z - Advanced topic: Handling packages with remote dependencies

Introduction

Packages published on CRAN must have their dependencies on either CRAN or Bioconductor, but not on GitHub. However, there are many packages available on GitHub that never get published on CRAN, and some of these packages may even depend on other packages that are also only available on GitHub. {rix} makes it possible to install packages from GitHub and if these packages have dependencies that are also on GitHub, these also get correctly added to the generated default.nix.

There are however certain caveats you should be aware of.

The {lookup} package

As an example we are going to use the {lookup} package which has only been released on GitHub. Here is the repository. This package comes with the lookup() function which makes it possible to check the source code of any function from a loaded package, even if the source of that function is in C or Fortran. To create a reproducible development environment that makes {lookup} available to you, you could use the following rix::rix() call:

path_default_nix <- tempdir()

rix(
  r_ver = "latest-upstream",
  r_pkgs = NULL,
  system_pkgs = NULL,
  git_pkgs = list(
    package_name = "lookup",
    repo_url = "https://github.com/jimhester/lookup/",
    commit = "eba63db477dd2f20153b75e2949eb333a36cccfc"
  ),
  ide = "other",
  project_path = path_default_nix,
  overwrite = TRUE,
  print = TRUE
)

This will generate the following default.nix:

let
 pkgs = import (fetchTarball "https://github.com/NixOS/nixpkgs/archive/6a25f33c843a45b8d67ba782b6782973a7265774.tar.gz") {};

    httr2 = (pkgs.rPackages.buildRPackage {
      name = "httr2";
      src = pkgs.fetchgit {
        url = "https://github.com/r-lib/httr2";
        rev = "HEAD";
        sha256 = "sha256-UgJCFPO47mgUt3esRRPhXjr0oNDRrR9XAAIxMhZYbFc=";
      };
      propagatedBuildInputs = builtins.attrValues {
        inherit (pkgs.rPackages)
          cli
          curl
          glue
          lifecycle
          magrittr
          openssl
          R6
          rappdirs
          rlang
          vctrs
          withr;
      };
    });

    gh = (pkgs.rPackages.buildRPackage {
      name = "gh";
      src = pkgs.fetchgit {
        url = "https://github.com/gaborcsardi/gh";
        rev = "HEAD";
        sha256 = "sha256-VpxFIfUEk0PudytQ3boMhEJhT0AnelWkSU++WD/HAyo=";
      };
      propagatedBuildInputs = builtins.attrValues {
        inherit (pkgs.rPackages) 
          cli
          gitcreds
          glue
          ini
          jsonlite
          lifecycle
          rlang;
      } ++ [ httr2 ];
    });


    highlite = (pkgs.rPackages.buildRPackage {
      name = "highlite";
      src = pkgs.fetchgit {
        url = "https://github.com/jimhester/highlite";
        rev = "HEAD";
        sha256 = "sha256-lkWMlAi75MYxiBUYnLwxLK9ApXkWanA4Mt7g4qtLpxM=";
      };
      propagatedBuildInputs = builtins.attrValues {
        inherit (pkgs.rPackages) 
          Rcpp
          BH;
      };
    });


    memoise = (pkgs.rPackages.buildRPackage {
      name = "memoise";
      src = pkgs.fetchgit {
        url = "https://github.com/hadley/memoise";
        rev = "HEAD";
        sha256 = "sha256-FDMNgrgctzkN8dXKRoWsOKe3tXxmm8Cqdu/Sh6WKx/Q=";
      };
      propagatedBuildInputs = builtins.attrValues {
        inherit (pkgs.rPackages) 
          rlang
          cachem;
      };
    });

    lookup = (pkgs.rPackages.buildRPackage {
      name = "lookup";
      src = pkgs.fetchgit {
        url = "https://github.com/jimhester/lookup/";
        rev = "eba63db477dd2f20153b75e2949eb333a36cccfc";
        sha256 = "sha256-arl7LVxL8xGUW3LhuDCSUjcfswX0rdofL/7v8Klw8FM=";
      };
      propagatedBuildInputs = builtins.attrValues {
        inherit (pkgs.rPackages) 
          Rcpp
          codetools
          crayon
          rex
          jsonlite
          rstudioapi
          withr
          httr;
      } ++ [ highlite gh memoise ];
    });

  system_packages = builtins.attrValues {
    inherit (pkgs)
      glibcLocales
      nix
      R;
  };

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 = [ lookup   system_packages   ];
 
}

as you can see, several other packages hosted on GitHub were added automatically. This is because these were listed as remote dependencies in {lookup}’s DESCRIPTION file:

Remotes:
    jimhester/highlite,
    gaborcsardi/gh,
    hadley/memoise

Caveats

{highlite} is a dependency of {lookup} that is only available on GitHub. {gh} and {memoise} are also listed as remote dependencies, however, they are also available on CRAN. What likely happened here was that {gh} and {memoise} were not yet available on CRAN at the time when {lookup} was written (which was more than 6 years ago as of 2025). Because they are listed as remote dependencies, they will also be built from GitHub instead of CRAN. Here, it is up to you to decide if you want to keep the GitHub version of these packages, or if you should instead include the released CRAN version. Depending on what you want to do, going for the CRAN release of the packages might be advisable. For example in this case, trying to build this expression will not work.

This is because {httr2} is a package that needs to be compiled from source and which needs some Nix-specific fixes applied to its source code for it to build successfully. Installing the version provided by nixpkgs, which builds upon the released CRAN version will succeed however. To do so, change the default.nix manually to this (essentially remove the definition of {httr2} and put it as a propagatedBuildInput to {gh}):

let
 pkgs = import (fetchTarball "https://github.com/NixOS/nixpkgs/archive/6a25f33c843a45b8d67ba782b6782973a7265774.tar.gz") {};

    gh = (pkgs.rPackages.buildRPackage {
      name = "gh";
      src = pkgs.fetchgit {
        url = "https://github.com/gaborcsardi/gh";
        rev = "HEAD";
        sha256 = "sha256-VpxFIfUEk0PudytQ3boMhEJhT0AnelWkSU++WD/HAyo=";
      };
      propagatedBuildInputs = builtins.attrValues {
        inherit (pkgs.rPackages)
          cli
          gitcreds
          glue
          httr2 # <- httr2 is now declared here, so it's the CRAN version
          ini
          jsonlite
          lifecycle
          rlang;
      };
    });

    highlite = (pkgs.rPackages.buildRPackage {
      name = "highlite";
      src = pkgs.fetchgit {
        url = "https://github.com/jimhester/highlite";
        rev = "HEAD";
        sha256 = "sha256-lkWMlAi75MYxiBUYnLwxLK9ApXkWanA4Mt7g4qtLpxM=";
      };
      propagatedBuildInputs = builtins.attrValues {
        inherit (pkgs.rPackages) 
          Rcpp
          BH;
      };
    });

    memoise = (pkgs.rPackages.buildRPackage {
      name = "memoise";
      src = pkgs.fetchgit {
        url = "https://github.com/hadley/memoise";
        rev = "HEAD";
        sha256 = "sha256-FDMNgrgctzkN8dXKRoWsOKe3tXxmm8Cqdu/Sh6WKx/Q=";
      };
      propagatedBuildInputs = builtins.attrValues {
        inherit (pkgs.rPackages)
          rlang
          cachem;
      };
    });

    lookup = (pkgs.rPackages.buildRPackage {
      name = "lookup";
      src = pkgs.fetchgit {
        url = "https://github.com/jimhester/lookup/";
        rev = "eba63db477dd2f20153b75e2949eb333a36cccfc";
        sha256 = "sha256-arl7LVxL8xGUW3LhuDCSUjcfswX0rdofL/7v8Klw8FM=";
      };
      propagatedBuildInputs = builtins.attrValues {
        inherit (pkgs.rPackages)
          Rcpp
          codetools
          crayon
          rex
          jsonlite
          rstudioapi
          withr
          httr;
      } ++ [ highlite gh memoise ];
    });

  system_packages = builtins.attrValues {
    inherit (pkgs)
      glibcLocales
      nix
      R;
  };

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 = [ lookup   system_packages   ];

}

In this manually edited expression, {httr2} will now build successfully because Nix is instructed to build the CRAN version by applying this fix which was added there by packagers and maintainers of the R programming language for nixpkgs (it is exactly the same if you tried to install {httr2} from GitHub on Windows: you would need to build it from source and thus make sure that you have the required system-level dependencies to build it. Instead, it is easier to install a pre-compiled binary from CRAN).

Another important point to address is that if remote dependencies are listed in a DESCRIPTION file like this:

Remotes:
    jimhester/highlite,
    gaborcsardi/gh,
    hadley/memoise

{rix} will automatically use the latest commit from these repositories as the revision. This also means that if these repositories are being actively worked on, rebuilding these environments will actually pull another version of these packages. Instead, it is advisable to edit the default.nix yet again, and replace mentions of HEAD with an actual commit. For example, edit this:

    gh = (pkgs.rPackages.buildRPackage {
      name = "gh";
      src = pkgs.fetchgit {
        url = "https://github.com/gaborcsardi/gh";
        rev = "HEAD";
        sha256 = "sha256-VpxFIfUEk0PudytQ3boMhEJhT0AnelWkSU++WD/HAyo=";
      };
      propagatedBuildInputs = builtins.attrValues {
        inherit (pkgs.rPackages) 
          cli
          gitcreds
          glue
          ini
          jsonlite
          lifecycle
          rlang;
      } ++ [ httr2 ];
    });

to this:

    gh = (pkgs.rPackages.buildRPackage {
      name = "gh";
      src = pkgs.fetchgit {
        url = "https://github.com/gaborcsardi/gh";
        rev = "27db16cf363dc";
        sha256 = ""; # <- You will need to try to build the expression once, and then
      };             # <- put the sha256 that nix-build returns
      propagatedBuildInputs = builtins.attrValues {
        inherit (pkgs.rPackages)
          cli
          gitcreds
          glue
          ini
          jsonlite
          lifecycle
          rlang;
      } ++ [ httr2 ];
    });

However, if instead the remotes are listed like this:

Remotes:
    jimhester/highlite@abc123,
    gaborcsardi/gh@def123,
    hadley/memoise@ghi123

then the listed commits will be used, which will make sure that the build process is reproducible. Only commits can be used, anything else listed there (such as pull request numbers or release tags) will not work with {rix}.

In conclusion, {rix} makes it easier to build packages from GitHub which have themselves dependencies hosted on GitHub, you should however make sure that the expression that is generated uses fixed commits instead of HEAD for the packages being built from GitHub, and you should also decide if you want to use the version of a packages hosted on GitHub instead of the CRAN release. These are decisions that {rix} cannot take for you.