1  Nix

This book template uses the Nix packager manager to handle the book’s dependencies. This chapter introduces the Nix packager manager and nixpkgs quickly.

1.1 The Nix package manager

Nix is a package manager available for Linux, Windows (on WSL2) and macOS. Its mono-repository, nixpkgs, contains more than 80’000 packages, among them the entirety of the R packages released on CRAN and Bioconductor, as well as R itself (and RStudio, but only for Linux and Windows, as of writing). This means that it is possible to use the Nix package manager to install R, the R packages you require for your day-to-day work, and any other packages that you might need (for example, if you need Python and Python packages, you can install these as well).

The question that remains unanswered though, is why use the Nix package manager to install all this software instead of using the usual ways of first installing R, and then using install.packages() to install any required packages?

There are at least three reasons. The first is that it is possible to define so-called default.nix files that define an environment. This environment will contain all the packages that you require, and will not interfere with any other packages installed on your system. This essentially means that you can have project-specific default.nix files, each specifying the requirements for specific projects. The second reason is that when installing a package that requires system-level dependencies, {rJava} for example, all the lower-level dependencies get automatically installed. Forget about reading error messages of install.packages() to find which system development library you need to install first. The third reason, is that you can pin a specific revision of nixpkgs to ensure reproducibility.

1.2 Ensuring reproducibility with Nix

The nixpkgs mono-repository is “just” a Github repsitory which you can find here: https://github.com/NixOS/nixpkgs. This repository contains Nix expressions to build and install more than 80’000 packages and you can search for installable Nix packages here.

Because nixpkgs is a Github repository, it is possible to use a specific commit hash to install the packages as they were at a specific point in time. For example, if you use this commit, 7c9cc5a6e, you’ll get the very latest packages as of the 19th of October 2023, but if you used this one instead: 976fa3369, you’ll get packages from the 19th of August 2023.

You can declare which revision of nixpkgs to use at the top of a default.nix file. Here is what such a file looks like:

 pkgs = import (fetchTarball "https://github.com/NixOS/nixpkgs/archive/976fa3369d722e76f37c77493d99829540d43845.tar.gz") {};
 rpkgs = builtins.attrValues {
  inherit (pkgs.rPackages) tidymodels vetiver targets xgboost;
 system_packages = builtins.attrValues {
  inherit (pkgs) R;
 pkgs.mkShell {
  buildInputs = [  rpkgs system_packages  ];

As you can see, we import a specific revision of the nixpkgs Github repository to ensure that we always get the same packages in our environment.

If you’re unfamiliar with Nix, this file can be quite scary. But don’t worry, with my co-author Philipp Baumann we developed an R package called {rix} which generate this default.nix files for you.

1.3 The R {rix} package

{rix} is an R package that makes it very easy to generate very complex default.nix files. These files can in turn be used by the Nix package manager to build project-specific environments. The book’s Github repository contains a file called define_env.R with the following content:


rix(r_ver = "4.3.1",
    r_pkgs = c("quarto"),
    system_pkgs = "quarto",
    tex_pkgs = c(
    ide = "other",
    shell_hook = "",
    project_path = ".",
    overwrite = TRUE,
    print = TRUE)

{rix} ships the rix() function which takes several arguments. These arguments allow you to specify an R version, a list of R packages, a list of system packages, TeXLive packages and other options that allow you to specify your requirements. Running this code generates this default.nix file:

# This file was generated by the {rix} R package v0.4.1 on 2023-10-19
# with following call:
# >rix(r_ver = "976fa3369d722e76f37c77493d99829540d43845",
#  > r_pkgs = c("quarto"),
#  > system_pkgs = "quarto",
#  > tex_pkgs = c("amsmath",
#  > "framed",
#  > "fvextra",
#  > "environ",
#  > "fontawesome5",
#  > "orcidlink",
#  > "pdfcol",
#  > "tcolorbox",
#  > "tikzfill"),
#  > ide = "other",
#  > project_path = ".",
#  > overwrite = TRUE,
#  > print = TRUE,
#  > shell_hook = "")
# It uses nixpkgs' revision 976fa3369d722e76f37c77493d99829540d43845 for reproducibility purposes
# which will install R version 4.3.1
# Report any issues to https://github.com/b-rodrigues/rix
 pkgs = import (fetchTarball "https://github.com/NixOS/nixpkgs/archive/976fa3369d722e76f37c77493d99829540d43845.tar.gz") {};
 rpkgs = builtins.attrValues {
  inherit (pkgs.rPackages) quarto;
  tex = (pkgs.texlive.combine {
  inherit (pkgs.texlive) scheme-small amsmath framed fvextra environ fontawesome5 orcidlink pdfcol tcolorbox tikzfill;
 system_packages = builtins.attrValues {
  inherit (pkgs) R glibcLocalesUtf8 quarto;
  pkgs.mkShell {
    LOCALE_ARCHIVE = if pkgs.system == "x86_64-linux" then  "${pkgs.glibcLocalesUtf8}/lib/locale/locale-archive" else "";
    LANG = "en_US.UTF-8";
    LC_ALL = "en_US.UTF-8";
    LC_TIME = "en_US.UTF-8";
    LC_MONETARY = "en_US.UTF-8";
    LC_PAPER = "en_US.UTF-8";

    buildInputs = [  rpkgs tex system_packages  ];

You can now use this file to work on your book locally by first building the environment and then use it. To know more about using default.nix files on a day-to-day basis, read this vignette.

In the next chapter, I’m going to explain how this book gets built on Github Actions.