{"id":14986011,"url":"https://github.com/insightsengineering/bioc-check-action","last_synced_at":"2025-04-11T22:13:19.273Z","repository":{"id":45405280,"uuid":"427349325","full_name":"insightsengineering/bioc-check-action","owner":"insightsengineering","description":"Github Action that runs Bioconductor-specific R package checks with BiocCheck.","archived":false,"fork":false,"pushed_at":"2024-03-15T15:35:18.000Z","size":22,"stargazers_count":3,"open_issues_count":1,"forks_count":2,"subscribers_count":3,"default_branch":"main","last_synced_at":"2025-04-11T22:13:17.211Z","etag":null,"topics":["actions","bioconductor","github-actions","r"],"latest_commit_sha":null,"homepage":"https://github.com/marketplace/actions/bioc-check-action","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/insightsengineering.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":".github/CODEOWNERS","security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null},"funding":{"custom":["https://pharmaverse.org"]}},"created_at":"2021-11-12T12:17:39.000Z","updated_at":"2023-08-18T19:55:53.000Z","dependencies_parsed_at":"2024-10-13T23:20:38.431Z","dependency_job_id":null,"html_url":"https://github.com/insightsengineering/bioc-check-action","commit_stats":{"total_commits":17,"total_committers":8,"mean_commits":2.125,"dds":0.7647058823529411,"last_synced_commit":"97971bdd29d882668332f82e34fba62dcdc86673"},"previous_names":[],"tags_count":11,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/insightsengineering%2Fbioc-check-action","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/insightsengineering%2Fbioc-check-action/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/insightsengineering%2Fbioc-check-action/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/insightsengineering%2Fbioc-check-action/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/insightsengineering","download_url":"https://codeload.github.com/insightsengineering/bioc-check-action/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248487684,"owners_count":21112190,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["actions","bioconductor","github-actions","r"],"created_at":"2024-09-24T14:12:07.969Z","updated_at":"2025-04-11T22:13:19.248Z","avatar_url":"https://github.com/insightsengineering.png","language":"R","funding_links":["https://pharmaverse.org"],"categories":[],"sub_categories":[],"readme":"# BiocCheck Action\n\n[![Action Test](https://github.com/insightsengineering/bioc-check-action/actions/workflows/test-action.yaml/badge.svg)](https://github.com/insightsengineering/bioc-check-action/actions/workflows/test-action.yaml)\n[![SuperLinter](https://github.com/insightsengineering/bioc-check-action/actions/workflows/linter.yaml/badge.svg)](https://github.com/insightsengineering/bioc-check-action/actions/workflows/linter.yaml)\n\n## Description\n\nGithub Action that implements Bioconductor-specific R package checks with [BiocCheck](https://bioconductor.org/packages/release/bioc/html/BiocCheck.html).\n\n## Action Type\n\nComposite\n\n## Quick Start\n\n1. Create a new GitHub Actions workflow file `.github/workflows/bioc-check.yaml` and add the following as content:\n\n```yaml\n---\nname: BiocCheck\n\non:\n  push:\n    branches:\n      - main\n  pull_request:\n\njobs:\n  bioccheck:\n    runs-on: ubuntu-latest\n    name: BiocCheck\n    steps:\n      - name: Checkout Repo\n        uses: actions/checkout@v3\n      - name: Setup Pandoc\n        uses: r-lib/actions/setup-pandoc@v2\n      - name: Setup R\n        uses: r-lib/actions/setup-r@v2\n        with:\n          r-version: release\n          http-user-agent: release\n          use-public-rspm: true\n      - name: Install Deps\n        uses: r-lib/actions/setup-r-dependencies@v2\n        with:\n          cache: true\n      - name: Run BiocCheck\n        uses: insightsengineering/bioc-check-action@v1\n```\n\n2. Create a PR against your repository to test and use the action.\n\n## Standalone Usage\n\nNote that you may also use the script from this action in standalone mode by running the following:\n\n```bash\n# Download the script\nwget -O BiocCheck.R \\\n  https://raw.githubusercontent.com/insightsengineering/bioc-check-action/main/BiocCheck.R\n# Making the script executable\nchmod +x BiocCheck.R\n# Run the script\n./BiocCheck.R --help\n```\n\n## Example Output\n\nYou may view an example output of this action [here](https://github.com/insightsengineering/hermes/pull/166#issuecomment-1016147947).\n\n## Inputs\n\n* `path`:\n\n  _Description_: Path to package's root\n\n  _Required_: `false`\n\n  _Default_: `.`\n\n* `new-package`:\n\n  _Description_: enable checks specific to new packages\n\n  _Required_: `false`\n\n  _Default_: `false`\n\n* `post-result-as-comment`:\n\n  _Description_: post the check result as a PR comment\n\n  _Required_: `false`\n\n  _Default_: `true`\n\n* `no-check-dependencies`:\n\n  _Description_: disable check for bad dependencies\n\n  _Required_: `false`\n\n  _Default_: `false`\n\n* `no-check-deprecated`:\n\n  _Description_: disable check for usage of deprecated packages\n\n  _Required_: `false`\n\n  _Default_: `false`\n\n* `no-check-remotes`:\n\n  _Description_: disable check for usage of remote packages other than those hosted on CRAN or Bioconductor\n\n  _Required_: `false`\n\n  _Default_: `false`\n\n* `no-check-version-num`:\n\n  _Description_: disable check for valid version number\n\n  _Required_: `false`\n\n  _Default_: `false`\n\n* `no-check-R-ver`:\n\n  _Description_: disable check for valid R version\n\n  _Required_: `false`\n\n  _Default_: `false`\n\n* `no-check-pkg-size`:\n\n  _Description_: disable check for package tarball size\n\n  _Required_: `false`\n\n  _Default_: `false`\n\n* `no-check-file-size`:\n\n  _Description_: disable check for individual file size\n\n  _Required_: `false`\n\n  _Default_: `false`\n\n* `no-check-bioc-views`:\n\n  _Description_: disable biocViews-specific checks (for non-BioC packages)\n\n  _Required_: `false`\n\n  _Default_: `false`\n\n* `no-check-bbs`:\n\n  _Description_: disable BBS-specific checks (for non-BioC packages). Valid DESCRIPTION\n\n  _Required_: `false`\n\n  _Default_: `false`\n\n* `no-check-description`:\n\n  _Description_: disable DESCRIPTION file checks\n\n  _Required_: `false`\n\n  _Default_: `false`\n\n* `no-check-namespace`:\n\n  _Description_: disable namespace checks\n\n  _Required_: `false`\n\n  _Default_: `false`\n\n* `no-check-vignettes`:\n\n  _Description_: disable vignette checks\n\n  _Required_: `false`\n\n  _Default_: `false`\n\n* `no-check-library-calls`:\n\n  _Description_: disable check usage of functions that install or update packages\n\n  _Required_: `false`\n\n  _Default_: `false`\n\n* `no-check-install-self`:\n\n  _Description_: disable check for require or library of itself\n\n  _Required_: `false`\n\n  _Default_: `false`\n\n* `no-check-coding-practices`:\n\n  _Description_: disable check for some common best coding practices\n\n  _Required_: `false`\n\n  _Default_: `false`\n\n* `no-check-function-len`:\n\n  _Description_: disable check for function length\n\n  _Required_: `false`\n\n  _Default_: `false`\n\n* `no-check-man-doc`:\n\n  _Description_: disable checks for man page documentation\n\n  _Required_: `false`\n\n  _Default_: `false`\n\n* `no-check-news`:\n\n  _Description_: disable checks for NEWS file\n\n  _Required_: `false`\n\n  _Default_: `false`\n\n* `no-check-unit-tests`:\n\n  _Description_: disable checks for unit tests\n\n  _Required_: `false`\n\n  _Default_: `false`\n\n* `no-check-skip-bioc-tests`:\n\n  _Description_: disable check for tests that skip when on bioc\n\n  _Required_: `false`\n\n  _Default_: `false`\n\n* `no-check-formatting`:\n\n  _Description_: disable checks for file formatting\n\n  _Required_: `false`\n\n  _Default_: `false`\n\n* `no-check-CRAN`:\n\n  _Description_: disable check for if package exists in CRAN\n\n  _Required_: `false`\n\n  _Default_: `false`\n\n* `no-check-bioc-help`:\n\n  _Description_: disable check for registration on Bioconductor mailing list and support site\n\n  _Required_: `false`\n\n  _Default_: `false`\n\n* `build-output-file`:\n\n  _Description_: file containing R CMD build output, for additional analysis\n\n  _Required_: `false`\n\n* `quit-with-status`:\n\n  _Description_: enable exit code option when performing check\n\n  _Required_: `false`\n\n  _Default_: `false`\n\n* `no-cache`:\n\n  _Description_: disable github action R dependency caching\n\n  _Required_: `false`\n\n  _Default_: `false`\n\n* `cache-version`:\n\n  _Description_: version of cache. To clean cache bump this version\n\n  _Required_: `false`\n\n  _Default_: `cache-v1`\n\n* `allow-failure`:\n\n  _Description_: BiocCheck errors will not fail, but will give a warning\n\n  _Required_: `false`\n\n  _Default_: `false`\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Finsightsengineering%2Fbioc-check-action","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Finsightsengineering%2Fbioc-check-action","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Finsightsengineering%2Fbioc-check-action/lists"}