Automate package and project setup for Bioconductor packages • biocthis

biocthis is an R package that expands usethis with Bioconductor-friendly templates. These templates will help you quickly create an R package that either has Bioconductor dependencies or that you are thinking of submitting to Bioconductor one day. biocthis has functions that can also enhance your current R packages that either are already distributed by Bioconductor or have Bioconductor dependencies. biocthis also includes a Bioconductor-friendly GitHub Actions workflow for your R package(s).

Note that biocthis is not a Bioconductor-core package and as such it is not a Bioconductor official package. It was made by and for Leonardo Collado-Torres so he could more easily maintain and create Bioconductor packages as listed at lcolladotor.github.io/pkgs/. Hopefully biocthis will be helpful for you too.

Installation instructions

Get the latest stable R release from CRAN. Then install biocthis from Bioconductor using the following code:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

BiocManager::install("biocthis")

And the development version from GitHub with:

BiocManager::install("lcolladotor/biocthis")

Example

Here is how you can use biocthis to create a new Bioconductor-friendly R package (illustrated using a temporary directory):

## Load biocthis
library("biocthis")

## Create an example package for illustrative purposes.
## Note: you do not need to run this for your own package!
pkgdir <- biocthis_example_pkg()
#> ✔ Creating '/var/folders/9f/82m1lr2n1fv1mk91plf2l_dr0000gn/T/Rtmp4fYodr/biocthisexample/'
#> ✔ Setting active project to '/private/var/folders/9f/82m1lr2n1fv1mk91plf2l_dr0000gn/T/Rtmp4fYodr/biocthisexample'
#> ✔ Creating 'R/'
#> ✔ Writing 'DESCRIPTION'
#> Package: biocthisexample
#> Title: What the Package Does (One Line, Title Case)
#> Version: 0.0.0.9000
#> Authors@R (parsed):
#>     * First Last <first.last@example.com> [aut, cre] (YOUR-ORCID-ID)
#> Description: What the package does (one paragraph).
#> License: `use_mit_license()`, `use_gpl3_license()` or friends to pick a
#>     license
#> Encoding: UTF-8
#> Roxygen: list(markdown = TRUE)
#> RoxygenNote: 7.2.1
#> ✔ Writing 'NAMESPACE'
#> ✔ Setting active project to '<no active project>'
#> ✔ Setting active project to '/private/var/folders/9f/82m1lr2n1fv1mk91plf2l_dr0000gn/T/Rtmp4fYodr/biocthisexample'

## Create the bioc templates
biocthis::use_bioc_pkg_templates()
#> ✔ Creating 'dev/'
#> ✔ Adding '^dev$' to '.Rbuildignore'
#> ✔ Writing 'dev/01_create_pkg.R'
#> ✔ Writing 'dev/02_git_github_setup.R'
#> ✔ Writing 'dev/03_core_files.R'
#> ✔ Writing 'dev/04_update.R'

The template dev scripts include comments and steps you can follow for making your Bioconductor-friendly R package or updating a current package. In particular, you might want to use a Bioconductor-friendly GitHub Actions workflow. If this is your first time seeings this words, we highly recommend that you watch Jim Hester’s rstudio::conf(2020) talk on this subject.

## Create a GitHub Actions workflow that is Bioconductor-friendly
biocthis::use_bioc_github_action()
#> ✔ Creating '.github/'
#> ✔ Adding '^\\.github$' to '.Rbuildignore'
#> ✔ Adding '*.html' to '.github/.gitignore'
#> ✔ Creating '.github/workflows/'
#> ✔ Writing '.github/workflows/check-bioc.yml'

## Alternatively, use the general GitHub Actions workflow maintained by
## r-lib/actions
usethis::use_github_action("check-standard")
#> ✔ Saving 'r-lib/actions/examples/check-standard.yaml@v2' to '.github/workflows/check-standard.yaml'
#> • Learn more at <https://github.com/r-lib/actions/blob/v2/examples/README.md>.

Citation

Below is the citation output from using citation('biocthis') in R. Please run this yourself to check for any updates on how to cite biocthis.

print(citation("biocthis"), bibtex = TRUE)
#> 
#> To cite package 'biocthis' in publications use:
#> 
#>   Collado-Torres L (2022). _Automate package and project setup for
#>   Bioconductor packages_. doi:10.18129/B9.bioc.biocthis
#>   <https://doi.org/10.18129/B9.bioc.biocthis>,
#>   https://github.com/lcolladotor/biocthisbiocthis - R package version
#>   1.9.1, <http://www.bioconductor.org/packages/biocthis>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     title = {Automate package and project setup for Bioconductor packages},
#>     author = {Leonardo Collado-Torres},
#>     year = {2022},
#>     url = {http://www.bioconductor.org/packages/biocthis},
#>     note = {https://github.com/lcolladotor/biocthisbiocthis - R package version 1.9.1},
#>     doi = {10.18129/B9.bioc.biocthis},
#>   }
#> 
#>   Collado-Torres L (2022). "Automate package and project setup for
#>   Bioconductor packages." _bioRxiv_. doi:10.1101/TODO
#>   <https://doi.org/10.1101/TODO>,
#>   <https://www.biorxiv.org/content/10.1101/TODO>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Article{,
#>     title = {Automate package and project setup for Bioconductor packages},
#>     author = {Leonardo Collado-Torres},
#>     year = {2022},
#>     journal = {bioRxiv},
#>     doi = {10.1101/TODO},
#>     url = {https://www.biorxiv.org/content/10.1101/TODO},
#>   }

Please note that the biocthis was only made possible thanks to many other R and bioinformatics software authors, which are cited either in the vignettes and/or the paper(s) describing this package.

Code of Conduct

Please note that the biocthis project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Development tools

Continuous code testing is possible thanks to GitHub actions through usethis, remotes, and rcmdcheck customized to use Bioconductor’s docker containers and BiocCheck.
Code coverage assessment is possible thanks to codecov and covr.
The documentation website is automatically updated thanks to pkgdown.
The code is styled automatically thanks to styler.
The documentation is formatted thanks to devtools and roxygen2.