vignettes/biocthis.Rmd
biocthis.RmdNote 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.
biocthis
R is an open-source statistical environment which can be
easily modified to enhance its functionality via packages. biocthis
is a R package available via the Bioconductor repository for packages.
R can be installed on any operating system from CRAN after which you can install
biocthis
by using the following commands in your R session:
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("biocthis")
## Check that you have a valid Bioconductor installation
BiocManager::valid()You can install the development version from GitHub with:
BiocManager::install("lcolladotor/biocthis")biocthis is based on many other packages and in particular in those that have implemented the infrastructure needed for creating tidyverse-style R packages. That is usethis (Wickham, Bryan, Barrett, and Teucher, 2024), devtools (Wickham, Hester, Chang, and Bryan, 2022), and testthat (Wickham, 2011). It will also be helpful if you are familiar with styler (Müller and Walthert, 2024). Finally, we highly recommend that you run biocthis within RStudio Desktop.
If you are asking yourself the question “Where do I start using Bioconductor?” you might be interested in this blog post.
As package developers, we try to explain clearly how to use our
packages and in which order to use the functions. But R and
Bioconductor have a steep learning curve so it is critical
to learn where to ask for help. The blog post quoted above mentions some
but we would like to highlight the Bioconductor support site
as the main resource for getting help: remember to use the
biocthis tag and check the older
posts. Other alternatives are available such as creating GitHub
issues and tweeting. However, please note that if you want to receive
help you should adhere to the posting
guidelines. It is particularly critical that you provide a small
reproducible example and your session information so package developers
can track down the source of the error.
biocthis
We hope that biocthis will be useful for your work. Please use the following information to cite the package and the overall approach. Thank you!
## Citation info
citation("biocthis")
#> To cite package 'biocthis' in publications use:
#>
#> Collado-Torres L (2025). _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
#> 1.17.4, <http://www.bioconductor.org/packages/biocthis>.
#>
#> Collado-Torres L (2025). "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>.
#>
#> To see these entries in BibTeX format, use 'print(<citation>,
#> bibtex=TRUE)', 'toBibtex(.)', or set
#> 'options(citation.bibtex.max=999)'.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). To use the functions in this package, you need to load it as shown below.
library("biocthis")
## Load other R packages used in this vignette
library("usethis")
library("styler")biocthis in your R package
If you haven’t made an R package yet, you can do so using usethis. That
is, utilize usethis::create_package() with the package name
of your choice. If you are using RStudio
Desktop this function will open a new RStudio window and open R in
the correct location. Otherwise, you might need to use
setwd() to change directories.
In this vignette we will create an example package called
biocthispkg on a temporary directory and work in this
directory in order to illustrate how the functions work. In a real world
scenario, you would be working inside your R package and would not run
biocthis_example_pkg().
## Create an example package for illustrative purposes.
## Note: you do not need to run this for your own package!
pkgdir <- biocthis_example_pkg("biocthispkg", use_git = TRUE)
#> ✔ Creating /tmp/Rtmpq2Qnp9/biocthispkg/.
#> ✔ Setting active project to "/tmp/Rtmpq2Qnp9/biocthispkg".
#> ✔ Creating R/.
#> ✔ Writing DESCRIPTION.
#> Package: biocthispkg
#> 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]
#> 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: 7.3.2
#> ✔ Writing NAMESPACE.
#> ✔ Setting active project to "<no active project>".
#> ✔ Setting active project to "/tmp/Rtmpq2Qnp9/biocthispkg".
#> ✔ Initialising Git repo.
#> ✔ Adding ".Rproj.user", ".Rhistory", ".Rdata", ".httr-oauth", ".DS_Store", and
#> ".quarto" to .gitignore.Once you have created a package, you can use
use_bioc_pkg_templates() to create a set of scripts in the
dev (developer) directory.
## Create the bioc templates
biocthis::use_bioc_pkg_templates()
#> ✔ Creating dev/.
#> ✔ Adding "^dev$" to .Rbuildignore.
#> ✔ Adding "dev" to .gitignore.
#> ✔ Writing dev/01_create_pkg.R.
#> ✔ Writing dev/02_git_github_setup.R.
#> ✔ Writing dev/03_core_files.R.
#> ✔ Writing dev/04_update.R.If you run use_bioc_pkg_templates() inside RStudio
Desktop, then all the scripts will open on your RStudio window. Each
script contains comments that will guide you on the steps you need to do
to create your Bioconductor-friendly R package. These scripts are:
01_create_pkg.R
use_bioc_pkg_templates().02_git_github_setup.R
*.Rproj files to comply with Bioconductor’s
requirements03_core_files.R
README.Rmd and
NEWS.md filesCITATION
fileREADME.Rmd file 1
pkgdown/extra.css file for configuring pkgdown
(Wickham, Hesselberth, Salmon, Roy, and Brüggemann, 2024) documentation
websites with Bioconductor’s official colors04_update.R
Many of these steps are powered by usethis (Wickham, Bryan, Barrett et al., 2024) with some of them utilizing biocthis (Collado-Torres, 2025).
biocthis functions overview
The dev scripts use the different functions provided by
biocthis
in the suggested order. However, below we give a brief overview of what
they do.
use_bioc_badges()
Creates several Bioconductor badges for software packages (you will
need to edit them for experiment data, annotation,
workflow, or book packages) on your
README files.
## Create some Bioconductor software package badges on your README files
biocthis::use_bioc_badges()
#> ! Can't find a README for the current project.
#> ℹ See `usethis::use_readme_rmd()` for help creating this file.
#> ℹ Badge link will only be printed to screen.
#> ☐ Copy and paste the following lines into README:
#> <!-- badges: start -->
#> [](https://bioconductor.org/checkResults/release/bioc-LATEST/biocthispkg)
#> <!-- badges: end -->
#> ! Can't find a README for the current project.
#> ℹ See `usethis::use_readme_rmd()` for help creating this file.
#> ℹ Badge link will only be printed to screen.
#> ☐ Copy and paste the following lines into README:
#> <!-- badges: start -->
#> [](https://bioconductor.org/checkResults/devel/bioc-LATEST/biocthispkg)
#> <!-- badges: end -->
#> ! Can't find a README for the current project.
#> ℹ See `usethis::use_readme_rmd()` for help creating this file.
#> ℹ Badge link will only be printed to screen.
#> ☐ Copy and paste the following lines into README:
#> <!-- badges: start -->
#> [](http://bioconductor.org/packages/stats/bioc/biocthispkg/)
#> <!-- badges: end -->
#> ! Can't find a README for the current project.
#> ℹ See `usethis::use_readme_rmd()` for help creating this file.
#> ℹ Badge link will only be printed to screen.
#> ☐ Copy and paste the following lines into README:
#> <!-- badges: start -->
#> [](https://support.bioconductor.org/tag/biocthispkg)
#> <!-- badges: end -->
#> ! Can't find a README for the current project.
#> ℹ See `usethis::use_readme_rmd()` for help creating this file.
#> ℹ Badge link will only be printed to screen.
#> ☐ Copy and paste the following lines into README:
#> <!-- badges: start -->
#> [](https://bioconductor.org/packages/release/bioc/html/biocthispkg.html#since)
#> <!-- badges: end -->
#> ! Can't find a README for the current project.
#> ℹ See `usethis::use_readme_rmd()` for help creating this file.
#> ℹ Badge link will only be printed to screen.
#> ☐ Copy and paste the following lines into README:
#> <!-- badges: start -->
#> [](http://bioconductor.org/checkResults/devel/bioc-LATEST/biocthispkg/)
#> <!-- badges: end -->
#> ! Can't find a README for the current project.
#> ℹ See `usethis::use_readme_rmd()` for help creating this file.
#> ℹ Badge link will only be printed to screen.
#> ☐ Copy and paste the following lines into README:
#> <!-- badges: start -->
#> [](https://bioconductor.org/packages/release/bioc/html/biocthispkg.html#since)
#> <!-- badges: end -->This function was contributed by Milan Malfait
(@milanmlft) at pull request
35.
bioc_style()
bioc_style() helps you automatically apply a coding
style to your R package files using styler (Müller
and Walthert, 2024) that is based on the tidyverse coding style guide but
modified to make it more similar to the Bioconductor
coding style guide.
## Automatically style the example package
styler::style_pkg(pkgdir, transformers = biocthis::bioc_style())
#> ────────────────────────────────────────
#> Status Count Legend
#> ✔ 0 File unchanged.
#> ℹ 0 File changed.
#> ✖ 0 Styling threw an error.
#> ────────────────────────────────────────use_bioc_citation()
use_bioc_citation() creates an R package
CITATION file at inst/CITATION that is
pre-populated with information you might want to use for your (future)
Bioconductor package such as the Bioconductor DOIs and reference a
journal article describing your package (that you might consider
submitting to bioRxiv as a
pre-print first). Alternatively, use
usethis::use_citation().
## Create a template CITATION file that is Bioconductor-friendly
biocthis::use_bioc_citation()
#> ✔ Creating inst/.
#> ✔ Writing inst/CITATION.
#> ☐ Edit inst/CITATION.use_bioc_description()
use_bioc_description() creates an R package
DESCRIPTION file that is pre-populated with information you
might want to use for your (future) Bioconductor package such as links
to the Bioconductor Support Website and biocViews. You will
still need to manually edit the file. Alternatively, use
usethis::use_description().
## Create a template DESCRIPTION file that is Bioconductor-friendly
biocthis::use_bioc_description()
#> ℹ Leaving DESCRIPTION unchanged.
#> Package: biocthispkg
#> Title: What the Package Does (One Line, Title Case)
#> Version: 0.99.0
#> Date: 2025-03-21
#> Authors@R (parsed):
#> * First Last <first.last@example.com> [aut, cre]
#> Description: What the package does (one paragraph).
#> License: Artistic-2.0
#> URL:
#> BugReports:
#> biocViews: Software
#> Encoding: UTF-8
#> Roxygen: list(markdown = TRUE)
#> RoxygenNote: 7.3.2use_bioc_feature_request_template()
This function is related to use_bioc_issue_template(),
as it creates a GitHub issue template file specifically tailored for
feature requests. It is pre-populated with information you might want to
users to provide when giving this type of feedback.
## Create a GitHub template for feature requests that is Bioconductor-friendly
biocthis::use_bioc_feature_request_template()
#> ✔ Creating .github/.
#> ✔ Adding "^\\.github$" to .Rbuildignore.
#> ✔ Adding "*.html" to .github/.gitignore.
#> ✔ Creating .github/ISSUE_TEMPLATE/.
#> ✔ Writing .github/ISSUE_TEMPLATE/feature_request_template.md.This function was added after a related contribution by Marcel Ramos
(@LiNk-NY) at pull request
33.
use_bioc_github_action()
use_bioc_github_action() creates a GitHub Actions (GHA)
workflow file that is configured to be Bioconductor-friendly.
Alternatively, use usethis::use_github_action() for the
general GitHub Actions workflow maintained by
r-lib/actions. If this is your first time seeing the words
GitHub Actions, we highly recommend that you watch Jim
Hester’s rstudio::conf(2020) talk on this subject. Here
is how you can add this GHA workflow to your R package:
## Create a GitHub Actions workflow that is Bioconductor-friendly
biocthis::use_bioc_github_action()
#> ✔ Creating .github/workflows/.
#> ✔ Writing .github/workflows/check-bioc.yml.This GitHub Actions
(GHA) workflow is based on r-lib/actions//examples/check-standard.yaml
and others. The goal is to provide on demand R CMD checks
on Linux, macOS and Windows using a similar setup to Bioconductor-devel
and release branches. Some key features that make this GHA workflow
Bioconductor-friendly are:
R CMD check on the same platforms (Linux, macOS
and Windows) that Bioconductor supports.BiocCheck::BiocCheck() on all these platforms,
unlike the Bioconductor nightly builds. BiocCheck
is complementary to R CMD check and can help you improve
your R package.Furthermore, the use_bioc_github_action() GHA workflow
provides the following features:
run_covr (see the first few lines of the
workflow).run_pkgdown (see the
first few lines of the workflow). With
use_bioc_pkgdown_css() you can also create the
pkgdown/extra.css file that will configure your pkgdown
(Wickham, Hesselberth, Salmon et al., 2024) documentation website with
Bioconductor’s official colors.has_testthat (see the first few lines of
the workflow). Similarly, has_RUnit
controls whether you want to run the RUnit tests described
in the Bioconductor
unit testing guidelines./nocache in your commit message. Using
/nocache can be helpful for debugging
purposes. The caches are specific to the platform, the R version, and
the Bioconductor version 2. These caches help you speed up your checks
and are updated after a successful build.To help you set some of these configuration environment variables in
the GHA workflow, use_bioc_github_action() has a few
arguments that are used to update a template and customize it for your
particular repository. Several of the arguments in
use_bioc_github_action() use
base::getOption(), which enables you to edit your R profile
file with usethis::edit_r_profile() and add lines such as
the ones mentioned in the code below.
You could also edit the resulting GHA workflow to run automatically
every few days (for example, every Monday) by adding a cron
line as described in the official
GHA documentation. This could of interest to you in some situations,
though you should also be aware that it will use your GHA compute time
that can have limits depending on your GitHub account and repository
settings. If you are setting up a cron scheduled job, you
might find crontab.guru useful.
Ultimately, there are many things you can do with GHA and you might
want to use workflow as the basis for building bookdown or
rmarkdown
websites, or even docker images. Some examples are:
docker image at the end.Using a GitHub Actions workflow with Bioconductor-devel (R-devel six months in the year), regardless of which GHA workflow you use specifically, will expose you to issues with installing R packages in the latest versions of Bioconductor, CRAN, GitHub and elsewhere. At r-lib/actions#where-to-find-help you can find a list of steps you can take to get help for R GHA workflows. In the end, you might have to ask for help in:
That is, the GHA workflow provided by biocthis can break depending on changes upstream of it. In particular, it can stop working:
r-lib/actions
supports R alpha releases),rocker and other upstream tools) 3.We highly recommend watching any developments as they happen at
actions since
the r-lib team does an excellent job keeping their GHA
workflows updated. You can do so by subscribing to the RSS atom
feed for commits in their repository processed through RSS
FeedBurner that you can subscribe
to by email.
If you are interested in learning more details about how this GHA
workflow came to be, check the biocthis developer notes
vignette.
use_bioc_issue_template()
use_bioc_issue_template() creates a GitHub issue
template file that is pre-populated with information you might want to
use for your (future) Bioconductor package such as links to the
Bioconductor Support Website and examples of the information you can ask
users to provide that will make it easier for you to help your users.
Alternatively, use usethis::use_tidy_issue_template().
## Create a GitHub issue template file that is Bioconductor-friendly
biocthis::use_bioc_issue_template()
#> ✔ Writing .github/ISSUE_TEMPLATE/issue_template.md.This function was greatly modified in a contribution by Marcel Ramos
(@LiNk-NY) at pull request
33
use_bioc_news_md()
use_bioc_news_md() creates a NEWS.md
template file that is pre-populated with information you might want to
use for your (future) Bioconductor package. Alternatively, use
usethis::use_news_md().
## Create a template NEWS.md file that is Bioconductor-friendly
biocthis::use_bioc_news_md()
#> ✔ Writing NEWS.md.use_bioc_pkg_templates()
This function was already described in detail in the previous main section.
use_bioc_pkgdown_css()
use_bioc_pkgdown_css() creates the
pkgdown/extra.css file that configures your pkgdown
(Wickham, Hesselberth, Salmon et al., 2024) documentation website with
Bioconductor’s official colors.
## Create the pkgdown/extra.css file to configure pkgdown with
## Bioconductor's official colors
biocthis::use_bioc_pkgdown_css()
#> ✔ Creating pkgdown/.
#> ✔ Writing pkgdown/extra.css.This function was created after issue 34
contributed by Kevin Rue-Albrecht
@kevinrue.
use_bioc_readme_rmd()
use_bioc_readme_rmd() creates a README.Rmd
template file that is pre-populated with information you might want to
use for your (future) Bioconductor package such as Bioconductor’s
installation instructions, how to cite your package and links to the
development tools you used. Alternatively, use
usethis::use_readme_rmd().
## Create a template README.Rmd file that is Bioconductor-friendly
biocthis::use_bioc_readme_rmd()
#> ✔ Writing README.Rmd.
#> ✔ Adding "^README\\.Rmd$" to .Rbuildignore.
#> ✔ Writing .git/hooks/pre-commit.use_bioc_support()
use_bioc_support() creates a template GitHub support
template file that is pre-populated with information you might want to
use for your (future) Bioconductor package such where to ask for help
including the Bioconductor Support website. Alternatively, use
usethis::use_tidy_support().
## Create a template GitHub support file that is Bioconductor-friendly
biocthis::use_bioc_support()
#> ✔ Writing .github/SUPPORT.md.use_bioc_vignette()
use_bioc_vignette() creates a template vignette file
that is pre-populated with information you might want to use for your
(future) Bioconductor package. This template includes information on how
to cite other packages using RefManageR,
styling your vignette with BiocStyle,
instructions on how to install your package from Bioconductor, where to
ask for help, information a user might need to know before they use your
package, as well as the reproducibility information on how the vignette
was made powered by sessioninfo.
You will need to spend a significant amount of time editing this
vignette as you develop your R package. Alternatively, use
usethis::use_vignette().
## Create a template vignette file that is Bioconductor-friendly
biocthis::use_bioc_vignette("biocthispkg", "Introduction to biocthispkg")
#> ✔ Adding knitr to Suggests field in DESCRIPTION.
#> ☐ Use `requireNamespace("knitr", quietly = TRUE)` to test if knitr is
#> installed.
#> ☐ Then directly refer to functions with `knitr::fun()`.
#> ✔ Adding BiocStyle to Suggests field in DESCRIPTION.
#> ☐ Use `requireNamespace("BiocStyle", quietly = TRUE)` to test if BiocStyle is
#> installed.
#> ☐ Then directly refer to functions with `BiocStyle::fun()`.
#> ✔ Adding RefManageR to Suggests field in DESCRIPTION.
#> ☐ Use `requireNamespace("RefManageR", quietly = TRUE)` to test if RefManageR is
#> installed.
#> ☐ Then directly refer to functions with `RefManageR::fun()`.
#> ✔ Adding sessioninfo to Suggests field in DESCRIPTION.
#> ☐ Use `requireNamespace("sessioninfo", quietly = TRUE)` to test if sessioninfo
#> is installed.
#> ☐ Then directly refer to functions with `sessioninfo::fun()`.
#> ✔ Adding testthat to Suggests field in DESCRIPTION.
#> ☐ Use `requireNamespace("testthat", quietly = TRUE)` to test if testthat is
#> installed.
#> ☐ Then directly refer to functions with `testthat::fun()`.
#> ✔ Adding "knitr" to VignetteBuilder.
#> ✔ Adding "inst/doc" to .gitignore.
#> ✔ Creating vignettes/.
#> ✔ Adding "vignettes/*.html" and "vignettes/*.R" to .gitignore.
#> ✔ Adding rmarkdown to Suggests field in DESCRIPTION.
#> ☐ Use `requireNamespace("rmarkdown", quietly = TRUE)` to test if rmarkdown is
#> installed.
#> ☐ Then directly refer to functions with `rmarkdown::fun()`.
#> ✔ Writing vignettes/biocthispkg.Rmd.
#> ☐ Edit vignettes/biocthispkg.Rmd.biocthis
wouldn’t have been possible without the help of many other R package
developers. Please read the full story at the biocthis developer notes
vignette.
Thank you very much! 🙌🏽😊
The biocthis package (Collado-Torres, 2025) was made possible thanks to:
This package was developed using biocthis.
Code for creating the vignette
## Create the vignette
library("rmarkdown")
system.time(render("biocthis.Rmd", "BiocStyle::html_document"))
## Extract the R code
library("knitr")
knit("biocthis.Rmd", tangle = TRUE)Date the vignette was generated.
#> [1] "2025-03-21 15:43:19 UTC"Wallclock time spent generating the vignette.
#> Time difference of 4.546 secsR session information.
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.4.2 (2024-10-31)
#> os Ubuntu 24.04.1 LTS
#> system x86_64, linux-gnu
#> ui X11
#> language en
#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz UTC
#> date 2025-03-21
#> pandoc 3.6 @ /usr/bin/ (via rmarkdown)
#> quarto 1.5.57 @ /usr/local/bin/quarto
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
#> package * version date (UTC) lib source
#> askpass 1.2.1 2024-10-04 [2] RSPM (R 4.4.0)
#> backports 1.5.0 2024-05-23 [1] RSPM (R 4.4.0)
#> bibtex 0.5.1 2023-01-26 [1] RSPM (R 4.4.0)
#> BiocManager 1.30.25 2024-08-28 [2] CRAN (R 4.4.2)
#> BiocStyle * 2.34.0 2024-10-29 [1] Bioconductor 3.20 (R 4.4.2)
#> biocthis * 1.17.4 2025-03-21 [1] Bioconductor
#> bookdown 0.42 2025-01-07 [1] RSPM (R 4.4.0)
#> brio 1.1.5 2024-04-24 [2] RSPM (R 4.4.0)
#> bslib 0.9.0 2025-01-30 [2] RSPM (R 4.4.0)
#> cachem 1.1.0 2024-05-16 [2] RSPM (R 4.4.0)
#> cli 3.6.4 2025-02-13 [2] RSPM (R 4.4.0)
#> credentials 2.0.2 2024-10-04 [2] RSPM (R 4.4.0)
#> desc 1.4.3 2023-12-10 [2] RSPM (R 4.4.0)
#> digest 0.6.37 2024-08-19 [2] RSPM (R 4.4.0)
#> evaluate 1.0.3 2025-01-10 [2] RSPM (R 4.4.0)
#> fastmap 1.2.0 2024-05-15 [2] RSPM (R 4.4.0)
#> fs 1.6.5 2024-10-30 [2] RSPM (R 4.4.0)
#> generics 0.1.3 2022-07-05 [1] RSPM (R 4.4.0)
#> gert 2.1.4 2024-10-14 [2] RSPM (R 4.4.0)
#> glue 1.8.0 2024-09-30 [2] RSPM (R 4.4.0)
#> htmltools 0.5.8.1 2024-04-04 [2] RSPM (R 4.4.0)
#> htmlwidgets 1.6.4 2023-12-06 [2] RSPM (R 4.4.0)
#> httr 1.4.7 2023-08-15 [1] RSPM (R 4.4.0)
#> jquerylib 0.1.4 2021-04-26 [2] RSPM (R 4.4.0)
#> jsonlite 1.9.1 2025-03-03 [2] RSPM (R 4.4.0)
#> knitr 1.50 2025-03-16 [2] RSPM (R 4.4.0)
#> lifecycle 1.0.4 2023-11-07 [2] RSPM (R 4.4.0)
#> lubridate 1.9.4 2024-12-08 [1] RSPM (R 4.4.0)
#> magrittr 2.0.3 2022-03-30 [2] RSPM (R 4.4.0)
#> openssl 2.3.2 2025-02-03 [2] RSPM (R 4.4.0)
#> pillar 1.10.1 2025-01-07 [2] RSPM (R 4.4.0)
#> pkgconfig 2.0.3 2019-09-22 [2] RSPM (R 4.4.0)
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#> ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────This vignette was generated using BiocStyle (Oleś, 2024) with knitr (Xie, 2025) and rmarkdown (Allaire, Xie, Dervieux et al., 2024) running behind the scenes.
Citations made with RefManageR (McLean, 2017).
[1] J. Allaire, Y. Xie, C. Dervieux, et al. rmarkdown: Dynamic Documents for R. R package version 2.29. 2024. URL: https://github.com/rstudio/rmarkdown.
[2] L. Collado-Torres. Automate package and project setup for Bioconductor packages. https://github.com/lcolladotor/biocthisbiocthis - R package version 1.17.4. 2025. DOI: 10.18129/B9.bioc.biocthis. URL: http://www.bioconductor.org/packages/biocthis.
[3] L. Henry and H. Wickham. rlang: Functions for Base Types and Core R and ‘Tidyverse’ Features. R package version 1.1.5, https://github.com/r-lib/rlang. 2025. URL: https://rlang.r-lib.org.
[4] J. Hester. covr: Test Coverage for Packages. R package version 3.6.4, https://github.com/r-lib/covr. 2023. URL: https://covr.r-lib.org.
[5] J. Hester and J. Bryan. glue: Interpreted String Literals. R package version 1.8.0, https://github.com/tidyverse/glue. 2024. URL: https://glue.tidyverse.org/.
[6] J. Hester, H. Wickham, and G. Csárdi. fs: Cross-Platform File System Operations Based on ‘libuv’. R package version 1.6.5, https://github.com/r-lib/fs. 2024. URL: https://fs.r-lib.org.
[7] M. W. McLean. “RefManageR: Import and Manage BibTeX and BibLaTeX References in R”. In: The Journal of Open Source Software (2017). DOI: 10.21105/joss.00338.
[8] K. Müller and L. Walthert. styler: Non-Invasive Pretty Printing of R Code. R package version 1.10.3, https://styler.r-lib.org. 2024. URL: https://github.com/r-lib/styler.
[9] A. Oleś. BiocStyle: Standard styles for vignettes and other Bioconductor documents. R package version 2.34.0. 2024. DOI: 10.18129/B9.bioc.BiocStyle. URL: https://bioconductor.org/packages/BiocStyle.
[10] R Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing. Vienna, Austria, 2024. URL: https://www.R-project.org/.
[11] H. Wickham. “testthat: Get Started with Testing”. In: The R Journal 3 (2011), pp. 5–10. URL: https://journal.r-project.org/archive/2011-1/RJournal_2011-1_Wickham.pdf.
[12] H. Wickham, J. Bryan, M. Barrett, et al. usethis: Automate Package and Project Setup. R package version 3.1.0, https://github.com/r-lib/usethis. 2024. URL: https://usethis.r-lib.org.
[13] H. Wickham, W. Chang, R. Flight, et al. sessioninfo: R Session Information. R package version 1.2.3, https://sessioninfo.r-lib.org. 2025. URL: https://github.com/r-lib/sessioninfo#readme.
[14] H. Wickham, J. Hesselberth, M. Salmon, et al. pkgdown: Make Static HTML Documentation for a Package. R package version 2.1.1, https://github.com/r-lib/pkgdown. 2024. URL: https://pkgdown.r-lib.org/.
[15] H. Wickham, J. Hester, W. Chang, et al. devtools: Tools to Make Developing R Packages Easier. R package version 2.4.5, https://github.com/r-lib/devtools. 2022. URL: https://devtools.r-lib.org/.
[16] Y. Xie. knitr: A General-Purpose Package for Dynamic Report Generation in R. R package version 1.50. 2025. URL: https://yihui.org/knitr/.
You might want to use badger too, which has badges for Bioconductor download statistics. Some of the badges are only tailored for Bioconductor software packages, so you’ll have to edit them for annotation, experiment and workflow packages.↩︎
In some situations, you might want to change the
cache_version environment variable to
force GHA to use new caches.↩︎
See for example rocker-versioned2 issue 50. ↩︎