checkhelper

A package to help you deal with devtools::check() outputs and helps avoids problems with CRAN submissions

Complete documentation in the {pkgdown} site: https://thinkr-open.github.io/checkhelper/

Installation

You can install the last version of checkhelper from r-universe with:

install.packages('checkhelper', repos = 'https://thinkr-open.r-universe.dev')

Or from GitHub:

remotes::install_github("thinkr-open/checkhelper")

Examples

  • Check your current package under development and get all the globals missing: no visible global variable and no visible global function
  • Detect exported functions with missing or empty @return / @noRd tags

Directly in your package in development

  • Use checkhelper::find_missing_tags() on your package in development to find which functions are exported but missing @export roxygen2 tag.
    • CRAN policy asks for every exported function to have a value (named @export when using {roxygen2}).
    • This also checks that not exported functions don’t have roxygen title, or have @noRd in case you faced Please add \value to .Rd files CRAN message for documented but not exported functions.
  • You can directly use checkhelper::print_globals() on your package instead of devtools::check(). This is a wrapper around rcmdcheck::rcmdcheck(). This will run the checks and directly list the potential “globalVariables” to add in a globals.R file.
checkhelper::find_missing_tags()

checkhelper::print_globals(quiet = TRUE)

Reproducible example with a fake package in tempdir

  • Create a fake package with
    • a function having global variables
    • a function with @export but no @return
    • a function with title but without @export and thus missing @noRd 
library(checkhelper)

# Create fake package ----
pkg_path <- tempfile(pattern = "pkg.")
dir.create(pkg_path)

# Create fake package
usethis::create_package(pkg_path, open = FALSE)
#> ✔ Setting active project to '/tmp/RtmpWS1RKv/RtmpYskIAy/pkg.91a53e683a4'
#> ✔ Creating 'R/'
#> ✔ Writing 'DESCRIPTION'
#> ✔ Writing 'NAMESPACE'
#> ✔ Setting active project to '<no active project>'

# Create function no visible global variables and missing documented functions
cat("
#' Function
#' @importFrom dplyr filter
#' @export
my_fun <- function() {
data %>%
filter(col == 3) %>%
mutate(new_col = 1) %>%
ggplot() +
  aes(x, y, colour = new_col) +
  geom_point()
}

#' Function not exported but with doc
my_not_exported_doc <- function() {
  message('Not exported but with title, should have @noRd')
}
", file = file.path(pkg_path, "R", "function.R"))

attachment::att_amend_desc(path = pkg_path)
#> Updating pkg.91a53e683a4 documentation
#> ℹ Loading pkg.91a53e683a4Writing ']8;;file:///tmp/RtmpWS1RKv/RtmpYskIAy/pkg.91a53e683a4/NAMESPACENAMESPACE]8;;'Writing ']8;;file:///tmp/RtmpWS1RKv/RtmpYskIAy/pkg.91a53e683a4/NAMESPACENAMESPACE]8;;'Writing ']8;;ide:run:pkgload::dev_help('my_fun')my_fun.Rd]8;;'Writing ']8;;ide:run:pkgload::dev_help('my_not_exported_doc')my_not_exported_doc.Rd]8;;'ℹ Loading pkg.91a53e683a4[+] 1 package(s) added: dplyr.

# Files of the package
fs::dir_tree(pkg_path, recurse = TRUE)
  • Find missing @return and find missing @noRd for not exported function with documentation
find_missing_tags(pkg_path)
#> ℹ Loading pkg.91a53e683a4
#> Missing or empty return value for exported functions: my_fun
#> 
#> 
#> 
#> Doc available but need to choose between `@export` or `@noRd`: my_not_exported_doc
#> 
#> 
#> 
#> ℹ Loading pkg.91a53e683a4
#> # A tibble: 2 × 11
#>      id filename   topic has_e…¹ has_r…² retur…³ has_n…⁴ rdnam…⁵ not_e…⁶ test_…⁷
#>   <int> <chr>      <chr> <lgl>   <lgl>   <chr>   <lgl>   <chr>   <lgl>   <chr>  
#> 1     1 function.R my_f… TRUE    FALSE   ""      FALSE   my_fun  FALSE   not_ok 
#> 2     2 function.R my_n… FALSE   FALSE   ""      FALSE   my_not… FALSE   ok     
#> # … with 1 more variable: test_has_export_or_has_nord <chr>, and abbreviated
#> #   variable names ¹​has_export, ²​has_return, ³​return_value, ⁴​has_nord,
#> #   ⁵​rdname_value, ⁶​not_empty_return_value, ⁷​test_has_export_and_return
  • Get global variables
globals <- get_no_visible(pkg_path, quiet = TRUE)
globals
#> $globalVariables
#> # A tibble: 4 × 7
#>   notes                            filep…¹ fun   is_fu…² is_gl…³ varia…⁴ propo…⁵
#>   <chr>                            <chr>   <chr> <lgl>   <lgl>   <chr>   <chr>  
#> 1 my_fun: no visible binding for … -       my_f… FALSE   TRUE    data    " impo…
#> 2 my_fun: no visible binding for … -       my_f… FALSE   TRUE    x        <NA>  
#> 3 my_fun: no visible binding for … -       my_f… FALSE   TRUE    y        <NA>  
#> 4 my_fun: no visible binding for … -       my_f… FALSE   TRUE    new_col  <NA>  
#> # … with abbreviated variable names ¹​filepath, ²​is_function,
#> #   ³​is_global_variable, ⁴​variable, ⁵​proposed
#> 
#> $functions
#> # A tibble: 5 × 7
#>   notes                            filep…¹ fun   is_fu…² is_gl…³ varia…⁴ propo…⁵
#>   <chr>                            <chr>   <chr> <lgl>   <lgl>   <chr>   <chr>  
#> 1 my_fun: no visible global funct… -       my_f… TRUE    FALSE   %>%     <NA>   
#> 2 my_fun: no visible global funct… -       my_f… TRUE    FALSE   mutate  <NA>   
#> 3 my_fun: no visible global funct… -       my_f… TRUE    FALSE   ggplot  <NA>   
#> 4 my_fun: no visible global funct… -       my_f… TRUE    FALSE   aes     <NA>   
#> 5 my_fun: no visible global funct… -       my_f… TRUE    FALSE   geom_p… <NA>   
#> # … with abbreviated variable names ¹​filepath, ²​is_function,
#> #   ³​is_global_variable, ⁴​variable, ⁵​proposed
  • Print globals to copy-paste
print_globals(globals)
#> --- Functions to add in NAMESPACE (with @importFrom ?) ---
#> 
#> my_fun: %>%, aes, geom_point, ggplot, mutate
#> 
#> --- Potential GlobalVariables ---
#> -- code to copy to your R/globals.R file --
#> 
#> globalVariables(unique(c(
#> # my_fun: 
#> "data", "new_col", "x", "y"
#> )))
  • Store the output of print_globals() in package using usethis::use_r("globals"). Note that you can also transform all these variables with .data[[variable]]

Experimental: Check that the user space is clean after checks

Have you faced a note on CRAN about non-standard things in the check directory ?

Check: for non-standard things in the check directory
Result: NOTE
    Found the following files/directories:
     ‘extrapackage’

Maybe you do not understand where these files came from.
Then, you can run check_clean_userspace() in your package directory to detect every files that you created during the check.
They could be issued from examples, tests or vignettes: check_clean_userspace() will tell you.

#> Package: checkpackage
#> Title: What the Package Does (One Line, Title Case)
#> Version: 0.0.0.9000
#> Authors@R (parsed):
#>     * First Last <first.last@example.com> [aut, cre] (YOUR-ORCID-ID)
#> Description: What the package does (one paragraph).
#> License: `use_mit_license()`, `use_gpl3_license()` or friends to pick a
#>     license
#> Encoding: UTF-8
#> Roxygen: list(markdown = TRUE)
#> RoxygenNote: 7.2.2
#> ✔ | F W S  OK | Context
#> ⠏ |         0 | in_test                                                         
#> ══ Results ═════════════════════════════════════════════════════════════════════
#> [ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
#> Warning in normalizePath(file.path(tempdir(), "callr-"), winslash = "/"):
#> path[1]="/tmp/RtmpWS1RKv/RtmpYskIAy/callr-": Aucun fichier ou dossier de ce type
#> Warning in normalizePath(file.path(tempdir(), "test.*[.](o|c|so)$"), winslash =
#> "/"): path[1]="/tmp/RtmpWS1RKv/RtmpYskIAy/test.*[.](o|c|so)$": Aucun fichier ou
#> dossier de ce type
#> Warning in normalizePath(file.path(tempdir(), "foo[.]o$"), winslash = "/"):
#> path[1]="/tmp/RtmpWS1RKv/RtmpYskIAy/foo[.]o$": Aucun fichier ou dossier de ce
#> type
#> ── Running 4 example files ───────────────────────────────────── checkpackage ──
#> 
#> > cat("#in example", file = tempfile("in_example"))
#> Warning in normalizePath(file.path(tempdir(), "callr-"), winslash = "/"):
#> path[1]="/tmp/RtmpWS1RKv/RtmpYskIAy/callr-": Aucun fichier ou dossier de ce type
#> Warning in normalizePath(file.path(tempdir(), "test.*[.](o|c|so)$"), winslash =
#> "/"): path[1]="/tmp/RtmpWS1RKv/RtmpYskIAy/test.*[.](o|c|so)$": Aucun fichier ou
#> dossier de ce type
#> Warning in normalizePath(file.path(tempdir(), "foo[.]o$"), winslash = "/"):
#> path[1]="/tmp/RtmpWS1RKv/RtmpYskIAy/foo[.]o$": Aucun fichier ou dossier de ce
#> type
#> Warning in check_clean_userspace(pkg = path, check_dir = check_dir): One of the
#> 'Run examples' .R file was created to run examples. You should not bother about
#> it
#> Warning in normalizePath(file.path(tempdir(), "callr-"), winslash = "/"):
#> path[1]="/tmp/RtmpWS1RKv/RtmpYskIAy/callr-": Aucun fichier ou dossier de ce type
#> Warning in normalizePath(file.path(tempdir(), "test.*[.](o|c|so)$"), winslash =
#> "/"): path[1]="/tmp/RtmpWS1RKv/RtmpYskIAy/test.*[.](o|c|so)$": Aucun fichier ou
#> dossier de ce type
#> Warning in normalizePath(file.path(tempdir(), "foo[.]o$"), winslash = "/"):
#> path[1]="/tmp/RtmpWS1RKv/RtmpYskIAy/foo[.]o$": Aucun fichier ou dossier de ce
#> type
#> Warning in normalizePath(all_local[[what]], winslash = "/"):
#> path[1]="/tmp/RtmpWS1RKv/RtmpYskIAy/file91a55996461d/pkg.91a53e683a4_0.0.0.9000.tar.gz":
#> Aucun fichier ou dossier de ce type
#> Warning in normalizePath(all_local[[what]], winslash = "/"):
#> path[2]="/tmp/RtmpWS1RKv/RtmpYskIAy/file91a55996461d/pkg.91a53e683a4.Rcheck/00_pkg_src/pkg.91a53e683a4/DESCRIPTION":
#> Aucun fichier ou dossier de ce type
#> Warning in normalizePath(all_local[[what]], winslash = "/"):
#> path[3]="/tmp/RtmpWS1RKv/RtmpYskIAy/file91a55996461d/pkg.91a53e683a4.Rcheck/00_pkg_src/pkg.91a53e683a4/man/my_fun.Rd":
#> Aucun fichier ou dossier de ce type
#> Warning in normalizePath(all_local[[what]], winslash = "/"):
#> path[4]="/tmp/RtmpWS1RKv/RtmpYskIAy/file91a55996461d/pkg.91a53e683a4.Rcheck/00_pkg_src/pkg.91a53e683a4/man/my_not_exported_doc.Rd":
#> Aucun fichier ou dossier de ce type
#> Warning in normalizePath(all_local[[what]], winslash = "/"):
#> path[5]="/tmp/RtmpWS1RKv/RtmpYskIAy/file91a55996461d/pkg.91a53e683a4.Rcheck/00_pkg_src/pkg.91a53e683a4/NAMESPACE":
#> Aucun fichier ou dossier de ce type
#> Warning in normalizePath(all_local[[what]], winslash = "/"):
#> path[6]="/tmp/RtmpWS1RKv/RtmpYskIAy/file91a55996461d/pkg.91a53e683a4.Rcheck/00_pkg_src/pkg.91a53e683a4/R/function.R":
#> Aucun fichier ou dossier de ce type
#> Warning in normalizePath(all_local[[what]], winslash = "/"):
#> path[7]="/tmp/RtmpWS1RKv/RtmpYskIAy/file91a55996461d/pkg.91a53e683a4.Rcheck/00check.log":
#> Aucun fichier ou dossier de ce type
#> Warning in normalizePath(all_local[[what]], winslash = "/"):
#> path[8]="/tmp/RtmpWS1RKv/RtmpYskIAy/file91a55996461d/pkg.91a53e683a4.Rcheck/00install.out":
#> Aucun fichier ou dossier de ce type
#> Warning in normalizePath(all_local[[what]], winslash = "/"):
#> path[9]="/tmp/RtmpWS1RKv/RtmpYskIAy/file91a55996461d/pkg.91a53e683a4.Rcheck/pkg.91a53e683a4-manual.log":
#> Aucun fichier ou dossier de ce type
#> Warning in normalizePath(all_local[[what]], winslash = "/"):
#> path[10]="/tmp/RtmpWS1RKv/RtmpYskIAy/file91a55996461d/pkg.91a53e683a4.Rcheck/pkg.91a53e683a4-manual.pdf":
#> Aucun fichier ou dossier de ce type
#> Warning in normalizePath(all_local[[what]], winslash = "/"):
#> path[11]="/tmp/RtmpWS1RKv/RtmpYskIAy/file91a55996461d/pkg.91a53e683a4.Rcheck/pkg.91a53e683a4/DESCRIPTION":
#> Aucun fichier ou dossier de ce type
#> Warning in normalizePath(all_local[[what]], winslash = "/"):
#> path[12]="/tmp/RtmpWS1RKv/RtmpYskIAy/file91a55996461d/pkg.91a53e683a4.Rcheck/pkg.91a53e683a4/help/aliases.rds":
#> Aucun fichier ou dossier de ce type
#> Warning in normalizePath(all_local[[what]], winslash = "/"):
#> path[13]="/tmp/RtmpWS1RKv/RtmpYskIAy/file91a55996461d/pkg.91a53e683a4.Rcheck/pkg.91a53e683a4/help/AnIndex":
#> Aucun fichier ou dossier de ce type
#> Warning in normalizePath(all_local[[what]], winslash = "/"):
#> path[14]="/tmp/RtmpWS1RKv/RtmpYskIAy/file91a55996461d/pkg.91a53e683a4.Rcheck/pkg.91a53e683a4/help/paths.rds":
#> Aucun fichier ou dossier de ce type
#> Warning in normalizePath(all_local[[what]], winslash = "/"):
#> path[15]="/tmp/RtmpWS1RKv/RtmpYskIAy/file91a55996461d/pkg.91a53e683a4.Rcheck/pkg.91a53e683a4/help/pkg.91a53e683a4.rdb":
#> Aucun fichier ou dossier de ce type
#> Warning in normalizePath(all_local[[what]], winslash = "/"):
#> path[16]="/tmp/RtmpWS1RKv/RtmpYskIAy/file91a55996461d/pkg.91a53e683a4.Rcheck/pkg.91a53e683a4/help/pkg.91a53e683a4.rdx":
#> Aucun fichier ou dossier de ce type
#> Warning in normalizePath(all_local[[what]], winslash = "/"):
#> path[17]="/tmp/RtmpWS1RKv/RtmpYskIAy/file91a55996461d/pkg.91a53e683a4.Rcheck/pkg.91a53e683a4/html/00Index.html":
#> Aucun fichier ou dossier de ce type
#> Warning in normalizePath(all_local[[what]], winslash = "/"):
#> path[18]="/tmp/RtmpWS1RKv/RtmpYskIAy/file91a55996461d/pkg.91a53e683a4.Rcheck/pkg.91a53e683a4/html/R.css":
#> Aucun fichier ou dossier de ce type
#> Warning in normalizePath(all_local[[what]], winslash = "/"):
#> path[19]="/tmp/RtmpWS1RKv/RtmpYskIAy/file91a55996461d/pkg.91a53e683a4.Rcheck/pkg.91a53e683a4/INDEX":
#> Aucun fichier ou dossier de ce type
#> Warning in normalizePath(all_local[[what]], winslash = "/"):
#> path[20]="/tmp/RtmpWS1RKv/RtmpYskIAy/file91a55996461d/pkg.91a53e683a4.Rcheck/pkg.91a53e683a4/Meta/features.rds":
#> Aucun fichier ou dossier de ce type
#> Warning in normalizePath(all_local[[what]], winslash = "/"):
#> path[21]="/tmp/RtmpWS1RKv/RtmpYskIAy/file91a55996461d/pkg.91a53e683a4.Rcheck/pkg.91a53e683a4/Meta/hsearch.rds":
#> Aucun fichier ou dossier de ce type
#> Warning in normalizePath(all_local[[what]], winslash = "/"):
#> path[22]="/tmp/RtmpWS1RKv/RtmpYskIAy/file91a55996461d/pkg.91a53e683a4.Rcheck/pkg.91a53e683a4/Meta/links.rds":
#> Aucun fichier ou dossier de ce type
#> Warning in normalizePath(all_local[[what]], winslash = "/"):
#> path[23]="/tmp/RtmpWS1RKv/RtmpYskIAy/file91a55996461d/pkg.91a53e683a4.Rcheck/pkg.91a53e683a4/Meta/nsInfo.rds":
#> Aucun fichier ou dossier de ce type
#> Warning in normalizePath(all_local[[what]], winslash = "/"):
#> path[24]="/tmp/RtmpWS1RKv/RtmpYskIAy/file91a55996461d/pkg.91a53e683a4.Rcheck/pkg.91a53e683a4/Meta/package.rds":
#> Aucun fichier ou dossier de ce type
#> Warning in normalizePath(all_local[[what]], winslash = "/"):
#> path[25]="/tmp/RtmpWS1RKv/RtmpYskIAy/file91a55996461d/pkg.91a53e683a4.Rcheck/pkg.91a53e683a4/Meta/Rd.rds":
#> Aucun fichier ou dossier de ce type
#> Warning in normalizePath(all_local[[what]], winslash = "/"):
#> path[26]="/tmp/RtmpWS1RKv/RtmpYskIAy/file91a55996461d/pkg.91a53e683a4.Rcheck/pkg.91a53e683a4/NAMESPACE":
#> Aucun fichier ou dossier de ce type
#> Warning in normalizePath(all_local[[what]], winslash = "/"):
#> path[27]="/tmp/RtmpWS1RKv/RtmpYskIAy/file91a55996461d/pkg.91a53e683a4.Rcheck/pkg.91a53e683a4/R/pkg.91a53e683a4":
#> Aucun fichier ou dossier de ce type
#> Warning in normalizePath(all_local[[what]], winslash = "/"):
#> path[28]="/tmp/RtmpWS1RKv/RtmpYskIAy/file91a55996461d/pkg.91a53e683a4.Rcheck/pkg.91a53e683a4/R/pkg.91a53e683a4.rdb":
#> Aucun fichier ou dossier de ce type
#> Warning in normalizePath(all_local[[what]], winslash = "/"):
#> path[29]="/tmp/RtmpWS1RKv/RtmpYskIAy/file91a55996461d/pkg.91a53e683a4.Rcheck/pkg.91a53e683a4/R/pkg.91a53e683a4.rdx":
#> Aucun fichier ou dossier de ce type
#> Warning in normalizePath(all_local[[what]], winslash = "/"):
#> path[30]="/tmp/RtmpWS1RKv/RtmpYskIAy/file91a55996461d/pkg.91a53e683a4.Rcheck/Rdlatex.log":
#> Aucun fichier ou dossier de ce type
#> # A tibble: 6 × 4
#>   source       problem where                                               file 
#>   <chr>        <chr>   <chr>                                               <chr>
#> 1 Unit tests   added   /tmp/RtmpWS1RKv/RtmpYskIAy/pkg-91a5111d5f0c/checkp… /tmp…
#> 2 Unit tests   added   /tmp/RtmpWS1RKv/RtmpYskIAy                          /tmp…
#> 3 Run examples added   /tmp/RtmpWS1RKv/RtmpYskIAy                          /tmp…
#> 4 Run examples added   /tmp/RtmpWS1RKv/RtmpYskIAy                          /tmp…
#> 5 Full check   added   /tmp/RtmpWS1RKv/RtmpYskIAy                          /tmp…
#> 6 Full check   deleted /tmp/RtmpWS1RKv/RtmpYskIAy                          /tmp…

Experimental: Check as CRAN with CRAN global variables

Use the exploration of CRAN scripts by the RConsortium to check a package as CRAN does it with their env. variables. See https://github.com/RConsortium/r-repositories-wg/issues/17 for more details.

check_dir <- tempfile("example")
# Check the current directory
check_as_cran(check_dir = check_dir)
# Open directory with all outputs
utils::browseURL(check_dir)

Code of Conduct

Please note that the checkhelper project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.