addressed \value warning from BiocCheck::BiocCheck('new-package'=TRUE) #33
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| # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples | |
| # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help | |
| on: | |
| push: | |
| branches: [main] | |
| pull_request: | |
| branches: [main] | |
| 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: macos-latest, r: 'release'} | |
| - {os: windows-latest, r: 'release'} | |
| - {os: ubuntu-latest, r: 'release'} | |
| env: | |
| # environment setting created by JEFWorks-Lab | |
| # GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| # R_KEEP_PKG_SOURCE: yes | |
| # R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| # _R_CHECK_CRAN_INCOMING_REMOTE_: false | |
| # _R_CHECK_FORCE_SUGGESTS_: false | |
| # Bioconductor recommended environment (https://contributions.bioconductor.org/general.html) | |
| # https://www.rdocumentation.org/packages/base/versions/3.5.1/topics/Startup | |
| # https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Checking-and-building-packages | |
| # https://cran.r-project.org/doc/manuals/r-devel/R-ints.html#Tools | |
| _R_CHECK_FORCE_SUGGESTS_: true | |
| _R_CHECK_RD_LINE_WIDTHS_: true | |
| _R_CHECK_EXECUTABLES_: false | |
| _R_CHECK_EXECUTABLES_EXCLUSIONS_: false | |
| _R_CHECK_FF_DUP_: true | |
| _R_CHECK_VC_DIR_: true | |
| _R_CHECK_PKG_SIZES_: true | |
| _R_CHECK_PKG_SIZES_THRESHOLD_: 5 | |
| _R_CHECK_REPLACING_IMPORTS_: true | |
| _R_CHECK_TIMINGS_: "0" | |
| _R_CHECK_INSTALL_DEPENDS_: true | |
| _R_CHECK_SUGGESTS_ONLY_: true | |
| _R_CHECK_NO_RECOMMENDED_: true | |
| _R_CHECK_CODE_ASSIGN_TO_GLOBALENV_: true | |
| _R_CHECK_CODE_ATTACH_: true | |
| _R_CHECK_CODE_DATA_INTO_GLOBALENV_: true | |
| _R_CHECK_DOT_FIRSTLIB_: true | |
| _R_CHECK_DEPRECATED_DEFUNCT_: true | |
| _R_CHECK_TOPLEVELFILES_: true | |
| _R_CHECK_LIMIT_CORES_: true | |
| _R_CHECK_CODE_USAGE_VIA_NAMESPACES_: true | |
| _R_CHECK_S3_METHODS_NOT_REGISTERED_: true | |
| _R_CHECK_OVERWRITE_REGISTERED_S3_METHODS_: true | |
| _R_S3_METHOD_LOOKUP_BASEENV_AFTER_GLOBALENV_: true | |
| _R_CHECK_TESTS_NLINES_: 20 | |
| _R_CHECK_NATIVE_ROUTINE_REGISTRATION_: true | |
| _R_CHECK_NO_STOP_ON_TEST_ERROR_: true | |
| _R_CHECK_PRAGMAS_: true | |
| _R_CHECK_COMPILATION_FLAGS_: true | |
| _R_CHECK_R_DEPENDS_: "warn" | |
| _R_CHECK_SERIALIZATION_: true | |
| _R_CHECK_R_ON_PATH_: true | |
| _R_CHECK_PACKAGES_USED_IN_TESTS_USE_SUBDIRS_: true | |
| _R_CHECK_SHLIB_OPENMP_FLAGS_: true | |
| _R_CHECK_CONNECTIONS_LEFT_OPEN_: true | |
| _R_CHECK_FUTURE_FILE_TIMESTAMPS_: true | |
| _R_CHECK_LENGTH_1_CONDITION_ : package:_R_CHECK_PACKAGE_NAME_ | |
| _R_CHECK_LENGTH_1_LOGIC2_: package:_R_CHECK_PACKAGE_NAME_ | |
| IS_BIOC_BUILD_MACHINE: true | |
| _R_CHECK_NEWS_IN_PLAIN_TEXT_: true | |
| R_DEFAULT_INTERNET_TIMEOUT: 600 | |
| BIOCPARALLEL_WORKER_NUMBER: 4 | |
| OMP_THREAD_LIMIT: 2 | |
| OMP_NUM_THREADS: 2 | |
| KMP_DEVICE_THREAD_LIMIT: 2 | |
| KMP_TEAMS_THREAD_LIMIT: 2 | |
| _R_COMPARE_LANG_OBJECTS: eqonly | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| http-user-agent: ${{ matrix.config.http-user-agent }} | |
| use-public-rspm: true | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: any::rcmdcheck | |
| needs: check | |
| - uses: r-lib/actions/check-r-package@v2 | |
| with: | |
| error-on: '"error"' | |
| upload-snapshots: true | |