diff --git a/emcc.py b/emcc.py
index a98f33c33cc7e..a55c37282011b 100644
--- a/emcc.py
+++ b/emcc.py
@@ -711,7 +711,6 @@ def phase_setup(options, state, newargs):
   """
 
   if settings.RUNTIME_LINKED_LIBS:
-    diagnostics.warning('deprecated', 'RUNTIME_LINKED_LIBS is deprecated; you can simply list the libraries directly on the commandline now')
     newargs += settings.RUNTIME_LINKED_LIBS
 
   # Find input files
diff --git a/site/source/docs/tools_reference/settings_reference.rst b/site/source/docs/tools_reference/settings_reference.rst
index 53714034b38bf..9300709020657 100644
--- a/site/source/docs/tools_reference/settings_reference.rst
+++ b/site/source/docs/tools_reference/settings_reference.rst
@@ -1406,6 +1406,8 @@ RUNTIME_LINKED_LIBS
 
 Deprecated, list shared libraries directly on the command line instead.
 
+.. note:: This setting is deprecated
+
 .. _build_as_worker:
 
 BUILD_AS_WORKER
diff --git a/src/settings.js b/src/settings.js
index a673bee6257c1..0f4444c6144f4 100644
--- a/src/settings.js
+++ b/src/settings.js
@@ -1107,6 +1107,7 @@ var SIDE_MODULE = 0;
 
 // Deprecated, list shared libraries directly on the command line instead.
 // [link]
+// [deprecated]
 var RUNTIME_LINKED_LIBS = [];
 
 // If set to 1, this is a worker library, a special kind of library that is run
diff --git a/tools/settings.py b/tools/settings.py
index a394f8088b0d2..ee843de7d4d9d 100644
--- a/tools/settings.py
+++ b/tools/settings.py
@@ -119,6 +119,8 @@
     'SUPPORT_ERRNO': 'emscripten no longer uses the setErrNo library function',
     'EXTRA_EXPORTED_RUNTIME_METHODS': 'please use EXPORTED_RUNTIME_METHODS instead',
     'DEMANGLE_SUPPORT': 'mangled names no longer appear in stack traces',
+    'RUNTIME_LINKED_LIBS': 'you can simply list the libraries directly on the commandline now',
+    'CLOSURE_WARNINGS': 'use -Wclosure instead',
 }
 
 # Settings that don't need to be externalized when serializing to json because they