From 1c1c51deb092da4c8d3725fbb3794797eef03d3f Mon Sep 17 00:00:00 2001 From: maksymis <32574056+maksymiuks@users.noreply.github.com> Date: Fri, 19 Jun 2026 18:59:41 +0200 Subject: [PATCH 1/2] Basic tty improvements --- DESCRIPTION | 2 +- NEWS.md | 6 + R/checker.R | 8 + R/install.R | 39 ++-- R/next_task.R | 4 +- R/reporter.R | 8 +- R/reporter_basic_tty.R | 27 ++- R/run.R | 6 +- man/checker.Rd | 14 ++ man/options.Rd | 440 +++++++++++++++++++++++++++++++++-- man/options_params.Rd | 239 +++++++++++++++++-- man/print.checked_results.Rd | 2 +- man/reporters.Rd | 4 +- man/results.Rd | 2 +- man/run.Rd | 2 +- 15 files changed, 737 insertions(+), 66 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 01a5994..de0725c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: checked Title: Systematically Run R CMD Checks -Version: 0.5.3 +Version: 0.5.4 Authors@R: c( person( diff --git a/NEWS.md b/NEWS.md index d8e81bc..7534ead 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,9 @@ +# checked 0.5.4 + +* Improve error messaging when using basic_tty + +* Various improvements to reporters and minor display tweaks + # checked 0.5.3 * Make is possible to construct reporter environments with additional values diff --git a/R/checker.R b/R/checker.R index d631a3d..272fb16 100644 --- a/R/checker.R +++ b/R/checker.R @@ -228,6 +228,14 @@ checker <- R6::R6Class( all(V(self$graph)$status == STATUS$done) } + }, + #' @description + #' Tasks + #' + #' Returns what type of tasks the checker consists of and returns a unique + #' vector of primary classes + tasks = function() { + unique(vcapply(V(self$graph)$task, function(x) class(x)[[1]])) } ), private = list( diff --git a/R/install.R b/R/install.R index 0ab1056..93adbae 100644 --- a/R/install.R +++ b/R/install.R @@ -19,29 +19,22 @@ install_process <- R6::R6Class( private$package <- pkgs self$log <- log private$callr_r_bg( - function(..., escalate_warning, available_packages_filters) { + function(..., available_packages_filters) { options( timeout = 600, available_packages_filters = available_packages_filters ) - withCallingHandlers( + invisible(capture.output(withCallingHandlers( utils::install.packages(..., quiet = FALSE, verbose = TRUE), warning = function(w) { - if (escalate_warning(w)) { - print(w$message) - stop(w$message) - } else { - print(w$message) - warning(w) - } + print(w$message) } - ) + ), split = TRUE)) }, args = list( private$package, ..., lib = lib, - escalate_warning = is_install_failure_warning, available_packages_filters = available_packages_filters ), libpath = libpaths, @@ -49,6 +42,7 @@ install_process <- R6::R6Class( stderr = "2>&1", system_profile = options::opt("install_system_profile"), user_profile = options::opt("install_user_profile"), + cmdargs = c("--slave", "--no-save", "--no-restore", "--vanilla"), env = env ) }, @@ -68,7 +62,26 @@ install_process <- R6::R6Class( if (is.function(f <- private$finish_callback)) f(self) }, get_r_exit_status = function() { - as.integer(inherits(try(self$get_result(), silent = TRUE), "try-error")) + res <- self$get_results_safe() + if (inherits(self$get_results_safe(), "callr_error")) { + 1L + } else if (any(is_install_failure_warning(res))) { + 1L + } else { + 0L + } + + }, + get_results_safe = function() { + tryCatch( + gsub("\\n", "\n", self$get_result(), fixed = TRUE), + error = function(e) { + e + }, + warning = function(w) { + w + } + ) } ), private = list( @@ -115,5 +128,5 @@ is_install_failure_warning <- function(w) { ) re <- paste0("(", paste0(patterns, collapse = "|"), ")") - grepl(re, w$message) + grepl(re, w) } diff --git a/R/next_task.R b/R/next_task.R index a392601..8d9731a 100644 --- a/R/next_task.R +++ b/R/next_task.R @@ -87,9 +87,7 @@ start_task.install_task <- function( upgrade %nif% task$origin$version ) - if (is_installed && - is_lib_path_default(task) && - inherits(task$origin, "pkg_origin_repo")) + if (is_installed && is_lib_path_default(task) && inherits(task$origin, "pkg_origin_repo")) # nolint return(NULL) install_process$new( diff --git a/R/reporter.R b/R/reporter.R index fc0ba80..3b5c43b 100644 --- a/R/reporter.R +++ b/R/reporter.R @@ -22,6 +22,7 @@ #' a reporter with minimal assumptions about terminal capabilities. #' #' @param checks_only whether basic tty reporter should report only check tasks. +#' @param checker checker object required to properly derive default reporter. #' @param ... additional values which should be assigned to the reported #' environment. #' @@ -58,8 +59,11 @@ reporter_basic_tty <- function(checks_only = FALSE, ...) { #' @rdname reporters #' @export -reporter_default <- function() { - if (cli::is_ansi_tty()) { +reporter_default <- function(checker = NULL) { + is_revdep <- + !is.null(checker) && "rev_dep_check_meta_task" %in% checker$tasks() + + if (cli::is_ansi_tty() && is_revdep) { reporter_ansi_tty() } else if (cli::is_dynamic_tty()) { reporter_basic_tty() diff --git a/R/reporter_basic_tty.R b/R/reporter_basic_tty.R index 1ec4ef4..1880570 100644 --- a/R/reporter_basic_tty.R +++ b/R/reporter_basic_tty.R @@ -19,7 +19,13 @@ report_start_setup.reporter_basic_tty <- function( reporter$time_start <- Sys.time() - cli::cli_text("<", utils::packageName(), "> Checks") + type <- if (all(vlapply(v_reportable$task, inherits, "install_task"))) { + "> Installs" + } else { + "> Checks" + } + + cli::cli_text("<", utils::packageName(), type) } #' @export @@ -41,6 +47,7 @@ report_status.reporter_basic_tty <- function(reporter, checker, envir) { p <- node$process + failure_message <- NULL # report stating of new checks if (!identical(node$status, reporter$status[[node$name]])) { status <- switch( # nolint @@ -61,12 +68,19 @@ report_status.reporter_basic_tty <- function(reporter, checker, envir) { ) } else if (p$get_r_exit_status() != 0) { # checks processes don't have logs associated with it - message <- if (!is.null(p$log)) { - sprintf("failed (log: '%s')", p$log) - } else { - "failed" + failure_message <- if (inherits(p, "install_process")) { + paste( + p$get_results_safe(), + if (file.exists(p$log)) sprintf("\nfull log: '%s'", p$log), + sep = "\n", + collapse = "\n" + ) } - cli::cli_fmt(cli::cli_text(message)) + cli::cli_fmt( + cli::cli_text( + "failed", cli::format_inline(fmt_count) + ) + ) } else { dur <- if (!is.null(p$get_duration)) { p$get_duration() @@ -103,6 +117,7 @@ report_status.reporter_basic_tty <- function(reporter, checker, envir) { type <- format_task_type(node$task) # nolint (used via glue) prefix <- cli::col_cyan("[{format_time(time)}][{type}] ") cli::cli_text(prefix, "{.pkg {package(node$task)}} {status}") + if (!is.null(failure_message)) cli::cli_text(failure_message) reporter$status[[node$name]] <- node$status } } diff --git a/R/run.R b/R/run.R index 01005b5..2b12df6 100644 --- a/R/run.R +++ b/R/run.R @@ -13,12 +13,12 @@ #' most expressive command-line reporter given your terminal capabilities. #' #' @export -run <- function(checker, ..., reporter = reporter_default()) { +run <- function(checker, ..., reporter = reporter_default(checker)) { UseMethod("run") } #' @export -run.character <- function(checker, ..., reporter = reporter_default()) { +run.character <- function(checker, ..., reporter = reporter_default(checker)) { checker <- new_rev_dep_checker(checker, ...) report_start_setup( reporter, @@ -30,7 +30,7 @@ run.character <- function(checker, ..., reporter = reporter_default()) { } #' @export -run.checker <- function(checker, ..., reporter = reporter_default()) { +run.checker <- function(checker, ..., reporter = reporter_default(checker)) { on.exit(add = TRUE, { checker$terminate() report_finalize(reporter, checker) diff --git a/man/checker.Rd b/man/checker.Rd index f16eb06..10116f2 100644 --- a/man/checker.Rd +++ b/man/checker.Rd @@ -62,6 +62,7 @@ be created and stored.} \item \href{#method-checker-step}{\code{checker$step()}} \item \href{#method-checker-start_next_task}{\code{checker$start_next_task()}} \item \href{#method-checker-is_done}{\code{checker$is_done()}} +\item \href{#method-checker-tasks}{\code{checker$tasks()}} \item \href{#method-checker-clone}{\code{checker$clone()}} } } @@ -194,6 +195,19 @@ Checks whether all the scheduled tasks were successfully executed. \if{html}{\out{
}}\preformatted{checker$is_done()}\if{html}{\out{
}} } +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-checker-tasks}{}}} +\subsection{Method \code{tasks()}}{ +Tasks + +Returns what type of tasks the checker consists of and returns a unique +vector of primary classes +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{checker$tasks()}\if{html}{\out{
}} +} + } \if{html}{\out{
}} \if{html}{\out{}} diff --git a/man/options.Rd b/man/options.Rd index 71c9de2..bc79e91 100644 --- a/man/options.Rd +++ b/man/options.Rd @@ -20,17 +20,431 @@ options::opt(x, default, env = "checked") \section{Options}{ \describe{ +\item{quiet}{\describe{ +Whether execution should suppress output. When \code{TRUE}, only warnings +are emitted. When \code{FALSE}, a pretty-formatted log is emitted to the +console.\item{default: }{\preformatted{FALSE}} +\item{option: }{autovalidateutils.quiet} +\item{envvar: }{AUTOVALIDATEUTILS_QUIET (TRUE if one of 'TRUE', '1', FALSE otherwise)} +}} + +\item{clean}{\describe{ +Whether directories created by autovaldiateutils in /tmp directory +should be removed. Set to TRUE if you want to save space in your /tmp. Keep +FALSE to maintain all the output in /tmp. Does not affect regular output\item{default: }{\preformatted{TRUE}} +\item{option: }{autovalidateutils.clean} +\item{envvar: }{AUTOVALIDATEUTILS_CLEAN (TRUE if one of 'TRUE', '1', FALSE otherwise)} +}} + +\item{timeout}{\describe{ +A difftime object or a numeric value with a real number indicating +number of seconds that should pass before certain calls are timed out. Set to +Inf to turn off timeout. By deafult set to difftime 14 hours.\item{default: }{\preformatted{as.difftime(14, units = "hours")}} +\item{option: }{autovalidateutils.timeout} +\item{envvar: }{AUTOVALIDATEUTILS_TIMEOUT (evaluated if possible, raw string otherwise)} +}} + +\item{output}{\describe{ +A parent directory for all non-relative output files. Defaults to the +current working directory.\item{default: }{\preformatted{file.path(normalize_path(tempdir()), "autovalidateutils")}} +\item{option: }{autovalidateutils.output} +\item{envvar: }{AUTOVALIDATEUTILS_OUTPUT (evaluated if possible, raw string otherwise)} +}} + +\item{log_output}{\describe{ +path to the directory where log files will be created.\item{default: }{\preformatted{file.path(normalize_path(tempdir()), "log_autovalidateutils")}} +\item{option: }{autovalidateutils.log_output} +\item{envvar: }{AUTOVALIDATEUTILS_LOG_OUTPUT (evaluated if possible, raw string otherwise)} +}} + +\item{original_libpaths}{\describe{ +Vector storing original .libPaths before the vector was +altered by avu_install function. It is always overwritten during +autovalidateutils runtime.\item{default: }{\preformatted{NULL}} +\item{option: }{autovalidateutils.original_libpaths} +\item{envvar: }{AUTOVALIDATEUTILS_ORIGINAL_LIBPATHS (evaluated if possible, raw string otherwise)} +}} + +\item{lib.loc}{\describe{ +Character vector describing the location of R library trees to search +through. It will be passed to installed.packages() while deriving whether all +required dependencies are installed. +Defaults to c(.Library, .Library.site).\item{default: }{\preformatted{c(.Library, .Library.site)}} +\item{option: }{autovalidateutils.lib.loc} +\item{envvar: }{AUTOVALIDATEUTILS_LIB_LOC (evaluated if possible, raw string otherwise)} +}} + +\item{clear_description}{\describe{ +Logical value whether all non-utf8 characters should be removed from +the DESCRIPTION value. This is to avoid potential erros that might +occure when installing the package from the source.\item{default: }{\preformatted{FALSE}} +\item{option: }{autovalidateutils.clear_description} +\item{envvar: }{AUTOVALIDATEUTILS_CLEAR_DESCRIPTION (TRUE if one of 'TRUE', '1', FALSE otherwise)} +}} + +\item{subprocess_debug}{\describe{ +Logical whether certain functionalities shall be run in a debug mode. Debug +means functions are run in the main process rather that callr::r_vanilla\item{default: }{\preformatted{FALSE}} +\item{option: }{autovalidateutils.subprocess_debug} +\item{envvar: }{AUTOVALIDATEUTILS_SUBPROCESS_DEBUG (TRUE if one of 'TRUE', '1', FALSE otherwise)} +}} + +\item{install_n_workers}{\describe{ +Number of subprocesses used by the checked package for +executing tasks when installing package and dependencies.\item{default: }{\preformatted{20L}} +\item{option: }{autovalidateutils.install_n_workers} +\item{envvar: }{AUTOVALIDATEUTILS_INSTALL_N_WORKERS (evaluated if possible, raw string otherwise)} +}} + +\item{session}{\describe{ +The file path of the session information metadata file, a +yaml-formatted itemization of a few characteristic measures of an R session +environment.\item{default: }{\preformatted{"session.yml"}} +\item{option: }{autovalidateutils.session} +\item{envvar: }{AUTOVALIDATEUTILS_SESSION (evaluated if possible, raw string otherwise)} +}} + +\item{description}{\describe{ +The file path of the \code{DESCRIPTION} file contents, written out to +a plain text, yaml-formatted file.\item{default: }{\preformatted{"description.yml"}} +\item{option: }{autovalidateutils.description} +\item{envvar: }{AUTOVALIDATEUTILS_DESCRIPTION (evaluated if possible, raw string otherwise)} +}} + +\item{news}{\describe{ +The file path of the \code{NEWS} (or \code{NEWS.md}) file contents. If the \code{NEWS} file +is not already markdown formatted, it will be converted into a preformatted +markdown code block to be embedded in an \code{autovalidate} report.\item{default: }{\preformatted{"news.md"}} +\item{option: }{autovalidateutils.news} +\item{envvar: }{AUTOVALIDATEUTILS_NEWS (evaluated if possible, raw string otherwise)} +}} + +\item{conditions}{\describe{ +The file path of the file to which conditions should be emitted. They are +logged in yaml format, which is later read by \code{autovalidate} to +re-emit them as \code{autovalidate} checks and trigger failures when applicable\item{default: }{\preformatted{"conditions.yml"}} +\item{option: }{autovalidateutils.conditions} +\item{envvar: }{AUTOVALIDATEUTILS_CONDITIONS (evaluated if possible, raw string otherwise)} +}} + +\item{build_binaries}{\describe{ +Logical whether binary source of the package should be compiled during +validation.\item{default: }{\preformatted{FALSE}} +\item{option: }{autovalidateutils.build_binaries} +\item{envvar: }{AUTOVALIDATEUTILS_BUILD_BINARIES (TRUE if one of 'TRUE', '1', FALSE otherwise)} +}} + +\item{generalize_sources}{\describe{ +Logical whether sources produced during validation should be renamed to +general 'package_binary.tgz/tar.gz/zip' and 'package_source.tar.gz'.\item{default: }{\preformatted{FALSE}} +\item{option: }{autovalidateutils.generalize_sources} +\item{envvar: }{AUTOVALIDATEUTILS_GENERALIZE_SOURCES (TRUE if one of 'TRUE', '1', FALSE otherwise)} +}} + +\item{steps}{\describe{ +A listing of autovalidateutils steps to perform. Either a \code{character} vector +or \code{list}. Alternatively, the vector or list may consist of modifications +to a listing of all steps, which must be prefixed by \code{-} (for example, +\code{-write_revdep_check}, which will use all steps except reverse dependency +checks).\item{default: }{\preformatted{c("-write_checked")}} +\item{option: }{autovalidateutils.steps} +\item{envvar: }{AUTOVALIDATEUTILS_STEPS (evaluated if possible, raw string otherwise)} +}} + +\item{installed_packages}{\describe{ +The name of the installed packages json file. It keeps track of +the information about which packages were installed to the environemnt +and their versions. File will be written to the log_output directory\item{default: }{\preformatted{"installed_packages.json"}} +\item{option: }{autovalidateutils.installed_packages} +\item{envvar: }{AUTOVALIDATEUTILS_INSTALLED_PACKAGES (evaluated if possible, raw string otherwise)} +}} + +\item{use_remotes}{\describe{ +Logical flag or named character mapping dependency types to the mechanism of +handling remotes, one of "allow", "prefer" or "disallow". "allow" +option means that the remote sources are allowed but will not take precedence +over other standard sources if both available. "prefer" means allow and +overwrite standard sources while "disallow" stands for skipping remote +sources at all. If no value is provided for a dependency type it is +considered to be "disallow". Can also be set to TRUE to "prefer" all or +FALSE to "disallow all.\item{default: }{\preformatted{c(Depends = "disallow", Imports = "disallow", LinkingTo = "disallow", + Suggests = "allow", Enhances = "allow")}} +\item{option: }{autovalidateutils.use_remotes} +\item{envvar: }{AUTOVALIDATEUTILS_USE_REMOTES (evaluated if possible, raw string otherwise)} +}} + +\item{version_control}{\describe{ +The file path to which package version control metadata +should be captured.\item{default: }{\preformatted{"version_control.yml"}} +\item{option: }{autovalidateutils.version_control} +\item{envvar: }{AUTOVALIDATEUTILS_VERSION_CONTROL (evaluated if possible, raw string otherwise)} +}} + +\item{version_control.md5}{\describe{ +When a source control hash can't be derived from +the target directory, this option will be used to populate version control +metadata. This is of particular interest when the source code has been +extracted from a tar.gz package bundle. In this case, the md5 hash should +reflect the hash of the originating package bundle.\item{default: }{\preformatted{NULL}} +\item{option: }{autovalidateutils.version_control.md5} +\item{envvar: }{AUTOVALIDATEUTILS_VERSION_CONTROL_MD5 (evaluated if possible, raw string otherwise)} +}} + +\item{version_control.url}{\describe{ +When a source control origin can't be derived from +the target directory, this option will be used to populate version control +metadata. This is of particular interest when the source code has been +extracted from a tar.gz package bundle. In this case, the url should +reflect the url from which the originating package bundle was downloaded.\item{default: }{\preformatted{NULL}} +\item{option: }{autovalidateutils.version_control.url} +\item{envvar: }{AUTOVALIDATEUTILS_VERSION_CONTROL_URL (evaluated if possible, raw string otherwise)} +}} + +\item{vulnerabilities}{\describe{ +The file path to which metadata reagarding possible package's +vulnerabilities should be captured.\item{default: }{\preformatted{"vulnerabilities.yml"}} +\item{option: }{autovalidateutils.vulnerabilities} +\item{envvar: }{AUTOVALIDATEUTILS_VULNERABILITIES (evaluated if possible, raw string otherwise)} +}} + +\item{r_cmd_check}{\describe{ +The file path to which \verb{R CMD check} results should be written. +Contents are written in yaml format.\item{default: }{\preformatted{"r_cmd_check.yml"}} +\item{option: }{autovalidateutils.r_cmd_check} +\item{envvar: }{AUTOVALIDATEUTILS_R_CMD_CHECK (evaluated if possible, raw string otherwise)} +}} + +\item{r_cmd_check_variables}{\describe{ +The named character vector of environmental variables, +that will be passed to the \code{withr::with_envvar} function and used to execute +rcmdcheck::rcmdcheck. It can also be a single keyword, either 'cran' or +'internal' that will result in using predefined set of variables.\item{default: }{\preformatted{"internal"}} +\item{option: }{autovalidateutils.r_cmd_check_variables} +\item{envvar: }{AUTOVALIDATEUTILS_R_CMD_CHECK_VARIABLES (evaluated if possible, raw string otherwise)} +}} + +\item{r_cmd_check_clean_tests}{\describe{ +Logical flag whether the \if{html}{\out{}}.Rcheck/\if{html}{\out{}}/tests +directory should be cleared by removing all the directories in it\item{default: }{\preformatted{FALSE}} +\item{option: }{autovalidateutils.r_cmd_check_clean_tests} +\item{envvar: }{AUTOVALIDATEUTILS_R_CMD_CHECK_CLEAN_TESTS (TRUE if one of 'TRUE', '1', FALSE otherwise)} +}} + +\item{check_dir}{\describe{ +The directory R CMD check results should be written to +(.tag.gz, .Rcheck).\item{default: }{\preformatted{"check"}} +\item{option: }{autovalidateutils.check_dir} +\item{envvar: }{AUTOVALIDATEUTILS_CHECK_DIR (evaluated if possible, raw string otherwise)} +}} + +\item{sonarqube}{\describe{ +The file path in which to record a sonarqube xml coverage output file.\item{default: }{\preformatted{file.path("coverage", "sonarqube.xml")}} +\item{option: }{autovalidateutils.sonarqube} +\item{envvar: }{AUTOVALIDATEUTILS_SONARQUBE (evaluated if possible, raw string otherwise)} +}} + +\item{cov_report}{\describe{ +The file path in which to save coverage .html report.\item{default: }{\preformatted{file.path("coverage", "cov_report.html")}} +\item{option: }{autovalidateutils.cov_report} +\item{envvar: }{AUTOVALIDATEUTILS_COV_REPORT (evaluated if possible, raw string otherwise)} +}} + +\item{skip_cov_report}{\describe{ +Logical whether interactive coverage report calculation shall be skipped\item{default: }{\preformatted{FALSE}} +\item{option: }{autovalidateutils.skip_cov_report} +\item{envvar: }{AUTOVALIDATEUTILS_SKIP_COV_REPORT (TRUE if one of 'TRUE', '1', FALSE otherwise)} +}} + +\item{cov_table}{\describe{ +The file path in which to save markdown table with coverage percentage for +each file.\item{default: }{\preformatted{file.path("coverage", "cov_table.md")}} +\item{option: }{autovalidateutils.cov_table} +\item{envvar: }{AUTOVALIDATEUTILS_COV_TABLE (evaluated if possible, raw string otherwise)} +}} + +\item{cov_logs}{\describe{ +Directory where logs gathered during coverage execution are saved.\item{default: }{\preformatted{file.path("coverage", "logs")}} +\item{option: }{autovalidateutils.cov_logs} +\item{envvar: }{AUTOVALIDATEUTILS_COV_LOGS (evaluated if possible, raw string otherwise)} +}} + +\item{testing_session}{\describe{ +The file path of the yml parsed sessionInfo file that +captures the environment in which units tests were executed.\item{default: }{\preformatted{file.path("coverage", "testing_session.yml")}} +\item{option: }{autovalidateutils.testing_session} +\item{envvar: }{AUTOVALIDATEUTILS_TESTING_SESSION (evaluated if possible, raw string otherwise)} +}} + +\item{coverage_threshold}{\describe{ +The numeric value of the minimal code coverage percentage +required for package to be validated\item{default: }{\preformatted{80}} +\item{option: }{autovalidateutils.coverage_threshold} +\item{envvar: }{AUTOVALIDATEUTILS_COVERAGE_THRESHOLD (evaluated if possible, raw string otherwise)} +}} + +\item{reuse_check_source}{\describe{ +Logical whether the source generated when running +R CMD check should be used when calcualting coverage code coverage instead +of the raw source.\item{default: }{\preformatted{TRUE}} +\item{option: }{autovalidateutils.reuse_check_source} +\item{envvar: }{AUTOVALIDATEUTILS_REUSE_CHECK_SOURCE (TRUE if one of 'TRUE', '1', FALSE otherwise)} +}} + +\item{documentation}{\describe{ +The directory path into which R documentation should +be written as markdown-formatted files. Files will be named with a prefixed +index according to their lexical Rd name sorting. This index corresponds to +the requirements index in the \code{mapper_file} option, and is used by +\code{autovalidate} to generate a traceability matrix.\item{default: }{\preformatted{file.path("traceability_matrix", "documentation")}} +\item{option: }{autovalidateutils.documentation} +\item{envvar: }{AUTOVALIDATEUTILS_DOCUMENTATION (evaluated if possible, raw string otherwise)} +}} + +\item{documentation_fragments}{\describe{ +A \code{character} vector of the types of \code{Rd} fragments +to be included in the resulting documentation markdown files, or \code{NULL} to +include all \code{Rd} contents.\item{default: }{\preformatted{c("title", "usage", "description", "details")}} +\item{option: }{autovalidateutils.documentation_fragments} +\item{envvar: }{AUTOVALIDATEUTILS_DOCUMENTATION_FRAGMENTS (evaluated if possible, raw string otherwise)} +}} + +\item{rd_transform}{\describe{ +A function which will be applied to the raw rd object before +converting it to the markdown file. Identity function by default.\item{default: }{\preformatted{function(x) x}} +\item{option: }{autovalidateutils.rd_transform} +\item{envvar: }{AUTOVALIDATEUTILS_RD_TRANSFORM (evaluated if possible, raw string otherwise)} +}} + +\item{mapper}{\describe{ +The file path into which an \code{autovalidate}-style mapper file should +be written.\item{default: }{\preformatted{file.path("traceability_matrix", "mapper.yml")}} +\item{option: }{autovalidateutils.mapper} +\item{envvar: }{AUTOVALIDATEUTILS_MAPPER (evaluated if possible, raw string otherwise)} +}} + +\item{mapper_defaults}{\describe{ +If \code{TRUE}, default values will be injected into the +autovalidate mapper.yml file for fields that have no direct analog in a +typical testthat-generated junit.xml file. This includes the \code{author}, +\code{reviewer} and \code{review_date}.\item{default: }{\preformatted{TRUE}} +\item{option: }{autovalidateutils.mapper_defaults} +\item{envvar: }{AUTOVALIDATEUTILS_MAPPER_DEFAULTS (TRUE if one of 'TRUE', '1', FALSE otherwise)} +}} + +\item{add_missing_traces}{\describe{ +Logical if covr traces which are missing in the testresults file should be +added to the JUnit\item{default: }{\preformatted{TRUE}} +\item{option: }{autovalidateutils.add_missing_traces} +\item{envvar: }{AUTOVALIDATEUTILS_ADD_MISSING_TRACES (TRUE if one of 'TRUE', '1', FALSE otherwise)} +}} + +\item{test_exec_log}{\describe{ +The file path of a file in which console output generated during test +execution.\item{default: }{\preformatted{"tests.Rout"}} +\item{option: }{autovalidateutils.test_exec_log} +\item{envvar: }{AUTOVALIDATEUTILS_TEST_EXEC_LOG (evaluated if possible, raw string otherwise)} +}} + +\item{junit}{\describe{ +The file path into which a JUnit-style xml test results +file should be written.\item{default: }{\preformatted{file.path("traceability_matrix", "junit.xml")}} +\item{option: }{autovalidateutils.junit} +\item{envvar: }{AUTOVALIDATEUTILS_JUNIT (evaluated if possible, raw string otherwise)} +}} + +\item{junit_reporter}{\describe{ +A quoted expression, producing a \code{testthat} reporter. The +reporter's initialization is expected to match the signature of +\code{testthat::JunitReporter$new()}, notably expecting a \code{file} argument to +use as the output \code{junit.xml} filepath.\item{default: }{\preformatted{quote(testthat::JunitReporter)}} +\item{option: }{autovalidateutils.junit_reporter} +\item{envvar: }{AUTOVALIDATEUTILS_JUNIT_REPORTER (evaluated if possible, raw string otherwise)} +}} + +\item{use_testthat}{\describe{ +Whether testthat infrastructure should be available within +autovalidateutils. The actual usage will be determined based on the +uses_testthat function output. Defaults to \code{TRUE}.\item{default: }{\preformatted{TRUE}} +\item{option: }{autovalidateutils.use_testthat} +\item{envvar: }{AUTOVALIDATEUTILS_USE_TESTTHAT (TRUE if one of 'TRUE', '1', FALSE otherwise)} +}} + +\item{inst_deps}{\describe{ +Character vector of dependency types. All packages with those types +are permitted to be installed from any available repo during validation. +Defaults to only 'Suggests'\item{default: }{\preformatted{"Suggests"}} +\item{option: }{autovalidateutils.inst_deps} +\item{envvar: }{AUTOVALIDATEUTILS_INST_DEPS (evaluated if possible, raw string otherwise)} +}} + +\item{req_deps}{\describe{ +Character vector of dependecies types. All packages with those types +are required to be installed before the validation can start.\item{default: }{\preformatted{c("Depends", "Imports", "LinkingTo")}} +\item{option: }{autovalidateutils.req_deps} +\item{envvar: }{AUTOVALIDATEUTILS_REQ_DEPS (evaluated if possible, raw string otherwise)} +}} + +\item{upgrade_deps}{\describe{ +Whether packages should be upgraded if higher version than installed is +available. Keep NULL to use the default autovalidateutils behavior +which is upgrading for DEP_LIB_CORE and not upgrading for DEP_LIB_OPTIONAL.\item{default: }{\preformatted{NULL}} +\item{option: }{autovalidateutils.upgrade_deps} +\item{envvar: }{AUTOVALIDATEUTILS_UPGRADE_DEPS (evaluated if possible, raw string otherwise)} +}} + +\item{suggests_repos}{\describe{ +Character vector of libraries that will be appended to +standard repos during installation of suggested packages.\item{default: }{\preformatted{c("https://cran.r-project.org/")}} +\item{option: }{autovalidateutils.suggests_repos} +\item{envvar: }{AUTOVALIDATEUTILS_SUGGESTS_REPOS (evaluated if possible, raw string otherwise)} +}} + +\item{revdep_repos}{\describe{ +Repository used for identyfying reverse dependencies. It should +be the same as \code{repos} unless using linux binaries, then it should be +repo URL without binaires part.\item{default: }{\preformatted{getOption("repos")}} +\item{option: }{autovalidateutils.revdep_repos} +\item{envvar: }{AUTOVALIDATEUTILS_REVDEP_REPOS (evaluated if possible, raw string otherwise)} +}} + +\item{revdep_n_workers}{\describe{ +Number of subprocesses used by the checked package for +executing tasks when running reverse dependecy check.\item{default: }{\preformatted{20L}} +\item{option: }{autovalidateutils.revdep_n_workers} +\item{envvar: }{AUTOVALIDATEUTILS_REVDEP_N_WORKERS (evaluated if possible, raw string otherwise)} +}} + +\item{revdep_clean_sources}{\describe{ +Logical flag whether the sources of reverse dependencies should be removed.\item{default: }{\preformatted{TRUE}} +\item{option: }{autovalidateutils.revdep_clean_sources} +\item{envvar: }{AUTOVALIDATEUTILS_REVDEP_CLEAN_SOURCES (TRUE if one of 'TRUE', '1', FALSE otherwise)} +}} + +\item{revdep_clean_library}{\describe{ +Logical whether the source of the target package should be removed after +completing checks.\item{default: }{\preformatted{TRUE}} +\item{option: }{autovalidateutils.revdep_clean_library} +\item{envvar: }{AUTOVALIDATEUTILS_REVDEP_CLEAN_LIBRARY (TRUE if one of 'TRUE', '1', FALSE otherwise)} +}} + +\item{checked_debug}{\describe{ +Logical whether checked should use detailed reporter which reports every task +to allow debuging of the checked state.\item{default: }{\preformatted{FALSE}} +\item{option: }{autovalidateutils.checked_debug} +\item{envvar: }{AUTOVALIDATEUTILS_CHECKED_DEBUG (TRUE if one of 'TRUE', '1', FALSE otherwise)} +}} + \item{tty_tick_interval}{\describe{ tty refresh interval when reporting results in milliseconds\item{default: }{\preformatted{0.1}} \item{option: }{checked.tty_tick_interval} -\item{envvar: }{R_CHECKED_TTY_TICK_INTERVAL (evaluated if possible, raw string otherwise)} +\item{envvar: }{CHECKED_TTY_TICK_INTERVAL (evaluated if possible, raw string otherwise)} }} \item{tty_default_height}{\describe{ deafult tty height used for the ANSI reporter. Used only if correct values could not be acquired with system('tput lines')\item{default: }{\preformatted{50}} \item{option: }{checked.tty_default_height} -\item{envvar: }{R_CHECKED_TTY_DEFAULT_HEIGHT (evaluated if possible, raw string otherwise)} +\item{envvar: }{CHECKED_TTY_DEFAULT_HEIGHT (evaluated if possible, raw string otherwise)} }} \item{proactive_gc}{\describe{ @@ -41,7 +455,7 @@ is recommended to be used for designs with many sub-processes required as native garbage collection can lag leading to memory issues. Disable only when maximum prefromance is required and memory is not the issue.\item{default: }{\preformatted{TRUE}} \item{option: }{checked.proactive_gc} -\item{envvar: }{R_CHECKED_PROACTIVE_GC (evaluated if possible, raw string otherwise)} +\item{envvar: }{CHECKED_PROACTIVE_GC (evaluated if possible, raw string otherwise)} }} \item{results_error_on}{\describe{ @@ -50,7 +464,7 @@ are discovered when generating results. "never" means that no errors are thrown. If "issues" then errors are emitted only on issues, whereas "potential issues" stands for error on both issues and potential issues.\item{default: }{\preformatted{"never"}} \item{option: }{checked.results_error_on} -\item{envvar: }{R_CHECKED_RESULTS_ERROR_ON (evaluated if possible, raw string otherwise)} +\item{envvar: }{CHECKED_RESULTS_ERROR_ON (evaluated if possible, raw string otherwise)} }} \item{results_keep}{\describe{ @@ -59,7 +473,7 @@ character vector indicating which packages should be included in the results. with issues identified, whereas "potential_issues" stands for keeping packages with both "issues" and "potential_issues".\item{default: }{\preformatted{"all"}} \item{option: }{checked.results_keep} -\item{envvar: }{R_CHECKED_RESULTS_KEEP (evaluated if possible, raw string otherwise)} +\item{envvar: }{CHECKED_RESULTS_KEEP (evaluated if possible, raw string otherwise)} }} \item{restore}{\describe{ @@ -67,7 +481,7 @@ packages with both "issues" and "potential_issues".\item{default: }{\preformatte running checks. If \code{FALSE}, an attempt will me made to restore previous progress from the same \code{output}\item{default: }{\preformatted{NA}} \item{option: }{checked.restore} -\item{envvar: }{R_CHECKED_RESTORE (evaluated if possible, raw string otherwise)} +\item{envvar: }{CHECKED_RESTORE (evaluated if possible, raw string otherwise)} }} \item{add_remotes}{\describe{ @@ -75,7 +489,7 @@ progress from the same \code{output}\item{default: }{\preformatted{NA}} should be scanned for packages in the \code{remotes} field and added while constrocuting a plan \code{task_grap}\item{default: }{\preformatted{TRUE}} \item{option: }{checked.add_remotes} -\item{envvar: }{R_CHECKED_ADD_REMOTES (evaluated if possible, raw string otherwise)} +\item{envvar: }{CHECKED_ADD_REMOTES (evaluated if possible, raw string otherwise)} }} \item{check_envvars}{\describe{ @@ -84,40 +498,40 @@ the R CMD check.\item{default: }{\preformatted{c(`_R_CHECK_FORCE_SUGGESTS_` = "f `_R_CHECK_SYSTEM_CLOCK_` = "false", `_R_CHECK_SUGGESTS_ONLY_` = "true", `_R_CHECK_CRAN_INCOMING_` = "false")}} \item{option: }{checked.check_envvars} -\item{envvar: }{R_CHECKED_CHECK_ENVVARS (evaluated if possible, raw string otherwise)} +\item{envvar: }{CHECKED_CHECK_ENVVARS (evaluated if possible, raw string otherwise)} }} \item{check_build_args}{\describe{ \code{character} vector of args passed to the R CMD build.\item{default: }{\preformatted{c("--no-build-vignettes", "--no-manual")}} \item{option: }{checked.check_build_args} -\item{envvar: }{R_CHECKED_CHECK_BUILD_ARGS (space-separated R CMD build flags)} +\item{envvar: }{CHECKED_CHECK_BUILD_ARGS (space-separated R CMD build flags)} }} \item{check_args}{\describe{ \code{character} vector of args passed to the R CMD check.\item{default: }{\preformatted{c("--timings", "--ignore-vignettes", "--no-manual", "--as-cran")}} \item{option: }{checked.check_args} -\item{envvar: }{R_CHECKED_CHECK_ARGS (space-separated R CMD check flags)} +\item{envvar: }{CHECKED_CHECK_ARGS (space-separated R CMD check flags)} }} \item{install_envvars}{\describe{ named \code{character} vector of environment variables to use during the package installation.\item{default: }{\preformatted{callr::rcmd_safe_env()}} \item{option: }{checked.install_envvars} -\item{envvar: }{R_CHECKED_INSTALL_ENVVARS (evaluated if possible, raw string otherwise)} +\item{envvar: }{CHECKED_INSTALL_ENVVARS (evaluated if possible, raw string otherwise)} }} \item{install_system_profile}{\describe{ \code{logical} used as \code{sytem_profile} parameter passed to the \code{callr::r_bg()} function used to install packages\item{default: }{\preformatted{FALSE}} \item{option: }{checked.install_system_profile} -\item{envvar: }{R_CHECKED_INSTALL_SYSTEM_PROFILE (evaluated if possible, raw string otherwise)} +\item{envvar: }{CHECKED_INSTALL_SYSTEM_PROFILE (evaluated if possible, raw string otherwise)} }} \item{install_user_profile}{\describe{ value used as \code{user_profile} parameter passed to the \code{callr::r_bg()} function used to install packages\item{default: }{\preformatted{"project"}} \item{option: }{checked.install_user_profile} -\item{envvar: }{R_CHECKED_INSTALL_USER_PROFILE (evaluated if possible, raw string otherwise)} +\item{envvar: }{CHECKED_INSTALL_USER_PROFILE (evaluated if possible, raw string otherwise)} }} } diff --git a/man/options_params.Rd b/man/options_params.Rd index 4402e65..7b44e37 100644 --- a/man/options_params.Rd +++ b/man/options_params.Rd @@ -4,51 +4,248 @@ \alias{options_params} \title{Checked Options} \arguments{ +\item{build_binaries}{Logical whether binary source of the package should be compiled during +validation. (Defaults to \code{FALSE}, overwritable using option 'autovalidateutils.build_binaries' or environment variable 'AUTOVALIDATEUTILS_BUILD_BINARIES')} + +\item{check_build_args}{\code{character} vector of args passed to the R CMD build. (Defaults to \code{c("--no-build-vignettes", "--no-manual")}, overwritable using option 'checked.check_build_args' or environment variable 'CHECKED_CHECK_BUILD_ARGS')} + +\item{add_remotes}{\code{logical} indicating whether origins inheriting from \code{pkg_origin_local}, +should be scanned for packages in the \code{remotes} field and added while +constrocuting a plan \code{task_grap} (Defaults to \code{TRUE}, overwritable using option 'checked.add_remotes' or environment variable 'CHECKED_ADD_REMOTES')} + +\item{lib.loc}{Character vector describing the location of R library trees to search +through. It will be passed to installed.packages() while deriving whether all +required dependencies are installed. +Defaults to c(.Library, .Library.site). (Defaults to \code{c(.Library, .Library.site)}, overwritable using option 'autovalidateutils.lib.loc' or environment variable 'AUTOVALIDATEUTILS_LIB_LOC')} + +\item{tty_tick_interval}{tty refresh interval when reporting results in milliseconds (Defaults to \code{0.1}, overwritable using option 'checked.tty_tick_interval' or environment variable 'CHECKED_TTY_TICK_INTERVAL')} + +\item{checked_debug}{Logical whether checked should use detailed reporter which reports every task +to allow debuging of the checked state. (Defaults to \code{FALSE}, overwritable using option 'autovalidateutils.checked_debug' or environment variable 'AUTOVALIDATEUTILS_CHECKED_DEBUG')} + \item{proactive_gc}{\code{logical}, indicating whether additional garbage collection should be performed before starting a new task, if at least one process recently finalized. This can cause the checker to orchestrate tasks slower but is recommended to be used for designs with many sub-processes required as native garbage collection can lag leading to memory issues. Disable only -when maximum prefromance is required and memory is not the issue. (Defaults to \code{TRUE}, overwritable using option 'checked.proactive_gc' or environment variable 'R_CHECKED_PROACTIVE_GC')} +when maximum prefromance is required and memory is not the issue. (Defaults to \code{TRUE}, overwritable using option 'checked.proactive_gc' or environment variable 'CHECKED_PROACTIVE_GC')} + +\item{install_user_profile}{value used as \code{user_profile} parameter passed to the \code{callr::r_bg()} +function used to install packages (Defaults to \code{"project"}, overwritable using option 'checked.install_user_profile' or environment variable 'CHECKED_INSTALL_USER_PROFILE')} + +\item{use_testthat}{Whether testthat infrastructure should be available within +autovalidateutils. The actual usage will be determined based on the +uses_testthat function output. Defaults to \code{TRUE}. (Defaults to \code{TRUE}, overwritable using option 'autovalidateutils.use_testthat' or environment variable 'AUTOVALIDATEUTILS_USE_TESTTHAT')} + +\item{vulnerabilities}{The file path to which metadata reagarding possible package's +vulnerabilities should be captured. (Defaults to \code{"vulnerabilities.yml"}, overwritable using option 'autovalidateutils.vulnerabilities' or environment variable 'AUTOVALIDATEUTILS_VULNERABILITIES')} + +\item{news}{The file path of the \code{NEWS} (or \code{NEWS.md}) file contents. If the \code{NEWS} file +is not already markdown formatted, it will be converted into a preformatted +markdown code block to be embedded in an \code{autovalidate} report. (Defaults to \code{"news.md"}, overwritable using option 'autovalidateutils.news' or environment variable 'AUTOVALIDATEUTILS_NEWS')} + +\item{add_missing_traces}{Logical if covr traces which are missing in the testresults file should be +added to the JUnit (Defaults to \code{TRUE}, overwritable using option 'autovalidateutils.add_missing_traces' or environment variable 'AUTOVALIDATEUTILS_ADD_MISSING_TRACES')} + +\item{results_keep}{character vector indicating which packages should be included in the results. +"all" means that all packages are kept. If "issues" then only packages +with issues identified, whereas "potential_issues" stands for keeping +packages with both "issues" and "potential_issues". (Defaults to \code{"all"}, overwritable using option 'checked.results_keep' or environment variable 'CHECKED_RESULTS_KEEP')} + +\item{installed_packages}{The name of the installed packages json file. It keeps track of +the information about which packages were installed to the environemnt +and their versions. File will be written to the log_output directory (Defaults to \code{"installed_packages.json"}, overwritable using option 'autovalidateutils.installed_packages' or environment variable 'AUTOVALIDATEUTILS_INSTALLED_PACKAGES')} + +\item{junit}{The file path into which a JUnit-style xml test results +file should be written. (Defaults to \code{file.path("traceability_matrix", "junit.xml")}, overwritable using option 'autovalidateutils.junit' or environment variable 'AUTOVALIDATEUTILS_JUNIT')} + +\item{output}{A parent directory for all non-relative output files. Defaults to the +current working directory. (Defaults to \code{file.path(normalize_path(tempdir()), "autovalidateutils")}, overwritable using option 'autovalidateutils.output' or environment variable 'AUTOVALIDATEUTILS_OUTPUT')} \item{results_error_on}{character vector indicating whether R error should be thrown when issues are discovered when generating results. "never" means that no errors are thrown. If "issues" then errors are emitted only on issues, whereas -"potential issues" stands for error on both issues and potential issues. (Defaults to \code{"never"}, overwritable using option 'checked.results_error_on' or environment variable 'R_CHECKED_RESULTS_ERROR_ON')} +"potential issues" stands for error on both issues and potential issues. (Defaults to \code{"never"}, overwritable using option 'checked.results_error_on' or environment variable 'CHECKED_RESULTS_ERROR_ON')} + +\item{session}{The file path of the session information metadata file, a +yaml-formatted itemization of a few characteristic measures of an R session +environment. (Defaults to \code{"session.yml"}, overwritable using option 'autovalidateutils.session' or environment variable 'AUTOVALIDATEUTILS_SESSION')} + +\item{version_control}{The file path to which package version control metadata +should be captured. (Defaults to \code{"version_control.yml"}, overwritable using option 'autovalidateutils.version_control' or environment variable 'AUTOVALIDATEUTILS_VERSION_CONTROL')} + +\item{timeout}{A difftime object or a numeric value with a real number indicating +number of seconds that should pass before certain calls are timed out. Set to +Inf to turn off timeout. By deafult set to difftime 14 hours. (Defaults to \code{as.difftime(14, units = "hours")}, overwritable using option 'autovalidateutils.timeout' or environment variable 'AUTOVALIDATEUTILS_TIMEOUT')} + +\item{revdep_repos}{Repository used for identyfying reverse dependencies. It should +be the same as \code{repos} unless using linux binaries, then it should be +repo URL without binaires part. (Defaults to \code{getOption("repos")}, overwritable using option 'autovalidateutils.revdep_repos' or environment variable 'AUTOVALIDATEUTILS_REVDEP_REPOS')} \item{install_envvars}{named \code{character} vector of environment variables to use during -the package installation. (Defaults to \code{callr::rcmd_safe_env()}, overwritable using option 'checked.install_envvars' or environment variable 'R_CHECKED_INSTALL_ENVVARS')} +the package installation. (Defaults to \code{callr::rcmd_safe_env()}, overwritable using option 'checked.install_envvars' or environment variable 'CHECKED_INSTALL_ENVVARS')} -\item{check_args}{\code{character} vector of args passed to the R CMD check. (Defaults to \code{c("--timings", "--ignore-vignettes", "--no-manual", "--as-cran")}, overwritable using option 'checked.check_args' or environment variable 'R_CHECKED_CHECK_ARGS')} +\item{description}{The file path of the \code{DESCRIPTION} file contents, written out to +a plain text, yaml-formatted file. (Defaults to \code{"description.yml"}, overwritable using option 'autovalidateutils.description' or environment variable 'AUTOVALIDATEUTILS_DESCRIPTION')} -\item{install_system_profile}{\code{logical} used as \code{sytem_profile} parameter passed to the \code{callr::r_bg()} -function used to install packages (Defaults to \code{FALSE}, overwritable using option 'checked.install_system_profile' or environment variable 'R_CHECKED_INSTALL_SYSTEM_PROFILE')} +\item{cov_table}{The file path in which to save markdown table with coverage percentage for +each file. (Defaults to \code{file.path("coverage", "cov_table.md")}, overwritable using option 'autovalidateutils.cov_table' or environment variable 'AUTOVALIDATEUTILS_COV_TABLE')} -\item{results_keep}{character vector indicating which packages should be included in the results. -"all" means that all packages are kept. If "issues" then only packages -with issues identified, whereas "potential_issues" stands for keeping -packages with both "issues" and "potential_issues". (Defaults to \code{"all"}, overwritable using option 'checked.results_keep' or environment variable 'R_CHECKED_RESULTS_KEEP')} +\item{revdep_clean_sources}{Logical flag whether the sources of reverse dependencies should be removed. (Defaults to \code{TRUE}, overwritable using option 'autovalidateutils.revdep_clean_sources' or environment variable 'AUTOVALIDATEUTILS_REVDEP_CLEAN_SOURCES')} -\item{add_remotes}{\code{logical} indicating whether origins inheriting from \code{pkg_origin_local}, -should be scanned for packages in the \code{remotes} field and added while -constrocuting a plan \code{task_grap} (Defaults to \code{TRUE}, overwritable using option 'checked.add_remotes' or environment variable 'R_CHECKED_ADD_REMOTES')} +\item{generalize_sources}{Logical whether sources produced during validation should be renamed to +general 'package_binary.tgz/tar.gz/zip' and 'package_source.tar.gz'. (Defaults to \code{FALSE}, overwritable using option 'autovalidateutils.generalize_sources' or environment variable 'AUTOVALIDATEUTILS_GENERALIZE_SOURCES')} + +\item{r_cmd_check_variables}{The named character vector of environmental variables, +that will be passed to the \code{withr::with_envvar} function and used to execute +rcmdcheck::rcmdcheck. It can also be a single keyword, either 'cran' or +'internal' that will result in using predefined set of variables. (Defaults to \code{"internal"}, overwritable using option 'autovalidateutils.r_cmd_check_variables' or environment variable 'AUTOVALIDATEUTILS_R_CMD_CHECK_VARIABLES')} + +\item{tty_default_height}{deafult tty height used for the ANSI reporter. Used only +if correct values could not be acquired with system('tput lines') (Defaults to \code{50}, overwritable using option 'checked.tty_default_height' or environment variable 'CHECKED_TTY_DEFAULT_HEIGHT')} + +\item{r_cmd_check}{The file path to which \verb{R CMD check} results should be written. +Contents are written in yaml format. (Defaults to \code{"r_cmd_check.yml"}, overwritable using option 'autovalidateutils.r_cmd_check' or environment variable 'AUTOVALIDATEUTILS_R_CMD_CHECK')} + +\item{install_system_profile}{\code{logical} used as \code{sytem_profile} parameter passed to the \code{callr::r_bg()} +function used to install packages (Defaults to \code{FALSE}, overwritable using option 'checked.install_system_profile' or environment variable 'CHECKED_INSTALL_SYSTEM_PROFILE')} + +\item{coverage_threshold}{The numeric value of the minimal code coverage percentage +required for package to be validated (Defaults to \code{80}, overwritable using option 'autovalidateutils.coverage_threshold' or environment variable 'AUTOVALIDATEUTILS_COVERAGE_THRESHOLD')} \item{check_envvars}{named \code{character} vector of environment variables to use during -the R CMD check. (Defaults to \verb{c(}\emph{R_CHECK_FORCE_SUGGESTS}\verb{= "false",}\emph{R_CHECK_RD_XREFS}\verb{= "false", ; }\emph{R_CHECK_SYSTEM_CLOCK}\verb{= "false",}\emph{R_CHECK_SUGGESTS_ONLY}\verb{= "true", ; }\emph{R_CHECK_CRAN_INCOMING}\verb{ = "false")}, overwritable using option 'checked.check_envvars' or environment variable 'R_CHECKED_CHECK_ENVVARS')} +the R CMD check. (Defaults to \verb{c(}\emph{R_CHECK_FORCE_SUGGESTS}\verb{= "false",}\emph{R_CHECK_RD_XREFS}\verb{= "false", ; }\emph{R_CHECK_SYSTEM_CLOCK}\verb{= "false",}\emph{R_CHECK_SUGGESTS_ONLY}\verb{= "true", ; }\emph{R_CHECK_CRAN_INCOMING}\verb{ = "false")}, overwritable using option 'checked.check_envvars' or environment variable 'CHECKED_CHECK_ENVVARS')} + +\item{documentation_fragments}{A \code{character} vector of the types of \code{Rd} fragments +to be included in the resulting documentation markdown files, or \code{NULL} to +include all \code{Rd} contents. (Defaults to \code{c("title", "usage", "description", "details")}, overwritable using option 'autovalidateutils.documentation_fragments' or environment variable 'AUTOVALIDATEUTILS_DOCUMENTATION_FRAGMENTS')} + +\item{inst_deps}{Character vector of dependency types. All packages with those types +are permitted to be installed from any available repo during validation. +Defaults to only 'Suggests' (Defaults to \code{"Suggests"}, overwritable using option 'autovalidateutils.inst_deps' or environment variable 'AUTOVALIDATEUTILS_INST_DEPS')} + +\item{install_n_workers}{Number of subprocesses used by the checked package for +executing tasks when installing package and dependencies. (Defaults to \code{20L}, overwritable using option 'autovalidateutils.install_n_workers' or environment variable 'AUTOVALIDATEUTILS_INSTALL_N_WORKERS')} + +\item{revdep_n_workers}{Number of subprocesses used by the checked package for +executing tasks when running reverse dependecy check. (Defaults to \code{20L}, overwritable using option 'autovalidateutils.revdep_n_workers' or environment variable 'AUTOVALIDATEUTILS_REVDEP_N_WORKERS')} + +\item{req_deps}{Character vector of dependecies types. All packages with those types +are required to be installed before the validation can start. (Defaults to \code{c("Depends", "Imports", "LinkingTo")}, overwritable using option 'autovalidateutils.req_deps' or environment variable 'AUTOVALIDATEUTILS_REQ_DEPS')} + +\item{r_cmd_check_clean_tests}{Logical flag whether the \if{html}{\out{}}.Rcheck/\if{html}{\out{}}/tests +directory should be cleared by removing all the directories in it (Defaults to \code{FALSE}, overwritable using option 'autovalidateutils.r_cmd_check_clean_tests' or environment variable 'AUTOVALIDATEUTILS_R_CMD_CHECK_CLEAN_TESTS')} + +\item{documentation}{The directory path into which R documentation should +be written as markdown-formatted files. Files will be named with a prefixed +index according to their lexical Rd name sorting. This index corresponds to +the requirements index in the \code{mapper_file} option, and is used by +\code{autovalidate} to generate a traceability matrix. (Defaults to \code{file.path("traceability_matrix", "documentation")}, overwritable using option 'autovalidateutils.documentation' or environment variable 'AUTOVALIDATEUTILS_DOCUMENTATION')} + +\item{suggests_repos}{Character vector of libraries that will be appended to +standard repos during installation of suggested packages. (Defaults to \code{c("https://cran.r-project.org/")}, overwritable using option 'autovalidateutils.suggests_repos' or environment variable 'AUTOVALIDATEUTILS_SUGGESTS_REPOS')} + +\item{clean}{Whether directories created by autovaldiateutils in /tmp directory +should be removed. Set to TRUE if you want to save space in your /tmp. Keep +FALSE to maintain all the output in /tmp. Does not affect regular output (Defaults to \code{TRUE}, overwritable using option 'autovalidateutils.clean' or environment variable 'AUTOVALIDATEUTILS_CLEAN')} + +\item{mapper_defaults}{If \code{TRUE}, default values will be injected into the +autovalidate mapper.yml file for fields that have no direct analog in a +typical testthat-generated junit.xml file. This includes the \code{author}, +\code{reviewer} and \code{review_date}. (Defaults to \code{TRUE}, overwritable using option 'autovalidateutils.mapper_defaults' or environment variable 'AUTOVALIDATEUTILS_MAPPER_DEFAULTS')} + +\item{cov_logs}{Directory where logs gathered during coverage execution are saved. (Defaults to \code{file.path("coverage", "logs")}, overwritable using option 'autovalidateutils.cov_logs' or environment variable 'AUTOVALIDATEUTILS_COV_LOGS')} + +\item{cov_report}{The file path in which to save coverage .html report. (Defaults to \code{file.path("coverage", "cov_report.html")}, overwritable using option 'autovalidateutils.cov_report' or environment variable 'AUTOVALIDATEUTILS_COV_REPORT')} + +\item{check_args}{\code{character} vector of args passed to the R CMD check. (Defaults to \code{c("--timings", "--ignore-vignettes", "--no-manual", "--as-cran")}, overwritable using option 'checked.check_args' or environment variable 'CHECKED_CHECK_ARGS')} + +\item{test_exec_log}{The file path of a file in which console output generated during test +execution. (Defaults to \code{"tests.Rout"}, overwritable using option 'autovalidateutils.test_exec_log' or environment variable 'AUTOVALIDATEUTILS_TEST_EXEC_LOG')} + +\item{quiet}{Whether execution should suppress output. When \code{TRUE}, only warnings +are emitted. When \code{FALSE}, a pretty-formatted log is emitted to the +console. (Defaults to \code{FALSE}, overwritable using option 'autovalidateutils.quiet' or environment variable 'AUTOVALIDATEUTILS_QUIET')} -\item{tty_tick_interval}{tty refresh interval when reporting results in milliseconds (Defaults to \code{0.1}, overwritable using option 'checked.tty_tick_interval' or environment variable 'R_CHECKED_TTY_TICK_INTERVAL')} +\item{steps}{A listing of autovalidateutils steps to perform. Either a \code{character} vector +or \code{list}. Alternatively, the vector or list may consist of modifications +to a listing of all steps, which must be prefixed by \code{-} (for example, +\code{-write_revdep_check}, which will use all steps except reverse dependency +checks). (Defaults to \code{c("-write_checked")}, overwritable using option 'autovalidateutils.steps' or environment variable 'AUTOVALIDATEUTILS_STEPS')} -\item{check_build_args}{\code{character} vector of args passed to the R CMD build. (Defaults to \code{c("--no-build-vignettes", "--no-manual")}, overwritable using option 'checked.check_build_args' or environment variable 'R_CHECKED_CHECK_BUILD_ARGS')} +\item{subprocess_debug}{Logical whether certain functionalities shall be run in a debug mode. Debug +means functions are run in the main process rather that callr::r_vanilla (Defaults to \code{FALSE}, overwritable using option 'autovalidateutils.subprocess_debug' or environment variable 'AUTOVALIDATEUTILS_SUBPROCESS_DEBUG')} + +\item{reuse_check_source}{Logical whether the source generated when running +R CMD check should be used when calcualting coverage code coverage instead +of the raw source. (Defaults to \code{TRUE}, overwritable using option 'autovalidateutils.reuse_check_source' or environment variable 'AUTOVALIDATEUTILS_REUSE_CHECK_SOURCE')} + +\item{version_control.md5}{When a source control hash can't be derived from +the target directory, this option will be used to populate version control +metadata. This is of particular interest when the source code has been +extracted from a tar.gz package bundle. In this case, the md5 hash should +reflect the hash of the originating package bundle. (Defaults to \code{NULL}, overwritable using option 'autovalidateutils.version_control.md5' or environment variable 'AUTOVALIDATEUTILS_VERSION_CONTROL_MD5')} + +\item{upgrade_deps}{Whether packages should be upgraded if higher version than installed is +available. Keep NULL to use the default autovalidateutils behavior +which is upgrading for DEP_LIB_CORE and not upgrading for DEP_LIB_OPTIONAL. (Defaults to \code{NULL}, overwritable using option 'autovalidateutils.upgrade_deps' or environment variable 'AUTOVALIDATEUTILS_UPGRADE_DEPS')} + +\item{testing_session}{The file path of the yml parsed sessionInfo file that +captures the environment in which units tests were executed. (Defaults to \code{file.path("coverage", "testing_session.yml")}, overwritable using option 'autovalidateutils.testing_session' or environment variable 'AUTOVALIDATEUTILS_TESTING_SESSION')} + +\item{original_libpaths}{Vector storing original .libPaths before the vector was +altered by avu_install function. It is always overwritten during +autovalidateutils runtime. (Defaults to \code{NULL}, overwritable using option 'autovalidateutils.original_libpaths' or environment variable 'AUTOVALIDATEUTILS_ORIGINAL_LIBPATHS')} + +\item{sonarqube}{The file path in which to record a sonarqube xml coverage output file. (Defaults to \code{file.path("coverage", "sonarqube.xml")}, overwritable using option 'autovalidateutils.sonarqube' or environment variable 'AUTOVALIDATEUTILS_SONARQUBE')} + +\item{rd_transform}{A function which will be applied to the raw rd object before +converting it to the markdown file. Identity function by default. (Defaults to \code{function(x) x}, overwritable using option 'autovalidateutils.rd_transform' or environment variable 'AUTOVALIDATEUTILS_RD_TRANSFORM')} + +\item{junit_reporter}{A quoted expression, producing a \code{testthat} reporter. The +reporter's initialization is expected to match the signature of +\code{testthat::JunitReporter$new()}, notably expecting a \code{file} argument to +use as the output \code{junit.xml} filepath. (Defaults to \code{quote(testthat::JunitReporter)}, overwritable using option 'autovalidateutils.junit_reporter' or environment variable 'AUTOVALIDATEUTILS_JUNIT_REPORTER')} + +\item{version_control.url}{When a source control origin can't be derived from +the target directory, this option will be used to populate version control +metadata. This is of particular interest when the source code has been +extracted from a tar.gz package bundle. In this case, the url should +reflect the url from which the originating package bundle was downloaded. (Defaults to \code{NULL}, overwritable using option 'autovalidateutils.version_control.url' or environment variable 'AUTOVALIDATEUTILS_VERSION_CONTROL_URL')} + +\item{log_output}{path to the directory where log files will be created. (Defaults to \code{file.path(normalize_path(tempdir()), "log_autovalidateutils")}, overwritable using option 'autovalidateutils.log_output' or environment variable 'AUTOVALIDATEUTILS_LOG_OUTPUT')} + +\item{conditions}{The file path of the file to which conditions should be emitted. They are +logged in yaml format, which is later read by \code{autovalidate} to +re-emit them as \code{autovalidate} checks and trigger failures when applicable (Defaults to \code{"conditions.yml"}, overwritable using option 'autovalidateutils.conditions' or environment variable 'AUTOVALIDATEUTILS_CONDITIONS')} \item{restore}{\code{logical} indicating whether output directory should be unlinked before running checks. If \code{FALSE}, an attempt will me made to restore previous -progress from the same \code{output} (Defaults to \code{NA}, overwritable using option 'checked.restore' or environment variable 'R_CHECKED_RESTORE')} +progress from the same \code{output} (Defaults to \code{NA}, overwritable using option 'checked.restore' or environment variable 'CHECKED_RESTORE')} -\item{install_user_profile}{value used as \code{user_profile} parameter passed to the \code{callr::r_bg()} -function used to install packages (Defaults to \code{"project"}, overwritable using option 'checked.install_user_profile' or environment variable 'R_CHECKED_INSTALL_USER_PROFILE')} +\item{skip_cov_report}{Logical whether interactive coverage report calculation shall be skipped (Defaults to \code{FALSE}, overwritable using option 'autovalidateutils.skip_cov_report' or environment variable 'AUTOVALIDATEUTILS_SKIP_COV_REPORT')} -\item{tty_default_height}{deafult tty height used for the ANSI reporter. Used only -if correct values could not be acquired with system('tput lines') (Defaults to \code{50}, overwritable using option 'checked.tty_default_height' or environment variable 'R_CHECKED_TTY_DEFAULT_HEIGHT')} +\item{use_remotes}{Logical flag or named character mapping dependency types to the mechanism of +handling remotes, one of "allow", "prefer" or "disallow". "allow" +option means that the remote sources are allowed but will not take precedence +over other standard sources if both available. "prefer" means allow and +overwrite standard sources while "disallow" stands for skipping remote +sources at all. If no value is provided for a dependency type it is +considered to be "disallow". Can also be set to TRUE to "prefer" all or +FALSE to "disallow all. (Defaults to \verb{c(Depends = "disallow", Imports = "disallow", LinkingTo = "disallow", ; Suggests = "allow", Enhances = "allow")}, overwritable using option 'autovalidateutils.use_remotes' or environment variable 'AUTOVALIDATEUTILS_USE_REMOTES')} + +\item{mapper}{The file path into which an \code{autovalidate}-style mapper file should +be written. (Defaults to \code{file.path("traceability_matrix", "mapper.yml")}, overwritable using option 'autovalidateutils.mapper' or environment variable 'AUTOVALIDATEUTILS_MAPPER')} + +\item{clear_description}{Logical value whether all non-utf8 characters should be removed from +the DESCRIPTION value. This is to avoid potential erros that might +occure when installing the package from the source. (Defaults to \code{FALSE}, overwritable using option 'autovalidateutils.clear_description' or environment variable 'AUTOVALIDATEUTILS_CLEAR_DESCRIPTION')} + +\item{revdep_clean_library}{Logical whether the source of the target package should be removed after +completing checks. (Defaults to \code{TRUE}, overwritable using option 'autovalidateutils.revdep_clean_library' or environment variable 'AUTOVALIDATEUTILS_REVDEP_CLEAN_LIBRARY')} + +\item{check_dir}{The directory R CMD check results should be written to +(.tag.gz, .Rcheck). (Defaults to \code{"check"}, overwritable using option 'autovalidateutils.check_dir' or environment variable 'AUTOVALIDATEUTILS_CHECK_DIR')} } \description{ Checked Options diff --git a/man/print.checked_results.Rd b/man/print.checked_results.Rd index bea9075..a7ea5bd 100644 --- a/man/print.checked_results.Rd +++ b/man/print.checked_results.Rd @@ -22,7 +22,7 @@ \item{keep}{character vector indicating which packages should be included in the results. "all" means that all packages are kept. If "issues" then only packages with issues identified, whereas "potential_issues" stands for keeping -packages with both "issues" and "potential_issues". (Defaults to \code{"all"}, overwritable using option 'checked.results_keep' or environment variable 'R_CHECKED_RESULTS_KEEP')} +packages with both "issues" and "potential_issues". (Defaults to \code{"all"}, overwritable using option 'checked.results_keep' or environment variable 'CHECKED_RESULTS_KEEP')} } \description{ Print checked results diff --git a/man/reporters.Rd b/man/reporters.Rd index feb2287..05041c4 100644 --- a/man/reporters.Rd +++ b/man/reporters.Rd @@ -14,13 +14,15 @@ reporter_ansi_tty2(...) reporter_basic_tty(checks_only = FALSE, ...) -reporter_default() +reporter_default(checker = NULL) } \arguments{ \item{...}{additional values which should be assigned to the reported environment.} \item{checks_only}{whether basic tty reporter should report only check tasks.} + +\item{checker}{checker object required to properly derive default reporter.} } \description{ Reporters are used to configure how output is communicated while running diff --git a/man/results.Rd b/man/results.Rd index 90621d8..7c78e53 100644 --- a/man/results.Rd +++ b/man/results.Rd @@ -32,7 +32,7 @@ results(x, ...) \item{error_on}{character vector indicating whether R error should be thrown when issues are discovered when generating results. "never" means that no errors are thrown. If "issues" then errors are emitted only on issues, whereas -"potential issues" stands for error on both issues and potential issues. (Defaults to \code{"never"}, overwritable using option 'checked.results_error_on' or environment variable 'R_CHECKED_RESULTS_ERROR_ON')} +"potential issues" stands for error on both issues and potential issues. (Defaults to \code{"never"}, overwritable using option 'checked.results_error_on' or environment variable 'CHECKED_RESULTS_ERROR_ON')} \item{checker_obj}{\code{\link{checker}} object.} } diff --git a/man/run.Rd b/man/run.Rd index e6d7993..94cc504 100644 --- a/man/run.Rd +++ b/man/run.Rd @@ -4,7 +4,7 @@ \alias{run} \title{Run a Series of \verb{R CMD check}s} \usage{ -run(checker, ..., reporter = reporter_default()) +run(checker, ..., reporter = reporter_default(checker)) } \arguments{ \item{checker}{\code{character} or \code{checker} If a \code{character} value is From 06ac7df0eee74c3e712cc97b7afcc9314c89b5bf Mon Sep 17 00:00:00 2001 From: maksymis <32574056+maksymiuks@users.noreply.github.com> Date: Fri, 19 Jun 2026 19:01:02 +0200 Subject: [PATCH 2/2] Fix options --- man/options.Rd | 440 ++--------------------------------- man/options_params.Rd | 239 ++----------------- man/print.checked_results.Rd | 2 +- man/results.Rd | 2 +- 4 files changed, 36 insertions(+), 647 deletions(-) diff --git a/man/options.Rd b/man/options.Rd index bc79e91..71c9de2 100644 --- a/man/options.Rd +++ b/man/options.Rd @@ -20,431 +20,17 @@ options::opt(x, default, env = "checked") \section{Options}{ \describe{ -\item{quiet}{\describe{ -Whether execution should suppress output. When \code{TRUE}, only warnings -are emitted. When \code{FALSE}, a pretty-formatted log is emitted to the -console.\item{default: }{\preformatted{FALSE}} -\item{option: }{autovalidateutils.quiet} -\item{envvar: }{AUTOVALIDATEUTILS_QUIET (TRUE if one of 'TRUE', '1', FALSE otherwise)} -}} - -\item{clean}{\describe{ -Whether directories created by autovaldiateutils in /tmp directory -should be removed. Set to TRUE if you want to save space in your /tmp. Keep -FALSE to maintain all the output in /tmp. Does not affect regular output\item{default: }{\preformatted{TRUE}} -\item{option: }{autovalidateutils.clean} -\item{envvar: }{AUTOVALIDATEUTILS_CLEAN (TRUE if one of 'TRUE', '1', FALSE otherwise)} -}} - -\item{timeout}{\describe{ -A difftime object or a numeric value with a real number indicating -number of seconds that should pass before certain calls are timed out. Set to -Inf to turn off timeout. By deafult set to difftime 14 hours.\item{default: }{\preformatted{as.difftime(14, units = "hours")}} -\item{option: }{autovalidateutils.timeout} -\item{envvar: }{AUTOVALIDATEUTILS_TIMEOUT (evaluated if possible, raw string otherwise)} -}} - -\item{output}{\describe{ -A parent directory for all non-relative output files. Defaults to the -current working directory.\item{default: }{\preformatted{file.path(normalize_path(tempdir()), "autovalidateutils")}} -\item{option: }{autovalidateutils.output} -\item{envvar: }{AUTOVALIDATEUTILS_OUTPUT (evaluated if possible, raw string otherwise)} -}} - -\item{log_output}{\describe{ -path to the directory where log files will be created.\item{default: }{\preformatted{file.path(normalize_path(tempdir()), "log_autovalidateutils")}} -\item{option: }{autovalidateutils.log_output} -\item{envvar: }{AUTOVALIDATEUTILS_LOG_OUTPUT (evaluated if possible, raw string otherwise)} -}} - -\item{original_libpaths}{\describe{ -Vector storing original .libPaths before the vector was -altered by avu_install function. It is always overwritten during -autovalidateutils runtime.\item{default: }{\preformatted{NULL}} -\item{option: }{autovalidateutils.original_libpaths} -\item{envvar: }{AUTOVALIDATEUTILS_ORIGINAL_LIBPATHS (evaluated if possible, raw string otherwise)} -}} - -\item{lib.loc}{\describe{ -Character vector describing the location of R library trees to search -through. It will be passed to installed.packages() while deriving whether all -required dependencies are installed. -Defaults to c(.Library, .Library.site).\item{default: }{\preformatted{c(.Library, .Library.site)}} -\item{option: }{autovalidateutils.lib.loc} -\item{envvar: }{AUTOVALIDATEUTILS_LIB_LOC (evaluated if possible, raw string otherwise)} -}} - -\item{clear_description}{\describe{ -Logical value whether all non-utf8 characters should be removed from -the DESCRIPTION value. This is to avoid potential erros that might -occure when installing the package from the source.\item{default: }{\preformatted{FALSE}} -\item{option: }{autovalidateutils.clear_description} -\item{envvar: }{AUTOVALIDATEUTILS_CLEAR_DESCRIPTION (TRUE if one of 'TRUE', '1', FALSE otherwise)} -}} - -\item{subprocess_debug}{\describe{ -Logical whether certain functionalities shall be run in a debug mode. Debug -means functions are run in the main process rather that callr::r_vanilla\item{default: }{\preformatted{FALSE}} -\item{option: }{autovalidateutils.subprocess_debug} -\item{envvar: }{AUTOVALIDATEUTILS_SUBPROCESS_DEBUG (TRUE if one of 'TRUE', '1', FALSE otherwise)} -}} - -\item{install_n_workers}{\describe{ -Number of subprocesses used by the checked package for -executing tasks when installing package and dependencies.\item{default: }{\preformatted{20L}} -\item{option: }{autovalidateutils.install_n_workers} -\item{envvar: }{AUTOVALIDATEUTILS_INSTALL_N_WORKERS (evaluated if possible, raw string otherwise)} -}} - -\item{session}{\describe{ -The file path of the session information metadata file, a -yaml-formatted itemization of a few characteristic measures of an R session -environment.\item{default: }{\preformatted{"session.yml"}} -\item{option: }{autovalidateutils.session} -\item{envvar: }{AUTOVALIDATEUTILS_SESSION (evaluated if possible, raw string otherwise)} -}} - -\item{description}{\describe{ -The file path of the \code{DESCRIPTION} file contents, written out to -a plain text, yaml-formatted file.\item{default: }{\preformatted{"description.yml"}} -\item{option: }{autovalidateutils.description} -\item{envvar: }{AUTOVALIDATEUTILS_DESCRIPTION (evaluated if possible, raw string otherwise)} -}} - -\item{news}{\describe{ -The file path of the \code{NEWS} (or \code{NEWS.md}) file contents. If the \code{NEWS} file -is not already markdown formatted, it will be converted into a preformatted -markdown code block to be embedded in an \code{autovalidate} report.\item{default: }{\preformatted{"news.md"}} -\item{option: }{autovalidateutils.news} -\item{envvar: }{AUTOVALIDATEUTILS_NEWS (evaluated if possible, raw string otherwise)} -}} - -\item{conditions}{\describe{ -The file path of the file to which conditions should be emitted. They are -logged in yaml format, which is later read by \code{autovalidate} to -re-emit them as \code{autovalidate} checks and trigger failures when applicable\item{default: }{\preformatted{"conditions.yml"}} -\item{option: }{autovalidateutils.conditions} -\item{envvar: }{AUTOVALIDATEUTILS_CONDITIONS (evaluated if possible, raw string otherwise)} -}} - -\item{build_binaries}{\describe{ -Logical whether binary source of the package should be compiled during -validation.\item{default: }{\preformatted{FALSE}} -\item{option: }{autovalidateutils.build_binaries} -\item{envvar: }{AUTOVALIDATEUTILS_BUILD_BINARIES (TRUE if one of 'TRUE', '1', FALSE otherwise)} -}} - -\item{generalize_sources}{\describe{ -Logical whether sources produced during validation should be renamed to -general 'package_binary.tgz/tar.gz/zip' and 'package_source.tar.gz'.\item{default: }{\preformatted{FALSE}} -\item{option: }{autovalidateutils.generalize_sources} -\item{envvar: }{AUTOVALIDATEUTILS_GENERALIZE_SOURCES (TRUE if one of 'TRUE', '1', FALSE otherwise)} -}} - -\item{steps}{\describe{ -A listing of autovalidateutils steps to perform. Either a \code{character} vector -or \code{list}. Alternatively, the vector or list may consist of modifications -to a listing of all steps, which must be prefixed by \code{-} (for example, -\code{-write_revdep_check}, which will use all steps except reverse dependency -checks).\item{default: }{\preformatted{c("-write_checked")}} -\item{option: }{autovalidateutils.steps} -\item{envvar: }{AUTOVALIDATEUTILS_STEPS (evaluated if possible, raw string otherwise)} -}} - -\item{installed_packages}{\describe{ -The name of the installed packages json file. It keeps track of -the information about which packages were installed to the environemnt -and their versions. File will be written to the log_output directory\item{default: }{\preformatted{"installed_packages.json"}} -\item{option: }{autovalidateutils.installed_packages} -\item{envvar: }{AUTOVALIDATEUTILS_INSTALLED_PACKAGES (evaluated if possible, raw string otherwise)} -}} - -\item{use_remotes}{\describe{ -Logical flag or named character mapping dependency types to the mechanism of -handling remotes, one of "allow", "prefer" or "disallow". "allow" -option means that the remote sources are allowed but will not take precedence -over other standard sources if both available. "prefer" means allow and -overwrite standard sources while "disallow" stands for skipping remote -sources at all. If no value is provided for a dependency type it is -considered to be "disallow". Can also be set to TRUE to "prefer" all or -FALSE to "disallow all.\item{default: }{\preformatted{c(Depends = "disallow", Imports = "disallow", LinkingTo = "disallow", - Suggests = "allow", Enhances = "allow")}} -\item{option: }{autovalidateutils.use_remotes} -\item{envvar: }{AUTOVALIDATEUTILS_USE_REMOTES (evaluated if possible, raw string otherwise)} -}} - -\item{version_control}{\describe{ -The file path to which package version control metadata -should be captured.\item{default: }{\preformatted{"version_control.yml"}} -\item{option: }{autovalidateutils.version_control} -\item{envvar: }{AUTOVALIDATEUTILS_VERSION_CONTROL (evaluated if possible, raw string otherwise)} -}} - -\item{version_control.md5}{\describe{ -When a source control hash can't be derived from -the target directory, this option will be used to populate version control -metadata. This is of particular interest when the source code has been -extracted from a tar.gz package bundle. In this case, the md5 hash should -reflect the hash of the originating package bundle.\item{default: }{\preformatted{NULL}} -\item{option: }{autovalidateutils.version_control.md5} -\item{envvar: }{AUTOVALIDATEUTILS_VERSION_CONTROL_MD5 (evaluated if possible, raw string otherwise)} -}} - -\item{version_control.url}{\describe{ -When a source control origin can't be derived from -the target directory, this option will be used to populate version control -metadata. This is of particular interest when the source code has been -extracted from a tar.gz package bundle. In this case, the url should -reflect the url from which the originating package bundle was downloaded.\item{default: }{\preformatted{NULL}} -\item{option: }{autovalidateutils.version_control.url} -\item{envvar: }{AUTOVALIDATEUTILS_VERSION_CONTROL_URL (evaluated if possible, raw string otherwise)} -}} - -\item{vulnerabilities}{\describe{ -The file path to which metadata reagarding possible package's -vulnerabilities should be captured.\item{default: }{\preformatted{"vulnerabilities.yml"}} -\item{option: }{autovalidateutils.vulnerabilities} -\item{envvar: }{AUTOVALIDATEUTILS_VULNERABILITIES (evaluated if possible, raw string otherwise)} -}} - -\item{r_cmd_check}{\describe{ -The file path to which \verb{R CMD check} results should be written. -Contents are written in yaml format.\item{default: }{\preformatted{"r_cmd_check.yml"}} -\item{option: }{autovalidateutils.r_cmd_check} -\item{envvar: }{AUTOVALIDATEUTILS_R_CMD_CHECK (evaluated if possible, raw string otherwise)} -}} - -\item{r_cmd_check_variables}{\describe{ -The named character vector of environmental variables, -that will be passed to the \code{withr::with_envvar} function and used to execute -rcmdcheck::rcmdcheck. It can also be a single keyword, either 'cran' or -'internal' that will result in using predefined set of variables.\item{default: }{\preformatted{"internal"}} -\item{option: }{autovalidateutils.r_cmd_check_variables} -\item{envvar: }{AUTOVALIDATEUTILS_R_CMD_CHECK_VARIABLES (evaluated if possible, raw string otherwise)} -}} - -\item{r_cmd_check_clean_tests}{\describe{ -Logical flag whether the \if{html}{\out{}}.Rcheck/\if{html}{\out{}}/tests -directory should be cleared by removing all the directories in it\item{default: }{\preformatted{FALSE}} -\item{option: }{autovalidateutils.r_cmd_check_clean_tests} -\item{envvar: }{AUTOVALIDATEUTILS_R_CMD_CHECK_CLEAN_TESTS (TRUE if one of 'TRUE', '1', FALSE otherwise)} -}} - -\item{check_dir}{\describe{ -The directory R CMD check results should be written to -(.tag.gz, .Rcheck).\item{default: }{\preformatted{"check"}} -\item{option: }{autovalidateutils.check_dir} -\item{envvar: }{AUTOVALIDATEUTILS_CHECK_DIR (evaluated if possible, raw string otherwise)} -}} - -\item{sonarqube}{\describe{ -The file path in which to record a sonarqube xml coverage output file.\item{default: }{\preformatted{file.path("coverage", "sonarqube.xml")}} -\item{option: }{autovalidateutils.sonarqube} -\item{envvar: }{AUTOVALIDATEUTILS_SONARQUBE (evaluated if possible, raw string otherwise)} -}} - -\item{cov_report}{\describe{ -The file path in which to save coverage .html report.\item{default: }{\preformatted{file.path("coverage", "cov_report.html")}} -\item{option: }{autovalidateutils.cov_report} -\item{envvar: }{AUTOVALIDATEUTILS_COV_REPORT (evaluated if possible, raw string otherwise)} -}} - -\item{skip_cov_report}{\describe{ -Logical whether interactive coverage report calculation shall be skipped\item{default: }{\preformatted{FALSE}} -\item{option: }{autovalidateutils.skip_cov_report} -\item{envvar: }{AUTOVALIDATEUTILS_SKIP_COV_REPORT (TRUE if one of 'TRUE', '1', FALSE otherwise)} -}} - -\item{cov_table}{\describe{ -The file path in which to save markdown table with coverage percentage for -each file.\item{default: }{\preformatted{file.path("coverage", "cov_table.md")}} -\item{option: }{autovalidateutils.cov_table} -\item{envvar: }{AUTOVALIDATEUTILS_COV_TABLE (evaluated if possible, raw string otherwise)} -}} - -\item{cov_logs}{\describe{ -Directory where logs gathered during coverage execution are saved.\item{default: }{\preformatted{file.path("coverage", "logs")}} -\item{option: }{autovalidateutils.cov_logs} -\item{envvar: }{AUTOVALIDATEUTILS_COV_LOGS (evaluated if possible, raw string otherwise)} -}} - -\item{testing_session}{\describe{ -The file path of the yml parsed sessionInfo file that -captures the environment in which units tests were executed.\item{default: }{\preformatted{file.path("coverage", "testing_session.yml")}} -\item{option: }{autovalidateutils.testing_session} -\item{envvar: }{AUTOVALIDATEUTILS_TESTING_SESSION (evaluated if possible, raw string otherwise)} -}} - -\item{coverage_threshold}{\describe{ -The numeric value of the minimal code coverage percentage -required for package to be validated\item{default: }{\preformatted{80}} -\item{option: }{autovalidateutils.coverage_threshold} -\item{envvar: }{AUTOVALIDATEUTILS_COVERAGE_THRESHOLD (evaluated if possible, raw string otherwise)} -}} - -\item{reuse_check_source}{\describe{ -Logical whether the source generated when running -R CMD check should be used when calcualting coverage code coverage instead -of the raw source.\item{default: }{\preformatted{TRUE}} -\item{option: }{autovalidateutils.reuse_check_source} -\item{envvar: }{AUTOVALIDATEUTILS_REUSE_CHECK_SOURCE (TRUE if one of 'TRUE', '1', FALSE otherwise)} -}} - -\item{documentation}{\describe{ -The directory path into which R documentation should -be written as markdown-formatted files. Files will be named with a prefixed -index according to their lexical Rd name sorting. This index corresponds to -the requirements index in the \code{mapper_file} option, and is used by -\code{autovalidate} to generate a traceability matrix.\item{default: }{\preformatted{file.path("traceability_matrix", "documentation")}} -\item{option: }{autovalidateutils.documentation} -\item{envvar: }{AUTOVALIDATEUTILS_DOCUMENTATION (evaluated if possible, raw string otherwise)} -}} - -\item{documentation_fragments}{\describe{ -A \code{character} vector of the types of \code{Rd} fragments -to be included in the resulting documentation markdown files, or \code{NULL} to -include all \code{Rd} contents.\item{default: }{\preformatted{c("title", "usage", "description", "details")}} -\item{option: }{autovalidateutils.documentation_fragments} -\item{envvar: }{AUTOVALIDATEUTILS_DOCUMENTATION_FRAGMENTS (evaluated if possible, raw string otherwise)} -}} - -\item{rd_transform}{\describe{ -A function which will be applied to the raw rd object before -converting it to the markdown file. Identity function by default.\item{default: }{\preformatted{function(x) x}} -\item{option: }{autovalidateutils.rd_transform} -\item{envvar: }{AUTOVALIDATEUTILS_RD_TRANSFORM (evaluated if possible, raw string otherwise)} -}} - -\item{mapper}{\describe{ -The file path into which an \code{autovalidate}-style mapper file should -be written.\item{default: }{\preformatted{file.path("traceability_matrix", "mapper.yml")}} -\item{option: }{autovalidateutils.mapper} -\item{envvar: }{AUTOVALIDATEUTILS_MAPPER (evaluated if possible, raw string otherwise)} -}} - -\item{mapper_defaults}{\describe{ -If \code{TRUE}, default values will be injected into the -autovalidate mapper.yml file for fields that have no direct analog in a -typical testthat-generated junit.xml file. This includes the \code{author}, -\code{reviewer} and \code{review_date}.\item{default: }{\preformatted{TRUE}} -\item{option: }{autovalidateutils.mapper_defaults} -\item{envvar: }{AUTOVALIDATEUTILS_MAPPER_DEFAULTS (TRUE if one of 'TRUE', '1', FALSE otherwise)} -}} - -\item{add_missing_traces}{\describe{ -Logical if covr traces which are missing in the testresults file should be -added to the JUnit\item{default: }{\preformatted{TRUE}} -\item{option: }{autovalidateutils.add_missing_traces} -\item{envvar: }{AUTOVALIDATEUTILS_ADD_MISSING_TRACES (TRUE if one of 'TRUE', '1', FALSE otherwise)} -}} - -\item{test_exec_log}{\describe{ -The file path of a file in which console output generated during test -execution.\item{default: }{\preformatted{"tests.Rout"}} -\item{option: }{autovalidateutils.test_exec_log} -\item{envvar: }{AUTOVALIDATEUTILS_TEST_EXEC_LOG (evaluated if possible, raw string otherwise)} -}} - -\item{junit}{\describe{ -The file path into which a JUnit-style xml test results -file should be written.\item{default: }{\preformatted{file.path("traceability_matrix", "junit.xml")}} -\item{option: }{autovalidateutils.junit} -\item{envvar: }{AUTOVALIDATEUTILS_JUNIT (evaluated if possible, raw string otherwise)} -}} - -\item{junit_reporter}{\describe{ -A quoted expression, producing a \code{testthat} reporter. The -reporter's initialization is expected to match the signature of -\code{testthat::JunitReporter$new()}, notably expecting a \code{file} argument to -use as the output \code{junit.xml} filepath.\item{default: }{\preformatted{quote(testthat::JunitReporter)}} -\item{option: }{autovalidateutils.junit_reporter} -\item{envvar: }{AUTOVALIDATEUTILS_JUNIT_REPORTER (evaluated if possible, raw string otherwise)} -}} - -\item{use_testthat}{\describe{ -Whether testthat infrastructure should be available within -autovalidateutils. The actual usage will be determined based on the -uses_testthat function output. Defaults to \code{TRUE}.\item{default: }{\preformatted{TRUE}} -\item{option: }{autovalidateutils.use_testthat} -\item{envvar: }{AUTOVALIDATEUTILS_USE_TESTTHAT (TRUE if one of 'TRUE', '1', FALSE otherwise)} -}} - -\item{inst_deps}{\describe{ -Character vector of dependency types. All packages with those types -are permitted to be installed from any available repo during validation. -Defaults to only 'Suggests'\item{default: }{\preformatted{"Suggests"}} -\item{option: }{autovalidateutils.inst_deps} -\item{envvar: }{AUTOVALIDATEUTILS_INST_DEPS (evaluated if possible, raw string otherwise)} -}} - -\item{req_deps}{\describe{ -Character vector of dependecies types. All packages with those types -are required to be installed before the validation can start.\item{default: }{\preformatted{c("Depends", "Imports", "LinkingTo")}} -\item{option: }{autovalidateutils.req_deps} -\item{envvar: }{AUTOVALIDATEUTILS_REQ_DEPS (evaluated if possible, raw string otherwise)} -}} - -\item{upgrade_deps}{\describe{ -Whether packages should be upgraded if higher version than installed is -available. Keep NULL to use the default autovalidateutils behavior -which is upgrading for DEP_LIB_CORE and not upgrading for DEP_LIB_OPTIONAL.\item{default: }{\preformatted{NULL}} -\item{option: }{autovalidateutils.upgrade_deps} -\item{envvar: }{AUTOVALIDATEUTILS_UPGRADE_DEPS (evaluated if possible, raw string otherwise)} -}} - -\item{suggests_repos}{\describe{ -Character vector of libraries that will be appended to -standard repos during installation of suggested packages.\item{default: }{\preformatted{c("https://cran.r-project.org/")}} -\item{option: }{autovalidateutils.suggests_repos} -\item{envvar: }{AUTOVALIDATEUTILS_SUGGESTS_REPOS (evaluated if possible, raw string otherwise)} -}} - -\item{revdep_repos}{\describe{ -Repository used for identyfying reverse dependencies. It should -be the same as \code{repos} unless using linux binaries, then it should be -repo URL without binaires part.\item{default: }{\preformatted{getOption("repos")}} -\item{option: }{autovalidateutils.revdep_repos} -\item{envvar: }{AUTOVALIDATEUTILS_REVDEP_REPOS (evaluated if possible, raw string otherwise)} -}} - -\item{revdep_n_workers}{\describe{ -Number of subprocesses used by the checked package for -executing tasks when running reverse dependecy check.\item{default: }{\preformatted{20L}} -\item{option: }{autovalidateutils.revdep_n_workers} -\item{envvar: }{AUTOVALIDATEUTILS_REVDEP_N_WORKERS (evaluated if possible, raw string otherwise)} -}} - -\item{revdep_clean_sources}{\describe{ -Logical flag whether the sources of reverse dependencies should be removed.\item{default: }{\preformatted{TRUE}} -\item{option: }{autovalidateutils.revdep_clean_sources} -\item{envvar: }{AUTOVALIDATEUTILS_REVDEP_CLEAN_SOURCES (TRUE if one of 'TRUE', '1', FALSE otherwise)} -}} - -\item{revdep_clean_library}{\describe{ -Logical whether the source of the target package should be removed after -completing checks.\item{default: }{\preformatted{TRUE}} -\item{option: }{autovalidateutils.revdep_clean_library} -\item{envvar: }{AUTOVALIDATEUTILS_REVDEP_CLEAN_LIBRARY (TRUE if one of 'TRUE', '1', FALSE otherwise)} -}} - -\item{checked_debug}{\describe{ -Logical whether checked should use detailed reporter which reports every task -to allow debuging of the checked state.\item{default: }{\preformatted{FALSE}} -\item{option: }{autovalidateutils.checked_debug} -\item{envvar: }{AUTOVALIDATEUTILS_CHECKED_DEBUG (TRUE if one of 'TRUE', '1', FALSE otherwise)} -}} - \item{tty_tick_interval}{\describe{ tty refresh interval when reporting results in milliseconds\item{default: }{\preformatted{0.1}} \item{option: }{checked.tty_tick_interval} -\item{envvar: }{CHECKED_TTY_TICK_INTERVAL (evaluated if possible, raw string otherwise)} +\item{envvar: }{R_CHECKED_TTY_TICK_INTERVAL (evaluated if possible, raw string otherwise)} }} \item{tty_default_height}{\describe{ deafult tty height used for the ANSI reporter. Used only if correct values could not be acquired with system('tput lines')\item{default: }{\preformatted{50}} \item{option: }{checked.tty_default_height} -\item{envvar: }{CHECKED_TTY_DEFAULT_HEIGHT (evaluated if possible, raw string otherwise)} +\item{envvar: }{R_CHECKED_TTY_DEFAULT_HEIGHT (evaluated if possible, raw string otherwise)} }} \item{proactive_gc}{\describe{ @@ -455,7 +41,7 @@ is recommended to be used for designs with many sub-processes required as native garbage collection can lag leading to memory issues. Disable only when maximum prefromance is required and memory is not the issue.\item{default: }{\preformatted{TRUE}} \item{option: }{checked.proactive_gc} -\item{envvar: }{CHECKED_PROACTIVE_GC (evaluated if possible, raw string otherwise)} +\item{envvar: }{R_CHECKED_PROACTIVE_GC (evaluated if possible, raw string otherwise)} }} \item{results_error_on}{\describe{ @@ -464,7 +50,7 @@ are discovered when generating results. "never" means that no errors are thrown. If "issues" then errors are emitted only on issues, whereas "potential issues" stands for error on both issues and potential issues.\item{default: }{\preformatted{"never"}} \item{option: }{checked.results_error_on} -\item{envvar: }{CHECKED_RESULTS_ERROR_ON (evaluated if possible, raw string otherwise)} +\item{envvar: }{R_CHECKED_RESULTS_ERROR_ON (evaluated if possible, raw string otherwise)} }} \item{results_keep}{\describe{ @@ -473,7 +59,7 @@ character vector indicating which packages should be included in the results. with issues identified, whereas "potential_issues" stands for keeping packages with both "issues" and "potential_issues".\item{default: }{\preformatted{"all"}} \item{option: }{checked.results_keep} -\item{envvar: }{CHECKED_RESULTS_KEEP (evaluated if possible, raw string otherwise)} +\item{envvar: }{R_CHECKED_RESULTS_KEEP (evaluated if possible, raw string otherwise)} }} \item{restore}{\describe{ @@ -481,7 +67,7 @@ packages with both "issues" and "potential_issues".\item{default: }{\preformatte running checks. If \code{FALSE}, an attempt will me made to restore previous progress from the same \code{output}\item{default: }{\preformatted{NA}} \item{option: }{checked.restore} -\item{envvar: }{CHECKED_RESTORE (evaluated if possible, raw string otherwise)} +\item{envvar: }{R_CHECKED_RESTORE (evaluated if possible, raw string otherwise)} }} \item{add_remotes}{\describe{ @@ -489,7 +75,7 @@ progress from the same \code{output}\item{default: }{\preformatted{NA}} should be scanned for packages in the \code{remotes} field and added while constrocuting a plan \code{task_grap}\item{default: }{\preformatted{TRUE}} \item{option: }{checked.add_remotes} -\item{envvar: }{CHECKED_ADD_REMOTES (evaluated if possible, raw string otherwise)} +\item{envvar: }{R_CHECKED_ADD_REMOTES (evaluated if possible, raw string otherwise)} }} \item{check_envvars}{\describe{ @@ -498,40 +84,40 @@ the R CMD check.\item{default: }{\preformatted{c(`_R_CHECK_FORCE_SUGGESTS_` = "f `_R_CHECK_SYSTEM_CLOCK_` = "false", `_R_CHECK_SUGGESTS_ONLY_` = "true", `_R_CHECK_CRAN_INCOMING_` = "false")}} \item{option: }{checked.check_envvars} -\item{envvar: }{CHECKED_CHECK_ENVVARS (evaluated if possible, raw string otherwise)} +\item{envvar: }{R_CHECKED_CHECK_ENVVARS (evaluated if possible, raw string otherwise)} }} \item{check_build_args}{\describe{ \code{character} vector of args passed to the R CMD build.\item{default: }{\preformatted{c("--no-build-vignettes", "--no-manual")}} \item{option: }{checked.check_build_args} -\item{envvar: }{CHECKED_CHECK_BUILD_ARGS (space-separated R CMD build flags)} +\item{envvar: }{R_CHECKED_CHECK_BUILD_ARGS (space-separated R CMD build flags)} }} \item{check_args}{\describe{ \code{character} vector of args passed to the R CMD check.\item{default: }{\preformatted{c("--timings", "--ignore-vignettes", "--no-manual", "--as-cran")}} \item{option: }{checked.check_args} -\item{envvar: }{CHECKED_CHECK_ARGS (space-separated R CMD check flags)} +\item{envvar: }{R_CHECKED_CHECK_ARGS (space-separated R CMD check flags)} }} \item{install_envvars}{\describe{ named \code{character} vector of environment variables to use during the package installation.\item{default: }{\preformatted{callr::rcmd_safe_env()}} \item{option: }{checked.install_envvars} -\item{envvar: }{CHECKED_INSTALL_ENVVARS (evaluated if possible, raw string otherwise)} +\item{envvar: }{R_CHECKED_INSTALL_ENVVARS (evaluated if possible, raw string otherwise)} }} \item{install_system_profile}{\describe{ \code{logical} used as \code{sytem_profile} parameter passed to the \code{callr::r_bg()} function used to install packages\item{default: }{\preformatted{FALSE}} \item{option: }{checked.install_system_profile} -\item{envvar: }{CHECKED_INSTALL_SYSTEM_PROFILE (evaluated if possible, raw string otherwise)} +\item{envvar: }{R_CHECKED_INSTALL_SYSTEM_PROFILE (evaluated if possible, raw string otherwise)} }} \item{install_user_profile}{\describe{ value used as \code{user_profile} parameter passed to the \code{callr::r_bg()} function used to install packages\item{default: }{\preformatted{"project"}} \item{option: }{checked.install_user_profile} -\item{envvar: }{CHECKED_INSTALL_USER_PROFILE (evaluated if possible, raw string otherwise)} +\item{envvar: }{R_CHECKED_INSTALL_USER_PROFILE (evaluated if possible, raw string otherwise)} }} } diff --git a/man/options_params.Rd b/man/options_params.Rd index 7b44e37..4402e65 100644 --- a/man/options_params.Rd +++ b/man/options_params.Rd @@ -4,248 +4,51 @@ \alias{options_params} \title{Checked Options} \arguments{ -\item{build_binaries}{Logical whether binary source of the package should be compiled during -validation. (Defaults to \code{FALSE}, overwritable using option 'autovalidateutils.build_binaries' or environment variable 'AUTOVALIDATEUTILS_BUILD_BINARIES')} - -\item{check_build_args}{\code{character} vector of args passed to the R CMD build. (Defaults to \code{c("--no-build-vignettes", "--no-manual")}, overwritable using option 'checked.check_build_args' or environment variable 'CHECKED_CHECK_BUILD_ARGS')} - -\item{add_remotes}{\code{logical} indicating whether origins inheriting from \code{pkg_origin_local}, -should be scanned for packages in the \code{remotes} field and added while -constrocuting a plan \code{task_grap} (Defaults to \code{TRUE}, overwritable using option 'checked.add_remotes' or environment variable 'CHECKED_ADD_REMOTES')} - -\item{lib.loc}{Character vector describing the location of R library trees to search -through. It will be passed to installed.packages() while deriving whether all -required dependencies are installed. -Defaults to c(.Library, .Library.site). (Defaults to \code{c(.Library, .Library.site)}, overwritable using option 'autovalidateutils.lib.loc' or environment variable 'AUTOVALIDATEUTILS_LIB_LOC')} - -\item{tty_tick_interval}{tty refresh interval when reporting results in milliseconds (Defaults to \code{0.1}, overwritable using option 'checked.tty_tick_interval' or environment variable 'CHECKED_TTY_TICK_INTERVAL')} - -\item{checked_debug}{Logical whether checked should use detailed reporter which reports every task -to allow debuging of the checked state. (Defaults to \code{FALSE}, overwritable using option 'autovalidateutils.checked_debug' or environment variable 'AUTOVALIDATEUTILS_CHECKED_DEBUG')} - \item{proactive_gc}{\code{logical}, indicating whether additional garbage collection should be performed before starting a new task, if at least one process recently finalized. This can cause the checker to orchestrate tasks slower but is recommended to be used for designs with many sub-processes required as native garbage collection can lag leading to memory issues. Disable only -when maximum prefromance is required and memory is not the issue. (Defaults to \code{TRUE}, overwritable using option 'checked.proactive_gc' or environment variable 'CHECKED_PROACTIVE_GC')} - -\item{install_user_profile}{value used as \code{user_profile} parameter passed to the \code{callr::r_bg()} -function used to install packages (Defaults to \code{"project"}, overwritable using option 'checked.install_user_profile' or environment variable 'CHECKED_INSTALL_USER_PROFILE')} - -\item{use_testthat}{Whether testthat infrastructure should be available within -autovalidateutils. The actual usage will be determined based on the -uses_testthat function output. Defaults to \code{TRUE}. (Defaults to \code{TRUE}, overwritable using option 'autovalidateutils.use_testthat' or environment variable 'AUTOVALIDATEUTILS_USE_TESTTHAT')} - -\item{vulnerabilities}{The file path to which metadata reagarding possible package's -vulnerabilities should be captured. (Defaults to \code{"vulnerabilities.yml"}, overwritable using option 'autovalidateutils.vulnerabilities' or environment variable 'AUTOVALIDATEUTILS_VULNERABILITIES')} - -\item{news}{The file path of the \code{NEWS} (or \code{NEWS.md}) file contents. If the \code{NEWS} file -is not already markdown formatted, it will be converted into a preformatted -markdown code block to be embedded in an \code{autovalidate} report. (Defaults to \code{"news.md"}, overwritable using option 'autovalidateutils.news' or environment variable 'AUTOVALIDATEUTILS_NEWS')} - -\item{add_missing_traces}{Logical if covr traces which are missing in the testresults file should be -added to the JUnit (Defaults to \code{TRUE}, overwritable using option 'autovalidateutils.add_missing_traces' or environment variable 'AUTOVALIDATEUTILS_ADD_MISSING_TRACES')} - -\item{results_keep}{character vector indicating which packages should be included in the results. -"all" means that all packages are kept. If "issues" then only packages -with issues identified, whereas "potential_issues" stands for keeping -packages with both "issues" and "potential_issues". (Defaults to \code{"all"}, overwritable using option 'checked.results_keep' or environment variable 'CHECKED_RESULTS_KEEP')} - -\item{installed_packages}{The name of the installed packages json file. It keeps track of -the information about which packages were installed to the environemnt -and their versions. File will be written to the log_output directory (Defaults to \code{"installed_packages.json"}, overwritable using option 'autovalidateutils.installed_packages' or environment variable 'AUTOVALIDATEUTILS_INSTALLED_PACKAGES')} - -\item{junit}{The file path into which a JUnit-style xml test results -file should be written. (Defaults to \code{file.path("traceability_matrix", "junit.xml")}, overwritable using option 'autovalidateutils.junit' or environment variable 'AUTOVALIDATEUTILS_JUNIT')} - -\item{output}{A parent directory for all non-relative output files. Defaults to the -current working directory. (Defaults to \code{file.path(normalize_path(tempdir()), "autovalidateutils")}, overwritable using option 'autovalidateutils.output' or environment variable 'AUTOVALIDATEUTILS_OUTPUT')} +when maximum prefromance is required and memory is not the issue. (Defaults to \code{TRUE}, overwritable using option 'checked.proactive_gc' or environment variable 'R_CHECKED_PROACTIVE_GC')} \item{results_error_on}{character vector indicating whether R error should be thrown when issues are discovered when generating results. "never" means that no errors are thrown. If "issues" then errors are emitted only on issues, whereas -"potential issues" stands for error on both issues and potential issues. (Defaults to \code{"never"}, overwritable using option 'checked.results_error_on' or environment variable 'CHECKED_RESULTS_ERROR_ON')} - -\item{session}{The file path of the session information metadata file, a -yaml-formatted itemization of a few characteristic measures of an R session -environment. (Defaults to \code{"session.yml"}, overwritable using option 'autovalidateutils.session' or environment variable 'AUTOVALIDATEUTILS_SESSION')} - -\item{version_control}{The file path to which package version control metadata -should be captured. (Defaults to \code{"version_control.yml"}, overwritable using option 'autovalidateutils.version_control' or environment variable 'AUTOVALIDATEUTILS_VERSION_CONTROL')} - -\item{timeout}{A difftime object or a numeric value with a real number indicating -number of seconds that should pass before certain calls are timed out. Set to -Inf to turn off timeout. By deafult set to difftime 14 hours. (Defaults to \code{as.difftime(14, units = "hours")}, overwritable using option 'autovalidateutils.timeout' or environment variable 'AUTOVALIDATEUTILS_TIMEOUT')} - -\item{revdep_repos}{Repository used for identyfying reverse dependencies. It should -be the same as \code{repos} unless using linux binaries, then it should be -repo URL without binaires part. (Defaults to \code{getOption("repos")}, overwritable using option 'autovalidateutils.revdep_repos' or environment variable 'AUTOVALIDATEUTILS_REVDEP_REPOS')} +"potential issues" stands for error on both issues and potential issues. (Defaults to \code{"never"}, overwritable using option 'checked.results_error_on' or environment variable 'R_CHECKED_RESULTS_ERROR_ON')} \item{install_envvars}{named \code{character} vector of environment variables to use during -the package installation. (Defaults to \code{callr::rcmd_safe_env()}, overwritable using option 'checked.install_envvars' or environment variable 'CHECKED_INSTALL_ENVVARS')} - -\item{description}{The file path of the \code{DESCRIPTION} file contents, written out to -a plain text, yaml-formatted file. (Defaults to \code{"description.yml"}, overwritable using option 'autovalidateutils.description' or environment variable 'AUTOVALIDATEUTILS_DESCRIPTION')} - -\item{cov_table}{The file path in which to save markdown table with coverage percentage for -each file. (Defaults to \code{file.path("coverage", "cov_table.md")}, overwritable using option 'autovalidateutils.cov_table' or environment variable 'AUTOVALIDATEUTILS_COV_TABLE')} +the package installation. (Defaults to \code{callr::rcmd_safe_env()}, overwritable using option 'checked.install_envvars' or environment variable 'R_CHECKED_INSTALL_ENVVARS')} -\item{revdep_clean_sources}{Logical flag whether the sources of reverse dependencies should be removed. (Defaults to \code{TRUE}, overwritable using option 'autovalidateutils.revdep_clean_sources' or environment variable 'AUTOVALIDATEUTILS_REVDEP_CLEAN_SOURCES')} - -\item{generalize_sources}{Logical whether sources produced during validation should be renamed to -general 'package_binary.tgz/tar.gz/zip' and 'package_source.tar.gz'. (Defaults to \code{FALSE}, overwritable using option 'autovalidateutils.generalize_sources' or environment variable 'AUTOVALIDATEUTILS_GENERALIZE_SOURCES')} - -\item{r_cmd_check_variables}{The named character vector of environmental variables, -that will be passed to the \code{withr::with_envvar} function and used to execute -rcmdcheck::rcmdcheck. It can also be a single keyword, either 'cran' or -'internal' that will result in using predefined set of variables. (Defaults to \code{"internal"}, overwritable using option 'autovalidateutils.r_cmd_check_variables' or environment variable 'AUTOVALIDATEUTILS_R_CMD_CHECK_VARIABLES')} - -\item{tty_default_height}{deafult tty height used for the ANSI reporter. Used only -if correct values could not be acquired with system('tput lines') (Defaults to \code{50}, overwritable using option 'checked.tty_default_height' or environment variable 'CHECKED_TTY_DEFAULT_HEIGHT')} - -\item{r_cmd_check}{The file path to which \verb{R CMD check} results should be written. -Contents are written in yaml format. (Defaults to \code{"r_cmd_check.yml"}, overwritable using option 'autovalidateutils.r_cmd_check' or environment variable 'AUTOVALIDATEUTILS_R_CMD_CHECK')} +\item{check_args}{\code{character} vector of args passed to the R CMD check. (Defaults to \code{c("--timings", "--ignore-vignettes", "--no-manual", "--as-cran")}, overwritable using option 'checked.check_args' or environment variable 'R_CHECKED_CHECK_ARGS')} \item{install_system_profile}{\code{logical} used as \code{sytem_profile} parameter passed to the \code{callr::r_bg()} -function used to install packages (Defaults to \code{FALSE}, overwritable using option 'checked.install_system_profile' or environment variable 'CHECKED_INSTALL_SYSTEM_PROFILE')} - -\item{coverage_threshold}{The numeric value of the minimal code coverage percentage -required for package to be validated (Defaults to \code{80}, overwritable using option 'autovalidateutils.coverage_threshold' or environment variable 'AUTOVALIDATEUTILS_COVERAGE_THRESHOLD')} - -\item{check_envvars}{named \code{character} vector of environment variables to use during -the R CMD check. (Defaults to \verb{c(}\emph{R_CHECK_FORCE_SUGGESTS}\verb{= "false",}\emph{R_CHECK_RD_XREFS}\verb{= "false", ; }\emph{R_CHECK_SYSTEM_CLOCK}\verb{= "false",}\emph{R_CHECK_SUGGESTS_ONLY}\verb{= "true", ; }\emph{R_CHECK_CRAN_INCOMING}\verb{ = "false")}, overwritable using option 'checked.check_envvars' or environment variable 'CHECKED_CHECK_ENVVARS')} +function used to install packages (Defaults to \code{FALSE}, overwritable using option 'checked.install_system_profile' or environment variable 'R_CHECKED_INSTALL_SYSTEM_PROFILE')} -\item{documentation_fragments}{A \code{character} vector of the types of \code{Rd} fragments -to be included in the resulting documentation markdown files, or \code{NULL} to -include all \code{Rd} contents. (Defaults to \code{c("title", "usage", "description", "details")}, overwritable using option 'autovalidateutils.documentation_fragments' or environment variable 'AUTOVALIDATEUTILS_DOCUMENTATION_FRAGMENTS')} - -\item{inst_deps}{Character vector of dependency types. All packages with those types -are permitted to be installed from any available repo during validation. -Defaults to only 'Suggests' (Defaults to \code{"Suggests"}, overwritable using option 'autovalidateutils.inst_deps' or environment variable 'AUTOVALIDATEUTILS_INST_DEPS')} - -\item{install_n_workers}{Number of subprocesses used by the checked package for -executing tasks when installing package and dependencies. (Defaults to \code{20L}, overwritable using option 'autovalidateutils.install_n_workers' or environment variable 'AUTOVALIDATEUTILS_INSTALL_N_WORKERS')} - -\item{revdep_n_workers}{Number of subprocesses used by the checked package for -executing tasks when running reverse dependecy check. (Defaults to \code{20L}, overwritable using option 'autovalidateutils.revdep_n_workers' or environment variable 'AUTOVALIDATEUTILS_REVDEP_N_WORKERS')} - -\item{req_deps}{Character vector of dependecies types. All packages with those types -are required to be installed before the validation can start. (Defaults to \code{c("Depends", "Imports", "LinkingTo")}, overwritable using option 'autovalidateutils.req_deps' or environment variable 'AUTOVALIDATEUTILS_REQ_DEPS')} - -\item{r_cmd_check_clean_tests}{Logical flag whether the \if{html}{\out{}}.Rcheck/\if{html}{\out{}}/tests -directory should be cleared by removing all the directories in it (Defaults to \code{FALSE}, overwritable using option 'autovalidateutils.r_cmd_check_clean_tests' or environment variable 'AUTOVALIDATEUTILS_R_CMD_CHECK_CLEAN_TESTS')} - -\item{documentation}{The directory path into which R documentation should -be written as markdown-formatted files. Files will be named with a prefixed -index according to their lexical Rd name sorting. This index corresponds to -the requirements index in the \code{mapper_file} option, and is used by -\code{autovalidate} to generate a traceability matrix. (Defaults to \code{file.path("traceability_matrix", "documentation")}, overwritable using option 'autovalidateutils.documentation' or environment variable 'AUTOVALIDATEUTILS_DOCUMENTATION')} - -\item{suggests_repos}{Character vector of libraries that will be appended to -standard repos during installation of suggested packages. (Defaults to \code{c("https://cran.r-project.org/")}, overwritable using option 'autovalidateutils.suggests_repos' or environment variable 'AUTOVALIDATEUTILS_SUGGESTS_REPOS')} - -\item{clean}{Whether directories created by autovaldiateutils in /tmp directory -should be removed. Set to TRUE if you want to save space in your /tmp. Keep -FALSE to maintain all the output in /tmp. Does not affect regular output (Defaults to \code{TRUE}, overwritable using option 'autovalidateutils.clean' or environment variable 'AUTOVALIDATEUTILS_CLEAN')} - -\item{mapper_defaults}{If \code{TRUE}, default values will be injected into the -autovalidate mapper.yml file for fields that have no direct analog in a -typical testthat-generated junit.xml file. This includes the \code{author}, -\code{reviewer} and \code{review_date}. (Defaults to \code{TRUE}, overwritable using option 'autovalidateutils.mapper_defaults' or environment variable 'AUTOVALIDATEUTILS_MAPPER_DEFAULTS')} - -\item{cov_logs}{Directory where logs gathered during coverage execution are saved. (Defaults to \code{file.path("coverage", "logs")}, overwritable using option 'autovalidateutils.cov_logs' or environment variable 'AUTOVALIDATEUTILS_COV_LOGS')} - -\item{cov_report}{The file path in which to save coverage .html report. (Defaults to \code{file.path("coverage", "cov_report.html")}, overwritable using option 'autovalidateutils.cov_report' or environment variable 'AUTOVALIDATEUTILS_COV_REPORT')} - -\item{check_args}{\code{character} vector of args passed to the R CMD check. (Defaults to \code{c("--timings", "--ignore-vignettes", "--no-manual", "--as-cran")}, overwritable using option 'checked.check_args' or environment variable 'CHECKED_CHECK_ARGS')} - -\item{test_exec_log}{The file path of a file in which console output generated during test -execution. (Defaults to \code{"tests.Rout"}, overwritable using option 'autovalidateutils.test_exec_log' or environment variable 'AUTOVALIDATEUTILS_TEST_EXEC_LOG')} - -\item{quiet}{Whether execution should suppress output. When \code{TRUE}, only warnings -are emitted. When \code{FALSE}, a pretty-formatted log is emitted to the -console. (Defaults to \code{FALSE}, overwritable using option 'autovalidateutils.quiet' or environment variable 'AUTOVALIDATEUTILS_QUIET')} - -\item{steps}{A listing of autovalidateutils steps to perform. Either a \code{character} vector -or \code{list}. Alternatively, the vector or list may consist of modifications -to a listing of all steps, which must be prefixed by \code{-} (for example, -\code{-write_revdep_check}, which will use all steps except reverse dependency -checks). (Defaults to \code{c("-write_checked")}, overwritable using option 'autovalidateutils.steps' or environment variable 'AUTOVALIDATEUTILS_STEPS')} - -\item{subprocess_debug}{Logical whether certain functionalities shall be run in a debug mode. Debug -means functions are run in the main process rather that callr::r_vanilla (Defaults to \code{FALSE}, overwritable using option 'autovalidateutils.subprocess_debug' or environment variable 'AUTOVALIDATEUTILS_SUBPROCESS_DEBUG')} - -\item{reuse_check_source}{Logical whether the source generated when running -R CMD check should be used when calcualting coverage code coverage instead -of the raw source. (Defaults to \code{TRUE}, overwritable using option 'autovalidateutils.reuse_check_source' or environment variable 'AUTOVALIDATEUTILS_REUSE_CHECK_SOURCE')} - -\item{version_control.md5}{When a source control hash can't be derived from -the target directory, this option will be used to populate version control -metadata. This is of particular interest when the source code has been -extracted from a tar.gz package bundle. In this case, the md5 hash should -reflect the hash of the originating package bundle. (Defaults to \code{NULL}, overwritable using option 'autovalidateutils.version_control.md5' or environment variable 'AUTOVALIDATEUTILS_VERSION_CONTROL_MD5')} - -\item{upgrade_deps}{Whether packages should be upgraded if higher version than installed is -available. Keep NULL to use the default autovalidateutils behavior -which is upgrading for DEP_LIB_CORE and not upgrading for DEP_LIB_OPTIONAL. (Defaults to \code{NULL}, overwritable using option 'autovalidateutils.upgrade_deps' or environment variable 'AUTOVALIDATEUTILS_UPGRADE_DEPS')} - -\item{testing_session}{The file path of the yml parsed sessionInfo file that -captures the environment in which units tests were executed. (Defaults to \code{file.path("coverage", "testing_session.yml")}, overwritable using option 'autovalidateutils.testing_session' or environment variable 'AUTOVALIDATEUTILS_TESTING_SESSION')} - -\item{original_libpaths}{Vector storing original .libPaths before the vector was -altered by avu_install function. It is always overwritten during -autovalidateutils runtime. (Defaults to \code{NULL}, overwritable using option 'autovalidateutils.original_libpaths' or environment variable 'AUTOVALIDATEUTILS_ORIGINAL_LIBPATHS')} - -\item{sonarqube}{The file path in which to record a sonarqube xml coverage output file. (Defaults to \code{file.path("coverage", "sonarqube.xml")}, overwritable using option 'autovalidateutils.sonarqube' or environment variable 'AUTOVALIDATEUTILS_SONARQUBE')} - -\item{rd_transform}{A function which will be applied to the raw rd object before -converting it to the markdown file. Identity function by default. (Defaults to \code{function(x) x}, overwritable using option 'autovalidateutils.rd_transform' or environment variable 'AUTOVALIDATEUTILS_RD_TRANSFORM')} +\item{results_keep}{character vector indicating which packages should be included in the results. +"all" means that all packages are kept. If "issues" then only packages +with issues identified, whereas "potential_issues" stands for keeping +packages with both "issues" and "potential_issues". (Defaults to \code{"all"}, overwritable using option 'checked.results_keep' or environment variable 'R_CHECKED_RESULTS_KEEP')} -\item{junit_reporter}{A quoted expression, producing a \code{testthat} reporter. The -reporter's initialization is expected to match the signature of -\code{testthat::JunitReporter$new()}, notably expecting a \code{file} argument to -use as the output \code{junit.xml} filepath. (Defaults to \code{quote(testthat::JunitReporter)}, overwritable using option 'autovalidateutils.junit_reporter' or environment variable 'AUTOVALIDATEUTILS_JUNIT_REPORTER')} +\item{add_remotes}{\code{logical} indicating whether origins inheriting from \code{pkg_origin_local}, +should be scanned for packages in the \code{remotes} field and added while +constrocuting a plan \code{task_grap} (Defaults to \code{TRUE}, overwritable using option 'checked.add_remotes' or environment variable 'R_CHECKED_ADD_REMOTES')} -\item{version_control.url}{When a source control origin can't be derived from -the target directory, this option will be used to populate version control -metadata. This is of particular interest when the source code has been -extracted from a tar.gz package bundle. In this case, the url should -reflect the url from which the originating package bundle was downloaded. (Defaults to \code{NULL}, overwritable using option 'autovalidateutils.version_control.url' or environment variable 'AUTOVALIDATEUTILS_VERSION_CONTROL_URL')} +\item{check_envvars}{named \code{character} vector of environment variables to use during +the R CMD check. (Defaults to \verb{c(}\emph{R_CHECK_FORCE_SUGGESTS}\verb{= "false",}\emph{R_CHECK_RD_XREFS}\verb{= "false", ; }\emph{R_CHECK_SYSTEM_CLOCK}\verb{= "false",}\emph{R_CHECK_SUGGESTS_ONLY}\verb{= "true", ; }\emph{R_CHECK_CRAN_INCOMING}\verb{ = "false")}, overwritable using option 'checked.check_envvars' or environment variable 'R_CHECKED_CHECK_ENVVARS')} -\item{log_output}{path to the directory where log files will be created. (Defaults to \code{file.path(normalize_path(tempdir()), "log_autovalidateutils")}, overwritable using option 'autovalidateutils.log_output' or environment variable 'AUTOVALIDATEUTILS_LOG_OUTPUT')} +\item{tty_tick_interval}{tty refresh interval when reporting results in milliseconds (Defaults to \code{0.1}, overwritable using option 'checked.tty_tick_interval' or environment variable 'R_CHECKED_TTY_TICK_INTERVAL')} -\item{conditions}{The file path of the file to which conditions should be emitted. They are -logged in yaml format, which is later read by \code{autovalidate} to -re-emit them as \code{autovalidate} checks and trigger failures when applicable (Defaults to \code{"conditions.yml"}, overwritable using option 'autovalidateutils.conditions' or environment variable 'AUTOVALIDATEUTILS_CONDITIONS')} +\item{check_build_args}{\code{character} vector of args passed to the R CMD build. (Defaults to \code{c("--no-build-vignettes", "--no-manual")}, overwritable using option 'checked.check_build_args' or environment variable 'R_CHECKED_CHECK_BUILD_ARGS')} \item{restore}{\code{logical} indicating whether output directory should be unlinked before running checks. If \code{FALSE}, an attempt will me made to restore previous -progress from the same \code{output} (Defaults to \code{NA}, overwritable using option 'checked.restore' or environment variable 'CHECKED_RESTORE')} - -\item{skip_cov_report}{Logical whether interactive coverage report calculation shall be skipped (Defaults to \code{FALSE}, overwritable using option 'autovalidateutils.skip_cov_report' or environment variable 'AUTOVALIDATEUTILS_SKIP_COV_REPORT')} - -\item{use_remotes}{Logical flag or named character mapping dependency types to the mechanism of -handling remotes, one of "allow", "prefer" or "disallow". "allow" -option means that the remote sources are allowed but will not take precedence -over other standard sources if both available. "prefer" means allow and -overwrite standard sources while "disallow" stands for skipping remote -sources at all. If no value is provided for a dependency type it is -considered to be "disallow". Can also be set to TRUE to "prefer" all or -FALSE to "disallow all. (Defaults to \verb{c(Depends = "disallow", Imports = "disallow", LinkingTo = "disallow", ; Suggests = "allow", Enhances = "allow")}, overwritable using option 'autovalidateutils.use_remotes' or environment variable 'AUTOVALIDATEUTILS_USE_REMOTES')} +progress from the same \code{output} (Defaults to \code{NA}, overwritable using option 'checked.restore' or environment variable 'R_CHECKED_RESTORE')} -\item{mapper}{The file path into which an \code{autovalidate}-style mapper file should -be written. (Defaults to \code{file.path("traceability_matrix", "mapper.yml")}, overwritable using option 'autovalidateutils.mapper' or environment variable 'AUTOVALIDATEUTILS_MAPPER')} - -\item{clear_description}{Logical value whether all non-utf8 characters should be removed from -the DESCRIPTION value. This is to avoid potential erros that might -occure when installing the package from the source. (Defaults to \code{FALSE}, overwritable using option 'autovalidateutils.clear_description' or environment variable 'AUTOVALIDATEUTILS_CLEAR_DESCRIPTION')} - -\item{revdep_clean_library}{Logical whether the source of the target package should be removed after -completing checks. (Defaults to \code{TRUE}, overwritable using option 'autovalidateutils.revdep_clean_library' or environment variable 'AUTOVALIDATEUTILS_REVDEP_CLEAN_LIBRARY')} +\item{install_user_profile}{value used as \code{user_profile} parameter passed to the \code{callr::r_bg()} +function used to install packages (Defaults to \code{"project"}, overwritable using option 'checked.install_user_profile' or environment variable 'R_CHECKED_INSTALL_USER_PROFILE')} -\item{check_dir}{The directory R CMD check results should be written to -(.tag.gz, .Rcheck). (Defaults to \code{"check"}, overwritable using option 'autovalidateutils.check_dir' or environment variable 'AUTOVALIDATEUTILS_CHECK_DIR')} +\item{tty_default_height}{deafult tty height used for the ANSI reporter. Used only +if correct values could not be acquired with system('tput lines') (Defaults to \code{50}, overwritable using option 'checked.tty_default_height' or environment variable 'R_CHECKED_TTY_DEFAULT_HEIGHT')} } \description{ Checked Options diff --git a/man/print.checked_results.Rd b/man/print.checked_results.Rd index a7ea5bd..bea9075 100644 --- a/man/print.checked_results.Rd +++ b/man/print.checked_results.Rd @@ -22,7 +22,7 @@ \item{keep}{character vector indicating which packages should be included in the results. "all" means that all packages are kept. If "issues" then only packages with issues identified, whereas "potential_issues" stands for keeping -packages with both "issues" and "potential_issues". (Defaults to \code{"all"}, overwritable using option 'checked.results_keep' or environment variable 'CHECKED_RESULTS_KEEP')} +packages with both "issues" and "potential_issues". (Defaults to \code{"all"}, overwritable using option 'checked.results_keep' or environment variable 'R_CHECKED_RESULTS_KEEP')} } \description{ Print checked results diff --git a/man/results.Rd b/man/results.Rd index 7c78e53..90621d8 100644 --- a/man/results.Rd +++ b/man/results.Rd @@ -32,7 +32,7 @@ results(x, ...) \item{error_on}{character vector indicating whether R error should be thrown when issues are discovered when generating results. "never" means that no errors are thrown. If "issues" then errors are emitted only on issues, whereas -"potential issues" stands for error on both issues and potential issues. (Defaults to \code{"never"}, overwritable using option 'checked.results_error_on' or environment variable 'CHECKED_RESULTS_ERROR_ON')} +"potential issues" stands for error on both issues and potential issues. (Defaults to \code{"never"}, overwritable using option 'checked.results_error_on' or environment variable 'R_CHECKED_RESULTS_ERROR_ON')} \item{checker_obj}{\code{\link{checker}} object.} }