IssueTracker

Can you please upload __content__.json from build/intermediates/transforms/dexMerger/variant/ directory after the build fails? Also, please share:
- api of the device you are deploying to
- minSdkVersion in your build file
- if multiDexEnabled is true or false

I encountered the same issue with 3.2-beta01 and Instant Run (doesn't happen without Instant Run), here's my `__content__.json`:
```
[{"name":"directories","index":0,"scopes":["PROJECT"],"types":["DEX"],"format":"DIRECTORY","present":true},{"name":"nonExternalJars","index":1,"scopes":["MAIN_SPLIT"],"types":["DEX"],"format":"DIRECTORY","present":true},{"name":"externalLibs","index":2,"scopes":["EXTERNAL_LIBRARIES"],"types":["DEX"],"format":"DIRECTORY","present":true}]
```

Multidex is enabled, the device is on API 26, and the minSdk is 16.

Thanks, that is very helpful! Can you also upload build/intermediates/transforms/dexBuilder/variant/__content__.json and  build/intermediates/transforms/externalLibsDexMerger/variant/__content__.json?

I attached build/intermediates/transforms/dexBuilder/variant/__content__.json, but I don't have an externalLibsDexMerger folder, sorry!

I think we already have a fix for this, but I still do not understand how this can happen.

Do you have minifyEnabled for the debug variant? Also, can you please add to your app/build.gradle file:

project.afterEvaluate {
    println "External transforms are " + android.getTransforms()
}

and run from the IDE. You should be able to see the output under View -> Tool Windows -> Build.

minifyEnabled is not specified in debug (default value is disabled for debug builds, right?)

The only transform showing is the Firebase perf plugin: External transforms are [com.google.firebase.perf.plugin.FirebaseTransform@5a1ab286]

By default we do not minify, you are correct.

I was able to reproduce the issue by adding the Firebase performance plugin. The issue was on our end, we will fix this in 3.2.0-beta02. The workaround is to disable the Firebase performace plugin for your debug builds.

Before closing this bug, can someone else having the same issue add snippet from #6? I'd like to make sure we found the root cause.

Indeed, removing the Firebase perf plugin fixes the issue for now on my end. Thanks! Not sure #1 was using it though, he/she might be able to provide you another way to trigger it :-)

I'm also using the Firebase Performance Plugin so it sounds like that's the issue.

I've attached the files requested in case you need to confirm though.

I'm having the same issue but I'm not using the Firebase Performance Plugin.
I'm trying to disable every plugin I can but it doesn't seem to go away, I'm disabling Instant Run.
These are the plugins that are left and I'm running:
-Android Support
-Coverage
-EditorConfig
-Gradle
-Groovy
-IntelliLang
-JUnit
-Kotlin
-Properties Support
-Settings Repository
-Smali Support
-Task Management
-Terminal

#11 - The Firebase Performance Plugin is a Gradle plugin rather than an Android Studio/Intellij plugin - it's applied in a build.gradle file.

I would suggest uploading the files requested above and adding that small Gradle snippet to determine what is actually causing the issue.

Same problem with a very small test project setup with only the standard AS templates. No reference to firebase. I can build project and 'installDebug', but run app produces (and no instant run fixes):

org.gradle.initialization.ReportedException: org.gradle.internal.exceptions.LocationAwareException: Execution failed for task ':app:transformDexWithInstantRunSlicesApkForDebug'.
        at org.gradle.initialization.DefaultGradleLauncher.doBuildStages(DefaultGradleLauncher.java:145)
        at org.gradle.initialization.DefaultGradleLauncher.executeTasks(DefaultGradleLauncher.java:115)
        at org.gradle.internal.invocation.GradleBuildController$1.call(GradleBuildController.java:78)
        at org.gradle.internal.invocation.GradleBuildController$1.call(GradleBuildController.java:75)
        at org.gradle.internal.work.DefaultWorkerLeaseService.withLocks(DefaultWorkerLeaseService.java:152)
        at org.gradle.internal.invocation.GradleBuildController.doBuild(GradleBuildController.java:100)
        at org.gradle.internal.invocation.GradleBuildController.run(GradleBuildController.java:75)
        at org.gradle.tooling.internal.provider.runner.ClientProvidedBuildActionRunner.run(ClientProvidedBuildActionRunner.java:62)
        at org.gradle.launcher.exec.ChainingBuildActionRunner.run(ChainingBuildActionRunner.java:35)
        at org.gradle.launcher.exec.ChainingBuildActionRunner.run(ChainingBuildActionRunner.java:35)
        at org.gradle.tooling.internal.provider.ValidatingBuildActionRunner.run(ValidatingBuildActionRunner.java:32)
        at org.gradle.launcher.exec.RunAsBuildOperationBuildActionRunner$1.run(RunAsBuildOperationBuildActionRunner.java:43)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:199)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:110)
        at org.gradle.launcher.exec.RunAsBuildOperationBuildActionRunner.run(RunAsBuildOperationBuildActionRunner.java:40)
        at org.gradle.tooling.internal.provider.SubscribableBuildActionRunner.run(SubscribableBuildActionRunner.java:51)
        at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:49)
        at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:32)
        at org.gradle.launcher.exec.BuildTreeScopeBuildActionExecuter.execute(BuildTreeScopeBuildActionExecuter.java:39)
        at org.gradle.launcher.exec.BuildTreeScopeBuildActionExecuter.execute(BuildTreeScopeBuildActionExecuter.java:25)
        at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:80)
        at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:53)
        at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:57)
        at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:32)
        at org.gradle.tooling.internal.provider.GradleThreadBuildActionExecuter.execute(GradleThreadBuildActionExecuter.java:36)
        at org.gradle.tooling.internal.provider.GradleThreadBuildActionExecuter.execute(GradleThreadBuildActionExecuter.java:25)
        at org.gradle.tooling.internal.provider.ParallelismConfigurationBuildActionExecuter.execute(ParallelismConfigurationBuildActionExecuter.java:43)
        at org.gradle.tooling.internal.provider.ParallelismConfigurationBuildActionExecuter.execute(ParallelismConfigurationBuildActionExecuter.java:29)
        at org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:64)
        at org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:29)
        at org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:59)
        at org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:44)
        at org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:45)
        at org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:30)
        at org.gradle.launcher.daemon.server.exec.ExecuteBuild.doBuild(ExecuteBuild.java:67)
        at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36)
        at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122)
        at org.gradle.launcher.daemon.server.exec.WatchForDisconnection.execute(WatchForDisconnection.java:37)
        at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122)
        at org.gradle.launcher.daemon.server.exec.ResetDeprecationLogger.execute(ResetDeprecationLogger.java:26)
        at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122)
        at org.gradle.launcher.daemon.server.exec.RequestStopIfSingleUsedDaemon.execute(RequestStopIfSingleUsedDaemon.java:34)
        at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122)
        at org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.call(ForwardClientInput.java:74)
        at org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.call(ForwardClientInput.java:72)
        at org.gradle.util.Swapper.swap(Swapper.java:38)
        at org.gradle.launcher.daemon.server.exec.ForwardClientInput.execute(ForwardClientInput.java:72)
        at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122)
        at org.gradle.launcher.daemon.server.exec.LogAndCheckHealth.execute(LogAndCheckHealth.java:55)
        at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122)
        at org.gradle.launcher.daemon.server.exec.LogToClient.doBuild(LogToClient.java:62)
        at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36)
        at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122)
        at org.gradle.launcher.daemon.server.exec.EstablishBuildEnvironment.doBuild(EstablishBuildEnvironment.java:82)
        at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36)
        at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:122)
        at org.gradle.launcher.daemon.server.exec.StartBuildOrRespondWithBusy$1.run(StartBuildOrRespondWithBusy.java:50)
        at org.gradle.launcher.daemon.server.DaemonStateCoordinator$1.run(DaemonStateCoordinator.java:295)
        at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63)
        at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
        at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55)
        at java.lang.Thread.run(Thread.java:745)
Caused by: org.gradle.internal.exceptions.LocationAwareException: Execution failed for task ':app:transformDexWithInstantRunSlicesApkForDebug'.
        at org.gradle.initialization.DefaultExceptionAnalyser.transform(DefaultExceptionAnalyser.java:74)
        at org.gradle.initialization.MultipleBuildFailuresExceptionAnalyser.transform(MultipleBuildFailuresExceptionAnalyser.java:47)
        at org.gradle.initialization.DefaultGradleLauncher.doBuildStages(DefaultGradleLauncher.java:143)
        ... 65 more
Caused by: org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':app:transformDexWithInstantRunSlicesApkForDebug'.
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:103)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:73)
        at org.gradle.api.internal.tasks.execution.OutputDirectoryCreatingTaskExecuter.execute(OutputDirectoryCreatingTaskExecuter.java:51)
        at org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:59)
        at org.gradle.api.internal.tasks.execution.ResolveTaskOutputCachingStateExecuter.execute(ResolveTaskOutputCachingStateExecuter.java:54)
        at org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:59)
        at org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:101)
        at org.gradle.api.internal.tasks.execution.FinalizeInputFilePropertiesTaskExecuter.execute(FinalizeInputFilePropertiesTaskExecuter.java:44)
        at org.gradle.api.internal.tasks.execution.CleanupStaleOutputsExecuter.execute(CleanupStaleOutputsExecuter.java:91)
        at org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.java:62)
        at org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:59)
        at org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:54)
        at org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43)
        at org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:34)
        at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker$1.run(DefaultTaskGraphExecuter.java:256)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:199)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:110)
        at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:249)
        at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:238)
        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.processTask(DefaultTaskPlanExecutor.java:123)
        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.access$200(DefaultTaskPlanExecutor.java:79)
        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:104)
        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:98)
        at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.execute(DefaultTaskExecutionPlan.java:663)
        at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.executeWithTask(DefaultTaskExecutionPlan.java:597)
        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.run(DefaultTaskPlanExecutor.java:98)
        ... 6 more
Caused by: java.lang.IllegalArgumentException: java.lang.IllegalArgumentException: !zip.isFile()
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
        at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
        at java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:593)
        at java.util.concurrent.ForkJoinTask.reportException(ForkJoinTask.java:677)
        at java.util.concurrent.ForkJoinTask.join(ForkJoinTask.java:720)
        at com.android.ide.common.internal.WaitableExecutor.waitForTasksWithQuickFail(WaitableExecutor.java:146)
        at com.android.build.gradle.internal.transforms.InstantRunSliceSplitApkBuilder.transform(InstantRunSliceSplitApkBuilder.java:245)
        at com.android.build.gradle.internal.pipeline.TransformTask$2.call(TransformTask.java:239)
        at com.android.build.gradle.internal.pipeline.TransformTask$2.call(TransformTask.java:235)
        at com.android.builder.profile.ThreadRecorder.record(ThreadRecorder.java:102)
        at com.android.build.gradle.internal.pipeline.TransformTask.transform(TransformTask.java:230)
        at sun.reflect.GeneratedMethodAccessor350.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.gradle.internal.reflect.JavaMethod.invoke(JavaMethod.java:73)
        at org.gradle.api.internal.project.taskfactory.IncrementalTaskAction.doExecute(IncrementalTaskAction.java:50)
        at org.gradle.api.internal.project.taskfactory.StandardTaskAction.execute(StandardTaskAction.java:39)
        at org.gradle.api.internal.project.taskfactory.StandardTaskAction.execute(StandardTaskAction.java:26)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$1.run(ExecuteActionsTaskExecuter.java:124)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:199)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:110)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:113)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:95)
        ... 33 more
Caused by: java.lang.IllegalArgumentException: !zip.isFile()
        at com.google.common.base.Preconditions.checkArgument(Preconditions.java:135)
        at com.android.builder.files.IncrementalRelativeFileSets.fromZip(IncrementalRelativeFileSets.java:96)
        at com.android.builder.files.IncrementalRelativeFileSets.fromZip(IncrementalRelativeFileSets.java:79)
        at com.android.builder.core.AndroidBuilder.packageCodeSplitApk(AndroidBuilder.java:1453)
        at com.android.build.gradle.internal.transforms.InstantRunSliceSplitApkBuilder.generateSplitApk(InstantRunSliceSplitApkBuilder.java:260)
        at com.android.build.gradle.internal.transforms.InstantRunSliceSplitApkBuilder.lambda$null$1(InstantRunSliceSplitApkBuilder.java:234)
        at java.util.concurrent.ForkJoinTask$AdaptedCallable.exec(ForkJoinTask.java:1424)
        at java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:289)
        at java.util.concurrent.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1056)
        at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1692)
        at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:157)

Re #13: Can you please apply the snippet from #6, and share __content__.json files from build/intermediates/transforms/dexBuilder, and build/intermediates/transforms/dexMerger?

I started getting this issue on another project, without Firebase Performance plugin.

External transforms logged as []

I've attached content.json files.

I am now able to reproduce the issue myself, without any additional plugins. To repro:
- create a new sample project, File -> New -> Import Sample -> HelloJNI
- cd $PROJECT
- ./gradlew  :app:assembleArm7Debug
- ./gradlew -Pandroid.injected.invoked.from.ide=true  -Pandroid.optional.compilation=INSTANT_DEV,RESTART_ONLY  -Pandroid.injected.build.api=23  -Pandroid.injected.build.density=560dpi  -Pandroid.injected.build.abi=armeabi-v7a,armeabi  -Pandroid.injected.coldswap.mode=default  :app:assembleArm7Debug

The issue is that we do not clean the merged dex file for the project classes. Reason seems to be that in non-IR build and IR build, path to the dex archive directory is the same, but the stream name is different. In the non-IR case, name is a hash value, while in IR, it is "slice_0". Because this file is not cleaned up, we fail to find compiled resources for it, causing the exception.

Glad to see progress being made.

There is some history dependence to the issue. I did a fresh source checkout on  a rebooted host, and did many successful instant runs (looking at just ui changes via xml edits).

After a couple of hours of this make a tiny edit to activity and all of a sudden instant run fails. I cleared all the build and .gradle, cleared and restarted AS and problem remains. Have not rebooted, but wonder if the problems is connected to temp files that will be removed on reboot...

Re #17: Once the build fails, can you please execute clean, try to build with Instant Run, and if the build fails again, please upload __content__.json files that I've mentioned in #14.

The fix is ready for Android Gradle plugin 3.2.0-beta02, and that addresses #16, which I believe most of you are hitting.

Here are the files requested in #18

Re #19: Artifacts listed in the second __content__.json suggest this was an incremental build. Just to double check, did you run execute clean, before trying to use Instant Run again? Can you please describes steps in details? Also, if you have Gradle caching enabled (org.gradle.caching=true in gradle.properties), please try disabling it.

What caused the predictability  in my case is if the problem happens and you select from the IDE "clean" followed by "Rebuild Project" followed by "Run" the problem remains.

If you lose the paranoia, and simply do "clean" followed by "Run" the problem is gone (at least temporarily).

Thanks for the additional info Mike. This confirms that the issue is the same as in #16. "Rebuilt project" will execute a non-IR build, and when you hit the run button again, Instant Run build will be executed. As a temporary workaround, you can disable Instant Run, and re-enable it once we release a new version of the Android Gradle plugin.

As I've already mentioned, the fix will be in 3.2.0-beta02.