diff --git a/src/library/tools/R/QC.R b/src/library/tools/R/QC.R
index 6c99a7edb2..af665fd6c9 100644
--- a/src/library/tools/R/QC.R
+++ b/src/library/tools/R/QC.R
@@ -2379,6 +2379,39 @@ function(x, ...)
    res
 }
 
+### Additional functions for checkS3methods
+checkTopLevelCall <- function(expr, fun_name) {
+    if (inherits(expr, "if") || !is.call(expr)) {
+        return(FALSE)
+    }
+    fun_name <- as.name(fun_name)
+    fun_called <- expr[[1]]
+    if (is.call(fun_called)) {
+        inner_called <- fun_called[[1]]
+        if (identical(inner_called, quote(`:::`)) ||
+            identical(inner_called, quote(`::`))) {
+           fun_called <- fun_called[[3]]
+        }
+    }
+    identical(fun_called, fun_name)
+}
+
+containsTopLevelCall <- function(x, fun_name) {
+    fun_body <- body(x)
+    if (inherits(fun_body, "{")) {
+        any(vapply(fun_body, checkTopLevelCall, TRUE, fun = fun_name))
+    } else {
+        checkTopLevelCall(fun_body, fun_name)
+    }
+}
+
+isDeprecated <- function(fun) {
+    containsTopLevelCall(fun, quote(.Deprecated))
+}
+isDefunct <- function(fun) {
+    containsTopLevelCall(fun, quote(.Defunct))
+}
+
 ### * checkS3methods
 
 checkS3methods <-
@@ -2603,6 +2636,11 @@ function(package, dir, lib.loc = NULL)
                   function(g) {
                       methods <-
                           gen_dot_cls_matches(g, functions_in_code)
+                      method_funs <-
+                          Filter(Negate(function(x) {
+                              isDefunct(x) || isDeprecated(x)
+                              }), mget(methods, code_env))
+                      methods <- names(method_funs)
                       if((n <- length(methods)) > 0L) {
                           gargs <- nfg(g, code_env)
                           entries <-