Foo.php

<?php
class Foo {
	public function tested() {
		return true;
	}
	
	public function untested() {
		return true;
	}
}

FooTest.php

<?php

require_once 'Foo.php';

class FooTest extends PHPUnit_Framework_TestCase
{
	public function testTested() {
		$foo = new Foo();
		$this->assertEquals(true, $foo->tested());
	}
}

FooTestSuite.php

<?php
require_once 'FooTest.php';

class FooTestSuite extends PHPUnit_Framework_TestSuite {
	public static function suite() {
		$suite = new FooTestSuite('Foo test suite');
		$suite->addTestSuite('FooTest');
		$suite->addTestSuite('FooTest');
		return $suite;
	}
}

gistfile4.txt

Generating the code coverage report from FooTest.php is fine: statements="2" coveredstatements="1".

phpunit --coverage-clover coverage.xml FooTest.php

<?xml version="1.0" encoding="UTF-8"?>
<coverage generated="1286194796">
  <project timestamp="1286194796">
    <file name="/Users/yannooo/testcase/Foo.php">
      <class name="Foo" namespace="global">
        <metrics methods="2" coveredmethods="1" conditionals="0" coveredconditionals="0" statements="2" coveredstatements="1" elements="4" coveredelements="2"/>
      </class>
      <line num="3" type="method" name="tested" crap="1" count="1"/>
      <line num="4" type="stmt" count="1"/>
      <line num="7" type="method" name="untested" crap="2" count="0"/>
      <line num="8" type="stmt" count="0"/>
      <metrics loc="9" ncloc="9" classes="1" methods="2" coveredmethods="1" conditionals="0" coveredconditionals="0" statements="2" coveredstatements="1" elements="4" coveredelements="2"/>
    </file>
    <metrics files="1" loc="9" ncloc="9" classes="1" methods="2" coveredmethods="1" conditionals="0" coveredconditionals="0" statements="2" coveredstatements="1" elements="4" coveredelements="2"/>
  </project>
</coverage>

gistfile5.txt

When the TestCase is run twice from the test suite the results doesn't account for uncovered statements: statements="1" coveredstatements="1"

phpunit --coverage-clover coverage.xml FooTestSuite.php

<?xml version="1.0" encoding="UTF-8"?>
<coverage generated="1286194842">
  <project timestamp="1286194842">
    <file name="/Users/yannooo/testcase/Foo.php">
      <class name="Foo" namespace="global">
        <metrics methods="2" coveredmethods="1" conditionals="0" coveredconditionals="0" statements="1" coveredstatements="1" elements="3" coveredelements="2"/>
      </class>
      <line num="3" type="method" name="tested" crap="1" count="1"/>
      <line num="4" type="stmt" count="1"/>
      <line num="7" type="method" name="untested" crap="1" count="0"/>
      <metrics loc="9" ncloc="9" classes="1" methods="2" coveredmethods="1" conditionals="0" coveredconditionals="0" statements="1" coveredstatements="1" elements="3" coveredelements="2"/>
    </file>
    <metrics files="1" loc="9" ncloc="9" classes="1" methods="2" coveredmethods="1" conditionals="0" coveredconditionals="0" statements="1" coveredstatements="1" elements="3" coveredelements="2"/>
  </project>
</coverage>