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Spring: Error creating bean with name 'entityManagerFactory' caused by: java.lang.AbstractMethodError: null

I am developing a simple application in Spring and I just encountered this common problem, but for which I can find no solution, since the ones mentioned in other posts aren't working for some reason.
The error triggers when I run the application for the first time, and this is what it says:
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityManagerFactory' defined in class path resource [org/springframework/boot/autoconfigure/orm/jpa/HibernateJpaConfiguration.class]: Invocation of init method failed; nested exception is java.lang.AbstractMethodError
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1745) ~[spring-beans-5.1.4.RELEASE.jar:5.1.4.RELEASE]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:576) ~[spring-beans-5.1.4.RELEASE.jar:5.1.4.RELEASE]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:498) ~[spring-beans-5.1.4.RELEASE.jar:5.1.4.RELEASE]
at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:320) ~[spring-beans-5.1.4.RELEASE.jar:5.1.4.RELEASE]
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222) ~[spring-beans-5.1.4.RELEASE.jar:5.1.4.RELEASE]
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:318) ~[spring-beans-5.1.4.RELEASE.jar:5.1.4.RELEASE]
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:199) ~[spring-beans-5.1.4.RELEASE.jar:5.1.4.RELEASE]
at org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:1083) ~[spring-context-5.1.4.RELEASE.jar:5.1.4.RELEASE]
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:853) ~[spring-context-5.1.4.RELEASE.jar:5.1.4.RELEASE]
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:546) ~[spring-context-5.1.4.RELEASE.jar:5.1.4.RELEASE]
at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.refresh(ServletWebServerApplicationContext.java:142) ~[spring-boot-2.1.2.RELEASE.jar:2.1.2.RELEASE]
at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:775) [spring-boot-2.1.2.RELEASE.jar:2.1.2.RELEASE]
at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:397) [spring-boot-2.1.2.RELEASE.jar:2.1.2.RELEASE]
at org.springframework.boot.SpringApplication.run(SpringApplication.java:316) [spring-boot-2.1.2.RELEASE.jar:2.1.2.RELEASE]
at org.springframework.boot.SpringApplication.run(SpringApplication.java:1260) [spring-boot-2.1.2.RELEASE.jar:2.1.2.RELEASE]
at org.springframework.boot.SpringApplication.run(SpringApplication.java:1248) [spring-boot-2.1.2.RELEASE.jar:2.1.2.RELEASE]
at com.project.booklibrary.library.LibraryApplication.main(LibraryApplication.java:22) [classes/:na]
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.8.0_151]
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[na:1.8.0_151]
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.8.0_151]
at java.lang.reflect.Method.invoke(Method.java:498) ~[na:1.8.0_151]
at org.springframework.boot.devtools.restart.RestartLauncher.run(RestartLauncher.java:49) [spring-boot-devtools-2.1.2.RELEASE.jar:2.1.2.RELEASE]
Caused by: java.lang.AbstractMethodError: null
at org.hibernate.internal.SessionFactoryImpl.<init>(SessionFactoryImpl.java:276) ~[hibernate-core-5.3.7.Final.jar:5.3.7.Final]
at org.hibernate.boot.internal.SessionFactoryBuilderImpl.build(SessionFactoryBuilderImpl.java:467) ~[hibernate-core-5.3.7.Final.jar:5.3.7.Final]
at org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl.build(EntityManagerFactoryBuilderImpl.java:939) ~[hibernate-core-5.3.7.Final.jar:5.3.7.Final]
at org.springframework.orm.jpa.vendor.SpringHibernateJpaPersistenceProvider.createContainerEntityManagerFactory(SpringHibernateJpaPersistenceProvider.java:57) ~[spring-orm-5.1.4.RELEASE.jar:5.1.4.RELEASE]
at org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean.createNativeEntityManagerFactory(LocalContainerEntityManagerFactoryBean.java:365) ~[spring-orm-5.1.4.RELEASE.jar:5.1.4.RELEASE]
at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.buildNativeEntityManagerFactory(AbstractEntityManagerFactoryBean.java:390) ~[spring-orm-5.1.4.RELEASE.jar:5.1.4.RELEASE]
at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.afterPropertiesSet(AbstractEntityManagerFactoryBean.java:377) ~[spring-orm-5.1.4.RELEASE.jar:5.1.4.RELEASE]
at org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean.afterPropertiesSet(LocalContainerEntityManagerFactoryBean.java:341) ~[spring-orm-5.1.4.RELEASE.jar:5.1.4.RELEASE]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1804) ~[spring-beans-5.1.4.RELEASE.jar:5.1.4.RELEASE]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1741) ~[spring-beans-5.1.4.RELEASE.jar:5.1.4.RELEASE]
... 21 common frames omitted
Here is my pom.xml
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-parent</artifactId>
<version>2.1.2.RELEASE</version>
<relativePath/> <!-- lookup parent from repository -->
</parent>
<groupId>com.project.booklibrary</groupId>
<artifactId>library</artifactId>
<version>1.0.0</version>
<packaging>war</packaging>
<name>library</name>
<description>Library project</description>
<properties>
<java.version>1.8</java.version>
<mysql.version>5.1.31</mysql.version>
<joda-time.version>2.3</joda-time.version>
</properties>
<dependencies>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-aop</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-cache</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-data-jpa</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-integration</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-security</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-thymeleaf</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-validation</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-web</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.retry</groupId>
<artifactId>spring-retry</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.session</groupId>
<artifactId>spring-session-core</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-devtools</artifactId>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-configuration-processor</artifactId>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-tomcat</artifactId>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-test</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.springframework.security</groupId>
<artifactId>spring-security-test</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
<version>2.3.0</version>
</dependency>
<!-- Apache Commons FileUpload -->
<dependency>
<groupId>commons-fileupload</groupId>
<artifactId>commons-fileupload</artifactId>
<version>1.3.1</version>
</dependency>
<!-- Apache Commons IO -->
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.4</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.webjars/jquery -->
<dependency>
<groupId>org.webjars</groupId>
<artifactId>jquery</artifactId>
<version>2.1.4</version>
</dependency>
<!-- MySQL -->
<dependency>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
<version>${mysql.version}</version>
</dependency>
<!-- Joda-Time -->
<dependency>
<groupId>joda-time</groupId>
<artifactId>joda-time</artifactId>
<version>${joda-time.version}</version>
</dependency>
<!-- To map JodaTime with database type -->
<dependency>
<groupId>org.jadira.usertype</groupId>
<artifactId>usertype.core</artifactId>
<version>3.0.0.CR1</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.threeten/threetenbp -->
<dependency>
<groupId>org.threeten</groupId>
<artifactId>threetenbp</artifactId>
<version>1.3.6</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-maven-plugin</artifactId>
</plugin>
</plugins>
</build>
And here is my hibernate configuration
# ===============================
# DATABASE
# ===============================
spring.datasource.driver-class-name=com.mysql.jdbc.Driver
spring.datasource.url=jdbc:mysql://localhost:3306/library
spring.datasource.username=root
spring.datasource.password=
# ===============================
# JPA / HIBERNATE
# ===============================
spring.jpa.show-sql=true
spring.jpa.hibernate.ddl-auto = create
spring.jpa.properties.hibernate.dialect=org.hibernate.dialect.MySQLDialect
What I am trying to do is to develop a spring boot application that uses hibernate to connect to a mysql database provided by xampp, but this error is giving me a hard time.

I found the problem after searching for more answers. Looks like the fact that the following dependency
<dependency>
<groupId>org.jadira.usertype</groupId>
<artifactId>usertype.core</artifactId>
<version>3.0.0.CR1</version>
</dependency>
was included entered in conflict with the hibernate framework. Simply removing this dependency made the project work as it should.

Deploying Spring Boot WAR on WildFly

I have followed the steps mentioned here Create a Deployable War File
Things are working fine when I run (mvn spring-boot:run) and when I package using (mvn clean package)
But the created WAR is never deployed to WildFly 8 and I receive the below exception:
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'halObjectMapper' defined in class path resource [org/springframework/data/rest/webmvc/config/RepositoryRestMvcConfiguration.class]: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [com.fasterxml.jackson.databind.ObjectMapper]: Factory method 'halObjectMapper' threw exception; nested exception is java.lang.NoSuchMethodError: com.fasterxml.jackson.databind.ser.ContainerSerializer: method <init>(Lcom/fasterxml/jackson/databind/JavaType;)V not found
at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:599)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1173)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1067)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:513)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
at org.springframework.context.annotation.ConfigurationClassEnhancer$BeanMethodInterceptor.obtainBeanInstanceFromFactory(ConfigurationClassEnhancer.java:389)
at org.springframework.context.annotation.ConfigurationClassEnhancer$BeanMethodInterceptor.intercept(ConfigurationClassEnhancer.java:361)
at org.springframework.data.rest.webmvc.config.RepositoryRestMvcConfiguration$$EnhancerBySpringCGLIB$$ea277463.halObjectMapper(<generated>)
at org.springframework.data.rest.webmvc.config.RepositoryRestMvcConfiguration.halJacksonHttpMessageConverter(RepositoryRestMvcConfiguration.java:501)
at org.springframework.data.rest.webmvc.config.RepositoryRestMvcConfiguration$$EnhancerBySpringCGLIB$$ea277463.CGLIB$halJacksonHttpMessageConverter$22(<generated>)
at org.springframework.data.rest.webmvc.config.RepositoryRestMvcConfiguration$$EnhancerBySpringCGLIB$$ea277463$$FastClassBySpringCGLIB$$12fca279.invoke(<generated>)
at org.springframework.cglib.proxy.MethodProxy.invokeSuper(MethodProxy.java:228)
at org.springframework.context.annotation.ConfigurationClassEnhancer$BeanMethodInterceptor.intercept(ConfigurationClassEnhancer.java:358)
at org.springframework.data.rest.webmvc.config.RepositoryRestMvcConfiguration$$EnhancerBySpringCGLIB$$ea277463.halJacksonHttpMessageConverter(<generated>)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) [rt.jar:1.7.0_79]
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) [rt.jar:1.7.0_79]
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) [rt.jar:1.7.0_79]
at java.lang.reflect.Method.invoke(Method.java:606) [rt.jar:1.7.0_79]
at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:162)
... 91 more
Caused by: org.springframework.beans.BeanInstantiationException: Failed to instantiate [com.fasterxml.jackson.databind.ObjectMapper]: Factory method 'halObjectMapper' threw exception; nested exception is java.lang.NoSuchMethodError: com.fasterxml.jackson.databind.ser.ContainerSerializer: method <init>(Lcom/fasterxml/jackson/databind/JavaType;)V not found
at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:189)
at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:588)
... 113 more
Caused by: java.lang.NoSuchMethodError: com.fasterxml.jackson.databind.ser.ContainerSerializer: method <init>(Lcom/fasterxml/jackson/databind/JavaType;)V not found
at org.springframework.hateoas.hal.Jackson2HalModule$HalResourcesSerializer.<init>(Jackson2HalModule.java:325)
Also this is my pom.xml:
http://maven.apache.org/xsd/maven-4.0.0.xsd">
4.0.0
<groupId>com.companyname.dept.project</groupId>
<artifactId>test-spring-boot-wildfly</artifactId>
<version>0.0.1-SNAPSHOT</version>
<packaging>war</packaging>
<name>test-spring-boot-wildfly</name>
<description>Demo project for Spring Boot</description>
<parent>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-parent</artifactId>
<version>1.5.10.RELEASE</version>
<relativePath/>
</parent>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
<java.version>1.7</java.version>
</properties>
<dependencies>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-test</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-data-jpa</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-data-rest</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-web</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-logging</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-tomcat</artifactId>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
</dependency>
<!-- https://mvnrepository.com/artifact/org.modelmapper/modelmapper -->
<dependency>
<groupId>org.modelmapper</groupId>
<artifactId>modelmapper</artifactId>
<version>0.3.5</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
<version>3.0</version>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>19.0</version>
<type>jar</type>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
<version>4.5.3</version>
<type>jar</type>
</dependency>
<dependency>
<groupId>com.googlecode.json-simple</groupId>
<artifactId>json-simple</artifactId>
<version>1.1.1</version>
<type>jar</type>
</dependency>
<dependency>
<groupId>jaxen</groupId>
<artifactId>jaxen</artifactId>
<version>1.1.6</version>
</dependency>
<dependency>
<groupId>org.kie</groupId>
<artifactId>kie-internal</artifactId>
<version>6.4.0.Final</version>
</dependency>
<!-- missing this dependency raises this error during the build: class file for groovy.lang.Closure not found -->
<dependency>
<groupId>org.codehaus.groovy</groupId>
<artifactId>groovy-all</artifactId>
<version>2.4.7</version>
</dependency>
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-core</artifactId>
<version>1.1.9</version>
</dependency>
<!--
need this dependency fixes logback 1.1.11 exception during deployment
https://github.com/spring-projects/spring-boot/issues/8354
-->
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
<version>1.1.9</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-core</artifactId>
<version>2.9.2</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
<version>2.9.2</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-annotations</artifactId>
<version>2.9.2</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-maven-plugin</artifactId>
</plugin>
</plugins>
</build>
Any clue about what I'm missing?

Wildfly includes it own version of Jackson that leaks into the class space for your application. These Jackson classes are overwriting those that are packaged in your war. You can avoid this pollution by excluding some modules in a WEB-INF/jboss-deployment-structure.xml file in your war. Its contents should be something like the following:
<?xml version='1.0' encoding='UTF-8'?>
<jboss-deployment-structure xmlns="urn:jboss:deployment-structure:1.1">
<deployment>
<exclusions>
<module name="com.fasterxml.jackson.core.jackson-annotations" />
<module name="com.fasterxml.jackson.core.jackson-core" />
<module name="com.fasterxml.jackson.core.jackson-databind" />
<module name="com.fasterxml.jackson.datatype.jackson-datatype-jdk8"/>
<module name="com.fasterxml.jackson.datatype.jackson-datatype-jsr310"/>
<module name="com.fasterxml.jackson.jaxrs.jackson-jaxrs-json-provider" />
<module name="org.jboss.resteasy.resteasy-jackson2-provider" />
</exclusions>
</deployment>
</jboss-deployment-structure>
The above is a slightly modified version of the configuration that's used in Spring Boot's Wildfly deployment test.

Error running Junit Tests in maven

I have a SpringBoot app, where I pass the Junit tests successfully from Eclipse, and the app works perfeclty: the tests and the application itself.
But from maven mvn clean package
I got this error:
Caused by: java.lang.NoClassDefFoundError: javax/xml/bind/JAXBException
at org.hibernate.boot.spi.XmlMappingBinderAccess.<init>(XmlMappingBinderAccess.java:43)
at org.hibernate.boot.MetadataSources.<init>(MetadataSources.java:87)
at org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl.<init>(EntityManagerFactoryBuilderImpl.java:179)
at org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl.<init>(EntityManagerFactoryBuilderImpl.java:149)
at org.springframework.orm.jpa.vendor.SpringHibernateJpaPersistenceProvider.createContainerEntityManagerFactory(SpringHibernateJpaPersistenceProvider.java:54)
at org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean.createNativeEntityManagerFactory(LocalContainerEntityManagerFactoryBean.java:360)
at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.buildNativeEntityManagerFactory(AbstractEntityManagerFactoryBean.java:382)
at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.afterPropertiesSet(AbstractEntityManagerFactoryBean.java:371)
at org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean.afterPropertiesSet(LocalContainerEntityManagerFactoryBean.java:336)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1687)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1624)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:555)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
at org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:1080)
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:857)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:543)
at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:693)
at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:360)
at org.springframework.boot.SpringApplication.run(SpringApplication.java:303)
at org.springframework.boot.test.context.SpringBootContextLoader.loadContext(SpringBootContextLoader.java:120)
at org.springframework.test.context.cache.DefaultCacheAwareContextLoaderDelegate.loadContextInternal(DefaultCacheAwareContextLoaderDelegate.java:98)
at org.springframework.test.context.cache.DefaultCacheAwareContextLoaderDelegate.loadContext(DefaultCacheAwareContextLoaderDelegate.java:116)
at org.springframework.test.context.support.DefaultTestContext.getApplicationContext(DefaultTestContext.java:83)
at org.springframework.test.context.web.ServletTestExecutionListener.setUpRequestContextIfNecessary(ServletTestExecutionListener.java:189)
at org.springframework.test.context.web.ServletTestExecutionListener.prepareTestInstance(ServletTestExecutionListener.java:131)
at org.springframework.test.context.TestContextManager.prepareTestInstance(TestContextManager.java:230)
at org.springframework.test.context.junit4.SpringJUnit4ClassRunner.createTest(SpringJUnit4ClassRunner.java:228)
at org.springframework.test.context.junit4.SpringJUnit4ClassRunner$1.runReflectiveCall(SpringJUnit4ClassRunner.java:287)
at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
at org.springframework.test.context.junit4.SpringJUnit4ClassRunner.methodBlock(SpringJUnit4ClassRunner.java:289)
at org.springframework.test.context.junit4.SpringJUnit4ClassRunner.runChild(SpringJUnit4ClassRunner.java:247)
at org.springframework.test.context.junit4.SpringJUnit4ClassRunner.runChild(SpringJUnit4ClassRunner.java:94)
at org.junit.runners.ParentRunner$3.run(ParentRunner.java:290)
at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:71)
at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:288)
at org.junit.runners.ParentRunner.access$000(ParentRunner.java:58)
at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:268)
at org.springframework.test.context.junit4.statements.RunBeforeTestClassCallbacks.evaluate(RunBeforeTestClassCallbacks.java:61)
at org.springframework.test.context.junit4.statements.RunAfterTestClassCallbacks.evaluate(RunAfterTestClassCallbacks.java:70)
at org.junit.runners.ParentRunner.run(ParentRunner.java:363)
at org.springframework.test.context.junit4.SpringJUnit4ClassRunner.run(SpringJUnit4ClassRunner.java:191)
at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:283)
at org.apache.maven.surefire.junit4.JUnit4Provider.executeWithRerun(JUnit4Provider.java:173)
at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:153)
at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:128)
at org.apache.maven.surefire.booter.ForkedBooter.invokeProviderInSameClassLoader(ForkedBooter.java:203)
at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:155)
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:103)
If I execute this command mvn clean package -Dmaven.test.skip=true everything is fine
and here it is the pom I use for the project, only the dependencies
<dependencies>
<!-- Spring Boot dependencies -->
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-data-jpa</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-thymeleaf</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-web</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-tomcat</artifactId>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-aop</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-jdbc</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-mail</artifactId>
</dependency>
<dependency>
<groupId>it.ozimov</groupId>
<artifactId>spring-boot-email-core</artifactId>
<version>0.5.1</version>
</dependency>
<dependency>
<groupId>it.ozimov</groupId>
<artifactId>spring-boot-thymeleaf-email</artifactId>
<version>0.5.1</version>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-security</artifactId>
</dependency>
<!-- Test dependencies -->
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-test</artifactId>
<scope>test</scope>
</dependency>
<!-- Logging dependencies -->
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
</dependency>
<!-- Webjars for JQuery and Bootstrap -->
<dependency>
<groupId>org.webjars</groupId>
<artifactId>bootstrap</artifactId>
<version>3.3.7-1</version>
</dependency>
<dependency>
<groupId>org.webjars</groupId>
<artifactId>jquery</artifactId>
<version>3.2.0</version>
</dependency>
<!-- Spring Security -->
<dependency>
<groupId>org.thymeleaf.extras</groupId>
<artifactId>thymeleaf-extras-springsecurity4</artifactId>
<!-- <version>3.0.2.RELEASE</version> -->
</dependency>
<!-- Hibernate dependencies -->
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-validator</artifactId>
</dependency>
<dependency>
<groupId>com.googlecode.libphonenumber</groupId>
<artifactId>libphonenumber</artifactId>
<version>8.4.3</version>
</dependency>
<dependency>
<groupId>commons-codec</groupId>
<artifactId>commons-codec</artifactId>
<!-- <version>1.10</version> -->
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-core</artifactId>
<!-- <version>2.9.0.pr3</version> -->
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-annotations</artifactId>
<!-- <version>2.9.0.pr3</version> -->
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
</dependency>
<dependency>
<groupId>org.codehaus.jackson</groupId>
<artifactId>jackson-mapper-asl</artifactId>
<version>1.9.9</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.apache.httpcomponents/httpcore -->
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpcore</artifactId>
</dependency>
<!-- https://mvnrepository.com/artifact/org.apache.httpcomponents/httpclient -->
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
</dependency>
<!-- https://mvnrepository.com/artifact/com.icegreen/greenmail -->
<dependency>
<groupId>com.icegreen</groupId>
<artifactId>greenmail</artifactId>
<version>1.5.3</version>
<optional>true</optional>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.h2database</groupId>
<artifactId>h2</artifactId>
</dependency>
<dependency>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
<scope>runtime</scope>
</dependency>
</dependencies>

NoSuchMethodError: org.jboss.logging.Logger.debugf(Ljava/lang/String;I)V

I am developing a JSF + Spring integrated web application. I am using javaconfig instead of applicationContext.xml to configure. I got an error telling that
NoSuchMethodError: org.jboss.logging.Logger.debugf(Ljava/lang/String;I)V
but I added jboss logging dependency in pom.xml already. This is my dependencies:
<dependencyManagement>
<dependencies>
<dependency>
<groupId>io.spring.platform</groupId>
<artifactId>platform-bom</artifactId>
<version>Brussels-SR3</version>
<type>pom</type>
<scope>import</scope>
</dependency>
</dependencies>
</dependencyManagement>
<dependencies>
<!-- MySQL database driver -->
<dependency>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
</dependency>
<!-- Apache Commons -->
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
</dependency>
<dependency>
<groupId>org.jboss.logging</groupId>
<artifactId>jboss-logging</artifactId>
<version>3.3.1.Final</version>
</dependency>
<!--Spring Framework-->
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-aspects</artifactId>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-context-support</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.data</groupId>
<artifactId>spring-data-jpa</artifactId>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-web</artifactId>
</dependency>
<!--<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-core</artifactId>
</dependency>-->
<dependency>
<groupId>javax.el</groupId>
<artifactId>el-api</artifactId>
<version>2.2.1-b04</version>
</dependency>
<dependency>
<groupId>org.glassfish.web</groupId>
<artifactId>el-impl</artifactId>
<version>2.2</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<scope>test</scope>
</dependency>
<!--JSF-->
<dependency>
<groupId>com.sun.faces</groupId>
<artifactId>jsf-api</artifactId>
</dependency>
<dependency>
<groupId>com.sun.faces</groupId>
<artifactId>jsf-impl</artifactId>
</dependency>
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>jstl</artifactId>
</dependency>
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>javax.servlet-api</artifactId>
</dependency>
<dependency>
<groupId>javax.servlet.jsp</groupId>
<artifactId>jsp-api</artifactId>
<version>2.2.1-b03</version>
</dependency>
<!-- PrimeFaces -->
<dependency>
<groupId>org.primefaces</groupId>
<artifactId>primefaces</artifactId>
<version>6.1</version>
</dependency>
<!-- Database (H2) -->
<dependency>
<groupId>com.h2database</groupId>
<artifactId>h2</artifactId>
</dependency>
<!-- DataSource (HikariCP) -->
<dependency>
<groupId>com.zaxxer</groupId>
<artifactId>HikariCP</artifactId>
</dependency>
<!-- Hibernate JPA -->
<!--<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-core</artifactId>
</dependency>-->
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-entitymanager</artifactId>
<exclusions>
<exclusion>
<groupId>org.jboss.logging</groupId>
<artifactId>jboss-logging</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-validator</artifactId>
</dependency>
<!-- Hibernate library dependecy start -->
<dependency>
<groupId>dom4j</groupId>
<artifactId>dom4j</artifactId>
</dependency>
<!--<dependency>
<groupId>commons-logging</groupId>
<artifactId>commons-logging</artifactId>
</dependency>-->
<dependency>
<groupId>commons-collections</groupId>
<artifactId>commons-collections</artifactId>
</dependency>
<dependency>
<groupId>antlr</groupId>
<artifactId>antlr</artifactId>
</dependency>
<!-- Hibernate library dependecy end -->
</dependencies>
Most of the dependencies doesn't have version since I am using io.spring.platform. Can anyone tell me where is the conflict or error?
Error stack
org.apache.catalina.LifecycleException: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityManagerFactory' defined in com.peter.uass.config.PersistenceContext: Invocation of init method failed; nested exception is java.lang.NoSuchMethodError: org.jboss.logging.Logger.debugf(Ljava/lang/String;I)V
at org.apache.catalina.core.StandardContext.start(StandardContext.java:5985)
at com.sun.enterprise.web.WebModule.start(WebModule.java:691)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:1041)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:1024)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:747)
at com.sun.enterprise.web.WebContainer.loadWebModule(WebContainer.java:2286)
at com.sun.enterprise.web.WebContainer.loadWebModule(WebContainer.java:1932)
at com.sun.enterprise.web.WebApplication.start(WebApplication.java:139)
at org.glassfish.internal.data.EngineRef.start(EngineRef.java:122)
at org.glassfish.internal.data.ModuleInfo.start(ModuleInfo.java:291)
at org.glassfish.internal.data.ApplicationInfo.start(ApplicationInfo.java:352)
at com.sun.enterprise.v3.server.ApplicationLifecycle.deploy(ApplicationLifecycle.java:500)
at com.sun.enterprise.v3.server.ApplicationLifecycle.deploy(ApplicationLifecycle.java:219)
at org.glassfish.deployment.admin.DeployCommand.execute(DeployCommand.java:491)
at com.sun.enterprise.v3.admin.CommandRunnerImpl$2$1.run(CommandRunnerImpl.java:539)
at com.sun.enterprise.v3.admin.CommandRunnerImpl$2$1.run(CommandRunnerImpl.java:535)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.Subject.doAs(Subject.java:360)
at com.sun.enterprise.v3.admin.CommandRunnerImpl$2.execute(CommandRunnerImpl.java:534)
at com.sun.enterprise.v3.admin.CommandRunnerImpl$3.run(CommandRunnerImpl.java:565)
at com.sun.enterprise.v3.admin.CommandRunnerImpl$3.run(CommandRunnerImpl.java:557)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.Subject.doAs(Subject.java:360)
at com.sun.enterprise.v3.admin.CommandRunnerImpl.doCommand(CommandRunnerImpl.java:556)
at com.sun.enterprise.v3.admin.CommandRunnerImpl.doCommand(CommandRunnerImpl.java:1464)
at com.sun.enterprise.v3.admin.CommandRunnerImpl.access$1300(CommandRunnerImpl.java:109)
at com.sun.enterprise.v3.admin.CommandRunnerImpl$ExecutionContext.execute(CommandRunnerImpl.java:1846)
at com.sun.enterprise.v3.admin.CommandRunnerImpl$ExecutionContext.execute(CommandRunnerImpl.java:1722)
at com.sun.enterprise.v3.admin.AdminAdapter.doCommand(AdminAdapter.java:534)
at com.sun.enterprise.v3.admin.AdminAdapter.onMissingResource(AdminAdapter.java:224)
at org.glassfish.grizzly.http.server.StaticHttpHandlerBase.service(StaticHttpHandlerBase.java:189)
at com.sun.enterprise.v3.services.impl.ContainerMapper$HttpHandlerCallable.call(ContainerMapper.java:459)
at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:167)
at org.glassfish.grizzly.http.server.HttpHandler.runService(HttpHandler.java:206)
at org.glassfish.grizzly.http.server.HttpHandler.doHandle(HttpHandler.java:180)
at org.glassfish.grizzly.http.server.HttpServerFilter.handleRead(HttpServerFilter.java:235)
at org.glassfish.grizzly.filterchain.ExecutorResolver$9.execute(ExecutorResolver.java:119)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeFilter(DefaultFilterChain.java:283)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeChainPart(DefaultFilterChain.java:200)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.execute(DefaultFilterChain.java:132)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.process(DefaultFilterChain.java:111)
at org.glassfish.grizzly.ProcessorExecutor.execute(ProcessorExecutor.java:77)
at org.glassfish.grizzly.nio.transport.TCPNIOTransport.fireIOEvent(TCPNIOTransport.java:536)
at org.glassfish.grizzly.strategies.AbstractIOStrategy.fireIOEvent(AbstractIOStrategy.java:112)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.run0(WorkerThreadIOStrategy.java:117)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.access$100(WorkerThreadIOStrategy.java:56)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy$WorkerThreadRunnable.run(WorkerThreadIOStrategy.java:137)
at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:591)
at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.run(AbstractThreadPool.java:571)
at java.lang.Thread.run(Thread.java:745)
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityManagerFactory' defined in com.peter.uass.config.PersistenceContext: Invocation of init method failed; nested exception is java.lang.NoSuchMethodError: org.jboss.logging.Logger.debugf(Ljava/lang/String;I)V
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1628)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:555)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
at org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:1078)
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:857)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:543)
at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:443)
at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:325)
at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:107)
at org.apache.catalina.core.StandardContext.contextListenerStart(StandardContext.java:5394)
at com.sun.enterprise.web.WebModule.contextListenerStart(WebModule.java:743)
at org.apache.catalina.core.StandardContext.start(StandardContext.java:5963)
... 49 more
Caused by: java.lang.NoSuchMethodError: org.jboss.logging.Logger.debugf(Ljava/lang/String;I)V
at org.hibernate.internal.NamedQueryRepository.checkNamedQueries(NamedQueryRepository.java:149)
at org.hibernate.internal.SessionFactoryImpl.checkNamedQueries(SessionFactoryImpl.java:771)
at org.hibernate.internal.SessionFactoryImpl.<init>(SessionFactoryImpl.java:486)
at org.hibernate.boot.internal.SessionFactoryBuilderImpl.build(SessionFactoryBuilderImpl.java:444)
at org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl.build(EntityManagerFactoryBuilderImpl.java:879)
at org.springframework.orm.jpa.vendor.SpringHibernateJpaPersistenceProvider.createContainerEntityManagerFactory(SpringHibernateJpaPersistenceProvider.java:60)
at org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean.createNativeEntityManagerFactory(LocalContainerEntityManagerFactoryBean.java:353)
at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.buildNativeEntityManagerFactory(AbstractEntityManagerFactoryBean.java:370)
at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.afterPropertiesSet(AbstractEntityManagerFactoryBean.java:359)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1687)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1624)
... 64 more

Block Glassfish from using its own lib when project lib(lib in maven) is provided.
Just create a glassfish-web.xml file in the WEB-INF directory. The contents of the file are shown below:
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE glassfish-web-app PUBLIC "-//GlassFish.org//DTD GlassFish Application Server 3.1 Servlet 3.0//EN" "http://glassfish.org/dtds/glassfish-web-app_3_0-1.dtd">
<glassfish-web-app>
 <class-loader delegate="false"/>
</glassfish-web-app>
This ensures that glassfish does not load it's internal libraries, but libraries from your project.

I was able to resolve the issue by upgrading the hibernate-core jar version to 5.4.1.Final
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-core</artifactId>
<version>5.4.1.Final</version>
</dependency>

Springboot JPA dependency Exception

I am using Spring boot 1.4.2.RELEASE and Hibernate-core-5.0.5.Final , hibernate-entitymanager5.1.0.Final .
But i am facing below exception,Anyone have answer for this Exception let me know.
below is my Exception StrackTrace.
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityManagerFactory' defined in class path resource [org/springframework/boot/autoconfigure/orm/jpa/HibernateJpaAutoConfiguration.class]: Invocation of init method failed; nested exception is java.lang.NoClassDefFoundError: org/hibernate/tool/schema/spi/DelayedDropRegistry
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1583) ~[spring-beans-4.3.4.RELEASE.jar:4.3.4.RELEASE]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:553) ~[spring-beans-4.3.4.RELEASE.jar:4.3.4.RELEASE]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:482) ~[spring-beans-4.3.4.RELEASE.jar:4.3.4.RELEASE]
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306) ~[spring-beans-4.3.4.RELEASE.jar:4.3.4.RELEASE]
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230) ~[spring-beans-4.3.4.RELEASE.jar:4.3.4.RELEASE]
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302) ~[spring-beans-4.3.4.RELEASE.jar:4.3.4.RELEASE]
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197) ~[spring-beans-4.3.4.RELEASE.jar:4.3.4.RELEASE]
at org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:1081) ~[spring-context-4.3.4.RELEASE.jar:4.3.4.RELEASE]
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:856) ~[spring-context-4.3.4.RELEASE.jar:4.3.4.RELEASE]
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:542) ~[spring-context-4.3.4.RELEASE.jar:4.3.4.RELEASE]
at org.springframework.boot.context.embedded.EmbeddedWebApplicationContext.refresh(EmbeddedWebApplicationContext.java:122) ~[spring-boot-1.4.2.RELEASE.jar:1.4.2.RELEASE]
at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:761) [spring-boot-1.4.2.RELEASE.jar:1.4.2.RELEASE]
at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:371) [spring-boot-1.4.2.RELEASE.jar:1.4.2.RELEASE]
at org.springframework.boot.SpringApplication.run(SpringApplication.java:315) [spring-boot-1.4.2.RELEASE.jar:1.4.2.RELEASE]
at org.springframework.boot.SpringApplication.run(SpringApplication.java:1186) [spring-boot-1.4.2.RELEASE.jar:1.4.2.RELEASE]
at org.springframework.boot.SpringApplication.run(SpringApplication.java:1175) [spring-boot-1.4.2.RELEASE.jar:1.4.2.RELEASE]
at com.SpringBootWebApplication.main(SpringBootWebApplication.java:23) [classes/:na]
Caused by: java.lang.NoClassDefFoundError: org/hibernate/tool/schema/spi/DelayedDropRegistry
at org.springframework.orm.jpa.vendor.SpringHibernateJpaPersistenceProvider.createContainerEntityManagerFactory(SpringHibernateJpaPersistenceProvider.java:54) ~[spring-orm-4.3.4.RELEASE.jar:4.3.4.RELEASE]
at org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean.createNativeEntityManagerFactory(LocalContainerEntityManagerFactoryBean.java:353) ~[spring-orm-4.3.4.RELEASE.jar:4.3.4.RELEASE]
at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.buildNativeEntityManagerFactory(AbstractEntityManagerFactoryBean.java:373) ~[spring-orm-4.3.4.RELEASE.jar:4.3.4.RELEASE]
at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.afterPropertiesSet(AbstractEntityManagerFactoryBean.java:362) ~[spring-orm-4.3.4.RELEASE.jar:4.3.4.RELEASE]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1642) ~[spring-beans-4.3.4.RELEASE.jar:4.3.4.RELEASE]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1579) ~[spring-beans-4.3.4.RELEASE.jar:4.3.4.RELEASE]
... 16 common frames omitted
Caused by: java.lang.ClassNotFoundException: org.hibernate.tool.schema.spi.DelayedDropRegistry
at java.net.URLClassLoader.findClass(URLClassLoader.java:381) ~[na:1.8.0_111]
at java.lang.ClassLoader.loadClass(ClassLoader.java:424) ~[na:1.8.0_111]
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331) ~[na:1.8.0_111]
at java.lang.ClassLoader.loadClass(ClassLoader.java:357) ~[na:1.8.0_111]
... 22 common frames omitted
POM.XML
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<artifactId>spring-boot-web</artifactId>
<packaging>war</packaging>
<name>Spring Boot Web JSP Example</name>
<description>Spring Boot Web JSP Example</description>
<url>https://www.mkyong.com</url>
<version>1.0</version>
<parent>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-parent</artifactId>
<version>1.4.2.RELEASE</version>
</parent>
<properties>
<java.version>1.8</java.version>
</properties>
<dependencies>
<!-- Web -->
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-web</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-data-jpa</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-security</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-data-rest</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-tomcat</artifactId>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>com.h2database</groupId>
<artifactId>h2</artifactId>
</dependency>
<!-- Web with Tomcat + Embed -->
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-tomcat</artifactId>
<scope>provided</scope>
</dependency>
<!-- JSTL -->
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>jstl</artifactId>
</dependency>
<!-- Need this to compile JSP -->
<dependency>
<groupId>org.apache.tomcat.embed</groupId>
<artifactId>tomcat-embed-jasper</artifactId>
<scope>provided</scope>
</dependency>
<!-- Need this to compile JSP -->
<dependency>
<groupId>org.eclipse.jdt.core.compiler</groupId>
<artifactId>ecj</artifactId>
<version>4.6.1</version>
<scope>provided</scope>
</dependency>
<!-- Optional, for bootstrap -->
<dependency>
<groupId>org.webjars</groupId>
<artifactId>bootstrap</artifactId>
<version>3.3.7</version>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.4</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.hibernate/hibernate-core -->
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-core</artifactId>
<version>5.0.11.Final</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.hibernate/hibernate-entitymanager -->
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-entitymanager</artifactId>
<version>5.0.11.Final</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.hibernate.javax.persistence/hibernate-jpa-2.1-api -->
<dependency>
<groupId>org.hibernate.javax.persistence</groupId>
<artifactId>hibernate-jpa-2.1-api</artifactId>
<version>1.0.0.Final</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.hibernate.common/hibernate-commons-annotations -->
<dependency>
<groupId>org.hibernate.common</groupId>
<artifactId>hibernate-commons-annotations</artifactId>
<version>5.0.1.Final</version>
</dependency>
<dependency>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
<version>5.1.26</version>
</dependency>
<dependency>
<groupId>commons-dbcp</groupId>
<artifactId>commons-dbcp</artifactId>
<version>1.4</version>
</dependency>
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>jstl</artifactId>
<version>1.2</version>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.10</version>
<scope>test</scope>
</dependency>
</dependencies>
<build>
<plugins>
<!-- Package as an executable jar/war -->
<plugin>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-maven-plugin</artifactId>
</plugin>
</plugins>
</build>
</project>

Without seeing your pom.xml, build.gradle, etc. file it is hard to say what's going on, but in general you don't need to specify the Hibernate version when you use Spring Boot.
If you are using Maven:
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
...
<parent>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-parent</artifactId>
<version>1.4.2.RELEASE</version>
<relativePath/>
</parent>
<dependencies>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-data-jpa</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-test</artifactId>
<scope>test</scope>
</dependency>
</dependencies>
...
</project>
This will pull in the following dependencies:
Try removing the explicit versions for the Hibernate dependencies or use version 5.0.11 for both.