d1 - Installing R packages in a Nix environment

Introduction

You now know how to declare and build reproducible development environments using {rix} and Nix. This vignette will explain how to install specific versions of CRAN packages and how to install packages from GitHub.

A word of caution

It is important at this stage to understand that you should not call install.packages() from a running Nix environment. If you want to add packages while analyzing data, you need to add it the default.nix expression and rebuild the environment. The same goes for installing packages from Github; use the method described in this vignette instead of using something like remotes::install_github().

We recommend you create a script called create_env.R or similar, and add the call to rix() there:

library(rix)

rix(r_ver = "4.4.0",
    r_pkgs = c("dplyr", "ggplot2"),
    system_pkgs = NULL,
    git_pkgs = NULL,
    ide = "code",
    project_path = path_default_nix,
    overwrite = TRUE,
    print = TRUE)

Then, add the packages you need to r_pkgs and run the script again. Then, build the environment using nix-build again, and drop into it using nix-shell. Calling install.packages() is a bad idea for several reasons:

• it goes against the idea of defining an environment in a declarative way. If you were able to add packages using install.packages(), your environment would end up in a state where the default.nix definition of the environment and the actual environment don’t match anymore.
• using install.packages() will likely simply not work, and if it does, will cause issues. For example, if you call install.packages("ggplot2") from one Nix shell, it will not install {ggplot2} “inside” the Nix shell, but will install it on your user’s system library of packages. This is because the Nix shell cannot be changed at run-time, and so, R will instead install the packages in the user’s library. This version of {ggplot2}, because it is in that system-wide library of packages, will be available to any other Nix shell. If you call install.packages("ggplot2") again from another Nix shell, say 6 months later, this will replace the first version of {ggplot2} with the latest version.

Ideally, you should only manage R versions and R packages using Nix, and uninstall any system-managed version of R and R packages. But if you do wish to keep a system-managed version of R and R packages, rix::rix() also runs rix::rix_init() automatically which generates an .Rprofile file that avoids any clashes between your global user library and Nix-managed libraries of R packages.

Installing old packages archived on CRAN

It is possible to install an arbitrary version of a package that has been archived on CRAN:

path_default_nix <- tempdir()

rix(
  r_ver = "4.2.1",
  r_pkgs = c("dplyr@0.8.0", "janitor@1.0.0"),
  system_pkgs = NULL,
  git_pkgs = NULL,
  ide = "other",
  project_path = path_default_nix,
  overwrite = TRUE
)

#> # This file was generated by the {rix} R package v0.7.1 on 2024-07-01
#> # with following call:
#> # >rix(r_ver = "79b3d4bcae8c7007c9fd51c279a8a67acfa73a2a",
#> #  > r_pkgs = c("dplyr@0.8.0",
#> #  > "janitor@1.0.0"),
#> #  > system_pkgs = NULL,
#> #  > git_pkgs = NULL,
#> #  > ide = "other",
#> #  > project_path = path_default_nix,
#> #  > overwrite = TRUE)
#> # It uses nixpkgs' revision 79b3d4bcae8c7007c9fd51c279a8a67acfa73a2a for reproducibility purposes
#> # which will install R version 4.2.1.
#> # Report any issues to https://github.com/ropensci/rix
#> let
#>  pkgs = import (fetchTarball "https://github.com/NixOS/nixpkgs/archive/79b3d4bcae8c7007c9fd51c279a8a67acfa73a2a.tar.gz") {};
#>   
#>   git_archive_pkgs = [ 
#>     (pkgs.rPackages.buildRPackage {
#>       name = "dplyr";
#>       src = pkgs.fetchzip {
#>        url = "https://cran.r-project.org/src/contrib/Archive/dplyr/dplyr_0.8.0.tar.gz";
#>        sha256 = "sha256-f30raalLd9KoZKZSxeTN71PG6BczXRIiP6g7EZeH09U=";
#>       };
#>       propagatedBuildInputs = builtins.attrValues {
#>         inherit (pkgs.rPackages) 
#>           assertthat
#>           glue
#>           magrittr
#>           pkgconfig
#>           R6
#>           Rcpp
#>           rlang
#>           tibble
#>           tidyselect
#>           BH
#>           plogr;
#>       };
#>     })
#> 
#> 
#>     (pkgs.rPackages.buildRPackage {
#>       name = "janitor";
#>       src = pkgs.fetchzip {
#>        url = "https://cran.r-project.org/src/contrib/Archive/janitor/janitor_1.0.0.tar.gz";
#>        sha256 = "sha256-3NJomE/CNbOZ+ohuVZJWe2n1RVGUm8x8a0A0qzLmdN4=";
#>       };
#>       propagatedBuildInputs = builtins.attrValues {
#>         inherit (pkgs.rPackages) 
#>           dplyr
#>           tidyr
#>           snakecase
#>           magrittr
#>           purrr
#>           rlang;
#>       };
#>     })
#>   ];
#>    
#>   system_packages = builtins.attrValues {
#>     inherit (pkgs) 
#>       R
#>       glibcLocales
#>       nix;
#>   };
#>   
#> in
#> 
#> pkgs.mkShell {
#>   LOCALE_ARCHIVE = if pkgs.system == "x86_64-linux" then  "${pkgs.glibcLocales}/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";
#>    LC_MEASUREMENT = "en_US.UTF-8";
#> 
#>   buildInputs = [ git_archive_pkgs   system_packages   ];
#>   
#> }

The above expression will install R version 4.2.1, and {dplyr} at version 0.8.0 and {janitor} at version 1.0.0. This can be useful, especially for packages that have been archived, but otherwise, this feature should ideally be used sparingly. If you want to reconstruct an environment as it was around 2019, use the version of R that was current at that time. This will ensure that every package that gets installed is at a version compatible with that version of R, which might not be the case if you need to install a very old version of one particular package.

Installing packages from Github

It is also possible to install packages from Github:

path_default_nix <- tempdir()

rix(
  r_ver = "4.2.1",
  r_pkgs = c("dplyr", "janitor"),
  git_pkgs = list(
    list(
      package_name = "housing",
      repo_url = "https://github.com/rap4all/housing/",
      commit = "1c860959310b80e67c41f7bbdc3e84cef00df18e"
    ),
    list(
      package_name = "fusen",
      repo_url = "https://github.com/ThinkR-open/fusen",
      commit = "d617172447d2947efb20ad6a4463742b8a5d79dc"
    )
  ),
  ide = "other",
  project_path = path_default_nix,
  overwrite = TRUE
)

This will install two packages from Github: the {housing} package and more specifically the code as it is in the fusen branch; however the branch name is not required, as the commit is enough to pin the exact version of the code needed. The {fusen} package is also installed, as of commit d617172447d.

Installing local archives

It is also possible to install packages from a local tar.gz file. For this, place the package in the same folder where the default.nix will be generated, and write something like this:

rix(
  r_ver = "4.3.1",
  local_r_pkgs = c("chronicler_0.2.1.tar.gz", "knitr_1.43.tar.gz"),
  overwrite = TRUE
)

This assumes that both chronicler_0.2.1.tar.gz and knitr_1.43.tar.gz have been downloaded beforehand. If you want to include a local package that you are developing, make sure to first build it using devtools::build() to build the .tar.gz archive, but if you can, consider uploading the source code to your package on Github and installing it from Github instead.

A complete example

This example shows how to install packages from CRAN, from the CRAN archives and from GitHub:

path_default_nix <- tempdir()

rix(
  r_ver = "4.2.1",
  r_pkgs = c("dplyr", "janitor", "AER@1.2-8"),
  git_pkgs = list(
    list(
      package_name = "housing",
      repo_url = "https://github.com/rap4all/housing/",
      commit = "1c860959310b80e67c41f7bbdc3e84cef00df18e"
    ),
    list(
      package_name = "fusen",
      repo_url = "https://github.com/ThinkR-open/fusen",
      commit = "d617172447d2947efb20ad6a4463742b8a5d79dc"
    )
  ),
  ide = "other",
  project_path = path_default_nix,
  overwrite = TRUE
)

#> # This file was generated by the {rix} R package v0.7.1 on 2024-07-01
#> # with following call:
#> # >rix(r_ver = "79b3d4bcae8c7007c9fd51c279a8a67acfa73a2a",
#> #  > r_pkgs = c("dplyr",
#> #  > "janitor",
#> #  > "AER@1.2-8"),
#> #  > git_pkgs = list(list(package_name = "housing",
#> #  > repo_url = "https://github.com/rap4all/housing/",
#> #  > commit = "1c860959310b80e67c41f7bbdc3e84cef00df18e"),
#> #  > list(package_name = "fusen",
#> #  > repo_url = "https://github.com/ThinkR-open/fusen",
#> #  > commit = "d617172447d2947efb20ad6a4463742b8a5d79dc")),
#> #  > ide = "other",
#> #  > project_path = path_default_nix,
#> #  > overwrite = TRUE)
#> # It uses nixpkgs' revision 79b3d4bcae8c7007c9fd51c279a8a67acfa73a2a for reproducibility purposes
#> # which will install R version 4.2.1.
#> # Report any issues to https://github.com/ropensci/rix
#> let
#>  pkgs = import (fetchTarball "https://github.com/NixOS/nixpkgs/archive/79b3d4bcae8c7007c9fd51c279a8a67acfa73a2a.tar.gz") {};
#>  
#>   rpkgs = builtins.attrValues {
#>     inherit (pkgs.rPackages) 
#>       dplyr
#>       janitor;
#>   };
#>  
#>   git_archive_pkgs = [
#>     (pkgs.rPackages.buildRPackage {
#>       name = "housing";
#>       src = pkgs.fetchgit {
#>         url = "https://github.com/rap4all/housing/";
#>         rev = "1c860959310b80e67c41f7bbdc3e84cef00df18e";
#>         sha256 = "sha256-s4KGtfKQ7hL0sfDhGb4BpBpspfefBN6hf+XlslqyEn4=";
#>       };
#>       propagatedBuildInputs = builtins.attrValues {
#>         inherit (pkgs.rPackages) 
#>           dplyr
#>           ggplot2
#>           janitor
#>           purrr
#>           readxl
#>           rlang
#>           rvest
#>           stringr
#>           tidyr;
#>       };
#>     })
#> 
#> 
#>     (pkgs.rPackages.buildRPackage {
#>       name = "fusen";
#>       src = pkgs.fetchgit {
#>         url = "https://github.com/ThinkR-open/fusen";
#>         rev = "d617172447d2947efb20ad6a4463742b8a5d79dc";
#>         sha256 = "sha256-TOHA1ymLUSgZMYIA1a2yvuv0799svaDOl3zOhNRxcmw=";
#>       };
#>       propagatedBuildInputs = builtins.attrValues {
#>         inherit (pkgs.rPackages) 
#>           attachment
#>           cli
#>           desc
#>           devtools
#>           glue
#>           here
#>           magrittr
#>           parsermd
#>           roxygen2
#>           stringi
#>           tibble
#>           tidyr
#>           usethis
#>           yaml;
#>       };
#>     })
#>  
#>     (pkgs.rPackages.buildRPackage {
#>       name = "AER";
#>       src = pkgs.fetchzip {
#>        url = "https://cran.r-project.org/src/contrib/Archive/AER/AER_1.2-8.tar.gz";
#>        sha256 = "sha256-OqxXcnUX/2C6wfD5fuNayc8OU+mstI3tt4eBVGQZ2S0=";
#>       };
#>       propagatedBuildInputs = builtins.attrValues {
#>         inherit (pkgs.rPackages) 
#>           car
#>           lmtest
#>           sandwich
#>           survival
#>           zoo
#>           Formula;
#>       };
#>     })
#>   ];
#>    
#>   system_packages = builtins.attrValues {
#>     inherit (pkgs) 
#>       R
#>       glibcLocales
#>       nix;
#>   };
#>   
#> in
#> 
#> pkgs.mkShell {
#>   LOCALE_ARCHIVE = if pkgs.system == "x86_64-linux" then  "${pkgs.glibcLocales}/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";
#>    LC_MEASUREMENT = "en_US.UTF-8";
#>
#>   buildInputs = [ git_archive_pkgs rpkgs  system_packages   ];
#>
#> }

The next vignette, vignette("d2-installing-system-tools-and-texlive-packages-in-a-nix-environment"), explains how you can install tools such as text editors, git, Quarto, TexLive packages, and any other tool available through nixpkgs for your development environments.