Awesome R Package Development Tools

Keywords

r packages, software development, software engineering, r

A curated list of awesome tools to assist 📦 development in R programming language.

What is included?

• Only tools helpful for package development are included, and not other resources (e.g. books).
• All relevant tools are included, irrespective of their availability on CRAN/Bioconductor.
• Tools which are part of publicly archived/retired GitHub repositories are not included.

If you wish to suggest any additional tools, please make a PR or create an issue here.

Code of Conduct

Please note that the awesome-r-pkgtools project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Swiss army knives 🛠

Tools useful across all stages of package development (some of these are meta-packages and their component packages are also included in respective sections for the sake of completeness), irrespective of whether the package is meant to be submitted to CRAN or Bioconductor.

• {usethis}

• {devtools}

• {biocthis}

• {packager}

• {pacs}

• {pkgmaker}

Package templates 💀

Generic

• {pkgkitten} (useful for creating new packages for R)

• {rcompendium} (to make the creation of R package/research compendium easier)

• {r.pkg.template} (an opinionated R package template with CI/CD built-in)

• {skeletor} (An R Package Skeleton Generator)

RMarkdown-based

• {fusen} (to build a package from RMarkdown files)

• {litr} (to write a complete R package in a single R markdown document)

Shiny

• {golem} (framework for building shiny applications)

• {leprechaun} (leaner framework for building shiny applications)

• {rhino} (a framework to build high quality, enterprise-grade Shiny apps at speed)

Meta-packages

• {pkgverse} (for package meta-verse)

• {metamakr} (for package meta-verse)

Naming things 🧸

• {available} (to check if a package name is available to use)

• {collidr} (to check for namespace collisions)

• {changer} (to change the name of an existing R package)

Working with package components

• {rprojroot} (accessing files w.r.t. package root directory)

• {desc} (manipulating DESCRIPTION files)

• {withr} (to manage package side effects by safely and temporarily modifying global states)

• {pkgload} (to simulate the process of installing and loading a package)

• {pkgbuild} (to find tools needed to build packages)

Package configuration

• {config} (to manage environment specific configuration values)

Package management tools

• {pkgcache} (to cache ‘CRAN’-like metadata and packages)

Documentation 📚

Manual

• {roxygen2} (to generate R package documentation from inline R comments)

• {Rd2roxygen} (in case you inherit a project where documentation was not written using {roxygen2})

• {roxyglobals} (to generate global variables with {roxygen2} documentation)

• {sinew} (generate {roxygen2} skeletons)

• {roclang} (helpers for diffusing content across function documentation)

• {Rdpack} (for inserting references, figures, and evaluated examples in Rd docs)

• {roxygen2md} (to allow Markdown syntax usage in {roxygen2} documentation)

• {rd2markdown} (to convert .Rd package documentation files into markdown files)

• {rd2list} (converts Rd docs to a human-readable list)

• {pasteAsComment} (RStudio addin for pasting copied code as roxygen comment)

• roxygen2Comment (Rstudio addin for adding and remove {roxygen2} comment)

Math rendering in HTML/PDF manual

• {katex} (to convert latex math expressions to HTML for use in package manual pages)

• {mathjaxr} (provides ‘MathJax’ and macros to enable its use within Rd files for rendering equations in the HTML help files)

• {mathml} (translates R expressions to ‘MathML’ or ‘MathJax’ so that they can be rendered in HTML manual and Shiny apps)

Vignettes

• {knitr} (a general-purpose tool for dynamic report generation to be used as a vignette builder for R package vignettes)

• {rmarkdown} (to convert R Markdown documents to a variety of formats)

• {quarto} (provides R interface to frequently used operations in the Quarto CLI)

• {R.rsp} (for incorporating static and dynamic vignettes)

• {RmdConcord} (to provide support for concordances in R Markdown files)

• {prettydoc} (creates lightweight yet pretty vignettes)

Tutorials

• {learnr} (to turn any R Markdown document into an interactive tutorial)

Website

• {pkgdown} (static website for package documentation)

• {gitdown} (software changes as a gitbook)

• {altdoc} (use docute, docsify, or MkDocs to create a static website for package documentation)

Translation

• {potools} (for translating messages and checking the “health” of the messaging corpus)

Lifecycle

• {lifecycle} (to manage the life cycle of exported functions)

Badges and stickers

• {badger} (to query information and generate badges for use in README)

• {badgen} (provides bindings to badgen to generate beautiful ‘svg’ badges in R without internet access)

• {hexSticker} (helper functions for creating reproducible hexagon sticker purely in R)

• {hexFinder} (to scavenge the web for possible hex logos for packages)

• hexwall (to create a wall of hexstickers)

Presentation

• {xaringan} (an RMarkdown output format for remark.js slides)

Book

• {bookdown} (authoring framework for books and technical documents with R Markdown)

Change log and versioning

• {fledge} (to streamline the process of updating change logs and versioning R packages developed in git repositories)

• {newsmd} (utilities to add updates to the NEWS.md file)

• {autonewsmd} (to auto-generate change log using conventional commits)

Documentation quality ✒️

• {docreview} (to check quality of docs)

• {spelling} (to check for spelling mistakes)

• {gramr} (for grammar suggestions)

Unit testing 🧪

Generic R Packages

• {testthat} (a testing framework for R that is easy to learn and use; also provides snapshot testing)

• {patrick} (for parameterized unit testing with {testthat})

• {testdat} (a family of functions and reporting tools focused on checking of data)

• {tinytest} (zero-dependency unit testing framework that installs tests with the package)

• {tinysnapshot} (snapshots for unit tests using the {tinytest} framework)

• {tinytest2JUnit} (to convert {tinytest} output to JUnit XML needed by CI/CD)

• {RUnit} (a standard unit testing framework, with additional code inspection and report generation tools)

• {testit} (a simple package for testing R packages)

• {realtest} (a framework unit testing that distinguishes between expected, acceptable, current, fallback, ideal, or regressive behaviours)

• {roxytest} (inline {testthat} tests with {roxygen2})

• {roxut} (to write the unit tests in the same file as the function)

• {exampletestr} (tests based on package examples)

• {unitizer} (simplifies regression tests by comparing objects produced by test code with earlier versions of those same objects)

• {r-hedgehog} (property based testing)

• {autotest} (automatic mutation testing of R packages)

• {cucumber} (an implementation of the Cucumber testing framework in R)

Markdown documents

• {pandoc} (to check Markdown documents across various version of Pandoc)

Shiny applications

• {shinytest} (testing Shiny apps)

• {shinytest2} (testing Shiny apps using a headless Chromium web browser)

• {shinyloadtest} (to load test deployed Shiny apps)

Web/database applications

• {httptest} (a test environment for HTTP requests in R)

• {httptest2} (the same for {httr2} package)

• {webfakes} (provides fake web apps for HTTP testing R packages)

• {dittodb} (makes testing against databases easy)

Visual regression testing

• {vdiffr} (for visual regression testing with {testthat})

• {gdiff} (for performing graphical difference different package or R versions)

Mock testing

• {mockthat} (provides a way to mock package function for unit testing, while coping with S3 dispatch)

• {mockr} (provides a way to mock package function for unit testing)

• {mockery} (provides a way to mock package function for unit testing and can be used with any testing framework)

Mutation testing

• {mutant} (mutation testing for R)

Helpers for testing frameworks

• {testthis} (RStudio addins for working with files that contain tests)

• {xpectr} (builds unit tests with the {testthat} package by providing tools for generating expectations)

• {testdown} (turn {testthat} results into a {bookdown} project)

• {ttdo} (provides ‘diff’-style comparison of R objects for {tinytest} framework)

Code/Document Formatting 🧽

• {styler} (to format code according to a style guide)

• {stylermd} (to format text in Markdown documents)

• {formatR} (to format R source code)

• {RFormatter} (extension of {formatR} with slightly improved heuristics)

• {grkstyle} (extension package for {styler} that supports author’s personal code style preferences)

• {codegrip} (addin for RStudio IDE to reshape R code and navigate across syntactic constructs)

• {BiocStyle} (provides standard formatting styles for Bioconductor PDF and HTML documents)

• AlignAssign (RStudio addin that aligns the assignment operators within a highlighted area)

• {snakecase} (helpful for having consistent case while naming objects in the package)

• {dotInternals} (to distinguish non-exported package functions by prepending their names with a dot)

Code analysis 🗂⏱

General

• {codetools} (code analysis tools for R)

• {goodpractice} (Swiss army knife for good practices)

• {inteRgrate} (provides an opinionated set of rules for R package development)

• {pkgcheck} (checks if package follows good practices recommended for packages in the rOpenSci ecosystem)

• {pkgstats} (a static code analysis tool)

• {rchk} (provides several bug-finding tools that look for memory protection errors in C source code using R API)

• {sourcetools} (tools for reading, tokenizing, and parsing R code)

• {precommit} (git hooks for common tasks like formatting files, spell checking, etc.)

Code review

• {PaRe} (reviews other packages during code review by looking at their dependencies, code style, code complexity, and how internally defined functions interact with one another)

Code coverage

• {covr} (to compute code coverage)

• {covrpage} (to include summary README of code coverage and more detailed information about tests)

• {covtracer} (provides tools for contextualizing tests)

Code quality

• {lintr} (static code analysis)

• {roxylint} (to lint {roxygen2}-generated documentation)

• {checkglobals} (to check R-packages for globals and imports)

• {CodeDepends} (analysis of R code for reproducible research and code view)

• {adaptalint} (infer code style from one package and use it to check another)

• {roger} (provides tools for grading the coding style and documentation of R scripts)

• {cleanr} (tests code for some of the most common code layout flaws)

Code complexity

• {cyclocomp} (to index the complexity of a function)

• {pkgGraphR} (to visualize the relationship between functions in an R package)

Code similarity

• {dupree} (identifies code blocks that have a high level of similarity within a set of R files)

• {rscc} (provides source code similarity evaluation by variable/function names)

• {SimilaR} (quantifies the similarity of the code-base of R functions by means of program dependence graphs)

Compiled code

• {memtools} (to solve memory leaks)

• {sanitizers} (to test for memory violations and other undefined behaviour)

• {cppcheckR} (to check C and C++ code using Cppcheck)

JavaScript code

• {jshintr} (to run JSHint for static code analysis for JavaScript code included in the package)

Lines of code

• {cloc} (counts blank lines, comment lines, and physical lines of source code in source files)

Refactoring

• {refactor} (to check speed and performance of both the original and refactored version of code)

Code performance ⏱️

Benchmarking

• {bench} (provides high precision benchmarks for R expressions)

• {microbenchmark} (provides infrastructure to accurately measure and compare the execution time of R expressions)

• {tictoc} (provides functions for timing R scripts)

• {touchstone} (benchmarking pull requests)

Profiling

• {profvis} (to profile and visualize profiling data)

• {proffer} (to create friendlier, faster visualizations for profiling data)

• {jointprof} (to profile packages with native code in C, C++, Fortran, etc.)

• {xrprof} (an external sampling profiler for R programs)

Dependency Management ⚖️

• {pkgdepends} (to find recursive dependencies of from various sources)

• {deepdep} (to visualize and explore package dependencies)

• {itdepends} (to assess usage, measure weights, visualize proportions, and assist removal of dependencies)

• {DependenciesGraphs} (to visualize package dependencies)

• {DependencyReviewer} (to investigate packages during code review by looking at their dependencies)

• {deps} (to manage source code dependencies by decorating R code with roxygen-style comments)

• {pkgnet} (to build a graph representation of a package and its dependencies)

• {functiondepends} (to find functions in an unstructured directory and explore their dependencies)

• {pkgndep} (checks the heaviness of the packages used)

• {oysteR} (to secure package against insecure dependencies)

• {attachment} (to deal with package dependencies during package development)

CRAN/Bioconductor checks, submission, and status 📬

• {rcmdcheck} (to run R CMD check form R programmatically)

• {BiocCheck} (to run Bioconductor-specific package checks)

• {rhub} (to run R CMD check on CRAN architectures)

• {checkhelper} (to help avoid problems with CRAN submissions)

• {extrachecks} (to run some additional CRAN checks)

• {foghorn} (to check for results and submission portal status)

• {urlchecker} (to checks for URL rot)

Usage 🙈

• {cranlogs} (for computing CRAN download counts)

• {packageRank} (for visualizing CRAN download counts)

• {dlstats} (provides download statistics for packages)

CI/CD 📟

CI/CD: continuous integration and either continuous delivery or continuous deployment

• actions (provides GitHub Actions relevant for R)

• actions-sync (to manage GitHub Actions workflows across repositories)

• {rworkflows} (GitHub Actions to automates testing, documentation website building, and containerized deployment)

• AzureR (a family of packages for working with Azure from R)

• r-appveyor (for AppVeyor)

• {tic} (for Circle CI and GitHub Actions)

• {circle} (for Circle CI)

• {jenkins} (for Jenkins CI)

• {cronR} (to schedule R scripts/processes with the cron scheduler)

Security/Privacy 👮

• {digest} (for the creation of hash digests of arbitrary R objects)

• {hash} (implements a data structure similar to hashes in Perl and dictionaries in Python but with a purposefully R flavor)

• {gpg} (GNU privacy guard for R)

Build systems

• {fakemake} (to mock Unix Make build system in case it is unavailable)

Validation frameworks

• {valtools} (in clinical research and drug development)

Debugging 🔭

• {debugme} (provides helpers to specify debug messages as special string constants, and control debugging of packages via environment variables)

• {debugr} (tools to print out the value of R objects/expressions while running an R script)

• {winch} (provides stack traces for call chains that cross between R and C/C++ function calls)

• {flow} (to visualize as flow diagrams the logic of functions, expressions, or scripts, which can ease debugging)

• {boomer} (provides debugging tools to inspect the intermediate steps of a call)

Input validation 🔬

• {checkmate} (fast and versatile argument checks)

• {assertthat} (to declare the pre and post conditions that you code should satisfy and to produce friendly error messages)

• {assertive} (provides readable check functions to ensure code integrity)

• {pkgcond} (better error messages for package users)

• {dreamerr} (a simple and intuitive, yet powerful and flexible, way to check the arguments passed to a function and to offer informative error messages)

• {erify} (to check arguments and generate readable error messages)

• {validate} (to check whether data lives up to expectations based on the domain-specific knowledge)

Package metadata 🖨

• {codemetar} (provides utilities to generate, parse, and modify codemeta.jsonld files automatically for R packages), or {codemeta} (a leaner version of {codemetar})

• {cffr} (provides utilities to generate, parse, modify and validate CITATION.cff files automatically for R packages)

• {citation} (creates CITATION.cff from R package metadata)

• {pkgapi} (to create the map of function calls in a package)

• {riskmetric} (provides a collection of risk metrics to evaluate the quality of R packages)

• {packagemetrics} (for comparing among packages)

• {devtoolbox} (to create a summary report for R package and to extract dependency statistics in a tidy data frame)

• {pkgattrs} (useful for getting information on the contents of any R package)

• {foreman} (for unpacking, interrogating and subsetting R packages)

• {sessioninfo} (to include R session information)

Reverse dependency checks 📡⚰️

• {revdepcheck} (for automated, isolated, reverse dependency checking)

• {xfun} (specifically, xfun::rev_check())

Gratitude 🙏💌

To thank the contributors or maintainers of packages you rely on.

• {thankr} (to find out who maintains the packages you are using)

• {allcontributors} (to help acknowledge all contributions)

Docker container 🛍

• {containerit} (to package R script/session/workspace and all dependencies as a Docker container by generating a suitable Dockerfile)

• {usethat} (to automate analytic project setup tasks)

Integration with other languages 🔗

C++

• {Rcpp}

• {cpp11}

Fortran

• {RFI}

Python

• {reticulate}

Rust

• {rextendr}

• {cargo}

• {hellorust}

.NET Framework

• {rClr}

JavaScript/HTML/CSS

• {htmltools}
• {packer}

Julia

• {JuliaCall}

Upkeep 🧹

• {TODOr} (RStudio addin to list things that you need to do or change)

Sundry 🗒

• {pkglite} (tools to represent and exchange R package source code as text files)

• {gpttools} (RStudio addin that allows using chatGPT to automate writing documentation, tests, etc.)

• {rfold} (to work with many R folders within an R package)

• {many} (to create R packages from many directories)

• {prefixer} (prefix function with their namespace )

• {options} (provides simple mechanisms for defining and interpreting package options)

• {onetime} (for package authors to run code only once for a given user on a given computer)

• {rstudioapi} (to conditionally access the RStudio API from CRAN packages)

• {rcheology} (to access data on base packages for previous versions of R)

• {gitignore} (to fetch gitignore templates)

• {DIZutils} (helpers for packages dealing with database connections)

Session information

Quarto version

[1] '1.5.29'

Session details

─ Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.3.3 (2024-02-29)
 os       Ubuntu 22.04.4 LTS
 system   x86_64, linux-gnu
 ui       X11
 language (EN)
 collate  C.UTF-8
 ctype    C.UTF-8
 tz       UTC
 date     2024-04-14
 pandoc   3.1.8 @ /opt/hostedtoolcache/pandoc/3.1.8/x64/ (via rmarkdown)

─ Packages ───────────────────────────────────────────────────────────────────
 package     * version date (UTC) lib source
 cli           3.6.2   2023-12-11 [1] RSPM
 clipr         0.8.0   2022-02-22 [1] RSPM
 desc          1.4.3   2023-12-10 [1] RSPM
 details     * 0.3.0   2022-03-27 [1] RSPM
 digest        0.6.35  2024-03-11 [1] RSPM
 evaluate      0.23    2023-11-01 [1] RSPM
 fastmap       1.1.1   2023-02-24 [1] RSPM
 htmltools     0.5.8.1 2024-04-04 [1] RSPM
 httr          1.4.7   2023-08-15 [1] RSPM
 jsonlite      1.8.8   2023-12-04 [1] RSPM
 knitr         1.46    2024-04-06 [1] RSPM
 later         1.3.2   2023-12-06 [1] RSPM
 magrittr      2.0.3   2022-03-30 [1] RSPM
 png           0.1-8   2022-11-29 [1] RSPM
 processx      3.8.4   2024-03-16 [1] RSPM
 ps            1.7.6   2024-01-18 [1] RSPM
 quarto        1.4.1   2024-03-10 [1] Github (quarto-dev/quarto-r@ba8485a)
 R6            2.5.1   2021-08-19 [1] RSPM
 Rcpp          1.0.12  2024-01-09 [1] RSPM
 rlang         1.1.3   2024-01-10 [1] RSPM
 rmarkdown     2.26    2024-03-05 [1] RSPM
 rstudioapi    0.16.0  2024-03-24 [1] RSPM
 sessioninfo   1.2.2   2021-12-06 [1] any (@1.2.2)
 withr         3.0.0   2024-01-16 [1] RSPM
 xfun          0.43    2024-03-25 [1] RSPM
 xml2          1.3.6   2023-12-04 [1] RSPM
 yaml          2.3.8   2023-12-11 [1] RSPM

 [1] /home/runner/work/_temp/Library
 [2] /opt/R/4.3.3/lib/R/site-library
 [3] /opt/R/4.3.3/lib/R/library

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