Using JaCoCo agent to scan Spring Boot application returns an error

[Alchnemesis]

• JaCoCo version: 0.8.7
• Tool integration: Maven
• Complete executable reproducer: https://github.com/spring-projects/spring-petclinic
• Steps: Run the agent along side spring petclinic application. Add .jar file to the list and use agent analyzer API to analyze files.

Actual behaviour

java.io.IOException: Error while analyzing /runtime/spring-petclinic-2.4.5.jar@BOOT-INF/lib/log4j-api-2.13.3.jar@org/apache/logging/log4j/util/ProcessIdUtil.class.
at org.jacoco.core.analysis.Analyzer.analyzerError(Analyzer.java:162)
at org.jacoco.core.analysis.Analyzer.analyzeClass(Analyzer.java:134)
at org.jacoco.core.analysis.Analyzer.analyzeClass(Analyzer.java:157)
at org.jacoco.core.analysis.Analyzer.analyzeAll(Analyzer.java:193)
at org.jacoco.core.analysis.Analyzer.analyzeZip(Analyzer.java:265)
at org.jacoco.core.analysis.Analyzer.analyzeAll(Analyzer.java:196)
at org.jacoco.core.analysis.Analyzer.analyzeZip(Analyzer.java:265)
at org.jacoco.core.analysis.Analyzer.analyzeAll(Analyzer.java:196)
at org.jacoco.core.analysis.Analyzer.analyzeAll(Analyzer.java:226)
at org.jacoco.core.analysis.Analyzer.analyzeAll(Analyzer.java:221)
at com.test.coverage.ReportGenerator.analyzeJarDirectory(ReportGenerator.java:117)
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 org.restexpress.route.Route.invoke(Route.java:281)
at org.restexpress.route.Action.invoke(Action.java:65)
at org.restexpress.pipeline.DefaultRequestHandler.processRequest(DefaultRequestHandler.java:156)
at org.restexpress.pipeline.DefaultRequestHandler.channelRead0(DefaultRequestHandler.java:131)
at org.restexpress.pipeline.DefaultRequestHandler.channelRead0(DefaultRequestHandler.java:51)
at io.netty.channel.SimpleChannelInboundHandler.channelRead(SimpleChannelInboundHandler.java:105)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:307)
at io.netty.channel.AbstractChannelHandlerContext.access$600(AbstractChannelHandlerContext.java:32)
at io.netty.channel.AbstractChannelHandlerContext$7.run(AbstractChannelHandlerContext.java:298)
at io.netty.util.concurrent.DefaultEventExecutor.run(DefaultEventExecutor.java:36)
at io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:112)
at io.netty.util.concurrent.DefaultThreadFactory$DefaultRunnableDecorator.run(DefaultThreadFactory.java:137)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.IllegalStateException: Can't add different class with same name: org/apache/logging/log4j/util/ProcessIdUtil
at org.jacoco.core.analysis.CoverageBuilder.visitCoverage(CoverageBuilder.java:106)
at org.jacoco.core.analysis.Analyzer$1.visitEnd(Analyzer.java:99)
at org.objectweb.asm.ClassVisitor.visitEnd(ClassVisitor.java:326)
at org.jacoco.core.internal.flow.ClassProbesAdapter.visitEnd(ClassProbesAdapter.java:100)
at org.objectweb.asm.ClassReader.accept(ClassReader.java:692)
at org.objectweb.asm.ClassReader.accept(ClassReader.java:400)
at org.jacoco.core.analysis.Analyzer.analyzeClass(Analyzer.java:116)
at org.jacoco.core.analysis.Analyzer.analyzeClass(Analyzer.java:132)
... 29 more

[Godin]

Please read FAQ - https://www.jacoco.org/jacoco/trunk/doc/faq.html :

Why do I get the error "Can't add different class with same name"?

For coverage report generation all classes within a group must have unique names. You get this error during report generation if JaCoCo is supplied with multiple different class files with the same name. To fix this remove those duplicate classes or create separate reports or report groups for each version.