

    - name: Setup R environment
      run: |
        echo "options(Ncpus=2)" > ${HOME}/.Rprofile
        echo "r <- getOption('repos')" >> ${HOME}/.Rprofile
        echo 'r["CRAN"] <- "https://cloud.r-project.org"' >> ${HOME}/.Rprofile
        echo "options(repos=r)" >> ${HOME}/.Rprofile
        mkdir -p ${HOME}/tmp
        mkdir -p ${HOME}/R
        sudo R CMD javareconf
        make prereq
        Rscript -e "devtools::install_github('abelew/EuPathDB')"
        Rscript -e "remotes::install_deps(dependencies=TRUE)"
        Rscript -e "remotes::install_deps(dependencies='Suggests')"
        #Rscript -e "remotes::install_cran('lintr')"
        #Rscript -e "devtools::install_github('YuLab-SMU/GOSemSim')"

        Rscript -e "devtools::install_github('js229/Vennerable')"
        #Rscript -e "devtools::install_github('kokrah/cbcbSEQ')"
        #Rscript -e "devtools::install_bioc('RDAVIDWebService')"
        #Rscript -e "devtools::install_github('dviraran/xCell')"
        make deps

    - name: Run tests
      run: |
        Rscript -e "print(nrow(installed.packages()))"
        make test