Check the path in the zip archive not the path to the file.

build/android/gyp/util/build_utils.py

 # Copyright 2013 The Chromium Authors. All rights reserved.
 # Use of this source code is governed by a BSD-style license that can be
 # found in the LICENSE file.
 
 import contextlib
 import fnmatch
 import json
 import os
 import pipes
 import shlex
@@ skipping 179 matching lines @@
           raise Exception(
               'Path already exists from zip: %s %s %s'
               % (zip_path, name, output_path))
 
     z.extractall(path=path)
 
 
 def DoZip(inputs, output, base_dir):
   with zipfile.ZipFile(output, 'w') as outfile:
     for f in inputs:
-      CheckZipPath(f)
+      CheckZipPath(os.path.relpath(f, base_dir))
       outfile.write(f, os.path.relpath(f, base_dir))
 
 
 def PrintWarning(message):
   print 'WARNING: ' + message
 
 
 def PrintBigWarning(message):
   print '*****     ' * 8
   PrintWarning(message)
   print '*****     ' * 8