Spring boot error starting ApplicationContext - spring-boot

Question

It's my first Spring boot application and having some issues getting it to run. I don't understand what I'm doing wrong.
The output from the console is:
. ____ _ __ _ _
/\\ / ___'_ __ _ _(_)_ __ __ _ \ \ \ \
( ( )\___ | '_ | '_| | '_ \/ _` | \ \ \ \
\\/ ___)| |_)| | | | | || (_| | ) ) ) )
' |____| .__|_| |_|_| |_\__, | / / / /
=========|_|==============|___/=/_/_/_/
:: Spring Boot :: (v2.2.1.RELEASE)
2019-11-27 09:46:46.029 INFO 13638 --- [ restartedMain] com.example.rdm.App : Starting App on nmigeo-VirtualBox with PID 13638 (/home/nmigeo/arch_repo/RDM/RDM_backend/target/classes started by nmigeo in /home/nmigeo/arch_repo/RDM/RDM_backend)
2019-11-27 09:46:46.031 INFO 13638 --- [ restartedMain] com.example.rdm.App : The following profiles are active: michel
2019-11-27 09:46:46.074 INFO 13638 --- [ restartedMain] o.s.b.devtools.restart.ChangeableUrls : The Class-Path manifest attribute in /home/nmigeo/.m2/repository/org/glassfish/jaxb/jaxb-runtime/2.3.2/jaxb-runtime-2.3.2.jar referenced one or more files that do not exist: file:/home/nmigeo/.m2/repository/org/glassfish/jaxb/jaxb-runtime/2.3.2/jakarta.xml.bind-api-2.3.2.jar,file:/home/nmigeo/.m2/repository/org/glassfish/jaxb/jaxb-runtime/2.3.2/txw2-2.3.2.jar,file:/home/nmigeo/.m2/repository/org/glassfish/jaxb/jaxb-runtime/2.3.2/istack-commons-runtime-3.0.8.jar,file:/home/nmigeo/.m2/repository/org/glassfish/jaxb/jaxb-runtime/2.3.2/stax-ex-1.8.1.jar,file:/home/nmigeo/.m2/repository/org/glassfish/jaxb/jaxb-runtime/2.3.2/FastInfoset-1.2.16.jar,file:/home/nmigeo/.m2/repository/org/glassfish/jaxb/jaxb-runtime/2.3.2/jakarta.activation-api-1.2.1.jar
2019-11-27 09:46:46.074 INFO 13638 --- [ restartedMain] .e.DevToolsPropertyDefaultsPostProcessor : Devtools property defaults active! Set 'spring.devtools.add-properties' to 'false' to disable
2019-11-27 09:46:46.075 INFO 13638 --- [ restartedMain] .e.DevToolsPropertyDefaultsPostProcessor : For additional web related logging consider setting the 'logging.level.web' property to 'DEBUG'
2019-11-27 09:46:46.964 INFO 13638 --- [ restartedMain] .s.d.r.c.RepositoryConfigurationDelegate : Bootstrapping Spring Data repositories in DEFAULT mode.
2019-11-27 09:46:46.986 INFO 13638 --- [ restartedMain] .s.d.r.c.RepositoryConfigurationDelegate : Finished Spring Data repository scanning in 14ms. Found 0 repository interfaces.
2019-11-27 09:46:47.339 INFO 13638 --- [ restartedMain] trationDelegate$BeanPostProcessorChecker : Bean 'org.springframework.ws.config.annotation.DelegatingWsConfiguration' of type [org.springframework.ws.config.annotation.DelegatingWsConfiguration$$EnhancerBySpringCGLIB$$7556ff8b] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying)
2019-11-27 09:46:47.385 INFO 13638 --- [ restartedMain] .w.s.a.s.AnnotationActionEndpointMapping : Supporting [WS-Addressing August 2004, WS-Addressing 1.0]
2019-11-27 09:46:47.411 INFO 13638 --- [ restartedMain] trationDelegate$BeanPostProcessorChecker : Bean 'org.springframework.transaction.annotation.ProxyTransactionManagementConfiguration' of type [org.springframework.transaction.annotation.ProxyTransactionManagementConfiguration] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying)
2019-11-27 09:46:47.763 INFO 13638 --- [ restartedMain] o.s.b.w.embedded.tomcat.TomcatWebServer : Tomcat initialized with port(s): 8080 (http)
2019-11-27 09:46:47.771 INFO 13638 --- [ restartedMain] o.apache.catalina.core.StandardService : Starting service [Tomcat]
2019-11-27 09:46:47.771 INFO 13638 --- [ restartedMain] org.apache.catalina.core.StandardEngine : Starting Servlet engine: [Apache Tomcat/9.0.27]
2019-11-27 09:46:47.831 INFO 13638 --- [ restartedMain] o.a.c.c.C.[Tomcat].[localhost].[/] : Initializing Spring embedded WebApplicationContext
2019-11-27 09:46:47.831 INFO 13638 --- [ restartedMain] o.s.web.context.ContextLoader : Root WebApplicationContext: initialization completed in 1756 ms
2019-11-27 09:46:48.456 INFO 13638 --- [ restartedMain] o.hibernate.jpa.internal.util.LogHelper : HHH000204: Processing PersistenceUnitInfo [name: default]
2019-11-27 09:46:48.659 INFO 13638 --- [ restartedMain] org.hibernate.Version : HHH000412: Hibernate Core {5.4.8.Final}
2019-11-27 09:46:48.876 INFO 13638 --- [ restartedMain] o.hibernate.annotations.common.Version : HCANN000001: Hibernate Commons Annotations {5.1.0.Final}
2019-11-27 09:46:48.991 INFO 13638 --- [ restartedMain] org.hibernate.dialect.Dialect : HHH000400: Using dialect: org.hibernate.dialect.PostgreSQL9Dialect
2019-11-27 09:46:49.025 INFO 13638 --- [ restartedMain] o.h.e.boot.internal.EnversServiceImpl : Envers integration enabled? : true
2019-11-27 09:46:50.725 INFO 13638 --- [ restartedMain] com.zaxxer.hikari.HikariDataSource : HikariPool-1 - Starting...
2019-11-27 09:46:50.839 INFO 13638 --- [ restartedMain] com.zaxxer.hikari.HikariDataSource : HikariPool-1 - Start completed.
2019-11-27 09:46:51.375 INFO 13638 --- [ restartedMain] o.h.e.t.j.p.i.JtaPlatformInitiator : HHH000490: Using JtaPlatform implementation: [org.hibernate.engine.transaction.jta.platform.internal.NoJtaPlatform]
2019-11-27 09:46:51.382 INFO 13638 --- [ restartedMain] j.LocalContainerEntityManagerFactoryBean : Initialized JPA EntityManagerFactory for persistence unit 'default'
2019-11-27 09:46:51.484 INFO 13638 --- [ restartedMain] o.s.b.d.a.OptionalLiveReloadServer : LiveReload server is running on port 35729
2019-11-27 09:46:51.767 WARN 13638 --- [ restartedMain] ConfigServletWebServerApplicationContext : Exception encountered during context initialization - cancelling refresh attempt: org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'repositorySearchController' defined in URL [jar:file:/home/nmigeo/.m2/repository/org/springframework/data/spring-data-rest-webmvc/3.2.1.RELEASE/spring-data-rest-webmvc-3.2.1.RELEASE.jar!/org/springframework/data/rest/webmvc/RepositorySearchController.class]: Unsatisfied dependency expressed through constructor parameter 1; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityLinks' 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 [org.springframework.data.rest.webmvc.support.RepositoryEntityLinks]: Factory method 'entityLinks' threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'backendIdConverterRegistry' 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 [org.springframework.plugin.core.PluginRegistry]: Factory method 'backendIdConverterRegistry' threw exception; nested exception is java.lang.NoSuchMethodError: org.springframework.plugin.core.PluginRegistry.of(Ljava/util/List;)Lorg/springframework/plugin/core/PluginRegistry;
2019-11-27 09:46:51.768 INFO 13638 --- [ restartedMain] j.LocalContainerEntityManagerFactoryBean : Closing JPA EntityManagerFactory for persistence unit 'default'
2019-11-27 09:46:51.774 INFO 13638 --- [ restartedMain] com.zaxxer.hikari.HikariDataSource : HikariPool-1 - Shutdown initiated...
2019-11-27 09:46:51.791 INFO 13638 --- [ restartedMain] com.zaxxer.hikari.HikariDataSource : HikariPool-1 - Shutdown completed.
2019-11-27 09:46:51.794 INFO 13638 --- [ restartedMain] o.apache.catalina.core.StandardService : Stopping service [Tomcat]
2019-11-27 09:46:51.819 INFO 13638 --- [ restartedMain] ConditionEvaluationReportLoggingListener :
Error starting ApplicationContext. To display the conditions report re-run your application with 'debug' enabled.
2019-11-27 09:46:51.825 ERROR 13638 --- [ restartedMain] o.s.b.d.LoggingFailureAnalysisReporter :
***************************
APPLICATION FAILED TO START
***************************
Description:
An attempt was made to call a method that does not exist. The attempt was made from the following location:
org.springframework.data.rest.webmvc.config.RepositoryRestMvcConfiguration.backendIdConverterRegistry(RepositoryRestMvcConfiguration.java:721)
The following method did not exist:
org.springframework.plugin.core.PluginRegistry.of(Ljava/util/List;)Lorg/springframework/plugin/core/PluginRegistry;
The method's class, org.springframework.plugin.core.PluginRegistry, is available from the following locations:
jar:file:/home/nmigeo/.m2/repository/org/springframework/plugin/spring-plugin-core/1.2.0.RELEASE/spring-plugin-core-1.2.0.RELEASE.jar!/org/springframework/plugin/core/PluginRegistry.class
It was loaded from the following location:
file:/home/nmigeo/.m2/repository/org/springframework/plugin/spring-plugin-core/1.2.0.RELEASE/spring-plugin-core-1.2.0.RELEASE.jar
Action:
Correct the classpath of your application so that it contains a single, compatible version of org.springframework.plugin.core.PluginRegistry
and from what I can see in the description of the error, it seems that /home/nmigeo/.m2/repository/org/springframework/plugin/spring-plugin-core/1.2.0.RELEASE/spring-plugin-core-1.2.0.RELEASE.jar is being loaded twice. and that's where the issue is.
Other than that, here are my dependencies in the pom.xml although I double checked them and I do not have any duplicates dependencies which according to other stackoverflow posts might be the source of the error.
<?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 https://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>2.2.1.RELEASE</version>
<relativePath />
<!-- lookup parent from repository -->
</parent>
<groupId>com.example</groupId>
<artifactId>RDM_backend</artifactId>
<version>0.0.1-SNAPSHOT</version>
<name>RDM_backend</name>
<description>Demo project for Spring Boot</description>
<properties>
<java.version>1.8</java.version>
</properties>
<dependencies>
<dependency>
<groupId>javax.interceptor</groupId>
<artifactId>javax.interceptor-api</artifactId>
<version>1.2</version>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-actuator</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-test</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-devtools</artifactId>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-web</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-web-services</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-data-jpa</artifactId>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-oxm</artifactId>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-beans</artifactId>
</dependency>
<dependency>
<groupId>org.xerial</groupId>
<artifactId>sqlite-jdbc</artifactId>
</dependency>
<dependency>
<groupId>org.postgresql</groupId>
<artifactId>postgresql</artifactId>
</dependency>
<dependency>
<groupId>com.vladmihalcea</groupId>
<artifactId>hibernate-types-52</artifactId>
<version>2.5.0</version>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-core</artifactId>
</dependency>
<dependency>
<groupId>io.springfox</groupId>
<artifactId>springfox-swagger2</artifactId>
<version>2.9.2</version>
</dependency>
<dependency>
<groupId>io.springfox</groupId>
<artifactId>springfox-swagger-ui</artifactId>
<version>2.9.2</version>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-configuration-processor</artifactId>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-envers</artifactId>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-maven-plugin</artifactId>
</plugin>
</plugins>
</build>
</project>
What's causing the error and as a future reference, what are the steps that I should take when trying to debug errors like those? Thank you very much.
EDIT:
The error says to check my classpath but as I have generated the spring boot project on eclipse I have a feeling that that's not the error
EDIT 2:
added the whole pom.xml instead of just the dependencies

Answer 1

The version of spring-plugin-core that you are using is incompatible with the version of Spring Data REST that you are using. Spring Boot 2.2 uses Spring Data REST 3.2 which requires spring-plugin-core 2.0.
When Maven encounters the same dependency multiple times in the dependency tree, the version of the dependency nearest the root of the tree wins. You can run mvn dependency:tree to see the tree. If you do so, you'll see that spring-plugin-core is listed as a dependency of io.springfox:springfox-swagger2 and it's using version 1.2.0.
You need to use 2.0 if you want to use Spring Data REST. Adding your own dependency on spring-plugin-core with the version 2.0.0.RELEASE will do that. However, I believe it will also break Springfox as it is not yet compatible. Please see this issue for some further details.
In short, you can either use Spring Boot 2.1.x and use Springfox or you can use Spring Boot 2.2.x but you'll have to stop using Springfox until the they've had a chance to restore compatibility and release a new version.