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Hi Liran, thanks for filling a bug report.

1) Does this happen when running the application, or when running the tests?
2) Can you please upload the application APK (and test one if it is relevant)? Alternatively, a list of classes in all dex files would be enough.

@3
1. Running the app. We don't have unit testing, as we have a tiny company and focus on the minimal things we can to work well on the project.
2. Yes, but only via private email (not public here), because this is closed sourced app, which is from the office.
Do note, that the issue has occurred on Android 4.4 , but not on later versions.

Thanks, please send them to gavra@google.com.

@5 OK sent.
Also wrote the steps needed.

Issue is due not tracing classes annotated with runtime visible annotations. After examining logcat, annotation that was in the main classes.dex, was used to annotate class in classes3.dex, which led to:

Class resolved by unexpected DEX: Lcom/AmazonWebService;(0x9d03f7c8):0x8a7de000 ref [Lcom/vrest/HttpMethod;] Lcom/vrest/HttpMethod;(0x9d03f7c8):0x8bc12000
W/dalvikvm( 3781): (Lcom/AmazonWebService; had used a different Lcom/vrest/HttpMethod; during pre-verification)

Liran has confirmed that adding explicit keep rule for com/AmazonWebService fixes the issue.

@7 I don't understand.
You mean that the gradle plugin decided to remove the annotation or its classes for some reason?

For more details, please see https://issuetracker.google.com/37008250.

Long story short, if there is an runtime visible annotation that is in the main dex, all classes annotated with it should be in the main dex as well.  From our conversation, it seems that AmazonWebService class is annotated with a class that references HttpMethod, which could be the cause of the issue.

To answer your question in #8, the plugin is not removing any classes, they are all in the APK, but AmazonWebService has to be in classes.dex, which is not currently the case, and that causes issue.

I've attached project that reproduces the issue when run on API 19. The issue is that annotation has an Enum reference, and both are in the main dex file, while the annotated class, Data, is in classes2.dex. Switching D8 main dex list, by adding to gradle.properties

android.enableD8MainDexList=false

produces a working APK.

Project: r8
Branch: master

commit ff562da903acc163f6d1f8c133618d20ecb5e454
Author: Ivan Gavrilovic <gavra@google.com>
Date:   Tue Mar 06 15:45:33 2018

    Analyze field and method annotations for main dex list
   
    Analyze annotations on fields and methods, in addion to
    ones on the class. Classes containing any annotation
    that references an enum should be in the main dex,
    as otherwise reflection APIs e.g.
    Method.getDeclaredAnnotations() cause runtime failures
    on API 19 and below.
   
    Test: updated multidex002 test
    BUG=73800636
   
    Change-Id: Ie56da36056b80ed1273b07bdf293046b39fc4126

M       src/main/java/com/android/tools/r8/graph/DexClass.java
M       src/main/java/com/android/tools/r8/shaking/MainDexListBuilder.java
A       src/test/examples/multidex002/AnnotatedDirectMethod.java
A       src/test/examples/multidex002/AnnotatedInstanceField.java
A       src/test/examples/multidex002/AnnotatedMethodParameter.java
A       src/test/examples/multidex002/AnnotatedNotKept.java
A       src/test/examples/multidex002/AnnotatedStaticField.java
A       src/test/examples/multidex002/AnnotatedVirtualMethod.java
A       src/test/examples/multidex002/AnnotationWithEnum3.java
A       src/test/examples/multidex002/AnnotationWithoutEnum.java
M       src/test/examples/multidex002/ref-list-1.txt

https://r8-review.googlesource.com/17660

Merged in studio-3.1-release under ag/I8c2235710c6725a126b2730c7338b2d6241f3698.

@12 Which version of 3.2 ?

It should be 3.2.0-alpha07.