diff --git a/.Rbuildignore b/.Rbuildignore index d87a92e..0752ae4 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,4 +1,10 @@ examples +repo +revdep +scripts +tools +wiki +www tests/Makefile tests/(.+?)\.png$ tests/(.+?)\.pdf$ @@ -7,6 +13,7 @@ inst/doc/Makefile inst/doc/(.+?).md inst/doc/(.+?).Rmd man/roxygen +Doxyfile LICENSE\.md$ README\.md$ CRAN\.md$ @@ -33,6 +40,7 @@ Makefile rules.mk scripts lib +libs library check www diff --git a/.github/workflows/r-cmd-check.yml b/.github/workflows/r-cmd-check.yml index eb080be..7510028 100644 --- a/.github/workflows/r-cmd-check.yml +++ b/.github/workflows/r-cmd-check.yml @@ -22,10 +22,8 @@ jobs: config: - {os: ubuntu-22.04, r: 'devel', http-user-agent: 'release'} - {os: ubuntu-latest, r: 'release'} - - {os: ubuntu-latest, r: 'oldrel-1'} - {os: ubuntu-latest, r: '4.1.0'} - - {os: macOS-11, r: 'release'} - - {os: macOS-12, r: 'release'} + - {os: macOS-latest, r: 'release'} - {os: windows-latest, r: 'release'} env: diff --git a/.gitignore b/.gitignore index 16ab8f2..ec9dce7 100644 --- a/.gitignore +++ b/.gitignore @@ -19,16 +19,15 @@ *.so *.gcda *.gcno -tests/*.pdf -scripts +*.pdf +/scripts lib library check +repo +wiki www -*.pdf -inst/doc/figure -inst/doc/cache -hub_cov.R +tmp covr.html covr.rds .DS_Store diff --git a/rules.mk b/rules.mk index 79a6f96..18e5089 100644 --- a/rules.mk +++ b/rules.mk @@ -1,4 +1,4 @@ -REXE = R --vanilla +REXE = $(shell which R) --vanilla RSESSION = emacs -f R RCMD = $(REXE) CMD RCMD_ALT = R --no-save --no-restore CMD diff --git a/tools/check.env b/tools/check.env new file mode 100644 index 0000000..a200412 --- /dev/null +++ b/tools/check.env @@ -0,0 +1,88 @@ +_R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_=true +_R_CHECK_ALL_NON_ISO_C_=false +_R_CHECK_ALWAYS_LOG_VIGNETTE_OUTPUT_=false +_R_CHECK_ASCII_CODE_=true +_R_CHECK_ASCII_DATA_=true +_R_CHECK_AUTOCONF_=true +_R_CHECK_BASHISMS_=true +_R_CHECK_BOGUS_RETURN_=true +_R_CHECK_BUILD_VIGNETTES_SEPARATELY_=true +_R_CHECK_CLEAN_VIGN_TEST_=true +_R_CHECK_CODE_ASSIGN_TO_GLOBALENV_=true +_R_CHECK_CODE_ATTACH_=true +_R_CHECK_CODE_CLASS_IS_STRING_=true +_R_CHECK_CODE_DATA_INTO_GLOBALENV_=true +_R_CHECK_CODE_USAGE_VIA_NAMESPACES_=true +_R_CHECK_CODE_USAGE_WITH_ONLY_BASE_ATTACHED_=true +_R_CHECK_CODOC_S4_METHODS_=true +_R_CHECK_COMPACT_DATA_=true +_R_CHECK_COMPILATION_FLAGS_=true +_R_CHECK_CONNECTIONS_LEFT_OPEN_=true +_R_CHECK_CRAN_INCOMING_=false +_R_CHECK_DATALIST_=true +_R_CHECK_DEPRECATED_DEFUNCT_=true +_R_CHECK_DONTTEST_EXAMPLES_=false +_R_CHECK_DOT_FIRSTLIB_=true +_R_CHECK_DOT_INTERNAL_=true +_R_CHECK_EXAMPLE_TIMING_THRESHOLD_=5 +_R_CHECK_EXCESSIVE_IMPORTS_=20 +_R_CHECK_EXECUTABLES_=true +_R_CHECK_EXECUTABLES_EXCLUSIONS_=false +_R_CHECK_EXIT_ON_FIRST_ERROR_=false +_R_CHECK_FF_CALLS_=true +_R_CHECK_FF_DUP_=true +_R_CHECK_FORCE_SUGGESTS_=false +_R_CHECK_FUTURE_FILE_TIMESTAMPS_=true +_R_CHECK_GCT_N_=0 +_R_CHECK_INSTALL_DEPENDS_=true +_R_CHECK_LENGTH_1_CONDITION_ =package:_R_CHECK_PACKAGE_NAME_ +_R_CHECK_LENGTH_1_LOGIC2_=package:_R_CHECK_PACKAGE_NAME_,abort,verbose +_R_CHECK_LICENSE_=true +_R_CHECK_LIMIT_CORES_=true +_R_CHECK_MATRIX_DATA_=true +_R_CHECK_NATIVE_ROUTINE_REGISTRATION_=true +_R_CHECK_NO_RECOMMENDED_=true +_R_CHECK_NO_STOP_ON_TEST_ERROR_=true +_R_CHECK_ORPHANED_=true +_R_CHECK_OVERWRITE_REGISTERED_S3_METHODS_=true +_R_CHECK_PACKAGES_USED_IN_TESTS_USE_SUBDIRS_=true +_R_CHECK_PKG_SIZES_=true +_R_CHECK_PKG_SIZES_THRESHOLD_=5 +_R_CHECK_PRAGMAS_=true +_R_CHECK_RD_CHECKRD_MINLEVEL_=-1 +_R_CHECK_RD_CONTENTS_=true +_R_CHECK_RD_EXAMPLES_T_AND_F_=false +_R_CHECK_RD_LINE_WIDTHS_=true +_R_CHECK_RD_STYLE_=true +_R_CHECK_RD_VALIDATE_RD2HTML_=true +_R_CHECK_RD_XREFS_=true +_R_CHECK_REPLACING_IMPORTS_=true +_R_CHECK_R_DEPENDS_="warn" +_R_CHECK_R_ON_PATH_=true +_R_CHECK_S3_METHODS_NOT_REGISTERED_=true +_R_CHECK_SERIALIZATION_=true +_R_CHECK_SHLIB_OPENMP_FLAGS_=true +_R_CHECK_SKIP_ARCH_=none +_R_CHECK_SRC_MINUS_W_IMPLICIT_=true +_R_CHECK_SRC_MINUS_W_UNUSED_=true +_R_CHECK_SUBDIRS_NOCASE_=true +_R_CHECK_SUBDIRS_STRICT_=default +_R_CHECK_SUGGESTS_ONLY_=true +_R_CHECK_SYSTEM_CLOCK_=false +_R_CHECK_TESTS_NLINES_=13 +_R_CHECK_THINGS_IN_CHECK_DIR_=true +_R_CHECK_THINGS_IN_OTHER_DIRS_=false +_R_CHECK_THINGS_IN_TEMP_DIR_=true +_R_CHECK_TIMINGS_=10 +_R_CHECK_TOPLEVEL_FILES_=true +_R_CHECK_UNSAFE_CALLS_=true +_R_CHECK_USE_CODETOOLS_=true +_R_CHECK_USE_INSTALL_LOG_=true +_R_CHECK_VC_DIRS_=true +_R_CHECK_VIGNETTES_NLINES_=10 +_R_CHECK_VIGNETTES_SKIP_RUN_MAYBE_=true +_R_CHECK_WALL_FORTRAN_=true +_R_CHECK_XREFS_MIND_SUSPECT_ANCHORS_=false +_R_CHECK_XREFS_PKGS_ARE_DECLARED_=false +_R_CHECK_XREFS_USE_ALIASES_FROM_CRAN_=false +_R_CHECK_CODETOOLS_PROFILE_="suppressLocalUnused=FALSE,suppressPartialMatchArgs=FALSE,suppressParamUnused=TRUE,suppressUndefined=FALSE"