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

> 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=<style>' works

to activate the rcli addons. To see it for yourself, call the following from the command line:

$ 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:

$ 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:

$ 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:

$ 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.

If you are submitting a new package to Bioconductor, make sure that BiocCheck is installed. Then run:

$ R CMD check --as=bioconductor::BiocCheck pkg_1.0.tar.gz

For available command-line options for the latter, see:

$ R CMD check --as=bioconductor::BiocCheck --help

Customized checking

$ 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:

$ R --vanilla CMD check ...
$ R --no-init-file CMD check ...

If attempted, we will get something like:

$ R --vanilla CMD check --as=rcli --hello
Warning: unknown option ‘--as=rcli’
Warning: unknown option ‘--hello’
Error: no packages were specified

Installation

R package rcli is only available via GitHub and can be installed in R as:

remotes::install_github("HenrikBengtsson/rcli")

Pre-release version

To install the pre-release version that is available in Git branch develop on GitHub, use:

remotes::install_github("HenrikBengtsson/rcli@develop")

This will install the package from source.

Contributions

This Git repository uses the Git Flow branching model (the git flow extension is useful for this). The develop branch contains the latest contributions and other code that will appear in the next release, and the master branch contains the code of the latest release.

Contributing to this package is easy. Just send a pull request. When you send your PR, make sure develop is the destination branch on the rcli repository. 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
Test coverage