check_dir <- file.path(normalizePath("~"), "tmp", "CRAN")
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")
Sys.setenv("POCL_KERNEL_CACHE" = 0,
"OMPI_MCA_btl_base_warn_component_unused" = 0
)
##
##
## For the time being set do not set for the incoming checks
## OMP_NUM_THREADS OMP_THREAD_LIMIT RCPP_PARALLEL_NUM_THREADS
## as this makes UL unhappy.
## We may need to set for the revdep checks ...?
##
## ## 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)
## ## Or maybe instead just
## Sys.setenv("OPENBLAS_NUM_THREADS" = 1)
## ## ???
##
##
## Remove eventually ...?
## Keep in sync with ~/.R/Makevars-clang.
if(endsWith(Sys.getenv("R_MAKEVARS_USER"), "-clang"))
Sys.setenv("_R_CHECK_COMPILATION_FLAGS_KNOWN_" =
"-Wno-error=enum-constexpr-conversion")
##
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
}
##
## Change eventually ...
Sys.setenv("_R_CHECK_NATIVE_ROUTINE_REGISTRATION_" =
Sys.getenv("_R_CHECK_NATIVE_ROUTINE_REGISTRATION_",
"false"))
##
reverse <- NULL
##
## Perhaps add a -p argument to be passed to getIncoming?
## Currently, -p KH/*.tar.gz is hard-wired.
##
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",
" -r~PKGLIST also check revdeps in PKGLIST",
" -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()
{
x <- system(". ~/lib/bash/check_R_stoplists.sh; 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, "-r~"))) {
reverse <- unlist(strsplit(substring(args[ind][1L], 4L), ", *"))
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()
} else {
list()
}
check_env_common <-
c(paste0("LANG=", Sys.getenv("_R_CHECK_LANG_", "C.UTF-8")),
## (allow checking with LANG different from C.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",
##
## Currently, tools::check_packages_in_dir() only uses
## _R_INSTALL_PACKAGES_ELAPSED_TIMEOUT_ when installing
## dependencies.
"_R_INSTALL_PACKAGES_ELAPSED_TIMEOUT_=90m",
##
"_R_CHECK_ELAPSED_TIMEOUT_=30m",
"_R_CHECK_INSTALL_ELAPSED_TIMEOUT_=90m",
character()
)
check_env <-
list(c(check_env_common,
"_R_CHECK_CRAN_INCOMING_=true",
"_R_CHECK_CRAN_INCOMING_REMOTE_=true",
"_R_CHECK_CRAN_INCOMING_CHECK_FILE_URIS_=true",
"_R_CHECK_CRAN_INCOMING_NOTE_GNU_MAKE_=true",
sprintf("_R_CHECK_CRAN_INCOMING_SKIP_DATES_=%s",
!run_CRAN_incoming_feasibility_checks),
sprintf("_R_CHECK_CRAN_INCOMING_SKIP_VERSIONS_=%s",
!run_CRAN_incoming_feasibility_checks),
"_R_CHECK_CRAN_INCOMING_USE_ASPELL_=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_PACKAGE_DEPENDS_IGNORE_MISSING_ENHANCES_=true",
## Used for '--as-cran':
"_R_CHECK_BASHISMS_=true",
"_R_CHECK_CODE_CLASS_IS_STRING_=true",
"_R_CHECK_CODOC_VARIABLES_IN_USAGES_=true",
"_R_CHECK_CONNECTIONS_LEFT_OPEN_=true",
"_R_CHECK_DATALIST_=true",
"_R_CHECK_NEWS_IN_PLAIN_TEXT_=true",
## "_R_CHECK_ORPHANED_=true",
"_R_CHECK_PACKAGES_USED_CRAN_INCOMING_NOTES_=true",
"_R_CHECK_RD_CONTENTS_KEYWORDS_=true",
"_R_CHECK_R_DEPENDS_=warn",
"_R_CHECK_S3_METHODS_SHOW_POSSIBLE_ISSUES_=true",
"_R_CHECK_THINGS_IN_TEMP_DIR_=true",
"_R_CHECK_UNDOC_USE_ALL_NAMES_=true",
"_R_CHECK_URLS_SHOW_301_STATUS_=true",
## "_R_CHECK_XREFS_MIND_SUSPECT_ANCHORS_=true",
## "_R_CHECK_XREFS_NOTE_MISSING_PACKAGE_ANCHORS_=true",
## "_R_CXX_USE_NO_REMAP_=true",
## "_R_USE_STRICT_R_HEADERS_=true",
character()),
c(check_env_common,
##
## Remove eventually ...
"_R_CHECK_CRAN_INCOMING_=false",
##
## Avoid getting check NOTEs about GNU Make being a
## SystemRequirement:
"_R_CHECK_CRAN_INCOMING_NOTE_GNU_MAKE_=true",
"_R_CHECK_CONNECTIONS_LEFT_OPEN_=false",
##
## Remove eventually ...
## "_R_CHECK_SRC_MINUS_W_FORMAT_EXCEPTIONS_",
##
"_R_CHECK_THINGS_IN_TEMP_DIR_=false",
"_R_CHECK_XREFS_USE_ALIASES_FROM_CRAN_=true",
## "_R_CHECK_XREFS_MIND_SUSPECT_ANCHORS_=false",
##
## Need to keep these in sync with what we use for the
## *regular* checks:
"OMP_NUM_THREADS=3",
"OMP_THREAD_LIMIT=3",
"RCPP_PARALLEL_NUM_THREADS=4",
## However, this may still give notes about excessive CPU
## usage not seen in the regular checks, so for now suppress
## these for simplicity.
"_R_CHECK_EXAMPLE_TIMING_CPU_TO_ELAPSED_THRESHOLD_=",
"_R_CHECK_TEST_TIMING_CPU_TO_ELAPSED_THRESHOLD_=",
"_R_CHECK_VIGNETTE_TIMING_CPU_TO_ELAPSED_THRESHOLD_=",
"_R_CHECK_INSTALL_TIMING_CPU_TO_ELAPSED_THRESHOLD_=",
##
"_R_CXX_USE_NO_REMAP_=false",
"_R_USE_STRICT_R_HEADERS_=false",
character())
)
if(!is.null(reverse) && !is.character(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)
}