trying to get Matrix to build from source #448
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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: | ||
| - main | ||
| - master | ||
| - devel | ||
| - genetic_case | ||
| pull_request: | ||
| branches: | ||
| - main | ||
| - master | ||
| - devel | ||
| name: R-CMD-check | ||
| jobs: | ||
| R-CMD-check: | ||
| runs-on: ${{ matrix.config.os }} | ||
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| config: | ||
| - {os: windows-latest, r: 'release'} | ||
| - {os: macOS-latest, r: 'release'} | ||
| - {os: ubuntu-20.04, r: 'release', 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 }} | ||
| steps: | ||
| - uses: actions/checkout@v2 | ||
| - uses: r-lib/actions/setup-r@v2 | ||
| with: | ||
| r-version: ${{ matrix.config.r }} | ||
| - uses: r-lib/actions/setup-pandoc@v2 | ||
| - name: Query dependencies | ||
| run: | | ||
| install.packages('remotes') | ||
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | ||
| writeLines(sprintf("R-%i.%i", getRversion()$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 | ||
| if: runner.os == 'Linux' | ||
| run: | | ||
| while read -r cmd | ||
| do | ||
| eval sudo $cmd | ||
| done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))') | ||
| - name: Install dependencies | ||
| run: | | ||
| remotes::install_deps(dependencies = TRUE) | ||
| remotes::install_cran(c("rcmdcheck", "XML", "RCurl")) | ||
| install.packages("irlba", type="source") | ||
| BiocManager::install(c("MouseGastrulationData", "MouseThymusAgeing", "scRNAseq")) | ||
| shell: Rscript {0} | ||
| - name: Check | ||
| env: | ||
| _R_CHECK_CRAN_INCOMING_REMOTE_: false | ||
| run: | | ||
| options(crayon.enabled = TRUE) | ||
| rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", "--no-build-vignettes"), error_on = "error", check_dir = "check") | ||
| shell: Rscript {0} | ||
| - name: Test coverage | ||
| run: | | ||
| install.packages("covr") | ||
| covr::codecov() | ||
| shell: Rscript {0} | ||
