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: testAnonCompoundjava.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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