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#' Run R CMD check from R and Capture Results
#'
#' Run R CMD check from R programmatically, and capture the results of the
#' individual checks.
#'
#' @docType package
#' @name rcmdcheck
NULL
#' Run `R CMD check` on a package or a directory
#'
#' Runs `R CMD check` as an external command, and parses its output and
#' returns the check failures.
#'
#' See [rcmdcheck_process] if you need to run `R CMD check` in a background
#' process.
#'
#' # Turning off package checks
#'
#' Sometimes it is useful to programmatically turn off some checks that
#' may report check NOTEs.
#' rcmdcehck provides two ways to do this.
#'
#' First, you may declare in `DESCRIPTION` that you don't want to see
#' NOTEs that are accepted on CRAN, with this entry:
#'
#' ```
#' Config/rcmdcheck/ignore-inconsequential-notes: true
#' ```
#'
#' Currently, this will make rcmdcheck ignore the following notes:
#' `r format_env_docs()`.
#'
#' The second way is more flexible, and lets you turn off individual checks
#' via setting environment variables.
#' You may provide a `tools/check.env` _environment file_ in your package
#' with the list of environment variable settings that rcmdcheck will
#' automatically use when checking the package.
#' See [Startup] for the format of this file.
#'
#' Here is an example `tools/check.env` file:
#' ```
#' # Report if package size is larger than 10 megabytes
#' _R_CHECK_PKG_SIZES_THRESHOLD_=10
#'
#' # Do not check Rd cross references
#' _R_CHECK_RD_XREFS_=false
#'
#' # Do not report if package requires GNU make
#' _R_CHECK_CRAN_INCOMING_NOTE_GNU_MAKE_=false
#'
#' # Do not check non-ASCII strings in datasets
#' _R_CHECK_PACKAGE_DATASETS_SUPPRESS_NOTES_=true
#' ```
#'
#' See the ["R internals" manual](https://cran.r-project.org/doc/manuals/r-devel/R-ints.html)
#' and the [R source code](https://github.com/wch/r-source) for the
#' environment variables that control the checks.
#'
#' Note that `Config/rcmdcheck/ignore-inconsequential-notes` and the
#' `check.env` file are only supported by rcmdcheck, and running
#' `R CMD check` from a shell (or GUI) will not use them.
#'
#' @param path Path to a package tarball or a directory.
#' @param quiet Whether to print check output during checking.
#' @param args Character vector of arguments to pass to `R CMD check`. Pass each
#' argument as a single element of this character vector (do not use spaces to
#' delimit arguments like you would in the shell). For example, to skip
#' running of examples and tests, use `args = c("--no-examples",
#' "--no-tests")` and not `args = "--no-examples --no-tests"`. (Note that
#' instead of the `--output` option you should use the `check_dir` argument,
#' because `--output` cannot deal with spaces and other special characters on
#' Windows.)
#' @param build_args Character vector of arguments to pass to `R CMD build`.
#' Pass each argument as a single element of this character vector (do not use
#' spaces to delimit arguments like you would in the shell). For example,
#' `build_args = c("--force", "--keep-empty-dirs")` is a correct usage and
#' `build_args = "--force --keep-empty-dirs"` is incorrect.
#' @param check_dir Path to a directory where the check is performed.
#' If this is not `NULL`, then the a temporary directory is used, that
#' is cleaned up when the returned object is garbage collected.
#' @param libpath The library path to set for the check.
#' The default uses the current library path.
#' @param repos The `repos` option to set for the check.
#' This is needed for cyclic dependency checks if you use the
#' `--as-cran` argument. The default uses the current value.
#' @param timeout Timeout for the check, in seconds, or as a
#' [base::difftime] object. If it is not finished before this, it will be
#' killed. `Inf` means no timeout. If the check is timed out,
#' that is added as an extra error to the result object.
#' @param error_on Whether to throw an error on `R CMD check` failures.
#' Note that the check is always completed (unless a timeout happens),
#' and the error is only thrown after completion. If `"never"`, then
#' no errors are thrown. If `"error"`, then only `ERROR` failures
#' generate errors. If `"warning"`, then `WARNING` failures generate
#' errors as well. If `"note"`, then any check failure generated an
#' error. Its default can be modified with the `RCMDCHECK_ERROR_ON`
#' environment variable. If that is not set, then `"never"` is used.
#' @param env A named character vector, extra environment variables to
#' set in the check process.
#' @return An S3 object (list) with fields `errors`,
#' `warnings` and `notes`. These are all character
#' vectors containing the output for the failed check.
#'
#' @export
#' @importFrom rprojroot find_package_root_file
#' @importFrom withr local_path with_dir
#' @importFrom callr rcmd_safe
#' @importFrom desc desc
rcmdcheck <- function(
path = ".",
quiet = FALSE,
args = character(),
build_args = character(),
check_dir = NULL,
libpath = .libPaths(),
repos = getOption("repos"),
timeout = Inf,
error_on = Sys.getenv(
"RCMDCHECK_ERROR_ON",
c("never", "error", "warning", "note")[1]
),
env = character()) {
error_on <- match.arg(error_on, c("never", "error", "warning", "note"))
if (file.info(path)$isdir) {
path <- find_package_root_file(path = path)
} else {
path <- normalizePath(path)
}
if (is.null(check_dir)) {
check_dir <- tempfile()
cleanup <- TRUE
} else {
cleanup <- FALSE
}
# Add pandoc to the PATH, for R CMD build and R CMD check
if (should_use_rs_pandoc()) local_path(Sys.getenv("RSTUDIO_PANDOC"))
pkgbuild::without_cache(pkgbuild::local_build_tools())
targz <- build_package(path, check_dir, build_args = build_args,
libpath = libpath, quiet = quiet)
start_time <- Sys.time()
desc <- desc(targz)
set_env(path, targz, desc)
out <- with_dir(
dirname(targz),
do_check(targz,
package = desc$get("Package")[[1]],
args = args,
libpath = libpath,
repos = repos,
quiet = quiet,
timeout = timeout,
env = env
)
)
on.exit(unlink(out$session_info, recursive = TRUE), add = TRUE)
if (isTRUE(out$timeout)) message("R CMD check timed out")
res <- new_rcmdcheck(
stdout = out$result$stdout,
stderr = out$result$stderr,
description = desc,
status = out$result$status,
duration = duration(start_time),
timeout = out$result$timeout,
session_info = out$session_info
)
# Automatically delete temporary files when this object disappears
if (cleanup) res$cleaner <- auto_clean(check_dir)
handle_error_on(res, error_on)
res
}
#' @importFrom withr with_envvar
do_check <- function(targz, package, args, libpath, repos,
quiet, timeout, env) {
# if the pkg.Rcheck directory already exists, unlink it
unlink(paste0(package, ".Rcheck"), recursive = TRUE)
# set up environment, start with callr safe set
chkenv <- callr::rcmd_safe_env()
libdir <- file.path(dirname(targz), paste0(package, ".Rcheck"))
# if R_TESTS is set here, we'll skip the session_info, because we are
# probably inside test cases of some package
if (Sys.getenv("R_TESTS", "") == "") {
session_output <- tempfile()
profile <- make_fake_profile(package, session_output, libdir)
on.exit(unlink(profile), add = TRUE)
chkenv["R_TESTS"] <- profile
} else {
session_output <- NULL
}
# user supplied env vars take precedence
if (length(env)) chkenv[names(env)] <- env
if (!quiet) cat_head("R CMD check")
callback <- if (!quiet) detect_callback(as_cran = "--as-cran" %in% args)
res <- rcmd_safe(
"check",
cmdargs = c(basename(targz), args),
libpath = c(libdir, libpath),
user_profile = FALSE,
repos = repos,
stderr = "2>&1",
block_callback = callback,
spinner = !quiet && should_add_spinner(),
timeout = timeout,
fail_on_status = FALSE,
env = chkenv
)
# To print an incomplete line on timeout or crash
if (!is.null(callback) && (res$timeout || res$status != 0)) callback("\n")
# Non-zero status is an error, the check process failed
# R CMD check returns 1 for installation errors, we don't want to error
# for those.
if (res$status != 0 && res$status != 1) {
stop(
call. = FALSE,
"R CMD check process failed with exit status ", res$status,
"\n\nStandard output and error:\n",
res$stdout
)
}
list(result = res, session_info = session_output)
}
handle_error_on <- function(res, error_on) {
level <- c(never = 0, error = 1, warning = 2, note = 3)[error_on]
if (isTRUE(res$timeout)) {
print(res)
stop(make_error(res, "R CMD check timed out"))
} else if (length(res$errors) && level >= 1) {
print(res)
stop(make_error(res, "R CMD check found ERRORs"))
} else if (length(res$warnings) && level >= 2) {
print(res)
stop(make_error(res, "R CMD check found WARNINGs"))
} else if (length(res$notes) && level >= 3) {
print(res)
stop(make_error(res, "R CMD check found NOTEs"))
}
}
make_error <- function(res, msg) {
structure(
list(result = res, message = msg, call = NULL),
class = c(
if (isTRUE(res$timeout)) "rcmdcheck_timeout",
if (length(res$errors)) "rcmdcheck_error",
if (length(res$warnings)) "rcmdcheck_warning",
if (length(res$notes)) "rcmdcheck_note",
"rcmdcheck_failure",
"error",
"condition"
)
)
}
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