Error while building and running the project, java web, with jpa and Hibernate

Question

I am developing a Java Web project, using JPA, Hibernate and Maven, and when running the project, or when building the project I get the following exception:

cd E:\NetBeansProjects\mercadinho; "JAVA_HOME=C:\\Program Files\\Java\\jdk1.8.0_161" cmd /c "\"\"C:\\Program Files\\NetBeans 8.2\\java\\maven\\bin\\mvn.bat\" -Dmaven.ext.class.path=\"C:\\Program Files\\NetBeans 8.2\\java\\maven-nblib\\netbeans-eventspy.jar\" -Dfile.encoding=UTF-8 install\""
Scanning for projects...

------------------------------------------------------------------------
Building mercadinho 1.0-SNAPSHOT
------------------------------------------------------------------------
The POM for unknown.binary:hibernate-jpamodelgen-4.3.1.Final:jar:SNAPSHOT is missing, no dependency information available

--- maven-dependency-plugin:2.6:copy (default) @ mercadinho ---

--- maven-resources-plugin:2.5:resources (default-resources) @ mercadinho ---
[debug] execute contextualize
Using 'UTF-8' encoding to copy filtered resources.
Copying 1 resource

--- maven-compiler-plugin:3.1:compile (default-compile) @ mercadinho ---
Changes detected - recompiling the module!
Compiling 29 source files to E:\NetBeansProjects\mercadinho\target\classes
------------------------------------------------------------------------
BUILD FAILURE
------------------------------------------------------------------------
Total time: 9.218s
Finished at: Mon Jun 04 10:42:13 GFT 2018
Final Memory: 28M/307M
------------------------------------------------------------------------
Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.1:compile (default-compile) on project mercadinho: Fatal error compiling: java.lang.RuntimeException: javax.annotation.processing.FilerException: Attempt to recreate a file for type model.entidade.Funcionario_ -> [Help 1]

To see the full stack trace of the errors, re-run Maven with the -e switch.
Re-run Maven using the -X switch to enable full debug logging.

For more information about the errors and possible solutions, please read the following articles:
[Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException

Follow my pom.xml file:

<?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>com.mycompany</groupId>
    <artifactId>mercadinho</artifactId>
    <version>1.0-SNAPSHOT</version>
    <packaging>war</packaging>

    <name>mercadinho</name>

    <properties>
        <endorsed.dir>${project.build.directory}/endorsed</endorsed.dir>
        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
    </properties>

    <dependencies>
        <dependency>
            <groupId>org.hibernate</groupId>
            <artifactId>hibernate-core</artifactId>
            <version>5.2.10.Final</version>
        </dependency>
        <dependency>
            <groupId>postgresql</groupId>
            <artifactId>postgresql</artifactId>
            <version>9.1-901.jdbc4</version>
        </dependency>
        <dependency>
            <groupId>org.glassfish</groupId>
            <artifactId>javax.faces</artifactId>
            <version>2.2.7</version>
        </dependency>
        <dependency>
            <groupId>org.hibernate</groupId>
            <artifactId>hibernate-entitymanager</artifactId>
            <version>4.3.1.Final</version>
        </dependency>
        <!-- https://mvnrepository.com/artifact/org.hibernate/hibernate-jpamodelgen -->
        <dependency>
            <groupId>org.hibernate</groupId>
            <artifactId>hibernate-jpamodelgen</artifactId>
            <version>5.2.6.Final</version>
        </dependency>
        <dependency>
            <groupId>unknown.binary</groupId>
            <artifactId>hibernate-jpamodelgen-4.3.1.Final</artifactId>
            <version>SNAPSHOT</version>
            <scope>provided</scope>
        </dependency>
        <dependency>
            <groupId>org.eclipse.persistence</groupId>
            <artifactId>eclipselink</artifactId>
            <version>2.5.2</version>
        </dependency>
        <dependency>
            <groupId>org.eclipse.persistence</groupId>
            <artifactId>org.eclipse.persistence.jpa.modelgen.processor</artifactId>
            <version>2.5.2</version>
            <scope>provided</scope>
        </dependency>
        <dependency>
            <groupId>javax</groupId>
            <artifactId>javaee-web-api</artifactId>
            <version>6.0</version>
            <scope>provided</scope>
        </dependency>    

        <!-- https://mvnrepository.com/artifact/org.primefaces/primefaces -->
        <dependency>
            <groupId>org.primefaces</groupId>
            <artifactId>primefaces</artifactId>
            <version>5.0</version>
        </dependency>


    </dependencies>

    <build>
        <plugins>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-compiler-plugin</artifactId>
                <version>3.1</version>
                <configuration>
                    <source>1.7</source>
                    <target>1.7</target>
                    <compilerArguments>
                        <endorseddirs>${endorsed.dir}</endorseddirs>
                    </compilerArguments>
                </configuration>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-war-plugin</artifactId>
                <version>2.3</version>
                <configuration>
                    <failOnMissingWebXml>false</failOnMissingWebXml>
                </configuration>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-dependency-plugin</artifactId>
                <version>2.6</version>
                <executions>
                    <execution>
                        <phase>validate</phase>
                        <goals>
                            <goal>copy</goal>
                        </goals>
                        <configuration>
                            <outputDirectory>${endorsed.dir}</outputDirectory>
                            <silent>true</silent>
                            <artifactItems>
                                <artifactItem>
                                    <groupId>javax</groupId>
                                    <artifactId>javaee-endorsed-api</artifactId>
                                    <version>7.0</version>
                                    <type>jar</type>
                                </artifactItem>
                            </artifactItems>
                        </configuration>
                    </execution>
                </executions>
            </plugin>
        </plugins>
    </build>
    <repositories>
        <repository>
            <id>unknown-jars-temp-repo</id>
            <name>A temporary repository created by NetBeans for libraries and jars it could not identify. Please replace the dependencies in this repository with correct ones and delete this repository.</name>
            <url>file:${project.basedir}/lib</url>
        </repository>
        <repository>
            <url>http://repository.primefaces.org/</url>
            <id>PrimeFaces-maven-lib</id>
            <layout>default</layout>
            <name>Repository for library PrimeFaces-maven-lib</name>
        </repository>
    </repositories>
</project>

pom.xml modified:

http://maven.apache.org/xsd/maven-4.0.0.xsd"> 4.0.0

<groupId>com.mycompany</groupId>
<artifactId>mercadinho</artifactId>
<version>1.0-SNAPSHOT</version>
<packaging>war</packaging>

<name>mercadinho</name>

<properties>
    <endorsed.dir>${project.build.directory}/endorsed</endorsed.dir>
    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>

<dependencies>
    <dependency>
        <groupId>org.hibernate</groupId>
        <artifactId>hibernate-core</artifactId>
        <version>5.2.10.Final</version>
    </dependency>
    <dependency>
        <groupId>postgresql</groupId>
        <artifactId>postgresql</artifactId>
        <version>9.1-901.jdbc4</version>
    </dependency>
    <dependency>
        <groupId>org.glassfish</groupId>
        <artifactId>javax.faces</artifactId>
        <version>2.2.7</version>
    </dependency>

    <!-- https://mvnrepository.com/artifact/org.hibernate/hibernate-jpamodelgen -->
    <dependency>
        <groupId>org.hibernate</groupId>
        <artifactId>hibernate-jpamodelgen</artifactId>
        <version>4.3.1.Final</version>
        <scope>provided</scope>
    </dependency>

    <!-- https://mvnrepository.com/artifact/org.primefaces/primefaces -->
    <dependency>
        <groupId>org.primefaces</groupId>
        <artifactId>primefaces</artifactId>
        <version>5.0</version>
    </dependency>  

    <!-- https://mvnrepository.com/artifact/javax/javaee-api -->
    <dependency>
        <groupId>javax</groupId>
        <artifactId>javaee-api</artifactId>
        <version>7.0</version>
        <scope>provided</scope>
    </dependency>



</dependencies>

<build>
    <plugins>
        <plugin>
            <groupId>org.apache.maven.plugins</groupId>
            <artifactId>maven-compiler-plugin</artifactId>
            <version>3.1</version>
            <configuration>
                <source>1.7</source>
                <target>1.7</target>
                <compilerArguments>
                    <endorseddirs>${endorsed.dir}</endorseddirs>
                </compilerArguments>
            </configuration>
        </plugin>
        <plugin>
            <groupId>org.apache.maven.plugins</groupId>
            <artifactId>maven-war-plugin</artifactId>
            <version>2.3</version>
            <configuration>
                <failOnMissingWebXml>false</failOnMissingWebXml>
            </configuration>
        </plugin>
        <plugin>
            <groupId>org.apache.maven.plugins</groupId>
            <artifactId>maven-dependency-plugin</artifactId>
            <version>2.6</version>
            <executions>
                <execution>
                    <phase>validate</phase>
                    <goals>
                        <goal>copy</goal>
                    </goals>
                    <configuration>
                        <outputDirectory>${endorsed.dir}</outputDirectory>
                        <silent>true</silent>
                        <artifactItems>
                            <artifactItem>
                                <groupId>javax</groupId>
                                <artifactId>javaee-endorsed-api</artifactId>
                                <version>7.0</version>
                                <type>jar</type>
                            </artifactItem>
                        </artifactItems>
                    </configuration>
                </execution>
            </executions>
        </plugin>
    </plugins>
</build>
<repositories>
    <repository>
        <id>unknown-jars-temp-repo</id>
        <name>A temporary repository created by NetBeans for libraries and jars it could not identify. Please replace the dependencies in this repository with correct ones and delete this repository.</name>
        <url>file:${project.basedir}/lib</url>
    </repository>
    <repository>
        <url>http://repository.primefaces.org/</url>
        <id>PrimeFaces-maven-lib</id>
        <layout>default</layout>
        <name>Repository for library PrimeFaces-maven-lib</name>
    </repository>
</repositories>

Answer 1

The problem you’re having is mostly in this part of pom.xml:

        <dependency>
            <groupId>org.hibernate</groupId>
            <artifactId>hibernate-core</artifactId>
            <version>5.2.10.Final</version>
        </dependency>
        <!-- ... Outras dependências aqui que não dizem respeito ao problema... -->
        <dependency>
            <groupId>org.hibernate</groupId>
            <artifactId>hibernate-entitymanager</artifactId>
            <version>4.3.1.Final</version>
        </dependency>
        <!-- https://mvnrepository.com/artifact/org.hibernate/hibernate-jpamodelgen -->
        <dependency>
            <groupId>org.hibernate</groupId>
            <artifactId>hibernate-jpamodelgen</artifactId>
            <version>5.2.6.Final</version>
        </dependency>
        <dependency>
            <groupId>unknown.binary</groupId>
            <artifactId>hibernate-jpamodelgen-4.3.1.Final</artifactId>
            <version>SNAPSHOT</version>
            <scope>provided</scope>
        </dependency>
        <dependency>
            <groupId>org.eclipse.persistence</groupId>
            <artifactId>eclipselink</artifactId>
            <version>2.5.2</version>
        </dependency>
        <dependency>
            <groupId>org.eclipse.persistence</groupId>
            <artifactId>org.eclipse.persistence.jpa.modelgen.processor</artifactId>
            <version>2.5.2</version>
            <scope>provided</scope>
        </dependency>

The dependencies that are declared in this section are the following:

• org.hibernate:hibernate-core:5.2.10.Final

• org.hibernate:hibernate-entitymanager:4.3.1.Final

• org.hibernate:hibernate-jpamodelgen:5.2.6.Final

• unknown.binary:hibernate-jpamodelgen-4.3.1.Final:SNAPSHOT (provided)

• org.eclipse.persistence:eclipselink:2.5.2

• org.eclipse.persistence:org.eclipse.persistence.jpa.modelgen.processor:2.5.2 (provided)

The first problem is that you are mixing dependencies from 4 different versions of Hibernate (5.2.10.Final, 4.3.1.Final, 5.2.6.Final and this weird thing with SNAPSHOT). Use only one and only one version. The most recent is the 5.3.1.Final. Incidentally, in the version 5.3.1.Final, the hibernate-entitymanager is found deprecated, only the use of hibernate-core.

The second problem is that you can only have one modelgen. That one modelgen is an annotation processor that generates additional classes at compile time, such as the class model.entidade.Funcionario_ from the class model.entidade.Funcionario (understand the _ at the end of the generated class name). However, you are trying to use 3 modelgens distinct. The result is that the second will error because the class to be generated already exists. This is the build error you have.

The third problem is that once you can only have one modelgen, You have to choose between Hibernate or Eclipselink, you can’t have both. If you really need to use both, I suggest separating the classes you need from the modelgen hibernate in a JAR or module A to be compiled separately and the classes that need the modelgen Eclipselink in JAR or B module also to be compiled separately.

The fourth problem is that whatever the modelgen that you will use, it should be provided. The org.hibernate:hibernate-jpamodelgen:5.2.6.Final is not provided.

The fifth problem is that unknown.binary:hibernate-jpamodelgen-4.3.1.Final:SNAPSHOT is an aberration. It appears to be just a misdefined duplicate of modelgen Hibernate. It makes no sense to use it. It seems to have been automatically placed by Netbeans into the repository he invented unknown-jars-temp-repo. However, this is just a ploy that Netbeans does so that individual Jars can be used in Maven. Even, see the description of this repository as it is in your pom.xml:

A Temporary Repository created by Netbeans for Libraries and jars it could not identify. Please replace the dependencies in this Repository with correct ones and delete this Repository.

Translating (my own emphasis):

A temporary repository created by Netbeans for libraries and jars that he could not identify. Please replace the dependencies of this repository with the correct ones and delete this repository.

There is also a sixth problem which is a different thing. See:

        <dependency>
            <groupId>javax</groupId>
            <artifactId>javaee-web-api</artifactId>
            <version>6.0</version>
            <scope>provided</scope>
        </dependency>   

        <!-- ... Um monte de coisas omitidas aqui... -->

                                <artifactItem>
                                    <groupId>javax</groupId>
                                    <artifactId>javaee-endorsed-api</artifactId>
                                    <version>7.0</version>
                                    <type>jar</type>
                                </artifactItem>

Note that in one of them you use the version 6.0 and the other 7.0.

Considering all this, it is recommended to use variables to declare the versions of the artifacts to facilitate the change of them when necessary in one place, avoiding that they remain incoherent. A few years ago, I already lost a few days of work bumping my head because of incoherent versions that could easily be solved if the project used this approach. The pom.xml also becomes easier to read and understand when different artifacts of the same version of the same project come together.

Another detail that I note is that the latest version of Hibernate that worked on Java 7 is the 5.1.14.Final. Despite this, you are already trying to use the 5.2.6.Final and the 5.2.10.Final that only run from Java 8. Therefore, I suggest changing your maven-compiler-plugin for Java 8 at least.

You can also put plugins in newer versions. 3.7.0 to the maven-compiler-plugin, 3.2.1 to the maven-war-plugin and 3.1.1 to the maven-dependency-plugin.

I have never seen a case where it makes sense to use both Hibernate and Eclipselink in the same project, so I believe you want to use only Hibernate and leave Eclipselink aside. Therefore, its pom.xml would look like this:

<?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>com.mycompany</groupId>
    <artifactId>mercadinho</artifactId>
    <version>1.0-SNAPSHOT</version>
    <packaging>war</packaging>

    <name>mercadinho</name>

    <properties>
        <endorsed.dir>${project.build.directory}/endorsed</endorsed.dir>
        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>

        <hibernate.version>5.3.1.Final</hibernate.version>
        <postgresql.version>9.1-901.jdbc4</postgresql.version>
        <jsf.version>2.2.7</jsf.version>
        <primefaces.version>5.0</primefaces.version>
        <javaee.version>7.0</javaee.version>

        <java.version>8</java.version>
        <compiler.plugin.version>3.7.0</compiler.plugin.version>
        <war.plugin.version>3.2.1</war.plugin.version>
        <dependency.plugin.version>3.1.1</dependency.plugin.version>
    </properties>

    <dependencies>

        <!-- PostgreSQL. -->
        <dependency>
            <groupId>postgresql</groupId>
            <artifactId>postgresql</artifactId>
            <version>${postgresql.version}</version>
        </dependency>

        <!-- JSF. -->
        <dependency>
            <groupId>org.glassfish</groupId>
            <artifactId>javax.faces</artifactId>
            <version>${jsf.version}</version>
        </dependency>

        <!-- Primefaces. -->
        <dependency>
            <groupId>org.primefaces</groupId>
            <artifactId>primefaces</artifactId>
            <version>${primefaces.version}</version>
        </dependency>

        <!-- Java EE. -->
        <dependency>
            <groupId>javax</groupId>
            <artifactId>javaee-web-api</artifactId>
            <version>${javaee.version}</version>
            <scope>provided</scope>
        </dependency>  

        <!-- Hibernate. -->
        <dependency>
            <groupId>org.hibernate</groupId>
            <artifactId>hibernate-core</artifactId>
            <version>${hibernate.version}</version>
        </dependency>
        <dependency>
            <groupId>org.hibernate</groupId>
            <artifactId>hibernate-jpamodelgen</artifactId>
            <version>${hibernate.version}</version>
            <scope>provided</scope>
        </dependency>  
    </dependencies>

    <build>
        <plugins>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-compiler-plugin</artifactId>
                <version>${compiler.plugin.version}</version>
                <configuration>
                    <source>${java.version}</source>
                    <target>${java.version}</target>
                    <compilerArguments>
                        <endorseddirs>${endorsed.dir}</endorseddirs>
                    </compilerArguments>
                </configuration>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-war-plugin</artifactId>
                <version>${war.plugin.version}</version>
                <configuration>
                    <failOnMissingWebXml>false</failOnMissingWebXml>
                </configuration>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-dependency-plugin</artifactId>
                <version>${dependency.plugin.version}</version>
                <executions>
                    <execution>
                        <phase>validate</phase>
                        <goals>
                            <goal>copy</goal>
                        </goals>
                        <configuration>
                            <outputDirectory>${endorsed.dir}</outputDirectory>
                            <silent>true</silent>
                            <artifactItems>
                                <artifactItem>
                                    <groupId>javax</groupId>
                                    <artifactId>javaee-endorsed-api</artifactId>
                                    <version>${javaee.version}</version>
                                    <type>jar</type>
                                </artifactItem>
                            </artifactItems>
                        </configuration>
                    </execution>
                </executions>
            </plugin>
        </plugins>
    </build>
    <repositories>
        <repository>
            <url>http://repository.primefaces.org/</url>
            <id>PrimeFaces-maven-lib</id>
            <layout>default</layout>
            <name>Repository for library PrimeFaces-maven-lib</name>
        </repository>
    </repositories>
</project>