{"id":22569039,"url":"https://github.com/henrikbengtsson/rcli","last_synced_at":"2025-07-12T16:37:44.369Z","repository":{"id":146695707,"uuid":"256118769","full_name":"HenrikBengtsson/rcli","owner":"HenrikBengtsson","description":"R package: rcli - R Command-Line Interface Extras","archived":false,"fork":false,"pushed_at":"2020-04-27T15:38:13.000Z","size":168,"stargazers_count":4,"open_issues_count":3,"forks_count":0,"subscribers_count":2,"default_branch":"develop","last_synced_at":"2025-03-28T13:46:29.373Z","etag":null,"topics":["addons","build","check","cli","command-line-interface","package","r"],"latest_commit_sha":null,"homepage":"https://github.com/HenrikBengtsson/rcli","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/HenrikBengtsson.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null}},"created_at":"2020-04-16T05:33:47.000Z","updated_at":"2022-05-14T08:12:58.000Z","dependencies_parsed_at":"2024-02-24T13:19:58.786Z","dependency_job_id":"01016ae1-bda4-4c61-97a9-4652351b317d","html_url":"https://github.com/HenrikBengtsson/rcli","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/HenrikBengtsson/rcli","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HenrikBengtsson%2Frcli","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HenrikBengtsson%2Frcli/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HenrikBengtsson%2Frcli/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HenrikBengtsson%2Frcli/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/HenrikBengtsson","download_url":"https://codeload.github.com/HenrikBengtsson/rcli/tar.gz/refs/heads/develop","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HenrikBengtsson%2Frcli/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":265024279,"owners_count":23699589,"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":["addons","build","check","cli","command-line-interface","package","r"],"created_at":"2024-12-08T00:17:23.503Z","updated_at":"2025-07-12T16:37:44.344Z","avatar_url":"https://github.com/HenrikBengtsson.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# rcli: R Command-Line Interface Extras\n\n![Life cycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)\n\nThe **[rcli]** package boosts `R CMD check` with extra options.  For example, `R CMD check --config=check.dcf pkg_1.0.tar.gz` checks the package tarball with additional command-line options and environment variables as given by the 'check.dcf' file.  Another example is `R CMD check --as=bioconductor pkg_1.0.tar.gz`, which checks the package according to Bioconductor settings.\n\n\n## One-time setup\n\nAfter installing the **rcli** package (see below), call\n\n```r\n\u003e rcli::install()\nBacked up R startup file: '~/.Rprofile' (316 bytes) -\u003e '~/.Rprofile.bak.20200425-210609' (316 bytes)\nAdded 'rcli::r_cmd_call()' to already existing R startup file: '~/.Rprofile'\nValidated that 'R CMD check --as=\u003cstyle\u003e' works\n```\n\nto activate the **rcli** addons.  To see it for yourself, call the following from the command line:\n\n```sh\n$ R CMD check --as=rcli --hello\n* using --as=rcli\nHello world!\n$ \n```\n\n\n## Usage\n\n### For CRAN developers\n\nWhen submitting to CRAN, you should validate your package with `R CMD check --as-cran`.  For the completeness of this package, an alias for that is:\n\n```sh\n$ R CMD check --as=cran pkg_1.0.tar.gz\n```\n\nIf you are offline, on a slow or an unstable internet connection, or for other reasons do not want to send out online queries to the CRAN servers, you can run these checks in an \"offline\" mode by:\n\n```sh\n$ R CMD check --as=cran --offline pkg_1.0.tar.gz\n```\n\nThis will _as far as possible_ try to skip the tests that require data to be pulled down from the CRAN servers.  \n\n\n\n### For Bioconductor developers\n\nTo check a package for the currently installed version of Bioconductor, use:\n\n```sh\n$ R CMD check --as=bioconductor pkg_1.0.tar.gz\n```\n\nThis will validate the package using the same \"check\" environment variables as the [Bioconductor servers](https://github.com/Bioconductor/BBS).\n\nIf you are submitting a [new package](https://bioconductor.org/developers/package-guidelines/) to Bioconductor, make sure that **[BiocCheck]** is installed.  Then run:\n\n```sh\n$ R CMD check --as=bioconductor::BiocCheck pkg_1.0.tar.gz\n```\n\nFor available command-line options for the latter, see:\n\n```sh\n$ R CMD check --as=bioconductor::BiocCheck --help\n```\n\n\n### Customized checking\n\n```sh\n$ R CMD check --config=~/.R/my_bioc-3.11_check.dcf pkg_1.0.tar.gz\n```\n\nwhere `~/.R/my_bioc-3.11_check.dcf` may look like:\n\n```\nassert:\n  getRversion() \u003e= \"4.0.0\"\n  utils::packageVersion(\"BiocVersion\") \u003e= \"3.11\"\n  \noptions:\n  --as=bioconductor\n  --no-examples\n\nenv:\n  _R_CHECK_CRAN_INCOMING_REMOTE_=false\n```\n\n\n## Known limitations\n\nThe above `R CMD` extensions work because **rcli** injects itself, during the R startup process, in the first step of the `R` -\u003e `R CMD` -\u003e `R CMD {command}` pipeline.  Because of this, none of the above will work if we call it as:\n\n```sh\n$ R --vanilla CMD check ...\n$ R --no-init-file CMD check ...\n```\n\nIf attempted, we will get something like:\n\n```sh\n$ R --vanilla CMD check --as=rcli --hello\nWarning: unknown option ‘--as=rcli’\nWarning: unknown option ‘--hello’\nError: no packages were specified\n```\n\n[BiocCheck]: https://bioconductor.org/packages/BiocCheck/\n[rcli]: https://github.com/HenrikBengtsson/rcli\n\n## Installation\nR package rcli is only available via [GitHub](https://github.com/HenrikBengtsson/rcli) and can be installed in R as:\n```r\nremotes::install_github(\"HenrikBengtsson/rcli\")\n```\n\n### Pre-release version\n\nTo install the pre-release version that is available in Git branch `develop` on GitHub, use:\n```r\nremotes::install_github(\"HenrikBengtsson/rcli@develop\")\n```\nThis will install the package from source.  \n\n\n\n## Contributions\n\nThis Git repository uses the [Git Flow](http://nvie.com/posts/a-successful-git-branching-model/) branching model (the [`git flow`](https://github.com/petervanderdoes/gitflow-avh) extension is useful for this).  The [`develop`](https://github.com/HenrikBengtsson/rcli/tree/develop) branch contains the latest contributions and other code that will appear in the next release, and the [`master`](https://github.com/HenrikBengtsson/rcli) branch contains the code of the latest release.\n\nContributing to this package is easy.  Just send a [pull request](https://help.github.com/articles/using-pull-requests/).  When you send your PR, make sure `develop` is the destination branch on the [rcli repository](https://github.com/HenrikBengtsson/rcli).  Your PR should pass `R CMD check --as-cran`, which will also be checked by  and  when the PR is submitted.\n\n\n## Software status\n\n| Resource      | GitHub        | GitHub Actions      | Travis CI       | AppVeyor CI      |\n| ------------- | ------------------- | ------------------- | --------------- | ---------------- |\n| _Platforms:_  | _Multiple_          | _Multiple_          | _Linux \u0026 macOS_ | _Windows_        |\n| R CMD check   |  | \u003ca href=\"https://github.com/HenrikBengtsson/rcli/actions?query=workflow%3AR-CMD-check\"\u003e\u003cimg src=\"https://github.com/HenrikBengtsson/rcli/workflows/R-CMD-check/badge.svg?branch=develop\" alt=\"Build status\"\u003e\u003c/a\u003e       |    |  |\n| Test coverage |                     |                     |      |                  |\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhenrikbengtsson%2Frcli","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fhenrikbengtsson%2Frcli","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhenrikbengtsson%2Frcli/lists"}