Gradle Glam: jacoco + coveralls

.travis.yml

language: java
script: ./gradlew build jacocoTestReport
jdk: oraclejdk7
env:
  matrix:
  - TERM=dumb
after_success:
- ./gradlew jacocoRootReport coveralls

BarTest.java

package sample;

import org.junit.Ignore;
import org.junit.Test;

import static junit.framework.Assert.fail;

public class BarTest {
    @Ignore @Test
    public void bar() {
        fail("Not yet implemented!");
    }
}

build.gradle

allprojects {
    apply plugin: 'base'
    apply plugin: 'jacoco'

    repositories {
        jcenter()
    }

    jacoco {
        toolVersion = '0.7.1.201405082137'
    }
}

subprojects {
    apply plugin: 'java'

    dependencies {
        testCompile 'junit:junit:4.11'
    }

    jacocoTestReport {
        reports {
            html.enabled = true
            xml.enabled = true
            csv.enabled = false
        }
    }
}

task jacocoRootReport(type: org.gradle.testing.jacoco.tasks.JacocoReport) {
    dependsOn = subprojects.test
    sourceDirectories = files(subprojects.sourceSets.main.allSource.srcDirs)
    classDirectories =  files(subprojects.sourceSets.main.output)
    executionData = files(subprojects.jacocoTestReport.executionData)
    reports {
        html.enabled = true
        xml.enabled = true
        csv.enabled = false
    }
}

build_coveralls.gradle

buildscript {
  repositories {
    jcenter()
  }
  dependencies {
    classpath 'org.kt3k.gradle.plugin:coveralls-gradle-plugin:1.0.2'
  }
}

apply plugin: 'com.github.kt3k.coveralls'

build_fixed.gradle

allprojects {
    apply plugin: 'base'
    apply plugin: 'jacoco'

    repositories {
        jcenter()
    }

    jacoco {
        toolVersion = '0.7.1.201405082137'
    }
}

subprojects {
    apply plugin: 'java'

    dependencies {
        testCompile 'junit:junit:4.11'
    }

    jacocoTestReport {
        reports {
            html.enabled = true
            xml.enabled = true
            csv.enabled = false
        }
    }
}

coveralls {
    sourceDirs = files(subprojects.sourceSets.main.allSource.srcDirs).files.absolutePath
}

task jacocoRootReport(type: org.gradle.testing.jacoco.tasks.JacocoReport) {
    dependsOn = subprojects.test
    sourceDirectories = files(subprojects.sourceSets.main.allSource.srcDirs)
    classDirectories =  files(subprojects.sourceSets.main.output)
    executionData = files(subprojects.jacocoTestReport.executionData)
    reports {
        html.enabled = true
        xml.enabled = true
        csv.enabled = false
        xml.destination = "${buildDir}/reports/jacoco/test/jacocoTestReport.xml"
    }
}

project-structure

.
├── build.gradle
├── one
│   └── src
│       ├── main
│       │   └── java
│       │       └── sample
│       │           └── Foo.java
│       └── test
│           └── java
│               └── sample
│                   └── FooTest.java
├── settings.gradle
└── two
    └── src
        ├── main
        │   └── java
        │       └── sample
        │           └── Bar.java
        └── test
            └── java
                └── sample
                    └── BarTest.java

report-command

$ gradle clean jacocoRootReport
:clean UP-TO-DATE
:one:clean UP-TO-DATE
:two:clean UP-TO-DATE
:one:compileJava
:one:processResources UP-TO-DATE
:one:classes
:one:compileTestJava
:one:processTestResources UP-TO-DATE
:one:testClasses
:one:test
:two:compileJava
:two:processResources UP-TO-DATE
:two:classes
:two:compileTestJava
:two:processTestResources UP-TO-DATE
:two:testClasses
:two:test
:jacocoRootReport

The subprojects.sourceSets.main.output includes classes from the resources directory as well. So if you have third-party jar files in there, the report will include these classes. But since you did not include the sources for them, it fails. Below is what I think should be the correct line.

classDirectories =  files(subprojects.sourceSets.main.output.classesDir)