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Create Jar from Checker Framework enabled build?

I'm adding Checker Framework to an existing Java Gradle build. I have Checker integrated and raising issues and that's all working great. But now that I've added it, my build is no longer producing a .jar file as it once did.
Previously, I'd get a .jar at build/libs/myproject.jar. Now instead I see build/checkerframework and build/main but no build/libs and no .jar.
My build.gradle is below. Anyone attempted this before? Any success?
I guess I'd also accept an answer that shows how run Checker outside of the build, e.g. gradle check to run a build with Checker, and gradle build to produce a .jar. But I'd really prefer to have just a single build step if at all possible.
Thanks!
plugins {
id "org.checkerframework" version "0.5.18"
id 'application'
}
apply plugin: 'org.checkerframework'
checkerFramework {
checkers = [
'org.checkerframework.checker.nullness.NullnessChecker',
'org.checkerframework.checker.units.UnitsChecker'
]
}
repositories {
jcenter()
}
java {
sourceCompatibility = JavaVersion.VERSION_11
targetCompatibility = JavaVersion.VERSION_11
}
jar {
duplicatesStrategy = DuplicatesStrategy.EXCLUDE
// Embed all dependencies to create a "fat jar" as required for AWS deployment.
// Exclude 3rd-party signing files to prevent security errors at runtime
from {
configurations.runtimeClasspath.collect { it.isDirectory() ? it : zipTree(it) }
} {
exclude 'META-INF/*.RSA', 'META-INF/*.SF', 'META-INF/*.DSA'
}
manifest {
attributes('Main-Class': 'client.CliMain')
}
}

If the build is passing, then adding -processor should not affect whether a .jar file is produced. (Unless you pass -proc:only or the like.)
If the build is failing, then Gradle won't build the jar files.
You said the Checker Framework is "raising issues", so maybe the build is failing.

A library corrupts classpath?

There's a strange issue I've never seen.
Adding a compile 'org.locationtech.spatial4j:spatial4j:0.7' to the dependencies list in my gradle project leads to a corrupt classpath. When I comment out that library and run java -verbose:class -jar sol_backend_full.jar > ok.log it outputs 4399 lines of class entries. However, with that library in classpath, java -verbose:class -jar sol_backend_full.jar > failed.log outputs only 953 lines, most of which are java.lang.* or sun.*.
It obviously results in Error: Could not find or load main class.
➥ Has anyone ever encountered that strange behaviour?
Of course, I can substitute that library with another spatial library, but what's happening is simply strange. It happens only with this library, removing/adding any other is fine.
Gradle version in question is 5.5.1, and that library manifest looks a bit long, but not suspicious at all. Falling back to 4.8 also reproduces it.
Here is the build script:
task customFatJar(type: Jar) {
manifest {
attributes 'Main-Class': 'ru.rxproject.sol.backend.BackendApplication',
'Implementation-Version': version + System.getenv('BUILD_NUMBER').toString(),
'Commit-Hash': 'git-' + System.getenv('GIT_COMMIT'),
'Build-Date': java.time.LocalDateTime.now().toString()
}
archiveName = 'sol_backend_full.jar'
from { configurations.compile.collect { it.isDirectory() ? it : zipTree(it) } }
with jar
}

The JAR dependancy org.locationtech.spatial4j:spatial4j:0.7 is a signed jar. When you create a fat jar, java Classloader is not able to load the other classes from your fat jar because these are not signed.
So, you can't create a fat jar with that dependancy without excluding the signatures.
Please refer - Gradle - FatJar - Could not find or load main class
Like mentioned in the above post, you may exclude the signatures like -
jar {
manifest {
attributes "Main-Class": mainClassName
}
from {
configurations.compile.collect { it.isDirectory() ? it : zipTree(it) }
}
exclude 'META-INF/*.RSA'
exclude 'META-INF/*.SF'
exclude 'META-INF/*.DSA'
}
But, I would suggest to keep the jar dependancy out of the fat jar.

Alternative to fat jar in gradle java project

I have started on gradle today itself. So I am trying out random things. I have below build.gradle file:
apply plugin: 'java'
repositories {
mavenCentral()
}
dependencies {
testImplementation('org.junit.jupiter:junit-jupiter-api:5.4.2')
testRuntime('org.junit.jupiter:junit-jupiter-engine:5.4.2')
compile 'com.googlecode.json-simple:json-simple:1.1.1'
}
test {
useJUnitPlatform()
}
jar {
manifest {
attributes(
'Main-Class': 'src.main.java.demo.Hello'
)
}
from {
configurations.runtimeClasspath.collect { it.isDirectory() ? it : zipTree(it)}
}
}
I have read somewhere that the method that I am using inside from block will create fat jar, which is not a good practice. As I am fairly new to this, I humbly want to ask the alternative to this. Is it adding classpath to manifest or something else??
The primary purpose is to bundle third party dependency jar files that will be used on runtime.
Thank You!

You could put all your dependencies into a ZIP file together with your own JAR and possibly external resources, or build an installer, or (if you're building a web app) build a WAR or EAR file. Gradle will take care of the manifest for you in any case.
(Also, there is nothing really wrong with fat JARs, they are fairly common these days and they do work.)

gradle fatjar include classes from nested Jar

My problem might be simple to gradle experts.
I am building fatJar. One of the dependencies contain Jar file itself. With following piece of code fat jar is being created with all other dependencies but the one that has jar, it just places jars in final jar. Which makes sense. How can I copy all the classes from those nested jars into final Jar. Any help would be highly appreciated.
jar {
from {configurations.runtime.collect { it.isDirectory() ? it : zipTree(it) }} {
exclude "META-INF/*.SF"
exclude "META-INF/*.DSA"
exclude "META-INF/*.RSA"
}
}

Removing Jar Signatures in Gradle Build

We are having an issue with a war built from gradle failing to load in tomcat because of a Security Exception specific to a signed Jar. The stack trace is not showing what jar is causing the problem and to get this thing running I'm wondering if I can exclude the signatures in the build when the war is getting built but don't know how to do that with Gradle. In maven I believe it would be a <filter><exclude> tag but not sure if this type of thing is available in Gradle. Any input would be appreciated, the Exception being thrown is below.
Caused by: java.lang.SecurityException: Invalid signature file digest for

To find out if a jar file is signed, you can unzip the jar file using any zip utility tool. If the jar is signed it will contain files like *.RSA, *.SF or *.DSA under META-INF folder.
To exclude these signature files in gradle build , I did the following in my build.gradle. If you are using any other plugin to create the jar than you should check that plugins documentation for more details.
jar {
from { (configurations.runtime).collect { it.isDirectory() ? it : zipTree(it) } } {
exclude 'META-INF/*.RSA', 'META-INF/*.SF', 'META-INF/*.DSA'
}
manifest {
attributes("Main-Class": "com.nk.social.shareit.streams.AppMain")
}}
My entire build.gradle file is as listed below:-
apply plugin: 'scala'
dependencies {
compile group: 'org.apache.kafka', name: 'kafka-streams', version: '0.11.0.1'
compile 'org.scala-lang:scala-library:2.12.2'
compile 'com.sksamuel.elastic4s:elastic4s-core_2.12:5.4.2'
compile 'com.sksamuel.elastic4s:elastic4s-http_2.12:5.4.2'
compile 'org.apache.lucene:lucene-core:6.5.1'
compile 'joda-time:joda-time:2.9.9'
testCompile group: 'org.scalatest', name: 'scalatest_2.12', version: '3.0.4'
}
jar {
from { (configurations.runtime).collect { it.isDirectory() ? it : zipTree(it) } } {
exclude 'META-INF/*.RSA', 'META-INF/*.SF', 'META-INF/*.DSA'
}
manifest {
attributes("Main-Class": "com.nk.social.shareit.streams.AppMain")
}
}
Hope this helps.

With the jar, for example given in this thread I have a problem building a fat jar.
The main motivation is that the build process will skip also some dependecens.
A solution found is the following one, it contains only a small change
jar {
manifest {
attributes(
'Class-Path': configurations.compile.collect { it.getName() }.join(' '),
'Main-Class': 'io.vincenzopalazzo.lightning.App'
)
}
from(configurations.runtimeClasspath.collect { it.isDirectory() ? it : zipTree(it) }) {
exclude 'META-INF/*.RSA', 'META-INF/*.SF', 'META-INF/*.DSA'
}
}