GraalVM native image not working with logs

GraalVM native image not working with logs - java

What I try to do:
mvn package -Dpackaging=docker-native -Dmicronaut.runtime=lambda -Pgraalvm
what I get:
Caused by: com.oracle.graal.pointsto.constraints.UnsupportedFeatureException:
No instances of org.apache.logging.slf4j.SLF4JLogger
are allowed in the image heap as this class should be initialized at image runtime.
ok! Let me just trace the instantiation and find the issue:
[INFO] Caused by: com.oracle.graal.pointsto.constraints.UnsupportedFeatureException: No instances of org.apache.logging.slf4j.SLF4JLogger are allowed in the image heap as this class should be initialized at image runtime. Object has been initialized by the org.hibernate.internal.util.SerializationHelper class initializer with a trace:
at org.apache.logging.slf4j.SLF4JLogger.<init>(SLF4JLogger.java:41)
at org.apache.logging.slf4j.SLF4JLoggerContext.getLogger(SLF4JLoggerContext.java:36)
at org.apache.logging.log4j.LogManager.getLogger(LogManager.java:666)
at org.jboss.logging.Log4j2Logger.<init>(Log4j2Logger.java:36)
at org.jboss.logging.Log4j2LoggerProvider.getLogger(Log4j2LoggerProvider.java:30)
at org.jboss.logging.Log4j2LoggerProvider.getLogger(Log4j2LoggerProvider.java:26)
at org.jboss.logging.Logger.getLogger(Logger.java:2465)
at org.jboss.logging.Logger.doGetMessageLogger(Logger.java:2573)
at org.jboss.logging.Logger.getMessageLogger(Logger.java:2530)
at org.jboss.logging.Logger.getMessageLogger(Logger.java:2516)
at org.hibernate.internal.CoreLogging.messageLogger(CoreLogging.java:28)
at org.hibernate.internal.CoreLogging.messageLogger(CoreLogging.java:24)
at org.hibernate.internal.util.SerializationHelper.<clinit>(SerializationHelper.java:47)
. To fix the issue mark org.apache.logging.slf4j.SLF4JLogger for build-time initialization with --initialize-at-build-time=org.apache.logging.slf4j.SLF4JLogger or use the the information from the trace to find the culprit and --initialize-at-run-time=<culprit> to prevent its instantiation.
Sounds promising!
Trying with --initialize-at-build-time=org.apache.logging.slf4j.SLF4JLogger:
[INFO] Error: Classes that should be initialized at run time got initialized during image building:
org.apache.logging.log4j.util.ProviderUtil was unintentionally initialized at build time. To see why org.apache.logging.log4j.util.ProviderUtil got initialized use --trace-class-initialization=org.apache.logging.log4j.util.ProviderUtil
org.apache.logging.log4j.util.PropertySource$Util was unintentionally initialized at build time. To see why org.apache.logging.log4j.util.PropertySource$Util got initialized use --trace-class-initialization=org.apache.logging.log4j.util.PropertySource$Util
org.apache.logging.log4j.LogManager was unintentionally initialized at build time. To see why org.apache.logging.log4j.LogManager got initialized use --trace-class-initialization=org.apache.logging.log4j.LogManager
org.apache.logging.log4j.spi.Provider was unintentionally initialized at build time. To see why org.apache.logging.log4j.spi.Provider got initialized use --trace-class-initialization=org.apache.logging.log4j.spi.Provider
org.apache.logging.log4j.Level was unintentionally initialized at build time. To see why org.apache.logging.log4j.Level got initialized use --trace-class-initialization=org.apache.logging.log4j.Level
org.apache.logging.slf4j.SLF4JLogger$1 was unintentionally initialized at build time. To see why org.apache.logging.slf4j.SLF4JLogger$1 got initialized use --trace-class-initialization=org.apache.logging.slf4j.SLF4JLogger$1
org.apache.logging.log4j.util.Constants was unintentionally initialized at build time. To see why org.apache.logging.log4j.util.Constants got initialized use --trace-class-initialization=org.apache.logging.log4j.util.Constants
org.apache.logging.log4j.util.LoaderUtil was unintentionally initialized at build time. To see why org.apache.logging.log4j.util.LoaderUtil got initialized use --trace-class-initialization=org.apache.logging.log4j.util.LoaderUtil
org.apache.logging.log4j.spi.StandardLevel was unintentionally initialized at build time. To see why org.apache.logging.log4j.spi.StandardLevel got initialized use --trace-class-initialization=org.apache.logging.log4j.spi.StandardLevel
org.apache.logging.log4j.util.Strings was unintentionally initialized at build time. To see why org.apache.logging.log4j.util.Strings got initialized use --trace-class-initialization=org.apache.logging.log4j.util.Strings
org.apache.logging.log4j.util.PropertiesUtil was unintentionally initialized at build time. To see why org.apache.logging.log4j.util.PropertiesUtil got initialized use --trace-class-initialization=org.apache.logging.log4j.util.PropertiesUtil
org.apache.logging.log4j.status.StatusLogger was unintentionally initialized at build time. To see why org.apache.logging.log4j.status.StatusLogger got initialized use --trace-class-initialization=org.apache.logging.log4j.status.StatusLogger
org.apache.logging.log4j.spi.LoggerRegistry was unintentionally initialized at build time. To see why org.apache.logging.log4j.spi.LoggerRegistry got initialized use --trace-class-initialization=org.apache.logging.log4j.spi.LoggerRegistry
okay.... but I can try the other option!
try with: --initialize-at-run-time=<culprit>. According to logs the culprit was org.hibernate.internal.util.SerializationHelper:
[INFO] Caused by: com.oracle.graal.pointsto.constraints.UnsupportedFeatureException: No instances of org.apache.logging.slf4j.SLF4JLogger are allowed in the image heap as this class should be initialized at image runtime. Object has been initialized by the org.hibernate.internal.log.DeprecationLogger class initializer with a trace:
at org.apache.logging.slf4j.SLF4JLogger.<init>(SLF4JLogger.java:41)
at org.apache.logging.slf4j.SLF4JLoggerContext.getLogger(SLF4JLoggerContext.java:36)
at org.apache.logging.log4j.LogManager.getLogger(LogManager.java:666)
at org.jboss.logging.Log4j2Logger.<init>(Log4j2Logger.java:36)
at org.jboss.logging.Log4j2LoggerProvider.getLogger(Log4j2LoggerProvider.java:30)
at org.jboss.logging.Log4j2LoggerProvider.getLogger(Log4j2LoggerProvider.java:26)
at org.jboss.logging.Logger.getLogger(Logger.java:2465)
at org.jboss.logging.Logger.doGetMessageLogger(Logger.java:2573)
at org.jboss.logging.Logger.getMessageLogger(Logger.java:2530)
at org.jboss.logging.Logger.getMessageLogger(Logger.java:2516)
at org.hibernate.internal.log.DeprecationLogger.<clinit>(DeprecationLogger.java:29)
. To fix the issue mark org.apache.logging.slf4j.SLF4JLogger for build-time initialization with --initialize-at-build-time=org.apache.logging.slf4j.SLF4JLogger or use the the information from the trace to find the culprit and --initialize-at-run-time=<culprit> to prevent its instantiation.
Looks like there wasn't only one culprit? okay this time for sure it will work!
including second cuplrit:
[INFO] Caused by: com.oracle.graal.pointsto.constraints.UnsupportedFeatureException:
No instances of org.apache.logging.slf4j.SLF4JLogger are allowed in the image heap as this class should be initialized at image runtime.
Object has been initialized by the org.hibernate.internal.SessionFactoryRegistry class initializer with a trace:
There is no end to this!
Going for the whole package: --initialize-at-run-time=org.hibernate:
[INFO] Caused by: com.oracle.graal.pointsto.constraints.UnsupportedFeatureException: No instances of org.apache.logging.slf4j.SLF4JLogger are allowed in the image heap as this class should be initialized at image runtime. Object has been initialized by the org.hibernate.internal.util.SerializationHelper class initializer with a trace:
Let's try to go back to --initialize-at-build-time=org.apache.logging.slf4j.SLF4JLogger but instead specify the whole package: --initialize-at-build-time=org.apache.logging
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 02:08 min
[INFO] Finished at: 2022-10-14T16:33:04+03:00
[INFO] ------------------------------------------------------------------------
It's built! Now let's see if it runs!
...
Caused by: com.amazonaws.serverless.exceptions.ContainerInitializationException: Error starting Micronaut container: Bean definition [io.micronaut.configuration.hibernate.jpa.conf.SessionFactoryPerDataSourceFactory] could not be loaded: Error instantiating bean of type [io.micronaut.configuration.hibernate.jpa.conf.SessionFactoryPerDataSourceFactory]
...
Caused by: java.lang.NoSuchMethodException: org.apache.logging.log4j.message.ParameterizedMessageFactory.<init>()
...
At this point I'm out of options.
GRAALVM_VERSION: 22.2.0
GRAALVM_JVM_VERSION: java17
GRAALVM_ARCH: amd64
CLASS_NAME: io.micronaut.function.aws.runtime.MicronautLambdaRuntime
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>
<groupId>moe.sigeemu</groupId>
<artifactId>si-gameless</artifactId>
<version>0.1</version>
<packaging>${packaging}</packaging>
<parent>
<groupId>io.micronaut</groupId>
<artifactId>micronaut-parent</artifactId>
<version>3.7.1</version>
</parent>
<properties>
<packaging>jar</packaging>
<jdk.version>17</jdk.version>
<release.version>17</release.version>
<micronaut.version>3.7.1</micronaut.version>
<exec.mainClass>io.micronaut.function.aws.runtime.MicronautLambdaRuntime</exec.mainClass>
<micronaut.test.resources.enabled>true</micronaut.test.resources.enabled>
<micronaut.runtime>lambda</micronaut.runtime>
<micronaut.data.version>3.8.0</micronaut.data.version>
<vavr.version>0.10.3</vavr.version>
</properties>
<repositories>
<repository>
<id>central</id>
<url>https://repo.maven.apache.org/maven2</url>
</repository>
</repositories>
<dependencies>
<dependency>
<groupId>io.micronaut</groupId>
<artifactId>micronaut-inject</artifactId>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>io.micronaut</groupId>
<artifactId>micronaut-validation</artifactId>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>io.micronaut.aws</groupId>
<artifactId>micronaut-function-aws-api-proxy</artifactId>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>io.micronaut.aws</groupId>
<artifactId>micronaut-function-aws-api-proxy-test</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>io.micronaut.aws</groupId>
<artifactId>micronaut-function-aws-custom-runtime</artifactId>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>io.micronaut</groupId>
<artifactId>micronaut-http-client</artifactId>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>io.micronaut</groupId>
<artifactId>micronaut-jackson-databind</artifactId>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.dataformat</groupId>
<artifactId>jackson-dataformat-xml</artifactId>
<version>2.11.1</version>
</dependency>
<dependency>
<groupId>io.vavr</groupId>
<artifactId>vavr</artifactId>
<version>${vavr.version}</version>
</dependency>
<dependency>
<groupId>io.micronaut.aws</groupId>
<artifactId>micronaut-aws-sdk-v2</artifactId>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>software.amazon.awssdk</groupId>
<artifactId>s3</artifactId>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>io.micronaut.data</groupId>
<artifactId>micronaut-data-hibernate-jpa</artifactId>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>io.micronaut.flyway</groupId>
<artifactId>micronaut-flyway</artifactId>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>io.micronaut.graphql</groupId>
<artifactId>micronaut-graphql</artifactId>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>io.micronaut.sql</groupId>
<artifactId>micronaut-jdbc-hikari</artifactId>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>jakarta.annotation</groupId>
<artifactId>jakarta.annotation-api</artifactId>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>org.flywaydb</groupId>
<artifactId>flyway-mysql</artifactId>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>org.projectlombok</groupId>
<artifactId>lombok</artifactId>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>io.micronaut.test</groupId>
<artifactId>micronaut-test-junit5</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.assertj</groupId>
<artifactId>assertj-core</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-api</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-engine</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-core</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.graphql-java-generator</groupId>
<artifactId>graphql-java-runtime</artifactId>
<version>1.18</version>
<exclusions>
<exclusion>
<groupId>com.graphql-java</groupId>
<artifactId>graphql-java-spring-boot-starter-webmvc</artifactId>
</exclusion>
<exclusion>
<groupId>com.graphql-java-generator</groupId>
<artifactId>graphql-java-spring-mvc</artifactId>
</exclusion>
<exclusion>
<groupId>org.springframework</groupId>
<artifactId>*</artifactId>
</exclusion>
</exclusions>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>io.micronaut.build</groupId>
<artifactId>micronaut-maven-plugin</artifactId>
<configuration>
<nativeImageBuildArgs combine.children="append">
<nativeImageBuildArg>--trace-object-instantiation=org.apache.logging.slf4j.SLF4JLogger</nativeImageBuildArg>
<!-- <nativeImageBuildArg>--initialize-at-run-time=org.hibernate.internal.log.DeprecationLogger</nativeImageBuildArg>-->
<nativeImageBuildArg>--initialize-at-build-time=org.apache.logging</nativeImageBuildArg>
</nativeImageBuildArgs>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<!-- Uncomment to enable incremental compilation -->
<!-- <useIncrementalCompilation>false</useIncrementalCompilation> -->
<annotationProcessorPaths combine.self="override">
<path>
<groupId>org.projectlombok</groupId>
<artifactId>lombok</artifactId>
<version>${lombok.version}</version>
</path>
<path>
<groupId>io.micronaut</groupId>
<artifactId>micronaut-inject-java</artifactId>
<version>${micronaut.version}</version>
</path>
<path>
<groupId>io.micronaut.data</groupId>
<artifactId>micronaut-data-processor</artifactId>
<version>${micronaut.data.version}</version>
</path>
<path>
<groupId>io.micronaut</groupId>
<artifactId>micronaut-graal</artifactId>
<version>${micronaut.version}</version>
</path>
<path>
<groupId>io.micronaut</groupId>
<artifactId>micronaut-http-validation</artifactId>
<version>${micronaut.version}</version>
</path>
<path>
<groupId>io.micronaut</groupId>
<artifactId>micronaut-validation</artifactId>
<version>${micronaut.version}</version>
</path>
</annotationProcessorPaths>
<compilerArgs>
<arg>-Amicronaut.processing.group=moe.sigeemu</arg>
<arg>-Amicronaut.processing.module=si-gameless</arg>
</compilerArgs>
</configuration>
</plugin>
<plugin>
<groupId>com.graphql-java-generator</groupId>
<artifactId>graphql-maven-plugin</artifactId>
<version>1.18</version>
<executions>
<execution>
<goals>
<goal>generateClientCode</goal>
</goals>
</execution>
</executions>
<configuration>
<packageName>moe.sigeemu.domain.model.graphql.generated</packageName>
<copyRuntimeSources>false</copyRuntimeSources>
<generateDeprecatedRequestResponse>false</generateDeprecatedRequestResponse>
<separateUtilityClasses>true</separateUtilityClasses>
<customScalars>
<customScalar>
<graphQLTypeName>CountryCode</graphQLTypeName>
<javaType>com.nimbusds.openid.connect.sdk.assurance.claims.ISO3166_1Alpha2CountryCode</javaType>
<graphQLScalarTypeStaticField>moe.sigeemu.domain.model.scalars.GraphQLScalarTypeCountryCode.CountryCode</graphQLScalarTypeStaticField>
</customScalar>
<customScalar>
<graphQLTypeName>FuzzyDateInt</graphQLTypeName>
<javaType>java.time.LocalDate</javaType>
<graphQLScalarTypeStaticField>moe.sigeemu.domain.model.scalars.GraphQLScalarTypeFuzzyDateInt.FuzzyDateInt</graphQLScalarTypeStaticField>
</customScalar>
<customScalar>
<graphQLTypeName>Json</graphQLTypeName>
<javaType>com.fasterxml.jackson.databind.JsonNode</javaType>
<graphQLScalarTypeStaticField>moe.sigeemu.domain.model.scalars.GraphQLScalarTypeJson.Json</graphQLScalarTypeStaticField>
</customScalar>
</customScalars>
</configuration>
</plugin>
</plugins>
</build>
</project>
A cry for help to anyone who was able to read through this post and knows a little bit more about Micronaut and GraalVM: what am doing wrong? I'm desperate and want to go back to Spring since there is little to no info on the internet about native images T_T

I had a similar issue:
First I had this error:
UnresolvedElementException: Discovered unresolved method during parsing: io.netty.util.internal.logging.Log4J2Logger
Then after adding the following dependency: implementation("org.jboss.logmanager:log4j2-jboss-logmanager") as documented here on Quarkus website I had this one:
Discovered unresolved type during parsing: org.apache.log4j.Logger
I finally added these two dependencies and I was passed that Logging related errors and on to other but its ok, its progress!!!
implementation("org.jboss.logging:commons-logging-jboss-logging")
implementation("org.jboss.logmanager:log4j-jboss-logmanager")
implementation("org.jboss.slf4j:slf4j-jboss-logmanager")

Related

Many errors while running Renjin with packages in Eclipse

I've been trying to run some simple code from the first lesson of R for Data Science using Renjin in Eclipse. The reason I'm using Renjin is because I'm eventually going to develop this into a Java data analysis program. Here is the link to the R for Data Science lesson I'm following: https://r4ds.had.co.nz/data-visualisation.html
I got all my dependencies in the pom.xml file of my Maven project, and when I test my pom.xml file, it builds successfully. Here's my pom.xml just in case:
<?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>Tests</groupId>
<artifactId>Test1</artifactId>
<version>0.0.1-SNAPSHOT</version>
<name>Test1</name>
<!-- FIXME change it to the project's website -->
<url>http://www.example.com</url>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<maven.compiler.source>1.7</maven.compiler.source>
<maven.compiler.target>1.7</maven.compiler.target>
</properties>
<dependencies>
<dependency>
<groupId>org.renjin</groupId>
<artifactId>renjin-script-engine</artifactId>
<version>3.5-beta76</version>
</dependency>
<dependency>
<groupId>org.renjin.cran</groupId>
<artifactId>ggplot2</artifactId>
<version>3.2.0-b8</version>
</dependency>
<dependency>
<groupId>org.renjin.cran</groupId>
<artifactId>dplyr</artifactId>
<version>0.8.2-b6</version>
</dependency>
<dependency>
<groupId>org.renjin.cran</groupId>
<artifactId>feather</artifactId>
<version>0.3.1-b9</version>
</dependency>
<dependency>
<groupId>org.renjin.cran</groupId>
<artifactId>hms</artifactId>
<version>0.4.2-b18</version>
</dependency>
<dependency>
<groupId>org.renjin.cran</groupId>
<artifactId>stringr</artifactId>
<version>1.4.0-b6</version>
</dependency>
<dependency>
<groupId>org.renjin.cran</groupId>
<artifactId>lubridate</artifactId>
<version>1.7.4-b4</version>
</dependency>
<dependency>
<groupId>org.renjin.cran</groupId>
<artifactId>forcats</artifactId>
<version>0.3.0-b9</version>
</dependency>
<dependency>
<groupId>org.renjin.cran</groupId>
<artifactId>haven</artifactId>
<version>2.0.0-b1</version>
</dependency>
<dependency>
<groupId>org.renjin.cran</groupId>
<artifactId>httr</artifactId>
<version>1.4.0-b1</version>
</dependency>
<dependency>
<groupId>org.renjin.cran</groupId>
<artifactId>jsonlite</artifactId>
<version>1.6-b1</version>
</dependency>
<dependency>
<groupId>org.renjin.cran</groupId>
<artifactId>readxl</artifactId>
<version>1.3.1-b11</version>
</dependency>
<dependency>
<groupId>org.renjin.cran</groupId>
<artifactId>rvest</artifactId>
<version>0.3.2-b115</version>
</dependency>
<dependency>
<groupId>org.renjin.cran</groupId>
<artifactId>xml2</artifactId>
<version>1.2-renjin-8</version>
</dependency>
<dependency>
<groupId>org.renjin.cran</groupId>
<artifactId>modelr</artifactId>
<version>0.1.1-b31</version>
</dependency>
<dependency>
<groupId>org.renjin.cran</groupId>
<artifactId>broom</artifactId>
<version>0.4.4-b1</version>
</dependency>
<dependency>
<groupId>org.renjin.cran</groupId>
<artifactId>tidyr</artifactId>
<version>0.8.0-b1</version>
</dependency>
<dependency>
<groupId>org.renjin.cran</groupId>
<artifactId>readr</artifactId>
<version>1.3.1-b3</version>
</dependency>
<dependency>
<groupId>org.renjin.cran</groupId>
<artifactId>purrr</artifactId>
<version>0.3.2-b11</version>
</dependency>
<dependency>
<groupId>org.renjin.cran</groupId>
<artifactId>tibble</artifactId>
<version>2.1.3-b9</version>
</dependency>
</dependencies>
<build>
<pluginManagement><!-- lock down plugins versions to avoid using Maven defaults (may be moved to parent pom) -->
<plugins>
<!-- clean lifecycle, see https://maven.apache.org/ref/current/maven-core/lifecycles.html#clean_Lifecycle -->
<plugin>
<artifactId>maven-clean-plugin</artifactId>
<version>3.1.0</version>
</plugin>
<!-- default lifecycle, jar packaging: see https://maven.apache.org/ref/current/maven-core/default-bindings.html#Plugin_bindings_for_jar_packaging -->
<plugin>
<artifactId>maven-resources-plugin</artifactId>
<version>3.0.2</version>
</plugin>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.8.0</version>
</plugin>
<plugin>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.22.1</version>
</plugin>
<plugin>
<artifactId>maven-jar-plugin</artifactId>
<version>3.0.2</version>
</plugin>
<plugin>
<artifactId>maven-install-plugin</artifactId>
<version>2.5.2</version>
</plugin>
<plugin>
<artifactId>maven-deploy-plugin</artifactId>
<version>2.8.2</version>
</plugin>
<!-- site lifecycle, see https://maven.apache.org/ref/current/maven-core/lifecycles.html#site_Lifecycle -->
<plugin>
<artifactId>maven-site-plugin</artifactId>
<version>3.7.1</version>
</plugin>
<plugin>
<artifactId>maven-project-info-reports-plugin</artifactId>
<version>3.0.0</version>
</plugin>
</plugins>
</pluginManagement>
</build>
<repositories>
<repository>
<id>bedatadriven</id>
<name>bedatadriven public repo</name>
<url>https://nexus.bedatadriven.com/content/groups/public/</url>
</repository>
</repositories>
</project>
However, when I try to run my App.java program with the R for Data Science code, it gives me loads of errors. Here is my App.java:
package Tests.Test1;
import javax.script.*;
import org.renjin.script.*;
import java.awt.*;
import javax.swing.*;
// ... add additional imports here ...
public class App {
public static void main(String[] args) throws Exception {
// create a script engine manager:
RenjinScriptEngineFactory factory = new RenjinScriptEngineFactory();
// create a Renjin engine:
ScriptEngine engine = factory.getScriptEngine();
// ... put your Java code here ...
engine.eval("library(dplyr)");
engine.eval("library(ggplot2)");
engine.eval("library(tidyr)");
engine.eval("library(readr)");
engine.eval("library(purrr)");
engine.eval("library(tibble)");
engine.eval("?mpg");
engine.eval("ggplot(data = mpg) + geom_point(mapping = aes(x = displ, y = hwy))");
}
}
And here's the long list of errors I'm getting:
EEK! colSums.computeMeans() called through getElementAsDouble()
EEK! colSums.computeMeans() called through getElementAsDouble()
EEK! colSums.computeMeans() called through getElementAsDouble()
EEK! colSums.computeMeans() called through getElementAsDouble()
org.renjin.eval.EvalException: Exception initializing compiled GNU R library class org.renjin.cran.dplyr.dplyr
at org.renjin.primitives.packaging.DllInfo.initialize(DllInfo.java:141)
at org.renjin.primitives.packaging.Namespace.loadDynamicLibrary(Namespace.java:383)
at org.renjin.primitives.packaging.Namespace.importDynamicLibrary(Namespace.java:296)
at org.renjin.primitives.packaging.Namespace.initImports(Namespace.java:274)
at org.renjin.primitives.packaging.NamespaceRegistry.load(NamespaceRegistry.java:175)
at org.renjin.primitives.packaging.NamespaceRegistry.getNamespace(NamespaceRegistry.java:143)
at org.renjin.primitives.packaging.NamespaceRegistry.getNamespace(NamespaceRegistry.java:114)
at org.renjin.primitives.packaging.Packages.library(Packages.java:39)
at org.renjin.primitives.R$primitive$library.doApply(R$primitive$library.java:68)
at org.renjin.primitives.R$primitive$library.applyPromised(R$primitive$library.java:33)
at org.renjin.sexp.BuiltinFunction.apply(BuiltinFunction.java:100)
at org.renjin.primitives.special.InternalFunction.apply(InternalFunction.java:46)
at org.renjin.sexp.FunctionCall.eval(FunctionCall.java:80)
at org.renjin.primitives.special.BeginFunction.apply(BeginFunction.java:39)
at org.renjin.sexp.FunctionCall.eval(FunctionCall.java:80)
at org.renjin.sexp.Closure.applyPromised(Closure.java:200)
at org.renjin.sexp.Closure.apply(Closure.java:133)
at org.renjin.sexp.FunctionCall.eval(FunctionCall.java:80)
at org.renjin.sexp.ExpressionVector.eval(ExpressionVector.java:85)
at org.renjin.eval.Context.evaluate(Context.java:280)
at org.renjin.script.RenjinScriptEngine.eval(RenjinScriptEngine.java:174)
at org.renjin.script.RenjinScriptEngine.eval(RenjinScriptEngine.java:133)
at Tests.Test1.App.main(App.java:19)
Caused by: java.lang.ArithmeticException: / by zero
at java.base/java.lang.Integer.remainderUnsigned(Integer.java:1564)
at org.renjin.cran.dplyr.hybrid__._ZN5boost9unordered6detail12prime_policyIjE9to_bucketEjj(hybrid.cpp)
at org.renjin.cran.dplyr.hybrid__._ZNK5boost9unordered6detail5tableINS1_3mapISaISt4pairIKP7SEXPRECN5dplyr6hybrid15hybrid_functionEEES6_SA_NS_4hashIS6_EESt8equal_toIS6_EEEE14hash_to_bucketEj(hybrid.cpp)
at org.renjin.cran.dplyr.hybrid__._ZNK5boost9unordered6detail5tableINS1_3mapISaISt4pairIKP7SEXPRECN5dplyr6hybrid15hybrid_functionEEES6_SA_NS_4hashIS6_EESt8equal_toIS6_EEEE14find_node_implIS6_SG_EEPNS1_8ptr_nodeISB_EEjRKT_RKT0_(hybrid.cpp)
at org.renjin.cran.dplyr.hybrid__._ZNK5boost9unordered6detail5tableINS1_3mapISaISt4pairIKP7SEXPRECN5dplyr6hybrid15hybrid_functionEEES6_SA_NS_4hashIS6_EESt8equal_toIS6_EEEE9find_nodeEjRS7_(hybrid.cpp)
at org.renjin.cran.dplyr.hybrid__._ZN5boost9unordered6detail5tableINS1_3mapISaISt4pairIKP7SEXPRECN5dplyr6hybrid15hybrid_functionEEES6_SA_NS_4hashIS6_EESt8equal_toIS6_EEEE14emplace_uniqueINS1_13emplace_args1ISB_EEEES4_INS0_15iterator_detail8iteratorINS1_8ptr_nodeISB_EEEEbERS7_RKT_(hybrid.cpp)
at org.renjin.cran.dplyr.hybrid__._ZN5boost9unordered13unordered_mapIP7SEXPRECN5dplyr6hybrid15hybrid_functionENS_4hashIS3_EESt8equal_toIS3_ESaISt4pairIKS3_S6_EEE7emplaceISD_EESB_INS0_15iterator_detail8iteratorINS0_6detail8ptr_nodeISD_EEEEbERKT_(hybrid.cpp)
at org.renjin.cran.dplyr.hybrid__._ZN5boost9unordered13unordered_mapIP7SEXPRECN5dplyr6hybrid15hybrid_functionENS_4hashIS3_EESt8equal_toIS3_ESaISt4pairIKS3_S6_EEE6insertERKSD_(hybrid.cpp)
at org.renjin.cran.dplyr.hybrid__._ZN5dplyr6hybrid11hybrid_initEP7SEXPRECS2_S2_NS0_9hybrid_idE(hybrid.cpp)
at org.renjin.cran.dplyr.hybrid__._ZN5dplyr6hybrid4initEv(hybrid.cpp)
at org.renjin.cran.dplyr.hybrid__._Z22init_hybrid_inline_mapP8_DllInfo(hybrid.cpp)
at org.renjin.cran.dplyr.RcppExports__.R_init_dplyr(RcppExports.cpp)
at org.renjin.cran.dplyr.dplyr.R_init_dplyr(Unknown Source)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:78)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:567)
at org.renjin.primitives.packaging.DllInfo.initialize(DllInfo.java:137)
... 22 more
org.renjin.eval.EvalException: Exception initializing compiled GNU R library class org.renjin.cran.tidyr.tidyr
at org.renjin.primitives.packaging.DllInfo.initialize(DllInfo.java:141)
at org.renjin.primitives.packaging.Namespace.loadDynamicLibrary(Namespace.java:383)
at org.renjin.primitives.packaging.Namespace.importDynamicLibrary(Namespace.java:296)
at org.renjin.primitives.packaging.Namespace.initImports(Namespace.java:274)
at org.renjin.primitives.packaging.NamespaceRegistry.load(NamespaceRegistry.java:175)
at org.renjin.primitives.packaging.NamespaceRegistry.getNamespace(NamespaceRegistry.java:143)
at org.renjin.primitives.packaging.NamespaceRegistry.getNamespace(NamespaceRegistry.java:114)
at org.renjin.primitives.packaging.Packages.library(Packages.java:39)
at org.renjin.primitives.R$primitive$library.doApply(R$primitive$library.java:68)
at org.renjin.primitives.R$primitive$library.applyPromised(R$primitive$library.java:33)
at org.renjin.sexp.BuiltinFunction.apply(BuiltinFunction.java:100)
at org.renjin.primitives.special.InternalFunction.apply(InternalFunction.java:46)
at org.renjin.sexp.FunctionCall.eval(FunctionCall.java:80)
at org.renjin.primitives.special.BeginFunction.apply(BeginFunction.java:39)
at org.renjin.sexp.FunctionCall.eval(FunctionCall.java:80)
at org.renjin.sexp.Closure.applyPromised(Closure.java:200)
at org.renjin.sexp.Closure.apply(Closure.java:133)
at org.renjin.sexp.FunctionCall.eval(FunctionCall.java:80)
at org.renjin.sexp.ExpressionVector.eval(ExpressionVector.java:85)
at org.renjin.eval.Context.evaluate(Context.java:280)
at org.renjin.script.RenjinScriptEngine.eval(RenjinScriptEngine.java:174)
at org.renjin.script.RenjinScriptEngine.eval(RenjinScriptEngine.java:133)
at Tests.Test1.App.main(App.java:21)
Caused by: java.lang.NoSuchFieldError: _ZTVN10__cxxabiv120__si_class_type_infoE
at org.renjin.cran.tidyr.RcppExports__._ZTIN4Rcpp9exceptionE$$clinit(RcppExports.cpp)
at org.renjin.cran.tidyr.RcppExports__.<clinit>(RcppExports.cpp)
at org.renjin.cran.tidyr.tidyr.R_init_tidyr(Unknown Source)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:78)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:567)
at org.renjin.primitives.packaging.DllInfo.initialize(DllInfo.java:137)
... 22 more
I'm not quite sure how to get the code to work. If you have any ideas on how to fix this, I'd love to hear them. Please keep in mind that I am a beginner though, and I may need things in simpler/more thorough terms. If you need any more information, let me know, and I'll respond as soon as possible. Any and all help is appreciated. Thank you.

Package 'com.example' reads package 'javafx.beans' from both 'javafx.base' and 'javafx.base' -- how to solve?

I try to add some class of java RMI that works fine in separate project.
When i added the classes to my java fx project , i have got this error:
Package 'com.example' reads package 'javafx.beans' from both 'javafx.base' and 'javafx.base'
this is my pom.xml:enter image description here
<?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>
<groupId>com.example</groupId>
<artifactId>FXtest</artifactId>
<version>1.0-SNAPSHOT</version>
<name>FXtest</name>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<junit.version>5.8.1</junit.version>
</properties>
<dependencies>
<dependency>
<groupId>org.openjfx</groupId>
<artifactId>javafx-controls</artifactId>
<version>17.0.1</version>
</dependency>
<dependency>
<groupId>org.openjfx</groupId>
<artifactId>javafx-fxml</artifactId>
<version>17.0.1</version>
</dependency>
<dependency>
<groupId>org.openjfx</groupId>
<artifactId>javafx-web</artifactId>
<version>17.0.1</version>
</dependency>
<dependency>
<groupId>org.controlsfx</groupId>
<artifactId>controlsfx</artifactId>
<version>11.1.0</version>
</dependency>
<dependency>
<groupId>com.dlsc.formsfx</groupId>
<artifactId>formsfx-core</artifactId>
<version>11.3.2</version>
<exclusions>
<exclusion>
<groupId>org.openjfx</groupId>
<artifactId>*</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>net.synedra</groupId>
<artifactId>validatorfx</artifactId>
<version>0.1.13</version>
<exclusions>
<exclusion>
<groupId>org.openjfx</groupId>
<artifactId>*</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.kordamp.ikonli</groupId>
<artifactId>ikonli-javafx</artifactId>
<version>12.2.0</version>
</dependency>
<dependency>
<groupId>org.kordamp.bootstrapfx</groupId>
<artifactId>bootstrapfx-core</artifactId>
<version>0.4.0</version>
</dependency>
<dependency>
<groupId>eu.hansolo</groupId>
<artifactId>tilesfx</artifactId>
<version>11.48</version>
<exclusions>
<exclusion>
<groupId>org.openjfx</groupId>
<artifactId>*</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-api</artifactId>
<version>${junit.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-engine</artifactId>
<version>${junit.version}</version>
<scope>test</scope>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.8.1</version>
<configuration>
<source>17</source>
<target>17</target>
</configuration>
</plugin>
<plugin>
<groupId>org.openjfx</groupId>
<artifactId>javafx-maven-plugin</artifactId>
<version>0.0.8</version>
<executions>
<execution>
<!-- Default configuration for running with: mvn clean javafx:run -->
<id>default-cli</id>
<configuration>
<mainClass>com.example.fxtest/com.example.fxtest.HelloApplication</mainClass>
<launcher>app</launcher>
<jlinkZipName>app</jlinkZipName>
<jlinkImageName>app</jlinkImageName>
<noManPages>true</noManPages>
<stripDebug>true</stripDebug>
<noHeaderFiles>true</noHeaderFiles>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>
this is the console error i get when i run my rmi-server:
Exception in thread "main" java.lang.reflect.InaccessibleObjectException: Unable to make public abstract void com.example.fxtest.shared.CardgameServer.toUpperCase(java.lang.String,com.example.fxtest.shared.CardgameClient) throws java.rmi.RemoteException accessible: module com.example.fxtest does not "exports com.example.fxtest.shared" to module java.rmi
at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:354)
at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:297)
at java.base/java.lang.reflect.Method.checkCanSetAccessible(Method.java:199)
at java.base/java.lang.reflect.Method.setAccessible(Method.java:193)
at java.rmi/sun.rmi.server.UnicastServerRef$HashToMethod_Maps$1.run(UnicastServerRef.java:598)
at java.rmi/sun.rmi.server.UnicastServerRef$HashToMethod_Maps$1.run(UnicastServerRef.java:596)
at java.base/java.security.AccessController.doPrivileged(AccessController.java:318)
at java.rmi/sun.rmi.server.UnicastServerRef$HashToMethod_Maps.computeValue(UnicastServerRef.java:595)
at java.rmi/sun.rmi.server.UnicastServerRef$HashToMethod_Maps.computeValue(UnicastServerRef.java:574)
at java.rmi/sun.rmi.server.WeakClassHashMap.get(WeakClassHashMap.java:74)
at java.rmi/sun.rmi.server.UnicastServerRef.exportObject(UnicastServerRef.java:236)
at java.rmi/java.rmi.server.UnicastRemoteObject.exportObject(UnicastRemoteObject.java:475)
at java.rmi/java.rmi.server.UnicastRemoteObject.exportObject(UnicastRemoteObject.java:360)
at com.example.fxtest/com.example.fxtest.server.ServerImpl.<init>(ServerImpl.java:13)
at com.example.fxtest/com.example.fxtest.server.RunServer.main(RunServer.java:15)
i addad a photo of my module-info.java where the error is found.
any adivce will be appreciated!
thanks

To address the issue reported in the exception trace in the question body:
java.rmi.RemoteException accessible: module com.example.fxtest does not "exports com.example.fxtest.shared" to module java.rmi
you need to do what the message says.
Add to the module-info.java:
exports com.example.fxtest.shared to java.rmi;
Related question:
Unable to export a package from java.base module
For the question in the title:
Package 'com.example' reads package 'javafx.beans' from both 'javafx.base' and 'javafx.base'
There is not enough information in the question to do more than speculate on the reason for that. It is likely related to an error in your local development environment or in some aspect of your project setup. It could be that:
you are using a Java runtime that includes a different version of JavaFX
OR
have dependencies transitively on different versions of JavaFX
OR
you have some manual command-line switches to modules configured incorrectly
OR
you added a JavaFX SDK version that clashes with your dependencies
OR
you may have manually added incompatible versions of the JavaFX library manually in the IDE
OR
some 3rd party libraries you use are bundling JavaFX framework code inside them (which they should not do).
Which it is, I don’t know, but I offer the information in case it is needed.

Curious what sort of troubleshooting you attempted.
Have you tried removing the javafx-controls dependency? I think javafx-web contains javafx.controls as a transitive dependency so it may not be needed according to https://openjfx.io/javadoc/18/javafx.web/module-summary.html. Otherwise, https://openjfx.io/openjfx-docs/#maven may be a noteworthy guide.

how to fix "java.lang.NoClassDefFoundError: org/slf4j/LoggerFactory" error when run java jar application

we are using eclipse+spring tool suite to build java application, we can start the application in eclipse IDE, but if we export as jar with all dependency jars, and run it on linux machine. we always gets error as following:
Exception in thread "main" java.lang.NoClassDefFoundError: org/slf4j/LoggerFactory
at com.ctrip.framework.apollo.demo.api.SimpleApolloConfigDemo.<clinit>(SimpleApolloConfigDemo.java:22)
Caused by: java.lang.ClassNotFoundException: org.slf4j.LoggerFactory
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:335)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
here is our POM.xml below:
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<parent>
<artifactId>apollo</artifactId>
<groupId>com.ctrip.framework.apollo</groupId>
<version>1.3.0-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>apollo-demo</artifactId>
<name>Apollo Demo</name>
<packaging>jar</packaging>
<properties>
<java.version>1.7</java.version>
<github.path>${project.artifactId}</github.path>
</properties>
<dependencies>
<dependency>
<groupId>com.ctrip.framework.apollo</groupId>
<artifactId>apollo-client</artifactId>
<version>${project.version}</version>
</dependency>
<!-- for spring demo -->
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-context</artifactId>
</dependency>
<!-- for spring boot demo -->
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter</artifactId>
<exclusions>
<exclusion>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-logging</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-log4j2</artifactId>
</dependency>
<!-- for refresh scope demo -->
<dependency>
<groupId>org.springframework.cloud</groupId>
<artifactId>spring-cloud-context</artifactId>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-core</artifactId>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-api</artifactId>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j-impl</artifactId>
</dependency>
<!-- take over jcl -->
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>jcl-over-slf4j</artifactId>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-log4j12</artifactId>
<version>1.7.25</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>1.7.25</version>
</dependency>
</dependencies>
</project>
2.1 we already included slf4j-log4j12 and slf4j-api as depdency.
2.2 the application can run normally in eclipse IDE window.
2.3 if we export executable jar including all dependencies, and ship jar on linux machine, run the jar file will get the above error.
2.4 we also checked generated jar package on windows with winRAR, the slf4j and log4j* jar package were there, see picture below.
we have struggled this for half day, but did not get any progress. Hope each expert can share with us some light or any suggestions. really appreciated!!!

You need to tell maven to compile the dependencys like this, the jars are compiled but you need the src in youre jar and not the jars in there:
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>3.0.0</version>
<configuration>
</configuration>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
and dependencys normaly have a <scope>compile</scope> tag, to tell the compile that they are needed at runtime

I've faced a similar problem few days ago, right I add the jar libraries but the core (scripts/classes) of the jar file are no included due some reason I was able to solve that problem by right click on the jar file go to properties and set the class path for the classes of that jar folder.
if you wanna check that the jar file has no class Def inside it explore the jar file from the explorer and double click on any class you'll see a page showing up and says there's no script for this class and it asks you to set the class path.
Another approach I tried which also worked for me is I've imported the same jar files on netbeans and they worked 100%

Jersey Guice Integration exception

I'm struggling to get Guice to work with my Jersey/Grizzly classes. I started with console Java app, added Guice and got my injection working as well as my domain objects. Then I proceeded to add webservices through Jersey/Grizzly. As you might be able to tell from my coding style, I've come from a C# background. So I'm sure some of my struggle is learning Javas way of doing things.
What I want is that my non webservices classes can get injected into the webservices handlers so they can use the functionality I've built.
In my class below, I have a database instance handler I want to inject into the webservices classes:
#Path("/options")
public class OptionsServices {
private IDatabaseService dbService;
#Inject
public void setService(IDatabaseService svc){
this.dbService = svc;
}
#GET
#Path("{symbol}")
#Produces(MediaType.APPLICATION_JSON)
public Quote getOptionQuote(#PathParam("symbol") String symbol) {
// do stuff
}
}
I tried adding in GuiceBridge and binding that in my extension of the ResourceConfig class. But no matter what version I used, I get some really crazy exceptions about missing properties when I tried to initialize the webservices. Simply removing GuiceBridge from my pom.xml removes the exception. It seems like its version compatibility problem but I am at a loss to understand what version of what library.
Exception in thread "main" java.lang.NoSuchMethodError: org.glassfish.hk2.utilities.general.GeneralUtilities.getSystemProperty(Ljava/lang/String;Ljava/lang/String;)Ljava/lang/String;
at org.jvnet.hk2.internal.ServiceLocatorImpl.<clinit>(ServiceLocatorImpl.java:122)
at org.jvnet.hk2.external.generator.ServiceLocatorGeneratorImpl.initialize(ServiceLocatorGeneratorImpl.java:66)
at org.jvnet.hk2.external.generator.ServiceLocatorGeneratorImpl.create(ServiceLocatorGeneratorImpl.java:98)
at org.glassfish.hk2.internal.ServiceLocatorFactoryImpl.internalCreate(ServiceLocatorFactoryImpl.java:312)
at org.glassfish.hk2.internal.ServiceLocatorFactoryImpl.create(ServiceLocatorFactoryImpl.java:268)
at org.glassfish.jersey.internal.inject.Injections._createLocator(Injections.java:138)
at org.glassfish.jersey.internal.inject.Injections.createLocator(Injections.java:123)
at org.glassfish.jersey.server.ApplicationHandler.<init>(ApplicationHandler.java:308)
at org.glassfish.jersey.server.ApplicationHandler.<init>(ApplicationHandler.java:289)
at org.glassfish.jersey.grizzly2.httpserver.GrizzlyHttpContainer.<init>(GrizzlyHttpContainer.java:334)
at org.glassfish.jersey.grizzly2.httpserver.GrizzlyHttpServerFactory.createHttpServer(GrizzlyHttpServerFactory.java:122)
at Application.Server.WebServer.startServer(WebServer.java:40)
at Application.Server.WebServer.Start(WebServer.java:45)
at Application.Startup.run(Startup.java:68)
at Application.Startup.main(Startup.java:87)
And my pom.xml
<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>tatmancapital</groupId>
<artifactId>ServerConsole</artifactId>
<version>R1</version>
<properties>
<jersey.version>2.17</jersey.version>
</properties>
<dependencyManagement>
<dependencies>
<dependency>
<groupId>org.glassfish.jersey</groupId>
<artifactId>jersey-bom</artifactId>
<version>${jersey.version}</version>
<type>pom</type>
<scope>import</scope>
</dependency>
</dependencies>
</dependencyManagement>
<dependencies>
<!-- https://mvnrepository.com/artifact/com.google.inject/guice -->
<dependency>
<groupId>com.google.inject</groupId>
<artifactId>guice</artifactId>
<version>4.1.0</version>
</dependency>
<dependency>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
<version>5.1.6</version>
</dependency>
<dependency>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
<version>1.2.15</version>
<exclusions>
<exclusion>
<groupId>com.sun.jmx</groupId>
<artifactId>jmxri</artifactId>
</exclusion>
<exclusion>
<groupId>com.sun.jdmk</groupId>
<artifactId>jmxtools</artifactId>
</exclusion>
<exclusion>
<groupId>javax.jms</groupId>
<artifactId>jms</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>commons-codec</groupId>
<artifactId>commons-codec</artifactId>
<version>1.3</version>
</dependency>
<dependency>
<groupId>commons-httpclient</groupId>
<artifactId>commons-httpclient</artifactId>
<version>3.1</version>
</dependency>
<dependency>
<groupId>com.thoughtworks.xstream</groupId>
<artifactId>xstream</artifactId>
<version>1.4.9</version>
</dependency>
<dependency>
<groupId>commons-lang</groupId>
<artifactId>commons-lang</artifactId>
<version>2.4</version>
</dependency>
<dependency>
<groupId>commons-logging</groupId>
<artifactId>commons-logging</artifactId>
<version>1.0.4</version>
</dependency>
<dependency>
<groupId>org.glassfish.jersey.containers</groupId>
<artifactId>jersey-container-grizzly2-http</artifactId>
</dependency>
<dependency>
<groupId>org.glassfish.jersey.media</groupId>
<artifactId>jersey-media-moxy</artifactId>
</dependency>
<dependency>
<groupId>org.glassfish.hk2</groupId>
<artifactId>guice-bridge</artifactId>
<version>2.5.0-b32</version>
</dependency>
<dependency>
<groupId>commons-httpclient-ssl-contrib</groupId>
<artifactId>commons-httpclient-ssl-contrib</artifactId>
<version>3.1</version>
<scope>system</scope>
<systemPath>${project.basedir}/libs/commons-httpclient-contrib-ssl-3.1.jar</systemPath>
</dependency>
<dependency>
<groupId>etrade</groupId>
<artifactId>com.etrade.accounts</artifactId>
<version>1.0</version>
<scope>system</scope>
<systemPath>${project.basedir}/libs/etws-accounts-sdk-1.0.jar</systemPath>
</dependency>
<dependency>
<groupId>etrade</groupId>
<artifactId>com.etrade.order</artifactId>
<version>1.0</version>
<scope>system</scope>
<systemPath>${project.basedir}/libs/etws-order-sdk-1.0.jar</systemPath>
</dependency>
<dependency>
<groupId>etrade</groupId>
<artifactId>com.etrade.oauth</artifactId>
<version>1.0</version>
<scope>system</scope>
<systemPath>${project.basedir}/libs/etws-oauth-sdk-1.0.jar</systemPath>
</dependency>
<dependency>
<groupId>etrade</groupId>
<artifactId>com.etrade.markets</artifactId>
<version>1.0</version>
<scope>system</scope>
<systemPath>${project.basedir}/libs/etws-market-sdk-1.0.jar</systemPath>
</dependency>
<dependency>
<groupId>etrade</groupId>
<artifactId>com.etrade.common</artifactId>
<version>1.0</version>
<scope>system</scope>
<systemPath>${project.basedir}/libs/etws-common-connections-1.0.jar</systemPath>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<version>3.0.0</version>
<configuration>
<archive>
<manifest>
<mainClass>Application.Startup</mainClass>
</manifest>
</archive>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<appendAssemblyId>false</appendAssemblyId>
<finalName>ServerConsole-V1</finalName>
</configuration>
<executions>
<execution>
<id>make-assembly</id> <!-- this is used for inheritance merges -->
<phase>package</phase> <!-- bind to the packaging phase -->
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>
I apologize I cannot explain this problem with more definitive here's what is wrong. I may have architected my app completely wrong and given this is just me learning, I am ok with that. I would like to avoid rewriting my domain logic construction and unit tests.
Thank you for your help
Matt

Error explanation
A java.lang.NoSuchMethodError is definitely an error with packages and library versions. It means that you have compiled code referencing a method that do not exist in your runtime code.
It's not an error commonly seen in your code because the compiler won't let you pass code referencing a non existent method. But in this case the code referencing the method and the referenced code are both libraries so that means that the code with the method reference was compiled against a different version of the target class.
Somehow this error is analogous to the more common ClassNotFoundException. But instead of not finding a class you are not finding a method inside a class.
Finding the source of your problem
Now you know what the problem is. Solving it, I'm afraid, is not that easy. Package managment and library resolution with Java is becoming harder every year. I see you are using the bom (Bill of Materials) for the Jersey library. Also, your pom file is not an easy one. I suggest you to build a test project only with the structure of your API (jax-rs) code with Guice and the HK2-Guice bridge. Maybe instead of using the BOM try this recent versions, they work for me:
com.google.inject:guice:4.1.0
org.glassfish.jersey.containers:jersey-container-servlet:2.25
org.glassfish.hk2:guice-bridge:2.5.+
I'm using the servlet container but you are using an standalone one. It doesn't matter, use yours but keep the version number.
Maven resolution
Also try to check which version of each package you are including in the final build. You may find useful this maven command to display the dependency tree:
https://maven.apache.org/plugins/maven-dependency-plugin/tree-mojo.html

Add my own bundle sources to pax-exam when building with pax-maven-plugin

I'm trying to build my OSGI bundle with pax-maven-build and in the same time test it with pax-exam. It have some bundle in provision than I can test with the following pax-exam test configuration:
#RunWith(JUnit4TestRunner.class)
#ExamReactorStrategy(AllConfinedStagedReactorFactory.class)
public class OSGILoaderTest {
#Inject
protected BundleContext bundleContext;
#Configuration
public Option[] config() throws MalformedURLException {
String projectRoot = // a path to my project
return options(
junitBundles(),
equinox(),
bundle(projectRoot + "libs/org.eclipse.core.variables_3.2.500.v20110511.jar"),
bundle(projectRoot + "libs/org.eclipse.core.contenttype_3.4.100.v20110423-0524.jar"),
bundle(projectRoot + "libs/org.eclipse.core.expressions_3.4.300.v20110228.jar"),
// etc...
);
}
#Test
public void getBundleContext() throws RodinDBException {
IRodinDB rodinDB = RodinCore.getRodinDB();
assertNotNull(rodinDB);
}
}
Here, I can see I can access to the IRodinDB instance from a jar I have provisonned.
Now I have code my own bundle, which is going to use all the jar provisionned. But I cannot even test my own code, for instance:
#Test
public void checkAccessToRodinDbTest() {
VTGService service = null;
assertTrue(true);
}
give an error at compilation time:
[ERROR] Failed to execute goal org.ops4j:maven-pax-plugin:1.5:testCompile (default-testCompile) : Compilation failure
[ERROR] cannot find symbol
[ERROR] symbol : class VTGService
It seems test compilation cannot see 'src/main/java', contrarly as expected by the default behavior of maven-compiler-plugin. But in my case, you can see than maven does not use the compiler plugin but instead maven-pax-plugin.
The question is: how can i test my own bundle with pax-exam ?
update1
It seems that this is a problem with recent version of maven-pax-plugin, as the basic example available in ops4j pax maven plugin (in section Using the Pax Plugin inside a POM) seems to suffer of the same problem.
update2
As requested by Dmytro, this is the pom.xml of my bundle:
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://maven.apache.org/POM/4.0.0"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<parent>
<relativePath>../poms/compiled/</relativePath>
<groupId>fr.xlim.ssd.vtg.build</groupId>
<artifactId>compiled-bundle-settings</artifactId>
<version>0.1-SNAPSHOT</version>
</parent>
<properties>
<bundle.symbolicName>fr.xlim.ssd.vtg.bundle</bundle.symbolicName>
<bundle.namespace>fr.xlim.ssd.vtg.bundle</bundle.namespace>
</properties>
<modelVersion>4.0.0</modelVersion>
<groupId>fr.xlim.ssd.vtg</groupId>
<artifactId>fr.xlim.ssd.vtg.bundle</artifactId>
<version>0.1-SNAPSHOT</version>
<name>${bundle.symbolicName}</name>
<packaging>bundle</packaging>
<dependencies>
<dependency>
<type>pom</type>
<groupId>${project.parent.groupId}</groupId>
<artifactId>provision</artifactId>
<optional>true</optional>
</dependency>
<!-- not needed as equinox bundle are available in provision -->
<dependency>
<groupId>org.osgi</groupId>
<artifactId>osgi_R4_core</artifactId>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.osgi</groupId>
<artifactId>osgi_R4_compendium</artifactId>
<optional>true</optional>
</dependency-->
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.9</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.ops4j.pax.exam</groupId>
<artifactId>pax-exam</artifactId>
<version>2.3.0</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.ops4j.pax.exam</groupId>
<artifactId>pax-exam-junit4</artifactId>
<version>2.3.0</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.ops4j.pax.exam</groupId>
<artifactId>pax-exam-inject</artifactId>
<version>2.3.0</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.ops4j.pax.url</groupId>
<artifactId>pax-url-mvn</artifactId>
<version>1.3.5</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.ops4j.pax.exam</groupId>
<artifactId>pax-exam-container-native</artifactId>
<version>2.3.0</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>javax.inject</groupId>
<artifactId>javax.inject</artifactId>
<version>1</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.ops4j.pax.exam</groupId>
<artifactId>pax-exam-link-mvn</artifactId>
<version>2.3.0</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
<version>1.0.0</version>
</dependency>
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-core</artifactId>
<version>1.0.0</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>2.3.2</version>
<configuration>
<source>1.6</source>
<target>1.6</target>
</configuration>
</plugin>
</plugins>
</build>
</project>
I am not sure it is the most elegant solution, but I created a new maven project when I can import my own bundle like in the source code of my question.
Is there an elegant way to add my own java sources directly as new bundle for test in the same Maven project ? It could be not possible (as the bundle assembly operation is done after the compilation and tests)...

I use the following setup to provision the bundle under test. When configuring the test, I provision the bundle using the reference-protocol (this is a non-standard feature of Equinox and Felix, see here):
#Configuration
public Option[] config() {
return options(
bundle("reference:file:target/classes"),
junitBundles(),
felix()
);
}
The test-cases also run when you specify knopplerfish() as the environment. I guess that is because the URL is resolved by Pax Exam, and not by the OSGi-runtime. I use the maven-bundle-plugin to build my bundles. To make this work as expected, you have to add the following configuration:
<build>
<plugins>
<plugin>
<groupId>org.apache.felix</groupId>
<artifactId>maven-bundle-plugin</artifactId>
<version>2.3.7</version>
<extensions>true</extensions>
<executions>
<!-- This execution makes sure that the manifest is available
when the tests are executed -->
<execution>
<goals>
<goal>manifest</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
Otherwise the manifest will not be available when the tests are run, since by default it is generated during the package-phase.
I hope I did not forget anything - please let me know if it worked for you!

Check PaxExam docs how to configure your Maven POM with PaxExam.
Samples here

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