Enforcing Style in an R Project | R-bloggers

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Enforcing Style in an R Project
Posted on September 19, 2022 by R - datawookie in R bloggers | 0 Comments
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In the previous post we looked at how to apply a linter and styler to a Python Project. Now we’re going to do the same for an R project. We’ll use the {precommit} R package to make the setup a breeze.
Install
Setup precommit for a project.
precommit::use_precommit()
That will create the .pre-commit-config.yaml configuration file and, if present, also add it to .Rbuildignore.
The content of the .pre-commit-config.yaml file should look something like this (I’ve stripped out comment for brevity):
repos: - repo: https://github.com/lorenzwalthert/precommit rev: v0.3.2.9001 hooks: - id: style-files args: [--style_pkg=styler, --style_fun=tidyverse_style] - id: roxygenize - id: use-tidy-description - id: spell-check exclude: > (?x)^( .*\.[rR]| .*\.feather| .*\.jpeg| .*\.pdf| .*\.png| .*\.py| .*\.RData| .*\.rds| .*\.Rds| .*\.Rproj| .*\.sh| (.*/|)\.gitignore| (.*/|)\.gitlab-ci\.yml| (.*/|)\.lintr| (.*/|)\.pre-commit-.*| (.*/|)\.Rbuildignore| (.*/|)\.Renviron| (.*/|)\.Rprofile| (.*/|)\.travis\.yml| (.*/|)appveyor\.yml| (.*/|)NAMESPACE| (.*/|)renv/settings\.dcf| (.*/|)renv\.lock| (.*/|)WORDLIST| \.github/workflows/.*| data/.*| )$ - id: lintr - id: readme-rmd-rendered - id: parsable-R - id: no-browser-statement - id: no-debug-statement - id: deps-in-desc - repo: https://github.com/pre-commit/pre-commit-hooks rev: v4.3.0 hooks: - id: check-added-large-files args: ['--maxkb=200'] - id: file-contents-sorter files: '^\.Rbuildignore$' - id: end-of-file-fixer exclude: '\.Rd' - repo: https://github.com/pre-commit-ci/pre-commit-ci-config rev: v1.5.1 hooks: - id: check-pre-commit-ci-config - repo: local hooks: - id: forbid-to-commit name: Don't commit common R artifacts entry: Cannot commit .Rhistory, .RData, .Rds or .rds. language: fail files: '\.(Rhistory|RData|Rds|rds)$' # `exclude:
` to allow committing specific files ci: autoupdate_schedule: monthly
If you’re using {roxygen2} then you might be prompted to run the following:
precommit::snippet_generate('additional-deps-roxygenize')
That will probably generate additional instructions about changes you need to make to the id: roxygenize key in the .pre-commit-config.yaml file. Apply those.
Extra Hooks
You might also want to add the trailing-whitespace and check-yaml rules to .pre-commit-config.yaml under the https://github.com/pre-commit/pre-commit-hooks repository.
Commit
Once you’ve configured {precommit}, stage the .pre-commit-config.yaml and .Rbuildignore files and then try to commit. You might need to work fairly hard to get all of the checks passing, especially if there’s quite a lot of code in the repository. Just be systematic in addressing each of the errors raised by the hook processes.
You might get an error about /usr/lib/R/Rscript not being found. This means that pre-commit is looking in the wrong place for Rscript. I simply made a link from /usr/lib/R/Rscript to the actual location of Rscript.
The {lintr} Package
The {lintr} package will perform static analysis on your R code and help identify syntatic problems.
Install
Create a .lintr file in the project root.
lintr::use_lintr()
You can update the .lintr file to tweak the way that {lintr} will treat your files.
linters: linters_with_defaults( line_length_linter(120), object_usage_linter = NULL, object_name_linter(c("snake_case", "SNAKE_CASE")), commented_code_linter = NULL ) exclusions: list() encoding: "UTF-8"
You might want to add in "dotted.case" as another argument to object_name_linter().
Excluding Code
You can exclude chunks of code from linting by adding nolint hints as comments.
# The following line of code will be ignored by {lintr}. n