Flyway / Picocli native build fail with ClassNotFoundException org.jboss.vfs.VirtualFileFilter

[fano-mipih]

Describe the bug

I try to build a native executable for a Quarkus project using Picocli and Flyway quarkus extensions.
The native build fail with the following exceptions :

Fatal error: java.lang.NoClassDefFoundError: software/amazon/awssdk/awscore/exception/AwsServiceException
        at java.base/java.lang.Class.getDeclaredFields0(Native Method)
        at java.base/java.lang.Class.privateGetDeclaredFields(Class.java:2930)
        at java.base/java.lang.Class.getDeclaredFields(Class.java:2249)
        at org.graalvm.nativeimage.builder/com.oracle.svm.hosted.reflect.ReflectionDataBuilder.lambda$registerAllDeclaredFieldsQuery$0(ReflectionDataBuilder.java:555)
        at org.graalvm.nativeimage.builder/com.oracle.svm.hosted.reflect.ReflectionDataBuilder.lambda$runConditionalInAnalysisTask$1(ReflectionDataBuilder.java:184)
        at org.graalvm.nativeimage.pointsto/com.oracle.graal.pointsto.util.CompletionExecutor.executeCommand(CompletionExecutor.java:166)
        at org.graalvm.nativeimage.pointsto/com.oracle.graal.pointsto.util.CompletionExecutor.lambda$executeService$0(CompletionExecutor.java:152)
        at java.base/java.util.concurrent.ForkJoinTask$RunnableExecuteAction.compute(ForkJoinTask.java:1735)
        at java.base/java.util.concurrent.ForkJoinTask$RunnableExecuteAction.compute(ForkJoinTask.java:1726)
        at java.base/java.util.concurrent.ForkJoinTask$InterruptibleTask.exec(ForkJoinTask.java:1650)
        at java.base/java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:507)
        at java.base/java.util.concurrent.ForkJoinPool.externalHelpQuiesce(ForkJoinPool.java:2458)
        at java.base/java.util.concurrent.ForkJoinPool.helpQuiescePool(ForkJoinPool.java:2492)
        at java.base/java.util.concurrent.ForkJoinPool.awaitQuiescence(ForkJoinPool.java:3740)
        at org.graalvm.nativeimage.pointsto/com.oracle.graal.pointsto.util.CompletionExecutor.complete(CompletionExecutor.java:208)
        at org.graalvm.nativeimage.pointsto/com.oracle.graal.pointsto.PointsToAnalysis.doTypeflow(PointsToAnalysis.java:640)
        at org.graalvm.nativeimage.pointsto/com.oracle.graal.pointsto.PointsToAnalysis.finish(PointsToAnalysis.java:627)
        at org.graalvm.nativeimage.pointsto/com.oracle.graal.pointsto.AbstractAnalysisEngine.runAnalysis(AbstractAnalysisEngine.java:160)
        at org.graalvm.nativeimage.builder/com.oracle.svm.hosted.NativeImageGenerator.runPointsToAnalysis(NativeImageGenerator.java:821)
        at org.graalvm.nativeimage.builder/com.oracle.svm.hosted.NativeImageGenerator.doRun(NativeImageGenerator.java:567)
        at org.graalvm.nativeimage.builder/com.oracle.svm.hosted.NativeImageGenerator.run(NativeImageGenerator.java:533)
        at org.graalvm.nativeimage.builder/com.oracle.svm.hosted.NativeImageGeneratorRunner.buildImage(NativeImageGeneratorRunner.java:545)
        at org.graalvm.nativeimage.builder/com.oracle.svm.hosted.NativeImageGeneratorRunner.build(NativeImageGeneratorRunner.java:732)
        at org.graalvm.nativeimage.builder/com.oracle.svm.hosted.NativeImageGeneratorRunner.start(NativeImageGeneratorRunner.java:151)
        at org.graalvm.nativeimage.builder/com.oracle.svm.hosted.NativeImageGeneratorRunner.main(NativeImageGeneratorRunner.java:99)
Caused by: java.lang.ClassNotFoundException: software.amazon.awssdk.awscore.exception.AwsServiceException
        at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:580)
        at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:490)
        at org.graalvm.nativeimage.builder/com.oracle.svm.hosted.NativeImageClassLoader.loadClass(NativeImageClassLoader.java:682)
        at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:490)
        ... 25 more
Fatal error: java.lang.NoClassDefFoundError: org/jboss/vfs/VirtualFileFilter
        at java.base/java.lang.Class.getDeclaredMethods0(Native Method)
        at java.base/java.lang.Class.privateGetDeclaredMethods(Class.java:3035)
        at java.base/java.lang.Class.getDeclaredMethods(Class.java:2331)
        at org.graalvm.nativeimage.builder/com.oracle.svm.hosted.reflect.ReflectionDataBuilder.lambda$registerAllDeclaredMethodsQuery$0(ReflectionDataBuilder.java:379)
        at org.graalvm.nativeimage.builder/com.oracle.svm.hosted.reflect.ReflectionDataBuilder.lambda$runConditionalInAnalysisTask$1(ReflectionDataBuilder.java:184)
        at org.graalvm.nativeimage.pointsto/com.oracle.graal.pointsto.util.CompletionExecutor.executeCommand(CompletionExecutor.java:166)
        at org.graalvm.nativeimage.pointsto/com.oracle.graal.pointsto.util.CompletionExecutor.lambda$executeService$0(CompletionExecutor.java:152)
        at java.base/java.util.concurrent.ForkJoinTask$RunnableExecuteAction.compute(ForkJoinTask.java:1735)
        at java.base/java.util.concurrent.ForkJoinTask$RunnableExecuteAction.compute(ForkJoinTask.java:1726)
        at java.base/java.util.concurrent.ForkJoinTask$InterruptibleTask.exec(ForkJoinTask.java:1650)
        at java.base/java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:507)
        at java.base/java.util.concurrent.ForkJoinPool$WorkQueue.topLevelExec(ForkJoinPool.java:1394)
        at java.base/java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1970)
        at java.base/java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:187)
Caused by: java.lang.ClassNotFoundException: org.jboss.vfs.VirtualFileFilter
        at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:580)
        at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:490)
        at org.graalvm.nativeimage.builder/com.oracle.svm.hosted.NativeImageClassLoader.loadClass(NativeImageClassLoader.java:682)
        at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:490)
        ... 14 more

My project doesn't make use of Amazon S3 or Jboss VFS but native build try to load these classes.

I tried to add quarkus.native.additional-build-args=--initialize-at-run-time=org.flywaydb.core.internal.scanner.classpath.jboss.JBossVFSv3ClassPathLocationScanner\\,org.flywaydb.core.internal.resource.s3.AwsS3Resource option but with no success.

How could i tell the native builder to ignore these optional dependencies ?

Expected behavior

Native build must ignore these classes because VFS and S3 are not used in this project.

Actual behavior

Native build try to load VFS and S3 related classes.

How to Reproduce?

I've uploaded a sample projet to Github :
https://github.com/fano-mipih/dumpbo-test

Steps to reproduce :

1. Clone project : https://github.com/fano-mipih/dumpbo-test
2. Run a native build : mvn clean package -Pnative

Output of uname -a or ver

Linux vdi-407 4.4.0-19041-Microsoft #1237-Microsoft Sat Sep 11 14:32:00 PST 2021 x86_64 x86_64 x86_64 GNU/Linux

Output of java -version

openjdk version "24.0.1" 2025-04-15 OpenJDK Runtime Environment GraalVM CE 24.0.1+9.1 (build 24.0.1+9-jvmci-b01) OpenJDK 64-Bit Server VM GraalVM CE 24.0.1+9.1 (build 24.0.1+9-jvmci-b01, mixed mode, sharing)

Mandrel or GraalVM version (if different from Java)

No response

Quarkus version or git rev

3.22.3

Build tool (ie. output of mvnw --version or gradlew --version)

Apache Maven 3.9.9

Additional information

No response

[quarkus-bot]

/cc @Karm (native-image), @cristhiank (flyway), @ebullient (picocli), @galderz (native-image), @gastaldi (flyway), @geoand (flyway), @gsmet (flyway), @zakkak (native-image)

[geoand]

cc @alesj

[geoand]

@zakkak I don't see why this would be happening as we have ClassPathScannerSubstitutions

[zakkak]

@geoand I see org.jboss.vfs.VirtualFileFilter being reached through https://github.com/flyway/flyway/blame/main/flyway-core/src/main/java/org/flywaydb/core/internal/scanner/classpath/jboss/JBossVFSv3ClassPathLocationScanner.java which is being registered for reflection:

  {
    "allDeclaredClasses": true,
    "allDeclaredConstructors": true,
    "name": "org.flywaydb.core.internal.scanner.classpath.jboss.JBossVFSv3ClassPathLocationScanner",
    "allDeclaredMethods": true,
    "allDeclaredFields": true
  },

Passing -Dquarkus.native.include-reasons-in-config-files to the build I see that the "reason" it is being registered is:

      "PicocliNativeImageProcessor > fr.mipih.dumpbo.SubCommand > org.flywaydb.core.Flyway > org.flywaydb.core.FlywayExecutor > org.flywaydb.core.internal.scanner.LocationScannerCache > java.util.Map > org.flywaydb.core.internal.scanner.classpath.ClassPathLocationScanner"

Similarly for org.flywaydb.core.internal.resource.s3.AwsS3Resource which leads to software.amazon.awssdk.awscore.exception.AwsServiceException:

      "PicocliNativeImageProcessor > fr.mipih.dumpbo.SubCommand > org.flywaydb.core.Flyway > org.flywaydb.core.api.configuration.ClassicConfiguration > org.flywaydb.core.api.ResourceProvider > java.util.HashMap > org.flywaydb.core.api.resource.LoadableResource"

Which indicates that the class is being registered for reflection by the picocli extension through the class hierarchy of fr.mipih.dumpbo.SubCommand. And more specifically by registering org.flywaydb.core.internal.scanner.classpath.ClassPathLocationScanner implementers in

quarkus/core/deployment/src/main/java/io/quarkus/deployment/steps/ReflectiveHierarchyStep.java

Lines 162 to 168 in 5cd8a5e

	for (ClassInfo subclass : combinedIndexBuildItem.getIndex().getAllKnownImplementors(type.name())) {
	addClassTypeHierarchy(combinedIndexBuildItem, capabilities, reflectiveHierarchyBuildItem, newSource,
	subclass.name(),
	subclass.name(),
	processedReflectiveHierarchies,
	unindexedClasses, finalFieldsWritable, reflectiveClass, visits);
	}

It looks like this could be fixed by:

1. augmenting

   quarkus/core/deployment/src/main/java/io/quarkus/deployment/builditem/nativeimage/ReflectiveHierarchyBuildItem.java

   Line 360 in 71538fb

   private static final List<String> DEFAULT_IGNORED_PACKAGES = Arrays.asList("java.", "io.reactivex.",

   but I can't tell if that's the right thing to do.
2. Removing JBossVFSv3ClassPathLocationScanner (and AwsS3Resource?) from the classpath when not needed.

[geoand]

Thanks a lot @zakkak!

[geoand]

I started #48179 but it seems like I am getting:

Error: Discovered unresolved type during parsing: org.osgi.framework.FrameworkUtil. This error is reported at image build time because class org.flywaydb.core.internal.scanner.classpath.OsgiClassPathLocationScanner is registered for linking at image build time by command line and command line.
Error encountered while parsing org.flywaydb.core.internal.scanner.classpath.OsgiClassPathLocationScanner.findResourceNames(OsgiClassPathLocationScanner.java:50) 
Parsing context:
   at root method.(Unknown Source)

Detailed message:

com.oracle.svm.core.util.UserError$UserException: Discovered unresolved type during parsing: org.osgi.framework.FrameworkUtil. This error is reported at image build time because class org.flywaydb.core.internal.scanner.classpath.OsgiClassPathLocationScanner is registered for linking at image build time by command line and command line.
Error encountered while parsing org.flywaydb.core.internal.scanner.classpath.OsgiClassPathLocationScanner.findResourceNames(OsgiClassPathLocationScanner.java:50) 
Parsing context:
   at root method.(Unknown Source)

Detailed message:

	at org.graalvm.nativeimage.builder/com.oracle.svm.core.util.UserError.abort(UserError.java:85)
	at org.graalvm.nativeimage.builder/com.oracle.svm.hosted.FallbackFeature.reportAsFallback(FallbackFeature.java:248)
	at org.graalvm.nativeimage.builder/com.oracle.svm.hosted.NativeImageGenerator.runPointsToAnalysis(NativeImageGenerator.java:814)
	at org.graalvm.nativeimage.builder/com.oracle.svm.hosted.NativeImageGenerator.doRun(NativeImageGenerator.java:592)
	at org.graalvm.nativeimage.builder/com.oracle.svm.hosted.NativeImageGenerator.run(NativeImageGenerator.java:550)
	at org.graalvm.nativeimage.builder/com.oracle.svm.hosted.NativeImageGeneratorRunner.buildImage(NativeImageGeneratorRunner.java:539)
	at org.graalvm.nativeimage.builder/com.oracle.svm.hosted.NativeImageGeneratorRunner.build(NativeImageGeneratorRunner.java:721)
	at org.graalvm.nativeimage.builder/com.oracle.svm.hosted.NativeImageGeneratorRunner.start(NativeImageGeneratorRunner.java:143)
	at org.graalvm.nativeimage.builder/com.oracle.svm.hosted.NativeImageGeneratorRunner.main(NativeImageGeneratorRunner.java:98)
Caused by: com.oracle.graal.pointsto.constraints.UnsupportedFeatureException: Discovered unresolved type during parsing: org.osgi.framework.FrameworkUtil. This error is reported at image build time because class org.flywaydb.core.internal.scanner.classpath.OsgiClassPathLocationScanner is registered for linking at image build time by command line and command line.
Error encountered while parsing org.flywaydb.core.internal.scanner.classpath.OsgiClassPathLocationScanner.findResourceNames(OsgiClassPathLocationScanner.java:50) 
Parsing context:
   at root method.(Unknown Source)

Detailed message:

	at org.graalvm.nativeimage.pointsto/com.oracle.graal.pointsto.constraints.UnsupportedFeatures.report(UnsupportedFeatures.java:126)
	at org.graalvm.nativeimage.builder/com.oracle.svm.hosted.NativeImageGenerator.runPointsToAnalysis(NativeImageGenerator.java:809)
	... 6 more
Caused by: com.oracle.graal.pointsto.constraints.UnresolvedElementException: Discovered unresolved type during parsing: org.osgi.framework.FrameworkUtil. This error is reported at image build time because class org.flywaydb.core.internal.scanner.classpath.OsgiClassPathLocationScanner is registered for linking at image build time by command line and command line.
	at org.graalvm.nativeimage.builder/com.oracle.svm.hosted.phases.SharedGraphBuilderPhase$SharedBytecodeParser.reportUnresolvedElement(SharedGraphBuilderPhase.java:550)
	at org.graalvm.nativeimage.builder/com.oracle.svm.hosted.phases.SharedGraphBuilderPhase$SharedBytecodeParser.reportUnresolvedElement(SharedGraphBuilderPhase.java:544)
	at org.graalvm.nativeimage.builder/com.oracle.svm.hosted.phases.SharedGraphBuilderPhase$SharedBytecodeParser.handleUnresolvedType(SharedGraphBuilderPhase.java:436)
	at org.graalvm.nativeimage.builder/com.oracle.svm.hosted.phases.SharedGraphBuilderPhase$SharedBytecodeParser.handleUnresolvedMethod(SharedGraphBuilderPhase.java:464)
	at org.graalvm.nativeimage.builder/com.oracle.svm.hosted.phases.SharedGraphBuilderPhase$SharedBytecodeParser.handleUnresolvedInvoke(SharedGraphBuilderPhase.java:368)
	at jdk.internal.vm.compiler/org.graalvm.compiler.java.BytecodeParser.genInvokeStatic(BytecodeParser.java:1698)
	at jdk.internal.vm.compiler/org.graalvm.compiler.java.BytecodeParser.genInvokeStatic(BytecodeParser.java:1677)
	at jdk.internal.vm.compiler/org.graalvm.compiler.java.BytecodeParser.processBytecode(BytecodeParser.java:5441)
	at jdk.internal.vm.compiler/org.graalvm.compiler.java.BytecodeParser.iterateBytecodesForBlock(BytecodeParser.java:3431)
	at org.graalvm.nativeimage.builder/com.oracle.svm.hosted.phases.SharedGraphBuilderPhase$SharedBytecodeParser.iterateBytecodesForBlock(SharedGraphBuilderPhase.java:743)
	at jdk.internal.vm.compiler/org.graalvm.compiler.java.BytecodeParser.handleBytecodeBlock(BytecodeParser.java:3391)
	at jdk.internal.vm.compiler/org.graalvm.compiler.java.BytecodeParser.processBlock(BytecodeParser.java:3233)
	at jdk.internal.vm.compiler/org.graalvm.compiler.java.BytecodeParser.build(BytecodeParser.java:1137)
	at org.graalvm.nativeimage.builder/com.oracle.svm.hosted.phases.SharedGraphBuilderPhase$SharedBytecodeParser.build(SharedGraphBuilderPhase.java:162)
	at jdk.internal.vm.compiler/org.graalvm.compiler.java.BytecodeParser.buildRootMethod(BytecodeParser.java:1029)
	at jdk.internal.vm.compiler/org.graalvm.compiler.java.GraphBuilderPhase$Instance.run(GraphBuilderPhase.java:101)
	at org.graalvm.nativeimage.builder/com.oracle.svm.hosted.phases.SharedGraphBuilderPhase.run(SharedGraphBuilderPhase.java:116)
	at jdk.internal.vm.compiler/org.graalvm.compiler.phases.Phase.run(Phase.java:49)
	at jdk.internal.vm.compiler/org.graalvm.compiler.phases.BasePhase.apply(BasePhase.java:434)
	at jdk.internal.vm.compiler/org.graalvm.compiler.phases.Phase.apply(Phase.java:42)
	at jdk.internal.vm.compiler/org.graalvm.compiler.phases.Phase.apply(Phase.java:38)
	at org.graalvm.nativeimage.pointsto/com.oracle.graal.pointsto.flow.AnalysisParsedGraph.parseBytecode(AnalysisParsedGraph.java:146)
	at org.graalvm.nativeimage.pointsto/com.oracle.graal.pointsto.meta.AnalysisMethod.parseGraph(AnalysisMethod.java:895)
	at org.graalvm.nativeimage.pointsto/com.oracle.graal.pointsto.meta.AnalysisMethod.ensureGraphParsedHelper(AnalysisMethod.java:860)
	at org.graalvm.nativeimage.pointsto/com.oracle.graal.pointsto.meta.AnalysisMethod.ensureGraphParsed(AnalysisMethod.java:843)
	at org.graalvm.nativeimage.pointsto/com.oracle.graal.pointsto.flow.MethodTypeFlowBuilder.parse(MethodTypeFlowBuilder.java:186)
	at org.graalvm.nativeimage.pointsto/com.oracle.graal.pointsto.flow.MethodTypeFlowBuilder.apply(MethodTypeFlowBuilder.java:621)
	at org.graalvm.nativeimage.pointsto/com.oracle.graal.pointsto.flow.MethodTypeFlow.createFlowsGraph(MethodTypeFlow.java:167)
	at org.graalvm.nativeimage.pointsto/com.oracle.graal.pointsto.flow.MethodTypeFlow.ensureFlowsGraphCreated(MethodTypeFlow.java:153)
	at org.graalvm.nativeimage.pointsto/com.oracle.graal.pointsto.flow.MethodTypeFlow.getOrCreateMethodFlowsGraphInfo(MethodTypeFlow.java:111)
	at org.graalvm.nativeimage.pointsto/com.oracle.graal.pointsto.typestate.DefaultVirtualInvokeTypeFlow.onObservedUpdate(DefaultVirtualInvokeTypeFlow.java:114)
	at org.graalvm.nativeimage.pointsto/com.oracle.graal.pointsto.flow.TypeFlow.update(TypeFlow.java:620)
	at org.graalvm.nativeimage.pointsto/com.oracle.graal.pointsto.PointsToAnalysis$1.run(PointsToAnalysis.java:491)
	at org.graalvm.nativeimage.pointsto/com.oracle.graal.pointsto.util.CompletionExecutor.executeCommand(CompletionExecutor.java:187)
	at org.graalvm.nativeimage.pointsto/com.oracle.graal.pointsto.util.CompletionExecutor.lambda$executeService$0(CompletionExecutor.java:171)
	at java.base/java.util.concurrent.ForkJoinTask$RunnableExecuteAction.exec(ForkJoinTask.java:1423)
	at java.base/java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:387)
	at java.base/java.util.concurrent.ForkJoinPool$WorkQueue.topLevelExec(ForkJoinPool.java:1312)
	at java.base/java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1843)
	at java.base/java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1808)
	at java.base/java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:188)

Any clues on why this is happening?

[zakkak]

Any clues on why this is happening?

Oh this is happening with Mandrel 23.1 for JDK 21, right? I only explored Mandrel 24.2 for JDK 24. I 'll have a look.

BTW in my experiments I apply the following to the reproducer:

diff --git a/src/main/resources/application.properties b/src/main/resources/application.properties
index 7f25435..a9f7e43 100755
--- a/src/main/resources/application.properties
+++ b/src/main/resources/application.properties
@@ -1,2 +1 @@
 quarkus.picocli.top-command=fr.mipih.dumpbo.TopCommand
-quarkus.native.additional-build-args=--initialize-at-run-time=org.flywaydb.core.internal.scanner.classpath.jboss.JBossVFSv3ClassPathLocationScanner\\,org.flywaydb.core.internal.resource.s3.AwsS3Resource
\ No newline at end of file

[geoand]

Any clues on why this is happening?

Oh this is happening with Mandrel 23.1 for JDK 21, right? I only explored Mandrel 24.2 for JDK 24. I 'll have a look.

Right