CITEViz.Rmd: Remove formatting fluff, still need to update contents #164
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| name: 'rcmdcheck' | |
| on: [push, pull_request] | |
| env: | |
| cache-version: v1 | |
| # source: https://github.com/seandavi/BuildABiocWorkshop | |
| jobs: | |
| r-check: | |
| runs-on: ubuntu-latest | |
| container: bioconductor/bioconductor_docker:devel | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Query dependencies and update old packages | |
| run: | | |
| BiocManager::install(ask=FALSE) | |
| 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: /usr/local/lib/R/site-library | |
| key: ${{ env.cache-version }}-${{ runner.os }}-r-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ${{ env.cache-version }}-${{ runner.os }}-r- | |
| # This lets us augment with additional dependencies | |
| - name: Install system dependencies | |
| run: | | |
| remotes::install_cran('Seurat') | |
| shell: Rscript {0} | |
| - name: Install dependencies | |
| run: | | |
| options(repos = c(CRAN = "https://cran.r-project.org")) | |
| BiocManager::repositories() | |
| remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories()) | |
| remotes::install_cran("rcmdcheck") | |
| remotes::install_bioc("BiocCheck") | |
| shell: Rscript {0} | |
| - name: rcmdcheck | |
| env: | |
| _R_CHECK_CRAN_INCOMING_REMOTE_: false | |
| run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--no-examples"), error_on = "warning", check_dir = "check") | |
| shell: Rscript {0} | |
| - name: BiocCheck | |
| run: BiocCheck::BiocCheck() | |
| shell: Rscript {0} |