MultiDex NoClassDefFound error

Question

I have converted my application into MultiDex to bear with 64k dex limit. Now it looks like this:

public class App extends MultiDexApplication {

private AppWrapper instance;

@Override
protected void attachBaseContext(Context base) {
    super.attachBaseContext(base);
    MultiDex.install(base);
}

@Override
public void onCreate() {
    super.onCreate();

    if (instance == null) {
        instance = new AppWrapper(this);
    }
}
}

I've pulled all the usual logic from App to AppWidget to make MultiDex work. And it works ok on other teammates' computers. But not with me. It keeps throwing java.lang.NoClassDefFoundError on application create:

I/dalvikvm﹕ Failed resolving     Lcom/playday/app/core/AppWrapper; interface 8940 'Lretrofit/ErrorHandler;'
W/dalvikvm﹕ Link of class     'Lcom/playday/app/core/AppWrapper;' failed
I/dalvikvm﹕ Failed resolving     Lcom/playday/app/core/AppWrapper; interface 8940 'Lretrofit/ErrorHandler;'
W/dalvikvm﹕ Link of class     'Lcom/playday/app/core/AppWrapper;' failed
E/dalvikvm﹕ Could not find class     'com.playday.app.core.AppWrapper', referenced from method com.playday.app.core.App.onCreate
W/dalvikvm﹕ VFY: unable to resolve     new-instance 7076 (Lcom/playday/app/core/AppWrapper;) in Lcom/playday/app/core/App;
D/dalvikvm﹕ VFY: replacing opcode     0x22 at 0x0007
I/dalvikvm﹕ Failed resolving     Lcom/playday/app/core/AppWrapper; interface 8940 'Lretrofit/ErrorHandler;'
W/dalvikvm﹕ Link of class     'Lcom/playday/app/core/AppWrapper;' failed
D/dalvikvm﹕ DexOpt: unable to opt     direct call 0xc21b at 0x09 in Lcom/playday/app/core/App;.onCreate
I/MultiDex﹕ VM with version 1.6.0     does not have multidex support
I/MultiDex﹕ install
I/MultiDex﹕ MultiDexExtractor.load(    /data/app/com.playdayteam.playday.debug-1.apk, false)
I/MultiDex﹕ Detected that     extraction must be performed.
I/MultiDex﹕ Trying to delete old     file /data/data/com.playdayteam.playday.debug/code_cache/secondary-dexes/com.playdayteam.playday.    debug-2.apk.classes2.dex of size 1484912
I/MultiDex﹕ Deleted old file     /data/data/com.playdayteam.playday.debug/code_cache/secondary-dexes/com.playdayteam.playday.debug-2    .apk.classes2.dex
I/MultiDex﹕ Trying to delete old     file /data/data/com.playdayteam.playday.debug/code_cache/secondary-dexes/com.playdayteam.playday.    debug-2.apk.classes2.zip of size 540964
I/MultiDex﹕ Deleted old file     /data/data/com.playdayteam.playday.debug/code_cache/secondary-dexes/com.playdayteam.playday.debug-2    .apk.classes2.zip
D/dalvikvm﹕ GC_CONCURRENT freed     186K, 11% free 3245K/3640K, paused 2ms+4ms, total 28ms
D/dalvikvm﹕ WAIT_FOR_CONCURRENT_GC     blocked 5ms
D/dalvikvm﹕ GC_CONCURRENT freed     156K, 8% free 3593K/3904K, paused 3ms+2ms, total 22ms
I/MultiDex﹕ Extraction is needed     for file /data/data/com.playdayteam.playday.debug/code_cache/secondary-dexes/com.playdayteam.    playday.debug-1.apk.classes2.zip
I/MultiDex﹕ Extracting     /data/data/com.playdayteam.playday.debug/code_cache/secondary-dexes/com.playdayteam.playday.debug-1    .apk.classes576886388.zip
I/MultiDex﹕ Renaming to     /data/data/com.playdayteam.playday.debug/code_cache/secondary-dexes/com.playdayteam.playday.debug-1    .apk.classes2.zip
I/MultiDex﹕ Extraction success -     length /data/data/com.playdayteam.playday.debug/code_cache/secondary-dexes/com.playdayteam.playday.    debug-1.apk.classes2.zip: 540964
I/MultiDex﹕ load found 1 secondary     dex files
D/dalvikvm﹕ DexOpt: --- BEGIN 'com.    playdayteam.playday.debug-1.apk.classes2.zip' (bootstrap=0) ---
D/dalvikvm﹕ DexOpt: --- END 'com.    playdayteam.playday.debug-1.apk.classes2.zip' (success) ---
D/dalvikvm﹕ DEX prep '/data/data/com    .playdayteam.playday.debug/code_cache/secondary-dexes/com.playdayteam.playday.debug-1.apk.classes2.    zip': unzip in 28ms, rewrite 387ms
I/MultiDex﹕ install done
I/MultiDex﹕ install
D/AndroidRuntime﹕ Shutting down VM
W/dalvikvm﹕ threadid=1: thread     exiting with uncaught exception (group=0x41c1d930)
E/AndroidRuntime﹕ FATAL EXCEPTION:     main
    java.lang.NoClassDefFoundError: com.playday.app.core.AppWrapper
            at com.playday.app.core.App.onCreate(App.java:22)
            at android.app.Instrumentation.callApplicationOnCreate(Instrumentation.java:1006)
            at android.app.ActivityThread.handleBindApplication(ActivityThread.java:4457)
            at android.app.ActivityThread.access$1300(ActivityThread.java:142)
            at android.app.ActivityThread$H.handleMessage(ActivityThread.java:1332)
            at android.os.Handler.dispatchMessage(Handler.java:99)
            at android.os.Looper.loop(Looper.java:137)
            at android.app.ActivityThread.main(ActivityThread.java:5105)
            at java.lang.reflect.Method.invokeNative(Native Method)
            at java.lang.reflect.Method.invoke(Method.java:511)
            at com.android.internal.os.ZygoteInit$MethodAndArgsCaller.run(ZygoteInit.java:793)
            at com.android.internal.os.ZygoteInit.main(ZygoteInit.java:560)
            at dalvik.system.NativeStart.main(Native Method)    

I have the same Android Studio, gradle, sdk, jdk versions, same code. I've even tried to format hard drive and reinstall OS to make sure that environment is the same. What can be the cause of this strange problem?

This is my build.gradle:

apply plugin: 'com.android.application'

repositories {
    maven { url 'http://dl.bintray.com/populov/maven' }
    mavenCentral()
    maven { url 'https://oss.sonatype.org/content/repositories/snapshots/' }
}

android {
    compileSdkVersion project.api_level
    buildToolsVersion project.build_tools_version

    defaultConfig {
        minSdkVersion 14
        targetSdkVersion project.api_level
    }

    sourceSets {
        instrumentTest.setRoot('src/test')
    }

    packagingOptions {
        exclude 'META-INF/LICENSE.txt'
        exclude 'META-INF/LICENSE'
        exclude 'META-INF/NOTICE.txt'
        exclude 'META-INF/NOTICE'
        exclude 'META-INF/ASL2.0'
        exclude 'AndroidManifest.xml'
    }

    defaultConfig {
        versionName "0.3.2"
        versionCode 23
    }

    buildTypes {

        debug {
            debuggable true
            applicationIdSuffix ".debug"
        }

        beta {
            debuggable true
            signingConfig signingConfigs.release
            applicationIdSuffix ".beta"
        }

        release {
            signingConfig signingConfigs.release
            runProguard false
            proguardFile file('proguard-rules.txt')
            proguardFile getDefaultProguardFile('proguard-android-optimize.txt')
        }
    }

    dexOptions {
        incremental false
        preDexLibraries false
    }
}

dependencies {
    compile "com.android.support:support-v13:$project.support_lib_version"
    compile "com.android.support:support-v4:$project.support_lib_version"
    compile "com.android.support:appcompat-v7:$project.support_lib_version"
    compile 'com.google.android.gms:play-services:6.1.11'
    compile('de.keyboardsurfer.android.widget:crouton:1.8.5@aar') {
        exclude group: 'com.google.android', module: 'support-v4'
    }
    compile('com.octo.android.robospice:robospice:1.4.14'){
        exclude group: 'commons-io', module: 'commons-io'
    }
    compile('com.octo.android.robospice:robospice-retrofit:1.4.14'){
        exclude group: 'commons-io', module: 'commons-io'
    }
    compile 'com.squareup.retrofit:retrofit:1.6.1'
    compile 'com.google.code.gson:gson:2.3'
    compile 'com.viewpagerindicator:library:2.4.1@aar'
    compile 'com.squareup.picasso:picasso:2.3.3'
    compile 'com.squareup.okhttp:okhttp:2.0.0'
    compile 'com.squareup.okhttp:okhttp-urlconnection:2.0.0'

    compile 'com.etsy.android.grid:library:1.0.5'
    compile 'com.squareup:otto:1.3.4'
    compile 'com.darwinsys:hirondelle-date4j:1.5.1'
    compile 'com.github.chrisbanes.photoview:library:1.2.3'
    compile 'me.grantland:autofittextview:0.2.0'
    compile 'it.sephiroth.android.library.horizontallistview:library:1.2.1'
    compile 'org.ocpsoft.prettytime:prettytime:3.2.4.Final'
    compile 'com.google.guava:guava:18.0'
    compile 'com.github.castorflex.smoothprogressbar:library:0.5.2'
    compile 'com.makeramen:roundedimageview:1.3.0'
    compile 'org.lucasr.twowayview:twowayview:0.1.1'
    compile 'com.michaelpardo:activeandroid:3.1.0-SNAPSHOT'

    compile project(':libs:LoopingViewPager')
    compile project(':libs:PhotoView-2.2.1')
    compile files('libs/localytics.jar')
    compile files('libs/android-support-multidex.jar')

    compile 'net.hockeyapp.android:HockeySDK:3.0.2'
}

afterEvaluate {
    tasks.matching {
        it.name.startsWith('dex')
    }.each { dx ->
        if (dx.additionalParameters == null) {
            dx.additionalParameters = []
        }
        dx.additionalParameters += '--multi-dex' // enable multidex
        dx.additionalParameters += "--main-dex-list=$projectDir/multidex.keep".toString()
    }
}

Update. My multidex.keep file:

android/support/multidex/BuildConfig.class
android/support/multidex/MultiDex$V14.class
android/support/multidex/MultiDex$V19.class
android/support/multidex/MultiDex$V4.class
android/support/multidex/MultiDex.class
android/support/multidex/MultiDexApplication.class
android/support/multidex/MultiDexExtractor$1.class
android/support/multidex/MultiDexExtractor.class
android/support/multidex/ZipUtil$CentralDirectory.class
android/support/multidex/ZipUtil.class
com/playday/app/models/notification/Badge.class
com/playday/app/models/User.class
com/playday/app/core/AppWrapper.class
com/playday/app/core/App.class

Answer 1

Your AppWrapper class fails to load because the retrofit.ErrorHandler interface is not included in main dex file.

How do you calculate which classes to put in your main-dex-list file?
There's a script that can generate it for you. I wrote a blogpost that shows how to use it.

Update (10/31/2014):
Gradle plugin v0.14.0 now does it automatically. See my answer here.

Update (24/04/2017):
The developer guide explains how to pick specific classes with a gradle option if it doesn't pick all the right ones automatically.