Bug#1019393: hdf5 breaks libsis-jhdf5-java autopkgtest: Could not initialize class

Paul Gevers Thu, 08 Sep 2022 07:15:47 -0700

Source: hdf5, libsis-jhdf5-java
Control: found -1 hdf5/1.10.8+repack-1
Control: found -1 libsis-jhdf5-java/19.04.1+dfsg-1
Severity: serious
Tags: sid bookworm
User: debian...@lists.debian.org
Usertags: breaks needs-update


Dear maintainer(s),

With a recent upload of hdf5 the autopkgtest of libsis-jhdf5-java fails in testing when that autopkgtest is run with the binary packages of hdf5 from unstable. It passes when run with only packages from testing. In tabular form:


                       pass            fail
hdf5                   from testing    1.10.8+repack-1
libsis-jhdf5-java      from testing    19.04.1+dfsg-1
all others             from testing    from testing

I copied some of the output at the bottom of this report.

Currently this regression is blocking the migration of hdf5 to testing [1]. Due to the nature of this issue, I filed this bug report against both packages. Can you please investigate the situation and reassign the bug to the right package?


More information about this bug and the reason for filing it can be found on
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation

Paul

[1] https://qa.debian.org/excuses.php?package=hdf5

https://ci.debian.net/data/autopkgtest/testing/amd64/libs/libsis-jhdf5-java/25831074/log.gz

Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.

[TestNGContentHandler] [WARN] It is strongly recommended to add "<!DOCTYPE suite SYSTEM "http://testng.org/testng-1.0.dtd"; >" at the top of your file, otherwise TestNG may fail or not work as expected.

[TestNG] Running:

/tmp/autopkgtest-lxc.50ajov7f/downtmp/build.MuO/src/sourceTest/java/tests.xml

sourceTest/java/ch/systemsx/cisd/hdf5/h5ar/test.h5ar
sourceTest/java/ch/systemsx/cisd/hdf5/h5ar/test_14_12_0.h5ar
[Utils] Attempting to create /tmp/tmp.FUdpvQH0CP/test-output/All/All.xml
[Utils]   Directory /tmp/tmp.FUdpvQH0CP/test-output/All exists: true
PASSED: testBitSetArrayRoundTrip([Ljava.util.BitSet;@697a0948)
PASSED: testBitSetArrayRoundTrip([Ljava.util.BitSet;@7cf63b9a)
PASSED: testBitSetArrayRoundTrip([Ljava.util.BitSet;@4776e209)
PASSED: testBitSetArrayRoundTrip([Ljava.util.BitSet;@265a094b)
PASSED: testBitSetArrayRoundTrip([Ljava.util.BitSet;@1f536481)
PASSED: testBitSetArrayRoundTrip([Ljava.util.BitSet;@5234b61a)
PASSED: testBitSetArrayRoundTrip([Ljava.util.BitSet;@22a260ff)
PASSED: testBitSetArrayRoundTrip([Ljava.util.BitSet;@54c425b1)
PASSED: testBitSetArrayRoundTrip([Ljava.util.BitSet;@50b734c4)
PASSED: testBitSetRoundTrip({})
PASSED: testBitSetRoundTrip({0})
PASSED: testBitSetRoundTrip({31})
PASSED: testBitSetRoundTrip({64})
PASSED: testBitSetRoundTrip({128})
PASSED: testBitSetRoundTrip({63, 191})
PASSED: testBitSetRoundTrip({64, 192})
PASSED: testBitSetRoundTrip({17, 88, 155})

PASSED: testBitSetRoundTrip({0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255})

PASSED: testAttributeTypeVariantAttributeName
PASSED: testConversion
PASSED: testTypeVariant
PASSED: testFileExistsOnFS
PASSED: testOnlyFileAndDirExistsOnFS
PASSED: testConcatLink
PASSED: testGetParentPath
PASSED: testNormalizePath
PASSED: testDescribeLink
PASSED: testGetPermissions
PASSED: testIdCache
PASSED: testToInt64
PASSED: testToInt64_Overflow
PASSED: testToUint16
PASSED: testToUint32
PASSED: testToUint8
PASSED: testIncrementIdx
PASSED: testConvertUnit
PASSED: testCompressAll
PASSED: testCompressBlackList
PASSED: testCompressBlackWhiteList
PASSED: testCompressDefault
PASSED: testCompressDefaultWithCompression
PASSED: testCompressWhiteList
FAILED: testAccessClosedReaderWriter
java.lang.ExceptionInInitializerError
        at hdf.hdf5lib.HDF5Constants.<clinit>(HDF5Constants.java:29)

at ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator$FileFormatVersion.<clinit>(IHDF5WriterConfigurator.java:74) at ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator$FileFormatVersionBounds.<clinit>(IHDF5WriterConfigurator.java:127) at ch.systemsx.cisd.hdf5.HDF5WriterConfigurator.<init>(HDF5WriterConfigurator.java:42) at ch.systemsx.cisd.hdf5.HDF5FactoryProvider$HDF5Factory.open(HDF5FactoryProvider.java:49) at ch.systemsx.cisd.hdf5.HDF5RoundtripTest.testAccessClosedReaderWriter(HDF5RoundtripTest.java:1653) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

        at java.base/java.lang.reflect.Method.invoke(Method.java:566)

at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100)

        at org.testng.internal.Invoker.invokeMethod(Invoker.java:646)
        at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811)
        at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129)

at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129)

        at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
        at org.testng.TestRunner.privateRun(TestRunner.java:746)
        at org.testng.TestRunner.run(TestRunner.java:600)
        at org.testng.SuiteRunner.runTest(SuiteRunner.java:366)
        at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361)
        at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319)
        at org.testng.SuiteRunner.run(SuiteRunner.java:268)
        at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
        at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
        at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264)
        at org.testng.TestNG.runSuitesLocally(TestNG.java:1189)
        at org.testng.TestNG.runSuites(TestNG.java:1104)
        at org.testng.TestNG.run(TestNG.java:1076)
        at org.testng.TestNG.privateMain(TestNG.java:1405)
        at org.testng.TestNG.main(TestNG.java:1374)

Caused by: java.lang.UnsupportedOperationException: No suitable HDF5 native library found for this platform.

        at hdf.hdf5lib.H5.loadH5Lib(H5.java:240)
        at hdf.hdf5lib.H5.<clinit>(H5.java:230)
        ... 30 more

FAILED: testAnonCompound

java.lang.NoClassDefFoundError: Could not initialize class ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator$FileFormatVersionBounds at ch.systemsx.cisd.hdf5.HDF5WriterConfigurator.<init>(HDF5WriterConfigurator.java:42) at ch.systemsx.cisd.hdf5.HDF5FactoryProvider$HDF5Factory.open(HDF5FactoryProvider.java:49)

        at ch.systemsx.cisd.hdf5.HDF5Factory.open(HDF5Factory.java:38)

at ch.systemsx.cisd.hdf5.HDF5RoundtripTest.testAnonCompound(HDF5RoundtripTest.java:8707) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

        at java.base/java.lang.reflect.Method.invoke(Method.java:566)

at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100)

        at org.testng.internal.Invoker.invokeMethod(Invoker.java:646)
        at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811)
        at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129)

at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129)

        at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
        at org.testng.TestRunner.privateRun(TestRunner.java:746)
        at org.testng.TestRunner.run(TestRunner.java:600)
        at org.testng.SuiteRunner.runTest(SuiteRunner.java:366)
        at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361)
        at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319)
        at org.testng.SuiteRunner.run(SuiteRunner.java:268)
        at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
        at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
        at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264)
        at org.testng.TestNG.runSuitesLocally(TestNG.java:1189)
        at org.testng.TestNG.runSuites(TestNG.java:1104)
        at org.testng.TestNG.run(TestNG.java:1076)
        at org.testng.TestNG.privateMain(TestNG.java:1405)
        at org.testng.TestNG.main(TestNG.java:1374)

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Bug#1019393: hdf5 breaks libsis-jhdf5-java autopkgtest: Could not initialize class

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