diff -up src/setup.py.orig src/setup.py
--- src/setup.py.orig	2019-01-04 11:05:11.337077724 -0700
+++ src/setup.py	2019-01-16 09:45:32.570933224 -0700
@@ -334,6 +334,9 @@ class sage_build_cython(Command):
         with open(self._version_file, 'w') as f:
             f.write(self._version_stamp)
 
+        # Remove buildroot paths from the generated files
+        subprocess.run(["find", "build/cythonized/sage", "-type", "f", "-exec", "sed", "-i", "s|@@BUILDROOT@@||g", "{}", "+"], check=True)
+
         # Finally, copy relevant cythonized files from build/cythonized
         # tree into the build-lib tree
         for (dst_dir, src_files) in self.get_cythonized_package_files():