Kotlin,Java,multidex,Dagger 2,Butterknife and Realm: transformClassesWithJarMergingForDebug: duplicate entry: org/jetbrains/annotations/NotNull.class

Question

We have existing Java Android code. We want to painlessly slowly start moving to Kotlin. We use Dagger 2, Butterknife and Realm. We use Java 8 compiler (but our targetCompatibility and sourceCompatibility are 1.7).

I've been roaming the web for hours, seen SO, GitHub conversations and so on, and managed to solve all problems except one:

The build is successful, but when trying to debug, we get:

Error:Execution failed for task ':app:transformClassesWithJarMergingForDebug'.
> com.android.build.api.transform.TransformException: java.util.zip.ZipException: duplicate entry: org/jetbrains/annotations/NotNull.class

Is there a way to resolve duplicate entries in Gradle (maybe using packagingOptions or resolutionStrategy? as it's a duplication that comes from the plugins...?) ?

Again - build project goes without any error, only transformClassesWithJarMergingForDebug fails!

Here's the app's gradle:

apply plugin: 'com.android.application'
apply plugin: 'kotlin-android'
//apply plugin: 'com.neenbedankt.android-apt'
apply plugin: 'realm-android'

kapt { generateStubs = true }

android {
    signingConfigs {
        config {
            keyAlias 'MyAndroidKey'
            keyPassword 'password'
            storeFile file('android.jks')
            storePassword 'password'
        }
    }
    compileSdkVersion 23
    buildToolsVersion '23.0.3'
    defaultConfig {
        vectorDrawables.useSupportLibrary = true
        applicationId "com.acme.app"
        minSdkVersion 15
        targetSdkVersion 23
        versionCode 1
        versionName "1.0"
        //testInstrumentationRunner "android.support.test.runner.AndroidJUnitRunner"
        testInstrumentationRunner "com.acme.app.utils.CustomAndroidJUnitRunner"

        // http://stackoverflow.com/a/26515860/587467:
        multiDexEnabled true
    }
    //dexOptions { incremental false }
    buildTypes {
        release {
            minifyEnabled true
            proguardFiles getDefaultProguardFile('proguard-android.txt'), 'proguard-rules.pro'
            signingConfig signingConfigs.config
        }
    }
    packagingOptions {
        exclude 'META-INF/services/javax.annotation.processing.Processor'
        exclude 'META-INF/DEPENDENCIES.txt'
        exclude 'META-INF/DEPENDENCIES'
        exclude 'META-INF/dependencies.txt'
        exclude 'META-INF/LICENSE.txt'
        exclude 'META-INF/LICENSE'
        exclude 'META-INF/license.txt'
        exclude 'META-INF/LGPL2.1'
        exclude 'META-INF/NOTICE.txt'
        exclude 'META-INF/NOTICE'
        exclude 'META-INF/notice.txt'
    }

    configurations.all {
        resolutionStrategy.force 'com.android.support:support-annotations:23.3.0', 'junit:junit:4.12'
    }

    targetCompatibility = 1.7
    sourceCompatibility = 1.7
    compileOptions {
        sourceCompatibility JavaVersion.VERSION_1_7
        targetCompatibility JavaVersion.VERSION_1_7
    }
    sourceSets { main.java.srcDirs += 'src/main/kotlin' }
}

dependencies {
    // http://stackoverflow.com/a/26515860/587467:
    compile 'com.android.support:multidex:1.0.1'

    compile fileTree(include: ['*.jar'], dir: 'libs')

    /// <Firebase> Cloud Messaging (FCM) - the Google Cloud Messaging (GCM) new version:
    compile 'com.google.firebase:firebase-messaging:9.0.2'
    /// </Firebase>

    /// <Dagger>
    //provided 'javax.annotation:jsr250-api:1.0'
    //apt 'com.google.dagger:dagger-compiler:2.5'
    //compile 'com.google.dagger:dagger:2.5'
    //compile 'com.google.dagger:dagger-compiler:2.4'
    /// </Dagger>

    /// <KotlinDagger>
    compile 'com.google.dagger:dagger:2.5'
    kapt 'com.google.dagger:dagger-compiler:2.5'
    kaptTest 'com.google.dagger:dagger-compiler:2.5'
    kaptAndroidTest 'com.google.dagger:dagger-compiler:2.5'
    //provided 'org.glassfish:javax.annotation:10.0-b28'
    /// </KotlinDagger>

    /// <JSON>
    //testCompile 'javax.json:javax.json-api:1.0'
    testCompile 'org.glassfish:javax.json:1.0.4'
    // https://github.com/FasterXML/jackson-docs/wiki/Using-Jackson2-with-Maven
    // http://www.mkyong.com/java/jackson-2-convert-java-object-to-from-json/
    //testCompile 'com.fasterxml.jackson.core:jackson-core:2.6.3'
    testCompile 'com.fasterxml.jackson.core:jackson-databind:2.7.4'
    /// </JSON>

    //apt 'com.jakewharton:butterknife-compiler:8.0.1'
    kapt 'com.jakewharton:butterknife-compiler:8.0.1'

    testCompile 'junit:junit:4.12'
    testCompile 'org.mockito:mockito-core:1.10.19'
    testCompile 'net.java.dev.jna:jna-platform:4.2.2'

    // <InstrumentedTests>
    // <MutualExclusive>
    // <Or>
          //androidTestCompile 'com.android.support.test:testing-support-lib:0.1'
    // </Or>
    // <Or>
    //    androidTestCompile 'com.android.support:support-annotations:23.0.0'
        androidTestCompile 'com.android.support.test:runner:0.4'
        //androidTestCompile 'com.android.support.test:rules:0.4'
        // <Espresso>
        androidTestCompile 'com.android.support.test.espresso:espresso-core:2.2.2'
        // </Espresso>
        //androidTestCompile "org.robolectric:robolectric:3.0"
    // </Or>
    // </MutualExclusive>
    // </InstrumentedTests>

    compile 'com.android.support:appcompat-v7:23.4.0'
    compile 'com.android.support:support-v13:23.4.0'
    compile 'com.android.support:design:23.4.0'
    compile 'com.jakewharton:butterknife:8.0.1'
    compile 'com.google.code.ksoap2-android:ksoap2-android:3.6.1'
    compile 'org.springframework.android:spring-android-rest-template:2.0.0.M3'

    compile 'com.squareup.retrofit2:retrofit:2.1.0'
    compile 'com.squareup.retrofit2:converter-gson:2.1.0'
    compile 'com.squareup.retrofit2:adapter-rxjava:2.1.0'

    compile 'com.android.support:support-v4:23.3.0'
    compile 'com.android.support:recyclerview-v7:23.3.0'
    compile 'com.android.support:cardview-v7:23.3.0'
    compile 'io.reactivex:rxandroid:1.2.1'
    compile 'joda-time:joda-time:2.9.4'
    //compile 'io.reactivex:rxjava:1.1.6'
    compile 'io.reactivex:rxjava-async-util:0.21.0'
    //<Floating Buttons>
    compile 'com.github.clans:fab:1.6.4'
    //</Floating Buttons>

    compile 'com.facebook.fresco:fresco:0.11.0'
    compile 'org.jetbrains:annotations-java5:15.0'
    compile 'com.fasterxml.jackson.core:jackson-databind:2.7.4'
    compile 'com.google.code.gson:gson:2.4'
    compile 'javax.annotation:javax.annotation-api:1.2'
    compile "org.jetbrains.kotlin:kotlin-stdlib:1.0.3"
}

// https://firebase.google.com/docs/android/setup#add_the_sdk
// Firebase Cloud Messaging (FCM) - the Google Cloud Messaging (GCM) new version:
apply plugin: 'com.google.gms.google-services'
repositories {
    mavenCentral()
}

Answer 1

Try to delete: compile 'org.jetbrains:annotations-java5:15.0'. If it won't work, follow these steps:

Go to your app/build.gradle file and add:

configurations {
    cleanedAnnotations

    compile.exclude group: 'org.jetbrains' , module:'annotations'
}

Change

compile 'org.jetbrains:annotations-java5:15.0'

with

 compile files("${buildDir}/libs/annotations-cleaned.jar") { builtBy 'cleanAnnotationsJar' }
    cleanedAnnotations 'org.jetbrains:nnotations-java5:15.0'

Finally add:

task cleanAnnotationsJar(type:Jar) {
    configurations.cleanedAnnotations.each { f ->
        from zipTree(f)
    }
    archiveName = "annotations-cleaned.jar"
    exclude 'org/jetbrains/annotations/NotNull.class'
    exclude 'org/jetbrains/annotations/Nullable.class'
}

Check: https://discuss.kotlinlang.org/t/duplicate-classes-in-kotlin-runtime-and-com-intellij-annotations/154/3