Package 'checktor'

Description

Runs a comprehensive diagnostic suite for common CRAN submission issues that are not caught by standard R CMD check. Like a doctor for your package, this function examines your code, DESCRIPTION file, documentation, general package structure, and CRAN policy compliance to identify potential problems that could cause CRAN submission delays or rejections.

Usage

checktor(
  path = ".",
  verbose = getOption("checktor.verbose", TRUE),
  progress = getOption("checktor.progress", verbose),
  severity = getOption("checktor.severity", c("policy", "robustness"))
)

Arguments

Details

The function runs five categories of diagnostics: Code, DESCRIPTION, Documentation, General, and Policy. See diagnose_code_issues(), diagnose_description_issues(), diagnose_documentation_issues(), diagnose_general_issues(), and diagnose_policy_violations() for the specific checks within each category.

The metadata$total_issues figure counts the individual findings of the checks in the severity tiers (e.g., 80 lines using T/F count as 80, not 1), and metadata$failed_checks counts how many of those checks reported anything. Findings in the other tiers are still in the result and are counted in metadata$advisory_issues instead.

A few checks never join a run, because no authority backs them or they ask about a submission workflow rather than the package. They are not skipped, since nothing tried to run them. metadata$on_request_checks names them; call ⁠lab_<name>()⁠ to run one.

A package can configure checktor from ⁠Config/checktor/*⁠ fields in its own DESCRIPTION (comma-separated lists; DESCRIPTION has no comment syntax, so anything after the last name becomes part of it):

• Config/checktor/disable: check names to skip entirely. A disabled check does not run and is not counted anywhere in the results. To turn a check off in every package, set options(checktor.disable = "news_file") once, for example in .Rprofile; the two lists are combined.

• Config/checktor/allow: check to mute a whole check, or check:substring to mute only findings whose text contains substring. The check still runs; muted findings are dropped from the results and tallied in metadata$suppressed, while a disabled check is removed entirely and never counted there.

• Config/checktor/software_names, Config/checktor/language_names, Config/checktor/format_names, Config/checktor/acronyms: names appended to those checks' vocabularies.

Value

A checktor_results object (list) containing:

• code_issues: Results from code diagnostics

• description_issues: Results from DESCRIPTION file diagnostics

• documentation_issues: Results from documentation diagnostics

• general_issues: Results from general package diagnostics

• policy_issues: Results from CRAN policy violation diagnostics

• metadata: List with the package path, the diagnosis time, the issue and failed-check counts (total_issues, failed_checks), the severity tiers they count, the findings outside those tiers (advisory_issues), the findings muted by Config/checktor/allow (suppressed), the checks that did not run (skipped_checks), the checks that run only when called (on_request_checks), and the checktor version (checktor_version)

Each diagnostic category contains a passed element showing which individual checks did not fail, plus detailed results for each check. A check that did not run is TRUE there, and its own skipped element records that it did not run.

Options

• checktor.verbose, checktor.progress: the defaults for verbose and progress. configure_doctor() sets both.

• checktor.severity: the default tiers for checktor() and checkup().

• checktor.disable: checks to leave out of every run, combined with Config/checktor/disable.

• checktor.url_check: TRUE or FALSE to run or skip lab_url_liveness() wherever you are. It defaults to interactive().

• checktor.spelling: FALSE turns off lab_spelling(), which is then reported as skipped.

See Also

health_report() to generate detailed reports, prescribe() for treatment recommendations, checkup() for quick health checks

Examples

# Run against a synthetic package with known T/F issues
pkg <- example_diagnose_scenario("code_examples/tf_usage_bad.R",
                                 show_content = FALSE)
results <- checktor(pkg, verbose = FALSE, progress = FALSE)

results              # the diagnosis summary
summary(results)     # per-category overview
issues(results)      # every issue as a tidy data frame
is_healthy(results)  # FALSE

Description

Constructor function for creating diagnostic category result objects used by multi-category diagnostic functions like diagnose_code_issues().

Usage

checktor_category_result(...)

Arguments

Value

An object of class checktor_category_result containing:

• Individual checktor_check_result objects for each check

• passed: Named logical vector showing which individual checks did not fail. A check that did not run is TRUE here, since it cannot fail a verdict; its own skipped element records that it did not run.

See Also

Multi-category functions like diagnose_code_issues(), diagnose_documentation_issues()

Examples

# Create individual check results
tf_check <- checktor_check_result(FALSE, "file.R:5", "T/F usage check")
seed_check <- checktor_check_result(TRUE, character(0), "Seed setting check")

# Create category result
code_results <- checktor_category_result(
  tf_usage = tf_check,
  seed_setting = seed_check
)
print(code_results)

Description

Constructor function for creating consistent diagnostic check result objects used by all individual diagnostic functions.

Usage

checktor_check_result(passed, issues, message, ...)

Arguments

Details

A check that could not run where it is, because it needs a network, a tool or a file that is not there, should say so rather than pass. Return checktor_check_result(TRUE, character(0), "<message>", skipped = TRUE, skip_reason = "<why>"). passed stays TRUE so the skip cannot fail a verdict, and skipped makes tidy(), summary(), metadata$skipped_checks, the printed report, health_report() and ci_report() report it as a check that did not run rather than one that passed. A result with passed = FALSE reads as failed whatever skipped says.

Value

An object of class checktor_check_result containing:

• passed: The passed status

• issues: Vector of issues found

• message: Description of the check

• Additional elements passed via ...

See Also

Individual diagnostic functions like lab_tf_usage(), lab_seed_setting()

Examples

# Create a passing check result
result <- checktor_check_result(
  passed = TRUE,
  issues = character(0),
  message = "Example check"
)
print(result)

# Create a failing check result with additional elements
result <- checktor_check_result(
  passed = FALSE,
  issues = c("file1.R:5", "file2.R:10"),
  message = "T/F usage check",
  file_issues = list("file1.R" = 5, "file2.R" = 10)
)
print(result)

# Report a check that could not run where it is
result <- checktor_check_result(
  passed = TRUE,
  issues = character(0),
  message = "License server check",
  skipped = TRUE,
  skip_reason = "no license server configured"
)
print(result)

Description

Runs checktor() with minimal output, suitable for CI/CD pipelines.

Usage

checkup(
  path = ".",
  severity = getOption("checktor.severity", c("policy", "robustness"))
)

Arguments

Value

Logical. TRUE if no finding in the severity tiers was found, FALSE otherwise. Findings in the other tiers do not change it.

Examples

# A package that uses a bare T fails the gate
pkg_bad <- example_diagnose_scenario("code_examples/tf_usage_bad.R",
                                     show_content = FALSE)
checkup(pkg_bad)

Description

Renders a checktor() result as machine-readable findings, so a build puts each one next to the line that caused it instead of leaving it in a log for someone to read. The format defaults to whichever forge the build is running on.

Usage

ci_report(
  results = NULL,
  format = c("auto", "github", "gitlab", "checkstyle", "sarif", "azure", "text"),
  file = NULL,
  severity = c("policy", "robustness", "opinion"),
  skipped = TRUE,
  path = "."
)

Arguments

Details

Each forge reads a different shape, and format picks it:

• "github" writes workflow commands to standard output, which GitHub Actions turns into annotations on the pull request diff. Gitea and Forgejo Actions read the same commands.

• "gitlab" writes a Code Quality report, which GitLab shows on the merge request diff. Name the file in ⁠artifacts:reports:codequality:⁠.

• "checkstyle" writes Checkstyle XML, which Jenkins, reviewdog and most review bots read. This is the one to reach for on a forge with no format of its own.

• "sarif" writes SARIF 2.1.0, which GitHub code scanning and Azure ingest.

• "azure" writes Azure Pipelines logging commands.

• "text" writes one plain line per finding, for a build with no forge at all.

Findings carry a file name rather than a path, so the path is recovered by looking for the file under ⁠R/⁠, ⁠man/⁠, ⁠vignettes/⁠ and the other places a package keeps code. A finding that names a file and no line, such as a help page with no ⁠\value⁠, is reported on that file's first line. A finding with no location at all, such as a DESCRIPTION field problem, is reported against DESCRIPTION so it still appears.

Value

Invisibly, the character vector written.

See Also

checkup() for the pass or fail gate, health_report() for a report a person reads.

Examples

pkg <- example_diagnose_scenario("code_examples/tf_usage_bad.R",
                                 show_content = FALSE)
results <- checktor(pkg, verbose = FALSE, progress = FALSE)

# What a GitHub Actions job would emit. Indented here, because a runner reads
# any line starting with `::` as a command, including one this example printed.
writeLines(paste0("  ", head(ci_report(results, format = "github", file = NULL), 3)))

Description

Recursively concatenates the text of a tools::parse_Rd() node, optionally skipping subsections by Rd_tag (for instance "\\dontrun" when collecting example code that is meant to run).

Usage

collect_rd_text(node, skip = character(0))

Arguments

Value

A single character string.

See Also

extract_rd_section().

Examples

rd_file <- tempfile(fileext = ".Rd")
writeLines(c("\\name{foo}", "\\title{Foo}",
             "\\examples{ f() \\dontrun{ g() } }"), rd_file)
rd <- tools::parse_Rd(rd_file)
collect_rd_text(extract_rd_section(rd, "\\examples"), skip = "\\dontrun")

Description

Sets session-wide defaults for checktor() behavior. Subsequent calls to checktor() (and helpers that delegate to it) pick up these defaults via getOption().

Usage

configure_doctor(verbose_default = TRUE, progress_default = TRUE, color = TRUE)

Arguments

Value

Invisibly returns the previous values of the changed options, so the call can be reversed with options(.).

Examples

# configure_doctor() returns the options it replaced
old <- configure_doctor(verbose_default = FALSE)
getOption("checktor.verbose")

# Put them back
options(old)

Description

Runs comprehensive diagnostics on R source code to identify common CRAN submission issues and coding best-practice violations.

Usage

diagnose_code_issues(path = ".", verbose = TRUE)

Arguments

Details

Each source file is parsed once with parse(keep.source = TRUE); checks run XPath queries against the parsed XML representation, so identifiers that appear only inside string literals or comments do not false-positive. Multi-line constructs (⁠set.seed(\n123\n)⁠), formula ~ versus path ~, and scope-aware patterns (an options() call guarded by a sibling on.exit() in the same function body) are all handled correctly.

Value

List of named checktor_check_result() objects (e.g., tf_usage, seed_setting) plus a passed named logical vector summarizing pass/fail for each sub-check.

See Also

checktor() for complete package diagnostics

Examples

pkg <- example_diagnose_scenario("code_examples/tf_usage_bad.R",
                                 show_content = FALSE)
code_results <- diagnose_code_issues(pkg, verbose = FALSE)
summary(code_results)   # per-category overview
issues(code_results)    # the issues found

Description

Runs diagnostics against the package DESCRIPTION file. Fields are parsed with base::read.dcf() so that multi-line fields like Description and Title are inspected in full, not just their first physical line.

Usage

diagnose_description_issues(path = ".", verbose = TRUE)

Arguments

Value

List containing one named element per check. Each element is a list with at least passed, issues, and message (see checktor_check_result()). When the DESCRIPTION is missing or R cannot read it, description_file fails, and every check that reads the parsed fields, registered ones included, is reported as skipped with the reason "DESCRIPTION could not be read", since it has nothing to examine.

See Also

checktor() for complete package diagnostics

Examples

pkg_path <- example_diagnose_scenario("description_examples/bad_description.txt",
                                      show_content = FALSE)
results <- diagnose_description_issues(pkg_path, verbose = FALSE)
issues(results)     # description-field problems, if any

Description

Runs diagnostics on package documentation to identify common issues that can cause CRAN submission problems or a poor user experience.

Usage

diagnose_documentation_issues(path = ".", verbose = TRUE)

Arguments

Details

This function checks for:

• Missing ⁠\value⁠ tags in function documentation

• Exported functions missing an ⁠\examples⁠ section

• Roxygen2 usage

• Example structure (appropriate use of ⁠\dontrun{}⁠)

• Examples that use Suggested packages without a guard

.Rd files are parsed structurally via tools::parse_Rd() so analyses look at sections by their Rd_tag rather than grepping LaTeX text.

Value

List of checktor_check_result() objects plus a passed named logical vector summarizing pass/fail per check.

See Also

checktor() for complete package diagnostics

Examples

pkg_path <- example_diagnose_scenario("documentation_examples/missing_value_tag.Rd",
                                      show_content = FALSE)
doc_results <- diagnose_documentation_issues(pkg_path, verbose = FALSE)
summary(doc_results)
issues(doc_results)

Description

Runs general diagnostics on package structure and content that don't fit into specific code, documentation, or DESCRIPTION categories.

Usage

diagnose_general_issues(path = ".", verbose = TRUE)

Arguments

Details

This function checks:

• Package size, measured against the files that would go into the tarball (.Rbuildignore and standard scratch dirs are excluded), with a 5 MB warning threshold matching CRAN's recommendation.

• ⁠http://⁠ URLs and URL shorteners, offline. ⁠R CMD check --as-cran⁠ does fetch every URL, but only with a network and only under --as-cran; this is the fast local pass.

• Presence of a NEWS file documenting user-facing changes.

• Relative links in the README that would break on CRAN.

• A package that exports code but has no examples, no tests and no vignettes to exercise it.

• An inst/CITATION that uses the old-style citEntry() or personList(), or calls packageDescription(), library() or require().

lab_cran_comments_file() is intentionally not part of this default run, since a cran-comments.md is a workflow convention rather than a CRAN requirement; call it directly to opt in.

Value

List of checktor_check_result() objects plus a passed summary.

See Also

checktor() for complete package diagnostics

Examples

pkg_path <- example_diagnose_scenario("code_examples/tf_usage_bad.R",
                                      show_content = FALSE)
general_results <- diagnose_general_issues(pkg_path, verbose = FALSE)
general_results$package_size$size_mb

Description

Runs additional diagnostics focused on CRAN policy: leftover browser() calls, raw system invocations, file writes outside tempdir(), and unwrapped network access in examples or vignettes. Code-side checks use the parsed AST so string/comment matches don't false-positive; Rd-side checks use tools::parse_Rd() for the same reason.

Usage

diagnose_policy_violations(path = ".", verbose = TRUE)

Arguments

Value

List of checktor_check_result() objects, plus a passed named logical vector summarizing pass/fail per check.

See Also

checktor() for complete package diagnostics

Examples

pkg <- example_diagnose_scenario("code_examples/browser_calls_bad.R",
                                 show_content = FALSE)
policy <- diagnose_policy_violations(pkg, verbose = FALSE)
summary(policy)
issues(policy)

Description

Creates a temporary package structure with a specified example file for testing diagnostic functions. This is primarily used in documentation examples to demonstrate diagnostic capabilities with known problematic code.

Usage

example_diagnose_scenario(
  example_path,
  show_content = TRUE,
  description_type = "minimal",
  cleanup = FALSE
)

Arguments

Details

This function:

1. Locates the specified example file in the package's ⁠inst/diagnose/⁠ directory

2. Creates a temporary package directory structure

3. Copies the example file to where a package keeps its kind: an .R file in ⁠R/⁠, an .Rd file in ⁠man/⁠, a vignette (.Rmd, .qmd, .Rnw) in ⁠vignettes/⁠, a DESCRIPTION scenario (.txt) as the DESCRIPTION, a citation scenario (.CITATION) as inst/CITATION, and a licence scenario (.LICENSE) as LICENSE

4. Optionally displays the example file content

5. Returns the path to the temporary package for diagnostic testing

The temporary package includes minimal structure (⁠R/⁠, ⁠man/⁠, etc.) needed for running diagnostics, plus a basic DESCRIPTION file.

Value

Character. Path to the temporary package directory containing the example file. Returns NULL, with a warning, if the example file cannot be found. An example_path that is not an .R, .Rd, .Rmd, .qmd, .Rnw, .txt, .CITATION or .LICENSE file is an error, since a package has no place for it.

Example File Structure

The temporary package created has this structure. The example file goes in the one place its extension names, and the other directories stay empty:

<tempdir>/checktor_example_XXXX/
|-- DESCRIPTION          # The template, or a .txt scenario itself
|-- LICENSE              # A .LICENSE scenario; made only for one
|-- NEWS.md              # So the NEWS check has nothing to report
|-- cran-comments.md     # So the cran-comments check has nothing to report
|-- R/                   # An .R scenario, such as tf_usage_bad.R
|-- man/                 # An .Rd scenario, such as missing_value_tag.Rd
|-- inst/CITATION        # A .CITATION scenario; made only for one
|-- tests/               # Always empty
`-- vignettes/           # An .Rmd, .qmd or .Rnw scenario; made only for one

See Also

Used in examples for diagnostic functions like lab_tf_usage(), lab_seed_setting(), etc.

Examples

# A scenario with T/F usage issues. show_content defaults to TRUE, so the
# offending file prints first
pkg_path <- example_diagnose_scenario("code_examples/tf_usage_bad.R")
lab_tf_usage(pkg_path, verbose = FALSE)$issues
issues(checktor(pkg_path, verbose = FALSE, progress = FALSE))
unlink(pkg_path, recursive = TRUE)

# A .txt scenario is the DESCRIPTION, so it needs no description_type
pkg_path <- example_diagnose_scenario("description_examples/bad_description.txt",
                                      show_content = FALSE)
issues(diagnose_description_issues(pkg_path, verbose = FALSE))
unlink(pkg_path, recursive = TRUE)

# With cleanup = TRUE the package is deleted when the calling function returns
count_tf <- function() {
  pkg_path <- example_diagnose_scenario("code_examples/tf_usage_bad.R",
                                        show_content = FALSE, cleanup = TRUE)
  length(lab_tf_usage(pkg_path, verbose = FALSE)$issues)
}
count_tf()

Description

Returns the first top-level node of a tools::parse_Rd() result whose Rd_tag matches tag, or NULL if absent. Use it to reach a specific section, such as ⁠\\value⁠ or ⁠\\examples⁠, when writing a documentation check.

Usage

extract_rd_section(rd, tag)

Arguments

Value

The matching Rd node, or NULL.

See Also

collect_rd_text().

Examples

rd_file <- tempfile(fileext = ".Rd")
writeLines(c("\\name{foo}", "\\title{Foo}", "\\value{A number.}"), rd_file)
rd <- tools::parse_Rd(rd_file)
collect_rd_text(extract_rd_section(rd, "\\value"))

Description

Walks up from path until it finds the directory holding a DESCRIPTION file, so checktor can be run from anywhere inside a package tree rather than only from the directory holding DESCRIPTION. That is what lets checktor() work with your working directory set to ⁠R/⁠, ⁠tests/testthat/⁠, or any other subdirectory.

Usage

find_package_root(path = ".")

Arguments

Details

Every checktor entry point calls this on the path it is given, so you rarely need it directly. It is exported for custom checks registered with register_check(), which receive a path that has already been resolved.

Value

Character. The package root, as an absolute path, when one is found above path. When path itself holds a DESCRIPTION it is returned unchanged, so an existing caller sees exactly what it passed in. When no package root is found at all, the search falls back to the directory it started from, meaning path for a directory and its parent for a file, which leaves the caller reporting the problem against the place the user pointed at.

See Also

checktor(), which resolves its path this way.

Examples

pkg <- example_diagnose_scenario("code_examples/tf_usage_bad.R",
                                 show_content = FALSE)

# From the package root, the path is handed back untouched
identical(find_package_root(pkg), pkg)

# From a subdirectory, the root is found by walking up
basename(find_package_root(file.path(pkg, "R")))

Description

Creates a report of every failing check, whatever its severity tier, with the treatment prescribe() gives for it. Every format carries the same treatment text.

Usage

health_report(results, file = NULL, format = "markdown")

Arguments

Value

The report as a character vector, one element per line. It is returned visibly even when file is given, so assign it to keep a console call from printing it.

Examples

pkg <- example_diagnose_scenario("code_examples/tf_usage_bad.R",
                                 show_content = FALSE)
results <- checktor(pkg, verbose = FALSE, progress = FALSE)
report <- health_report(results, format = "text")
head(report)

Description

Plain accessors over the objects returned by checktor() and the ⁠diagnose_*_issues()⁠ functions, so you never navigate nested sublists.

Usage

issues(x, ...)

## S3 method for class 'checktor_check_result'
issues(x, ...)

## S3 method for class 'checktor_category_result'
issues(x, ...)

## S3 method for class 'checktor_results'
issues(x, ...)

Arguments

Value

issues() returns a data.frame with one row per issue, whatever its severity tier. At the results level the columns are category, check, severity, file, line, location, message; a single category drops category; a single check drops category, check and severity. A healthy object yields a 0-row frame. file and line are read from location: a finding that names a file and no line, such as a help page with no ⁠\value⁠, has the file and an NA line, and a finding that names no file, such as one about a DESCRIPTION field, has NA for both.

Examples

pkg <- example_diagnose_scenario("code_examples/tf_usage_bad.R",
                                 show_content = FALSE)
results <- checktor(pkg, verbose = FALSE, progress = FALSE)
issues(results)

Description

Flags an acronym in Description that is never spelled out. A parenthetical gloss in either order counts as explained.

Usage

lab_acronyms(path = ".", verbose = TRUE, desc = NULL)

Arguments

Details

A name in single quotes, straight or typographic, is not read as an acronym, so 'YAML' or 'MATLAB' written as lab_language_names() and lab_format_names() ask is not reported here. Nor is anything inside a web address, a ⁠<doi:...>⁠, a function call or a quotation in double quotes, straight or typographic, such as the title of an article.

Value

checktor_check_result() with passed, issues, message.

Source

The CRAN Cookbook covers this under Explaining Acronyms. Reviewers ask for an acronym to be spelled out once, but nothing enforces it, which is why this sits at opinion tier. See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), which runs this and every other check.

Examples

pkg <- example_diagnose_scenario("description_examples/acronyms_bad.txt",
                                 show_content = FALSE)
lab_acronyms(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags a missing Authors@R, and an unfilled usethis or package.skeleton() template such as person("First", "Last", ...) or person("Givenname", "Familyname", ...), which is a hard CRAN rejection that ⁠R CMD check⁠ says nothing about.

Usage

lab_authors(path = ".", verbose = TRUE, desc = NULL)

Arguments

Details

The field is evaluated without running any code it contains: only person(), as.person(), c(), list(), paste(), paste0() and ( resolve, the calls R's own reader allows from R 4.6.0 on. Every other call in the field is reported, since ⁠R CMD build⁠ refuses it as a malformed Authors@R field. That includes a namespaced utils::person() and a function in parentheses, as in (c)(...), which are still read so the other checks see their roles.

Value

checktor_check_result() with passed, issues, message.

Source

The CRAN Repository Policy treats a placeholder or malformed Authors@R, including a missing maintainer, as a rejection. See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), which runs this and every other check.

Examples

pkg <- example_diagnose_scenario("description_examples/authors_bad.txt",
                                 show_content = FALSE)
lab_authors(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags a browser() call left in package code.

Usage

lab_browser_calls(path = ".", verbose = TRUE, parsed = NULL)

Arguments

Value

checktor_check_result() with passed, issues, message.

Source

The CRAN Repository Policy requires checks to run non-interactively, so a debugging leftover such as browser() must not be left in. See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), which runs this and every other check.

Examples

pkg <- example_diagnose_scenario("code_examples/browser_calls_bad.R",
                                 show_content = FALSE)
lab_browser_calls(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags an inst/CITATION that calls the old-style citEntry() (use bibentry()) or personList() and as.personList() (use c() on person objects), or that calls packageDescription(), library() or require(). R passes the file a meta object holding the package's DESCRIPTION, so it needs none of those, and each assumes the package is already installed.

Usage

lab_citation_file(path = ".", verbose = TRUE)

Arguments

Details

As in R, the fallback if (!exists("meta") || is.null(meta)) meta <- packageDescription("pkg") is exempt: a top-level if with exactly that condition and no ⁠else⁠. The file is parsed and never run, so a name in a comment or a string is not a call. A CITATION that does not parse is reported, with the line R stops at. A CITATION that .Rbuildignore excludes is not in the tarball and is not read.

Value

checktor_check_result() with passed, issues, message.

Source

The CRAN incoming check (⁠R CMD check --as-cran⁠) NOTEs "Package CITATION file contains call(s) to old-style citEntry(). Please use bibentry() instead." and "... old-style personList() or as.personList(). Please use c() on person objects instead.", and lists calls to packageDescription, library and require. Writing R Extensions, under "CITATION files", says "It is desirable (and essential for CRAN) that the CITATION file does not contain calls to functions such as packageDescription which assume the package is installed in a library tree on the package search path." devtools::check() turns the incoming check off by default. See vignette("check-sources", package = "checktor") for how every check maps to its source.

Examples

pkg <- example_diagnose_scenario("general_examples/citation_file_bad.CITATION",
                                 show_content = FALSE)
lab_citation_file(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags a package that exports something but ships no ⁠\examples⁠ in any help page, no tests and no vignettes, so a check runs none of its code. CRAN's incoming check raises this as a WARNING, which is an automatic rejection.

Usage

lab_code_exercised(path = ".", verbose = TRUE)

Arguments

Details

The conditions are R's own. An example counts even when all of it sits in ⁠\dontrun{}⁠, because R still writes it out. A test counts only as a file directly in ⁠tests/⁠ ending in .R, .r or .Rin, since that is what ⁠R CMD check⁠ runs: a ⁠tests/testthat/⁠ folder without the tests/testthat.R driver is never run, and the finding says so. Files .Rbuildignore excludes do not count, since they are not in the tarball. A package with no ⁠R/⁠ directory, or whose NAMESPACE exports nothing, passes. So does one whose NAMESPACE is missing or cannot be parsed, since its exports are then unknown.

Value

checktor_check_result() with passed, issues, message.

Source

The CRAN incoming check (⁠R CMD check --as-cran⁠) reports "checking for code which exercises the package ... WARNING" with "No examples, no tests, no vignettes" when all three are missing and the NAMESPACE exports anything. devtools::check() turns the incoming check off by default, so the WARNING is usually first seen at win-builder or on submission. The CRAN Repository Policy asks that "the checks that are left do exercise all the features of the package". See vignette("check-sources", package = "checktor") for how every check maps to its source.

Examples

pkg <- example_diagnose_scenario("general_examples/code_exercised_bad.R",
                                 show_content = FALSE)
# The scenario's function is exported, as roxygen2 would record it
writeLines("export(tidy_values)", file.path(pkg, "NAMESPACE"))
lab_code_exercised(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags an ⁠\examples{}⁠ block whose only content is commented out, so it demonstrates nothing. A comment beside live code is illustration and is not flagged.

Usage

lab_commented_examples(path = ".", verbose = TRUE)

Arguments

Value

checktor_check_result() with passed, issues, message.

Source

No formal rule. An ⁠\examples{}⁠ block that is entirely commented out demonstrates nothing, a convention which is why this sits at opinion tier. See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), which runs this and every other check.

Examples

pkg <- example_diagnose_scenario("documentation_examples/commented_examples_bad.Rd",
                                 show_content = FALSE)
lab_commented_examples(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags a worker count that can exceed CRAN's two-core limit. Understands parallel, snow, foreach, future, furrr, mirai, RcppParallel, data.table, and BiocParallel.

Usage

lab_core_usage(path = ".", verbose = TRUE, parsed = NULL)

Arguments

Value

checktor_check_result() with passed, issues, message.

Source

The CRAN Repository Policy states that "If running a package uses multiple threads/cores it must never use more than two simultaneously". See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), which runs this and every other check.

Examples

pkg <- example_diagnose_scenario("code_examples/core_usage_bad.R",
                                 show_content = FALSE)
lab_core_usage(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags a package that names no copyright holder: no person in Authors@R has the cph role and there is no Copyright field. It runs only when you call it: authors who are natural persons hold copyright by default, so most packages need neither. It is worth running when an organisation owns the copyright, since that is the case the role exists for.

Usage

lab_cph_role(path = ".", verbose = TRUE, desc = NULL)

Arguments

Details

The roles are read from the parsed person() object, never from the text of the field, so an address such as [email protected] is not a role. The field is parsed without running any code it contains, as in lab_authors(). A package with no Authors@R is read from its legacy Author field instead, where only a role written in square brackets, as in ⁠ACME Corporation [cph]⁠, counts, in any case, and not one inside a parenthesised comment.

Value

checktor_check_result() with passed, issues, message.

Source

utils::person() documents "cph" as the role for "all copyright holders", adding that "authors which are 'natural persons' are by default copyright holders and so do not need to be given this role". CRAN Repository Policy asks only that copyright ownership be clear, which a Copyright field also satisfies. See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), which runs this and every other check.

Examples

pkg <- example_diagnose_scenario("description_examples/cph_role_bad.txt",
                                 show_content = FALSE)
lab_cph_role(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

A cran-comments.md file carries the submission notes CRAN reviewers read (test environments, R CMD check results, downstream-dependency notes). Its absence is flagged so it can be added before submission.

Usage

lab_cran_comments_file(path = ".", verbose = TRUE)

Arguments

Details

This check is opt-in: it is not part of the default checktor() / diagnose_general_issues() run, because a cran-comments.md is a workflow convention rather than a CRAN requirement. Call it directly to use it.

Value

checktor_check_result() with passed, issues, message.

Source

No formal rule. A cran-comments.md is a submission-workflow convention rather than a CRAN requirement, which is why this check is opt-in and not part of a default run. See vignette("check-sources", package = "checktor") for how every check maps to its source.

Examples

pkg <- example_diagnose_scenario("code_examples/tf_usage_bad.R",
                                 show_content = FALSE)
invisible(file.remove(file.path(pkg, "cran-comments.md")))
lab_cran_comments_file(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags a Date field that is not ISO 8601 yyyy-mm-dd, is over a month old, or lies in the future. Mirrors the CRAN incoming check; an absent Date field (the common, preferred case) passes.

Usage

lab_date_format(path = ".", verbose = TRUE, desc = NULL)

Arguments

Value

checktor_check_result() with passed, issues, message.

Source

Writing R Extensions, under "The DESCRIPTION file", says "the 'yyyy-mm-dd' format of the ISO 8601 standard is strongly recommended"; the incoming check also flags a stale or future date. See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), which runs this and every other check.

Examples

pkg <- example_diagnose_scenario("description_examples/date_format_bad.txt",
                                 show_content = FALSE)
lab_date_format(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags a DESCRIPTION field that is not one of the fields R knows, which is how CRAN's incoming check reads it. The usual one is Remotes, which devtools and pak read but CRAN does not, since CRAN installs dependencies from CRAN and Bioconductor alone. The others are typos such as Bugreports, Import, Suggest or URLs, which R ignores, so the field meant is silently missing; the finding names the field that was probably meant.

Usage

lab_description_fields(path = ".", verbose = TRUE, desc = NULL)

Arguments

Details

The fields R allows beyond its own list are allowed here too: any ⁠Config/⁠ field, such as Config/testthat/edition, and fields starting X-CRAN, X-schema.org, Repository/R-Forge or ⁠VCS/⁠, and a standard field name followed by Note, such as RoxygenNote.

Value

checktor_check_result() with passed, issues, message.

Source

The CRAN incoming check run by ⁠R CMD check --as-cran⁠ NOTEs "Unknown, possibly misspelled, fields in DESCRIPTION". The CRAN Repository Policy says "The strong dependencies ... should be available from CRAN or the Bioconductor software repository", which is why a Remotes field has no place in a submission. See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), which runs this and every other check.

Examples

pkg <- example_diagnose_scenario("description_examples/description_fields_bad.txt",
                                 show_content = FALSE)
lab_description_fields(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags a DESCRIPTION that is missing or that R cannot read: a line that is neither a Field: value pair nor an indented continuation, or a blank line that splits the file in two. ⁠R CMD build⁠ and ⁠R CMD INSTALL⁠ both stop on such a file, so the package cannot be built or installed. A DESCRIPTION R cannot open at all fails with the reason, a directory in its place or a file without read permission, which is found from the file system and so reads the same in any language. Every other DESCRIPTION check reads the parsed fields, so while this one fails they are reported as skipped.

Usage

lab_description_file(path = ".", verbose = TRUE, desc = NULL)

Arguments

Value

checktor_check_result() with passed, issues, message.

Source

Writing R Extensions, under "The DESCRIPTION file", specifies the format of a Debian Control File: "Fields start with an ASCII name immediately followed by a colon" and "Continuation lines ... start with a space or tab". R reads it with base::read.dcf() and refuses a file that yields more than one record. See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), which runs this and every other check.

Examples

pkg <- example_diagnose_scenario("description_examples/unparseable_description.txt",
                                 show_content = FALSE)
lab_description_file(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags a single-quoted function name in Title/Description. Single quotes are reserved for software names.

Usage

lab_description_function_quotes(path = ".", verbose = TRUE, desc = NULL)

Arguments

Value

checktor_check_result() with passed, issues, message.

Source

No rule. This was an invented rule and is kept callable but off by default. See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), which runs this and every other check.

Examples

pkg <- example_diagnose_scenario("description_examples/description_function_quotes_bad.txt",
                                 show_content = FALSE)
lab_description_function_quotes(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags a Description of fewer than 10 words.

Usage

lab_description_length(path = ".", verbose = TRUE, desc = NULL)

Arguments

Value

checktor_check_result() with passed, issues, message.

Source

The CRAN Cookbook covers this under Description Length. A one-line Description is thin and reviewers ask for more, a convention rather than a rule, which is why this sits at opinion tier. See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), which runs this and every other check.

Examples

pkg <- example_diagnose_scenario("description_examples/description_length_bad.txt",
                                 show_content = FALSE)
lab_description_length(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags a Title, Description, Author or Maintainer that still holds the text a package template wrote: the usethis template's "What the Package Does (One Line, Title Case)" and "What the package does (one paragraph).", and package.skeleton()'s "What the Package Does (Short Line)", "More about what it does (maybe more than one line).", "Who wrote it" and "Who to complain to". It applies R's own tests, so it flags what CRAN flags. A template Authors@R is lab_authors()'s to report.

Usage

lab_description_placeholders(path = ".", verbose = TRUE, desc = NULL)

Arguments

Value

checktor_check_result() with passed, issues, message.

Source

The CRAN incoming check run by ⁠R CMD check --as-cran⁠ NOTEs "DESCRIPTION fields with placeholder content". Writing R Extensions asks for a Title and Description that describe the package. See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), which runs this and every other check.

Examples

pkg <- example_diagnose_scenario("description_examples/description_placeholders_bad.txt",
                                 show_content = FALSE)
lab_description_placeholders(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags a software name in double quotes in Title or Description. Writing R Extensions reserves double quotes for quotations and requires single quotes for software names, so scare-quoted jargon is left alone. A lower-case span matches only a name written in lower case, such as shiny, so an English "rust" or a parameter "r" is not read as Rust or R. In the Title, where Title Case capitalises every word, a capitalised "Bugs" is likewise the word and not BUGS.

Usage

lab_description_quoted_quotes(path = ".", verbose = TRUE, desc = NULL)

Arguments

Details

The names are those lab_software_names() and lab_language_names() ask to see in single quotes, and a few more. Format names such as JSON or HTML, which CRAN accepts bare, are not among them, so one in double quotes is not reported; lab_format_names() reports them bare, on request.

Value

checktor_check_result() with passed, issues, message.

Source

Writing R Extensions, under "The DESCRIPTION file", reserves double quotes for book titles and similar; software names take single quotes. See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), which runs this and every other check.

Examples

pkg <- example_diagnose_scenario("description_examples/description_quoted_quotes_bad.txt",
                                 show_content = FALSE)
lab_description_quoted_quotes(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags a Description opening with a phrase CRAN forbids ("This package..."), or one that does not begin with a capital letter.

Usage

lab_description_starts_with(path = ".", verbose = TRUE, desc = NULL)

Arguments

Value

checktor_check_result() with passed, issues, message.

Source

Writing R Extensions, under "The DESCRIPTION file", says "It is good practice not to start with the package name, 'This package' or similar"; the incoming check flags it. See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), which runs this and every other check.

Examples

pkg <- example_diagnose_scenario("description_examples/description_starts_with_bad.txt",
                                 show_content = FALSE)
lab_description_starts_with(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags a parallel::detectCores() call whose result is used without an NA guard.

Usage

lab_detect_cores_robustness(path = ".", verbose = TRUE, parsed = NULL)

Arguments

Details

?detectCores says so in as many words: "An integer, NA if the answer is unknown", and R's own advice is to avoid it, "First because it may return NA". NA then propagates silently through the arithmetic packages usually do next, and the failure surfaces far from its cause:

n <- parallel::detectCores() - 1   # NA - 1 is NA
if (cores > n) cores <- n          # Error: missing value where TRUE/FALSE needed

This is a robustness defect rather than a policy one, and it is distinct from the core_usage check, which asks how many cores you use. A package can cap itself at two cores perfectly and still crash on the machine where detectCores() returns NA.

A call is treated as guarded when its enclosing function tests for NA (is.na()), passes na.rm = TRUE, or supplies a fallback with ⁠%||%⁠. The durable fix is parallelly::availableCores(), which never returns NA and also honours the CRAN core limit.

Value

checktor_check_result() with passed, issues, message.

Source

No formal rule. ?detectCores states it returns "NA if the answer is unknown", and the arithmetic that usually follows then crashes, which is why this sits at robustness tier. See vignette("check-sources", package = "checktor") for how every check maps to its source.

Examples

pkg <- example_diagnose_scenario("code_examples/detect_cores_bad.R",
                                 show_content = FALSE)
lab_detect_cores_robustness(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags ⁠\dontrun{}⁠ around code that is merely slow. ⁠\donttest{}⁠ is the right wrapper, since it still runs under --run-donttest.

Usage

lab_donttest_vs_dontrun(path = ".", verbose = TRUE)

Arguments

Details

A slow block that uses a Suggested package without a guard is left alone: ⁠R CMD check --as-cran⁠ runs ⁠\donttest{}⁠ code, so after the move lab_suggested_in_examples() would report it. Each ⁠\dontrun{}⁠ block is judged on its own, so such a block does not hold back the advice for another that is only slow.

Value

checktor_check_result() with passed, issues, message.

Source

The CRAN Cookbook covers the distinction under Structuring of Examples, where ⁠\donttest{}⁠ is the wrapper for an example that merely runs long. Nothing enforces the choice, which is why this sits at opinion tier. See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), which runs this and every other check.

Examples

pkg <- example_diagnose_scenario("documentation_examples/donttest_vs_dontrun_bad.Rd",
                                 show_content = FALSE)
lab_donttest_vs_dontrun(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags an Encoding that is anything but exactly UTF-8, which is the test CRAN's incoming check applies. latin1 and latin2 are still legal R, but CRAN NOTEs them as deprecated, and the comparison is case-sensitive, so a lower-case utf-8 is NOTEd too. An absent Encoding passes.

Usage

lab_encoding_utf8(path = ".", verbose = TRUE, desc = NULL)

Arguments

Value

checktor_check_result() with passed, issues, message.

Source

Writing R Extensions, under "The DESCRIPTION file", says a non-ASCII DESCRIPTION "should contain an 'Encoding' field"; the incoming check run by ⁠R CMD check --as-cran⁠ NOTEs any value but UTF-8 with "Package encoding '...' is deprecated. Please change to UTF-8 for non-ASCII content." See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), which runs this and every other check.

Examples

pkg <- example_diagnose_scenario("description_examples/encoding_utf8_bad.txt",
                                 show_content = FALSE)
lab_encoding_utf8(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags a call that installs a package or external software from an example, a vignette or a demo. CRAN asks maintainers not to install anything from these, because a check then has to do the install too, and the user did not ask for it.

Usage

lab_example_installs(path = ".", verbose = TRUE)

Arguments

Value

checktor_check_result() with passed, issues, message.

Source

The CRAN Cookbook covers this under Installing Software, and it is a rejection maintainers receive verbatim: "Please do not install packages in your functions, examples or vignette." See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), lab_software_install() for the same rule in ⁠R/⁠.

Examples

pkg <- example_diagnose_scenario("documentation_examples/example_installs_bad.Rd",
                                 show_content = FALSE)
lab_example_installs(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags an interactive call, such as a shiny app, a viewer or a prompt, that an example hides in ⁠\\dontrun{}⁠ or ⁠\\donttest{}⁠ instead of guarding with ⁠if (interactive())⁠.

Usage

lab_example_interactive(path = ".", verbose = TRUE)

Arguments

Details

In ⁠\\dontrun{}⁠, CRAN asks for the guard instead, so a reader can see that the function needs a session, not only that it does not run. In ⁠\\donttest{}⁠ the call is a failure waiting to happen: ⁠R CMD check --as-cran⁠ runs that code, where a prompt errors and an app waits for input until the check times out.

The example is read as parsed R, so a function named in a comment or a string is not a call, and only a guard that actually encloses the call excuses it, including roxygen's ⁠@examplesIf interactive()⁠. An app that shinyApp() builds is reported only where it is printed, which is what runs it; kept in a variable or handed to another function, it starts nothing.

Value

checktor_check_result() with passed, issues, message.

Source

The CRAN Cookbook covers this under Structuring of Examples, and the rejection reads "Functions which are supposed to only run interactively (e.g. shiny) should be wrapped in if(interactive()). Please replace \dontrun with if(interactive()) if possible". ⁠R CMD check --as-cran⁠ has run ⁠\\donttest{}⁠ examples since R 4.0.0. See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), lab_example_structure().

Examples

pkg <- example_diagnose_scenario("documentation_examples/example_interactive_bad.Rd",
                                 show_content = FALSE)
lab_example_interactive(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags a pkg:::fn() call in an example. The triple colon reaches an unexported object, whose behaviour the author is free to change, so CRAN asks for one colon or for the object to be exported.

Usage

lab_example_internal_ns(path = ".", verbose = TRUE)

Arguments

Value

checktor_check_result() with passed, issues, message.

Source

CRAN sends this back verbatim as "Using foo:::f instead of foo::f allows access to unexported objects ... Please omit one colon", listing the .Rd files it appears in. See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), lab_unexported_example_ns().

Examples

pkg <- example_diagnose_scenario("documentation_examples/example_internal_ns_bad.Rd",
                                 show_content = FALSE)
lab_example_internal_ns(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags an example, vignette or demo that changes options(), par() or the working directory without putting it back. A reader who runs the example is left with a session that behaves differently afterwards.

Usage

lab_example_state(path = ".", verbose = TRUE)

Arguments

Value

checktor_check_result() with passed, issues, message.

Source

The CRAN Cookbook covers this under Change of Options, Graphical Parameters and Working Directory, and the rejection reads "Please always make sure to reset to user's options(), working directory or par() after you changed it in examples and vignettes and demos." See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), lab_option_changes() for the same rule in ⁠R/⁠.

Examples

pkg <- example_diagnose_scenario("documentation_examples/example_state_bad.Rmd",
                                 show_content = FALSE)
lab_example_state(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Walks ⁠\examples{}⁠ sections via tools::parse_Rd() and flags ⁠\dontrun{}⁠ subtrees that don't appear to have a justifying reason (interactive, network, credentials, long-running, etc.).

Usage

lab_example_structure(path = ".", verbose = TRUE)

Arguments

Value

checktor_check_result() with passed, issues, message.

Source

The CRAN Cookbook covers this under Structuring of Examples. ⁠\dontrun{}⁠ should wrap only code that genuinely cannot run inside a check, a convention rather than a rule, which is why this sits at opinion tier. See vignette("check-sources", package = "checktor") for how every check maps to its source.

Examples

pkg <- example_diagnose_scenario("documentation_examples/example_structure_bad.Rd",
                                 show_content = FALSE)
lab_example_structure(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags a bare T or F in an example, a vignette chunk that runs, or a demo, judged exactly as lab_tf_usage() judges ⁠R/⁠: a T in a string, a comment, an argument name, x$T or language built by quote() is not reported.

Usage

lab_example_tf_usage(path = ".", verbose = TRUE, tests = FALSE)

Arguments

Value

checktor_check_result() with passed, issues, message.

Source

The CRAN Cookbook recipe T/F Instead of TRUE/FALSE says T and F "should not be used as variable names in your code, examples, tests or vignettes", and the reviewer's letter names the .Rd file: "'T' and 'F' instead of TRUE and FALSE: man/quiet.Rd: quiet(x, be_quiet = T)". No rule makes it binding, so it sits at robustness tier like lab_tf_usage(). Tests are left out unless tests = TRUE, since CRAN rarely reads them. See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), lab_tf_usage() for the same rule in ⁠R/⁠.

Examples

pkg <- example_diagnose_scenario("documentation_examples/example_tf_usage_bad.Rd",
                                 show_content = FALSE)
lab_example_tf_usage(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags an ⁠\examples{}⁠ section whose code does not parse as R, reporting the .Rd file and the line the parser stopped on. The code inside ⁠\dontrun{}⁠ is read too. ⁠R CMD check⁠ writes it out as comments and never parses it, so a missing bracket or a ⁠<your key>⁠ placeholder there passes every check.

Usage

lab_example_unparseable(path = ".", verbose = TRUE)

Arguments

Value

checktor_check_result() with passed, issues, message.

Source

A rejection CRAN reviewers send verbatim: "Warning: Unexecutable code in man/make.trait.model.Rd". Writing R Extensions, under "Documenting functions", says example code outside ⁠\dontrun{}⁠ "must be executable", and that the text inside it "need not be valid R code". Reviewers run the examples with ⁠\dontrun{}⁠ included all the same, so a placeholder belongs in a string or a variable, as in key <- "<your key>". An example that is deliberately not R, such as C++ source shown for reading, can be turned off with Config/checktor/disable. See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), lab_example_structure().

Examples

pkg <- example_diagnose_scenario("documentation_examples/example_unparseable_bad.Rd",
                                 show_content = FALSE)
lab_example_unparseable(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags a write from an example, vignette or demo whose destination is a literal path, so it lands in the user's filespace rather than in tempdir(). A destination the caller supplies is permission and is not flagged.

Usage

lab_example_writes(path = ".", verbose = TRUE)

Arguments

Value

checktor_check_result() with passed, issues, message.

Source

The CRAN Cookbook covers this under Writing Files and Directories to the Home Filespace, and the rejection reads "Please ensure that your functions do not write by default or in your examples/vignettes/tests in the user's home filespace". See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), lab_file_operations() for the same rule in ⁠R/⁠.

Examples

pkg <- example_diagnose_scenario("documentation_examples/example_writes_bad.Rd",
                                 show_content = FALSE)
lab_example_writes(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags a write whose destination is a literal path, so it provably lands in the working directory or the user's home. A caller-supplied or computed destination is permission, and is not flagged.

Usage

lab_file_operations(path = ".", verbose = TRUE, parsed = NULL)

Arguments

Value

checktor_check_result() with passed, issues, message.

Source

The CRAN Repository Policy states that "Packages should not write ... anywhere ... apart from the R session's temporary directory". See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), which runs this and every other check.

Examples

pkg <- example_diagnose_scenario("code_examples/file_operations_bad.R",
                                 show_content = FALSE)
lab_file_operations(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags a data, markup, typesetting or query format name – JSON, HTML, XML, CSS, YAML, TOML, Markdown, LaTeX, TeX or SQL – or one of the languages CRAN packages write either way (⁠C++⁠, Fortran, Tcl) that appears in Title or Description without single quotes. It runs only when you call it, for a maintainer who wants the quoting consistent. CRAN accepts these names bare, so a finding here never counts against a clean result.

Usage

lab_format_names(path = ".", verbose = TRUE, desc = NULL)

Arguments

Details

Occurrences are judged as in lab_software_names(): a name inside a quoted longer name such as 'R Markdown' or 'JSON-stat' is quoted, and so is one in a web address or a double-quoted span. A format name alone in double quotes, such as "JSON", is therefore reported by no check, by design: double quotes are the wrong kind for a name, but CRAN accepts the name with no quotes at all, so lab_description_quoted_quotes() leaves it alone too. A package can extend the list through Config/checktor/format_names in its own DESCRIPTION.

Value

checktor_check_result() with passed, issues, message.

Source

Writing R Extensions asks for single quotes around "other packages and external software", and a format is not software. A census of CRAN in September 2026 found that packages accepted at new-package review in the previous 18 months wrote these names bare 62% of the time, against 28% for the languages lab_language_names() covers, so this is a matter of style and sits at opinion tier. See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), lab_language_names().

Examples

pkg <- example_diagnose_scenario("description_examples/format_names_bad.txt",
                                 show_content = FALSE)
lab_format_names(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags a ⁠<<-⁠ whose target binds in neither an enclosing function nor the package, and so reaches .GlobalEnv. A closure updating its parent, or a package-level cache, is not flagged.

Usage

lab_globalenv_mod(path = ".", verbose = TRUE, parsed = NULL)

Arguments

Value

checktor_check_result() with passed, issues, message.

Source

The CRAN Repository Policy states that "Packages should not modify the global environment (user's workspace)." See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), which runs this and every other check.

Examples

pkg <- example_diagnose_scenario("code_examples/globalenv_bad.R",
                                 show_content = FALSE)
lab_globalenv_mod(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags a secret that looks like an API key, access token, or private key sitting in a string literal in ⁠R/⁠. ⁠R CMD check⁠ does not scan for leaked credentials, yet a token committed to a package is a security problem: once the package is published to CRAN the secret is public and must be revoked.

Usage

lab_hardcoded_credentials(path = ".", verbose = TRUE, parsed = NULL)

Arguments

Details

Only string literals in the parsed sources are examined, so the same text in a comment or a variable name never matches, and the check's own pattern strings never flag themselves.

Each format is anchored on a provider-specific prefix so ordinary code does not match. The recognised credentials, and the prefix each is keyed on, are:

• Version control and registries: GitHub tokens (ghp_, gho_, ghu_, ghs_, ghr_, and fine-grained github_pat_), GitLab tokens (⁠glpat-⁠), npm tokens (npm_), and PyPI upload tokens (pypi-AgEIcHlwaS5vcmc).

• Cloud providers: AWS access keys (AKIA, ASIA, AROA, AIDA, AGPA, ABIA, ACCA), Google API keys (AIza), Google OAuth client secrets (⁠GOCSPX-⁠), and DigitalOcean tokens (dop_v1_).

• AI and ML providers: OpenAI keys (⁠sk-⁠, ⁠sk-proj-⁠), Anthropic keys (⁠sk-ant-⁠), and Hugging Face tokens (hf_).

• Payments: Stripe secret and restricted keys (sk_live_, sk_test_, rk_live_, rk_test_) and Square tokens (⁠sq0atp-⁠, ⁠sq0csp-⁠, EAAA).

• Messaging: Slack tokens (⁠xoxb-⁠, ⁠xoxp-⁠, ...) and incoming webhooks (hooks.slack.com/services/...), SendGrid keys (SG.), and Telegram bot tokens (⁠<id>:AA...⁠).

• Platforms: Shopify tokens (shpat_, shpss_, shpca_, shppa_), Databricks tokens (dapi), and Postman keys (⁠PMAK-⁠).

• Generic: JSON Web Tokens (eyJ...) and PEM private-key headers (⁠-----BEGIN ... PRIVATE KEY-----⁠).

The prefixes and lengths follow each provider's published token format and the community-maintained gitleaks secret-detection ruleset.

Value

checktor_check_result() with passed, issues, message.

Source

No formal rule. A token or key committed to a package is public the moment it reaches CRAN and must be revoked, which is why this sits at robustness tier. See vignette("check-sources", package = "checktor") for how every check maps to its source.

References

Provider token formats and the gitleaks ruleset: https://github.com/gitleaks/gitleaks

Examples

pkg <- example_diagnose_scenario("code_examples/credentials_bad.R",
                                 show_content = FALSE)
lab_hardcoded_credentials(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags a write whose destination resolves to ~ or ⁠$HOME⁠.

Usage

lab_home_writing(path = ".", verbose = TRUE, parsed = NULL)

Arguments

Value

checktor_check_result() with passed, issues, message.

Source

The CRAN Repository Policy states that "Packages should not write in the user's home filespace ... nor anywhere else on the file system apart from the R session's temporary directory". See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), which runs this and every other check.

Examples

pkg <- example_diagnose_scenario("code_examples/home_writing_bad.R",
                                 show_content = FALSE)
lab_home_writing(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Validates ORCID and ROR identifiers carried in Authors@R person comment fields, mirroring CRAN's bad_ORCID_iDs and bad_ROR_IDs incoming checks. ORCID iDs are checked against their checksum, ROR IDs against their shape.

Usage

lab_identifier_format(path = ".", verbose = TRUE, desc = NULL)

Arguments

Details

An Authors@R that cannot be read has no identifiers to judge, so the check is reported as skipped and lab_authors() reports the field.

Value

checktor_check_result() with passed, issues, message.

Source

The CRAN incoming check run by ⁠R CMD check --as-cran⁠ NOTEs a malformed ORCID or ROR identifier in Authors@R. See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), which runs this and every other check.

Examples

pkg <- example_diagnose_scenario("description_examples/identifier_format_bad.txt",
                                 show_content = FALSE)
lab_identifier_format(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags installed.packages(), which is slow and is discouraged by its own help page.

Usage

lab_installed_packages(path = ".", verbose = TRUE, parsed = NULL)

Arguments

Value

checktor_check_result() with passed, issues, message.

Source

The CRAN Repository Policy does not let a package install other packages when it runs. See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), which runs this and every other check.

Examples

pkg <- example_diagnose_scenario("code_examples/installed_packages_bad.R",
                                 show_content = FALSE)
lab_installed_packages(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags a pkg:::fn() call in ⁠R/⁠. The triple colon reaches an object another package does not export, whose behaviour its author is free to change in routine maintenance, so a release elsewhere can break your package without warning.

Usage

lab_internal_ns(path = ".", verbose = TRUE, parsed = NULL)

Arguments

Details

A call into your own package is reported too, since a package almost never needs ::: for its own objects: everything in the namespace is already visible to the rest of it.

Value

checktor_check_result() with passed, issues, message.

Source

CRAN sends this back as "Using foo:::f instead of foo::f allows access to unexported objects. This is generally not recommended ... Please omit one colon." ⁠R CMD check⁠ reports it too, under dependencies in R code, so this check is the same finding without waiting for a full check. See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), lab_example_internal_ns() for the same rule in examples.

Examples

pkg <- example_diagnose_scenario("code_examples/internal_ns_bad.R",
                                 show_content = FALSE)
lab_internal_ns(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags a bare programming-language or statistical-computing name – Python, Java, JavaScript, Rust, MATLAB, SAS, Stata and more – in Title or Description that CRAN asks to see single-quoted. This is the language counterpart to lab_software_names(): both are policy-tier quoting checks, kept separate because a language name and a package name are different kinds of thing. R itself is never flagged in either form. No authority names it, and a bare R and a quoted 'R' both clear CRAN, so checktor takes no position on which you write. Single-letter or common-word names (C, Go, Swift) are left out because they cannot be told from ordinary prose.

Usage

lab_language_names(path = ".", verbose = TRUE, desc = NULL)

Arguments

Details

Data, markup and query formats (JSON, HTML, YAML, SQL, Markdown, LaTeX and the like) and the languages CRAN packages write either way (⁠C++⁠, Fortran, Tcl) are not flagged here. A census of CRAN in September 2026 found that packages accepted at new-package review in the previous 18 months wrote them bare 62% of the time, against 28% for the languages this check covers, so a bare one is not a policy finding. lab_format_names() reports them when you ask.

A package can extend the list through Config/checktor/language_names in its own DESCRIPTION.

Each occurrence is judged on its own, as in lab_software_names(): a term inside a quoted longer name such as 'MATLAB Runtime' or 'AWS Python SDK' is quoted, and so is one in a web address, a ⁠<doi:...>⁠ or a double-quoted book title.

Value

checktor_check_result() with passed, issues, message.

Source

Writing R Extensions, under "The DESCRIPTION file", asks for single quotes around other software; checktor applies the same to programming-language and markup names. See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), lab_software_names(), lab_format_names().

Examples

pkg <- example_diagnose_scenario("description_examples/language_names_bad.txt",
                                 show_content = FALSE)
lab_language_names(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags library() / require() in package code, which alters the user's search path. Code destined for a parallel worker is exempt, since a daemon starts with an empty search path.

Usage

lab_library_in_pkg(path = ".", verbose = TRUE, parsed = NULL)

Arguments

Value

checktor_check_result() with passed, issues, message.

Source

Writing R Extensions, under "Package Dependencies", asks package code to reach its dependencies through Imports and :: rather than attaching them with library(). See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), which runs this and every other check.

Examples

pkg <- example_diagnose_scenario("code_examples/library_in_pkg_bad.R",
                                 show_content = FALSE)
lab_library_in_pkg(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags a License that tools::analyze_license() cannot standardize, and a ⁠+ file LICENSE⁠ pointing at a file that does not exist. For MIT and the BSD licenses it also reads that file as ⁠R CMD check⁠ does: it must be the stub of YEAR and ⁠COPYRIGHT HOLDER⁠ fields (and ORGANIZATION for BSD 3-clause), so the full license text in its place is reported, as R's "License stub is invalid DCF" NOTE.

Usage

lab_license(path = ".", verbose = TRUE, desc = NULL)

Arguments

Value

checktor_check_result() with passed, issues, message.

Source

The CRAN Repository Policy treats an invalid or unrecognised License field as a rejection. See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), which runs this and every other check.

Examples

pkg <- example_diagnose_scenario("description_examples/license_bad.txt",
                                 show_content = FALSE)
lab_license(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags ⁠+ file LICENSE⁠ added to a standard license R knows, such as ⁠GPL-3 + file LICENSE⁠, ⁠LGPL-3 + file LICENSE⁠ or ⁠Apache License 2.0 + file LICENSE⁠. MIT and the BSD licenses are templates that need a LICENSE file naming the year and copyright holder, so they are left alone, as is a bare ⁠file LICENSE⁠. Each alternative of a dual license such as ⁠GPL-3 + file LICENSE | MIT + file LICENSE⁠ is judged on its own.

Usage

lab_license_file_unneeded(path = ".", verbose = TRUE, desc = NULL)

Arguments

Details

A LICENSE that adds attribution requirements or other restrictions is the exception CRAN allows. Explain it in cran-comments.md and allow the finding with Config/checktor/allow: license_file_unneeded.

Value

checktor_check_result() with passed, issues, message.

Source

The CRAN Cookbook's LICENSE files recipe gives the reviewers' text: "We do not need \"+ file LICENSE\" and the file as these are part of R. This is only needed in case of attribution requirements or other possible restrictions. Hence please omit it." R agrees in two places. ⁠R CMD check⁠ NOTEs "License components with restrictions not permitted" for a license that takes no extension, such as ⁠GPL (>= 2)⁠ or Apache, and the incoming check NOTEs "License components with restrictions and base license permitting such" for one that does, such as GPL-3. See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

lab_license() for a license R cannot read; checktor(), which runs this and every other check.

Examples

pkg <- example_diagnose_scenario("description_examples/license_file_unneeded_bad.txt",
                                 show_content = FALSE)
lab_license_file_unneeded(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags a LICENSE file still carrying template placeholders such as ⁠<YEAR>⁠ or ⁠<COPYRIGHT HOLDER>⁠.

Usage

lab_license_year(path = ".", verbose = TRUE)

Arguments

Value

checktor_check_result() with passed, issues, message.

Source

The CRAN Cookbook covers the file itself under LICENSE files. An unfilled template, with ⁠<YEAR>⁠ or ⁠<COPYRIGHT HOLDER>⁠ left in, leaves a placeholder, and no binding rule names it, which is why this sits at robustness tier. See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), which runs this and every other check.

Examples

pkg <- example_diagnose_scenario("description_examples/license_year_bad.LICENSE",
                                 show_content = FALSE)
lab_license_year(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

CRAN expects exported functions to carry a runnable ⁠\examples{}⁠ section. Walks .Rd files via tools::parse_Rd() and reports exported function topics that lack one. Data, class, methods, package-level, and re-export topics are skipped, and only topics whose name appears in NAMESPACE export() are considered (so internal helpers and S3 methods aren't required to have examples). A function that exists only for its side effect may be reported here even though it is fine, so use your judgement.

Usage

lab_missing_examples(path = ".", verbose = TRUE)

Arguments

Value

checktor_check_result() with passed, issues, missing, message.

Source

The CRAN Cookbook covers examples under Structuring of Examples. Exported functions are expected to carry an ⁠\examples{}⁠ block, a convention rather than a rule, which is why this sits at opinion tier. See vignette("check-sources", package = "checktor") for how every check maps to its source.

Examples

pkg <- example_diagnose_scenario("documentation_examples/missing_examples_bad.Rd",
                                 show_content = FALSE)
writeLines("export(undocumented_fn)", file.path(pkg, "NAMESPACE"))
lab_missing_examples(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags network access in code or examples that runs without a guard.

Usage

lab_network_operations(path = ".", verbose = TRUE)

Arguments

Details

An example is read as parsed R, so a function named in a comment, a string or an Rd ⁠%⁠ comment is not a call. A request counts as guarded when it sits in ⁠\dontrun{}⁠ or ⁠\donttest{}⁠, or in the branch of an if whose condition confines it to a connection or a session: curl::has_internet(), pingr::is_online(), capabilities("libcurl") or interactive(), including roxygen's ⁠@examplesIf⁠ with any of them. Only a guard that encloses the call excuses it, and a guard kept in a variable counts only when it is assigned in the same function and on every path to the test. A request function handed to something that calls it, as in lapply(urls, download.file), purrr::map(reqs, httr2::req_perform), do.call(httr::GET, args) or do.call("download.file", args), is a request too, and so is one called through parentheses, as in (download.file)(u, f), or wrapped by Vectorize(), memoise() or an adverb such as purrr::possibly(), which return a function that calls it. Named anywhere else, as in args(download.file) or a mock that redefines it, it is not. Neither is a helper from a network package that only builds a request, such as curl::form_file().

Value

checktor_check_result() with passed, issues, message.

Source

The CRAN Repository Policy states that "Packages which use Internet resources should fail gracefully with an informative message if the resource is not available". See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), which runs this and every other check.

Examples

pkg <- example_diagnose_scenario("network_examples/bad_network_example.Rd",
                                 show_content = FALSE)
lab_network_operations(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

CRAN expects packages (especially on resubmission) to document user-facing changes in a NEWS file. Accepts NEWS.md, NEWS, or NEWS.Rd at the package root or under ⁠inst/⁠.

Usage

lab_news_file(path = ".", verbose = TRUE)

Arguments

Value

checktor_check_result() with passed, issues, message.

Source

No formal rule. A NEWS file is expected but not required, a convention which is why this sits at opinion tier. See vignette("check-sources", package = "checktor") for how every check maps to its source.

Examples

pkg <- example_diagnose_scenario("code_examples/tf_usage_bad.R",
                                 show_content = FALSE)
invisible(file.remove(file.path(pkg, "NEWS.md")))
lab_news_file(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags a call to options(), par() or setwd() that changes the user's session state without restoring it.

Usage

lab_option_changes(path = ".", verbose = TRUE, parsed = NULL)

Arguments

Value

checktor_check_result() with passed, issues, message.

Source

The CRAN Cookbook covers this under Change of Options, Graphical Parameters and Working Directory, which asks that a function restore any options(), par() graphics parameters, or working directory it changes, using on.exit(). No clause in the Repository Policy or Writing R Extensions states it, yet it is among the most common reasons a package is sent back, because a function that quietly runs options(digits = 3) and returns has changed how the rest of the session behaves. See vignette("check-sources", package = "checktor") for how every check maps to its source.

Exemptions

Two shapes leak nothing and are exempt. A setter that captures the old value and hands it back, as in ⁠old <- options(...); invisible(old)⁠, honours the base R contract and lets the caller restore. And an option in the package's own namespace, written ⁠options(<PackageName>.key = ...)⁠, is the package managing its own configuration rather than the user's, so a deliberate session preference like options(mypkg.threshold = 5) is fine. If you keep a user setting for the session, give it a namespaced name rather than a bare global one, and restore a genuinely temporary change with on.exit(options(old)).

See Also

checktor(), which runs this and every other check.

Examples

pkg <- example_diagnose_scenario("code_examples/option_changes_bad.R",
                                 show_content = FALSE)
lab_option_changes(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Estimates the size of the source package that would be sent to CRAN (files matched by .Rbuildignore, plus standard scratch directories like .git, .Rproj.user, are excluded). Warns at the 5 MB threshold.

Usage

lab_package_size(path = ".", verbose = TRUE)

Arguments

Value

checktor_check_result() with passed, issues, message, and size_mb.

Source

The CRAN Repository Policy limits the size of the built tarball. See vignette("check-sources", package = "checktor") for how every check maps to its source.

Examples

pkg <- example_diagnose_scenario("code_examples/tf_usage_bad.R",
                                 show_content = FALSE)
# About 7 MB of data that gzip cannot shrink much
dir.create(file.path(pkg, "inst", "extdata"), recursive = TRUE)
writeBin(sin(seq_len(1e6) * 1.1), file.path(pkg, "inst", "extdata", "series.bin"))
lab_package_size(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags print() / cat() calls not guarded by an enclosing ⁠if()⁠, ⁠for()⁠, or ⁠while()⁠. The check uses the ancestor axis, so guard detection is robust regardless of formatting. Calls inside S3 ⁠print.*⁠ and ⁠format.*⁠ methods are exempt, since cat() is the required idiom there (base R's own print.default() / print.lm() use it).

Usage

lab_print_cat_usage(path = ".", verbose = TRUE, parsed = NULL)

Arguments

Value

checktor_check_result() with passed, issues, message.

Source

The CRAN Cookbook covers this under Using print()/cat(). Diagnostic output belongs in message() or warning(), which a user can suppress, rather than in cat() or print(), which they cannot. Neither the Repository Policy nor Writing R Extensions states this, but reviewers ask for it consistently. See vignette("check-sources", package = "checktor") for how every check maps to its source.

Examples

pkg <- example_diagnose_scenario("code_examples/print_cat_bad.R",
                                 show_content = FALSE)
lab_print_cat_usage(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Reads the ⁠\bibcitet{}⁠, ⁠\bibcitep{}⁠ and ⁠\bibshow{}⁠ macros R 4.6.0 added to .Rd files and reports what ⁠R CMD check⁠ would: a key that no bibliography holds, which R drops from the page, and a key cited in a file whose ⁠\bibshow{}⁠ never lists it. A REFERENCES file at the top level of the package is reported too, since ⁠R CMD check --as-cran⁠ notes it as a non-standard file.

Usage

lab_rd_bibliography(path = ".", verbose = TRUE)

Arguments

Details

A key is looked up as R looks it up: in the package's first REFERENCES.rds, REFERENCES.R or REFERENCES.bib, in the root and then ⁠inst/⁠, and in R's own bibliography. A pkg::key is looked up in that package's bibliography when the package is in Depends, Imports or Suggests and installed here. Nothing is run to read the files: a key REFERENCES.R does not give as a string is not guessed at, and no key is reported missing from a bibliography that could not be read.

Value

checktor_check_result() with passed, issues, message. It is skipped when R's own bibliography, which R 4.6.0 added, is not there to look a key up in.

Source

Writing R Extensions, under "Bibliographic citations and references", describes the macros and says the bibliography is kept in ⁠inst/⁠. ⁠R CMD check⁠ in R 4.6 warns "Could not find bibentries for the following keys" and notes "Bibentries cited but not shown in Rd file", and --as-cran notes a "Non-standard file/directory found at top level". See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), lab_rd_bibliography_files().

Examples

pkg <- example_diagnose_scenario("documentation_examples/rd_bibliography_bad.Rd",
                                 show_content = FALSE)
lab_rd_bibliography(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

For a package that cites with R 4.6.0's ⁠\bibcitet{}⁠, ⁠\bibcitep{}⁠ or ⁠\bibshow{}⁠ macros, reports a REFERENCES.bib whose package, bibtex, is not in Depends, Imports or Suggests, and a REFERENCES file that is not installed because it is outside ⁠inst/⁠ or excluded by .Rbuildignore.

Usage

lab_rd_bibliography_files(path = ".", verbose = TRUE)

Arguments

Details

R reads the bibliography when it builds the package, wherever it is, so the package's own pages are fine. But a .bib file is read with bibtex::read.bib(), so a build on a machine that installed only the declared dependencies, as r-universe and pak do, has no way to read it. And R installs only what is in ⁠inst/⁠, while another package's ⁠\bibcitet{pkg::key}⁠ looks for the bibliography in the installed package.

Value

checktor_check_result() with passed, issues, message.

Source

Writing R Extensions makes the bibliography available as inst/REFERENCES.R or inst/REFERENCES.bib, the latter "needs bibtex to be installed". No check enforces either, so this is robustness tier. See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), lab_rd_bibliography().

Examples

pkg <- example_diagnose_scenario("documentation_examples/rd_bibliography_bad.Rd",
                                 show_content = FALSE)
# Give the page a REFERENCES.bib, without 'bibtex' in Suggests to read it
dir.create(file.path(pkg, "inst"))
writeLines("@book{smith2020, author = {Ann Smith}, title = {Smoothing}, year = {2020}}",
           file.path(pkg, "inst", "REFERENCES.bib"))
lab_rd_bibliography_files(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Relative links in README.md/README.Rmd render on GitHub but break on CRAN when the target is not included in the built tarball. This flags relative links whose target is missing on disk or excluded by .Rbuildignore (and therefore absent after ⁠R CMD build⁠). Relative links to files that are included (e.g. man/figures/logo.png) are not flagged.

Usage

lab_readme_links(path = ".", verbose = TRUE)

Arguments

Details

Only what a renderer turns into a link counts. Fenced code blocks, inline code spans and HTML comments are left out of the scan, so a setup chunk calling knitr::opts_chunk[["set"]](...) is read as the code it is rather than as a link to a file named after its arguments.

Value

checktor_check_result() with passed, issues, message.

Source

No formal rule. A relative README link whose target is excluded from the tarball breaks on the package page, which is why this sits at robustness tier. See vignette("check-sources", package = "checktor") for how every check maps to its source.

Examples

pkg <- example_diagnose_scenario("code_examples/tf_usage_bad.R",
                                 show_content = FALSE)
# A relative link to a file the package does not have
writeLines("See [the guide](docs/guide.md) for details.",
           file.path(pkg, "README.md"))
lab_readme_links(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags the links in the Description that CRAN's incoming check NOTEs, applying its own rules to the same wrapped lines R reads:

Usage

lab_references(path = ".", verbose = TRUE, desc = NULL)

Arguments

Details

• a URL not enclosed in angle brackets, which should read ⁠<https://...>⁠;

• a DOI not written as ⁠<doi:prefix/suffix>⁠, such as a ⁠https://doi.org/⁠ link, a bare ⁠doi:⁠, ⁠<doi⁠ with no colon, or ⁠<10.xxxx/...>⁠;

• a publisher link that embeds a DOI, such as ⁠<https://onlinelibrary.wiley.com/doi/10.1002/...>⁠, reported only when no DOI is malformed, as R does;

• an arXiv id or link, such as ⁠<arXiv:1509.03700>⁠ or ⁠<https://arxiv.org/abs/...>⁠, which should be the e-print's arXiv DOI, ⁠<doi:10.48550/arXiv.1509.03700>⁠.

It also flags a reference with no closing >, which CRAN's page does not render as a link. Each rule is one finding, quoting every reference that breaks it. A space after the colon, as in ⁠<doi: 10.1000/xyz>⁠, is left alone: R does not NOTE it and CRAN's page links it all the same.

Value

checktor_check_result() with passed, issues, message.

Source

The CRAN incoming check run by ⁠R CMD check --as-cran⁠ NOTEs each of the four forms, with "Please enclose URLs in angle brackets (<...>).", "Please write DOIs as https://doi.org/prefix/suffix.", "Please use permanent DOI markup for linking to publications as in https://doi.org/prefix/suffix." and "Please refer to arXiv e-prints via their arXiv DOI https://doi.org/10.48550/arXiv.YYMM.NNNNN.". The submission checklist says "arXiv preprints should be referred to via their arXiv DOI", and the Cookbook's References recipe asks for "angle brackets for auto-linking". devtools::check() turns the incoming check off, so these usually surface first on win-builder or at CRAN. See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), which runs this and every other check.

Examples

pkg <- example_diagnose_scenario("description_examples/references_bad.txt",
                                 show_content = FALSE)
lab_references(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags a package whose NAMESPACE and ⁠man/⁠ no longer match the roxygen comments they were generated from, i.e. you edited roxygen and forgot to run devtools::document().

Usage

lab_roxygen_usage(path = ".", verbose = TRUE)

Arguments

Details

Two signals, both deliberately clock-free:

• A name tagged ⁠@export⁠ in a roxygen block that does not appear in NAMESPACE. This is the real cost of a forgotten document() call: the function is not exported, so users cannot call it, and ⁠R CMD check⁠ says nothing because a package is free to export whatever it likes.

• An .Rd file whose roxygen2 backlink names a source file that no longer exists, which is the orphan left behind when a source file is renamed or deleted without re-documenting.

File modification times are deliberately not used. git does not preserve them, so on a fresh clone every file carries roughly the checkout time in arbitrary order, and an mtime comparison would pass or fail at random in CI.

The check is skipped entirely unless NAMESPACE carries the roxygen2 "do not edit by hand" banner, so a hand-managed package is never flagged.

Value

checktor_check_result() with passed, issues, message.

Source

The CRAN Cookbook covers the roxygen2 side of this under Repeated Rejections of Issues in Manuals, where documentation is regenerated rather than hand-edited. A function tagged ⁠@export⁠ that never reached NAMESPACE is not actually exported, and no binding rule names it, which is why this sits at robustness tier. See vignette("check-sources", package = "checktor") for how every check maps to its source.

Examples

pkg <- example_diagnose_scenario("code_examples/roxygen_usage_bad.R",
                                 show_content = FALSE)
# NAMESPACE as roxygen2 wrote it before rescale01() was tagged @export
writeLines("# Generated by roxygen2: do not edit by hand",
           file.path(pkg, "NAMESPACE"))
lab_roxygen_usage(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags ⁠set.seed(<numeric>)⁠ calls. Multi-line forms are handled because the check matches the call AST node, not raw text.

Usage

lab_seed_setting(path = ".", verbose = TRUE, parsed = NULL)

Arguments

Value

checktor_check_result() with passed, issues, message.

Source

The CRAN Repository Policy asks a package not to modify the user's workspace, and set.seed() writes .Random.seed there, changing the random-number stream for the rest of the session. See vignette("check-sources", package = "checktor") for how every check maps to its source.

Examples

pkg <- example_diagnose_scenario("code_examples/seed_setting_bad.R",
                                 show_content = FALSE)
lab_seed_setting(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags install.packages() and friends. A package may not install software on the user's machine.

Usage

lab_software_install(path = ".", verbose = TRUE, parsed = NULL)

Arguments

Value

checktor_check_result() with passed, issues, message.

Source

The CRAN Repository Policy does not let a package download and install external software when it loads or runs. See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), which runs this and every other check.

Examples

pkg <- example_diagnose_scenario("code_examples/software_install_bad.R",
                                 show_content = FALSE)
lab_software_install(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags a package or external-software name in Title/Description that is not in single quotes, as Writing R Extensions requires.

Usage

lab_software_names(path = ".", verbose = TRUE, desc = NULL)

Arguments

Details

Each occurrence is judged on its own, so one quoted mention does not excuse a bare one elsewhere. A name is not bare inside a single-quoted span such as 'shiny.semantic', a ⁠<https://...>⁠ or ⁠<doi:...>⁠, or a function call such as purrr::map(), which are the spans CRAN's own incoming spell check skips. Nor is it bare in a plain web address, or in a double-quoted quotation such as the title of a book. A name alone in double quotes, in either field, is reported by lab_description_quoted_quotes() instead.

Value

checktor_check_result() with passed, issues, message.

Source

Writing R Extensions, under "The DESCRIPTION file", asks you to "Refer to other packages and external software in single quotes". See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), which runs this and every other check.

Examples

pkg <- example_diagnose_scenario("description_examples/software_names_bad.txt",
                                 show_content = FALSE)
lab_software_names(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Spell-checks the Title and Description fields with utils::aspell(), mirroring the aspell pass in CRAN's incoming check. It reports only words that are not already accepted somewhere: a package ⁠.aspell/⁠ dictionary, inst/WORDLIST, or a Config/checktor/acronyms, software_names, language_names or format_names field.

Usage

lab_spelling(path = ".", verbose = TRUE, desc = NULL)

Arguments

Details

The check needs a spell-check backend (aspell or hunspell) on the system. Without one it is reported as skipped, the same way CRAN's incoming check skips spelling when no backend is present, so a run on one machine may find words a run on another does not. It is therefore an opinion-tier check. When it does fire, prescribe() hands back a ready-to-paste ⁠.aspell/⁠ snippet with the flagged words filled in.

Value

checktor_check_result() with passed, issues, message; the issues are the possibly-misspelled words.

Source

The CRAN incoming check runs aspell over the Title and Description; it needs a spell-check backend and is noisy, so checktor keeps it at opinion tier. See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), prescribe().

Examples

# Needs aspell or hunspell; without one the check is skipped and finds nothing
pkg <- example_diagnose_scenario("description_examples/spelling_bad.txt",
                                 show_content = FALSE)
lab_spelling(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Under CRAN's noSuggests check a package must work without its Suggested packages installed. This flags an example that needs a Suggested package, through ⁠pkg::⁠, library() or require(), in code that runs without a guard naming that package: an enclosing ⁠if (requireNamespace("pkg", quietly = TRUE))⁠ or ⁠if (require("pkg"))⁠, including roxygen's ⁠@examplesIf⁠ with one of them. rlang::is_installed("pkg") counts too, but it needs rlang, so it is a use of rlang when rlang is only suggested.

Usage

lab_suggested_in_examples(path = ".", verbose = TRUE)

Arguments

Details

The example is read as parsed R, so a package named in a comment or a string is not a use, and a guard in a comment, a guard for another package, or one that does not enclose the use excuses nothing. Usage inside ⁠\dontrun{}⁠ is not flagged, since it never runs. Usage inside ⁠\donttest{}⁠ is, since ⁠R CMD check --as-cran⁠ runs it. A condition that is false under R CMD check keeps the use out of the check as surely as ⁠\dontrun{}⁠ does, so interactive(), identical(Sys.getenv("IN_PKGDOWN"), "true"), nzchar(Sys.getenv("IN_PKGDOWN")) and a test that NOT_CRAN is "true" excuse it too. A bare as.logical(Sys.getenv("NOT_CRAN")) does not: it is NA there, and ⁠if (NA)⁠ stops the example with an error. R's base packages, such as parallel and tools, and its recommended packages, such as MASS, Matrix and survival, ship with R and are never flagged.

Value

checktor_check_result() with passed, issues, message.

Source

Writing R Extensions, under "Suggested packages", asks that a package from Suggests used in an example be guarded so the example still runs without it. See vignette("check-sources", package = "checktor") for how every check maps to its source.

Examples

pkg <- example_diagnose_scenario("documentation_examples/suggested_in_examples_bad.Rd",
                                 show_content = FALSE)
cat("Suggests: somesuggest\n",
    file = file.path(pkg, "DESCRIPTION"), append = TRUE)
lab_suggested_in_examples(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags Sys.setenv() with no matching cleanup in the same function.

Usage

lab_sys_setenv(path = ".", verbose = TRUE, parsed = NULL)

Arguments

Value

checktor_check_result() with passed, issues, message.

Source

No clause names environment variables, but they are session state exactly as options() are, so the same restore-on-exit requirement applies. The CRAN Cookbook states it for options under Change of Options, Graphical Parameters and Working Directory. See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), which runs this and every other check.

Examples

pkg <- example_diagnose_scenario("code_examples/sys_setenv_bad.R",
                                 show_content = FALSE)
lab_sys_setenv(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags system() / system2() / shell(), which need review for portability and for shell-injection risk.

Usage

lab_system_calls(path = ".", verbose = TRUE, parsed = NULL)

Arguments

Value

checktor_check_result() with passed, issues, message.

Source

No flat rule. A raw system() or system2() call needs review for portability rather than being an automatic violation, which is why this sits at robustness tier. See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), which runs this and every other check.

Examples

pkg <- example_diagnose_scenario("code_examples/system_calls_bad.R",
                                 show_content = FALSE)
lab_system_calls(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags a temporary file created without a matching cleanup.

Usage

lab_temp_cleanup(path = ".", verbose = TRUE, parsed = NULL)

Arguments

Value

checktor_check_result() with passed, issues, message.

Source

The CRAN Cookbook covers this under Leaving Files in the Temporary Directory. tempdir() is removed at session end, so an un-unlink()ed tempfile breaks no rule, and tidiness rather than policy is why this sits at opinion tier. See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), which runs this and every other check.

Examples

pkg <- example_diagnose_scenario("temp_examples/bad_temp_usage.R",
                                 show_content = FALSE)
lab_temp_cleanup(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags bare T / F symbols that should be TRUE / FALSE. Operates on the parsed syntax tree, so T inside a string or a comment is not reported, which a plain text search could not tell apart. Named-argument names (f(T = 1)) and ⁠$T⁠ / ⁠@T⁠ extractions are excluded.

Usage

lab_tf_usage(path = ".", verbose = TRUE, parsed = NULL)

Arguments

Value

checktor_check_result() with passed, issues, message.

Source

No binding rule forbids T and F, though the CRAN Cookbook keeps a recipe for it under T/F Instead of TRUE/FALSE. They are ordinary variables (see ?logical) that R sets to TRUE and FALSE at startup but that any code can rebind, so a function reading T after something has run T <- 0 gets the wrong answer. A real risk that no rule makes citable is why this sits at robustness tier rather than policy. See vignette("check-sources", package = "checktor") for how every check maps to its source.

Examples

# show_content defaults to TRUE, so the offending file prints first
pkg <- example_diagnose_scenario("code_examples/tf_usage_bad.R")
lab_tf_usage(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags a Title that is not in title case, delegating to tools::toTitleCase(), which restores single-quoted spans so 'shiny' keeps its own capitalisation.

Usage

lab_title_case(path = ".", verbose = TRUE, desc = NULL)

Arguments

Value

checktor_check_result() with passed, issues, message.

Source

Writing R Extensions, under "The DESCRIPTION file", says the Title "should use title case"; the --as-cran incoming check flags one that does not. See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), which runs this and every other check.

Examples

pkg <- example_diagnose_scenario("description_examples/title_case_bad.txt",
                                 show_content = FALSE)
lab_title_case(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags a Title longer than 65 characters.

Usage

lab_title_length(path = ".", verbose = TRUE, desc = NULL)

Arguments

Value

checktor_check_result() with passed, issues, message.

Source

Writing R Extensions §1.1.1 notes that some package listings may truncate the title to 65 characters. That is a display width rather than a limit, so a title of exactly 65 characters still shows in full and only a longer one loses its tail. Nothing rejects a long title, which is why this sits at opinion tier. See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), which runs this and every other check.

Examples

pkg <- example_diagnose_scenario("description_examples/title_length_bad.txt",
                                 show_content = FALSE)
lab_title_length(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags a Title that is just the package name, or that opens with the name followed by a colon, as in ⁠toypkg: Fit Simple Models⁠. Package listings already show the name beside the Title, so it reads twice.

Usage

lab_title_package_name(path = ".", verbose = TRUE, desc = NULL)

Arguments

Details

R's incoming check also NOTEs a Title that opens with the name followed by a space, but that form is left alone here: when the name is an ordinary word, as in survival's "Survival Analysis", CRAN accepts it routinely, and over a hundred packages on CRAN carry one. R drops the NOTE for an update whose Title is unchanged since the version on CRAN, which checktor cannot see offline, so an older package may pass CRAN with a finding here.

Value

checktor_check_result() with passed, issues, message.

Source

Writing R Extensions, under "The DESCRIPTION file", says of the Title: "Do not repeat the package name: it is often used prefixed by the name." The incoming check NOTEs "The Title field is just the package name: provide a real title." and "The Title field starts with the package name.". See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), which runs this and every other check.

Examples

pkg <- example_diagnose_scenario("description_examples/title_package_name_bad.txt",
                                 show_content = FALSE)
lab_title_package_name(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags a Title carrying a phrase CRAN asks you to drop, such as "for R".

Usage

lab_title_redundant_phrases(path = ".", verbose = TRUE, desc = NULL)

Arguments

Value

checktor_check_result() with passed, issues, message.

Source

No formal rule. Phrases like "R package to" are redundant in a Title, a convention which is why this sits at opinion tier. See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), which runs this and every other check.

Examples

pkg <- example_diagnose_scenario("description_examples/title_redundant_phrases_bad.txt",
                                 show_content = FALSE)
lab_title_redundant_phrases(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags a Title beginning with A, An, or The.

Usage

lab_title_starts_with_article(path = ".", verbose = TRUE, desc = NULL)

Arguments

Value

checktor_check_result() with passed, issues, message.

Source

No rule. This was a mis-transplant of a real CRAN rule and is kept callable but off by default. See vignette("check-sources", package = "checktor") for how every check maps to its source.

See Also

checktor(), which runs this and every other check.

Examples

pkg <- example_diagnose_scenario("description_examples/title_starts_with_article_bad.txt",
                                 show_content = FALSE)
lab_title_starts_with_article(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Flags an ⁠\examples{}⁠ block that calls its own topic bare when that topic is not exported. Examples run with only the package's exports attached, so the call fails.

Usage

lab_unexported_example_ns(path = ".", verbose = TRUE)

Arguments

Details

⁠R CMD check⁠ does catch this, but only by RUNNING the examples, which is late and slow, and it is skipped entirely when examples are wrapped in ⁠\dontrun{}⁠ or when you check with --no-examples. This finds it statically in a second.

Value

checktor_check_result() with passed, issues, message.

Source

No formal rule. An example that reaches for an unexported object will error when it runs, which is why this sits at robustness tier. See vignette("check-sources", package = "checktor") for how every check maps to its source.

Examples

pkg <- example_diagnose_scenario("documentation_examples/unexported_example_ns_bad.Rd",
                                 show_content = FALSE)
# The package exports something, but not internal_values()
writeLines("export(public_values)", file.path(pkg, "NAMESPACE"))
lab_unexported_example_ns(pkg, verbose = FALSE)$issues
unlink(pkg, recursive = TRUE)

Description

Fetches every URL in the package, across DESCRIPTION, .Rd files and vignettes, and reports the ones that fail: 404s, other error statuses, and redirects that ought to point at their final target. This is what ⁠R CMD check --as-cran⁠ does, through the same base R machinery (tools::check_package_urls()), so you can see those findings without a full --as-cran pass and without depending on the urlchecker package.

Usage

lab_url_liveness(path = ".", verbose = TRUE)