GitHub - ankane/jetpack: A friendly package manager for R (original) (raw)

Jetpack

🔥 A friendly package manager for R

• Lightweight - adds just three files to your project
• Designed for reproducibility - thanks to renv, no more global installs!
• Works from both R and the command line

Inspired by Yarn, Bundler, and Pipenv

Installation

Install Jetpack

install.packages("jetpack")

How It Works

Jetpack uses the DESCRIPTION file to store your project dependencies. It stores the specific version of each package in renv.lock. This makes it possible to have a reproducible environment. You can edit dependencies in the DESCRIPTION file directly, but Jetpack provides functions to help with this.

Getting Started

Open a project and run:

Commands

Install

Install packages for a project

This ensures all the right versions are installed locally. As dependencies change, collaborators should run this command to stay synced.

Be sure to prefix commands with jetpack::. Jetpack isn’t installed in your virtual environment, so library(jetpack) won’t work.

Add

Add a package

jetpack::add("randomForest")

Add multiple packages

jetpack::add(c("randomForest", "DBI"))

Add a specific version

jetpack::add("DBI@1.0.0")

Add from GitHub or another remote source

jetpack::add("plyr", remote="hadley/plyr")

Supports these remotes

Add from a specific tag, branch, or commit

jetpack::add("plyr", remote="hadley/plyr@v1.8.4")

Add from a local source

jetpack::add("plyr", remote="local::/path/to/plyr")

The local directory must have the same name as the package

Update

Update a package

jetpack::update("randomForest")

For local packages, run this anytime the package code is changed

Update multiple packages

jetpack::update(c("randomForest", "DBI"))

Update all packages

Remove

Remove a package

jetpack::remove("randomForest")

Remove multiple packages

jetpack::remove(c("randomForest", "DBI"))

Remove remotes as well

jetpack::remove("plyr", remote="hadley/plyr")

Check

Check that all dependencies are installed

Outdated

Show outdated packages

Source Control

Be sure to commit the files Jetpack generates to source control.

Bioconductor

For Bioconductor, add the BiocManager package first:

jetpack::add("BiocManager")

Then add other packages:

jetpack::add("Biobase", remote="bioc::release/Biobase")

Deployment

Server

Install Jetpack on the server and run:

jetpack::install(deployment=TRUE)

Docker

Create init.R with:

install.packages("jetpack") jetpack::install(deployment=TRUE)

And add it into your Dockerfile:

FROM r-base

RUN apt-get update && apt-get install -qq -y --no-install-recommends
libxml2-dev libssl-dev libcurl4-openssl-dev libssh2-1-dev

RUN mkdir -p /app WORKDIR /app

COPY init.R DESCRIPTION renv.lock ./ RUN Rscript init.R

COPY . .

CMD Rscript app.R

Heroku

For the R buildpack, create init.R with:

install.packages("jetpack") jetpack::install(deployment=TRUE)

Alternatively, you can use Docker Deploys on Heroku.

Command Line

Jetpack can also be run from the command line. To install the CLI, run:

On Windows, add C:\ProgramData\jetpack\bin to your PATH. See instructions for how to do this.

All the Jetpack commands are now available

jetpack init jetpack install jetpack add randomForest jetpack add DBI@1.0.0 jetpack add plyr --remote=hadley/plyr jetpack update randomForest jetpack remove DBI jetpack check jetpack outdated

You can also use it to manage global packages

jetpack global add randomForest jetpack global update DBI jetpack global update jetpack global remove plyr jetpack global list jetpack global outdated

You can even use it to update itself

jetpack global update jetpack

For the full list of commands, use:

Upgrading

To upgrade, rerun the installation instructions.

History

View the changelog

Contributing

Everyone is encouraged to help improve this project. Here are a few ways you can help:

• Report bugs
• Fix bugs and submit pull requests
• Write, clarify, or fix documentation
• Suggest or add new features

To get started with development and testing:

git clone https://github.com/ankane/jetpack.git cd jetpack

In R, do:

install.packages("devtools") devtools::install_deps(dependencies=TRUE) devtools::test()

To test a single file, use:

devtools::install() # to use latest updates devtools::test_active_file("tests/testthat/test-jetpack.R")