build.gradle

plugins {
  id 'java'
}

repositories {
  jcenter()
}

dependencies {
  compileOnly 'com.google.code.findbugs:jsr305:3.0.2'
}

compileJava {
  doFirst {
    println("compileOnly = ${configurations.compileOnly.files}")
    println("compile = ${configurations.compile.files}")
    println("compileClasspath = ${configurations.compileClasspath.files}")
  }
}

configurations.compile.exclude group: 'com.google.code.findbugs', module: 'jsr305'

output.txt

> Task :compileJava FAILED
compileOnly = [/Users/martijn/.gradle/caches/modules-2/files-2.1/com.google.code.findbugs/jsr305/3.0.2/25ea2e8b0c338a877313bd4672d3fe056ea78f0d/jsr305-3.0.2.jar]
compile = []
compileClasspath = []
/private/tmp/gradletest/src/main/java/Main.java:1: error: cannot find symbol
import javax.annotation.Nullable;
                       ^
  symbol:   class Nullable
  location: package javax.annotation
/private/tmp/gradletest/src/main/java/Main.java:7: error: cannot find symbol
  public void x(@Nullable String s) {
                 ^
  symbol:   class Nullable
  location: class Main
2 errors

FAILURE: Build failed with an exception.

* What went wrong:
Execution failed for task ':compileJava'.
> Compilation failed; see the compiler error output for details.