Bug#1019393: marked as done (hdf5 breaks libsis-jhdf5-java autopkgtest: Could not initialize class)

Debian Bug Tracking System Mon, 19 Sep 2022 15:09:18 -0700

Your message dated Mon, 19 Sep 2022 22:06:25 +0000
with message-id <[email protected]>
and subject line Bug#1019393: fixed in libsis-jhdf5-java 19.04.1+dfsg-2
has caused the Debian Bug report #1019393,
regarding hdf5 breaks libsis-jhdf5-java autopkgtest: Could not initialize class
to be marked as done.


This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

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-- 
1019393: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1019393
Debian Bug Tracking System
Contact [email protected] with problems

--- Begin Message ---
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: [email protected]
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)
OpenPGP_signature
Description: OpenPGP digital signature

--- End Message ---

--- Begin Message ---

Source: libsis-jhdf5-java
Source-Version: 19.04.1+dfsg-2
Done: Pierre Gruet <[email protected]>

We believe that the bug you reported is fixed in the latest version of
libsis-jhdf5-java, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Pierre Gruet <[email protected]> (supplier of updated libsis-jhdf5-java package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 1.8
Date: Mon, 19 Sep 2022 23:13:29 +0200
Source: libsis-jhdf5-java
Architecture: source
Version: 19.04.1+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<[email protected]>
Changed-By: Pierre Gruet <[email protected]>
Closes: 1019393 1020139
Changes:
 libsis-jhdf5-java (19.04.1+dfsg-2) unstable; urgency=medium
 .
   * Adding a missing directive from removed H5private.h file of hdf5
     (Closes: #1019393, #1020139)
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--- End Message ---

Bug#1019393: marked as done (hdf5 breaks libsis-jhdf5-java autopkgtest: Could not initialize class)

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