I replaced google cardboard sdk with Google VR sdk and getting this famous error: unable to convert classes into dex format

I have tried the many solutions. I searched *.jar files in the project folder. There are duplicate jar files. When I delete the duplicates as mentioned in many solutions, and when I tried to build it again those duplicated files were again created.

To be exact here is the detailed error message:

CommandInvokationFailure: Unable to convert classes into dex format.
C:\Program Files\Java\jdk1.8.0_121\bin\java.exe -Xmx2048M -Dcom.android.sdkmanager.toolsdir="C:/Users/Ahsan Naeem/AppData/Local/Android/Sdk	ools" -Dfile.encoding=UTF8 -jar "C:\Program Files\Unity\Editor\Data\PlaybackEngines\AndroidPlayer/Tools\sdktools.jar" -

stderr[
Uncaught translation error: java.lang.IllegalArgumentException: already added: Lcom/google/protobuf/nano/CodedInputByteBufferNano;
Uncaught translation error: java.lang.IllegalArgumentException: already added: Lcom/google/protobuf/nano/CodedOutputByteBufferNano;
Uncaught translation error: java.lang.IllegalArgumentException: already added: Lcom/google/protobuf/nano/CodedOutputByteBufferNano$OutOfSpaceException;
Uncaught translation error: java.lang.IllegalArgumentException: already added: Lcom/google/protobuf/nano/ExtendableMessageNano;
Uncaught translation error: java.lang.IllegalArgumentException: already added: Lcom/google/protobuf/nano/Extension;
Uncaught translation error: java.lang.IllegalArgumentException: already added: Lcom/google/protobuf/nano/Extension$1;
Uncaught translation error: java.lang.IllegalArgumentException: already added: Lcom/google/protobuf/nano/Extension$PrimitiveExtension;
Uncaught translation error: java.lang.IllegalArgumentException: already added: Lcom/google/protobuf/nano/FieldArray;
Uncaught translation error: java.lang.IllegalArgumentException: already added: Lcom/google/protobuf/nano/FieldData;

UNEXPECTED TOP-LEVEL EXCEPTION:
java.lang.RuntimeException: Translation has been interrupted
	at com.android.dx.command.dexer.Main.processAllFiles(Main.java:613)
	at com.android.dx.command.dexer.Main.runMonoDex(Main.java:311)
	at com.android.dx.command.dexer.Main.run(Main.java:277)
	at com.android.dx.command.dexer.Main.main(Main.java:245)
	at com.android.dx.command.Main.main(Main.java:106)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at SDKMain.main(SDKMain.java:129)
Caused by: java.lang.InterruptedException: Too many errors
	at com.android.dx.command.dexer.Main.processAllFiles(Main.java:605)
	... 9 more
]
stdout[
processing archive D:\ChuTech\Unity Games\vRealizerstest\vRealizersTest\Temp\StagingArea\android-libraries\gvr-permissionsupport-release\libs\.\classes.jar...
processing com/google/gvr/permissionsupport/BuildConfig.class...
processing com/google/gvr/permissionsupport/PermissionsFragment.class...
processing com/google/gvr/permissionsupport/PermissionsFragment$1.class...
processing com/google/gvr/permissionsupport/PermissionsFragment$PermissionsCallback.class...
processing com/google/gvr/permissionsupport/TransitionVRActivity.class...
processing com/google/gvr/permissionsupport/TransitionVRActivity$1.class...
processing archive D:\ChuTech\Unity Games\vRealizerstest\vRealizersTest\Temp\StagingArea\android-libraries\gvr_android_common\libs\.\classes.jar...
ignored resource clearcut/
ignored resource clearcut/nano/
processing clearcut/nano/EventCodeEnumProto.class...
ignored resource com/
ignored resource com/google/
ignored resource com/google/common/
ignored resource com/google/common/logging/
ignored resource com/google/common/logging/nano/
processing com/google/common/logging/nano/Vr.class...
processing com/google/common/logging/nano/Vr$VREvent.class...
processing com/google/common/logging/nano/Vr$VREvent$Application.class...
processing com/google/common/logging/nano/Vr$VREvent$AudioStats.class...
processing com/google/common/logging/nano/Vr$VREvent$AudioStats$RenderingMode.class...
processing com/google/common/logging/nano/Vr$VREvent$Bucket.class...
processing com/google/common/logging/nano/Vr$VREvent$Cyclops.class...
processing com/google/common/logging/nano/Vr$VREvent$Cyclops$Capture.class...
processing com/google/common/logging/nano/Vr$VREvent$Cyclops$Capture$Outcome.class...
processing com/google/common/logging/nano/Vr$VREvent$Cyclops$Share.class...
processing com/google/common/logging/nano/Vr$VREvent$Cyclops$Share$Type.class...
processing com/google/common/logging/nano/Vr$VREvent$Cyclops$ShareStart.class...
processing com/google/common/logging/nano/Vr$VREvent$Cyclops$ShareStart$OriginScreen.class...
processing com/google/common/logging/nano/Vr$VREvent$Cyclops$View.class...
processing com/google/common/logging/nano/Vr$VREvent$Cyclops$View$Orientation.class...
processing com/google/common/logging/nano/Vr$VREvent$DoublePrecisionTransform.class...
processing com/google/common/logging/nano/Vr$VREvent$EarthVr.class...
processing com/google/common/logging/nano/Vr$VREvent$EarthVr$Actor.class...
processing com/google/common/logging/nano/Vr$VREvent$EarthVr$Actor$ControllerState.class...
processing com/google/common/logging/nano/Vr$VREvent$EarthVr$Actor$ControllerState$Role.class...
processing com/google/common/logging/nano/Vr$VREvent$EarthVr$AppState.class...
processing com/google/common/logging/nano/Vr$VREvent$EarthVr$ControllerState.class...
processing com/google/common/logging/nano/Vr$VREvent$EarthVr$ControllerState$Role.class...
processing com/google/common/logging/nano/Vr$VREvent$EarthVr$Environment.class...
processing com/google/common/logging/nano/Vr$VREvent$EarthVr$Menu.class...
processing com/google/common/logging/nano/Vr$VREvent$EarthVr$Preferences.class...
processing com/google/common/logging/nano/Vr$VREvent$EarthVr$Preferences$ComfortModeState.class...
processing com/google/common/logging/nano/Vr$VREvent$EarthVr$Preferences$GuestMode.class...
processing com/google/common/logging/nano/Vr$VREvent$EarthVr$Preferences$HumanScaleMode.class...
processing com/google/common/logging/nano/Vr$VREvent$EarthVr$Preferences$LabelsState.class...
processing com/google/common/logging/nano/Vr$VREvent$EarthVr$Preferences$MusicMode.class...
processing com/google/common/logging/nano/Vr$VREvent$EarthVr$Preferences$StartConfiguration.class...
processing com/google/common/logging/nano/Vr$VREvent$EarthVr$SplashScreen.class...
processing com/google/common/logging/nano/Vr$VREvent$EarthVr$SplashScreen$ExitType.class...
processing com/google/common/logging/nano/Vr$VREvent$EarthVr$Tour.class...
processing com/google/common/logging/nano/Vr$VREvent$EarthVr$Tutorial.class...
processing com/google/common/logging/nano/Vr$VREvent$EarthVr$View.class...
processing com/google/common/logging/nano/Vr$VREvent$EarthVr$View$Mode.class...
processing com/google/common/logging/nano/Vr$VREvent$EmbedVrWidget.class...
processing com/google/common/logging/nano/Vr$VREvent$EmbedVrWidget$Pano.class...
processing com/google/common/logging/nano/Vr$VREvent$EmbedVrWidget$StereoFormat.class...
processing com/google/common/logging/nano/Vr$VREvent$EmbedVrWidget$Video.class...
processing com/google/common/logging/nano/Vr$VREvent$EmbedVrWidget$ViewMode.class...
processing com/google/common/logging/nano/Vr$VREvent$EventType.class...
processing com/google/common/logging/nano/Vr$VREvent$GConfigUpdate.class...
processing com/google/common/logging/nano/Vr$VREvent$GConfigUpdate$GConfigValue.class...
processing com/google/common/logging/nano/Vr$VREvent$HeadMount.class...
processing com/google/common/logging/nano/Vr$VREvent$HistogramBucket.class...
processing com/google/common/logging/nano/Vr$VREvent$JumpInspector.class...
processing com/google/common/logging/nano/Vr$VREvent$JumpInspector$AudioDetails.class...
processing com/google/common/logging/nano/Vr$VREvent$JumpInspector$ImageDetails.class...
processing com/google/common/logging/nano/Vr$VREvent$JumpInspector$ImagePlaybackDetails.class...
processing com/google/common/logging/nano/Vr$VREvent$JumpInspector$MediaDetails.class...
processing com/google/common/logging/nano/Vr$VREvent$JumpInspector$MediaDetails$AudioCodec.class...
processing com/google/common/logging/nano/Vr$VREvent$JumpInspector$MediaDetails$VideoCodec.class...
processing com/google/common/logging/nano/Vr$VREvent$JumpInspector$PickerDetails.class...
processing com/google/common/logging/nano/Vr$VREvent$JumpInspector$PlaybackDetails.class...
processing com/google/common/logging/nano/Vr$VREvent$JumpInspector$PlaybackDetails$PlaybackEngine.class...
processing com/google/common/logging/nano/Vr$VREvent$JumpInspector$PlaybackDetails$PlaybackMode.class...
processing com/google/common/logging/nano/Vr$VREvent$JumpInspector$PlaybackDetails$PlaybackState.class...
processing com/google/common/logging/nano/Vr$VREvent$JumpInspector$Resolution.class...
processing com/google/common/logging/nano/Vr$VREvent$JumpInspector$SphericalMetadata.class...
processing com/google/common/logging/nano/Vr$VREvent$JumpInspector$SphericalMetadata$ProjectionType.class...
processing com/google/common/logging/nano/Vr$VREvent$JumpInspector$VideoDetails.class...
processing com/google/common/logging/nano/Vr$VREvent$JumpInspector$VideoPlaybackDetails.class...
processing com/google/common/logging/nano/Vr$VREvent$Keyboard.class...
processing com/google/common/logging/nano/Vr$VREvent$Keyboard$KeyboardEvent.class...
processing com/google/common/logging/nano/Vr$VREvent$Keyboard$KeyboardEventType.class...
processing com/google/common/logging/nano/Vr$VREvent$Keyboard$KeyboardInputType.class...
processing com/google/common/logging/nano/Vr$VREvent$Keyboard$KeyboardTextEntry.class...
processing com/google/common/logging/nano/Vr$VREvent$Keyboard$KeyboardTextType.class...
processing com/google/common/logging/nano/Vr$VREvent$Launcher.class...
processing com/google/common/logging/nano/Vr$VREvent$Launcher$NavItem.class...
processing com/google/common/logging/nano/Vr$VREvent$Lullaby.class...
processing com/google/common/logging/nano/Vr$VREvent$Lullaby$LoadTime.class...
processing com/google/common/logging/nano/Vr$VREvent$Lullaby$LoadTime$AssetType.class...
processing com/google/common/logging/nano/Vr$VREvent$Lullaby$UiElement.class...
processing com/google/common/logging/nano/Vr$VREvent$PerformanceStats.class...
processing com/google/common/logging/nano/Vr$VREvent$PerformanceStats$ThermalEventFlags.class...
processing com/google/common/logging/nano/Vr$VREvent$Photos.class...
processing com/google/common/logging/nano/Vr$VREvent$Photos$OpenMedia.class...
processing com/google/common/logging/nano/Vr$VREvent$Photos$OpenMedia$MediaSource.class...
processing com/google/common/logging/nano/Vr$VREvent$Photos$OpenMedia$MediaType.class...
processing com/google/common/logging/nano/Vr$VREvent$Photos$WarmWelcome.class...
processing com/google/common/logging/nano/Vr$VREvent$QrCodeScan.class...
processing com/google/common/logging/nano/Vr$VREvent$QrCodeScan$Status.class...
processing com/google/common/logging/nano/Vr$VREvent$Renderer.class...
processing com/google/common/logging/nano/Vr$VREvent$SdkConfigurationParams.class...
processing com/google/common/logging/nano/Vr$VREvent$SdkConfigurationParams$AsyncReprojectionConfig.class...
processing com/google/common/logging/nano/Vr$VREvent$SdkConfigurationParams$AsyncReprojectionConfig$Flags.class...
processing com/google/common/logging/nano/Vr$VREvent$SdkConfigurationParams$DaydreamImageAlignment.class...
processing com/google/common/logging/nano/Vr$VREvent$SensorStats.class...
processing com/google/common/logging/nano/Vr$VREvent$SensorStats$GyroscopeStats.class...
processing com/google/common/logging/nano/Vr$VREvent$SensorStats$Vector3.class...
processing com/google/common/logging/nano/Vr$VREvent$StreetView.class...
processing com/google/common/logging/nano/Vr$VREvent$StreetView$PanoSession.class...
processing com/google/common/logging/nano/Vr$VREvent$StreetView$PanoSession$Source.class...
processing com/google/common/logging/nano/Vr$VREvent$TimeSeriesData.class...
processing com/google/common/logging/nano/Vr$VREvent$TimeSeriesData$TimeIntervalData.class...
processing com/google/common/logging/nano/Vr$VREvent$Transform.class...
processing com/google/common/logging/nano/Vr$VREvent$VrCore.class...
processing com/google/common/logging/nano/Vr$VREvent$VrCore$Controller.class...
processing com/google/common/logging/nano/Vr$VREvent$VrCore$Controller$ControllerAxis.class...
processing com/google/common/logging/nano/Vr$VREvent$VrCore$Controller$SensorType.class...
processing com/google/common/logging/nano/Vr$VREvent$VrCore$ErrorCode.class...
processing com/google/common/logging/nano/Vr$VREvent$VrCore$Permission.class...
processing com/google/common/logging/nano/Vr$VREvent$VrHome.class...
processing com/google/common/logging/nano/Vr$VREvent$VrHome$DialogAction.class...
processing com/google/common/logging/nano/Vr$VREvent$VrHome$DialogAction$DialogActionType.class...
processing com/google/common/logging/nano/Vr$VREvent$VrHome$DialogAction$DialogType.class...
processing com/google/common/logging/nano/Vr$VREvent$VrHome$GetViewerClick.class...
processing com/google/common/logging/nano/Vr$VREvent$VrHome$Setup.class...
processing com/google/common/logging/nano/Vr$VREvent$VrHome$Setup$Step.class...
processing com/google/common/logging/nano/Vr$VREvent$VrHome$Setup$StepStateChange.class...
processing com/google/common/logging/nano/Vr$VREvent$VrHome$Setup$StepStateChange$StepState.class...
processing com/google/common/logging/nano/Vr$VREvent$VrHome$Setup$View.class...
ignored resource com/google/protobuf/
processing com/google/protobuf/AbstractMessageLite.class...
processing com/google/protobuf/AbstractMessageLite$Builder.class...
processing com/google/protobuf/AbstractMessageLite$Builder$LimitedInputStream.class...
processing com/google/protobuf/AbstractMutableMessageLite.class...
processing com/google/protobuf/AbstractMutableMessageLite$1.class...
processing com/google/protobuf/AbstractParser.class...
processing com/google/protobuf/AbstractProtobufList.class...
processing com/google/protobuf/AllocatedBuffer.class...
processing com/google/protobuf/AllocatedBuffer$1.class...
processing com/google/protobuf/AllocatedBuffer$2.class...
processing com/google/protobuf/BinaryProtocolUtil.class...
processing com/google/protobuf/BinaryReader.class...
processing com/google/protobuf/BinaryReader$1.class...
processing com/google/protobuf/BinaryReader$SafeHeapReader.class...
processing com/google/protobuf/BinaryWriter.class...
processing com/google/protobuf/BinaryWriter$1.class...
processing com/google/protobuf/BinaryWriter$SafeDirectWriter.class...
processing com/google/protobuf/BinaryWriter$SafeHeapWriter.class...
processing com/google/protobuf/BinaryWriter$UnsafeDirectWriter.class...
processing com/google/protobuf/BinaryWriter$UnsafeHeapWriter.class...
processing com/google/protobuf/BooleanArrayList.class...
processing com/google/protobuf/BufferAllocator.class...
processing com/google/protobuf/BufferAllocator$1.class...
processing com/google/protobuf/ByteBufferWriter.class...
processing com/google/protobuf/ByteOutput.class...
processing com/google/protobuf/ByteString.class...
processing com/google/protobuf/ByteString$1.class...
processing com/google/protobuf/ByteString$ArraysByteArrayCopier.class...
processing com/google/protobuf/ByteString$BoundedByteString.class...
processing com/google/protobuf/ByteString$ByteArrayCopier.class...
processing com/google/protobuf/ByteString$ByteIterator.class...
processing com/google/protobuf/ByteString$CodedBuilder.class...
processing com/google/protobuf/ByteString$LeafByteString.class...
processing com/google/protobuf/ByteString$LiteralByteString.class...
processing com/google/protobuf/ByteString$Output.class...
processing com/google/protobuf/ByteString$SystemByteArrayCopier.class...
processing com/google/protobuf/CodedInputStream.class...
processing com/google/protobuf/CodedInputStream$1.class...
processing com/google/protobuf/CodedInputStream$ArrayDecoder.class...
processing com/google/protobuf/CodedInputStream$StreamDecoder.class...
processing com/google/protobuf/CodedInputStream$StreamDecoder$RefillCallback.class...
processing com/google/protobuf/CodedInputStream$StreamDecoder$SkippedDataSink.class...
processing com/google/protobuf/CodedInputStream$UnsafeDirectNioDecoder.class...
processing com/google/protobuf/CodedInputStreamReader.class...
processing com/google/protobuf/CodedInputStreamReader$1.class...
processing com/google/protobuf/CodedOutputStream.class...
processing com/google/protobuf/CodedOutputStream$1.class...
processing com/google<message truncated>

The issue is resolved by recreating the application. Earlier I had the cardboard sdk and I added GVR sdk. Now in new project I only have GVR sdk and it worked for me.