[Debian-med-packaging] Trying to update htsjdk but some tests are failing
Vincent Danjean
vdanjean.ml at free.fr
Fri Jun 24 18:57:17 UTC 2016
Le 24/06/2016 à 19:34, Andreas Tille a écrit :
> Vincent, did you got this mail.
Yes, but I forgot it.
> Any idea how to fix the build issue?
No idea but I remember it passed on my laptop. Perhaps it is only
a missing build-dependency. I will try to recheck and look more
carefully.
That said, the "problem" seems to be a small difference in
rounding. Perhaps the test nedd only to be relaxed.
Regards,
Vincent
> 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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>
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