IssueTracker

Android Studio is actually 0.8.11

The stack trace seems to say you are running with several definitions of one annotation. This seems to often be caused by including 2 different versions of the same library in an instrumentation apk and its tested application apk. Could you please check it's not your case here? If it's your case, you should fix that.

Looking at dx about this report, it seems that DX may fail to check a duplicate class definition when running multidex, I've recorded a bug about this point.

That said, it does not look like we could be in the DX lack of check case here, because mainDexClasses is keeping all the annotations in the main dex (and dx seems to correctly identify the duplicate definition when the 2 definitions are added to the same dex). (Can you confirm that you're using mainDexClasses to create your main dex list?)

I'm assigning back to you xav in case you want to add some check in the SDK.

The error is not reproducible in other machines, so it's probably a local config problem. We'll try the mainDexClasses approach.

[Comment deleted]

We're still looking into it. We're *not* using mainDexClasses because it wasn't documented or included on the SDK, and the only blog file that references it (written on Monday) mentions libraries to be preDexed, which isn't available while --multi-dex, and removing --multi-dex doesn't allow our app to build due to the 64k method limit.

The error is localized to my computer and only in 4/10 builds, so whenever I want something and it doesn't work I have to edit a file, rebuild and hope for the best.

We've run into the same issue as well. Right before the AndroidRuntime error, you should see dalvikvm error saying which class resolved by unexpected DEX (the orm-lite class). I suspect that has a nested static enum or classes? If you add that class in your multidex.keep file, does it fix your problem? Could you paste the dalvikvm log line you are seeing?

10-29 18:26:26.140  31690-31690/com.myapp.app W/dalvikvm﹕ Class resolved by unexpected DEX: Lcom/myapp/model/MyClass;(0x427a7898):0x596d1000 ref [Lcom/j256/ormlite/field/DataType;] Lcom/j256/ormlite/field/DataType;(0x427a7898):0x5910f000
10-29 18:26:26.140  31690-31690/com.myapp.app W/dalvikvm﹕ (Lcom/myapp/model/MyClass; had used a different Lcom/j256/ormlite/field/DataType; during pre-verification)
10-29 18:26:26.140  31690-31690/com.myapp.app W/dalvikvm﹕ Failed processing annotation value
10-29 18:26:26.140  31690-31690/com.myapp.app W/dalvikvm﹕ threadid=1: thread exiting with uncaught exception (group=0x41d28700)

I'll try and add that class to the multidex.keep

[Comment deleted]

After several attempts with mainDexClasses this is as far as I got

sudo ./mainDexClasses --output multidex.keep /Users/myuser/my_workspace/myapp/app/build/intermediates/dex/dev/debug;/Users/myuser/my_workspace/myapp/app/libs/android-support-multidex.jar;/Users/myuser/.gradle/caches/modules-2/files-2.1/com.j256.ormlite/ormlite-core/4.48/e579bd2905d0399af5029aaaf9817d5fa0ca88a5/ormlite-core-4.48.jar;/Users/myuser/.gradle/caches/modules-2/files-2.1/com.fasterxml.jackson.core/jackson-core/2.2.4/95705b2e89a4101f2a82af6b303945755d7f93ab/jackson-core-2.2.4.jar;/Users/myuser/.gradle/caches/modules-2/files-2.1/com.fasterxml.jackson.core/jackson-annotations/2.2.4/9de62c96bb3e17eb909c107f2759c73650b5a8f1/jackson-annotations-2.2.4.jar;/Users/myuser/.gradle/caches/modules-2/files-2.1/com.fasterxml.jackson.core/jackson-databind/2.2.4/906cf5deb56ec1fb3ecbeceb08a1734ce9fed664/jackson-databind-2.2.4.jar
Password:
Error: The input doesn't contain any classes. Did you specify the proper '-injars' options?
-bash: /Users/myuser/my_workspace/myapp/app/libs/android-support-multidex.jar: cannot execute binary file
/Users/myuser/.gradle/caches/modules-2/files-2.1/com.j256.ormlite/ormlite-core/4.48/e579bd2905d0399af5029aaaf9817d5fa0ca88a5/ormlite-core-4.48.jar: line 1: PK: command not found
/Users/myuser/.gradle/caches/modules-2/files-2.1/com.j256.ormlite/ormlite-core/4.48/e579bd2905d0399af5029aaaf9817d5fa0ca88a5/ormlite-core-4.48.jar: line 2: xj?C: command not found
K-*??ϳR0?3??r,J??,K-?V?+????RKRSt?*?ules-2/files-2.1/com.j256.ormlite/ormlite-core/4.48/e579bd2905d0399af5029aaaf9817d5fa0ca88a5/ormlite-core-4.48.jar: line 3:wj?C?I5?x?META-INF/MANIFEST.MF?M??LK-.?
                                    ?3R: No such file or directory
/Users/myuser/.gradle/caches/modules-2/files-2.1/com.j256.ormlite/ormlite-core/4.48/e579bd2905d0399af5029aaaf9817d5fa0ca88a5/ormlite-core-4.48.jar: line 3: ?R?x??J3sJ???E???%??P?]??l?fz?f?@{: command not found
/Users/myuser/.gradle/caches/modules-2/files-2.1/com.j256.ormlite/ormlite-core/4.48/e579bd2905d0399af5029aaaf9817d5fa0ca88a5/ormlite-core-4.48.jar: line 5: r2?K?V: command not found
/Users/myuser/.gradle/caches/modules-2/files-2.1/com.j256.ormlite/ormlite-core/4.48/e579bd2905d0399af5029aaaf9817d5fa0ca88a5/ormlite-core-4.48.jar: line 6: sj?Ccom/PK: No such file or directory
/Users/myuser/.gradle/caches/modules-2/files-2.1/com.j256.ormlite/ormlite-core/4.48/e579bd2905d0399af5029aaaf9817d5fa0ca88a5/ormlite-core-4.48.jar: line 7: sj?C: command not found
/Users/myuser/.gradle/caches/modules-2/files-2.1/com.j256.ormlite/ormlite-core/4.48/e579bd2905d0399af5029aaaf9817d5fa0ca88a5/ormlite-core-4.48.jar: line 8: tj?Ccom/j256/ormlite/PK: No such file or directory
/Users/myuser/.gradle/caches/modules-2/files-2.1/com.j256.ormlite/ormlite-core/4.48/e579bd2905d0399af5029aaaf9817d5fa0ca88a5/ormlite-core-4.48.jar: line 9: sj?Ccom/j256/ormlite/core/PK: No such file or directory
/Users/myuser/.gradle/caches/modules-2/files-2.1/com.j256.ormlite/ormlite-core/4.48/e579bd2905d0399af5029aaaf9817d5fa0ca88a5/ormlite-core-4.48.jar: line 10: tj?Ccom/j256/ormlite/dao/PK: No such file or directory
/Users/myuser/.gradle/caches/modules-2/files-2.1/com.j256.ormlite/ormlite-core/4.48/e579bd2905d0399af5029aaaf9817d5fa0ca88a5/ormlite-core-4.48.jar: line 11: tj?Ccom/j256/ormlite/db/PK: No such file or directory
/Users/myuser/.gradle/caches/modules-2/files-2.1/com.j256.ormlite/ormlite-core/4.48/e579bd2905d0399af5029aaaf9817d5fa0ca88a5/ormlite-core-4.48.jar: line 12: tj?Ccom/j256/ormlite/field/PK: No such file or directory
/Users/myuser/.gradle/caches/modules-2/files-2.1/com.j256.ormlite/ormlite-core/4.48/e579bd2905d0399af5029aaaf9817d5fa0ca88a5/ormlite-core-4.48.jar: line 13: tj?Ccom/j256/ormlite/field/types/PK: No such file or directory
/Users/myuser/.gradle/caches/modules-2/files-2.1/com.j256.ormlite/ormlite-core/4.48/e579bd2905d0399af5029aaaf9817d5fa0ca88a5/ormlite-core-4.48.jar: line 14: tj?Ccom/j256/ormlite/logger/PK: No such file or directory
/Users/myuser/.gradle/caches/modules-2/files-2.1/com.j256.ormlite/ormlite-core/4.48/e579bd2905d0399af5029aaaf9817d5fa0ca88a5/ormlite-core-4.48.jar: line 15: tj?Ccom/j256/ormlite/misc/PK: No such file or directory
/Users/myuser/.gradle/caches/modules-2/files-2.1/com.j256.ormlite/ormlite-core/4.48/e579bd2905d0399af5029aaaf9817d5fa0ca88a5/ormlite-core-4.48.jar: line 16: tj?Ccom/j256/ormlite/stmt/PK: No such file or directory
/Users/myuser/.gradle/caches/modules-2/files-2.1/com.j256.ormlite/ormlite-core/4.48/e579bd2905d0399af5029aaaf9817d5fa0ca88a5/ormlite-core-4.48.jar: line 17: tj?Ccom/j256/ormlite/stmt/mapped/PK: No such file or directory
/Users/myuser/.gradle/caches/modules-2/files-2.1/com.j256.ormlite/ormlite-core/4.48/e579bd2905d0399af5029aaaf9817d5fa0ca88a5/ormlite-core-4.48.jar: line 18: tj?Ccom/j256/ormlite/stmt/query/PK: No such file or directory
/Users/myuser/.gradle/caches/modules-2/files-2.1/com.j256.ormlite/ormlite-core/4.48/e579bd2905d0399af5029aaaf9817d5fa0ca88a5/ormlite-core-4.48.jar: line 19: tj?Ccom/j256/ormlite/support/PK: No such file or directory
/Users/myuser/.gradle/caches/modules-2/files-2.1/com.j256.ormlite/ormlite-core/4.48/e579bd2905d0399af5029aaaf9817d5fa0ca88a5/ormlite-core-4.48.jar: line 20: tj?Ccom/j256/ormlite/table/PK: No such file or directory
/Users/myuser/.gradle/caches/modules-2/files-2.1/com.j256.ormlite/ormlite-core/4.48/e579bd2905d0399af5029aaaf9817d5fa0ca88a5/ormlite-core-4.48.jar: line 21:sj?C?0??L!com/j256/ormlite/core/LICENSE.txtURMs?: No such file or directory
/Users/myuser/.gradle/caches/modules-2/files-2.1/com.j256.ormlite/ormlite-core/4.48/e579bd2905d0399af5029aaaf9817d5fa0ca88a5/ormlite-core-4.48.jar: line 24: syntax error near unexpected token `)'
/Users/myuser/.gradle/caches/modules-2/files-2.1/com.j256.ormlite/ormlite-core/4.48/e579bd2905d0399af5029aaaf9817d5fa0ca88a5/ormlite-core-4.48.jar: line 24: `"?@?h/Ѯ??)???????j?
p??ah5EbH???Ь.a_S???c"'                                                                                                                                                              {`M??d??c????N?[n????
-bash: /Users/myuser/.gradle/caches/modules-2/files-2.1/com.fasterxml.jackson.core/jackson-core/2.2.4/95705b2e89a4101f2a82af6b303945755d7f93ab/jackson-core-2.2.4.jar: cannot execute binary file
-bash: /Users/myuser/.gradle/caches/modules-2/files-2.1/com.fasterxml.jackson.core/jackson-annotations/2.2.4/9de62c96bb3e17eb909c107f2759c73650b5a8f1/jackson-annotations-2.2.4.jar: cannot execute binary file
-bash: /Users/myuser/.gradle/caches/modules-2/files-2.1/com.fasterxml.jackson.core/jackson-databind/2.2.4/906cf5deb56ec1fb3ecbeceb08a1734ce9fed664/jackson-databind-2.2.4.jar: cannot execute binary file


The output file is empty.

[Comment deleted]

Changed /Users/myuser/my_workspace/myapp/app/build/intermediates/dex/dev/debug to /Users/myuser/my_workspace/myapp/app/build/intermediates/classes/dev/debug and the multidex.keep at least got my project's classes

Seems to be working so far.

Same error with the new multiDex system (multiDexEnabled true)
I added the multidex instrumentation but it conflicts with the multidex lib added automatically by multiDexEnabled.
And the classes with annotation doesn't works.

Same issue as well after updating to the new multiDex system, Nitro have you had any luck yet?

No, I reverted to the old multidex system for now (I'm working on a project with a dead-line).
What I could find :
Using Build-Tools 21.1.0, gradle plugin 0.14.1 and AS 0.9.1

Having multiDexEnabled true :
in dependencies, you need to remove
compile 'com.android.support:multidex:1.0.0'
because it's already included by multiDexEnabled

same for
androidTestCompile('com.android.support:multidex-instrumentation:1.0.0') that include com.android.support:multidex:1.0.0
so need to do :
androidTestCompile('com.android.support:multidex-instrumentation:1.0.0') {
        exclude module: 'multidex'
    }

Then sometimes it couldn't find the instrumentation MultiDexTestRunner so I created a class implementing it for my tests and added it with :
testInstrumentationRunner "com.package.DexInstrumentationTestRunner"


So... it should works but on my project we use jackson annotations and it results with the error :
java.lang.IllegalAccessError: Class ref in pre-verified class resolved to unexpected implementation
    at java.lang.reflect.Field.getAnnotation(Native Method)

and the same :

10-29 18:26:26.140  31690-31690/com.myapp.app W/dalvikvm﹕ Class resolved by unexpected DEX: JsonInclude$Include...
10-29 18:26:26.140  31690-31690/com.myapp.app W/dalvikvm﹕ xxx had used a different xxx; during pre-verification)
10-29 18:26:26.140  31690-31690/com.myapp.app W/dalvikvm﹕ Failed processing annotation value

target version 21, same for subprojects...
Here's my dependencies :

androidTestCompile - Classpath for compiling the androidTest sources.
\--- com.squareup.okhttp:mockwebserver:2.0.0
     \--- org.bouncycastle:bcprov-jdk15on:1.50

compile - Classpath for compiling the main sources.
+--- project :libraries:extendedCalendarView
|    \--- com.android.support:multidex:1.0.0
+--- project :libraries:facebook
|    +--- com.android.support:multidex:1.0.0
|    +--- com.android.support:support-v4:20.0.0 -> 21.0.0
|    |    \--- com.android.support:support-annotations:21.0.0
|    \--- com.parse.bolts:bolts-android:1.1.3
+--- project :libraries:viewpagerindicator
|    +--- com.android.support:multidex:1.0.0
|    \--- com.android.support:support-v4:20.0.0 -> 21.0.0 (*)
+--- com.android.support:support-v4:21.0.0 (*)
+--- com.google.android.gms:play-services:4.+ -> 4.4.52
|    \--- com.android.support:support-v4:19.0.1 -> 21.0.0 (*)
+--- com.google.http-client:google-http-client-android:1.12.0-beta
+--- com.google.guava:guava-jdk5:17.0
+--- com.google.protobuf:protobuf-java:2.5.0
+--- com.google.api-client:google-api-client:1.19.0
|    +--- com.google.oauth-client:google-oauth-client:1.19.0
|    |    +--- com.google.http-client:google-http-client:1.19.0
|    |    |    \--- com.google.code.findbugs:jsr305:1.3.9
|    |    \--- com.google.code.findbugs:jsr305:1.3.9
|    +--- com.google.http-client:google-http-client-jackson2:1.19.0
|    |    +--- com.google.http-client:google-http-client:1.19.0 (*)
|    |    \--- com.fasterxml.jackson.core:jackson-core:2.1.3 -> 2.4.3
|    \--- com.google.guava:guava-jdk5:13.0 -> 17.0
+--- com.squareup.retrofit:retrofit:1.6.1
|    \--- com.google.code.gson:gson:2.2.4
+--- de.greenrobot:eventbus:2.2.1
+--- com.fasterxml.jackson.core:jackson-annotations:2.4.3
+--- com.fasterxml.jackson.core:jackson-databind:2.4.3
|    \--- com.fasterxml.jackson.core:jackson-core:2.4.3
+--- com.fasterxml.jackson.core:jackson-core:2.4.3
+--- com.path:android-priority-jobqueue:1.1.2
|    \--- com.google.android:android:2.2.1
|         +--- commons-logging:commons-logging:1.1.1
|         +--- org.apache.httpcomponents:httpclient:4.0.1
|         |    +--- org.apache.httpcomponents:httpcore:4.0.1
|         |    +--- commons-logging:commons-logging:1.1.1
|         |    \--- commons-codec:commons-codec:1.3 -> 1.9
|         +--- org.khronos:opengl-api:gl1.1-android-2.1_r1
|         +--- xerces:xmlParserAPIs:2.6.2
|         +--- xpp3:xpp3:1.1.4c
|         \--- org.json:json:20080701
+--- com.squareup.okhttp:okhttp:2.0.0
|    \--- com.squareup.okio:okio:1.0.0 -> 1.0.1
+--- com.squareup.okhttp:okhttp-urlconnection:2.0.0
|    \--- com.squareup.okhttp:okhttp:2.0.0 (*)
+--- com.squareup.okio:okio:1.0.1
+--- org.chalup.microorm:microorm:0.4.1
|    \--- com.google.guava:guava:16.0
+--- commons-codec:commons-codec:1.9
+--- com.squareup.picasso:picasso:2.3.4
+--- com.jakewharton:butterknife:5.1.2
+--- info.hoang8f:android-segmented:1.0.2
+--- com.github.chrisbanes.photoview:library:1.2.3
+--- com.google.maps.android:android-maps-utils:0.3.1
|    \--- com.google.android.gms:play-services:4.3+ -> 4.4.52 (*)
+--- com.jayway.android.robotium:robotium-solo:5.2.1
\--- org.fusesource.mqtt-client:mqtt-client:1.10
     +--- org.fusesource.hawtdispatch:hawtdispatch-transport:1.20
     |    \--- org.fusesource.hawtdispatch:hawtdispatch:1.20
     \--- org.fusesource.hawtbuf:hawtbuf:1.10

As you can see there are only one jackson include ! I tried everything and was pretty pissed... But I'm not mad against anyone, and the multiDexEnabled is pretty awesome (though the new guide that came out is already outdated http://developer.android.com/tools/building/multidex.html#testing ). I hope it will be fixed as soon as possible !

From the documentation:

There are complex requirements regarding what classes are needed in the primary dex file when executing in the Dalvik runtime. The Android build tooling updates handle the Android requirements, but it is possible that other included libraries have additional dependency requirements including the use of introspection or invocation of Java methods from native code. Some libraries may not be able to be used until the multidex build tools are updated to allow you to specify classes that must be included in the primary dex file.


So as of today multidex builds are not deterministic.

Yeah, I read that part. But as I said, the doc seems to have been made before the new multiDexEnabled = true system.
Why ? because in the build folder, there is a folder multidex containing a file with all the class that should be on the first dex (mainDexClasses).
And there was the JsonInclude.Class that made all my run failed, so it seems it should work !
I don't know where the problem is but my doubt are about the dx command.

[Comment deleted]

The file is called maindexlist.txt and here's the result (without my app's packages) :
com/fasterxml/jackson/annotation/JsonTypeId.class
android/support/annotation/RawRes.class
com/dsi/ant/AntInterface.class
com/google/android/gms/common/GooglePlayServicesClient$ConnectionCallbacks.class
com/facebook/model/GraphObjectList.class
android/support/annotation/LayoutRes.class
com/fasterxml/jackson/annotation/JsonGetter.class
com/fasterxml/jackson/annotation/JsonAutoDetect$1.class
android/support/annotation/XmlRes.class
com/fasterxml/jackson/annotation/JsonValue.class
com/facebook/AuthorizationClient$BackgroundProcessingListener.class
javax/annotation/meta/When.class
javax/annotation/Nullable.class
android/support/annotation/ColorRes.class
com/fasterxml/jackson/annotation/JsonUnwrapped.class
javax/annotation/Untainted.class
android/support/v4/app/FragmentManagerImpl$3.class
retrofit/http/GET.class
com/path/android/jobqueue/BaseJob.class
com/google/common/annotations/GwtCompatible.class
com/fasterxml/jackson/annotation/JsonManagedReference.class
com/fasterxml/jackson/annotation/JsonAutoDetect$Visibility.class
com/fasterxml/jackson/databind/annotation/JacksonStdImpl.class
com/fasterxml/jackson/annotation/JsonCreator.class
butterknife/OnItemClick.class
javax/annotation/meta/TypeQualifierValidator.class
android/support/v4/app/FragmentContainer.class
android/support/multidex/MultiDex$V19.class
com/facebook/model/GraphMultiResult.class
com/google/ads/mediation/MediationServerParameters$MappingException.class
com/path/android/jobqueue/Job.class
com/facebook/SessionState.class
com/path/android/jobqueue/config/Configuration.class
com/fasterxml/jackson/databind/util/Converter$None.class
retrofit/http/EncodedQueryMap.class
com/fasterxml/jackson/annotation/SimpleObjectIdResolver.class
android/support/v4/util/DebugUtils.class
com/facebook/AuthorizationClient$Result.class
com/fasterxml/jackson/annotation/JsonAnyGetter.class
retrofit/http/Field.class
retrofit/http/Multipart.class
android/support/v4/app/LoaderManager.class
android/support/multidex/MultiDex.class
javax/annotation/WillNotClose.class
com/facebook/Settings.class
com/facebook/Request.class
com/google/api/client/util/Key.class
com/fasterxml/jackson/annotation/JsonAnySetter.class
com/facebook/widget/LoginButton.class
android/support/annotation/AttrRes.class
android/support/annotation/StyleRes.class
javax/annotation/Nonnull$Checker.class
android/support/v4/app/NotificationCompat.class
javax/annotation/meta/TypeQualifierNickname.class
android/support/v4/app/NoSaveStateFrameLayout.class
com/fasterxml/jackson/annotation/JsonFilter.class
com/facebook/Session$4.class
android/support/annotation/PluralsRes.class
android/support/v4/app/FragmentManager$BackStackEntry.class
com/fasterxml/jackson/annotation/JsonRootName.class
android/support/v4/widget/MaterialProgressDrawable$3.class
com/fasterxml/jackson/databind/annotation/JsonPOJOBuilder$Value.class
android/support/v4/widget/MaterialProgressDrawable$StartCurveInterpolator.class
butterknife/OnEditorAction.class
android/support/annotation/NonNull.class
butterknife/Optional.class
android/support/v4/widget/DrawerLayoutImpl.class
retrofit/http/PATCH.class
com/facebook/Session$StatusCallback.class
com/fasterxml/jackson/databind/jsonFormatVisitors/JsonFormatVisitorWithSerializerProvider.class
com/fasterxml/jackson/annotation/JsonSubTypes.class
com/google/gson/annotations/Since.class
org/sidibe/mqtt/android/lib/MqttPushEventListener.class
butterknife/OnTextChanged.class
com/google/common/annotations/GwtIncompatible.class
com/google/protobuf/AbstractMessageLite.class
butterknife/OnCheckedChanged.class
com/path/android/jobqueue/JobManager.class
android/support/v4/app/Fragment.class
butterknife/internal/ListenerClass.class
com/google/android/gms/location/DetectedActivity.class
android/support/v4/widget/MaterialProgressDrawable$4.class
com/facebook/SessionDefaultAudience.class
android/support/v4/app/ActivityCompat.class
android/support/v4/view/ViewPager$OnPageChangeListener.class
retrofit/http/RestMethod.class
fr/openium/androkit/ConfigApp.class
android/support/v4/widget/MaterialProgressDrawable$EndCurveInterpolator.class
retrofit/http/Streaming.class
com/google/common/annotations/VisibleForTesting.class
com/fasterxml/jackson/annotation/ObjectIdGenerator.class
com/google/api/client/util/NullValue.class
com/google/api/client/util/Beta.class
retrofit/http/POST.class
retrofit/http/PUT.class
javax/annotation/Signed.class
butterknife/OnItemSelected$Callback.class
com/google/gson/annotations/Expose.class
com/path/android/jobqueue/log/CustomLogger.class
javax/annotation/ParametersAreNonnullByDefault.class
android/support/v4/app/FragmentActivity.class
android/support/v4/widget/MaterialProgressDrawable$1.class
com/fasterxml/jackson/databind/annotation/JsonPOJOBuilder.class
com/google/api/client/json/JsonPolymorphicTypeMap$TypeDef.class
android/support/annotation/StringDef.class
com/google/gson/annotations/Until.class
com/fasterxml/jackson/annotation/JsonInclude.class
com/fasterxml/jackson/databind/KeyDeserializer.class
com/facebook/AccessTokenSource.class
android/support/v4/app/ListFragment.class
com/facebook/AppEventsLogger.class
android/support/v4/app/FragmentActivity$NonConfigurationInstances.class
com/fasterxml/jackson/databind/JsonMappingException.class
com/fasterxml/jackson/databind/JsonSerializer$None.class
com/facebook/AuthorizationClient$Result$Code.class
com/fasterxml/jackson/core/JsonProcessingException.class
com/fasterxml/jackson/databind/JsonDeserializer$None.class
retrofit/http/DELETE.class
com/fasterxml/jackson/databind/annotation/JsonDeserialize.class
com/fasterxml/jackson/databind/JsonSerializer.class
com/facebook/Session$TokenRefreshRequestHandler.class
org/chalup/microorm/annotations/Column.class
com/facebook/AuthorizationClient$AuthorizationRequest.class
com/facebook/android/R.class
com/google/api/client/json/JsonString.class
com/fasterxml/jackson/annotation/JacksonAnnotationsInside.class
android/support/annotation/IntDef.class
com/google/android/gms/location/LocationListener.class
android/support/v4/widget/DrawerLayout.class
butterknife/OnLongClick.class
android/support/v4/widget/MaterialProgressDrawable$ProgressDrawableSize.class
com/fasterxml/jackson/annotation/JsonIdentityInfo.class
butterknife/OnPageChange$Callback.class
android/support/v4/app/ActivityCompatHoneycomb.class
com/google/common/annotations/Beta.class
com/google/protobuf/MessageLiteOrBuilder.class
com/fasterxml/jackson/annotation/JsonTypeInfo$As.class
javax/annotation/Nonnegative.class
com/google/gson/annotations/SerializedName.class
com/fasterxml/jackson/annotation/JsonIgnore.class
com/google/api/client/repackaged/com/google/common/annotations/VisibleForTesting.class
com/fasterxml/jackson/databind/util/Converter.class
android/support/v4/app/FragmentManager$OnBackStackChangedListener.class
com/facebook/internal/Utility.class
retrofit/http/FormUrlEncoded.class
javax/annotation/RegEx.class
butterknife/OnClick.class
android/support/v4/app/FragmentActivity$1.class
butterknife/ButterKnife.class
com/facebook/internal/Validate.class
butterknife/OnTouch.class
android/support/v4/app/LoaderManagerImpl.class
com/fasterxml/jackson/annotation/JsonTypeInfo$None.class
com/google/protobuf/InvalidProtocolBufferException.class
android/support/annotation/Nullable.class
android/support/multidex/MultiDex$V14.class
android/support/v4/app/FragmentManagerImpl$4.class
android/support/multidex/MultiDexApplication.class
retrofit/http/EncodedPath.class
com/fasterxml/jackson/databind/jsonschema/JsonSerializableSchema.class
com/facebook/AccessToken.class
com/facebook/model/CreateGraphObject.class
com/facebook/Session$2.class
com/google/common/eventbus/AllowConcurrentEvents.class
android/support/v4/content/LocalBroadcastManager.class
android/support/v4/content/ContextCompat.class
com/facebook/android/R$id.class
android/support/v4/app/FragmentManagerState.class
com/fasterxml/jackson/annotation/JsonIgnoreProperties.class
com/google/android/gms/location/ActivityRecognitionClient.class
com/google/ads/mediation/MediationServerParameters.class
android/support/v4/app/ActionBarDrawerToggle.class
butterknife/OnItemLongClick.class
javax/annotation/meta/Exhaustive.class
com/fasterxml/jackson/annotation/JsonSubTypes$Type.class
javax/annotation/WillClose.class
javax/annotation/Nonnull.class
fr/openium/androkit/utils/ToastUtils.class
retrofit/http/Headers.class
com/facebook/Session$PermissionsPair.class
javax/annotation/WillCloseWhenClosed.class
android/support/v4/app/FragmentManagerImpl$FragmentTag.class
android/support/annotation/IdRes.class
com/facebook/Response.class
android/support/v4/app/FragmentManagerImpl$5.class
retrofit/http/HEAD.class
javax/annotation/CheckForSigned.class
javax/annotation/CheckForNull.class
com/google/ads/mediation/MediationServerParameters$Parameter.class
com/facebook/Session$1.class
butterknife/InjectViews.class
com/fasterxml/jackson/annotation/JsonFormat$Value.class
android/support/annotation/FractionRes.class
com/fasterxml/jackson/annotation/JsonTypeInfo$Id.class
com/fasterxml/jackson/annotation/JsonIgnoreType.class
com/fasterxml/jackson/annotation/ObjectIdGenerator$IdKey.class
com/facebook/FacebookAuthorizationException.class
javax/annotation/ParametersAreNullableByDefault.class
com/facebook/Session.class
javax/annotation/Nonnegative$Checker.class
android/support/annotation/DimenRes.class
android/support/annotation/AnyRes.class
com/fasterxml/jackson/annotation/JacksonAnnotation.class
com/facebook/model/GraphObject.class
javax/annotation/CheckReturnValue.class
com/facebook/FacebookOperationCanceledException.class
android/support/annotation/IntegerRes.class
android/support/multidex/MultiDexExtractor$1.class
com/facebook/UiLifecycleHelper.class
android/support/v4/app/BackStackRecord$TransitionState.class
com/fasterxml/jackson/annotation/JsonView.class
android/support/annotation/MenuRes.class
com/fasterxml/jackson/annotation/JsonRawValue.class
retrofit/http/Query.class
com/google/android/gms/common/annotation/KeepName.class
org/chalup/microorm/MicroOrm.class
com/facebook/FacebookException.class
android/support/multidex/MultiDexExtractor.class
android/support/v4/app/FragmentManagerImpl$2.class
android/support/v4/util/SimpleArrayMap.class
javax/annotation/MatchesPattern$Checker.class
com/fasterxml/jackson/databind/annotation/JsonNaming.class
android/support/multidex/MultiDex$V4.class
android/support/annotation/DrawableRes.class
android/support/v4/app/BackStackState.class
javax/annotation/concurrent/GuardedBy.class
android/support/v4/app/NotificationCompat$Builder.class
com/fasterxml/jackson/databind/jsonFormatVisitors/JsonFormatVisitable.class
com/facebook/Session$TokenRefreshRequest.class
com/facebook/AuthorizationClient$OnCompletedListener.class
com/facebook/LoginActivity.class
org/sidibe/mqtt/android/lib/MqttTopic.class
com/fasterxml/jackson/annotation/JsonPropertyOrder.class
butterknife/OnTextChanged$Callback.class
com/google/android/gms/common/GooglePlayServicesClient.class
javax/annotation/Tainted.class
retrofit/http/FieldMap.class
com/google/android/gms/internal/dw.class
com/fasterxml/jackson/databind/KeyDeserializer$None.class
retrofit/http/QueryMap.class
javax/annotation/Detainted.class
org/fusesource/hawtdispatch/jmx/MBeanInfo.class
android/support/annotation/ArrayRes.class
android/support/v4/app/Fragment$SavedState.class
butterknife/OnItemSelected.class
com/facebook/LoginActivity$1.class
retrofit/http/PartMap.class
android/support/v4/app/FragmentState.class
android/support/v4/app/FragmentActivity$2.class
com/fasterxml/jackson/databind/annotation/JsonSerialize$Inclusion.class
android/support/v4/app/FragmentManagerImpl$1.class
com/fasterxml/jackson/annotation/JsonSetter.class
javax/annotation/OverridingMethodsMustInvokeSuper.class
android/support/multidex/ZipUtil$CentralDirectory.class
com/fasterxml/jackson/databind/jsontype/TypeDeserializer.class
com/facebook/Session$StartActivityDelegate.class
com/facebook/AuthorizationClient.class
retrofit/http/EncodedQuery.class
javax/annotation/Syntax.class
com/facebook/Session$3.class
com/fasterxml/jackson/annotation/JsonFormat$Shape.class
com/facebook/SessionLoginBehavior.class
com/facebook/android/R$layout.class
com/facebook/Session$SerializationProxyV2.class
android/support/v4/util/LogWriter.class
retrofit/http/Body.class
com/google/android/gms/maps/SupportMapFragment.class
javax/annotation/meta/TypeQualifierDefault.class
com/path/android/jobqueue/config/Configuration$Builder.class
com/fasterxml/jackson/annotation/JsonAutoDetect.class
fr/openium/androkit/utils/MemoryUtils.class
com/tyczj/extendedcalendarview/CalendarProvider$DatabaseHelper.class
com/facebook/Request$Callback.class
com/facebook/internal/SessionAuthorizationType.class
android/support/annotation/AnimatorRes.class
javax/annotation/meta/Exclusive.class
android/support/v4/app/SuperNotCalledException.class
android/support/annotation/AnimRes.class
com/facebook/Session$AutoPublishAsyncTask.class
com/fasterxml/jackson/annotation/JsonInclude$Include.class
com/google/protobuf/MessageLite.class
com/google/api/client/json/JsonPolymorphicTypeMap.class
com/google/android/gms/location/ActivityRecognitionResult.class
com/fasterxml/jackson/databind/annotation/JsonSerialize$Typing.class
com/fasterxml/jackson/databind/annotation/JsonValueInstantiator.class
android/support/v4/widget/DrawerLayout$DrawerListener.class
com/google/api/client/util/Value.class
org/chalup/microorm/annotations/Embedded.class
com/fasterxml/jackson/annotation/JsonFormat.class
com/path/android/jobqueue/network/NetworkEventProvider$Listener.class
android/support/annotation/StringRes.class
javax/annotation/concurrent/Immutable.class
com/google/android/gms/common/GooglePlayServicesClient$OnConnectionFailedListener.class
android/support/annotation/StyleableRes.class
android/support/v4/widget/MaterialProgressDrawable$2.class
com/facebook/SharedPreferencesTokenCachingStrategy.class
android/support/v4/app/LoaderManager$LoaderCallbacks.class
android/support/annotation/InterpolatorRes.class
javax/annotation/concurrent/NotThreadSafe.class
android/support/v4/widget/MaterialProgressDrawable$Ring.class
org/sidibe/mqtt/android/lib/MqttAndroidClient.class
com/facebook/Session$5.class
butterknife/internal/ListenerClass$NONE.class
com/google/protobuf/GeneratedMessageLite.class
butterknife/OnFocusChange.class
com/fasterxml/jackson/annotation/JsonIdentityReference.class
com/tyczj/extendedcalendarview/CalendarProvider.class
com/facebook/Session$OpenRequest.class
com/fasterxml/jackson/annotation/JsonPropertyDescription.class
com/google/android/gms/maps/model/LatLng.class
javax/annotation/RegEx$Checker.class
retrofit/http/Path.class
javax/annotation/concurrent/ThreadSafe.class
com/fasterxml/jackson/annotation/JsonTypeName.class
com/facebook/Session$NewPermissionsRequest.class
com/fasterxml/jackson/databind/annotation/JsonSerialize.class
retrofit/http/Part.class
com/fasterxml/jackson/annotation/JsonTypeInfo.class
com/facebook/Session$Builder.class
com/fasterxml/jackson/annotation/ObjectIdResolver.class
android/support/v4/widget/MaterialProgressDrawable.class
com/google/android/gms/common/internal/safeparcel/SafeParcelable.class
com/facebook/model/PropertyName.class
com/fasterxml/jackson/annotation/JsonProperty.class
com/fasterxml/jackson/databind/JsonDeserializer.class
android/support/v4/app/DialogFragment.class
com/facebook/TokenCachingStrategy.class
com/google/api/client/repackaged/com/google/common/annotations/GwtCompatible.class
butterknife/InjectView.class
android/support/v4/app/FragmentTransaction.class
com/facebook/Session$SerializationProxyV1.class
android/support/v4/widget/MaterialProgressDrawable$5.class
android/support/v4/app/FragmentManagerImpl.class
android/support/v4/app/BackStackRecord.class
retrofit/http/Header.class
butterknife/OnPageChange.class
javax/annotation/meta/TypeQualifier.class
com/google/common/eventbus/Subscribe.class
butterknife/internal/ListenerMethod.class
com/facebook/Session$AuthorizationRequest.class
com/facebook/LoginActivity$2.class
com/fasterxml/jackson/databind/annotation/JsonTypeResolver.class
javax/annotation/PropertyKey.class
com/google/protobuf/Internal$EnumLite.class
com/fasterxml/jackson/annotation/JsonBackReference.class
com/fasterxml/jackson/databind/annotation/JsonTypeIdResolver.class
javax/annotation/MatchesPattern.class
com/google/api/client/repackaged/com/google/common/annotations/Beta.class
android/support/multidex/ZipUtil.class
android/support/annotation/BoolRes.class
com/fasterxml/jackson/annotation/JacksonInject.class
android/support/v4/app/FragmentManager.class
org/sidibe/mqtt/android/lib/MqttClientState.class
com/fasterxml/jackson/databind/jsonFormatVisitors/JsonFormatVisitorWrapper.class

You can see that jackson is present so it should be in the first dex, so it should works ! (lots of should).

I've looked into this problem a little more today: unlike what I've said before, you don't need to have different versions of one class to face it. Having the exact same class defined twice in 2 different dexes is enough.

In the following error:
"0-29 18:26:26.140  31690-31690/com.myapp.app W/dalvikvm﹕ Class resolved by unexpected DEX: Lcom/myapp/model/MyClass;(0x427a7898):0x596d1000 ref [Lcom/j256/ormlite/field/DataType;] Lcom/j256/ormlite/field/DataType;(0x427a7898):0x5910f000
10-29 18:26:26.140  31690-31690/com.myapp.app W/dalvikvm﹕ (Lcom/myapp/model/MyClass; had used a different Lcom/j256/ormlite/field/DataType; during pre-verification)
10-29 18:26:26.140  31690-31690/com.myapp.app W/dalvikvm﹕ Failed processing annotation value
10-29 18:26:26.140  31690-31690/com.myapp.app W/dalvikvm﹕ threadid=1: thread exiting with uncaught exception (group=0x41d28700)"
My guess is that you face it because of com/j256/ormlite/field/DataType defined in the instrumentation apk and in the application apk. I can't be sure without seeing those apks but you can try to do it yourself by running dexdump on each dex of the application apk and on the instrumentation apk.

If you give me a safe sharing place or I can run it through the business unit I'm happy to share.

The safest would probably be you running dexdump:
You can find the tool in <sdk-path>/build-tools/<version>/dexdump<.exe?>

You'll have then to run
dexdump <instrumentation.apk>  | grep "Class descriptor" | grep com/j256/ormlite/field/DataType
then unzip the application apk in a folder and run in this folder
dexdump classes.dex  | grep "Class descriptor" | grep com/j256/ormlite/field/DataType
dexdump classes2.dex  | grep "Class descriptor" | grep com/j256/ormlite/field/DataType
dexdump classes3.dex  | grep "Class descriptor" | grep com/j256/ormlite/field/DataType
... untill you've run it on all dex files

do the same for com/myapp/model/MyClass and just report here where the 2 classes were found.

If you're running a Windows I think you can replace grep by something like:
findstr /c:"com/j256/ormlite/field/DataType"

Here's my result :
Background =>
-An application using Retrofit and Jackson for get/post query. I have an object Form that I use to post data to a rest service. Form have the annotation JsonInclude(NonNull) that remove the fields of the class Form that are null.

I have a Test Application that send a fake Form but the problem occurs also in the app alone (not in test environement).

-------

So the two classes are :
com/fasterxml/jackson/annotation/JsonInclude$Include <= annotation
and
com/myapp/Form <= class using annotation

--------

I ran dexdump and I could see that :
-Neither are in the test apk (apk-debug-test-unaligned.apk)
-In the app apk (apk-debug.apk) the classes.dex contains the annotation (com/fasterxml/jackson/annotation/JsonInclude$Include and com/fasterxml/jackson/annotation/JsonInclude) and classes2.dex contains the class (com/myapp/Form)
No duplications.
I hope it helps.

Ok I have good news :)
I succeeded in reproducing the bug on a test project (in attachment).
Import it in Android studio, and run the class TestBugReplicator (from androidTest), with the Runner "com.testbug.DexInstrumentation".
You'll get the error. (at least I have)
I tried to make the project as little/simple as I could.
Thank you !
BTW : I use OS X Yosemite 10.10 on a Macbook Air.

So if you have no duplicate this does not look like a packaging issue any more. Can you please tell me which device + android version you used to run the test?

Thank you for the reproduction project, I'll try it soon.