Title: Deal with Check Outputs
Version: 0.1.1
Description: Deal with packages 'check' outputs and reduce the risk of rejection by 'CRAN' by following policies.
License: MIT + file LICENSE
URL: https://thinkr-open.github.io/checkhelper/, https://github.com/ThinkR-open/checkhelper
BugReports: https://github.com/ThinkR-open/checkhelper/issues
Depends: R (≥ 2.10)
Imports: cli, desc, devtools, dplyr, glue, lifecycle, magrittr, pkgbuild, purrr, rcmdcheck, roxygen2, stringr, tools, utils, whisker (≥ 0.4), withr
Suggests: attachment, callr, knitr, rmarkdown, testthat, usethis
VignetteBuilder: knitr
Config/fusen/version: 0.5.0.9009
Config/Needs/website: ThinkR-open/thinkrtemplate
Encoding: UTF-8
Language: en-US
RoxygenNote: 7.3.0
NeedsCompilation: no
Packaged: 2024-01-22 08:39:34 UTC; murielle
Author: Sebastien Rochette ORCID iD [aut, cre], Vincent Guyader ORCID iD [aut], Arthur Bréant ORCID iD [aut], Murielle Delmotte ORCID iD [aut], ThinkR [cph]
Maintainer: Sebastien Rochette <sebastien@thinkr.fr>
Repository: CRAN
Date/Publication: 2024-01-22 09:22:46 UTC

checkhelper: Deal with Check Outputs

Description

Deal with packages 'check' outputs and reduce the risk of rejection by 'CRAN' by following policies.

Author(s)

Maintainer: Sebastien Rochette sebastien@thinkr.fr (ORCID)

Authors:

Other contributors:

See Also

Useful links:

Pipe operator

Description

See magrittr::%>% for details.

Usage

lhs %>% rhs

Arguments

lhs

A value or the magrittr placeholder.

rhs

A function call using the magrittr semantics.

Value

The result of calling rhs(lhs).

Check your package with real CRAN default environment variables and check strategy

Description

[Experimental]

Usage

check_as_cran(
  pkg = ".",
  check_output = tempfile("check_output"),
  scratch = tempfile("scratch_dir"),
  Ncpus = 1,
  as_command = FALSE,
  clean_before = TRUE,
  open = FALSE
)

Arguments

pkg

pkg directory to check

check_output

Where to store check outputs. Default is a temporary directory

scratch

Where to store temporary files (cleaned after). Default is another temporary directory

Ncpus

Number of CPU used to build the package

as_command

Whether to run the check as Linux command line, instead of directly in R

clean_before

Whether to delete the previous check_output

open

Whether to open the check dir at the end of the process

Details

When you send your package on CRAN, there are multiple options set before running the checks. Here we use the CRAN settings and way of managing incoming packages used for Linux in this function check_as_cran().

Scripts and options used are directly issued from the GitHub mirror repository of the CRAN machines: https://github.com/r-devel/r-dev-web/tree/master/CRAN/. Although check_as_cran() should run on any OS, it will run CRAN parameters originally set up for Linux machines.

In the check_output, you will get the same outputs, in the same format as used by CRAN, for the pre-test of incoming packages.

Value

An object containing errors, warnings, and notes.

References

https://github.com/r-devel/r-dev-web/tree/master/CRAN/

Examples

## Not run: 
# This runs a check of the current package
# Directory to store the check outputs
check_output <- tempfile("example")
# Check the current package
check_as_cran(check_output = check_output)
# Open directory with all outputs
utils::browseURL(check_output)

## End(Not run)

check_clean_userspace

Description

[Experimental]

Usage

check_clean_userspace(pkg = ".", check_output = tempfile("dircheck"))

Arguments

pkg

Path to package to check

check_output

Path to directory where to store check results

Value

data.frame of files that are left after checks

Examples

## Not run: 
# This runs a check of the current package
all_files <- check_clean_userspace()
all_files

## End(Not run)

Create a package example producing notes and errors

Description

Create a package example producing notes and errors

Usage

create_example_pkg(
  path = tempfile(pattern = "pkg-"),
  with_functions = TRUE,
  with_extra_notes = FALSE
)

Arguments

path

Path where to store the example package

with_functions

Logical. Whether there will be functions or not (with notes)

with_extra_notes

Logical. Whether there are extra notes or not

Value

Path where the example package is stored.

Examples

create_example_pkg()

Find missing 'return' tag when function exported

Description

Find missing 'return' tag when function exported

Usage

find_missing_tags(
  package.dir = ".",
  roclets = NULL,
  load_code = NULL,
  clean = FALSE
)

Arguments

package.dir

Location of package top level directory. Default is working directory.

roclets

Character vector of roclet names to use with package. The default, NULL, uses the roxygen roclets option, which defaults to c("collate", "namespace", "rd").

load_code

A function used to load all the R code in the package directory. The default, NULL, uses the strategy defined by the load roxygen option, which defaults to load_pkgload(). See load for more details.

clean

If TRUE, roxygen will delete all files previously created by roxygen before running each roclet.

Value

a list with the 3 data.frames with the missing tags

Examples

## Not run: 
# What you will do from inside your package
find_missing_tags()

## End(Not run)
# A reproducible example on a test package
pkg_path <- create_example_pkg()
find_missing_tags(pkg_path)

Get information of a .Rda file stored inside the 'data/' folder

Description

Get information of a .Rda file stored inside the 'data/' folder

Usage

get_data_info(name, description, source)

Arguments

name

name of the file that exists in "data/"

description

description for the data

source

source of data

Value

list of information from a data.frame

See Also

use_data_doc() to add the information directly as roxygen documentation in your package.

Examples

# Store a dataset as rda file
path_project <- tempfile(pattern = "data-")
path_data <- file.path(path_project, "data")
dir.create(path_data, recursive = TRUE)
path_rda <- file.path(path_data, "iris.rda")
save(iris, file = path_rda)

# Get its information
withr::with_dir(
  path_project,
  {
    get_data_info("iris", "Iris data frame", source = "ThinkR")
  }
)

# Clean userspace
unlink(path_project, recursive = TRUE)

List no visible globals from check and separate by category

Description

List no visible globals from check and separate by category

Usage

get_no_visible(path = ".", checks, ...)

Arguments

path

Path to a package tarball or a directory.

checks

Output of rcmdcheck if already computed

...

Other parameters for rcmdcheck

Value

A list with no visible globals

Examples

## Not run: 
# This runs a check of the example package
tempdir <- tempdir()
# Create fake package
usethis::create_package(file.path(tempdir, "checkpackage"), 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()
}
", file = file.path(tempdir, "checkpackage", "R", "function.R"))

path <- file.path(tempdir, "checkpackage")
attachment::att_to_description(path = path)
get_no_visible(path)

## End(Not run)

List notes from check and identify global variables

Description

List notes from check and identify global variables

Usage

get_notes(path = ".", checks, ...)

Arguments

path

Path to a package tarball or a directory.

checks

Output of rcmdcheck if already computed

...

Other parameters for rcmdcheck

Value

A tibble with notes and information about the global variables

Examples

## Not run: 
# This runs a check of the example package
tempdir <- tempdir()
# Create fake package
usethis::create_package(file.path(tempdir, "checkpackage"), 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()
}
", file = file.path(tempdir, "checkpackage", "R", "function.R"))

path <- file.path(tempdir, "checkpackage")
attachment::att_to_description(path = path)
get_notes(path)

## End(Not run)

Description

Print no visible globals from check and separate by category

Usage

print_globals(globals, path = ".", ..., message = TRUE)

Arguments

globals

A list as issued from get_no_visible or empty

path

Path to a package tarball or a directory.

...

Other parameters for rcmdcheck

message

Logical. Whether to return message with content (Default) or return as list

Value

A message with no visible globals or a list with no visible globals

Examples

## Not run: 
# This runs a check of the example package
tempdir <- tempdir()
# Create fake package
usethis::create_package(file.path(tempdir, "checkpackage"), open = FALSE)

# Create function no visible global variables and missing documented functions
cat("
#' Function
#' @importFrom dplyr filter
#' @export
my_fun <- function() {
data %>%
ggplot2::ggplot() +
  aes(x, y, colour = new_col) +
  geom_point()
}
", file = file.path(tempdir, "checkpackage", "R", "function.R"))

path <- file.path(tempdir, "checkpackage")
attachment::att_to_description(path = path)
globals <- get_no_visible(path)
print_globals(globals = globals)

## End(Not run)

Create documentation of a rda / RData dataset in a package

Description

Create documentation of a rda / RData dataset in a package

Usage

use_data_doc(
  name,
  prefix = "doc_",
  description = "Description",
  source = "Source"
)

Arguments

name

Name of your data without extension

prefix

Add prefix for the name of the output R script

description

Description of the dataset that will be added in the documentation

source

Source of the dataset that will be presented in the documentation

Value

Creates a data documentation in a R file and returns path to the file

See Also

get_data_info() to only retrieve information without writing the documentation

Examples

## Not run: 
# This adds a R file in the current user directory
# This works if there is a "my_data.rda" file in your "data/" directory
use_data_doc("my_data", description = "Description of my_data", source = "Here the source")

## End(Not run)