checklist

An R package for checking R packages and R code

https://github.com/inbo/checklist

Keywords

Repository

An R package for checking R packages and R code

README.Rmd

---
output: github_document
---




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# The Checklist Package 

```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE, comment = "#>", fig.path = "man/figures/README-",
  out.width = "100%", eval = FALSE
)
```

The goal of `checklist` is to provide an elaborate and strict set of checks for R packages and R code.

## Installation

You can install the package from the [INBO universe](https://inbo.r-universe.dev/builds) via

```{r universe}
# Enable the INBO universe
options(
  repos = c(
    inbo = "https://inbo.r-universe.dev", CRAN = "https://cloud.r-project.org"
  )
)
# Install the packages
install.packages("checklist", dependencies = TRUE)
```

If that doesn't work, you can install the version from [GitHub](https://github.com/inbo/checklist/) with:

```{r installation}
# install.packages("remotes")
remotes::install_github("inbo/checklist", dependencies = TRUE)
```

## Setting a default organisation

We created `checklist` with the Research Institute for Nature and Forest (INBO) in mind.
When you don't specify the organisation, `checklist` assumes the code was written by INBO personnel.
INBO has specific requirements which are not relevant for external users of `checklist`.

When you are not writing code for INBO, we recommend that you set a default `organisation`.
Below we specify the defaults for INBO.
More details in `vignette("organisation", package = "checklist")`.

```{r organisation}
library(checklist)
org <- organisation$new(
  github = "inbo", community = "inbo", email = "info@inbo.be",
  rightsholder = "Research Institute for Nature and Forest (INBO)",
  funder = "Research Institute for Nature and Forest (INBO)",
  organisation = list(
    "inbo.be" = list(
      affiliation = c(
        en = "Research Institute for Nature and Forest (INBO)",
        nl = "Instituut voor Natuur en Bosonderzoek (INBO)"
      ),
      orcid = TRUE
    ) 
  )
)
default_organisation(org = org)
```

## Using `checklist` on a package.

Before you can run the checks, you must initialise `checklist` on the package.
Either use `create_package()` to create a new package from scratch.
Or use `setup_package()` on an existing package.
More details in `vignette("getting_started", package = "checklist")`.

```{r package-initialise}
create_package()
```

Once initialised, you can run all the checks with `check_package()`.
Or run the individual checks.

```{r package-checks}
check_cran()
check_description()
check_documentation()
check_lintr()
check_filename()
check_folder()
update_citation()
```

To allow some of the warnings or notes, first run the checks and store them in an object.
Update `checklist.yml` by writing that object.

```{r package-allow-warnings}
x <- check_package()
write_checklist(x)
```

## Using `checklist` on a project.

Before you can run the checks, you must initialise `checklist` on the project.
Either use `create_project()` to create a new package from scratch.
Or use `setup_project()` on an existing package.
More details in `vignette("getting_started_project", package = "checklist")`.

```{r project-initialise}
library(checklist)
create_project()
```

Once initialised, you can run all the checks with `check_project()`.
Or run the individual checks.

```{r project-checks}
check_lintr()
check_filename()
check_folder()
update_citation()
```

To allow some of the warnings or notes, first run the checks and store them in an object.
Update `checklist.yml` by writing that object.


```{r project-allow-warnings}
x <- check_project()
write_checklist(x)
```

Owner

Citation (CITATION.cff)

cff-version: 1.2.0
message: If you use this software, please cite it using these metadata.
title: "checklist: A Thorough and Strict Set of Checks for R Packages and Source Code"
authors:
- given-names: Thierry
  family-names: Onkelinx
  affiliation: Research Institute for Nature and Forest (INBO)
  orcid: 0000-0001-8804-4216
keywords:
- quality control
- documentation
- publication
contact:
- given-names: Thierry
  family-names: Onkelinx
  affiliation: Research Institute for Nature and Forest (INBO)
  orcid: 0000-0001-8804-4216
doi: 10.5281/zenodo.4028303
license: GPL-3.0
repository-code: https://github.com/inbo/checklist/
type: software
abstract: "An opinionated set of rules for R packages and R source code projects."
identifiers:
- type: doi
  value: 10.5281/zenodo.4028303
- type: url
  value: https://inbo.github.io/checklist/
version: 0.4.2

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