native-image fails to compile fat-jar of scala-2.12.6 project

[smabie]

I run with:
$ native-image -H:+ReportExceptionStackTraces -jar metaswarm-assembly-0.1.jar run

And the output is:

Build on Server(pid: 7945, port: 46753)                                                                                              
[run:7945]    classlist:   9,237.07 ms                                                                                               
[run:7945]        (cap):     603.49 ms                                                                                               
[run:7945]        setup:     924.41 ms                                                                                               
[run:7945]     analysis:   2,636.08 ms                                                                                               
Error: Error encountered while parsing metaswarm.Main$.<init>()                                                                      
Parsing context:                                                                                                                     
        parsing metaswarm.Main$.<clinit>(Main.scala)                                                                                 
                                                                                                                                     
com.oracle.graal.pointsto.util.AnalysisError$ParsingError: Error encountered while parsing metaswarm.Main$.<init>()                  
Parsing context:                                                                                                                     
        parsing metaswarm.Main$.<clinit>(Main.scala)                                                                                 
                                                                                                                                     
        at com.oracle.graal.pointsto.util.AnalysisError.parsingError(AnalysisError.java:138)                                         
        at com.oracle.graal.pointsto.flow.MethodTypeFlow.doParse(MethodTypeFlow.java:323)                                            
        at com.oracle.graal.pointsto.flow.MethodTypeFlow.ensureParsed(MethodTypeFlow.java:300)                                       
        at com.oracle.graal.pointsto.flow.MethodTypeFlow.addContext(MethodTypeFlow.java:107)                                         
        at com.oracle.graal.pointsto.flow.SpecialInvokeTypeFlow.onObservedUpdate(InvokeTypeFlow.java:421)                            
        at com.oracle.graal.pointsto.flow.TypeFlow.notifyObservers(TypeFlow.java:343)                                                
        at com.oracle.graal.pointsto.flow.TypeFlow.update(TypeFlow.java:385)                                                         
        at com.oracle.graal.pointsto.flow.SourceTypeFlowBase.update(SourceTypeFlowBase.java:121)                                     
        at com.oracle.graal.pointsto.BigBang$2.run(BigBang.java:510)                                                                 
        at com.oracle.graal.pointsto.util.CompletionExecutor.lambda$execute$0(CompletionExecutor.java:171)                           
        at java.util.concurrent.ForkJoinTask$RunnableExecuteAction.exec(ForkJoinTask.java:1402)                                      
        at java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:289)                                                           
        at java.util.concurrent.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1056)
        at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1692)
        at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:157)
Caused by: org.graalvm.compiler.java.BytecodeParser$BytecodeParserError: java.lang.IncompatibleClassChangeError: metaswarm.Main and $
etaswarm.Main$delayedInit$body disagree on InnerClasses attribute
        at parsing metaswarm.Main$.<init>(Main.scala:24)
        at org.graalvm.compiler.java.BytecodeParser.throwParserError(BytecodeParser.java:2470)
        at com.oracle.svm.hosted.phases.SharedGraphBuilderPhase$SharedBytecodeParser.throwParserError(SharedGraphBuilderPhase.java:9$
)
        at org.graalvm.compiler.java.BytecodeParser.iterateBytecodesForBlock(BytecodeParser.java:3272)
        at org.graalvm.compiler.java.BytecodeParser.processBlock(BytecodeParser.java:3074)
        at org.graalvm.compiler.java.BytecodeParser.build(BytecodeParser.java:976)
        at org.graalvm.compiler.java.BytecodeParser.buildRootMethod(BytecodeParser.java:870)
        at org.graalvm.compiler.java.GraphBuilderPhase$Instance.run(GraphBuilderPhase.java:84)
        at org.graalvm.compiler.phases.Phase.run(Phase.java:49)
        at org.graalvm.compiler.phases.BasePhase.apply(BasePhase.java:197)
        at org.graalvm.compiler.phases.Phase.apply(Phase.java:42)
        at org.graalvm.compiler.phases.Phase.apply(Phase.java:38)
        at com.oracle.graal.pointsto.flow.MethodTypeFlowBuilder.parse(MethodTypeFlowBuilder.java:221)
        at com.oracle.graal.pointsto.flow.MethodTypeFlowBuilder.apply(MethodTypeFlowBuilder.java:340)
        at com.oracle.graal.pointsto.flow.MethodTypeFlow.doParse(MethodTypeFlow.java:310)
        ... 13 more
Caused by: java.lang.IncompatibleClassChangeError: metaswarm.Main and metaswarm.Main$delayedInit$body disagree on InnerClasses attrib
ute
        at java.lang.Class.getDeclaringClass0(Native Method)
        at java.lang.Class.getDeclaringClass(Class.java:1235)
        at java.lang.Class.getEnclosingClass(Class.java:1277)
        at jdk.vm.ci.hotspot.HotSpotJDKReflection.getEnclosingClass(HotSpotJDKReflection.java:106)
        at jdk.vm.ci.hotspot.HotSpotResolvedObjectTypeImpl.getEnclosingType(HotSpotResolvedObjectTypeImpl.java:932)
        at jdk.vm.ci.hotspot.HotSpotResolvedObjectTypeImpl.getEnclosingType(HotSpotResolvedObjectTypeImpl.java:60)
        at com.oracle.graal.pointsto.meta.AnalysisUniverse.createType(AnalysisUniverse.java:294)
        at com.oracle.graal.pointsto.meta.AnalysisUniverse.lookupAllowUnresolved(AnalysisUniverse.java:203)
        at com.oracle.graal.pointsto.infrastructure.WrappedConstantPool.lookupType(WrappedConstantPool.java:155)
        at org.graalvm.compiler.java.BytecodeParser.lookupType(BytecodeParser.java:4080)
        at org.graalvm.compiler.java.BytecodeParser.genNewInstance(BytecodeParser.java:4330)
        at org.graalvm.compiler.java.BytecodeParser.processBytecode(BytecodeParser.java:5128)
        at org.graalvm.compiler.java.BytecodeParser.iterateBytecodesForBlock(BytecodeParser.java:3267)
        ... 24 more
Error: Image build request failed with exit status 1

The Main object is defined as:

object Main extends App {
  val conf = ConfigFactory.load(ConfigFactory.parseFile(File("/home/sturm/akbt/application.conf").toJava))

  implicit val system: ActorSystem = ActorSystem("tracker", conf)
  val path = "/home/sturm/misc/test.mkv.torrent"

  val supervisor = system.actorOf(Props(new ListenerSupervisor()), "listener-supervisor")
  supervisor ! ListenerSupervisor.Start

  implicit val timeout = Timeout(5 seconds)
  for {
    (trackerListener: ActorRef, peerListener: ActorRef) <- supervisor ? ListenerSupervisor.GetListenerRefs
  } yield {
    val torrent = system.actorOf(Props(new Torrent(torrentPath = path, filePath = "/home/sturm/tmp/", trackerListener,
      peerListener)),
      "torrent")
    torrent ! Torrent.Start
  }

  while(true) {
    Thread.sleep(500)
  }
}

[cstancu]

This is a Scala compiler bug: scala/bug#10487 that should have been fixed by scala/scala#6788. You may need to use a newer Scala version. A similar issue was reported in #384 which also proposed the use of

object Main {
  def main(args: Array[String]): Unit = {
  }
}

instead of

object Main extends App {
 }

as an workaround.