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Lifecycle: experimental

rix-run

Command line tool to run R scripts that are annotated with rix roxygen2 tags.

Supported tags

  • @rix r_ver
  • @rix r_pkgs
  • @rix system_pkgs
  • @rix git_pkgs

These annotations will be used in {rix} to generate the nix configuration of the environment that will run the R script.

Installation

Clone this repo and put rix-run in your path.

$ git clone git@github.com:jrosell/rix-run.git
$ chmod u+x rix-run/rix-run
$ cp rix-run/rix-run ./somewhere/in/your/search/path

Usage

Basic usage

The examples/data-visualize.R file include r_ver and r_pkgs annotated values.

Once rix-run is installed, to run the script execute:

$ rix-run examples/data-visualize.R

To use docker:

$ docker build -f Dockerfile -t rix-run-image . \
  && docker run --name rix-run-container --rm  -v $(pwd)/examples:/workspace/examples/:rw rix-run-image

To clean up the used docker images and containers:

(docker container rm -f rix-run-container || true) \
		&& (docker rmi $(docker images --format '{{.Repository}}:{{.ID}}'| egrep 'rix-run-image' | cut -d':' -f2 | uniq) --force || true)

Targets single file

The examples/targets-run1.R file is a _targets.R script file that will be exacuted with tar_make when using the --targets argument.

Once rix-run is installed, to run the target script execute:

$ rix-run examples/targets-run1.R --targets

First time result example:

> dispatched target file_url
o completed target file_url [0.089 seconds]
> dispatched target file
o completed target file [0.045 seconds]
> dispatched target data
o completed target data [0.147 seconds]
> dispatched target model
o completed target model [0.003 seconds]
> dispatched target plot
o completed target plot [0.013 seconds]
> ended pipeline [0.447 seconds]

Following times resul example:

v skipped target file_url
v skipped target file
v skipped target data
v skipped target model
v skipped target plot
v skipped pipeline [0.168 seconds]

Troubleshooting

  • It's tested on Ubuntu. If you want to help, please test Debian, Fedora, Centos, MacOS, etc. Windows it's not (yet?) supported.
  • Please, open an issue if you have any problem.
  • Feel free to open a PR to improve rix-run.