[Debian-med-packaging] Bug#1019393: hdf5 breaks libsis-jhdf5-java autopkgtest: Could not initialize class
Paul Gevers
elbrus at debian.org
Thu Sep 8 15:11:33 BST 2022
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-ci at 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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