use_bioc_pkg_templates: Create a biocthis package template R scripts

In lcolladotor/biocthis: Automate package and project setup for Bioconductor packages

Create a biocthis package template R scripts

Description

This function creates the dev directory and in it, it creates R script files that you can follow to create your own Bioconductor-friendly R package. These R scripts include all the commands you need to get started =) The commands are designed to be run on the order given, though we also encourage you to check the latest utility functions in the usethis package. The dev directory will not be version controlled as requested by Bioconductor package reviewers at https://github.com/Bioconductor/Contributions/issues/3503 and recommendations from https://contributions.bioconductor.org/general.html?q=unnec#undesirable-files.

Usage

use_bioc_pkg_templates(open = rlang::is_interactive())

Arguments

open	Open the newly created file for editing? Happens in RStudio, if applicable, or via utils::file.edit() otherwise. This argument has the same behavior as the open argument used in usethis functions.

Details

For more details on how this function came to be, check: https://github.com/r-lib/actions/issues/84 https://github.com/r-lib/styler/issues/636 https://github.com/Bioconductor/BiocCheck/issues/57 https://github.com/Bioconductor/bioconductor.org/issues/54 https://github.com/r-lib/usethis/issues/1108 as well as the "biocthis developer notes" vignette https://lcolladotor.github.io/biocthis/articles/biocthis_dev_notes.html.

Value

This function adds and/or replaces the dev files in your R package. That is:

• ⁠dev/01_create_pkg.R⁠

• ⁠dev/02_git_github_setup.R⁠

• ⁠dev/03_core_files.R⁠

• ⁠dev/04_update.R⁠

Examples

## Not run: 
## Run this function in your package
use_bioc_pkg_templates()

## End(Not run)

## Create an example package for illustrative purposes.
## Note: you do not need to run this for your own package!
pkgdir <- biocthis_example_pkg()

## Create the biocthis templates
biocthis::use_bioc_pkg_templates()

lcolladotor/biocthis documentation built on March 29, 2025, 4:22 a.m.