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 <[email protected]> [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.

For more details, check the dev directory.

This package was developed using biocthis.