R CMD Issues

Common R CMD Check Issues

R CMD check is a command line tool that checks R packages against a standard set of criteria. For a pull request to pass the check must not issue any notes, warnings or errors. Below is a list of common issues and how to resolve them.

Check Fails Only on One Version

If the R CMD check workflow fails only on one or two R versions it can be helpful to reproduce the testing environment locally.

To reproduce a particular R version environment open the admiral project in the corresponding R version, comment the line source("renv/activate.R") in the .Rprofile file, restart the R session and then run the following commands in the R console.

Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS = "true")

if (!dir.exists(".library")) {
  dir.create(".library")
}

base_recommended_pkgs <- row.names(installed.packages(priority = "high"))
for (pkg in base_recommended_pkgs) {
  path <- file.path(.Library, pkg)
  cmd <- sprintf("cp -r %s .library", path)
  system(cmd)
}
assign(".lib.loc", ".library", envir = environment(.libPaths))

r_version <- getRversion()
if (grepl("^4.1", r_version)) {
  options(repos = "https://packagemanager.posit.co/cran/2021-05-03/")
} else if (grepl("^4.2", r_version)) {
  options(repos = "https://packagemanager.posit.co/cran/2022-01-03/")
} else if (grepl("^4.3", r_version)) {
  options(repos = "https://packagemanager.posit.co/cran/2023-04-20/")
} else {
  options(repos = "https://cran.rstudio.com")
}

if (!requireNamespace("remotes", quietly = TRUE)) {
  install.packages("remotes")
}
remotes::install_deps(dependencies = TRUE)
remotes::install_github("pharmaverse/pharmaversesdtm", ref = "devel")
remotes::install_github("pharmaverse/admiraldev", ref = "devel")
rcmdcheck::rcmdcheck()

This will ensure that the exact package versions we use in the workflow are installed into the hidden folder .library. That way your existing R packages are not overwritten.

Package Dependencies

> checking package dependencies ... ERROR
  Namespace dependency not required: ‘pkg’

Add pkg to the Imports or Suggests field in the DESCRIPTION file. In general, dependencies should be listed in the Imports field. However, if a package is only used inside vignettes or unit tests it should be listed in Suggests because all admiral functions would work without these “soft” dependencies being installed.

Global Variables

❯ checking R code for possible problems ... NOTE
  function_xyz: no visible binding for global variable ‘some_var’

Add some_var to the list of “global” variables in R/globals.R.

Undocumented Function Parameter

❯ checking Rd \usage sections ... WARNING
  Undocumented arguments in documentation object 'function_xyz'
    ‘some_param’

Add an @param some_param section in the header of function_xyz() and run devtools::document() afterwards.

Outdated Documentation

❯ checking for code/documentation mismatches ... WARNING
  Codoc mismatches from documentation object 'function_xyz':
  ...
  Argument names in code not in docs:
    new_param_name
  Argument names in docs not in code:
    old_param_name
  Mismatches in argument names:
    Position: 6 Code: new_param_name Docs: old_param_name

The name of a parameter has been changed in the function code but not yet in the header. Change @param old_param_name to @param new_param_name and run devtools::document().

For further reading we recommend the R-pkg manual r-cmd chapter