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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

Install from CRAN

install.packages("checkhelper")

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/RtmprzMcDg/pkg.2b822dec9ea8'
#> ✔ 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)
#> Saving attachment parameters to yaml config file
#> Updating pkg.2b822dec9ea8 documentation
#> ℹ Loading pkg.2b822dec9ea8Writing ']8;;file:///tmp/RtmprzMcDg/pkg.2b822dec9ea8/NAMESPACENAMESPACE]8;;'Writing ']8;;file:///tmp/RtmprzMcDg/pkg.2b822dec9ea8/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.2b822dec9ea8[+] 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.2b822dec9ea8
#> Problem: Missing or empty return value for exported functions: my_fun
#> 
#> 
#> 
#> Problem: Doc available but need to choose between `@export` or `@noRd`: my_not_exported_doc
#> 
#> 
#> 
#> ℹ Loading pkg.2b822dec9ea8
#> $package_doc
#> # A tibble: 0 × 0
#> 
#> $data
#> # A tibble: 0 × 0
#> 
#> $functions
#> # 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.

check_clean_userspace()

#> 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 ]
#> 
#> 🌈 Your tests are over the rainbow 🌈
#> ── Running 4 example files ───────────────────────────────────── checkpackage ──
#> 
#> > text <- "in_example"
#> 
#> > file <- tempfile("in_example")
#> 
#> > cat(text, file = file)
#> Warning in check_clean_userspace(pkg = path, check_output = check_output): One
#> of the 'Run examples' .R file was created to run examples. You should not bother
#> about it
#> # A tibble: 5 × 4
#>   source       problem where                                        file        
#>   <chr>        <chr>   <chr>                                        <chr>       
#> 1 Unit tests   added   /tmp/RtmprzMcDg/pkg-2b82ce31126/checkpackage /tmp/Rtmprz…
#> 2 Unit tests   added   /tmp/RtmprzMcDg                              /tmp/Rtmprz…
#> 3 Run examples added   /tmp/RtmprzMcDg                              /tmp/Rtmprz…
#> 4 Run examples added   /tmp/RtmprzMcDg                              /tmp/Rtmprz…
#> 5 Full check   added   /tmp/RtmprzMcDg                              /tmp/Rtmprz…

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 the current directory
check_as_cran()

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.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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