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Gradle Build Jar with Local Dependencies

I am building a jar file using gradle. I have local jar files as dependencies. Those jars have additional local dependencies stored in the same directory. I used the following build.gradle file
plugins { id 'application' }
repositories {
flatDir{ dirs 'lib'
}
dependencies {
implementation name: 'localjar1'
implementation name: 'localjar2'
}
application { mainClass = 'mypackage.MyApp' }
jar {
from { configurations.runtimeClasspath.collect {it.isDirectory ? : zipTree(it) } }
manifest { attributes 'Main-Class': 'mypackage.MyApp' }
}
I built the jar using gradle jar, but when I try to run the jar:
java -jar myapp\build\libs\myapp.jar
I get the following error:
Unable to initialize main class mypackage.MyApp
Caused by java.lang.NoClassDefFoundError: com/localpackage/SomeClass
How do bring that dependency in correctly?
I also tried to include the entire local library as a dependency
implementation fileTree(dir: 'lib', include: '*jar')
But when I do this I get the error: java.lang.ClassNotFoundException: mypackage.MyApp
What else should I try?
** Note: I can run the application using gradle run

How to exclude dependencies from BOOT-INF/classes?

I have a spring boot project and I get this error when I try to build it:
> gradle build
:processResources
:compileJava
:classes
:jar FAILED
FAILURE: Build failed with an exception.
* What went wrong:
Execution failed for task ':jar'.
> archive contains more than 65535 entries.
To build this archive, please enable the zip64 extension.
See: https://docs.gradle.org/3.5.1/dsl/org.gradle.api.tasks.bundling.Zip.html#org.gradle.api.tasks.bundling.Zip:zip64
* Try:
Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output.
Ok, I added the zip64 = true option to the jar task in the gradle configuration.
Now it can build the jar successfully but when I try to execute the jar, I get the following exception:
Exception in thread "main" java.lang.IllegalStateException: java.lang.IndexOutOfBoundsException
at org.springframework.boot.loader.ExecutableArchiveLauncher.<init>(ExecutableArchiveLauncher.java:43)
at org.springframework.boot.loader.JarLauncher.<init>(JarLauncher.java:37)
at org.springframework.boot.loader.JarLauncher.main(JarLauncher.java:58)
Caused by: java.lang.IndexOutOfBoundsException
at org.springframework.boot.loader.jar.AsciiBytes.<init>(AsciiBytes.java:69)
at org.springframework.boot.loader.jar.CentralDirectoryFileHeader.load(CentralDirectoryFileHeader.java:95)
at org.springframework.boot.loader.jar.CentralDirectoryParser.parseEntries(CentralDirectoryParser.java:68)
at org.springframework.boot.loader.jar.CentralDirectoryParser.parse(CentralDirectoryParser.java:57)
at org.springframework.boot.loader.jar.JarFile.<init>(JarFile.java:118)
at org.springframework.boot.loader.jar.JarFile.<init>(JarFile.java:106)
at org.springframework.boot.loader.jar.JarFile.<init>(JarFile.java:92)
at org.springframework.boot.loader.jar.JarFile.<init>(JarFile.java:83)
at org.springframework.boot.loader.archive.JarFileArchive.<init>(JarFileArchive.java:61)
at org.springframework.boot.loader.archive.JarFileArchive.<init>(JarFileArchive.java:57)
at org.springframework.boot.loader.Launcher.createArchive(Launcher.java:129)
at org.springframework.boot.loader.ExecutableArchiveLauncher.<init>(ExecutableArchiveLauncher.java:40)
... 2 more
It turned out that SpringBoot doesn't even support the zip64 format, so I had to make further investigation.
Where do the 65535+ entries come from? Obviously these come from dependencies, because the issue exists since
I added a new dependency in the build.gradle file. While examining the zip64 jar, I have found that
all the dependency classes! are under the BOOT-INF/classes folder.
As I understand, the structure must look like
BOOT-INF/
classes/
<only this application's compiled classes>
libs/
<all the dependency jars>
But my classes folder has all the dependency jars "extracted" to it.
(As you can see)
I extracted the jar, removed all the dependency classes from this folder and rezipped it. (Like this)
This way it can be run without any problem, so I'm sure these files are unneccesary.
Can somebody help me, how to exclude these dependency classes from the structure? Thank you in advance!
Here's my relevant gradle configuration:
apply plugin: 'java'
apply plugin: 'eclipse'
apply plugin: 'application'
apply plugin: 'org.springframework.boot'
ext.springBootVersion = '1.4.2.RELEASE'
buildscript {
repositories {
mavenCentral()
}
dependencies {
classpath("org.springframework.boot:spring-boot-gradle-plugin:1.4.2.RELEASE")
}
}
configurations {
provided.all*.exclude group: 'javax.servlet'
}
mainClassName = 'com.path.to.my.MainClass'
repositories {
mavenCentral()
maven {
url "https://repository.jboss.org/nexus/content/repositories/releases"
}
maven {
url "https://repo.eclipse.org/content/groups/releases/"
}
}
jar {
//zip64 = true
from {
configurations.compile.collect {
it.isDirectory() ? it : zipTree(it)
}
}
manifest {
attributes("Main-Class": mainClassName)
}
exclude 'META-INF/*.RSA', 'META-INF/*.SF','META-INF/*.DSA'
}
sourceCompatibility = 1.8
targetCompatibility = 1.8
dependencies {
compile 'aopalliance:aopalliance:1.0'
compile 'com.google.code.gson:gson:2.7'
compile 'com.google.gdata:core:1.47.1'
compile 'com.google.guava:guava:19.0'
compile 'commons-io:commons-io:2.4'
compile 'javax.json:javax.json-api:1.0'
compile 'mysql:mysql-connector-java:5.1.22'
compile 'org.apache.commons:commons-csv:1.4'
compile 'org.flywaydb:flyway-core:4.0.3'
compile 'org.glassfish:javax.json:1.0.4'
......
testCompile 'org.springframework.boot:spring-boot-starter-test'
}
bootRun {
addResources = true
}
task wrapper(type: Wrapper) {
gradleVersion = '2.3'
}

Gradle dependency issue, java.lang.NoClassDefFoundError, but compiles

new to gradle and java here and I am trying to use Android's Log method from android.util.Log. It seems I can compile and it finds what it needs, but it can not find it at runtime. I have tried using 'runtime' instead of 'compile' in the dependencies section, but not luck.
java -jar build/libs/testJavaHttp.jar
Exception in thread "main" java.lang.NoClassDefFoundError: android/util/Log
at myproject.test.HttpToFile.downloadFile(HttpToFile.java:20)
at myproject.test.Main.main(Main.java:12)
Caused by: java.lang.ClassNotFoundException: android.util.Log
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
... 2 more
In build.gradle
apply plugin: 'java'
dependencies {
compile files('../androidsdk/platforms/android-25/android.jar')
}
jar {
manifest {
attributes 'Main-Class': 'myproject.test.Main'
}
}

You are trying to run the jar and the jar is not packed with dependencies, use shadow jar plugin or pack required artifacts in, by extending the jar task.
jar {
archiveName = 'Name.jar'
manifest {
attributes 'Main-Class': 'myproject.test.Main',
'Class-Path': configurations.runtime.files.collect { "lib/$it.name" }.join(' '),
'Implementation-Version': 1.0
}
from(configurations.myconfig.collect { it.isDirectory() ? it : zipTree(it) }) {
// in here you can exclude what you need as well if needed.
}
}
To not pull the 'entire world' into a jar you can create configuration just with libraries you require:
configurations{
myconfig // to create configuration
compile.extendsFrom(myConfig) //to include it in compile as well
}
and then use this config in the jar creation and in dependecies.
dependencies {
myconfig files('../androidsdk/platforms/android-25/android.jar')
}
But looking at your code there is not much to pull there. You need to consider packing all needed artifacts and transitives if you expect it to be a runnable jar, as you run it with 'java -jar [...]' command.
PS. Everything that is in compile is going to be included in runtime configuration as well.

Successful Gradle project build produces NoClassDefFoundError at runtime

I am using Gradle to build my Java project in Eclipse. gradle.build is as follows
apply plugin: 'java'
repositories {
mavenCentral()
}
dependencies {
compile group: 'com.flowpowered', name: 'flow-nbt', version: '1.0.0'
compile group: 'org.reflections', name: 'reflections', version: '0.9.10'
}
All libraries are functioning properly when run through Eclipse. But sometimes it is useful to work on the command line. When run on the command line, the runtime error Exception in thread "main" java.lang.NoClassDefFoundError: com/flowpowered/nbt/regionfile/SimpleRegionFileReader occurs, even though the build is successful and the code contains imports from those libraries. I have tried cleans and rebuilds, along with gradlew build --refresh-dependencies, but I still encounter the same runtime error.
I would assume that the libraries are just never actually imported? Or that they are not being stored where the java project thinks they are? I'm unfamiliar with Gradle, so any advice on this is welcome.

Based on the posted build.gradle file you are not packaging the application as an executable JAR.
First apply the application plugin. But this will not be enough as you won't be able to run the executable as a single JAR without all of its dependencies. Apply the shadow plugin too.
These two plugins will give you access to the following tasks:
run: execute the application from gradle's command line.
runShadow: execute the application but with all dependencies packaged in a single JAR, alongside your compiled classes and resources.
shadowJar: create a single "fat JAR" with compiled classes and all dependencies.
Thus your build.gradle may look like this
plugins {
id 'java'
id 'application'
id 'com.github.johnrengelman.shadow' version '1.2.4'
}
mainClassName = 'com.acme.YourMainClassName'
repositories {
mavenCentral()
}
dependencies {
compile group: 'com.flowpowered', name: 'flow-nbt', version: '1.0.0'
compile group: 'org.reflections', name: 'reflections', version: '0.9.10'
}
Plugin documentation:
https://github.com/johnrengelman/shadow
https://docs.gradle.org/3.4/userguide/application_plugin.html#useApplicationPlugin

Another solution without using any plugins and still end up with a runnable fat jar
jar {
archiveName = 'NameOfYourApp.jar'
manifest {
attributes 'Main-Class': 'uk.co.cdl.Main',
'Class-Path': configurations.runtime.files.collect { "lib/$it.name" }.join(' '),
'Implementation-Version': project.version
}
from(configurations.compile.collect { it.isDirectory() ? it : zipTree(it) }) {
include/exclude anything if need to if not take the curlys off
}
}

NoClassDefFoundError in jar but not in Intellij

I'm trying to run a jar with dependencies. The application runs fine in Intellij but when I try to run the jar I get:
>> java -jar test-0.1.0.jar
Exception in thread "main" java.lang.NoClassDefFoundError: com/atlassian/httpclient/apache/httpcomponents/DefaultHttpClient
at com.atlassian.jira.rest.client.internal.async.AsynchronousHttpClientFactory.createClient(AsynchronousHttpClientFactory.java:53)
at com.atlassian.jira.rest.client.internal.async.AsynchronousJiraRestClientFactory.create(AsynchronousJiraRestClientFactory.java:35)
at com.atlassian.jira.rest.client.internal.async.AsynchronousJiraRestClientFactory.createWithBasicHttpAuthentication(AsynchronousJiraRestClientFactory.java:42)
at Main.main(Main.java:19)
Caused by: java.lang.ClassNotFoundException: com.atlassian.httpclient.apache.httpcomponents.DefaultHttpClient
at java.net.URLClassLoader.findClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
... 4 more
My build.gradle looks like this:
group 'test'
version '1.0-SNAPSHOT'
task wrapper(type: Wrapper) {
gradleVersion = '2.9'
distributionUrl = "https://services.gradle.org/distributions/gradle-$gradleVersion-all.zip"
}
apply plugin: 'java'
apply plugin: 'idea'
apply plugin: 'application'
sourceCompatibility = 1.8
mainClassName = "Main"
repositories {
mavenCentral()
maven {
url 'https://maven.atlassian.com/content/repositories/atlassian-public/'
}
}
jar {
baseName = 'test'
version = '0.1.0'
from {
configurations.compile.collect { it.isDirectory() ? it : zipTree(it) }
configurations.runtime.collect { it.isDirectory() ? it : zipTree(it) }
}
manifest {
attributes 'Main-Class': 'Main'
}
}
dependencies {
testCompile group: 'junit', name: 'junit', version: '4.11'
compile 'com.atlassian.jira:jira-rest-java-client-parent:4.0.0'
compile 'com.atlassian.jira:jira-rest-java-client-core:4.0.0'
compile 'com.atlassian.jira:jira-rest-java-client-api:4.0.0'
compile 'com.atlassian.jira:jira-rest-java-client-plugin:3.0.0'
compile 'com.atlassian.fugue:fugue-parent:2.6.1'
compile 'com.atlassian.fugue:fugue:2.6.1'
}
I've also tried adding transitive=true to each compile clause to no avail.

You need to set CLASSPATH
The class path is the path that the Java runtime environment searches for classes and other resource files. The class search path (more commonly known by the shorter name, "class path") can be set using either the -classpath option when calling a JDK tool (the preferred method) or by setting the CLASSPATH environment variable. The -classpath option is preferred because you can set it individually for each application without affecting other applications and without other applications modifying its value.
UPDATE:
By default, Gradle doesn't copy dependencies to build folder or include it into the jar. There are three ways to solve the problem with dependencies:
Download them separately and put into the appropriate directory.
Use plugins to build fat jar. Something like shadow.
Add to build.gradle task that copies dependencies into build folder.
For example
task copyDependencies(type: Copy) {
into "$buildDir/libs"
from configurations.runtime
}