Upload CRAN scripts for Linux

Documents/CRAN_scripts/CRAN_incoming/CRAN_incoming.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes

Documents/CRAN_scripts/CRAN_incoming/check.Renviron

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+## KH's personal ~/.R/check.Renviron.
+## Last updated on 2022-08-10
+
+### Defaults for '--as-cran": commented out where not appropriate for
+### all KH checks.
+_R_CHECK_AUTOCONF_=true
+## _R_CHECK_BASHISMS_=true
+_R_CHECK_BOGUS_RETURN_=true
+_R_CHECK_CODE_USAGE_VIA_NAMESPACES_=true
+_R_CHECK_CODE_USAGE_WITH_ONLY_BASE_ATTACHED_=true
+## _R_CHECK_CODOC_VARIABLES_IN_USAGES_=true
+_R_CHECK_COMPILATION_FLAGS_=true
+## _R_CHECK_CONNECTIONS_LEFT_OPEN_=true
+_R_CHECK_DEPENDS_ONLY_DATA_=true
+## _R_CHECK_DONTTEST_EXAMPLES_=true
+_R_CHECK_DOT_FIRSTLIB_=true
+_R_CHECK_FF_AS_CRAN_=true
+_R_CHECK_FUTURE_FILE_TIMESTAMPS_=true
+_R_CHECK_INSTALL_DEPENDS_=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_PACKAGE_DATASETS_SUPPRESS_NOTES_=true
+## _R_CHECK_PACKAGES_USED_CRAN_INCOMING_NOTES_=true
+_R_CHECK_PACKAGES_USED_IGNORE_UNUSED_IMPORTS_=true
+_R_CHECK_PACKAGES_USED_IN_TESTS_USE_SUBDIRS_=true
+_R_CHECK_PRAGMAS_=true
+## _R_CHECK_R_DEPENDS_=warn
+_R_CHECK_R_ON_PATH_=true
+_R_CHECK_RD_VALIDATE_RD2HTML_=${_R_CHECK_RD_VALIDATE_RD2HTML_-true}
+## _R_CHECK_RD_CONTENTS_KEYWORDS_=true
+_R_CHECK_SCREEN_DEVICE_=stop
+_R_CHECK_S3_METHODS_NOT_REGISTERED_=true
+_R_CHECK_SHLIB_OPENMP_FLAGS_=true
+_R_CHECK_TIMINGS_=10
+_R_CHECK_THINGS_IN_CHECK_DIR_=true
+## _R_CHECK_THINGS_IN_TEMP_DIR_=true
+_R_CHECK_VIGNETTE_TITLES_=true
+## _R_CHECK_XREFS_PKGS_ARE_DECLARED_=true
+## _R_CHECK_XREFS_MIND_SUSPECT_ANCHORS_=true
+_R_SHLIB_BUILD_OBJECTS_SYMBOL_TABLES_=true
+
+_R_OPTIONS_STRINGS_AS_FACTORS_=${_R_OPTIONS_STRINGS_AS_FACTORS_-false}
+
+### Additional settings used for all KH checks.
+_R_CHECK_ALWAYS_LOG_VIGNETTE_OUTPUT_=true
+_R_CHECK_CODE_ASSIGN_TO_GLOBALENV_=true
+_R_CHECK_CODE_ATTACH_=true
+_R_CHECK_CODE_DATA_INTO_GLOBALENV_=true
+_R_CHECK_CODETOOLS_PROFILE_="suppressPartialMatchArgs=false"
+_R_CHECK_CRAN_INCOMING_CHECK_URLS_IN_PARALLEL_=true
+_R_CHECK_DEPRECATED_DEFUNCT_=true
+_R_CHECK_DOC_SIZES2_=true
+_R_CHECK_DOTCODE_RETVAL_=true
+_R_CHECK_EXECUTABLES_EXCLUSIONS_=false
+## _R_CHECK_FF_CALLS_=registration
+_R_CHECK_FUTURE_FILE_TIMESTAMPS_LEEWAY_=6h
+_R_GC_FAIL_ON_ERROR_=true
+_R_CHECK_LENGTH_1_CONDITION_="package:_R_CHECK_PACKAGE_NAME_,verbose"
+## _R_CHECK_LENGTH_1_CONDITION_=${_R_CHECK_LENGTH_1_CONDITION_-warn}
+## _R_CHECK_LENGTH_1_LOGIC2_="package:_R_CHECK_PACKAGE_NAME_,verbose"
+_R_CHECK_OVERWRITE_REGISTERED_S3_METHODS_=true
+_R_CHECK_PACKAGE_DATASETS_SUPPRESS_NOTES_=true
+_R_CHECK_PKG_SIZES_=false
+_R_CHECK_R_DEPENDS_=true
+_R_CHECK_RD_LINE_WIDTHS_=true
+_R_CHECK_RD_MATH_RENDERING_=true
+_R_CHECK_REPLACING_IMPORTS_=true
+_R_CHECK_SERIALIZATION_=true
+_R_CHECK_SRC_MINUS_W_IMPLICIT_=true
+_R_CHECK_SUGGESTS_ONLY_=${_R_CHECK_SUGGESTS_ONLY_-true}
+_R_CHECK_SYSTEM_CLOCK_=false
+_R_CHECK_THINGS_IN_TEMP_DIR_EXCLUDE_="^(ompi|pulse|runtime-)"
+_R_CHECK_TOPLEVEL_FILES_=true
+_R_CHECK_VC_DIRS_=true
+_R_CHECK_VIGNETTES_SKIP_RUN_MAYBE_=true
+_R_CHECK_XREFS_USE_ALIASES_FROM_CRAN_=true
+## Outputs
+_R_CHECK_TESTS_NLINES_=0
+_R_CHECK_VIGNETTES_NLINES_=10000
+## Timings
+_R_CHECK_TIMINGS_=0
+_R_CHECK_EXAMPLE_TIMING_CPU_TO_ELAPSED_THRESHOLD_=2.5
+_R_CHECK_TEST_TIMING_=yes
+_R_CHECK_TEST_TIMING_CPU_TO_ELAPSED_THRESHOLD_=2.5
+_R_CHECK_VIGNETTE_TIMING_=yes
+_R_CHECK_VIGNETTE_TIMING_CPU_TO_ELAPSED_THRESHOLD_=2.5
+
+## FIXME: remove eventually ...
+## _R_CLASS_MATRIX_ARRAY_=${_R_CLASS_MATRIX_ARRAY_-true}
+

Documents/CRAN_scripts/CRAN_incoming/check_CRAN_incoming.R

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+check_dir <- file.path(normalizePath("~"), "tmp", "CRAN")
+if (!dir.exists(check_dir)) {
+  dir.create(check_dir)
+  message(check_dir, " Created")
+}
+
+# Place lib directory with all .sh files is
+lib_dir <- "../lib/"
+
+user <- Sys.info()["user"]
+if(user == "unknown") user <- Sys.getenv("LOGNAME")
+Sys.setenv("R_USER_DATA_DIR" =
+               sprintf("/tmp/check-CRAN-incoming-%s/data", user),
+           "R_USER_CACHE_DIR" =
+               sprintf("/tmp/check-CRAN-incoming-%s/cache", user),
+           "R_USER_CONFIG_DIR" =
+               sprintf("/tmp/check-CRAN-incoming-%s/config", user))
+
+Sys.setenv("_R_CHECK_INSTALL_DEPENDS_" = "true")
+
+Sys.setenv("R_GC_MEM_GROW" = "2",
+           "R_C_BOUNDS_CHECK" = "yes")
+
+## <FIXME>
+## Need OMP thread limit as 3 instead of 4 when using OpenBLAS.
+Sys.setenv("OMP_NUM_THREADS" = 3,      # 4?
+           "OMP_THREAD_LIMIT" = 3,     # 4?
+           "RCPP_PARALLEL_NUM_THREADS" = 4,
+           "POCL_KERNEL_CACHE" = 0,
+           "OMPI_MCA_btl_base_warn_component_unused" = 0
+           )
+## Or maybe instead just
+Sys.setenv("OPENBLAS_NUM_THREADS" = 1)
+## ???
+## </FIXME>
+
+Sys.setenv("_R_CHECK_FORCE_SUGGESTS_" = "false",
+           "_R_CHECK_PACKAGE_DEPENDS_IGNORE_MISSING_ENHANCES_" = "true")
+
+if(dir.exists(path <- file.path(normalizePath("~"), "tmp", "scratch")))
+    Sys.setenv("TMPDIR" = path)
+
+check_args <- character()               # No longer "--as-cran" ...
+update_check_dir <- TRUE
+use_check_stoplists <- FALSE
+Ncpus <- 6
+
+hostname <- system2("hostname", "-f", stdout = TRUE)
+if(hostname == "xmanduin.wu.ac.at") {
+    Sys.setenv("_R_CHECK_EXAMPLE_TIMING_THRESHOLD_" = "10")
+    Ncpus <- 10
+}
+if(hostname %in% c("anduin2.wu.ac.at", "anduin3.wu.ac.at")) {
+    Ncpus <- 28
+}
+
+Sys.setenv("_R_S3_METHOD_LOOKUP_BASEENV_AFTER_GLOBALENV_" =
+               Sys.getenv("_R_S3_METHOD_LOOKUP_BASEENV_AFTER_GLOBALENV_",
+                          "true"))
+
+## <FIXME>
+## Change eventually ...
+Sys.setenv("_R_CHECK_NATIVE_ROUTINE_REGISTRATION_" =
+               Sys.getenv("_R_CHECK_NATIVE_ROUTINE_REGISTRATION_",
+                          "false"))
+## </FIXME>
+
+## <FIXME>
+## Remove eventually ...
+Sys.setenv("_R_S3_METHOD_LOOKUP_USE_TOPENV_AS_DEFENV_" =
+               Sys.getenv("_R_S3_METHOD_LOOKUP_USE_TOPENV_AS_DEFENV_",
+                          "true"))
+## </FIXME>
+
+## <FIXME>
+## Remove eventually ..
+Sys.setenv("_R_STOP_ON_XTFRM_DATA_FRAME_" =
+               Sys.getenv("_R_STOP_ON_XTFRM_DATA_FRAME_",
+                          "true"))
+## </FIXME>
+
+reverse <- NULL
+
+## <FIXME>
+## Perhaps add a -p argument to be passed to getIncoming?
+## Currently, -p KH/*.tar.gz is hard-wired.
+## </FIXME>
+
+usage <- function() {
+    cat("Usage: check_CRAN_incoming [options]",
+        "",
+        "Run KH CRAN incoming checks.",
+        "",
+        "Options:",
+        "  -h, --help      print short help message and exit",
+        "  -n              do not update check dir",
+        "  -s              use stop lists",
+        "  -c              run CRAN incoming feasibility checks",
+        "  -r              also check strong reverse depends",
+        "  -r=WHICH        also check WHICH reverse depends",
+        "  -N=N            use N CPUs",
+        "  -f=FLAVOR       use flavor FLAVOR ('g' or 'c' for the GCC or Clang",
+        "                  defaults, 'g/v' or 'c/v' for the version 'v' ones)",
+        "  -d=DIR          use DIR as check dir (default: ~/tmp/CRAN)",
+        "  -l              run local incoming checks only",
+        "  -a=ARGS         pass ARGS to R CMD check",
+        "",
+        "The CRAN incoming feasibility checks are always used for CRAN",
+        "incoming checks (i.e., unless '-n' is given), and never when",
+        "checking the reverse dependencies.",
+        sep = "\n")
+}
+
+check_args_db_from_stoplist_sh <-
+  function(stoplist_path = "../lib/check_R_stoplists.sh")
+  {
+    x <- system(paste(".", stoplist_path, "; set"), intern = TRUE)
+    x <- grep("^check_args_db_", x, value = TRUE)
+    db <- sub(".*='(.*)'$", "\\1", x)
+    names(db) <-
+      chartr("_", ".", sub("^check_args_db_([^=]*)=.*", "\\1", x))
+    db
+  }
+
+args <- commandArgs(trailingOnly = TRUE)
+if(any(ind <- (args %in% c("-h", "--help")))) {
+    usage()
+    q("no", runLast = FALSE)
+}
+if(any(ind <- (args == "-n"))) {
+    update_check_dir <- FALSE
+    args <- args[!ind]
+}
+if(any(ind <- (args == "-s"))) {
+    use_check_stoplists <- TRUE
+    args <- args[!ind]
+}
+run_CRAN_incoming_feasibility_checks <- update_check_dir
+if(any(ind <- (args == "-c"))) {
+    run_CRAN_incoming_feasibility_checks <- TRUE
+    args <- args[!ind]
+}
+if(any(ind <- (args == "-r"))) {
+    reverse <- list()
+    args <- args[!ind]
+}
+if(any(ind <- (args == "-l"))) {
+    Sys.setenv("_R_CHECK_CRAN_INCOMING_SKIP_URL_CHECKS_IF_REMOTE_" = "true",
+               "_R_CHECK_CRAN_INCOMING_SKIP_DOI_CHECKS_" = "true")
+    args <- args[!ind]
+}
+if(any(ind <- startsWith(args, "-r="))) {
+    which <- substring(args[ind][1L], 4L)
+    reverse <- if(which == "most") {
+        list(which = list(c("Depends", "Imports", "LinkingTo"),
+                          "Suggests"),
+             reverse = c(TRUE, FALSE))
+    } else {
+        list(which = which)
+    }
+    args <- args[!ind]
+}
+if(any(ind <- startsWith(args, "-N="))) {
+    Ncpus <- list(which = substring(args[ind][1L], 4L))
+    args <- args[!ind]
+}
+if(any(ind <- startsWith(args, "-d="))) {
+    check_dir <- substring(args[ind][1L], 4L)
+    args <- args[!ind]
+}
+if(any(ind <- startsWith(args, "-a="))) {
+    check_args <- substring(args[ind][1L], 4L)
+    args <- args[!ind]
+}
+if(length(args)) {
+    stop(paste("unknown option(s):",
+               paste(sQuote(args), collapse = ", ")))
+}
+
+# if(update_check_dir) {
+#     unlink(check_dir, recursive = TRUE)
+#     if(system2("getIncoming",
+#                c("-p KH/*.tar.gz", "-d", check_dir),
+#                stderr = FALSE)) {
+#         message("no packages to check")
+#         q("no", status = 1, runLast = FALSE)
+#     }
+#     message("")
+# }
+
+
+
+check_args_db <- if(use_check_stoplists) {
+    check_args_db_from_stoplist_sh(stoplist_path = file.path(lib_dir, "check_R_stoplists.sh"))
+} else {
+    list()
+}
+check_env_common <-
+    c(paste0("LANG=", Sys.getenv("_R_CHECK_LANG_", "en_US.UTF-8")),
+      ## (allow checking with LANG different from en_US.UTF-8)
+      "LC_COLLATE=C",
+      "LANGUAGE=en@quot",
+      sprintf("_R_CHECK_CRAN_STATUS_SUMMARY_=%s",
+              Sys.getenv("_R_CHECK_CRAN_STATUS_SUMMARY_", "true")),
+      "_R_TOOLS_C_P_I_D_ADD_RECOMMENDED_MAYBE_=true",
+      ## These could be conditionalized according to hostname.
+      ##   "R_SESSION_TIME_LIMIT_CPU=900",
+      ##   "R_SESSION_TIME_LIMIT_ELAPSED=1800",
+      ## <FIXME>
+      ## Currently, tools::check_packages_in_dir() only uses
+      ## _R_INSTALL_PACKAGES_ELAPSED_TIMEOUT_ when installing
+      ## dependencies.
+      "_R_INSTALL_PACKAGES_ELAPSED_TIMEOUT_=90m",
+      ## </FIXME>
+      "_R_CHECK_ELAPSED_TIMEOUT_=30m",
+      "_R_CHECK_INSTALL_ELAPSED_TIMEOUT_=90m",
+      character()
+      )
+check_env <-
+    list(c(check_env_common,
+           "_R_CHECK_WARN_BAD_USAGE_LINES_=TRUE",
+           sprintf("_R_CHECK_CRAN_INCOMING_SKIP_VERSIONS_=%s",
+                   !run_CRAN_incoming_feasibility_checks),
+           sprintf("_R_CHECK_CRAN_INCOMING_SKIP_DATES_=%s",
+                   !run_CRAN_incoming_feasibility_checks),
+           "_R_CHECK_CODOC_VARIABLES_IN_USAGES_=true",
+           "_R_CHECK_CONNECTIONS_LEFT_OPEN_=true",
+           "_R_CHECK_CRAN_INCOMING_=true",
+           "_R_CHECK_CRAN_INCOMING_NOTE_GNU_MAKE_=true",
+           "_R_CHECK_CRAN_INCOMING_REMOTE_=true",
+           "_R_CHECK_CRAN_INCOMING_USE_ASPELL_=true",
+           "_R_CHECK_CRAN_INCOMING_CHECK_FILE_URIS_=true",
+           "_R_CHECK_DATALIST_=true",
+           if(run_CRAN_incoming_feasibility_checks)
+               c("_R_CHECK_LENGTH_1_CONDITION_=package:_R_CHECK_PACKAGE_NAME_,abort,verbose",
+                 ## "_R_CHECK_LENGTH_1_LOGIC2_=package:_R_CHECK_PACKAGE_NAME_,abort,verbose",
+                 character()),
+           ## "_R_CHECK_ORPHANED_=true",
+           "_R_CHECK_PACKAGE_DEPENDS_IGNORE_MISSING_ENHANCES_=true",
+           "_R_CHECK_PACKAGES_USED_CRAN_INCOMING_NOTES_=true",
+           "_R_CHECK_RD_CONTENTS_KEYWORDS_=true",
+           "_R_CHECK_R_DEPENDS_=warn",
+           "_R_CHECK_THINGS_IN_TEMP_DIR_=true",
+           "_R_CHECK_BASHISMS_=true",
+           ## "_R_CHECK_XREFS_MIND_SUSPECT_ANCHORS_=true",
+           "_R_CHECK_URLS_SHOW_301_STATUS_=true",
+           "_R_CHECK_CODE_CLASS_IS_STRING_=true",
+           "_R_CHECK_NEWS_IN_PLAIN_TEXT_=true",
+           character()),
+         c(check_env_common,
+           ## <FIXME>
+           ## Remove eventually ...
+           "_R_CHECK_CRAN_INCOMING_=false",
+           ## </FIXME>
+           "_R_CHECK_CONNECTIONS_LEFT_OPEN_=false",
+           "_R_CHECK_THINGS_IN_TEMP_DIR_=false",
+           ## "_R_CHECK_XREFS_MIND_SUSPECT_ANCHORS_=false",
+           ## <FIXME>
+           character())
+         )
+
+if(!is.null(reverse))
+    reverse$repos <- getOption("repos")["CRAN"]
+
+pfiles <-
+    tools::check_packages_in_dir(check_dir,
+                                 check_args = check_args,
+                                 check_args_db = check_args_db,
+                                 reverse = reverse,
+                                 xvfb = TRUE,
+                                 check_env = check_env,
+                                 Ncpus = Ncpus)
+
+if(length(pfiles)) {
+    writeLines("\nDepends:")
+    tools::summarize_check_packages_in_dir_depends(check_dir)
+    writeLines("\nTimings:")
+    tools::summarize_check_packages_in_dir_timings(check_dir)
+    writeLines("\nResults:")
+    tools::summarize_check_packages_in_dir_results(check_dir)
+}
+