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If you use the templateR R package template, or any of the
rworkflows suite tools,
please cite:
Brian M. Schilder, Alan E. Murphy, & Nathan G. Skene (2023) The rworkflows suite: automated continuous integration for quality checking, documentation website creation, and containerised deployment of R packages, Research Square; https://doi.org/10.21203/rs.3.rs-2399015/v1
templateR is a template designed to make developing new R packages
easy by providing:
- DESCRIPTION, vignettes/, tests/, R/, man/, inst/: Basic skeleton for the package itself.
- README.Rmd: Auto-populates based on the DESCRIPTION file (that can be knit to create README.md). Also contains badges that automatically update themselves.
- inst/hex/hexSticker.Rmd: Template for creating hex stickers.
- .github/workflows/*.yml: GitHub
Actions
workflow files that will automatically trigger code checks and pushing
images to DockerHub every time you
make a push to your GitHub repo (from
rworkflows). - inst/CITATION : Allows users of your package to call
citation("<packageName>"). Also used to auto-populate the README.Rmd.
To get started, simply click on the green Use this template button
at the top right of the templateR repo.
To use certain features of rworkflows, you may need to set up one or
more GitHub
Secrets:
PAT_GITHUB[Optional]: Can grant access to private repos on GitHub Actions. You can generate your very own Personal Authentication Token withusethis::create_github_token(). See the GitHub docs for details.DOCKER_TOKEN[Optional]: Allows GitHub Actions to push to a DockerHub account.
The GitHub Actions workflows included in this template will automatically create a documentation website for your package via GitHub Pages.
After the rworkflows action has successfully run on Ubuntu for the
first time, a new branch will appear in your repo called “gh-pages”.
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If you use templateR, please cite:
author1, author2, author3 (publicationYear) articleTitle, journalName; volumeNumber, linkToPublication
if(!require("BiocManager")) install.packages("BiocManager")
BiocManager::install("neurogenomics/templateR")
library(templateR)utils::sessionInfo()## R version 4.4.2 (2024-10-31)
## Platform: aarch64-apple-darwin20
## Running under: macOS Sequoia 15.5
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## time zone: America/New_York
## tzcode source: internal
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## loaded via a namespace (and not attached):
## [1] gtable_0.3.6 jsonlite_2.0.0 renv_1.1.5
## [4] dplyr_1.1.4 compiler_4.4.2 BiocManager_1.30.26
## [7] tidyselect_1.2.1 dichromat_2.0-0.1 rvcheck_0.2.1
## [10] scales_1.4.0 yaml_2.3.10 fastmap_1.2.0
## [13] here_1.0.1 ggplot2_3.5.2 R6_2.6.1
## [16] generics_0.1.4 knitr_1.50 yulab.utils_0.2.0
## [19] tibble_3.3.0 desc_1.4.3 dlstats_0.1.7
## [22] rprojroot_2.1.0 pillar_1.11.0 RColorBrewer_1.1-3
## [25] rlang_1.1.6 badger_0.2.5 xfun_0.52
## [28] fs_1.6.6 cli_3.6.5 magrittr_2.0.3
## [31] rworkflows_1.0.6 digest_0.6.37 grid_4.4.2
## [34] rstudioapi_0.17.1 lifecycle_1.0.4 vctrs_0.6.5
## [37] evaluate_1.0.4 glue_1.8.0 data.table_1.17.8
## [40] farver_2.1.2 rmarkdown_2.29 tools_4.4.2
## [43] pkgconfig_2.0.3 htmltools_0.5.8.1