d1 - Installing R packages in a Nix environment • rix

library(rix)

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.

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It is possible to install an arbitrary version of a package that has been archived on CRAN: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 v0.6.0 on 2024-05-19
#> # 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/b-rodrigues/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:

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/",
                   branch_name = "fusen",
                   commit = "1c860959310b80e67c41f7bbdc3e84cef00df18e"),
                 list(package_name = "fusen",
                   repo_url = "https://github.com/ThinkR-open/fusen",
                   branch_name = "main",
                   commit = "d617172447d2947efb20ad6a4463742b8a5d79dc")
    ),
    ide = "other",
    project_path = path_default_nix,
    overwrite = TRUE)

#> # This file was generated by the {rix} R package v0.6.0 on 2024-05-19
#> # with following call:
#> # >rix(r_ver = "79b3d4bcae8c7007c9fd51c279a8a67acfa73a2a",
#> #  > r_pkgs = c("dplyr",
#> #  > "janitor"),
#> #  > git_pkgs = list(list(package_name = "housing",
#> #  > repo_url = "https://github.com/rap4all/housing/",
#> #  > branch_name = "fusen",
#> #  > commit = "1c860959310b80e67c41f7bbdc3e84cef00df18e"),
#> #  > list(package_name = "fusen",
#> #  > repo_url = "https://github.com/ThinkR-open/fusen",
#> #  > branch_name = "main",
#> #  > 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/b-rodrigues/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/";
#>       branchName = "fusen";
#>       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";
#>       branchName = "main";
#>       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;
#>     };
#>   }) ];
#>   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  ];
#>       
#>   }

This will install two packages from Github: the {housing} package and more specifically the code as it is in the fusen branch. The commit is also provided, to pin the exact version of the package needed. The fusen package is also installed, from the main branch at commit d617172447d.

A complete example

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

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/",
                   branch_name = "fusen",
                   commit = "1c860959310b80e67c41f7bbdc3e84cef00df18e"),
                 list(package_name = "fusen",
                   repo_url = "https://github.com/ThinkR-open/fusen",
                   branch_name = "main",
                   commit = "d617172447d2947efb20ad6a4463742b8a5d79dc")
    ),
    ide = "other",
    project_path = path_default_nix,
    overwrite = TRUE)

#> # This file was generated by the {rix} R package v0.6.0 on 2024-05-19
#> # 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/",
#> #  > branch_name = "fusen",
#> #  > commit = "1c860959310b80e67c41f7bbdc3e84cef00df18e"),
#> #  > list(package_name = "fusen",
#> #  > repo_url = "https://github.com/ThinkR-open/fusen",
#> #  > branch_name = "main",
#> #  > 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/b-rodrigues/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/";
#>       branchName = "fusen";
#>       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";
#>       branchName = "main";
#>       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.