fix(r): resolve R6 self$ and private$ intra-class method calls

An R6 method reaches a sibling only through self$method() or private$method(),
never as a bare name, but walk_calls only handled a bare identifier callee. So
every intra-class call inside an R6 class was dropped, leaving methods that
clearly call each other disconnected in the graph.

Handle an extract_operator callee whose receiver is self or private: resolve
the method against the enclosing class scope, which is already reachable from
the caller via scope_parent. super$ is deliberately excluded — it dispatches to
a parent class this single-file pass cannot see, so a local binding would be
wrong.

Added a regression test covering both self$ and private$ calls.

graphify/extractors/r.py

@@ -399,6 +399,22 @@ def extract_r(path: Path) -> dict:
                         "source_file": source_file,
                         "source_location": f"L{line}",
                     })
+            elif callee_node is not None and callee_node.type == "extract_operator":
+                # `self$method()` / `private$method()`: an R6 method reaches its
+                # siblings only through self/private, never as a bare name, so
+                # these intra-class calls were dropped entirely. Resolve the
+                # method against the enclosing class scope (walked from the caller
+                # via scope_parent). super$ is left out: it dispatches to a parent
+                # class this pass cannot see, so binding it locally would be wrong.
+                parts = [c for c in callee_node.children if c.type == "identifier"]
+                if (
+                    len(parts) == 2
+                    and _read_text(parts[0], source) in ("self", "private")
+                ):
+                    method = _read_text(parts[1], source)
+                    target = resolve_local(caller_id, method)
+                    if target is not None:
+                        add_edge(caller_id, target, "calls", node.start_point[0] + 1)
             elif callee_node is not None and callee_node.type == "namespace_operator":
                 package_node = callee_node.child_by_field_name("lhs")
                 function_node = callee_node.child_by_field_name("rhs")

tests/test_r_extractor.py

@@ -16,7 +16,7 @@ from pathlib import Path
 
 
 
-from graphify.extract import extract
+from graphify.extract import extract, extract_r
 
 
 
@@ -111,6 +111,30 @@ def test_r_malformed_tail_comments_and_strings_do_not_create_phantoms(tmp_path):
     assert labels.isdisjoint({'ghost()', 'hidden()'})
 
 
+def test_r6_self_and_private_method_calls_resolve(tmp_path):
+    """R6 methods reach their siblings through `self$` / `private$`, never as a
+    bare name. Those intra-class calls were dropped because walk_calls only
+    handled a bare identifier callee."""
+    source = tmp_path / "counter.R"
+    source.write_text(
+        'Counter <- R6Class("Counter",\n'
+        "  public = list(\n"
+        "    increment = function() self$report(),\n"
+        "    report = function() print(1)\n"
+        "  ),\n"
+        "  private = list(\n"
+        "    log = function() private$fmt(),\n"
+        "    fmt = function() 2\n"
+        "  )\n"
+        ")\n",
+        encoding="utf-8",
+    )
+    result = extract_r(source)
+    calls = _edge_labels(result, "calls")
+    assert ("increment()", "report()") in calls, "self$ call dropped"
+    assert ("log()", "fmt()") in calls, "private$ call dropped"
+
+
 def test_r_missing_parser_reports_install_hint(tmp_path, monkeypatch, capsys):
     source = tmp_path / "missing.R"
     source.write_text('run <- function() 1\n', encoding="utf-8")