Fixing github actions #31
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| # For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag. | |
| # https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions | |
| on: | |
| push: | |
| branches: | |
| - github_actions | |
| - master | |
| pull_request: | |
| branches: | |
| - github_actions | |
| - master | |
| name: Ubuntu | |
| jobs: | |
| R-CMD-check: | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}, Java ${{ matrix.config.java }}, ${{ matrix.config.pkgs }} packages) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - {os: ubuntu-20.04, r: 'release', pkgs: 'all', java: 8} | |
| - {os: ubuntu-20.04, r: 'release', pkgs: 'all', java: 11} | |
| - {os: ubuntu-20.04, r: 'devel', pkgs: 'all', java: 8} | |
| - {os: ubuntu-20.04, r: 'devel', pkgs: 'all', java: 11} | |
| - {os: ubuntu-20.04, r: 'devel', pkgs: 'depends only', java: 11} | |
| env: | |
| _R_REMOTES_NO_ERRORS_FROM_WARNINGS_: true | |
| _R_CHECK_FORCE_SUGGESTS_: false | |
| _R_CHECK_TIMINGS_: 10 | |
| _R_CHECK_CRAN_INCOMING_REMOTE_: false | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| CI: true | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| - uses: actions/setup-java@v1 | |
| with: | |
| java-version: ${{ matrix.config.java }} | |
| #- uses: r-lib/actions/setup-pandoc@v1 | |
| - name: Query dependencies | |
| run: | | |
| install.packages('remotes') | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | |
| writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") | |
| shell: Rscript {0} | |
| - name: Cache R packages | |
| if: runner.os != 'Windows' | |
| uses: actions/cache@v2 | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- | |
| - name: Install system dependencies | |
| run: | | |
| sudo apt-get -y install \ | |
| libcurl4-openssl-dev \ | |
| libudunits2-dev libgdal-dev libgeos-dev libproj-dev libglpk-dev | |
| while read -r cmd | |
| do | |
| eval sudo $cmd | |
| done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))') | |
| echo export PATH=$PATH > reconf.sh; echo export JAVA_HOME=$JAVA_HOME >> reconf.sh; echo R CMD javareconf >> reconf.sh; sudo bash reconf.sh | |
| rm -f reconf.sh | |
| - name: Install dependencies | |
| run: | | |
| remotes::install_deps(dependencies = TRUE) | |
| remotes::install_cran("rcmdcheck") | |
| remotes::install_cran("covr") | |
| remotes::install_bioc("lpsymphony") | |
| remotes::install_cran("urlchecker") | |
| shell: Rscript {0} | |
| - name: Session information | |
| run: | | |
| options(width = 100) | |
| pkgs <- installed.packages()[, "Package"] | |
| sessioninfo::session_info(pkgs, include_base = TRUE) | |
| shell: Rscript {0} | |
| - name: Java information | |
| run: java -version && which java && echo $PATH && echo $JAVA_HOME | |
| shell: bash | |
| - name: Set environmental variables for package checks | |
| if: matrix.config.pkgs == 'depends only' | |
| run: | | |
| echo "_R_CHECK_DEPENDS_ONLY_=true" >> $GITHUB_ENV | |
| - name: Check | |
| run: | | |
| rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", "--no-build-vignettes", "--no-multiarch"), error_on = "warning", check_dir = "check") | |
| shell: Rscript {0} | |
| - name: Upload check results | |
| if: failure() | |
| uses: actions/upload-artifact@main | |
| with: | |
| name: ${{ runner.os }}-r${{ matrix.config.r }}-results | |
| path: check | |
| - name: Show testthat output | |
| if: always() | |
| run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true | |
| shell: bash | |
| - name: Test coverage | |
| if: runner.os == 'Linux' && matrix.config.r == 'release' | |
| run: covr::codecov() | |
| shell: Rscript {0} |