The rworkflows suite: automated continuous integration for quality checking, documentation website creation, and containerised deployment of R packages
File(s)
Working paper
Author(s)
Schilder, Brian
Murphy, Alan
Skene, Nathan
Type
Working Paper
Abstract
Reproducibility is essential to the progress of research, yet achieving it remains elusive even in computational fields. Continuous Integration (CI) platforms offer a powerful way to launch automated workflows to check and document code, but often require considerable time, effort, and technical expertise to setup. We therefore developed the rworkflows suite to make robust CI workflows easy and freely accessible to all R package developers (https://github.com/neurogenomics/rworkflows). rworkflows consists of 1) a CRAN/Bioconductor-compatible R package template, 2) an R package to quickly implement a standardised workflow, and 3) a centrally maintained GitHub Action. Each time it is triggered by a push to a GitHub repository, it automatically creates virtual machines across multiple OS, installs all dependencies, runs code checks, builds/deploys a documentation website, and builds/deploys version-controlled containers with a built-in RStudio interface. Additional analyses demonstrate that >50% of all R packages are only available via GitHub, highlighting the need for accessible solutions. Thus, rworkflows greatly reduces the barriers to implementing robust and reproducible best practices.
Date Issued
2023-01-05
Citation
2023
Publisher
Research Square
Copyright Statement
© 2023 The Author(s). This work is licensed under a Creative Commons Attribution 4.0 International License.
License URL
Identifier
https://www.researchsquare.com/article/rs-2399015/v1
Publication Status
Published