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https://github.com/HenrikBengtsson/rcli
R package: rcli - R Command-Line Interface Extras
https://github.com/HenrikBengtsson/rcli
addons build check cli command-line-interface package r
Last synced: about 1 month ago
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R package: rcli - R Command-Line Interface Extras
- Host: GitHub
- URL: https://github.com/HenrikBengtsson/rcli
- Owner: HenrikBengtsson
- Created: 2020-04-16T05:33:47.000Z (over 4 years ago)
- Default Branch: develop
- Last Pushed: 2020-04-27T15:38:13.000Z (over 4 years ago)
- Last Synced: 2024-06-11T08:46:24.533Z (3 months ago)
- Topics: addons, build, check, cli, command-line-interface, package, r
- Language: R
- Homepage: https://github.com/HenrikBengtsson/rcli
- Size: 164 KB
- Stars: 4
- Watchers: 3
- Forks: 0
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
- jimsghstars - HenrikBengtsson/rcli - R package: rcli - R Command-Line Interface Extras (R)
README
# rcli: R Command-Line Interface Extras
The **[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.
## One-time setup
After installing the **rcli** package (see below), call
```r
> rcli::install()
Backed up R startup file: '~/.Rprofile' (316 bytes) -> '~/.Rprofile.bak.20200425-210609' (316 bytes)
Added 'rcli::r_cmd_call()' to already existing R startup file: '~/.Rprofile'
Validated that 'R CMD check --as=' works
```
to activate the **rcli** addons. To see it for yourself, call the following from the command line:
```sh
$ R CMD check --as=rcli --hello
* using --as=rcli
Hello world!
$
```
## Usage
### For CRAN developers
When 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:
```sh
$ R CMD check --as=cran pkg_1.0.tar.gz
```
If 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:
```sh
$ R CMD check --as=cran --offline pkg_1.0.tar.gz
```
This will _as far as possible_ try to skip the tests that require data to be pulled down from the CRAN servers.
### For Bioconductor developers
To check a package for the currently installed version of Bioconductor, use:
```sh
$ R CMD check --as=bioconductor pkg_1.0.tar.gz
```
This will validate the package using the same "check" environment variables as the [Bioconductor servers](https://github.com/Bioconductor/BBS).
If you are submitting a [new package](https://bioconductor.org/developers/package-guidelines/) to Bioconductor, make sure that **[BiocCheck]** is installed. Then run:
```sh
$ R CMD check --as=bioconductor::BiocCheck pkg_1.0.tar.gz
```
For available command-line options for the latter, see:
```sh
$ R CMD check --as=bioconductor::BiocCheck --help
```
### Customized checking
```sh
$ R CMD check --config=~/.R/my_bioc-3.11_check.dcf pkg_1.0.tar.gz
```
where `~/.R/my_bioc-3.11_check.dcf` may look like:
```
assert:
getRversion() >= "4.0.0"
utils::packageVersion("BiocVersion") >= "3.11"
options:
--as=bioconductor
--no-examples
env:
_R_CHECK_CRAN_INCOMING_REMOTE_=false
```
## Known limitations
The above `R CMD` extensions work because **rcli** injects itself, during the R startup process, in the first step of the `R` -> `R CMD` -> `R CMD {command}` pipeline. Because of this, none of the above will work if we call it as:
```sh
$ R --vanilla CMD check ...
$ R --no-init-file CMD check ...
```
If attempted, we will get something like:
```sh
$ R --vanilla CMD check --as=rcli --hello
Warning: unknown option ‘--as=rcli’
Warning: unknown option ‘--hello’
Error: no packages were specified
```
[BiocCheck]: https://bioconductor.org/packages/BiocCheck/
[rcli]: https://github.com/HenrikBengtsson/rcli
## Installation
R package rcli is only available via [GitHub](https://github.com/HenrikBengtsson/rcli) and can be installed in R as:
```r
remotes::install_github("HenrikBengtsson/rcli")
```
### Pre-release version
To install the pre-release version that is available in Git branch `develop` on GitHub, use:
```r
remotes::install_github("HenrikBengtsson/rcli@develop")
```
This will install the package from source.
## Contributions
This 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.
Contributing 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.
## Software status
| Resource | GitHub | GitHub Actions | Travis CI | AppVeyor CI |
| ------------- | ------------------- | ------------------- | --------------- | ---------------- |
| _Platforms:_ | _Multiple_ | _Multiple_ | _Linux & macOS_ | _Windows_ |
| R CMD check | | <a href="https://github.com/HenrikBengtsson/rcli/actions?query=workflow%3AR-CMD-check"><img src="https://github.com/HenrikBengtsson/rcli/workflows/R-CMD-check/badge.svg?branch=develop" alt="Build status"></a> | | |
| Test coverage | | | | |