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README.md

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# r.pkg.template
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![GitHub forks](https://img.shields.io/github/forks/insightsengineering/r.pkg.template?style=social)
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![GitHub Repo stars](https://img.shields.io/github/stars/insightsengineering/r.pkg.template?style=social)
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![GitHub commit activity](https://img.shields.io/github/commit-activity/m/insightsengineering/r.pkg.template)
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![GitHub contributors](https://img.shields.io/github/contributors/insightsengineering/r.pkg.template)
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![GitHub last commit](https://img.shields.io/github/last-commit/insightsengineering/r.pkg.template)
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![GitHub pull requests](https://img.shields.io/github/issues-pr/insightsengineering/r.pkg.template)
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![GitHub repo size](https://img.shields.io/github/repo-size/insightsengineering/r.pkg.template)
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![GitHub language count](https://img.shields.io/github/languages/count/insightsengineering/r.pkg.template)
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[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
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[![Downloads](https://img.shields.io/github/downloads/insightsengineering/r.pkg.template/latest/total)](https://tooomm.github.io/github-release-stats/?username=insightsengineering\&repository=r.pkg.template)
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[![Current Version](https://img.shields.io/github/r-package/v/insightsengineering/r.pkg.template/main?color=purple\&label=package%20version)](https://github.com/insightsengineering/r.pkg.template/tree/main)
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[![Open Issues](https://img.shields.io/github/issues-raw/insightsengineering/r.pkg.template?color=red\&label=open%20issues)](https://github.com/insightsengineering/r.pkg.template/issues?q=is%3Aissue+is%3Aopen+sort%3Aupdated-desc)
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[![Audit Dependencies](https://github.com/insightsengineering/r.pkg.template/actions/workflows/audit.yaml/badge.svg)](https://github.com/insightsengineering/r.pkg.template/actions/workflows/audit.yaml)
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[![BiocCheck](https://github.com/insightsengineering/r.pkg.template/actions/workflows/bioccheck.yaml/badge.svg)](https://github.com/insightsengineering/r.pkg.template/actions/workflows/bioccheck.yaml)
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[![Check URLs](https://github.com/insightsengineering/r.pkg.template/actions/workflows/links.yaml/badge.svg)](https://github.com/insightsengineering/r.pkg.template/actions/workflows/links.yaml)
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[![Version bump](https://github.com/insightsengineering/r.pkg.template/actions/workflows/version-bump.yaml/badge.svg)](https://github.com/insightsengineering/r.pkg.template/actions/workflows/version-bump.yaml)
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[![Version check](https://github.com/insightsengineering/r.pkg.template/actions/workflows/version.yaml/badge.svg)](https://github.com/insightsengineering/r.pkg.template/actions/workflows/version.yaml)
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[![gitleaks](https://github.com/insightsengineering/r.pkg.template/actions/workflows/gitleaks.yaml/badge.svg)](https://github.com/insightsengineering/r.pkg.template/actions/workflows/gitleaks.yaml)
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[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
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[![Downloads](https://img.shields.io/github/downloads/insightsengineering/r.pkg.template/latest/total)](https://tooomm.github.io/github-release-stats/?username=insightsengineering&repository=r.pkg.template)
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[![Current Version](https://img.shields.io/github/r-package/v/insightsengineering/r.pkg.template/main?color=purple&label=Version@main)](https://github.com/insightsengineering/r.pkg.template/tree/main)
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[![Open Issues](https://img.shields.io/github/issues-raw/insightsengineering/r.pkg.template?color=red&label=Open%20Issues)](https://github.com/insightsengineering/r.pkg.template/issues?q=is%3Aissue+is%3Aopen+sort%3Aupdated-desc)
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<!-- links -->
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[pre-commit]: https://pre-commit.com
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[pre-commit installation]: https://pre-commit.com/#installation
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[git hooks]: https://git-scm.com/book/en/v2/Customizing-Git-Git-Hooks
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An R package template with built-in GitHub Actions-based CI/CD workflows.
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#### Clone this template
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- Clone this repository:
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* Clone this repository:
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```bash
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git clone https://github.com/insightsengineering/r.pkg.template.git
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cd r.pkg.template
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```
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- Run the initializer script:
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* Run the initializer script:
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```bash
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./init.sh
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```
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#### Use GitHub's template importer
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- Click [here](https://github.com/insightsengineering/r.pkg.template/generate) to generate a copy of this template directly within GitHub.
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* Click [here](https://github.com/insightsengineering/r.pkg.template/generate) to generate a copy of this template directly within GitHub.
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- Clone the repository from your account/organization.
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* Clone the repository from your account/organization.
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- Run the initializer script:
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* Run the initializer script:
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```bash
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./init.sh
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All workflows originating from this repository can be repurposed by other R package GitHub repositories.
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For more information including detailed description and screenshots of workflows, please refer to [Workflows](./workflows.md).
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👉 For more information including detailed description and screenshots of workflows, please refer to the [Workflows documentation](./workflows.md).
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### Pre-commit
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### Setting up pre-commit for R project
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1. Install the `pre-commit` framework. Use the official [installation guide][pre-commit installation].
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2. Install R package `precommit`
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* Install the `pre-commit` framework. Use the official [installation guide][pre-commit installation].
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```sh
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R -e 'install.packages("precommit")'
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```
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* Install R package `precommit`
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1. Run the `use_precommit()` function to generate an example pre-commit configuration called `.pre-commit-config.yaml`:
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```sh
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R -e 'install.packages("precommit")'
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```
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```sh
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[ ! -f ".pre-commit-config.yaml" ] && R -e 'precommit::use_precommit()'
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```
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* Run the `use_precommit()` function to generate an example pre-commit configuration called `.pre-commit-config.yaml`:
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1. Install the git hooks script:
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```sh
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[ ! -f ".pre-commit-config.yaml" ] && R -e 'precommit::use_precommit()'
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```
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```sh
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pre-commit install
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```
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* Install the git hooks script:
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```sh
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pre-commit install
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```
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1. From this moment all scripts from `.pre-commit-config.yaml` will run before every `git commit`
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command. If you want to run them manually without committing you can use command
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`pre-commit run --all-files`. For more information refer official [pre-commit] documentation.
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* From this moment on, all scripts from `.pre-commit-config.yaml` will run before every `git commit` command. If you want to run them manually without committing you can use command `pre-commit run --all-files`. For more information, please refer to the official [pre-commit] documentation.
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> NOTE:
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> Frequently run `pre-commit autoupdate` to update all repositories
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> in `.pre-commit-config.yaml`.
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> NOTE: Frequently run `pre-commit autoupdate` to update all hooks in the `.pre-commit-config.yaml` configuration file.
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### Example output from pre-commit
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