Rix: Reproducible Environments with Nix

Reproducible Environments with Nix

Introduction

rix is an R package that leverages Nix, a powerful package manager focusing on reproducible builds. With Nix, it is possible to create project-specific environments that contain a project-specific version of R and R packages (as well as other tools or languages, if needed). You can use rix and Nix to replace renv and Docker with one single tool. Nix is an incredibly useful piece of software for ensuring reproducibility of projects, in research or otherwise. For example, it allows you run web applications like Shiny apps or plumber APIs in a controlled environment.

Nix has a fairly high entry cost though. Nix is a complex piece of software that comes with its own programming language, which is also called Nix. Its purpose is to solve a complex problem: defining instructions on how to build software packages and manage configurations in a declarative way. This makes sure that software gets installed in fully reproducible manner, on any operating system or hardware.

rix provides functions to help you write and deploy Nix expressions (written in the Nix language). These expressions will be the inputs for the Nix package manager, to build sets of software packages and provide them in a reproducible development environment. These environments can be used for interactive data analysis, or reproduced when running pipelines in CI/CD systems. On the Nixpkgs collection, there are currently more than 80.000 pieces of software available through the Nix package manager. Through {rix}, you can define and build isolated R environments through Nix package manager with ease. Like this, environments contain R and all the required packages that you need for your project. You can also add any other software tool available. The Nix R ecosystem currently includes the entirety of CRAN and Bioconductor packages. Like with any other programming language and software, it is also possible to install older releases of R packages, or install packages from GitHub at defined states.

The Nix package manager is extremely powerful. Not only does it handle all the dependencies of any package extremely well in a deterministic manner, it is also possible with it to reproduce environments containing old releases of software. It is thus possible to build environments containing R version 4.0.0 (for example) to run an old project that was originally developed on that version of R.

As stated above, with Nix, it is essentially possible to replace {renv} and Docker combined. If you need other tools or languages like Python or Julia, this can also be done easily. Nix is available for Linux, macOS and Windows (via WSL2) and rix comes with the following features:

install any version of R and R packages for specific projects;
have several versions of R and R packages installed at the same time on the same system;
define complete development environments as code and use them anywhere;
run single R functions (and objects in the call stack) in a different environment (potentially with a different R version and R packages) for an interactive R session, and get back the output of that function using with_nix();

rix does not require Nix to be installed on your system to generate expressions. This means that you can generate expressions on a system on which you cannot easily install software, and then use these expressions on the cloud or on a CI/CD environment to build the project there.

If you have R installed, you can start straight away from your R session by first installing rix:

install.packages("rix", repos = c("https://b-rodrigues.r-universe.dev",
  "https://cloud.r-project.org"))

library("rix")

path_default_nix <- "."

rix(r_ver = "latest",
    r_pkgs = c("dplyr", "ggplot2"),
    system_pkgs = NULL,
    git_pkgs = NULL,
    ide = "code",
    project_path = path_default_nix,
    overwrite = TRUE,
    print = TRUE)

This generates a file called default.nix in the path path_default_nix with the correct expression to build this environment. To build the environment, the Nix package manager must be installed.

Quick start for returning users

If you are not familiar with Nix or rix skip to the next section.

Click to expand

If you are already familiar with Nix and R, and simply want to get started as quickly as possible, you can start by installing Nix using the installer from Determinate Systems a company that provides services and tools built on Nix:

curl --proto '=https' --tlsv1.2 -sSf \
    -L https://install.determinate.systems/nix | \
     sh -s -- install

You can check that everything works well by trying to build the Nix expression that ships with rix. Nix expressions are typically saved into files with the name default.nix or shell.nix. This expression installs the latest version of R and rix in a separate, reproducible environment:

file.copy(
  # default.nix is the file containing the Nix expression
  from = system.file("extdata", "default.nix", package = "rix"),
  to = ".", overwrite = TRUE
)

# nix_build() is a wrapper around the command line tool `nix-build`
nix_build(project_path = ".")

If everything worked well, you should see a file called result next to default.nix. You can now enter this newly built development environment by opening a terminal in that folder and typing nix-shell. You should be immediately dropped into an interactive R session.

If you don’t have R installed, but have the Nix package manager installed, you can run a temporary R session with R using this command (it will build the same environment as the one above):

nix-shell --expr "$(curl -sl https://raw.githubusercontent.com/b-rodrigues/rix/master/inst/extdata/default.nix)"

You can then create new development environment definitions, build them, and start using them.

Getting started for new users

To get started with rix and Nix, you should read the following vignette vignette("a-getting-started") (online documentation). The vignettes are numbered to get you to learn how to use rix and Nix smoothly. There’s a lot of info, so take your time reading the vignettes. Don’t hesitate to open an issue if something is not clear.

Docker

You can also try out Nix inside Docker. To do so, you can start your image from the NixOS Docker image. NixOS is a full GNU/Linux distribution that uses Nix as its system package manager.

Contributing

This package is developed using the fusen package. If you want to contribute, please edit the .Rmd files found in the dev/ folder. Then, inflate the package using fusen::inflate_all(). If no errors are found (warning and notes are OK), then commit and open a PR. To learn how to use fusen (don’t worry, it’s super easy), refer to this vignette. In our development workflow, we use semantic versioning via {fledge}.

Thanks