update subset.FRASER drop argument #178
Workflow file for this run
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
| # 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: | |
| pull_request: | |
| name: Build | |
| jobs: | |
| Build: | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - {os: windows-latest, r: '4.2', bioc: '3.15'} | |
| - {os: macOS-latest, r: '4.2', bioc: '3.15'} | |
| - {os: ubuntu-20.04, r: '4.2', bioc: '3.15', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | |
| - {os: ubuntu-20.04, r: 'next', bioc: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| RSPM: ${{ matrix.config.rspm }} | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| BIOC_VERSION: ${{ matrix.config.bioc }} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: r-lib/actions/setup-r@v1 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| - uses: r-lib/actions/setup-pandoc@v1 | |
| - name: Query dependencies | |
| run: | | |
| install.packages('remotes') | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | |
| writeLines(sprintf("R-%i.%i", getRversion()$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 (Linux) | |
| if: runner.os == 'Linux' | |
| run: | | |
| sudo apt-get install libgit2-dev | |
| while read -r cmd | |
| do | |
| eval sudo $cmd | |
| done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))') | |
| - name: Install system dependencies (macOS) | |
| if: runner.os == 'macos' | |
| run: | | |
| brew install libgit2 | |
| brew install --force --overwrite gcc | |
| - uses: r-lib/actions/setup-tinytex@v1 | |
| - name: Init and install packages for tex | |
| run: | | |
| system("tlmgr --version") | |
| install.packages("tinytex") | |
| tinytex::tlmgr_install(pkgs = c("bera", "caption", "changepage", "enumitem", "everysel", "fancyhdr", "footmisc", "grfext", "index", "marginfix", "mathtools", "ms", "nowidow", "parnotes", "parskip", "placeins", "preprint", "ragged2e", "side", "soul", "titlesec", "tocbibind", "xstring")) | |
| shell: Rscript {0} | |
| - name: Install dependencies | |
| run: | | |
| source(".github/helperScripts/setupEnv.R") | |
| remotes::install_cran("rcmdcheck") | |
| shell: Rscript {0} | |
| - name: Check build | |
| run: | | |
| devtools::build(vignettes = FALSE) | |
| shell: Rscript {0} | |
| - name: Check BiocCheck | |
| run: | | |
| BiocCheck::BiocCheck('.', `quit-with-status`=TRUE) | |
| shell: Rscript {0} | |
| - name: Check R check | |
| run: | | |
| devtools::check(vignettes = FALSE, args = '--timings') | |
| shell: Rscript {0} | |
| - name: Check Examples | |
| run: | | |
| devtools::run_examples() | |
| shell: Rscript {0} | |
| - name: Check tests | |
| run: | | |
| devtools::test() | |
| shell: Rscript {0} | |
| - name: Check vignette | |
| run: | | |
| devtools::build_vignettes() | |
| 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 | |
| - uses: codecov/codecov-action@v1 |