# 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.