[Debian-med-packaging] Trying to update htsjdk but some tests are failing

[Andreas Tille]

Hi Vincent,

On Sat, May 21, 2016 at 11:40:11PM +0200, Vincent Danjean wrote:
> Le 20/05/2016 23:50, Andreas Tille a écrit :
> > On Fri, May 20, 2016 at 09:18:09PM +0200, Vincent Danjean wrote:
> >> I'm not sure if the right fix is in the test suite (as I propose)
> >> or in the DeflaterFactory class. So, I did not commit anything for
> >> now.
> > 
> > Please be so kind to commit.  Thanks.
> 
> Done

The current state in Git does not build for me:

   [testng] PASSED: testReadAndSkipWithMultipleBlocks([null of CHAR, null of CHAR, null of CHAR])
   [testng] FAILED: testLazyInstance
   [testng] java.lang.AssertionError: expected [1.46426744E12] but found [1.46426757E12]
   [testng]     at org.testng.Assert.fail(Assert.java:94)
   [testng]     at org.testng.Assert.failNotEquals(Assert.java:513)
   [testng]     at org.testng.Assert.assertEquals(Assert.java:260)
   [testng]     at org.testng.Assert.assertEquals(Assert.java:273)
   [testng]     at htsjdk.samtools.util.RelativeIso8601DateTest.testLazyInstance(RelativeIso8601DateTest.java:19)
   [testng]     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
   [testng]     at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
   [testng]     at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
   [testng]     at java.lang.reflect.Method.invoke(Method.java:498)
   [testng]     at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:86)
   [testng]     at org.testng.internal.Invoker.invokeMethod(Invoker.java:643)
   [testng]     at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:820)
   [testng]     at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1128)
   [testng]     at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129)
   [testng]     at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
   [testng]     at org.testng.TestRunner.privateRun(TestRunner.java:782)
   [testng]     at org.testng.TestRunner.run(TestRunner.java:632)
   [testng]     at org.testng.SuiteRunner.runTest(SuiteRunner.java:366)
   [testng]     at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361)
   [testng]     at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319)
   [testng]     at org.testng.SuiteRunner.run(SuiteRunner.java:268)
   [testng]     at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
   [testng]     at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
   [testng]     at org.testng.TestNG.runSuitesSequentially(TestNG.java:1244)
   [testng]     at org.testng.TestNG.runSuitesLocally(TestNG.java:1169)
   [testng]     at org.testng.TestNG.run(TestNG.java:1064)
   [testng]     at org.testng.TestNG.privateMain(TestNG.java:1385)
   [testng]     at org.testng.TestNG.main(TestNG.java:1354)
   [testng] 
   [testng] 
   [testng] ===============================================
   [testng]     Ant test
   [testng]     Tests run: 22478, Failures: 1, Skips: 0
   [testng] ===============================================
   [testng] 
   [testng] 
   [testng] ===============================================
   [testng] htsjdk-tests
   [testng] Total tests run: 22478, Failures: 1, Skips: 0
   [testng] ===============================================
   [testng] 
   [testng] [TestNG] Time taken by org.testng.reporters.SuiteHTMLReporter at 3d82c5f3: 429 ms
   [testng] [TestNG] Time taken by [FailedReporter passed=0 failed=0 skipped=0]: 27 ms
   [testng] [TestNG] Time taken by org.testng.reporters.EmailableReporter2 at 73a8dfcc: 541 ms
   [testng] [TestNG] Time taken by org.testng.reporters.XMLReporter at 4cdf35a9: 960 ms
   [testng] [TestNG] Time taken by org.testng.reporters.JUnitReportReporter at 3f8f9dd6: 302 ms
   [testng] [TestNG] Time taken by org.testng.reporters.jq.Main at 66cd51c3: 1994 ms
   [testng] The tests failed.
[junitreport] the file /build/htsjdk-2.3.0+dfsg.1/dist/test/TESTS-TestSuites.xml is not a valid testsuite XML document
[junitreport] Error while accessing file /build/htsjdk-2.3.0+dfsg.1/dist/test/testng-failed.xml: testng.org
[junitreport] the file /build/htsjdk-2.3.0+dfsg.1/dist/test/testng-results.xml is not a valid testsuite XML document
[junitreport] Processing /build/htsjdk-2.3.0+dfsg.1/dist/test/TESTS-TestSuites.xml to /build/htsjdk-2.3.0+dfsg.1/dist/test/junit-noframes.html
[junitreport] Loading stylesheet /build/htsjdk-2.3.0+dfsg.1/etc/test/junit-noframes.xsl
[junitreport] Transform time: 45ms
     [copy] Copying 1 file to /build/htsjdk-2.3.0+dfsg.1/dist/test

BUILD FAILED
/build/htsjdk-2.3.0+dfsg.1/build.xml:180: The following error occurred while executing this line:
/build/htsjdk-2.3.0+dfsg.1/build.xml:174: There were failed unit tests

Total time: 1 minute 26 seconds
dh_auto_build: ant -Dant.build.javac.source=1.8 -Dant.build.javac.target=1.8 -Ddebug=true test returned exit code 1
debian/rules:26: recipe for target 'override_dh_auto_test' failed


Could you confirm that it builds for you in a clean pbuilder chroot?

Kind regards

       Andreas.

-- 
http://fam-tille.de