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.
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")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>.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.
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.
- 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.
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