How to fix this issue?
FAILURE: Build failed with an exception.
Resolving dependency configuration ‘runtimeOnly’ is not allowed as it is defined as ‘canBeResolved=false’.
Instead, a resolvable (‘canBeResolved=true’) dependency configuration that extends ‘runtimeOnly’ should be resolved.
Well, hard to guess without you showing any relevant code.
But let me repeat what the error already told you.
You try to use the runtimeOnly configuration as input for the classPathJar task and that is not allowed, as runtimeOnly must not be resolved.
Maybe you wanted to runtimeClasspath instead.
Or if you really just wanted the runtimeOnly dependencies, then the error also already told you what to do, i.e. create a new configuration that is resolvable and extends it.
For your reference code snippet:
if (project.plugins.hasPlugin('java')) {
project.tasks.compileJava {
options.incremental = true
options.compilerArgs << '-parameters'
}
project.task 'classPathJar', type: Jar, {
dependsOn project.configurations.runtimeOnly
classifier = "classpath"
doFirst {
manifest {
attributes "Class-Path": project.configurations.runtime.files.collect {
"/" + it.absolutePath.replace("\\", "/")
}.join(" ")
}
}
}
}
final Closure configureRunTask = {
dependsOn project.tasks.classPathJar
classpath = project.files(project.sourceSets.main.output.files, project.tasks.classPathJar.archivePath)
System.properties.each { key, val ->
if (key.startsWith('run.')) {
systemProperties[key - 'run.'] = val
}
}
if (project.hasProperty('args')) {
args project.properties['args'].split(" +")
}
doFirst {
println " System properties: $systemProperties"
println " Command arguments: $args"
}
}
Puh, there is so much suboptimal in this snippet. 
Here some points:
runtime configuration is deprecated since many many years and since Gradle 7 also removed, so you are on a very old version most probably)project.plugins as per its JavaDoc it shouldn’t be used, but either the PluginAware methods on project directly, or in your case pluginManager
hasPlugin as it imposes an ordering requirement, instead either use pluginManager.withPlugin('java') to react to that plugin being applied even if it is applied later, or first apply the java plugin if it is always required thereproject.task and some other things to leverage Task Configuration Avoidance
runtimeOnly which is not meant and not supported for resolving dependencies but for declaring dependencies, besides that you depend on it, but not use it at all which also makes no senseruntime, besides that it is deprecated since years it is also not for resolving dependencies, but for declaring, you probably want to use runtimeClasspath insteaddoFirst), that works against properly working up-to-date checks (and if the task were cacheable would also cause wrong cache entries)classPathJar task) to inputs (classpath of the run task), but properly wire the outputs to the inputs, then you get implicit task dependencies where necessary automatically. Almost any explicit dependsOn is a code smell unless the left-hand side of the dependsOn is a lifecycle taskapplication plugin you already get a properly configured run task where you just have to add your system properties and so onargs through gradle.properties, don’t use a Gradle property for the args to your program. I guess you intend to use it like ./gradlew run -P args="a b c", simply use the the --args parameter instead like ./gradlew run --args a --args b --args c.providers.systemPropertiesPrefixedBy...