check.js: Ignore dedup warnings for bundled dependencies

__tests__/commands/check.js

@@ -313,3 +313,12 @@ test.concurrent('--integrity --check-files should not die on broken symlinks', a
     },
   );
 });
+
+test.concurrent('should ignore bundled dependencies',
+async (): Promise<void> => {
+  await runInstall({}, path.join('..', 'check', 'bundled-dep-check'),
+  async (config, reporter, install, getStdout): Promise<void> => {
+    await checkCmd.run(config, reporter, {}, []);
+    expect(getStdout().indexOf('warning')).toEqual(-1);
+  });
+});

__tests__/fixtures/check/bundled-dep-check/package.json

@@ -0,0 +1,9 @@
+{
+  "name": "bundled-dep-check",
+  "description": "A package with bundled dependencies",
+  "version": "2.0.1",
+  "dependencies": {
+    "nyc": "file:./nyc-10.3.2.tgz"
+  },
+  "license": "MIT"
+}

__tests__/fixtures/check/bundled-dep-check/yarn.lock

@@ -0,0 +1,13 @@
+# THIS IS AN AUTOGENERATED FILE. DO NOT EDIT THIS FILE DIRECTLY.
+# yarn lockfile v1
+
+
+archy@^1.0.0:
+  version "1.0.0"
+  resolved "https://registry.yarnpkg.com/archy/-/archy-1.0.0.tgz#f9c8c13757cc1dd7bc379ac77b2c62a5c2868c40"
+
+"nyc@file:./nyc-10.3.2.tgz":
+  version "10.3.2"
+  resolved "./nyc-10.3.2.tgz#35563cb271637e2dc922a1145d8981e948a9f5c3"
+  dependencies:
+    archy "^1.0.0"

src/cli/commands/check.js

@@ -218,6 +218,7 @@ export async function run(config: Config, reporter: Reporter, flags: Object, arg
     }
   }
 
+  const bundledDeps = {};
   // check if any of the node_modules are out of sync
   const res = await install.linker.getFlatHoistedTree(patterns);
   for (const [loc, {originalKey, pkg, ignore}] of res) {
@@ -268,6 +269,7 @@ export async function run(config: Config, reporter: Reporter, flags: Object, arg
     }
 
     const deps = Object.assign({}, packageJson.dependencies, packageJson.peerDependencies);
+    bundledDeps[packageJson.name] = packageJson.bundledDependencies || [];
 
     for (const name in deps) {
       const range = deps[name];
@@ -321,10 +323,14 @@ export async function run(config: Config, reporter: Reporter, flags: Object, arg
         }
 
         const packageJson = await config.readJson(loc);
-        if (
-          packageJson.version === depPkg.version ||
-          (semver.satisfies(packageJson.version, range, config.looseSemver) &&
-            semver.gt(packageJson.version, depPkg.version, config.looseSemver))
+        const packagePath = originalKey.split('#');
+        const rootDep = packagePath[0];
+        const packageName = packagePath[1] || packageJson.name;
+
+        const bundledDep = bundledDeps[rootDep] && bundledDeps[rootDep].includes(packageName);
+        if (!bundledDep && (packageJson.version === depPkg.version ||
+        (semver.satisfies(packageJson.version, range, config.looseSemver) &&
+          semver.gt(packageJson.version, depPkg.version, config.looseSemver)))
         ) {
           reporter.warn(
             reporter.lang(