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

[Andreas Tille]

Vincent, did you got this mail.  Any idea how to fix the build issue?

Kind regards

     Andreas.

On Thu, May 26, 2016 at 03:07:25PM +0200, Andreas Tille wrote:
> 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
> 
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