vignette edits #333
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| ## This is a test | |
| ## Template from here: https://github.com/r-lib/actions/tree/master/examples#standard-ci-workflow | |
| ## ubuntu-latest | |
| on: | |
| push: | |
| branches: | |
| - devel | |
| pull_request: | |
| branches: | |
| - devel | |
| name: R-CMD-check | |
| jobs: | |
| R-CMD-check: | |
| if: "contains(toJSON(github.event.commits.*.message), 'build_check')" | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - {os: ubuntu-20.04, r: '4.3.3', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | |
| - {os: macOS-latest, r: '4.3.3'} | |
| - {os: windows-latest, r: '4.3.3'} | |
| 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) | |
| shell: Rscript {0} | |
| - name: Cache R packages | |
| if: runner.os != 'Windows' | |
| uses: actions/cache@v1 | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: ${{ runner.os }}-r-${{ matrix.config.r }}-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}- | |
| - name: Install system dependencies | |
| if: runner.os == 'Linux' | |
| env: | |
| RHUB_PLATFORM: linux-x86_64-ubuntu-gcc | |
| run: | | |
| sudo apt-get install libv8-dev | |
| sudo apt install libcurl4-openssl-dev | |
| - name: Install dependencies | |
| run: | | |
| remotes::install_deps(dependencies = TRUE) | |
| remotes::install_cran("rcmdcheck") | |
| install.packages(c("BiocManager", "knitcitations", "docopt")) | |
| remotes::install_github("HenrikBengtsson/matrixStats", ref="develop") ## temp fix - 03/15/22 | |
| BiocManager::install("tgirke/systemPipeR", dependencies=TRUE) | |
| BiocManager::install("tgirke/systemPipeRdata") | |
| shell: Rscript {0} | |
| - name: Check | |
| env: | |
| _R_CHECK_CRAN_INCOMING_REMOTE_: false | |
| run: rcmdcheck::rcmdcheck(build_args = c('--compact-vignettes=gs+qpdf'), args = c("--no-manual", "--no-build-vignettes", "--timings"), 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 |