update

.github/workflows/check-standard.yaml

@@ -23,12 +23,65 @@ jobs:
           - {os: ubuntu-latest,   r: 'release'}
 
     env:
-      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
-
+      # 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
 

DESCRIPTION

@@ -49,6 +49,7 @@ Imports:
     BiocParallel,
     ggplot2,
     Matrix,
+    methods,
     rearrr,
     sf,
     SpatialExperiment,