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LintR

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Source: vignettes/lintr.Rmd
lintr.Rmd

Lint Workflow

This GitHub Actions workflow performs linting tasks for an R package. It runs on a docker container instance using admiralci images (ghcr.io/pharmaverse/admiralci-${{ inputs.r-version }}:latest) for the R environment.

Workflow Triggers

This workflow is triggered in the following ways:

  • Manual Dispatch: You can manually trigger the workflow using the “workflow_dispatch” event.

  • Workflow Call: The workflow can also be triggered by another workflow using the “workflow_call” event.

Workflow Inputs

The workflow accepts the following inputs during manual dispatch or workflow call:

  • r-version: The version of R to use, with options ‘4.1’, ‘4.2’, and ‘4.3’.

  • lint-all-files: Boolean indicating whether to lint all files every time.

  • latest-lintr: Boolean indicating whether to install the latest lintr CRAN release.

  • install-package: Boolean indicating whether to install the R package locally.

Workflow Setup

  • Concurrency: Lint jobs are organized by the pull request number or branch.

  • Cancel-in-progress: Allows canceling in-progress lint jobs.

Job: lint

This job performs linting tasks.

Steps

  1. Get branch names: Gets the branch names using the tj-actions/branch-names action.

  2. Checkout repo (PR): Checks out the repository for pull requests.

  3. Checkout repository: Checks out the repository for non-pull request events.

  4. Normalize inputs: Normalizes the R version input.

  5. Restore cache: Restores the cache for staged dependencies.

  6. Run Staged dependencies: Runs staged dependencies action to set up the environment.

  7. Install dependencies from DESCRIPTION: install dependencies from DESCRIPTION (in case of missing dependencies in parent admiralci docker image)

  8. Install latest release of lintr: Installs the latest release of lintr from the CRAN repository if specified.

  9. Install package: Installs the R package locally if specified.

  10. Changed files: Gets the list of changed files using the Ana06/get-changed-files action.

  11. Lint: Performs linting using lintr on the R package. Excludes files based on the changed files list.

  12. Error if lints are detected: Raises an error if lints are detected, prompting a review and adjustment of the code.

Note : a .lintr file can be configured at the upstream repository level, to be able for example to exclude some lint rules such as this example :

exclusions: list(
    "R/data.R" = Inf,
    "inst" = list(undesirable_function_linter = Inf),
    "vignettes" = list(undesirable_function_linter = Inf)
  )