z - Advanced topic: Understanding the rPackages set release cycle and using bleeding edge packages

Introduction

It is important to understand the release cycle of the rPackages set and what steps you should take if you need bleeding edge packages. R packages on nixpkgs tend to get updated alongside a new release of R, and the reason is to ensure a certain level of quality. The vast majority of CRAN (and Bioconductor) packages are made available through nixpkgs in a fully automated way. But some packages do require some manual intervention to work on Nix, and we only know this if we try to build these packages, but building packages requires quite a lot of resources. We can’t build CRAN packages every single day to see if everything works well on Nix, so we only rebuild the whole tree whenever there’s a new release of R. Packages get built on a CI infrastructure called Hydra, and then these packages get cached on cache.nixos.org so whenever someone wants to install a package, a pre-built binary gets download from the cache. This avoids having to build software from source locally. For packages that don’t need compiling this is not that big of a time save, but for packages that do need to get compiled it is huge. Depending on which packages you want to install, if you had to build everything from source, it could potentially take hours, but if you can install pre-built binaries it’s just a matter of how quick your internet connection is.

R packages available through Nix

As explained in the introduction, the rPackages set on nixpkgs gets updated shortly after a new release of R. The process involves first updating the package definitions found here, and then building the whole tree on a CI platform called Hydra. Build failures then get fixed by volunteers (to learn how you can contribute, read the vignette("z-contributing_to_nixpkgs")). After the most important packages have been fixed, the whole rPackages set gets updated and made available through nixpkgs master branch.

Essentially this means that if you start a project with rix using "latest" as the r_ver just after the rPackages set got updated, this project will use very fresh packages. But if instead you start a project just before an R release, then the environment will be using older packages. In practice this rarely matters, unless you absolutely need a very recent version of a specific package because you need a specific feature, or if you need an environment with bleeding edge packages for development. For cases like this, we provide the r_ver = "bleeding_edge" and r_ver = "frozen_edge" options that makes it possible to use the most recent packages for your environment, but at a cost. You must be aware of this cost which we detail in the next section.

Using bleeding and frozen edge package for your environments

CRAN is continuously getting new or updated packages. When you use R outside of Nix, running install.packages(pkg) will install the latest version of the {pkg} package available from CRAN (unless you changed the default repository url). With Nix, packages do not get downloaded from CRAN but for the nixpkgs repository and they may be outdated as explained above. If you require bleeding edge packages, use the "bleeding_edge" option to r_ver. This will NOT download packages from the official nixpkgs repository anymore, but from a fork that we maintain that you can find here. This fork gets updated every 12 hours with the latest commits from both the nixpkgs repository and CRAN. This means that environments generated using this fork will contain bleeding packages for both the CRAN (and Bioconductor) packages as well as system-level dependencies. Also, be aware that this will generate an expression that is NOT reproducible! Each time you will rebuild the environment generated using the "bleeding_edge" option, you will get exactly that: an environment with bleeding edge packages at build time. If you want instead to have bleeding edge packages at the time you generate the expression, but then want reproducibility (in other words, building should always result in the same environment), then use the "frozen_edge" option instead.

In any case, whatever option you choose, using them comes at a cost of which you must be aware.

First, because these packages are bleeding edge, they have not had the chance to be built by Hydra yet. Hydra periodically builds packages and these get cached. So if you’re using Nix, pre-compiled binaries get used instead of being built from source. This is not the case if you use our fork, unless you also use the cache that we provide, courtesy of cachix.org. Cachix provides a cache for your own projects and works seamlessly with the official Nix cache. However, we are limited in space, and cannot possible cache all the CRAN packages. So only the most popular packages get built and cached, and hopefully the packages you need are part of this limited set. To use the cache, run the following commands on your computer. First, install the Cachix client:

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

then use the cache:

cachix use rstats-on-nix

that’s it! Packages now not only will get pulled from the official cache, but also from the dedicated rstats-on-nix cache. Our cache also contains the latest version of R, which sometimes can also lag behind on the official nixpkgs repository.

Making your own cache

If you need packages that are not included in the rstats-on-nix cache, you can very easily roll out your own binary cache. Simply build the environment once on one machine, and then push the binaries in a cache for re-use. Refer to the vignette vignette("z-binary_cache") to learn how to set up your own cache.