Add summary statistic for the number of detected features #141
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: | |
| - main | |
| schedule: | |
| - cron: '0 9 * * 2' | |
| name: R-CMD-check | |
| jobs: | |
| R-CMD-check: | |
| runs-on: ${{ matrix.config.os }} | |
| container: ${{ matrix.config.image }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.bioc }} - ${{ matrix.config.image }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - { os: macOS-latest, bioc: 'release', curlConfigPath: '/usr/bin/'} | |
| - { os: windows-latest, bioc: 'release'} | |
| - { os: ubuntu-latest, image: "bioconductor/bioconductor_docker:RELEASE_3_18", cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"} | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| _R_CHECK_FORCE_SUGGESTS_: false | |
| CRAN: ${{ matrix.config.cran }} | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| CURL_CONFIG: ${{ matrix.config.curlConfigPath }}curl-config | |
| cache-version: v1 | |
| steps: | |
| - name: Check out repo | |
| uses: actions/checkout@v3 | |
| - name: Set up R and install BiocManager | |
| uses: grimbough/bioc-actions/setup-bioc@v1 | |
| if: matrix.config.image == null | |
| with: | |
| bioc-version: ${{ matrix.config.bioc }} | |
| - name: Set up pandoc | |
| uses: r-lib/actions/setup-pandoc@v2 | |
| if: matrix.config.image == null | |
| - name: Install remotes | |
| run: | | |
| install.packages('remotes') | |
| 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: ${{ env.cache-version }}-${{ runner.os }}-bioc-${{ matrix.config.bioc }}-${{ hashFiles('depends.Rds') }} | |
| restore-keys: ${{ env.cache-version }}-${{ runner.os }}-bioc-${{ matrix.config.bioc }}- | |
| - name: Install system dependencies (Linux) | |
| if: runner.os == 'Linux' | |
| env: | |
| RHUB_PLATFORM: linux-x86_64-ubuntu-gcc | |
| run: | | |
| Rscript -e "remotes::install_github('r-hub/sysreqs')" | |
| sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))") | |
| sudo -s eval "$sysreqs" | |
| sudo apt-get update && sudo apt-get -y install libcurl4-openssl-dev libharfbuzz-dev libfribidi-dev | |
| - name: Install system dependencies (macOS) | |
| if: runner.os == 'macOS' | |
| run: | | |
| brew install harfbuzz | |
| brew install fribidi | |
| brew install gcc | |
| brew install --cask xquartz | |
| - name: Install dependencies | |
| run: | | |
| local_deps <- remotes::local_package_deps(dependencies = TRUE) | |
| deps <- remotes::dev_package_deps(dependencies = TRUE, repos = BiocManager::repositories()) | |
| BiocManager::install(local_deps[local_deps %in% deps$package[deps$diff != 0]], Ncpu = 2L) | |
| remotes::install_cran('rcmdcheck', Ncpu = 2L) | |
| 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: Build, Install, Check | |
| id: build-install-check | |
| uses: grimbough/bioc-actions/build-install-check@v1 | |
| - name: Upload install log if the build/install/check step fails | |
| if: always() && (steps.build-install-check.outcome == 'failure') | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: install-log | |
| path: | | |
| ${{ steps.build-install-check.outputs.install-log }} | |
| # - name: Run BiocCheck | |
| # uses: grimbough/bioc-actions/run-BiocCheck@v1 | |
| # with: | |
| # arguments: '--no-check-bioc-views --no-check-bioc-help' | |
| # error-on: 'error' | |
| - name: Show testthat output (windows) | |
| if: always() && runner.os == 'Windows' | |
| run: | | |
| type ${{ steps.build-install-check.outputs.check-dir }}\tests\testthat.Rout | |
| shell: cmd | |
| - name: Show testthat output (non-windows) | |
| if: always() && runner.os != 'Windows' | |
| run: | | |
| cat ${{ steps.build-install-check.outputs.check-dir }}/tests/testthat.Rout | |
| shell: bash | |
| - name: Upload check results | |
| if: failure() | |
| uses: actions/upload-artifact@master | |
| with: | |
| name: ${{ runner.os }}-bioc-${{ matrix.config.bioc }}-results | |
| path: ${{ steps.build-install-check.outputs.check-dir }} | |
| - name: Test coverage | |
| if: matrix.config.os == 'macOS-latest' | |
| run: | | |
| install.packages("covr") | |
| covr::codecov(token = "${{secrets.CODECOV_TOKEN}}") | |
| shell: Rscript {0} | |
| - name: Deploy | |
| if: github.event_name == 'push' && github.ref == 'refs/heads/main' && matrix.config.os == 'macOS-latest' | |
| run: | | |
| R CMD INSTALL . | |
| Rscript -e "remotes::install_dev('pkgdown'); pkgdown::deploy_to_branch(new_process = FALSE)" |