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rix: Reproducible Environments with Nix

Introduction

rix is an R package that leverages Nix, a package manager focused on reproducible builds. With Nix, you can create project-specific environments with a custom version of R, its packages, and all system dependencies (e.g., GDAL). Nix ensures full reproducibility, which is crucial for research and development projects.

Use cases include running web apps (e.g., Shiny, plumber APIs) or targets pipelines with a controlled R environment. Unlike renv, which snapshots package versions, rix provides an entire ecosystem snapshot, including system-level dependencies.

While Nix has a steep learning curve, rix

  1. simplifies creating Nix expressions, which define reproducible environments, also from renv.lock files;
  2. lets you work interactively in IDEs like RStudio or VS Code, or use Nix in CI/CD workflows;
  3. makes it easy to create Docker images with the right packages;
  4. provides helpers that make it easy to build those environments, evaluate the same code in different development environments, and finally to deploy software environments in production.

If you want to watch a 5-Minute video introduction click here.

Nix includes nearly all CRAN and Bioconductor packages, with the ability to install specific package versions or GitHub snapshots. Nix also includes Python, Julia (and many of their respective packages) as well as many, many other tools (up to 120’000 pieces of software as of writing). Expressions generated by rix point to our fork of Nixpkgs which provides improved compatibility for older versions of R and R packages, especially for Apple Silicon computers.

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

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

Now try to generate an expression using rix():

# Choose the path to your project
# This will create two files: .Rprofile and default.nix
path_default_nix <- "."

rix(
  r_ver = "4.3.3",
  r_pkgs = c("dplyr", "ggplot2"),
  system_pkgs = NULL,
  git_pkgs = NULL,
  ide = "code",
  project_path = path_default_nix,
  overwrite = TRUE,
  print = TRUE
)

This will generate two files, default.nix and .Rprofile in project_default_nix. default.nix is the environment definition written in the Nix programming language, and .Rprofile prevents conflicts with library paths from system-installed R versions, offering better control over your environment and improving isolation of Nix environments. .Rprofile is created by rix_init() which is called automatically by the main function, rix().

It is also possible to provide a date instead of an R version:

# Choose the path to your project
# This will create two files: .Rprofile and default.nix
path_default_nix <- "."

rix(
  date = "2024-12-14",
  r_pkgs = c("dplyr", "ggplot2"),
  system_pkgs = NULL,
  git_pkgs = NULL,
  ide = "code",
  project_path = path_default_nix,
  overwrite = TRUE,
  print = TRUE
)

The table below illustrates this all the different types of environment you can generate:

r_ver or date Intended use State of R version State of CRAN packages State of Bioconductor packages State of other packages in Nixpkgs
r_ver = “latest-upstream” Start of new project where versions don’t matter Current or previous Outdated (up to 6 months) Outdated (up to 6 months) Current at time of generation
r_ver = “4.4.2” (or other) Reproducing old project or starting a new project where versions don’t matter Same as in r_ver, check available_r() Outdated (up to 2 months if using latest release) Outdated (up to 2 months if using latest release) Potentially outdated (up to 12 months)
date = “2024-12-14” Reproducing old project or starting a new project using the most recent date Current at that date, check available_dates() Current at that date, check available_dates() Current at that date, check available_dates() Potentially outdated (up to 12 months)
r_ver = “bleeding-edge” To develop against the latest release of CRAN Always current Always current Always current Always current
r_ver = “frozen-edge” To develop against the latest release of CRAN, but manually manage updates Current at time of generation Current at time of generation Current at time of generation Current at time of generation
r_ver = “r-devel” To develop/test against the development version of R Development version Always current Always current Always current
r_ver = “r-devel-bioc-devel” To develop/test against the development version of R and Bioconductor Development version Always current Development version Always current
r_ver = “bioc-devel” To develop/test against the development version of Bioconductor Always current Always current Development version Always current

If you want to benefit from relatively fresh packages and have a stable environment for production purposes, using a date for r_ver is likely your best option.

Quick-start for returning users

Click to expand

If you’re already familiar with Nix and rix, install Nix using the Determinate Systems installer: (if you’re using WSL, do check out the detailed installation instructions though):

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

Then, install the cachix client and configure our rstats-on-nix cache; this will install binary versions of many R packages which will speed up the building process of environments:

nix-env -iA cachix -f https://cachix.org/api/v1/install

then use the cache:

cachix use rstats-on-nix

You only need to do this once per machine you want to use rix on. Many thanks to Cachix for sponsoring the rstats-on-nix cache!

rix also includes a function called setup_cachix() which will configure the cache but it is recommended to use the cachix client instead. This is because setup_cachix() will not edit the files that require admin/root privileges and only edit the user-level files. This may not be enough depending on how you installed Nix. Using the cachix client takes care of everything.

You can then use rix to build and enter a Nix-based R environment:

library(rix)

path_default_nix <- "."

rix(
  r_ver = "4.3.3",
  r_pkgs = c("dplyr", "ggplot2"),
  system_pkgs = NULL,
  git_pkgs = NULL,
  ide = "code",
  project_path = path_default_nix,
  overwrite = TRUE,
  print = TRUE
)

To build the environment, call nix_build()

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

If you don’t have R installed, but have the Nix package manager installed, you can run a temporary terminal session which includes R and the development version of rix:

nix-shell --expr "$(curl -sl https://raw.githubusercontent.com/ropensci/rix/main/inst/extdata/default.nix)"
You can then create new development environment definitions, build them, and start using them.

Getting started for new users

New to rix and Nix? Start by reading the vignette("a-getting-started") (online documentation). to learn how to set up and use Nix smoothly.

Docker

Try Nix inside Docker by following this vignette("z-advanced-topic-using-nix-inside-docker") vignette.

How is Nix different from Docker+renv/{groundhog}/{rang}/(Ana/Mini)Conda/Guix? or Why Nix?

Docker + {renv}

Docker and {renv} provide robust reproducibility by combining package snapshots with system-level dependencies. However, for long-term reproducibility, Nix offers a simpler approach by bundling everything (R, packages, and dependencies) in a single environment.

Ana/Miniconda & Mamba

Conda is similar to Nix, but Nix offers immutable environments, making it more reliable for preventing accidental changes. Nix also supports nearly all CRAN and Bioconductor packages, which Conda lacks.

Nix vs. Guix

Guix, like Nix, focuses on reproducibility, but Nix supports more CRAN/Bioconductor packages and works across Windows, macOS, and Linux.

Is {rix} all there is?

No, there are other tools that you might want to check out, especially if you want to set up polyglot environments (even though it is possible to use rix to set up an environment with R and Python packages for example).

Take a look at https://devenv.sh/ and https://prefix.dev/ if you want to explore other tools that make using Nix easier!

Ideally, you shouldn’t be using a system-wide installation of R, and instead use dedicated Nix environments for each of your projects.

Start a new project by writing a file called generate_env.R and write something like:

library(rix)

path_default_nix <- "."

rix(
  r_ver = "4.3.3",                # Change to whatever R version you need
  r_pkgs = c("dplyr", "ggplot2")  # Change to whatever packages you need
  system_pkgs = NULL
  git_pkgs = NULL,
  ide = "code",
  project_path = path_default_nix,
  overwrite = TRUE,
  print = TRUE
)

Then use the following command to bootstrap an enivronment with R and rix only (from the same directory):

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

and then simply run Rscript generate_env.R which will run the above script, thus generating the project’s default.nix. If you need to add packages, open the generate_env.R file again, modify it, and run it again, do not edit the default.nix directly. Also, commit all the files to version control to avoid any issues.

Contributing

Refer to Contributing.md to learn how to contribute to the package.

Please note that this package is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Thanks

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).

Finally, thanks to David Solito for creating rix’s logo!