Spring MVC + Spring Data

Подозреваю что проблема с зависимостями при добавлении Spring Data, без data, напрямую с EntityManager всё работает, но нужно построить приложение с data. При запуске получаю:

C:\apache-tomcat-7.0.67\bin\catalina.bat run
[2017-03-19 11:56:45,987] Artifact unnamed: Server is not connected. Deploy is not available.
Using CATALINA_BASE:   "C:\Users\k2\.IntelliJIdea2016.2\system\tomcat\Unnamed_Message"
Using CATALINA_HOME:   "C:\apache-tomcat-7.0.67"
Using CATALINA_TMPDIR: "C:\apache-tomcat-7.0.67\temp"
Using JRE_HOME:        "C:\Program Files\Java\jdk1.8.0_112"
Using CLASSPATH:       "C:\apache-tomcat-7.0.67\bin\bootstrap.jar;C:\apache-tomcat-7.0.67\bin\tomcat-juli.jar"
мар 19, 2017 11:56:46 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server version:        Apache Tomcat/7.0.67
мар 19, 2017 11:56:46 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server built:          Dec 7 2015 13:07:11 UTC
мар 19, 2017 11:56:46 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server number:         7.0.67.0
мар 19, 2017 11:56:46 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: OS Name:               Windows 10
мар 19, 2017 11:56:46 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: OS Version:            10.0
мар 19, 2017 11:56:46 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Architecture:          amd64
мар 19, 2017 11:56:46 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Java Home:             C:\Program Files\Java\jdk1.8.0_112\jre
мар 19, 2017 11:56:46 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: JVM Version:           1.8.0_112-b15
мар 19, 2017 11:56:46 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: JVM Vendor:            Oracle Corporation
мар 19, 2017 11:56:46 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: CATALINA_BASE:         C:\Users\k2\.IntelliJIdea2016.2\system\tomcat\Unnamed_Message
мар 19, 2017 11:56:46 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: CATALINA_HOME:         C:\apache-tomcat-7.0.67
мар 19, 2017 11:56:46 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dcom.sun.management.jmxremote=
мар 19, 2017 11:56:46 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dcom.sun.management.jmxremote.port=1099
мар 19, 2017 11:56:46 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dcom.sun.management.jmxremote.ssl=false
мар 19, 2017 11:56:46 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dcom.sun.management.jmxremote.authenticate=false
мар 19, 2017 11:56:46 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.rmi.server.hostname=127.0.0.1
мар 19, 2017 11:56:46 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.util.logging.config.file=C:\Users\k2\.IntelliJIdea2016.2\system\tomcat\Unnamed_Message\conf\logging.properties
мар 19, 2017 11:56:46 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
мар 19, 2017 11:56:46 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.endorsed.dirs=C:\apache-tomcat-7.0.67\endorsed
мар 19, 2017 11:56:46 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dcatalina.base=C:\Users\k2\.IntelliJIdea2016.2\system\tomcat\Unnamed_Message
мар 19, 2017 11:56:46 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dcatalina.home=C:\apache-tomcat-7.0.67
мар 19, 2017 11:56:46 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.io.tmpdir=C:\apache-tomcat-7.0.67\temp
мар 19, 2017 11:56:46 PM org.apache.catalina.core.AprLifecycleListener lifecycleEvent
INFO: The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: C:\Program Files\Java\jdk1.8.0_112\bin;C:\Windows\Sun\Java\bin;C:\Windows\system32;C:\Windows;C:\ProgramData\Oracle\Java\javapath;C:\Program Files\Broadcom\Broadcom 802.11 Network Adapter;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Program Files\Java\jdk1.8.0_112\bin\;C:\Program Files (x86)\MySQL\MySQL Fabric 1.5 & MySQL Utilities 1.5\;C:\Program Files (x86)\MySQL\MySQL Fabric 1.5 & MySQL Utilities 1.5\Doctrine extensions for PHP\;C:\apache-maven-3.3.9\bin;C:\Program Files (x86)\Skype\Phone\;C:\Program Files\Git\cmd;C:\Users\k2\AppData\Local\Microsoft\WindowsApps;;.
мар 19, 2017 11:56:46 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
мар 19, 2017 11:56:46 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["ajp-bio-8009"]
мар 19, 2017 11:56:46 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 545 ms
мар 19, 2017 11:56:46 PM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
мар 19, 2017 11:56:46 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.67
мар 19, 2017 11:56:46 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
мар 19, 2017 11:56:47 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["ajp-bio-8009"]
мар 19, 2017 11:56:47 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 106 ms
Connected to server
[2017-03-19 11:56:47,181] Artifact unnamed: Artifact is being deployed, please wait...
мар 19, 2017 11:56:47 PM org.apache.catalina.loader.WebappClassLoaderBase validateJarFile
INFO: validateJarFile(C:\Users\k2\IdeaProjects\Message\out\artifacts\unnamed\WEB-INF\lib\javax.servlet-api-3.1.0.jar) - jar not loaded. See Servlet Spec 3.0, section 10.7.2. Offending class: javax/servlet/Servlet.class
мар 19, 2017 11:56:48 PM org.apache.catalina.startup.TldConfig execute
INFO: At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
мар 19, 2017 11:56:48 PM org.apache.catalina.core.ContainerBase addChildInternal
SEVERE: ContainerBase.addChild: start: 
org.apache.catalina.LifecycleException: Failed to start component [StandardEngine[Catalina].StandardHost[localhost].StandardContext[]]
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:154)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:901)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:877)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
    at org.apache.catalina.startup.HostConfig.manageApp(HostConfig.java:1836)
    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.apache.tomcat.util.modeler.BaseModelMBean.invoke(BaseModelMBean.java:301)
    at com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.invoke(DefaultMBeanServerInterceptor.java:819)
    at com.sun.jmx.mbeanserver.JmxMBeanServer.invoke(JmxMBeanServer.java:801)
    at org.apache.catalina.mbeans.MBeanFactory.createStandardContext(MBeanFactory.java:618)
    at org.apache.catalina.mbeans.MBeanFactory.createStandardContext(MBeanFactory.java:565)
    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.apache.tomcat.util.modeler.BaseModelMBean.invoke(BaseModelMBean.java:301)
    at com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.invoke(DefaultMBeanServerInterceptor.java:819)
    at com.sun.jmx.mbeanserver.JmxMBeanServer.invoke(JmxMBeanServer.java:801)
    at javax.management.remote.rmi.RMIConnectionImpl.doOperation(RMIConnectionImpl.java:1468)
    at javax.management.remote.rmi.RMIConnectionImpl.access$300(RMIConnectionImpl.java:76)
    at javax.management.remote.rmi.RMIConnectionImpl$PrivilegedOperation.run(RMIConnectionImpl.java:1309)
    at javax.management.remote.rmi.RMIConnectionImpl.doPrivilegedOperation(RMIConnectionImpl.java:1401)
    at javax.management.remote.rmi.RMIConnectionImpl.invoke(RMIConnectionImpl.java:829)
    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 sun.rmi.server.UnicastServerRef.dispatch(UnicastServerRef.java:324)
    at sun.rmi.transport.Transport$1.run(Transport.java:200)
    at sun.rmi.transport.Transport$1.run(Transport.java:197)
    at java.security.AccessController.doPrivileged(Native Method)
    at sun.rmi.transport.Transport.serviceCall(Transport.java:196)
    at sun.rmi.transport.tcp.TCPTransport.handleMessages(TCPTransport.java:568)
    at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(TCPTransport.java:826)
    at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.lambda$run$0(TCPTransport.java:683)
    at java.security.AccessController.doPrivileged(Native Method)
    at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(TCPTransport.java:682)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
Caused by: org.springframework.beans.factory.BeanDefinitionStoreException: Failed to read candidate component class: file [C:\Users\k2\IdeaProjects\Message\out\artifacts\unnamed\WEB-INF\classes\ru\rambler\skanerxxl\controller\MainController.class]; nested exception is java.lang.IncompatibleClassChangeError: class org.springframework.core.type.classreading.ClassMetadataReadingVisitor has interface org.springframework.asm.ClassVisitor as super class
    at org.springframework.context.annotation.ClassPathScanningCandidateComponentProvider.findCandidateComponents(ClassPathScanningCandidateComponentProvider.java:303)
    at org.springframework.context.annotation.ClassPathBeanDefinitionScanner.doScan(ClassPathBeanDefinitionScanner.java:248)
    at org.springframework.context.annotation.ComponentScanAnnotationParser.parse(ComponentScanAnnotationParser.java:137)
    at org.springframework.context.annotation.ConfigurationClassParser.doProcessConfigurationClass(ConfigurationClassParser.java:267)
    at org.springframework.context.annotation.ConfigurationClassParser.processConfigurationClass(ConfigurationClassParser.java:231)
    at org.springframework.context.annotation.ConfigurationClassParser.parse(ConfigurationClassParser.java:198)
    at org.springframework.context.annotation.ConfigurationClassParser.parse(ConfigurationClassParser.java:167)
    at org.springframework.context.annotation.ConfigurationClassPostProcessor.processConfigBeanDefinitions(ConfigurationClassPostProcessor.java:321)
    at org.springframework.context.annotation.ConfigurationClassPostProcessor.postProcessBeanDefinitionRegistry(ConfigurationClassPostProcessor.java:243)
    at org.springframework.context.support.PostProcessorRegistrationDelegate.invokeBeanDefinitionRegistryPostProcessors(PostProcessorRegistrationDelegate.java:273)
    at org.springframework.context.support.PostProcessorRegistrationDelegate.invokeBeanFactoryPostProcessors(PostProcessorRegistrationDelegate.java:98)
    at org.springframework.context.support.AbstractApplicationContext.invokeBeanFactoryPostProcessors(AbstractApplicationContext.java:673)
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:519)
    at ru.rambler.skanerxxl.init.WebInitializer.onStartup(WebInitializer.java:24)
    at org.springframework.web.SpringServletContainerInitializer.onStartup(SpringServletContainerInitializer.java:175)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5580)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    ... 42 more
Caused by: java.lang.IncompatibleClassChangeError: class org.springframework.core.type.classreading.ClassMetadataReadingVisitor has interface org.springframework.asm.ClassVisitor as super class
    at java.lang.ClassLoader.defineClass1(Native Method)
    at java.lang.ClassLoader.defineClass(ClassLoader.java:763)
    at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
    at org.apache.catalina.loader.WebappClassLoaderBase.findClassInternal(WebappClassLoaderBase.java:3116)
    at org.apache.catalina.loader.WebappClassLoaderBase.findClass(WebappClassLoaderBase.java:1344)
    at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1825)
    at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1705)
    at java.lang.ClassLoader.defineClass1(Native Method)
    at java.lang.ClassLoader.defineClass(ClassLoader.java:763)
    at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
    at org.apache.catalina.loader.WebappClassLoaderBase.findClassInternal(WebappClassLoaderBase.java:3116)
    at org.apache.catalina.loader.WebappClassLoaderBase.findClass(WebappClassLoaderBase.java:1344)
    at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1825)
    at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1705)
    at org.springframework.core.type.classreading.SimpleMetadataReader.<init>(SimpleMetadataReader.java:63)
    at org.springframework.core.type.classreading.SimpleMetadataReaderFactory.getMetadataReader(SimpleMetadataReaderFactory.java:98)
    at org.springframework.core.type.classreading.CachingMetadataReaderFactory.getMetadataReader(CachingMetadataReaderFactory.java:102)
    at org.springframework.context.annotation.ClassPathScanningCandidateComponentProvider.findCandidateComponents(ClassPathScanningCandidateComponentProvider.java:279)
    ... 58 more
мар 19, 2017 11:56:48 PM org.apache.tomcat.util.modeler.BaseModelMBean invoke
SEVERE: Exception invoking method manageApp
java.lang.IllegalStateException: ContainerBase.addChild: start: org.apache.catalina.LifecycleException: Failed to start component [StandardEngine[Catalina].StandardHost[localhost].StandardContext[]]
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:905)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:877)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
    at org.apache.catalina.startup.HostConfig.manageApp(HostConfig.java:1836)
    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.apache.tomcat.util.modeler.BaseModelMBean.invoke(BaseModelMBean.java:301)
    at com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.invoke(DefaultMBeanServerInterceptor.java:819)
    at com.sun.jmx.mbeanserver.JmxMBeanServer.invoke(JmxMBeanServer.java:801)
    at org.apache.catalina.mbeans.MBeanFactory.createStandardContext(MBeanFactory.java:618)
    at org.apache.catalina.mbeans.MBeanFactory.createStandardContext(MBeanFactory.java:565)
    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.apache.tomcat.util.modeler.BaseModelMBean.invoke(BaseModelMBean.java:301)
    at com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.invoke(DefaultMBeanServerInterceptor.java:819)
    at com.sun.jmx.mbeanserver.JmxMBeanServer.invoke(JmxMBeanServer.java:801)
    at javax.management.remote.rmi.RMIConnectionImpl.doOperation(RMIConnectionImpl.java:1468)
    at javax.management.remote.rmi.RMIConnectionImpl.access$300(RMIConnectionImpl.java:76)
    at javax.management.remote.rmi.RMIConnectionImpl$PrivilegedOperation.run(RMIConnectionImpl.java:1309)
    at javax.management.remote.rmi.RMIConnectionImpl.doPrivilegedOperation(RMIConnectionImpl.java:1401)
    at javax.management.remote.rmi.RMIConnectionImpl.invoke(RMIConnectionImpl.java:829)
    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 sun.rmi.server.UnicastServerRef.dispatch(UnicastServerRef.java:324)
    at sun.rmi.transport.Transport$1.run(Transport.java:200)
    at sun.rmi.transport.Transport$1.run(Transport.java:197)
    at java.security.AccessController.doPrivileged(Native Method)
    at sun.rmi.transport.Transport.serviceCall(Transport.java:196)
    at sun.rmi.transport.tcp.TCPTransport.handleMessages(TCPTransport.java:568)
    at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(TCPTransport.java:826)
    at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.lambda$run$0(TCPTransport.java:683)
    at java.security.AccessController.doPrivileged(Native Method)
    at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(TCPTransport.java:682)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
мар 19, 2017 11:56:48 PM org.apache.tomcat.util.modeler.BaseModelMBean invoke
SEVERE: Exception invoking method createStandardContext
javax.management.RuntimeOperationsException: Exception invoking method manageApp
    at org.apache.tomcat.util.modeler.BaseModelMBean.invoke(BaseModelMBean.java:309)
    at com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.invoke(DefaultMBeanServerInterceptor.java:819)
    at com.sun.jmx.mbeanserver.JmxMBeanServer.invoke(JmxMBeanServer.java:801)
    at org.apache.catalina.mbeans.MBeanFactory.createStandardContext(MBeanFactory.java:618)
    at org.apache.catalina.mbeans.MBeanFactory.createStandardContext(MBeanFactory.java:565)
    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.apache.tomcat.util.modeler.BaseModelMBean.invoke(BaseModelMBean.java:301)
    at com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.invoke(DefaultMBeanServerInterceptor.java:819)
    at com.sun.jmx.mbeanserver.JmxMBeanServer.invoke(JmxMBeanServer.java:801)
    at javax.management.remote.rmi.RMIConnectionImpl.doOperation(RMIConnectionImpl.java:1468)
    at javax.management.remote.rmi.RMIConnectionImpl.access$300(RMIConnectionImpl.java:76)
    at javax.management.remote.rmi.RMIConnectionImpl$PrivilegedOperation.run(RMIConnectionImpl.java:1309)
    at javax.management.remote.rmi.RMIConnectionImpl.doPrivilegedOperation(RMIConnectionImpl.java:1401)
    at javax.management.remote.rmi.RMIConnectionImpl.invoke(RMIConnectionImpl.java:829)
    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 sun.rmi.server.UnicastServerRef.dispatch(UnicastServerRef.java:324)
    at sun.rmi.transport.Transport$1.run(Transport.java:200)
    at sun.rmi.transport.Transport$1.run(Transport.java:197)
    at java.security.AccessController.doPrivileged(Native Method)
    at sun.rmi.transport.Transport.serviceCall(Transport.java:196)
    at sun.rmi.transport.tcp.TCPTransport.handleMessages(TCPTransport.java:568)
    at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(TCPTransport.java:826)
    at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.lambda$run$0(TCPTransport.java:683)
    at java.security.AccessController.doPrivileged(Native Method)
    at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(TCPTransport.java:682)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.IllegalStateException: ContainerBase.addChild: start: org.apache.catalina.LifecycleException: Failed to start component [StandardEngine[Catalina].StandardHost[localhost].StandardContext[]]
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:905)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:877)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
    at org.apache.catalina.startup.HostConfig.manageApp(HostConfig.java:1836)
    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.apache.tomcat.util.modeler.BaseModelMBean.invoke(BaseModelMBean.java:301)
    ... 33 more
[2017-03-19 11:56:48,947] Artifact unnamed: Error during artifact deployment. See server log for details.
мар 19, 2017 11:56:56 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory C:\apache-tomcat-7.0.67\webapps\manager
мар 19, 2017 11:56:57 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory C:\apache-tomcat-7.0.67\webapps\manager has finished in 94 ms

Проблема возникает в инициалайзере на данном этапе(ctx.refresh();)

at ru.rambler.skanerxxl.init.WebInitializer.onStartup(WebInitializer.java:24)

Контролёр. В строке браузера переходим по /qwe и сохраняем сущность с помощью метода save интерфейса JpaRepository

@Controller
@RequestMapping("/")
public class MainController {
    @Autowired
    private ServiceMessage serviceMessage;
    @RequestMapping("/qwe")
    public String crr(){
        serviceMessage.addMessage(new Message("zxc"));
        return "start";
    }
}

Инициалайзер

public class WebInitializer implements WebApplicationInitializer {
    @Override
    public void onStartup(ServletContext servletContext) throws ServletException {
        AnnotationConfigWebApplicationContext ctx = new AnnotationConfigWebApplicationContext();
        ctx.register(AppConfig.class);
        ctx.setServletContext(servletContext);
        ctx.refresh();
        ServletRegistration.Dynamic servlet = servletContext.addServlet("dispatcher", new DispatcherServlet(ctx));
        servlet.addMapping("/");
        servlet.setLoadOnStartup(1);
    }
}

Репозиторий

public interface MessageRepository extends JpaRepository<Message, Long> {
}

Сервис

@Service
public class ServiceMessage {
    @Autowired
    private MessageRepository messageRepository;
    @Transactional
    public void addMessage(Message message) {
        messageRepository.save(message);
    }
}

Pom

<?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>
    <groupId>message</groupId>
    <artifactId>message</artifactId>
    <version>1.0</version>
    <packaging>war</packaging>
    <name>mess</name>
    <dependencies>
        <dependency>
            <groupId>org.springframework</groupId>
            <artifactId>spring-webmvc</artifactId>
            <version>4.2.1.RELEASE</version>
        </dependency>
        <dependency>
            <groupId>org.springframework</groupId>
            <artifactId>spring-orm</artifactId>
            <version>4.2.1.RELEASE</version>
        </dependency>
        <dependency>
            <groupId>org.springframework.data</groupId>
            <artifactId>spring-data-jpa</artifactId>
            <version>1.3.4.RELEASE</version>
        </dependency>
        <dependency>
            <groupId>mysql</groupId>
            <artifactId>mysql-connector-java</artifactId>
            <version>5.1.34</version>
        </dependency>
        <dependency>
            <groupId>org.hibernate</groupId>
            <artifactId>hibernate-entitymanager</artifactId>
            <version>4.3.11.Final</version>
        </dependency>
        <dependency>
            <groupId>javax.servlet</groupId>
            <artifactId>javax.servlet-api</artifactId>
            <version>3.1.0</version>
        </dependency>
        <dependency>
            <groupId>javax.servlet</groupId>
            <artifactId>jstl</artifactId>
            <version>1.2</version>
        </dependency>
    </dependencies>
    <build>
        <finalName>mess</finalName>
        <plugins>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-compiler-plugin</artifactId>
                <configuration>
                    <source>1.7</source>
                    <target>1.7</target>
                </configuration>
            </plugin>
        </plugins>
    </build>
</project>

В сущности всё стандартно

@Entity
@Table(name = "message")
public class Message {
    @Id
    @GeneratedValue
    @Column(name = "id")
    private long idUser;
...

Добавил изменения на комментарий от mrchebik: 1) изменил версию зависимости

        <dependency>
            <groupId>org.springframework.data</groupId>
            <artifactId>spring-data-jpa</artifactId>
            <version>1.10.5.RELEASE</version>
        </dependency>

2) вместо реализации WebApplicationInitializer использовал наследник от AbstractAnnotationConfigDispatcherServletInitializer

public class AppInit extends AbstractAnnotationConfigDispatcherServletInitializer {

    @Override
    protected Class<?>[] getRootConfigClasses() {
        return new Class<?>[]{
                AppConfig.class
        };
    }

    @Override
    protected Class<?>[] getServletConfigClasses() {
        return new Class<?>[]{
                AppConfig.class
        };
    }
    @Override
    protected String[] getServletMappings() {
        return new String[]{"/"};
    }
}

Но результат тот же самый

WARNING: Exception thrown from LifecycleProcessor on context close
java.lang.IllegalStateException: LifecycleProcessor not initialized - call 'refresh' before invoking lifecycle methods via the context: Root WebApplicationContext: startup date [Mon Mar 20 11:13:44 EET 2017]; root of context hierarchy