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

2022-09-15 Thread Pierre Gruet 

Control: tags -1 + confirmed

Hello,

The issue showing up in the tests is the native library cannot be loaded 
properly. Some symbols (at least HDfprintf) cannot be found. I can 
investigate next week.


Surprisingly, using sbuild and working in the chroot after the failure 
of the tests, running

debian/rules override_dh_auto_build
debian/rules override_dh_auto_test
leads to all the tests passing...

Cheers,

--
Pierre


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

2022-09-14 Thread Steven Robbins 
On Thu, 8 Sep 2022 16:11:33 +0200 Paul Gevers  wrote:

> 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.

I find the same holds for simple BUILDING of the libsis-jhdf5-java source 
package.  The build succeeds when using libhdf5-dev from testing, but fails 
with the  package from  unstable. 

The failure happens when running tests.  Below is output from first test 
failure.

-Steve

FAILED: testCreateVerifyContentArtificialRootRoundtripOK
java.lang.ExceptionInInitializerError
at hdf.hdf5lib.HDF5Constants.(HDF5Constants.java:29)
at 
ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator$FileFormatVersion.(IHDF5WriterConfigurator.java:
74)
at 
ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator$FileFormatVersionBounds.(IHDF5WriterConfigurator.java:
127)
at 
ch.systemsx.cisd.hdf5.h5ar.HDF5Archiver.(HDF5Archiver.java:112)
at 
ch.systemsx.cisd.hdf5.h5ar.HDF5ArchiverFactory.open(HDF5ArchiverFactory.java:
41)
at 
ch.systemsx.cisd.hdf5.h5ar.HDF5ArchiverTest.testCreateVerifyContentArtificialRootRoundtripOK(HDF5ArchiverTest.java:
330)
at java.base/
jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:
104)
at java.base/java.lang.reflect.Method.invoke(Method.java:577)
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.(H5.java:230)
... 28 more

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

2022-09-08 Thread Paul Gevers 

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:


   passfail
hdf5   from testing1.10.8+repack-1
libsis-jhdf5-java  from testing19.04.1+dfsg-1
all others from testingfrom 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 
"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.(HDF5Constants.java:29)
	at 
ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator$FileFormatVersion.(IHDF5WriterConfigurator.java:74)
	at