{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.
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 -- installYou 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.
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.
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.
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 to the Nix community for making Nix possible, and thanks to the community of R users on Nix for their work packaging R and CRAN/Bioconductor packages for Nix (in particular Justin Bedő, Rémi Nicole, nviets, Chris Hammill, László Kupcsik, Simon Lackerbauer, MrTarantoga and every other person from the Matrix Nixpkgs R channel).
- NixOS’s website
- Nixpkgs’s GitHub repository
- Nix for R series from Bruno’s blog. Or, in case you like video tutorials, watch this one on Reproducible R development environments with Nix
- nix.dev tutorials
- INRIA’s Nix tutorial
- Nix pills
- Nix for Data Science
- NixOS explained: NixOS is an entire Linux distribution that uses Nix as its package manager.
- Blog post: Nix with R and devtools
- Blog post: Statistical Rethinking and Nix
- Blog post: Searching and installing old versions of Nix packages