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b2 - Setting up and using Nix and rix on macOS

Source: vignettes/b2-setting-up-and-using-rix-on-macos.Rmd
b2-setting-up-and-using-rix-on-macos.Rmd

This vignette will discuss macOS-specific topics. If you’re not using macOS, you can ignore this vignette, and read the vignette("b1-setting-up-and-using-rix-on-linux-and-windows") vignette instead.

Introduction

When it comes to Nix, there are really only two supported operating systems: macOS and Linux distributions. Windows is “supported” because it is actually running Linux thanks to WSL2. In practice this means that Linux distributions and Windows can be considered one system, and macOS another, separate, system, with its own idiosyncrasies. This vignette details these.

Why rix and Nix?

You don’t have to install Nix to use rix: you can generate valid Nix expressions using rix even on a system where Nix isn’t present. However, this means that you won’t be able to build these expressions on that system.

Installing Nix

You can use rix to generate Nix expressions even if you don’t have Nix installed on your system, but obviously, you need to install Nix if you actually want to build the defined development environment and use them. Installing (and uninstalling) Nix is quite simple, thanks to the installer from Determinate Systems, a company that provides services and tools built on Nix. Simply open a terminal and run the following line:

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. Use setup_cachix() when building a Docker image or if you somehow mess up the configuration file (which should be located in ~/.config/nix.conf).

Once you have Nix installed, you can build the expressions you generate with rix!

What if you don’t have R already installed?

If you have successfully installed Nix, but don’t have yet R installed on your system, you could install R as you would usually do on your operating system, and then install the rix package, and from there, generated project-specific expressions and build them. But you could also install R using Nix. Running the following line in a terminal will drop you in an interactive R session that you can use to start generating expressions:

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

This should immediately start an R session inside your terminal. You can now run something like this:

rix(r_ver = "4.4.2",
    r_pkgs = c("dplyr", "ggplot2"),
    system_pkgs = NULL,
    git_pkgs = NULL,
    ide = "other",
    project_path = ".",
    overwrite = TRUE)

to generate a default.nix, and then use that file to generate an environment with R, dplyr and ggplot2. If you need to add packages for your project, rerun the command above, but add the needed packages to r_pkgs. This is detailed in the vignettes vignette("d1-installing-r-packages-in-a-nix-environment") and vignette("d2-installing-system-tools-and-texlive-packages-in-a-nix-environment").

Generating expressions

Once you have R installed, either through the usual installer for your operating system, or through Nix as explained previously, you can now start building project-specific development environments.

On macOS, generating expressions works just like on Linux and Windows. Start an R session, and install rix if that’s not already done. Because rix is not yet on CRAN, the easiest way is to install it from its r-universe:

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

You can then use the rix package to generate expressions. Consult the next vignette vignette("c-using-rix-to-build-project-specific-environments") to learn more.

More macOS specificities

R Support for Apple Silicon in Nixpkgs

The Apple Silicon architecture wasn’t well supported before 2021 on Nix. Our rstats-on-nix fork of nixpkgs provides improved compatibility by backporting fixes to R and R packages, but only from 2021 onwards. If you need to use an older R version, it is quite unlikely that it is going to work.

Shared libraries issue

When using environments built with Nix on macOS, you might get crashes (segmentation faults) refering to “shared libraries”. These indicate that your user library of R packages is interfering with the project-specific Nix environment. The system’s user library that Nix packaged R by default includes appears in the search paths (check libPaths()). For macOS, the user library is at /Library/Frameworks/R.framework/Versions/<major>.<minor>-<arch>/Resources/library; we have observed crashes with R packages that depend on system libraries, such as data.table or dplyr, and their (reverse) dependencies. Because user libraries from the system would also appear on the search path in R from nixpkgs for Linux, running rix() also runs rix_init() which creates a custom .Rprofile in your project’s path. This custom .Rprofile ensures that only packages declaratively defined in your default.nix and built to be part of the Nix store (one R package is one separate derivation listed in a unique Nix path) appear on the R library path.

RStudio and other development interfaces on macOS

As of writing, RStudio cannot be installed through nixpkgs for macOS, and if you wish to use RStudio with a Nix environment, you have to install it through nixpkgs. This means that it is impossible to use RStudio and a Nix environment on macOS. When you try to generate an expression with ide = "rstudio" on macOS, this will raise a warning. Here are the options you have:

  • ignore the warning, because the environment will be built on a Linux distribution (even though you generated the expression on macOS) and used on a Linux distribution;
  • change the ide = argument to either "other" or "code". Use "code" if you want to use VS Code and "other" for any other editor, like Vim or Emacs. These other editors don’t need to be installed through nixpkgs to use Nix environments, unlike RStudio;
  • if you’re working on a pipeline with the targets package, you could run it on GitHub Actions. This means you could work on the code on RStudio outside of the Nix environment, as the code will only be executed on GitHub Actions runners. See this vignette vignette("z-advanced-topic-reproducible-analytical-pipelines-with-nix") for further details;
  • work on your project as usual, using your usual installation of R and RStudio, but generate a default.nix at the end with ide = "other" with the right version of R for reproducibility purposes;
  • use subshells to execute only the code you need to run in a specific environment. See this vignette vignette("z-advanced-topic-running-r-or-shell-code-in-nix-from-r");
  • help us package RStudio for macOS on nixpgs. See here, the Nix expression for RStudio.

We recommend you continue with the next vignette before tackling the more advanced topics listed above: vignette("c-using-rix-to-build-project-specific-environments").

Why do we need all these special tweaks?

Path of Nix installation not in PATH

When using RStudio Desktop on macOS, you typically launch it from the Applications folder. However, RStudio currently lacks an option to start an integrated R session via a shell startup on macOS (see this issue. On RStudio for Linux flavors, PATH is properly inherited in R sessions. As a result, key environmental variables for UNIX systems, like PATH, are not be properly loaded from your default shell (e.g., zsh, via ~/.zshrc). Also, RStudio overwrites a PATH variable set via .Rprofile or .Renviron with its own defaults, which makes it impossible to find Nix and standard Nix tools like nix-build. It’s worth noting that this doesn’t impact rix::rix(), which generates Nix expressions and doesn’t require a Nix installation. As a workaround, we have added mechanisms in nix_build() and with_nix() that append the path of the Nix store to the PATH variable in an active session automatically (via Sys.setenv(), when you use RStudio on macOS. You don’t have to do anything. We have you covered, and you get a friendly message that informs you.

Other “Nix”es

There are several implementations of the Nix package manager that you might want to try if you’re feeling adventurous… for now, we recommend to stick with Nix.

You can give Lix a try, or Tvix.