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https://github.com/ThinkR-open/checkhelper

A package to help deal with devtools::check outputs
https://github.com/ThinkR-open/checkhelper

r r-package rstats

Last synced: 3 months ago
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A package to help deal with devtools::check outputs

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README 

        
---

output: github_document

---



[![checkhelper status badge](https://thinkr-open.r-universe.dev/badges/checkhelper)](https://thinkr-open.r-universe.dev)

[![R-CMD-check](https://github.com/ThinkR-open/checkhelper/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ThinkR-open/checkhelper/actions/workflows/R-CMD-check.yaml)

[![Codecov test coverage](https://codecov.io/gh/ThinkR-open/checkhelper/branch/main/graph/badge.svg)](https://app.codecov.io/gh/ThinkR-open/checkhelper/tree/main)

[![](https://cranlogs.r-pkg.org/badges/checkhelper)](https://cran.r-project.org/package=checkhelper)

[![CRAN status](https://www.r-pkg.org/badges/version/checkhelper)](https://CRAN.R-project.org/package=checkhelper)



  

# 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/



```{r setup, include = FALSE}

knitr::opts_chunk$set(

  collapse = TRUE,

  comment = "#>",

  fig.path = "man/figures/README-",

  out.width = "100%"

)

```



## Installation



Install from CRAN



```r

install.packages("checkhelper")

```



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



```r

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

```



Or from GitHub:

``` r

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.



```{r, eval=FALSE}

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`

  

```{r, eval=TRUE, results='hide'}

library(checkhelper)



# Create fake package ----

pkg_path <- tempfile(pattern = "pkg.")

dir.create(pkg_path)



# Create fake package

usethis::create_package(pkg_path, open = FALSE)



# 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)



# Files of the package

fs::dir_tree(pkg_path, recurse = TRUE)

```



- Find missing `@return` and find missing `@noRd` for not exported function with documentation



```{r}

find_missing_tags(pkg_path)

```



- Get global variables

```{r}

globals <- get_no_visible(pkg_path, quiet = TRUE)

globals

```



- Print globals to copy-paste

```{r, eval=TRUE}

print_globals(globals)

```



- 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.



```{r examples-check_clean_userspace, eval=FALSE}

check_clean_userspace()

```

```{r, echo=FALSE, message=FALSE}

pkgload::load_all()

path <- suppressWarnings(create_example_pkg())

dir.create(file.path(path, "tests", "testthat"), recursive = TRUE)

# Add a test that let file in the testthat dir

cat(

  "cat(\"#in tests\", file = \"in_test.R\")",

  file = file.path(path, "tests", "testthat", "test-in_test.R")

)



# Add an example that let file in tempdir

cat(

  "#' Function",

  "#' @return 1",

  "#' @export",

  "#' @examples",

  "#' text <- \"in_example\"",

  "#' file <- tempfile(\"in_example\")",

  "#' cat(text, file = file)",

  "in_example <- function() {",

  "1",

  "}",

  sep = "\n",

  file = file.path(path, "R", "in_example.R")

)



suppressWarnings(attachment::att_amend_desc(path = path))



check_output <- tempfile("check_output")



suppressMessages(

  all_files <- check_clean_userspace(pkg = path, check_output = check_output),

)

all_files

```



### 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.  



```{r eval=FALSE}

# Check the current directory

check_as_cran()

```



## Code of Conduct

  

  Please note that the checkhelper project is released with a [Contributor Code of Conduct](https://thinkr-open.github.io/checkhelper/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.