rPackages.vegan: removed from packagesRequiringX list

[juliendiot42]

Dear @jbedo,

It seems that this vegan package do not actually require X.

As mentioned in #319189, R-packages requiring X are broken on darwin platform. It is therefore good to keep this list up-to-date to let MacOS users being able to install them if they do not actually require X.

Best regards,
@juliendiot42

Description of changes

vegan have been removed from packagesRequiringX

Things done

• Built on platform(s)

  • x86_64-linux
  • aarch64-linux
  • x86_64-darwin
  • aarch64-darwin

• Tested, as applicable:

  • NixOS test(s) (look inside nixos/tests)
  • and/or package tests
  • or, for functions and "core" functionality, tests in lib/tests or pkgs/test
  • made sure NixOS tests are linked to the relevant packages

This package builds successfully without X with the command:

nix build .\#pkgs.rPackages.vegan

• Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage

It seems so:

Console log, click to expand

❯ nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD"
these 2 paths will be fetched (0.11 MiB download, 0.63 MiB unpacked):
  /nix/store/rx6laqr63fhb15sysy8z4magbijb8g0i-nixpkgs-review-2.10.4
  /nix/store/abnch2ab1jfh3kvlrf1fshnx4i2p7kdf-python3.11-argcomplete-3.3.0
copying path '/nix/store/abnch2ab1jfh3kvlrf1fshnx4i2p7kdf-python3.11-argcomplete-3.3.0' from 'https://cache.nixos.org'...
copying path '/nix/store/rx6laqr63fhb15sysy8z4magbijb8g0i-nixpkgs-review-2.10.4' from 'https://cache.nixos.org'...
$ git -c fetch.prune=false fetch --no-tags --force https://github.com/NixOS/nixpkgs master:refs/nixpkgs-review/0
remote: Enumerating objects: 47280, done.
remote: Counting objects: 100% (16339/16339), done.
remote: Compressing objects: 100% (622/622), done.
remote: Total 47280 (delta 15901), reused 15984 (delta 15674), pack-reused 30941
Receiving objects: 100% (47280/47280), 23.03 MiB | 3.43 MiB/s, done.
Resolving deltas: 100% (24784/24784), completed with 5450 local objects.
From https://github.com/NixOS/nixpkgs
 * [new branch]                master     -> refs/nixpkgs-review/0
$ git worktree add /home/julien/.cache/nixpkgs-review/rev-149f81c8d00e5053308b5f225cf6bbabaeee79e7/nixpkgs 698c1d1aeb6a1dc2d86f2fc1e9c418379e90a2e8
Preparing worktree (detached HEAD 698c1d1aeb6a)
Updating files: 100% (41584/41584), done.
HEAD is now at 698c1d1aeb6a Merge pull request #319039 from 0x4A6F/master-atuin
$ nix-env --extra-experimental-features no-url-literals --option system x86_64-linux -f <nixpkgs> --nix-path nixpkgs=/home/julien/.cache/nixpkgs-review/rev-149f81c8d00e5053308b5f225cf6bbabaeee79e7/nixpkgs nixpkgs-overlays=/run/user/1000/tmppu_kgl_o -qaP --xml --out-path --show-trace --no-allow-import-from-derivation
$ git merge --no-commit --no-ff 149f81c8d00e5053308b5f225cf6bbabaeee79e7
Automatic merge went well; stopped before committing as requested
$ nix-env --extra-experimental-features no-url-literals --option system x86_64-linux -f <nixpkgs> --nix-path nixpkgs=/home/julien/.cache/nixpkgs-review/rev-149f81c8d00e5053308b5f225cf6bbabaeee79e7/nixpkgs nixpkgs-overlays=/run/user/1000/tmppu_kgl_o -qaP --xml --out-path --show-trace --no-allow-import-from-derivation --meta
Nothing to be built.
$ /nix/store/j7rp0y3ii1w3dlbflbxlv4g7hbaaz3bs-nix-2.18.2/bin/nix-shell --argstr system x86_64-linux --argstr nixpkgs-path /home/julien/.cache/nixpkgs-review/rev-149f81c8d00e5053308b5f225cf6bbabaeee79e7/nixpkgs --argstr nixpkgs-config-path /run/user/1000/tmpbkjqupmg.nix --argstr attrs-path /home/julien/.cache/nixpkgs-review/rev-149f81c8d00e5053308b5f225cf6bbabaeee79e7/attrs.nix --nix-path nixpkgs=/home/julien/.cache/nixpkgs-review/rev-149f81c8d00e5053308b5f225cf6bbabaeee79e7/nixpkgs nixpkgs-overlays=/run/user/1000/tmppu_kgl_o /nix/store/rx6laqr63fhb15sysy8z4magbijb8g0i-nixpkgs-review-2.10.4/lib/python3.11/site-packages/nixpkgs_review/nix/review-shell.nix

[nix-shell:~/.cache/nixpkgs-review/rev-149f81c8d00e5053308b5f225cf6bbabaeee79e7]$

But I am not sure this apply for r-packages.

• Tested basic functionality of all binary files (usually in ./result/bin/)

library('vegan')

Works.

I used this flake to test it:

`flake.nix`, click to expand

{
  description = "Flake for a R environment";
  inputs = {
    nixpkgs.url = "github:juliendiot42/nixpkgs?ref=rpackages-vegan_doesnt_requireX";
    flake-utils.url = "github:numtide/flake-utils";
  };

  outputs = {
    self,
    nixpkgs,
    flake-utils,
  }:
    flake-utils.lib.eachDefaultSystem (
      system: let
        pkgs = import nixpkgs {inherit system;};
        R-with-my-packages = pkgs.rWrapper.override {
          packages = with pkgs.rPackages; [
            vegan
          ];
        };
      in rec {
        devShells.default = pkgs.mkShell {
          LOCALE_ARCHIVE =
            if "${system}" == "x86_64-linux"
            then "${pkgs.glibcLocalesUtf8}/lib/locale/locale-archive"
            else "";
          R_LIBS_USER = "''"; # to no use users' installed R packages
          R_PROFILE_USER = "''"; # to disable`.Rprofile` files (eg. when the project already use `renv`)
          nativeBuildInputs = [pkgs.bashInteractive];
          buildInputs = [
            R-with-my-packages
          ];
        };
        apps = {
          simpleTest = let
            simpleTest = pkgs.writeShellApplication {
              name = "simpleTest";
              text = ''
                Rscript --vanilla -e "library('vegan'); q()"
              '';
            };
          in {
            type = "app";
            program = "${simpleTest}/bin/simpleTest";
          };
        };
      }
    );
}

and

nix run .\#simpleTest

Output:

nix-shell-env ❯ nix run .\#simpleTest
Loading required package: permute
Loading required package: lattice
This is vegan 2.6-4

• Fits CONTRIBUTING.md.

---

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[juliendiot42]

By the way, @jbedo, this is the origin of the PR #316086 I opened previously that let me think that it would be ok to bypass require X on MacOS. I just encountered this particular package that seems to not require X.

[b-rodrigues]

Can confirm it works, we are in the process of bumping the rPackages set, could you re-open this PR against r-updates? See for example this one: #319389

[jbedo]

Resolved as part of 29a69eb