`check_packages_available` reports base packages

[djvanderlaan]

I use the parallel package in a paper. initial_check_article reports that I didn't use CRANpkg or BIOpkg:

ℹ NOTE: 1 package(s) used in the text without CRANpkg or BIOpkg commands: parallel

However, parallel isn't on CRAN as it is in base.R so I use a plain \pkg to name the package.

[dicook]

Oh, are you using the old latex template or the new Rmarkdown template. If Rmarkdown you would use backticks. In latex, yes, the \pkg is appropriate to use. Make a note in the letter to editor about the initial_check_article() error. Thanks for checking your article!

[djvanderlaan]

Sorry forgot to mention that I am indeed using the latex template. This paper has been in the pipeline for a while, didn't know about the rmarkdown option untill now. And even now, it is not mentioned in the author instructions. And also on https://journal.r-project.org/submissions.html I initially read over it (perhaps make it a separate section).

Woiuld it be an option to change the following code in check_packages_available

  pkgs_used <- stringr::str_sub(
    unlist(
      stringr::str_extract_all(string = tex, "pkg\\{(.*?)\\}")),
    start = 5, end = -2)

  # Start with full list of pkgs
  declared_pkgs <- pkgs_used %in% c(CRANpkgs, BIOpkgs)

  if (any(!declared_pkgs)) {
    # Look for pkgs that were used in the text but did not have a CRANpkg{} commands
    pkgs_missing_ref <- unique(pkgs_used[!(declared_pkgs)])
    amount_missing <- length(pkgs_missing_ref)

    log_note("{amount_missing} package(s) used in the text without CRANpkg or BIOpkg commands: {paste(pkgs_missing_ref, collapse = ', ')}")
  }

into something like:

  pkgs_used <- stringr::str_sub(
    unlist(
      stringr::str_extract_all(string = tex, "pkg\\{(.*?)\\}")),
    start = 5, end = -2)

  pkgs_used <- setdiff(pkgs_used, r_base_packages)

  # Start with full list of pkgs
  declared_pkgs <- pkgs_used %in% c(CRANpkgs, BIOpkgs)

  if (any(!declared_pkgs)) {
    # Look for pkgs that were used in the text but did not have a CRANpkg{} commands
    pkgs_missing_ref <- unique(pkgs_used[!(declared_pkgs)])
    amount_missing <- length(pkgs_missing_ref)

    log_note("{amount_missing} package(s) used in the text without CRANpkg or BIOpkg commands: {paste(pkgs_missing_ref, collapse = ', ')}")
  }

#....

r_base_packages <- c("base",
    "compiler",
    "datasets",
    "graphics",
    "grDevices",
    "grid",
    "methods",
    "parallel",
    "splines",
    "stats",
    "stats4",
    "tcltk",
    "tools",
    "translations",
    "utils")

That would capture cases like this. Another option would be to only report the note when the declared_packages are also in allCRANpkgs or allBIOpkgs.