From b152943d4be721069db29b18137b040df69844e1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Felix=20H=C3=A4fele?= <fhaefelegit@gmail.com>
Date: Fri, 28 Aug 2026 19:56:10 +0200
Subject: [PATCH] fix(pixi-build-r): resolve recommended R packages

---
 crates/pixi_build_r/src/main.rs     | 69 +++++++++++++++++++++++++++++
 crates/pixi_build_r/src/metadata.rs | 31 +++----------
 2 files changed, 75 insertions(+), 25 deletions(-)

diff --git a/crates/pixi_build_r/src/main.rs b/crates/pixi_build_r/src/main.rs
index 2801acc8fd..eb2acc6b26 100644
--- a/crates/pixi_build_r/src/main.rs
+++ b/crates/pixi_build_r/src/main.rs
@@ -651,6 +651,75 @@ Imports:
         });
     }
 
+    #[tokio::test]
+    async fn test_recommended_packages_are_dependencies() {
+        let temp_dir = TempDir::new().unwrap();
+
+        fs::write(
+            temp_dir.path().join("DESCRIPTION"),
+            r#"Package: nlraa
+Version: 1.9.11
+Imports:
+    boot,
+    MASS,
+    Matrix,
+    mgcv,
+    nlme,
+    stats
+"#,
+        )
+        .await
+        .unwrap();
+
+        let project_model = project_fixture!({
+            "name": "r-nlraa",
+            "version": "1.9.11",
+            "targets": {
+                "defaultTarget": {}
+            }
+        });
+
+        let generated_recipe = RGenerator::default()
+            .generate_recipe(
+                &project_model,
+                &RBackendConfig::default(),
+                temp_dir.path().to_path_buf(),
+                Platform::Linux64,
+                None,
+                &HashSet::new(),
+                vec![],
+                None,
+                None,
+                None,
+                None,
+            )
+            .await
+            .expect("Failed to generate recipe");
+
+        let host_reqs = &generated_recipe.recipe.requirements.host;
+        let run_reqs = &generated_recipe.recipe.requirements.run;
+
+        for package in ["r-boot", "r-mass", "r-matrix", "r-mgcv", "r-nlme"] {
+            assert!(
+                host_reqs.iter().any(|req| req.to_string() == package),
+                "{package} should be in host requirements"
+            );
+            assert!(
+                run_reqs.iter().any(|req| req.to_string() == package),
+                "{package} should be in run requirements"
+            );
+        }
+
+        assert!(
+            host_reqs.iter().all(|req| req.to_string() != "r-stats"),
+            "base packages should not be separate host requirements"
+        );
+        assert!(
+            run_reqs.iter().all(|req| req.to_string() != "r-stats"),
+            "base packages should not be separate run requirements"
+        );
+    }
+
     #[tokio::test]
     async fn test_package_name_derived_from_description_is_r_prefixed() {
         // When the model carries no name (the inline source-dependency flow),
diff --git a/crates/pixi_build_r/src/metadata.rs b/crates/pixi_build_r/src/metadata.rs
index 8335f043de..8bcb3ca02a 100644
--- a/crates/pixi_build_r/src/metadata.rs
+++ b/crates/pixi_build_r/src/metadata.rs
@@ -15,11 +15,8 @@ static CRAN_SPDX_MAP: LazyLock<HashMap<String, String>> = LazyLock::new(|| {
 
 /// R packages that are built into r-base and should not be listed as separate dependencies.
 ///
-/// This includes:
-/// - Base packages (14): ship with every R installation
-/// - Recommended packages (15): included in all binary distributions of R
-///
-/// See: <https://cran.r-project.org/doc/FAQ/R-FAQ.html>
+/// Recommended packages are not listed because conda-forge packages them
+/// separately from r-base.
 pub const R_BUILTIN_PACKAGES: &[&str] = &[
     // Base packages (Priority: base)
     "base",
@@ -36,23 +33,6 @@ pub const R_BUILTIN_PACKAGES: &[&str] = &[
     "tcltk",
     "tools",
     "utils",
-    // Recommended packages (Priority: recommended)
-    // These are included in all binary distributions of R
-    "KernSmooth",
-    "MASS",
-    "Matrix",
-    "boot",
-    "class",
-    "cluster",
-    "codetools",
-    "foreign",
-    "lattice",
-    "mgcv",
-    "nlme",
-    "nnet",
-    "rpart",
-    "spatial",
-    "survival",
 ];
 
 /// Check if an R package is built into r-base
@@ -715,10 +695,11 @@ Imports:
         }
 
         #[test]
-        fn test_is_builtin_package() {
+        fn test_only_base_packages_are_builtin() {
             assert!(is_builtin_package("stats"));
-            assert!(is_builtin_package("MASS"));
-            assert!(is_builtin_package("mass")); // case insensitive
+            assert!(is_builtin_package("STATS"));
+            assert!(!is_builtin_package("MASS"));
+            assert!(!is_builtin_package("boot"));
             assert!(!is_builtin_package("curl"));
             assert!(!is_builtin_package("ggplot2"));
         }