diff --git a/tools/apollo/cppcheck b/tools/apollo/cppcheck
index e61d63ed6..4f504bb13 100755
--- a/tools/apollo/cppcheck
+++ b/tools/apollo/cppcheck
@@ -16,9 +16,9 @@ if [ "$mode" == diff ]; then
     flags=""
 else
     files=src/
-    flags="-j$THREADS"
+    flags="-j$THREADS -Isrc"
 fi
-cppcheck --enable=all --force --suppress=missingInclude $flags -Isrc $files 2>"$errfile"
+cppcheck --enable=all --force --suppress=missingInclude $flags $files 2>"$errfile"
 
 cat "$errfile" >&2
 
diff --git a/tools/apollo/generate b/tools/apollo/generate
index 547f8a743..e3c1f33de 100755
--- a/tools/apollo/generate
+++ b/tools/apollo/generate
@@ -105,7 +105,7 @@ check_dirs = list(map(lambda x: os.path.join(BASE_DIR, x), ["src", "tests",
 archive = create_archive("cppcheck", check_dirs, WORKSPACE_DIR)
 cmd = os.path.relpath(cppcheck, WORKSPACE_DIR)
 outfile_paths = "\./" + cmd.replace("cppcheck", ".cppcheck_errors").replace(".", "\\.")
-RUNS.append(generate_run("cppcheck", commands = './{} {}'.format(cmd, mode),
+RUNS.append(generate_run("cppcheck", commands = 'TIMEOUT=1000 ./{} {}'.format(cmd, mode),
         infile = archive, outfile_paths = outfile_paths))
 
 # ctest tests