feat: OOM label propagation #46
Workflow file for this run
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| on: | |
| pull_request: | |
| branches: | |
| - 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: 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-branch | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| - uses: r-lib/actions/setup-pandoc@v2-branch | |
| - name: Query dependencies | |
| run: | | |
| install.packages('remotes') | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | |
| writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") | |
| shell: Rscript {0} | |
| - name: Cache R packages | |
| if: runner.os != 'Windows' | |
| uses: actions/cache@v1 | |
| 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' | |
| 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" | |
| - name: Install R dependencies | |
| run: | | |
| remotes::install_deps(dependencies = TRUE) | |
| install.packages("BiocManager") | |
| BiocManager::repositories() | |
| remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories()) | |
| remotes::install_cran("devtools") | |
| remotes::install_cran("rcmdcheck") | |
| BiocManager::install("BiocCheck") | |
| 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: R CMD Check | |
| env: | |
| _R_CHECK_CRAN_INCOMING_: false | |
| run: rcmdcheck::rcmdcheck(build_args = c("--no-build-vignettes", "--no-manual"), | |
| args = c("--no-manual", "--no-build-vignettes", "--no-vignettes", "--ignore-vignettes"), | |
| error_on = "warning", | |
| check_dir = "check") | |
| shell: Rscript {0} | |
| - name: Bioconductor Check | |
| env: | |
| _R_CHECK_CRAN_INCOMING_REMOTE_: false | |
| run: | | |
| checkres <- BiocCheck::BiocCheck() | |
| print(checkres$warning) | |
| checkres$warning$checkVersionNumber <- NULL | |
| if (length(checkres$warning) > 0 || length(checkres$error) > 0){ | |
| if (!is.null(checkres$warning)) print(checkres$warning) | |
| if (!is.null(checkres$error)) print(checkres$error) | |
| error("Failed BiocCheck") | |
| } | |
| shell: Rscript {0} | |