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Diagnose Reference Formatting in DESCRIPTION

Source: R/diagnostics-description-references.R
lab_references.Rd

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

path

Character. Path to the package directory. Default: ".".

verbose

Logical. Print diagnostic output. Default: TRUE.

desc

Optional pre-parsed DESCRIPTION, as returned by base::read.dcf(). Defaults to reading it from path.

Value

checktor_check_result() with passed, issues, message.

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.

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 doi:prefix/suffix.", "Please use permanent DOI markup for linking to publications as in doi:prefix/suffix." and "Please refer to arXiv e-prints via their arXiv DOI doi: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
#> [1] "URL not enclosed in angle brackets (<...>): https://colorcet.com"                                                    
#> [2] "DOI not written as <doi:prefix/suffix>: doi:10.1000/xyz123"                                                          
#> [3] "arXiv reference, which CRAN asks to see as its arXiv DOI: <arXiv:1509.03700> (write <doi:10.48550/arXiv.1509.03700>)"
unlink(pkg, recursive = TRUE)