flake.lock: Update

Flake lock file updates:

• Updated input 'r-nvim-nix':
    'github:dwinkler1/r_nvim_nix/435103d' (2026-05-13)
  → 'github:dwinkler1/r_nvim_nix/c7b880d' (2026-05-13)

.Rprofile

@@ -0,0 +1,5 @@
+if (Sys.getenv("RNVIM_TMPDIR") == "") {
+  options(defaultPackages = c("utils", "grDevices", "graphics", "stats", "methods"))
+} else {
+  options(defaultPackages = c("utils", "grDevices", "graphics", "stats", "methods", "nvimcom"))
+}

.commandcode/taste/taste.md

@@ -0,0 +1,8 @@
+# nix
+- For R.nvim in the Nix wrapper, both RNVIM_COMPLDIR (C server compilation) and a writable R_LIBS_USER directory (nvimcom R package installation) must be configured — fixing only one leaves permission errors in the other. Confidence: 0.65
+- For R.nvim writable directories (RNVIM_COMPLDIR, R_LIBS_USER, TMPDIR), prefer project-local paths (e.g., $PWD/.Rlibs) over global cache paths — the cache approach may let the build succeed but still fail at runtime. Confidence: 0.70
+
+# Taste (Continuously Learned by [CommandCode][cmd])
+
+[cmd]: https://commandcode.ai/
+

flake.lock

@@ -22,11 +22,11 @@
     },
     "nixpkgs": {
       "locked": {
-        "lastModified": 1777954456,
-        "narHash": "sha256-hGdgeU2Nk87RAuZyYjyDjFL6LK7dAZN5RE9+hrDTkDU=",
+        "lastModified": 1778443072,
+        "narHash": "sha256-zi7/fsqM/kFdNuED//4WOCUtezGtKKqRNORjMvfwjnA=",
         "owner": "nixos",
         "repo": "nixpkgs",
-        "rev": "549bd84d6279f9852cae6225e372cc67fb91a4c1",
+        "rev": "da5ad661ba4e5ef59ba743f0d112cbc30e474f32",
         "type": "github"
       },
       "original": {
@@ -69,19 +69,42 @@
         "type": "github"
       }
     },
-    "rixpkgs": {
+    "r-nvim-nix": {
+      "inputs": {
+        "nixpkgs": [
+          "rixpkgs"
+        ],
+        "rnvimsrc": [
+          "plugins-r"
+        ]
+      },
       "locked": {
-        "lastModified": 1778520264,
-        "narHash": "sha256-OjpxoQsZSsyXJxtgKJsbNKX5KaSZRaEeaqQj3rmI5uM=",
+        "lastModified": 1778643549,
+        "narHash": "sha256-dJBdYawL+/IVtmXLFZ+kQGOo5fd1cliDJJdJEi0Mqqw=",
         "owner": "dwinkler1",
-        "repo": "rixpkgs",
-        "rev": "88147cbbf4be689ea32ed5cbf9370a6aa95fd08e",
+        "repo": "r_nvim_nix",
+        "rev": "c7b880dde56b4fcef09938e311415b63f2262498",
         "type": "github"
       },
       "original": {
         "owner": "dwinkler1",
-        "ref": "nixpkgs",
+        "repo": "r_nvim_nix",
+        "type": "github"
+      }
+    },
+    "rixpkgs": {
+      "locked": {
+        "lastModified": 1771303851,
+        "narHash": "sha256-tgveHozOJ2D/mi3LxVy/FcmLFDlM5XKZxsNB2XpvzaM=",
+        "owner": "dwinkler1",
         "repo": "rixpkgs",
+        "rev": "af2dd3f7b4b172077747c0869d4e30702fb71b0e",
+        "type": "github"
+      },
+      "original": {
+        "owner": "dwinkler1",
+        "repo": "rixpkgs",
+        "rev": "af2dd3f7b4b172077747c0869d4e30702fb71b0e",
         "type": "github"
       }
     },
@@ -91,6 +114,7 @@
         "nixpkgs": "nixpkgs",
         "plugins-cmp-pandoc-references": "plugins-cmp-pandoc-references",
         "plugins-r": "plugins-r",
+        "r-nvim-nix": "r-nvim-nix",
         "rixpkgs": "rixpkgs",
         "wrappers": "wrappers"
       }

flake.nix

@@ -10,7 +10,11 @@
       url = "github:BirdeeHub/nix-wrapper-modules";
       inputs.nixpkgs.follows = "nixpkgs";
     };
-    rixpkgs.url = "github:dwinkler1/rixpkgs/nixpkgs";
+    rixpkgs.url = "github:dwinkler1/rixpkgs/af2dd3f7b4b172077747c0869d4e30702fb71b0e";
+
+    r-nvim-nix.url = "github:dwinkler1/r_nvim_nix";
+    r-nvim-nix.inputs.rnvimsrc.follows = "plugins-r";
+    r-nvim-nix.inputs.nixpkgs.follows = "rixpkgs";
 
     fran = {
       url = "github:dwinkler1/fran";
@@ -46,7 +50,7 @@
         nix = true;
         optional = false;
         python = false;
-        r = false;
+        r = true;
       };
       settings = {
         lang_packages = {
@@ -61,6 +65,7 @@
             janitor
             languageserver
             styler
+            pkgs.nvimcom
           ];
           julia = ["DataFramesMeta" "QuackIO"];
         };
@@ -187,6 +192,8 @@
             air-formatter
             yaml-language-server
             updateR
+            nvimcom
+            rnvimserver
           ];
 
         juliaPackages = let
@@ -199,7 +206,8 @@
           zk
         ];
 
-        shellPackages = [nvimPkg]
+        shellPackages =
+          [nvimPkg]
           ++ pkgs.lib.optionals cfg.cats.python pythonPackages
           ++ pkgs.lib.optionals cfg.cats.r rPackages
           ++ pkgs.lib.optionals cfg.cats.julia juliaPackages
@@ -210,7 +218,13 @@
           packages = shellPackages;
           nativeBuildInputs = with pkgs; [] ++ (pkgs.lib.optionals cfg.cats.optional [devenv]);
           inputsFrom = [];
-          shellHook = "";
+          shellHook = ''
+            echo 'I am a NixShell'
+            export R_HOME=$(R RHOME)
+            export R_LIBS_SITE=$(strings "$(command -v R)" | grep -oP '/nix/store/[^:]+/library' | sort -u | paste -sd: -)
+            export R_LIBS_USER="$PWD/.r-libs"
+            mkdir -p "$R_LIBS_USER"
+          '';
         };
       }
     );

modules/module/settings/cats.nix

@@ -43,7 +43,7 @@
     nix = lib.mkDefault true;
     optional = lib.mkDefault false;
     python = lib.mkDefault false;
-    r = lib.mkDefault false;
+    r = lib.mkDefault true;
     test = lib.mkDefault false;
     treesitterParsers = lib.mkDefault true;
     utils = lib.mkDefault true;

modules/module/settings/env.nix

@@ -11,12 +11,17 @@
       UV_PYTHON_DOWNLOADS = "never";
       UV_PYTHON = pkgs.python.interpreter;
     })
+    (lib.mkIf (config.cats.r or false) {
+      RNVIM_COMPLDIR = "$PWD/.r-compl";
+      R_LIBS_USER = "${pkgs.nvimcom}/library:$PWD/.Rlibs";
+      TMPDIR = "$PWD/.r-tmp";
+    })
   ];
 
   # Environment variables with defaults (can be overridden by user)
   config.envDefault = lib.mkMerge [
     (lib.mkIf (config.cats.r or false) {
-      R_LIBS_USER =  "./.Rlibs";
+      R_LIBS_USER = "${pkgs.nvimcom}/library:$PWD/.Rlibs";
     })
   ];
 }

modules/module/specs/plugins.nix

@@ -11,7 +11,13 @@
 
   config.specs.r = {
     data = with pkgs.vimPlugins; [
-      config.nvim-lib.neovimPlugins.r
+      (config.nvim-lib.neovimPlugins.r.overrideAttrs (old: {
+        postInstall = (old.postInstall or "") + ''
+          mkdir -p $out/rnvimserver
+          cp ${pkgs.rnvimserver}/bin/rnvimserver $out/rnvimserver/rnvimserver
+          chmod +x $out/rnvimserver/rnvimserver
+        '';
+      }))
       quarto-nvim
       {
         data = otter-nvim;

overlays/default.nix

@@ -3,12 +3,14 @@ let
   lib = nixpkgs.lib;
 
   rOverlay = import ./r.nix {inherit inputs;};
+  rNvimNixOverlay = inputs.r-nvim-nix.overlays.default;
   franOverlay = inputs.fran.overlays.default;
   pythonOverlay = import ./python.nix inputs;
   pluginsOverlay = import ./plugins.nix inputs;
 
   dependencyOverlays = [
     rOverlay
+    rNvimNixOverlay
     pythonOverlay
     pluginsOverlay
   ];
@@ -17,6 +19,7 @@ in
 {
   inherit
     rOverlay
+    rNvimNixOverlay
     franOverlay
     pythonOverlay
     pluginsOverlay
@@ -30,6 +33,7 @@ in
   overlays = {
     inherit
       rOverlay
+      rNvimNixOverlay
       franOverlay
       pythonOverlay
       pluginsOverlay

overlays/r.nix

@@ -33,6 +33,9 @@
     overlays = [inputs.fran.overlays.default];
   }; # rixpkgs.legacyPackages.${prev.stdenv.hostPlatform.system};
 
+  # nvimcom and rnvimserver are provided by the r-nvim-nix flake overlay
+  # (inputs.r-nvim-nix.overlays.default)
+
   # Standard R packages used by default in rWrapper and quarto
   reqPkgs = with rpkgs.rPackages; [
     #    languageserver

plugin/21_datascience.lua

@@ -44,6 +44,12 @@ end)
 -- r
 now(function()
   if nix.get_cat("r", false) then
+    local cwd = vim.fn.getcwd(-1)
+    vim.env.RNVIM_COMPLDIR = cwd .. "/.r-compl"
+    vim.env.R_LIBS_USER = (vim.env.R_LIBS_USER or ""):gsub("%$PWD", cwd)
+    vim.env.TMPDIR = cwd .. "/.r-tmp"
+    vim.fn.mkdir(vim.env.RNVIM_COMPLDIR, "p")
+    vim.fn.mkdir(vim.env.TMPDIR, "p")
     vim.g.rout_follow_colorscheme = true
     require("r").setup({
       -- Create a table with the options to be passed to setup()