diff --git a/src/index.ts b/src/index.ts
index 92cb253e3..3efc3d0b4 100644
--- a/src/index.ts
+++ b/src/index.ts
@@ -170,12 +170,16 @@ function getTmpDir (): string {
  * Register TypeScript compiler.
  */
 export function register (opts: Options = {}): Register {
-  const emptyFileListWarnings = [18002, 18003]
   const options = Object.assign({}, DEFAULTS, opts)
   const cacheDirectory = options.cacheDirectory || getTmpDir()
-  const ignoreDiagnostics = arrify(options.ignoreDiagnostics).concat(emptyFileListWarnings).map(Number)
   const originalJsHandler = require.extensions['.js']
 
+  const ignoreDiagnostics = arrify(options.ignoreDiagnostics).concat([
+    6059, // "'rootDir' is expected to contain all source files."
+    18002, // "The 'files' list in config file is empty."
+    18003 // "No inputs were found in config file."
+  ]).map(Number)
+
   const memoryCache: MemoryCache = {
     contents: Object.create(null),
     versions: Object.create(null),
diff --git a/tsconfig.json b/tsconfig.json
index fede4771a..143c2c32d 100644
--- a/tsconfig.json
+++ b/tsconfig.json
@@ -2,6 +2,7 @@
   "compilerOptions": {
     "target": "es5",
     "lib": ["es2015"],
+    "rootDir": "src",
     "outDir": "dist",
     "module": "commonjs",
     "declaration": true,