update oncogene/TSG source #389
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| on: | |
| push: | |
| pull_request: | |
| branches: | |
| - master | |
| name: R-CMD-check | |
| jobs: | |
| R-CMD-check: | |
| runs-on: ${{ matrix.config.os }} | |
| container: ${{ matrix.config.image }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.r }} - ${{ matrix.config.bioc }} - ${{ matrix.config.image }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - { os: windows-latest, r: 'devel', bioc: 'devel'} | |
| - { os: macOS-latest, r: 'release', bioc: '3.12'} | |
| - { os: macOS-latest, r: 'devel', bioc: 'devel', curlConfigPath: '/usr/bin/'} | |
| - { os: ubuntu-latest, r: 'release', image: 'bioconductor/bioconductor_docker:devel'} | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| CRAN: ${{ matrix.config.cran }} | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - name: Check out repo | |
| uses: actions/checkout@v2 | |
| - name: Set up R | |
| uses: r-lib/actions/setup-r@master | |
| if: matrix.config.image == null | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| - name: Set up pandoc | |
| uses: r-lib/actions/setup-pandoc@master | |
| if: matrix.config.image == null | |
| - name: Install remotes | |
| run: | | |
| install.packages('remotes') | |
| shell: Rscript {0} | |
| - name: Set BiocManager version | |
| if: matrix.config.image == null | |
| run: | | |
| install.packages('BiocManager') | |
| BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE) | |
| shell: Rscript {0} | |
| - name: Query dependencies | |
| run: | | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE, repos = c(getOption('repos'), BiocManager::repositories())), 'depends.Rds', version = 2) | |
| shell: Rscript {0} | |
| - name: Cache R packages | |
| if: runner.os != 'Windows' && matrix.config.image == null | |
| uses: actions/cache@v1 | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: ${{ runner.os }}-r-${{ matrix.config.r }}-bioc-${{ matrix.config.bioc }}-${{ hashFiles('depends.Rds') }} | |
| restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-bioc-${{ matrix.config.bioc }}- | |
| - name: Install system dependencies (macOS) | |
| if: runner.os == 'macOS' | |
| run: | | |
| brew install harfbuzz | |
| brew install fribidi | |
| - name: Set up gfortran symlinks (macOS) | |
| if: runner.os == 'macOS' | |
| run: | | |
| set -x | |
| sudo ln -s /usr/local/Cellar/gcc@8/8.4.0_2/lib/gcc/8 /usr/local/gfortran/lib | |
| gfortran --version | |
| - name: Install system dependencies | |
| if: runner.os == 'Linux' | |
| env: | |
| RHUB_PLATFORM: linux-x86_64-ubuntu-gcc | |
| run: | | |
| Rscript -e "remotes::install_github('r-hub/sysreqs')" | |
| sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))") | |
| sudo -s eval "$sysreqs" | |
| sudo apt-get update && sudo apt-get -y install libcurl4-openssl-dev | |
| - name: Install dependencies | |
| run: | | |
| local_deps <- remotes::local_package_deps(dependencies = TRUE) | |
| deps <- remotes::dev_package_deps(dependencies = TRUE, repos = BiocManager::repositories()) | |
| BiocManager::install(local_deps[local_deps %in% deps$package[deps$diff != 0]], Ncpu = 2L) | |
| remotes::install_cran('rcmdcheck', Ncpu = 2L) | |
| BiocManager::install("federicomarini/annoFuseData") | |
| shell: Rscript {0} | |
| - name: Session info | |
| run: | | |
| options(width = 100) | |
| pkgs <- installed.packages()[, "Package"] | |
| sessioninfo::session_info(pkgs, include_base = TRUE) | |
| shell: Rscript {0} | |
| - name: Check | |
| run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error", check_dir = "check") | |
| shell: Rscript {0} | |
| - name: BiocCheck | |
| run: | | |
| BiocManager::install("BiocCheck") | |
| BiocCheck::BiocCheck(".") | |
| shell: Rscript {0} | |
| - name: Upload check results | |
| if: failure() | |
| uses: actions/upload-artifact@master | |
| 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: Upload check results | |
| if: failure() | |
| uses: actions/upload-artifact@master | |
| with: | |
| name: ${{ runner.os }}-r${{ matrix.config.r }}-bioc-${{ matrix.config.bioc }}-results | |
| path: check | |
| # - name: Test coverage | |
| # if: matrix.config.os == 'macOS-latest' && matrix.config.r == 'release' | |
| # run: | | |
| # install.packages("covr") | |
| # covr::codecov(token = "${{secrets.CODECOV_TOKEN}}") | |
| # shell: Rscript {0} | |
| # - name: Deploy | |
| # if: github.event_name == 'push' && github.ref == 'refs/heads/master' && matrix.config.os == 'macOS-latest' && matrix.config.r == 'release' && matrix.config.bioc == 'devel' | |
| # run: | | |
| # R CMD INSTALL . | |
| # Rscript -e "remotes::install_dev('pkgdown'); pkgdown::deploy_to_branch(new_process = FALSE)" |