Unable to instantiate activity ... Didn't find class WelcomeActivity on path: DexPathList (with instant run)

Question

I've been struggling with my project for a few days now, suddenly from one build/deploy to another I started getting the following exception. Nothing was updated or changed, I just wanted to run the app on a different device when it happened (just like any other day really).

java.lang.RuntimeException: Unable to instantiate activity ComponentInfo{com.my.app.flavor.debug/com.my.app.ui.activity.WelcomeActivity}: java.lang.ClassNotFoundException: Didn't find class "com.my.app.flavor.ui.activity.WelcomeActivity" on path: DexPathList[[zip file "/data/app/com.my.app.flavor.debug-2/base.apk"],nativeLibraryDirectories=[/data/app/**com.my.app.flavor.**debug-2/lib/x86, /data/app/com.my.app.flavor.debug-2/base.apk!/lib/x86, /vendor/lib, /system/lib]]
                  at android.app.ActivityThread.performLaunchActivity(ActivityThread.java:2327)
                  at android.app.ActivityThread.handleLaunchActivity(ActivityThread.java:2476)
                  at android.app.ActivityThread.-wrap11(ActivityThread.java)
                  at android.app.ActivityThread$H.handleMessage(ActivityThread.java:1344)
                  at android.os.Handler.dispatchMessage(Handler.java:102)
                  at android.os.Looper.loop(Looper.java:148)
                  at android.app.ActivityThread.main(ActivityThread.java:5417)
                  at java.lang.reflect.Method.invoke(Native Method)
                  at com.android.internal.os.ZygoteInit$MethodAndArgsCaller.run(ZygoteInit.java:726)
                  at com.android.internal.os.ZygoteInit.main(ZygoteInit.java:616)
               Caused by: java.lang.ClassNotFoundException: Didn't find class "com.my.app.ui.activity.WelcomeActivity" on path: DexPathList[[zip file "/data/app/com.my.app.flavor.debug-2/base.apk"],nativeLibraryDirectories=[/data/app/com.my.app.flavor.debug-2/lib/x86, /data/app/com.my.app.flavor.debug-2/base.apk!/lib/x86, /vendor/lib, /system/lib]]
                  at dalvik.system.BaseDexClassLoader.findClass(BaseDexClassLoader.java:56)
                  at java.lang.ClassLoader.loadClass(ClassLoader.java:511)
                  at java.lang.ClassLoader.loadClass(ClassLoader.java:469)
                  at android.app.Instrumentation.newActivity(Instrumentation.java:1067)
                  at android.app.ActivityThread.performLaunchActivity(ActivityThread.java:2317)
                  at android.app.ActivityThread.handleLaunchActivity(ActivityThread.java:2476) 
                  at android.app.ActivityThread.-wrap11(ActivityThread.java) 
                  at android.app.ActivityThread$H.handleMessage(ActivityThread.java:1344) 
                  at android.os.Handler.dispatchMessage(Handler.java:102) 
                  at android.os.Looper.loop(Looper.java:148) 
                  at android.app.ActivityThread.main(ActivityThread.java:5417) 
                  at java.lang.reflect.Method.invoke(Native Method) 
                  at com.android.internal.os.ZygoteInit$MethodAndArgsCaller.run(ZygoteInit.java:726) 
                  at com.android.internal.os.ZygoteInit.main(ZygoteInit.java:616) 
                Suppressed: java.lang.ClassNotFoundException: com.my.app.ui.activity.WelcomeActivity
                  at java.lang.Class.classForName(Native Method)
                  at java.lang.BootClassLoader.findClass(ClassLoader.java:781)
                  at java.lang.BootClassLoader.loadClass(ClassLoader.java:841)
                  at java.lang.ClassLoader.loadClass(ClassLoader.java:504)
                        ... 12 more
               Caused by: java.lang.NoClassDefFoundError: Class not found using the boot class loader; no stack trace available

Debug builds fail to deploy/start on all my 3 devices (Android 5.0.2, 6.0.1 and 7.0), and on emulators. Run works if I select two or more deployment targets, but not with only one (because instant run is disabled with multiple targets). Debug and Run works when instant run is disabled

My project has multiple flavors and applicationIds (like in Android wear project with 3 flavors, 3 buildTypes and 2 applicationIdSuffixes). None of the gradle files were changed when the error occured, neither was the manifest.

AndroidManifest.xml:

<?xml version="1.0" encoding="utf-8"?>
<manifest xmlns:android="http://schemas.android.com/apk/res/android"
android:installLocation="auto"
package="com.my.app">
<permission
    android:name="${applicationId}.permission.C2D_MESSAGE"
    android:protectionLevel="signature" />

<!-- PROTECTION_NORMAL -->
<uses-permission android:name="android.permission.INTERNET" />
<uses-permission android:name="android.permission.ACCESS_NETWORK_STATE" />
<uses-permission android:name="android.permission.WAKE_LOCK" />
<uses-permission android:name="android.permission.VIBRATE" />
<!-- PROTECTION_DANGEROUS -->
<uses-permission android:name="android.permission.ACCESS_COARSE_LOCATION" />
<uses-permission android:name="android.permission.ACCESS_FINE_LOCATION" />
<uses-permission android:name="android.permission.GET_ACCOUNTS" />
<uses-permission android:name="android.permission.USE_CREDENTIALS" />
<!-- Protection unknown -->
<uses-permission android:name="${applicationId}.permission.C2D_MESSAGE" />
<uses-permission android:name="com.google.android.c2dm.permission.RECEIVE" />
<uses-permission android:name="com.google.android.providers.gsf.permission.READ_GSERVICES" />

<uses-feature android:glEsVersion="0x00020000" android:required="true" />
<uses-feature android:name="android.hardware.location" android:required="true" />

<application
    android:allowBackup="true"
    android:icon="@mipmap/ic_launcher"
    android:label="@string/app_name"
    android:theme="@style/AppTheme">
    <activity android:name="net.hockeyapp.android.UpdateActivity" />
    <activity
        android:name=".ui.activity.WelcomeActivity"
        android:label="@string/app_name"
        android:screenOrientation="portrait">
        <intent-filter>
            <action android:name="android.intent.action.MAIN" />
            <category android:name="android.intent.category.LAUNCHER" />
        </intent-filter>
    </activity>
    <activity
        android:name=".ui.activity.StartActivity"
        android:label="@string/app_name"
        android:screenOrientation="portrait" />
    <activity
        android:name=".MainActivity"
        android:label="@string/app_name"
        android:screenOrientation="portrait" />

    <activity
        android:name="com.facebook.LoginActivity"
        android:screenOrientation="portrait" />
    <activity
        android:name=".ui.activity.NotificationActivity"
        android:screenOrientation="portrait" />

    <activity
        android:name=".ui.activity.OtherActivity"
        android:label="@string/cards_register_card"
        android:screenOrientation="portrait" />
    <activity
        android:name=".ui.activity.OneMoreActivity"
        android:label="@string/a_title"
        android:parentActivityName=".ui.activity.OtherActivity"
        android:screenOrientation="portrait">
        <meta-data
            android:name="android.support.PARENT_ACTIVITY"
            android:value=".ui.activity.OtherActivity" />
    </activity>

    <service android:name=".service.WearableListenerService">
        <intent-filter>
            <action android:name="com.google.android.gms.wearable.DATA_CHANGED" />
            <action android:name="com.google.android.gms.wearable.MESSAGE_RECEIVED" />

            <data
                android:host="*"
                android:pathPrefix="/path"
                android:scheme="wear" />
        </intent-filter>
    </service>

    <!-- GCM START -->
    <receiver
        android:name="com.google.android.gms.gcm.GcmReceiver"
        android:exported="true"
        android:permission="com.google.android.c2dm.permission.SEND">
        <intent-filter>
            <action android:name="com.google.android.c2dm.intent.RECEIVE" />

            <category android:name="${applicationId}" />
        </intent-filter>
    </receiver>

    <service
        android:name=".service.PushListenerService"
        android:exported="false">
        <intent-filter>
            <action android:name="com.google.android.c2dm.intent.RECEIVE" />
        </intent-filter>
    </service>
    <service
        android:name=".service.PushInstanceIDListenerService"
        android:exported="false">
        <intent-filter>
            <action android:name="com.google.android.gms.iid.InstanceID" />
        </intent-filter>
    </service>
    <service
        android:name=".service.PushRegistrationIntentService"
        android:exported="false"></service>
    <!-- GCM END -->

    <meta-data
        android:name="com.google.android.geo.API_KEY"
        android:value="@string/google_maps_api_key" />
    <meta-data
        android:name="com.google.android.gms.version"
        android:value="@integer/google_play_services_version" />
    <meta-data
        android:name="com.facebook.sdk.ApplicationId"
        android:value="@string/facebook_app_id" />

    <!-- Register AnalyticsReceiver and AnalyticsService to support background dispatching on non-Google Play devices -->
    <receiver
        android:name="com.google.android.gms.analytics.AnalyticsReceiver"
        android:enabled="true">
        <intent-filter>
            <action android:name="com.google.android.gms.analytics.ANALYTICS_DISPATCH" />
        </intent-filter>
    </receiver>

    <service
        android:name="com.google.android.gms.analytics.AnalyticsService"
        android:enabled="true"
        android:exported="false" />
</application>

So far I've tried the following:

• clean, clean, clean and even more cleaning
• delete all /build folders
• restarting Android Studio (2.2), my computer and all devices
• uninstalling all flavors of my apps on all devices and emulators
• trying to create a new Run configuration with the activity specified under Launch Options (sometimes works when running on a single deployment target, but never in Debug mode)
• running with instant run deactivated followed by a run with it activated
• re-installing Android Studio

Any help on getting this to work again with instant run is much appreciated!

Answer 1

This seems to happen from time to time with instant run enabled (though not that often in the later updates of Android Studio). Just disable instant run, run the app, enable instant run again.

Hopefully instant run will keep improving.

(For me, switching between branches seems to trigger this more often.)

Answer 2

It looks like a bug in the build tools version 24.0.2, I upgraded to 24.0.3 and finally got it working again!

buildToolsVersion '24.0.3'

Rolling back to 24.0.2 reproduces the problem every time.