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Started by upstream project "BIOFORMATS-test-repo" build number 193 originally caused by: Started by upstream project "Trigger" build number 215 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@6 [BIOFORMATS-test-folder@6] $ /bin/bash -xe /tmp/jenkins16894959411244373729.sh + '[' bdv = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_30614_merge_ci -v /uod/idr/repos/curated/bdv:/data -v /uod/idr-scratch/merge-ci/curated/bdv:/config snoopycrimecop/bioformats:merge_ci -Dtestng.memory=15g -Dtestng.threadCount=12 Buildfile: /bio-formats-build/bioformats/components/test-suite/build.xml [echo] isSnapshot = true init-title: [echo] ----------=========== bio-formats-testing-framework ===========---------- init-timestamp: init: copy-resources: compile: [resolver:resolve] Resolving artifacts compile-tests: [resolver:resolve] Resolving artifacts [javac] Compiling 1 source file to /bio-formats-build/bioformats/components/test-suite/test [javac] warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. [javac] 4 warnings test-automated: [testng] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket [testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket [testng] File leak detector installed [testng] 02:25:16,118 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:25:16,120 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 02:25:16,120 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:25:16,121 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:25:16,122 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:25:16,122 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:25:16,123 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:25:16,123 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:25:16,123 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:25:16,124 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:25:16,124 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:25:16,125 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:25:16,309 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:25:16,310 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:25:16,340 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:25:16,341 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:25:16,349 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:25:16,349 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:25:16,349 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:25:16,350 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:25:16,350 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 02:25:16,351 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 02:25:16,351 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 228 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-09-19 02:25:16,362] [main] java.version = 21 [testng] 02:25:16,365 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:25:16,366 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:25:16,413 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-19_02-25-16.log] [testng] 02:25:16,414 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-09-19 02:25:16,416] [main] testng.directory = /data [testng] [2024-09-19 02:25:16,416] [main] testng.configDirectory = /config [testng] [2024-09-19 02:25:16,425] [main] testng.multiplier = 1.0 [testng] [2024-09-19 02:25:16,426] [main] testng.in-memory = false [testng] [2024-09-19 02:25:16,426] [main] testng.allow-missing = false [testng] [2024-09-19 02:25:16,426] [main] user.language = en [testng] [2024-09-19 02:25:16,426] [main] user.country = ${user.country} [testng] [2024-09-19 02:25:16,426] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-09-19 02:25:18,708] [main] ---------------------------------------- [testng] [2024-09-19 02:25:18,708] [main] Total files: 12 [testng] [2024-09-19 02:25:18,708] [main] Scan time: 2.282 s (190 ms/file) [testng] [2024-09-19 02:25:18,709] [main] ---------------------------------------- [testng] [2024-09-19 02:25:19,240] [main] setId("/data/public/idr0038/Lam-Cytok-MV-f0.h5") failed [testng] hdf.hdf5lib.exceptions.HDF5FileInterfaceException: Bad file ID accessed ["H5FDsec2.c line 959 in H5FD_sec2_lock(): unable to lock file, errno = 37, error message = 'No locks available'"] [testng] at hdf.hdf5lib.H5._H5Fopen(Native Method) [testng] at hdf.hdf5lib.H5.H5Fopen(H5.java:2347) [testng] at ch.systemsx.cisd.hdf5.HDF5.openFileReadOnly(HDF5.java:236) [testng] at ch.systemsx.cisd.hdf5.HDF5BaseReader.openFile(HDF5BaseReader.java:235) [testng] at ch.systemsx.cisd.hdf5.HDF5BaseReader.<init>(HDF5BaseReader.java:177) [testng] at ch.systemsx.cisd.hdf5.HDF5BaseReader.<init>(HDF5BaseReader.java:155) [testng] at ch.systemsx.cisd.hdf5.HDF5ReaderConfigurator.reader(HDF5ReaderConfigurator.java:81) [testng] at ch.systemsx.cisd.hdf5.HDF5FactoryProvider$HDF5Factory.openForReading(HDF5FactoryProvider.java:55) [testng] at ch.systemsx.cisd.hdf5.HDF5Factory.openForReading(HDF5Factory.java:62) [testng] at loci.formats.services.JHDFServiceImpl.setFile(JHDFServiceImpl.java:92) [testng] at loci.formats.in.BDVReader.initializeJHDFService(BDVReader.java:378) [testng] at loci.formats.in.BDVReader.initFile(BDVReader.java:157) [testng] at loci.formats.FormatReader.setId(FormatReader.java:1480) [testng] at loci.formats.ImageReader.setId(ImageReader.java:864) [testng] at loci.tests.testng.FormatReaderTestFactory.createInstances(FormatReaderTestFactory.java:251) [testng] at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) [testng] at java.base/java.lang.reflect.Method.invoke(Method.java:580) [testng] at org.testng.internal.FactoryMethod.invoke(FactoryMethod.java:81) [testng] at org.testng.internal.TestNGClassFinder.<init>(TestNGClassFinder.java:140) [testng] at org.testng.TestRunner.initMethods(TestRunner.java:409) [testng] at org.testng.TestRunner.init(TestRunner.java:235) [testng] at org.testng.TestRunner.init(TestRunner.java:205) [testng] at org.testng.TestRunner.<init>(TestRunner.java:153) [testng] at org.testng.SuiteRunner$DefaultTestRunnerFactory.newTestRunner(SuiteRunner.java:522) [testng] at org.testng.SuiteRunner.init(SuiteRunner.java:157) [testng] at org.testng.SuiteRunner.<init>(SuiteRunner.java:111) [testng] at org.testng.TestNG.createSuiteRunner(TestNG.java:1273) [testng] at org.testng.TestNG.createSuiteRunners(TestNG.java:1260) [testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1114) [testng] at org.testng.TestNG.run(TestNG.java:1031) [testng] at org.testng.TestNG.privateMain(TestNG.java:1338) [testng] at org.testng.TestNG.main(TestNG.java:1307) [testng] [2024-09-19 02:25:19,318] [main] setId("/data/public/idr0038/Lam-Cytok-MV-f0.xml") failed [testng] hdf.hdf5lib.exceptions.HDF5FileInterfaceException: Bad file ID accessed ["H5FDsec2.c line 959 in H5FD_sec2_lock(): unable to lock file, errno = 37, error message = 'No locks available'"] [testng] at hdf.hdf5lib.H5._H5Fopen(Native Method) [testng] at hdf.hdf5lib.H5.H5Fopen(H5.java:2347) [testng] at ch.systemsx.cisd.hdf5.HDF5.openFileReadOnly(HDF5.java:236) [testng] at ch.systemsx.cisd.hdf5.HDF5BaseReader.openFile(HDF5BaseReader.java:235) [testng] at ch.systemsx.cisd.hdf5.HDF5BaseReader.<init>(HDF5BaseReader.java:177) [testng] at ch.systemsx.cisd.hdf5.HDF5BaseReader.<init>(HDF5BaseReader.java:155) [testng] at ch.systemsx.cisd.hdf5.HDF5ReaderConfigurator.reader(HDF5ReaderConfigurator.java:81) [testng] at ch.systemsx.cisd.hdf5.HDF5FactoryProvider$HDF5Factory.openForReading(HDF5FactoryProvider.java:55) [testng] at ch.systemsx.cisd.hdf5.HDF5Factory.openForReading(HDF5Factory.java:62) [testng] at loci.formats.services.JHDFServiceImpl.setFile(JHDFServiceImpl.java:92) [testng] at loci.formats.in.BDVReader.initializeJHDFService(BDVReader.java:378) [testng] at loci.formats.in.BDVReader.initFile(BDVReader.java:157) [testng] at loci.formats.FormatReader.setId(FormatReader.java:1480) [testng] at loci.formats.ImageReader.setId(ImageReader.java:864) [testng] at loci.tests.testng.FormatReaderTestFactory.createInstances(FormatReaderTestFactory.java:251) [testng] at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) [testng] at java.base/java.lang.reflect.Method.invoke(Method.java:580) [testng] at org.testng.internal.FactoryMethod.invoke(FactoryMethod.java:81) [testng] at org.testng.internal.TestNGClassFinder.<init>(TestNGClassFinder.java:140) [testng] at org.testng.TestRunner.initMethods(TestRunner.java:409) [testng] at org.testng.TestRunner.init(TestRunner.java:235) [testng] at org.testng.TestRunner.init(TestRunner.java:205) [testng] at org.testng.TestRunner.<init>(TestRunner.java:153) [testng] at org.testng.SuiteRunner$DefaultTestRunnerFactory.newTestRunner(SuiteRunner.java:522) [testng] at org.testng.SuiteRunner.init(SuiteRunner.java:157) [testng] at org.testng.SuiteRunner.<init>(SuiteRunner.java:111) [testng] at org.testng.TestNG.createSuiteRunner(TestNG.java:1273) [testng] at org.testng.TestNG.createSuiteRunners(TestNG.java:1260) [testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1114) [testng] at org.testng.TestNG.run(TestNG.java:1031) [testng] at org.testng.TestNG.privateMain(TestNG.java:1338) [testng] at org.testng.TestNG.main(TestNG.java:1307) [testng] [2024-09-19 02:25:19,523] [main] setId("/data/public/idr0048/WB.h5") failed [testng] hdf.hdf5lib.exceptions.HDF5FileInterfaceException: Bad file ID accessed ["H5FDsec2.c line 959 in H5FD_sec2_lock(): unable to lock file, errno = 37, error message = 'No locks available'"] [testng] at hdf.hdf5lib.H5._H5Fopen(Native Method) [testng] at hdf.hdf5lib.H5.H5Fopen(H5.java:2347) [testng] at ch.systemsx.cisd.hdf5.HDF5.openFileReadOnly(HDF5.java:236) [testng] at ch.systemsx.cisd.hdf5.HDF5BaseReader.openFile(HDF5BaseReader.java:235) [testng] at ch.systemsx.cisd.hdf5.HDF5BaseReader.<init>(HDF5BaseReader.java:177) [testng] at ch.systemsx.cisd.hdf5.HDF5BaseReader.<init>(HDF5BaseReader.java:155) [testng] at ch.systemsx.cisd.hdf5.HDF5ReaderConfigurator.reader(HDF5ReaderConfigurator.java:81) [testng] at ch.systemsx.cisd.hdf5.HDF5FactoryProvider$HDF5Factory.openForReading(HDF5FactoryProvider.java:55) [testng] at ch.systemsx.cisd.hdf5.HDF5Factory.openForReading(HDF5Factory.java:62) [testng] at loci.formats.services.JHDFServiceImpl.setFile(JHDFServiceImpl.java:92) [testng] at loci.formats.in.BDVReader.initializeJHDFService(BDVReader.java:378) [testng] at loci.formats.in.BDVReader.initFile(BDVReader.java:157) [testng] at loci.formats.FormatReader.setId(FormatReader.java:1480) [testng] at loci.formats.ImageReader.setId(ImageReader.java:864) [testng] at loci.tests.testng.FormatReaderTestFactory.createInstances(FormatReaderTestFactory.java:251) [testng] at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) [testng] at java.base/java.lang.reflect.Method.invoke(Method.java:580) [testng] at org.testng.internal.FactoryMethod.invoke(FactoryMethod.java:81) [testng] at org.testng.internal.TestNGClassFinder.<init>(TestNGClassFinder.java:140) [testng] at org.testng.TestRunner.initMethods(TestRunner.java:409) [testng] at org.testng.TestRunner.init(TestRunner.java:235) [testng] at org.testng.TestRunner.init(TestRunner.java:205) [testng] at org.testng.TestRunner.<init>(TestRunner.java:153) [testng] at org.testng.SuiteRunner$DefaultTestRunnerFactory.newTestRunner(SuiteRunner.java:522) [testng] at org.testng.SuiteRunner.init(SuiteRunner.java:157) [testng] at org.testng.SuiteRunner.<init>(SuiteRunner.java:111) [testng] at org.testng.TestNG.createSuiteRunner(TestNG.java:1273) [testng] at org.testng.TestNG.createSuiteRunners(TestNG.java:1260) [testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1114) [testng] at org.testng.TestNG.run(TestNG.java:1031) [testng] at org.testng.TestNG.privateMain(TestNG.java:1338) [testng] at org.testng.TestNG.main(TestNG.java:1307) [testng] [2024-09-19 02:25:19,660] [main] setId("/data/public/idr0048/WB.xml") failed [testng] hdf.hdf5lib.exceptions.HDF5FileInterfaceException: Bad file ID accessed ["H5FDsec2.c line 959 in H5FD_sec2_lock(): unable to lock file, errno = 37, error message = 'No locks available'"] [testng] at hdf.hdf5lib.H5._H5Fopen(Native Method) [testng] at hdf.hdf5lib.H5.H5Fopen(H5.java:2347) [testng] at ch.systemsx.cisd.hdf5.HDF5.openFileReadOnly(HDF5.java:236) [testng] at ch.systemsx.cisd.hdf5.HDF5BaseReader.openFile(HDF5BaseReader.java:235) [testng] at ch.systemsx.cisd.hdf5.HDF5BaseReader.<init>(HDF5BaseReader.java:177) [testng] at ch.systemsx.cisd.hdf5.HDF5BaseReader.<init>(HDF5BaseReader.java:155) [testng] at ch.systemsx.cisd.hdf5.HDF5ReaderConfigurator.reader(HDF5ReaderConfigurator.java:81) [testng] at ch.systemsx.cisd.hdf5.HDF5FactoryProvider$HDF5Factory.openForReading(HDF5FactoryProvider.java:55) [testng] at ch.systemsx.cisd.hdf5.HDF5Factory.openForReading(HDF5Factory.java:62) [testng] at loci.formats.services.JHDFServiceImpl.setFile(JHDFServiceImpl.java:92) [testng] at loci.formats.in.BDVReader.initializeJHDFService(BDVReader.java:378) [testng] at loci.formats.in.BDVReader.initFile(BDVReader.java:157) [testng] at loci.formats.FormatReader.setId(FormatReader.java:1480) [testng] at loci.formats.ImageReader.setId(ImageReader.java:864) [testng] at loci.tests.testng.FormatReaderTestFactory.createInstances(FormatReaderTestFactory.java:251) [testng] at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) [testng] at java.base/java.lang.reflect.Method.invoke(Method.java:580) [testng] at org.testng.internal.FactoryMethod.invoke(FactoryMethod.java:81) [testng] at org.testng.internal.TestNGClassFinder.<init>(TestNGClassFinder.java:140) [testng] at org.testng.TestRunner.initMethods(TestRunner.java:409) [testng] at org.testng.TestRunner.init(TestRunner.java:235) [testng] at org.testng.TestRunner.init(TestRunner.java:205) [testng] at org.testng.TestRunner.<init>(TestRunner.java:153) [testng] at org.testng.SuiteRunner$DefaultTestRunnerFactory.newTestRunner(SuiteRunner.java:522) [testng] at org.testng.SuiteRunner.init(SuiteRunner.java:157) [testng] at org.testng.SuiteRunner.<init>(SuiteRunner.java:111) [testng] at org.testng.TestNG.createSuiteRunner(TestNG.java:1273) [testng] at org.testng.TestNG.createSuiteRunners(TestNG.java:1260) [testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1114) [testng] at org.testng.TestNG.run(TestNG.java:1031) [testng] at org.testng.TestNG.privateMain(TestNG.java:1338) [testng] at org.testng.TestNG.main(TestNG.java:1307) [testng] [2024-09-19 02:25:19,800] [main] setId("/data/public/idr0048/astroP65.h5") failed [testng] hdf.hdf5lib.exceptions.HDF5FileInterfaceException: Bad file ID accessed ["H5FDsec2.c line 959 in H5FD_sec2_lock(): unable to lock file, errno = 37, error message = 'No locks available'"] [testng] at hdf.hdf5lib.H5._H5Fopen(Native Method) [testng] at hdf.hdf5lib.H5.H5Fopen(H5.java:2347) [testng] at ch.systemsx.cisd.hdf5.HDF5.openFileReadOnly(HDF5.java:236) [testng] at ch.systemsx.cisd.hdf5.HDF5BaseReader.openFile(HDF5BaseReader.java:235) [testng] at ch.systemsx.cisd.hdf5.HDF5BaseReader.<init>(HDF5BaseReader.java:177) [testng] at ch.systemsx.cisd.hdf5.HDF5BaseReader.<init>(HDF5BaseReader.java:155) [testng] at ch.systemsx.cisd.hdf5.HDF5ReaderConfigurator.reader(HDF5ReaderConfigurator.java:81) [testng] at ch.systemsx.cisd.hdf5.HDF5FactoryProvider$HDF5Factory.openForReading(HDF5FactoryProvider.java:55) [testng] at ch.systemsx.cisd.hdf5.HDF5Factory.openForReading(HDF5Factory.java:62) [testng] at loci.formats.services.JHDFServiceImpl.setFile(JHDFServiceImpl.java:92) [testng] at loci.formats.in.BDVReader.initializeJHDFService(BDVReader.java:378) [testng] at loci.formats.in.BDVReader.initFile(BDVReader.java:157) [testng] at loci.formats.FormatReader.setId(FormatReader.java:1480) [testng] at loci.formats.ImageReader.setId(ImageReader.java:864) [testng] at loci.tests.testng.FormatReaderTestFactory.createInstances(FormatReaderTestFactory.java:251) [testng] at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) [testng] at java.base/java.lang.reflect.Method.invoke(Method.java:580) [testng] at org.testng.internal.FactoryMethod.invoke(FactoryMethod.java:81) [testng] at org.testng.internal.TestNGClassFinder.<init>(TestNGClassFinder.java:140) [testng] at org.testng.TestRunner.initMethods(TestRunner.java:409) [testng] at org.testng.TestRunner.init(TestRunner.java:235) [testng] at org.testng.TestRunner.init(TestRunner.java:205) [testng] at org.testng.TestRunner.<init>(TestRunner.java:153) [testng] at org.testng.SuiteRunner$DefaultTestRunnerFactory.newTestRunner(SuiteRunner.java:522) [testng] at org.testng.SuiteRunner.init(SuiteRunner.java:157) [testng] at org.testng.SuiteRunner.<init>(SuiteRunner.java:111) [testng] at org.testng.TestNG.createSuiteRunner(TestNG.java:1273) [testng] at org.testng.TestNG.createSuiteRunners(TestNG.java:1260) [testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1114) [testng] at org.testng.TestNG.run(TestNG.java:1031) [testng] at org.testng.TestNG.privateMain(TestNG.java:1338) [testng] at org.testng.TestNG.main(TestNG.java:1307) [testng] [2024-09-19 02:25:19,886] [main] setId("/data/public/idr0048/astroP65.xml") failed [testng] hdf.hdf5lib.exceptions.HDF5FileInterfaceException: Bad file ID accessed ["H5FDsec2.c line 959 in H5FD_sec2_lock(): unable to lock file, errno = 37, error message = 'No locks available'"] [testng] at hdf.hdf5lib.H5._H5Fopen(Native Method) [testng] at hdf.hdf5lib.H5.H5Fopen(H5.java:2347) [testng] at ch.systemsx.cisd.hdf5.HDF5.openFileReadOnly(HDF5.java:236) [testng] at ch.systemsx.cisd.hdf5.HDF5BaseReader.openFile(HDF5BaseReader.java:235) [testng] at ch.systemsx.cisd.hdf5.HDF5BaseReader.<init>(HDF5BaseReader.java:177) [testng] at ch.systemsx.cisd.hdf5.HDF5BaseReader.<init>(HDF5BaseReader.java:155) [testng] at ch.systemsx.cisd.hdf5.HDF5ReaderConfigurator.reader(HDF5ReaderConfigurator.java:81) [testng] at ch.systemsx.cisd.hdf5.HDF5FactoryProvider$HDF5Factory.openForReading(HDF5FactoryProvider.java:55) [testng] at ch.systemsx.cisd.hdf5.HDF5Factory.openForReading(HDF5Factory.java:62) [testng] at loci.formats.services.JHDFServiceImpl.setFile(JHDFServiceImpl.java:92) [testng] at loci.formats.in.BDVReader.initializeJHDFService(BDVReader.java:378) [testng] at loci.formats.in.BDVReader.initFile(BDVReader.java:157) [testng] at loci.formats.FormatReader.setId(FormatReader.java:1480) [testng] at loci.formats.ImageReader.setId(ImageReader.java:864) [testng] at loci.tests.testng.FormatReaderTestFactory.createInstances(FormatReaderTestFactory.java:251) [testng] at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) [testng] at java.base/java.lang.reflect.Method.invoke(Method.java:580) [testng] at org.testng.internal.FactoryMethod.invoke(FactoryMethod.java:81) [testng] at org.testng.internal.TestNGClassFinder.<init>(TestNGClassFinder.java:140) [testng] at org.testng.TestRunner.initMethods(TestRunner.java:409) [testng] at org.testng.TestRunner.init(TestRunner.java:235) [testng] at org.testng.TestRunner.init(TestRunner.java:205) [testng] at org.testng.TestRunner.<init>(TestRunner.java:153) [testng] at org.testng.SuiteRunner$DefaultTestRunnerFactory.newTestRunner(SuiteRunner.java:522) [testng] at org.testng.SuiteRunner.init(SuiteRunner.java:157) [testng] at org.testng.SuiteRunner.<init>(SuiteRunner.java:111) [testng] at org.testng.TestNG.createSuiteRunner(TestNG.java:1273) [testng] at org.testng.TestNG.createSuiteRunners(TestNG.java:1260) [testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1114) [testng] at org.testng.TestNG.run(TestNG.java:1031) [testng] at org.testng.TestNG.privateMain(TestNG.java:1338) [testng] at org.testng.TestNG.main(TestNG.java:1307) [testng] [2024-09-19 02:25:19,982] [main] setId("/data/public/samples/HisYFP-SPIM.h5") failed [testng] hdf.hdf5lib.exceptions.HDF5FileInterfaceException: Bad file ID accessed ["H5FDsec2.c line 959 in H5FD_sec2_lock(): unable to lock file, errno = 37, error message = 'No locks available'"] [testng] at hdf.hdf5lib.H5._H5Fopen(Native Method) [testng] at hdf.hdf5lib.H5.H5Fopen(H5.java:2347) [testng] at ch.systemsx.cisd.hdf5.HDF5.openFileReadOnly(HDF5.java:236) [testng] at ch.systemsx.cisd.hdf5.HDF5BaseReader.openFile(HDF5BaseReader.java:235) [testng] at ch.systemsx.cisd.hdf5.HDF5BaseReader.<init>(HDF5BaseReader.java:177) [testng] at ch.systemsx.cisd.hdf5.HDF5BaseReader.<init>(HDF5BaseReader.java:155) [testng] at ch.systemsx.cisd.hdf5.HDF5ReaderConfigurator.reader(HDF5ReaderConfigurator.java:81) [testng] at ch.systemsx.cisd.hdf5.HDF5FactoryProvider$HDF5Factory.openForReading(HDF5FactoryProvider.java:55) [testng] at ch.systemsx.cisd.hdf5.HDF5Factory.openForReading(HDF5Factory.java:62) [testng] at loci.formats.services.JHDFServiceImpl.setFile(JHDFServiceImpl.java:92) [testng] at loci.formats.in.BDVReader.initializeJHDFService(BDVReader.java:378) [testng] at loci.formats.in.BDVReader.initFile(BDVReader.java:157) [testng] at loci.formats.FormatReader.setId(FormatReader.java:1480) [testng] at loci.formats.ImageReader.setId(ImageReader.java:864) [testng] at loci.tests.testng.FormatReaderTestFactory.createInstances(FormatReaderTestFactory.java:251) [testng] at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) [testng] at java.base/java.lang.reflect.Method.invoke(Method.java:580) [testng] at org.testng.internal.FactoryMethod.invoke(FactoryMethod.java:81) [testng] at org.testng.internal.TestNGClassFinder.<init>(TestNGClassFinder.java:140) [testng] at org.testng.TestRunner.initMethods(TestRunner.java:409) [testng] at org.testng.TestRunner.init(TestRunner.java:235) [testng] at org.testng.TestRunner.init(TestRunner.java:205) [testng] at org.testng.TestRunner.<init>(TestRunner.java:153) [testng] at org.testng.SuiteRunner$DefaultTestRunnerFactory.newTestRunner(SuiteRunner.java:522) [testng] at org.testng.SuiteRunner.init(SuiteRunner.java:157) [testng] at org.testng.SuiteRunner.<init>(SuiteRunner.java:111) [testng] at org.testng.TestNG.createSuiteRunner(TestNG.java:1273) [testng] at org.testng.TestNG.createSuiteRunners(TestNG.java:1260) [testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1114) [testng] at org.testng.TestNG.run(TestNG.java:1031) [testng] at org.testng.TestNG.privateMain(TestNG.java:1338) [testng] at org.testng.TestNG.main(TestNG.java:1307) [testng] [2024-09-19 02:25:20,042] [main] setId("/data/public/samples/HisYFP-SPIM.xml") failed [testng] hdf.hdf5lib.exceptions.HDF5FileInterfaceException: Bad file ID accessed ["H5FDsec2.c line 959 in H5FD_sec2_lock(): unable to lock file, errno = 37, error message = 'No locks available'"] [testng] at hdf.hdf5lib.H5._H5Fopen(Native Method) [testng] at hdf.hdf5lib.H5.H5Fopen(H5.java:2347) [testng] at ch.systemsx.cisd.hdf5.HDF5.openFileReadOnly(HDF5.java:236) [testng] at ch.systemsx.cisd.hdf5.HDF5BaseReader.openFile(HDF5BaseReader.java:235) [testng] at ch.systemsx.cisd.hdf5.HDF5BaseReader.<init>(HDF5BaseReader.java:177) [testng] at ch.systemsx.cisd.hdf5.HDF5BaseReader.<init>(HDF5BaseReader.java:155) [testng] at ch.systemsx.cisd.hdf5.HDF5ReaderConfigurator.reader(HDF5ReaderConfigurator.java:81) [testng] at ch.systemsx.cisd.hdf5.HDF5FactoryProvider$HDF5Factory.openForReading(HDF5FactoryProvider.java:55) [testng] at ch.systemsx.cisd.hdf5.HDF5Factory.openForReading(HDF5Factory.java:62) [testng] at loci.formats.services.JHDFServiceImpl.setFile(JHDFServiceImpl.java:92) [testng] at loci.formats.in.BDVReader.initializeJHDFService(BDVReader.java:378) [testng] at loci.formats.in.BDVReader.initFile(BDVReader.java:157) [testng] at loci.formats.FormatReader.setId(FormatReader.java:1480) [testng] at loci.formats.ImageReader.setId(ImageReader.java:864) [testng] at loci.tests.testng.FormatReaderTestFactory.createInstances(FormatReaderTestFactory.java:251) [testng] at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) [testng] at java.base/java.lang.reflect.Method.invoke(Method.java:580) [testng] at org.testng.internal.FactoryMethod.invoke(FactoryMethod.java:81) [testng] at org.testng.internal.TestNGClassFinder.<init>(TestNGClassFinder.java:140) [testng] at org.testng.TestRunner.initMethods(TestRunner.java:409) [testng] at org.testng.TestRunner.init(TestRunner.java:235) [testng] at org.testng.TestRunner.init(TestRunner.java:205) [testng] at org.testng.TestRunner.<init>(TestRunner.java:153) [testng] at org.testng.SuiteRunner$DefaultTestRunnerFactory.newTestRunner(SuiteRunner.java:522) [testng] at org.testng.SuiteRunner.init(SuiteRunner.java:157) [testng] at org.testng.SuiteRunner.<init>(SuiteRunner.java:111) [testng] at org.testng.TestNG.createSuiteRunner(TestNG.java:1273) [testng] at org.testng.TestNG.createSuiteRunners(TestNG.java:1260) [testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1114) [testng] at org.testng.TestNG.run(TestNG.java:1031) [testng] at org.testng.TestNG.privateMain(TestNG.java:1338) [testng] at org.testng.TestNG.main(TestNG.java:1307) [testng] [TestNG] [Error] [testng] The factory method class loci.tests.testng.FormatReaderTestFactory.createInstances() threw an exception [testng] [2024-09-19 02:25:20,193] [main] setId("/data/public/samples/drosophila.h5") failed [testng] hdf.hdf5lib.exceptions.HDF5FileInterfaceException: Bad file ID accessed ["H5FDsec2.c line 959 in H5FD_sec2_lock(): unable to lock file, errno = 37, error message = 'No locks available'"] [testng] at hdf.hdf5lib.H5._H5Fopen(Native Method) [testng] at hdf.hdf5lib.H5.H5Fopen(H5.java:2347) [testng] at ch.systemsx.cisd.hdf5.HDF5.openFileReadOnly(HDF5.java:236) [testng] at ch.systemsx.cisd.hdf5.HDF5BaseReader.openFile(HDF5BaseReader.java:235) [testng] at ch.systemsx.cisd.hdf5.HDF5BaseReader.<init>(HDF5BaseReader.java:177) [testng] at ch.systemsx.cisd.hdf5.HDF5BaseReader.<init>(HDF5BaseReader.java:155) [testng] at ch.systemsx.cisd.hdf5.HDF5ReaderConfigurator.reader(HDF5ReaderConfigurator.java:81) [testng] at ch.systemsx.cisd.hdf5.HDF5FactoryProvider$HDF5Factory.openForReading(HDF5FactoryProvider.java:55) [testng] at ch.systemsx.cisd.hdf5.HDF5Factory.openForReading(HDF5Factory.java:62) [testng] at loci.formats.services.JHDFServiceImpl.setFile(JHDFServiceImpl.java:92) [testng] at loci.formats.in.BDVReader.initializeJHDFService(BDVReader.java:378) [testng] at loci.formats.in.BDVReader.initFile(BDVReader.java:157) [testng] at loci.formats.FormatReader.setId(FormatReader.java:1480) [testng] at loci.formats.ImageReader.setId(ImageReader.java:864) [testng] at loci.tests.testng.FormatReaderTestFactory.createInstances(FormatReaderTestFactory.java:251) [testng] at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) [testng] at java.base/java.lang.reflect.Method.invoke(Method.java:580) [testng] at org.testng.internal.FactoryMethod.invoke(FactoryMethod.java:81) [testng] at org.testng.internal.TestNGClassFinder.<init>(TestNGClassFinder.java:140) [testng] at org.testng.TestRunner.initMethods(TestRunner.java:409) [testng] at org.testng.TestRunner.init(TestRunner.java:235) [testng] at org.testng.TestRunner.init(TestRunner.java:205) [testng] at org.testng.TestRunner.<init>(TestRunner.java:153) [testng] at org.testng.SuiteRunner$DefaultTestRunnerFactory.newTestRunner(SuiteRunner.java:522) [testng] at org.testng.SuiteRunner.init(SuiteRunner.java:157) [testng] at org.testng.SuiteRunner.<init>(SuiteRunner.java:111) [testng] at org.testng.TestNG.createSuiteRunner(TestNG.java:1273) [testng] at org.testng.TestNG.createSuiteRunners(TestNG.java:1260) [testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1114) [testng] at org.testng.TestNG.run(TestNG.java:1031) [testng] at org.testng.TestNG.privateMain(TestNG.java:1338) [testng] at org.testng.TestNG.main(TestNG.java:1307) [testng] [2024-09-19 02:25:20,254] [main] setId("/data/public/samples/drosophila.xml") failed [testng] hdf.hdf5lib.exceptions.HDF5FileInterfaceException: Bad file ID accessed ["H5FDsec2.c line 959 in H5FD_sec2_lock(): unable to lock file, errno = 37, error message = 'No locks available'"] [testng] at hdf.hdf5lib.H5._H5Fopen(Native Method) [testng] at hdf.hdf5lib.H5.H5Fopen(H5.java:2347) [testng] at ch.systemsx.cisd.hdf5.HDF5.openFileReadOnly(HDF5.java:236) [testng] at ch.systemsx.cisd.hdf5.HDF5BaseReader.openFile(HDF5BaseReader.java:235) [testng] at ch.systemsx.cisd.hdf5.HDF5BaseReader.<init>(HDF5BaseReader.java:177) [testng] at ch.systemsx.cisd.hdf5.HDF5BaseReader.<init>(HDF5BaseReader.java:155) [testng] at ch.systemsx.cisd.hdf5.HDF5ReaderConfigurator.reader(HDF5ReaderConfigurator.java:81) [testng] at ch.systemsx.cisd.hdf5.HDF5FactoryProvider$HDF5Factory.openForReading(HDF5FactoryProvider.java:55) [testng] at ch.systemsx.cisd.hdf5.HDF5Factory.openForReading(HDF5Factory.java:62) [testng] at loci.formats.services.JHDFServiceImpl.setFile(JHDFServiceImpl.java:92) [testng] at loci.formats.in.BDVReader.initializeJHDFService(BDVReader.java:378) [testng] at loci.formats.in.BDVReader.initFile(BDVReader.java:157) [testng] at loci.formats.FormatReader.setId(FormatReader.java:1480) [testng] at loci.formats.ImageReader.setId(ImageReader.java:864) [testng] at loci.tests.testng.FormatReaderTestFactory.createInstances(FormatReaderTestFactory.java:251) [testng] at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) [testng] at java.base/java.lang.reflect.Method.invoke(Method.java:580) [testng] at org.testng.internal.FactoryMethod.invoke(FactoryMethod.java:81) [testng] at org.testng.internal.TestNGClassFinder.<init>(TestNGClassFinder.java:140) [testng] at org.testng.TestRunner.initMethods(TestRunner.java:409) [testng] at org.testng.TestRunner.init(TestRunner.java:235) [testng] at org.testng.TestRunner.init(TestRunner.java:205) [testng] at org.testng.TestRunner.<init>(TestRunner.java:153) [testng] at org.testng.SuiteRunner$DefaultTestRunnerFactory.newTestRunner(SuiteRunner.java:522) [testng] at org.testng.SuiteRunner.init(SuiteRunner.java:157) [testng] at org.testng.SuiteRunner.<init>(SuiteRunner.java:111) [testng] at org.testng.TestNG.createSuiteRunner(TestNG.java:1273) [testng] at org.testng.TestNG.createSuiteRunners(TestNG.java:1260) [testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1114) [testng] at org.testng.TestNG.run(TestNG.java:1031) [testng] at org.testng.TestNG.privateMain(TestNG.java:1338) [testng] at org.testng.TestNG.main(TestNG.java:1307) [testng] [2024-09-19 02:25:20,254] [main] setId failed on [/data/public/idr0038/Lam-Cytok-MV-f0.h5, /data/public/idr0038/Lam-Cytok-MV-f0.xml, /data/public/idr0048/WB.h5, /data/public/idr0048/WB.xml, /data/public/idr0048/astroP65.h5, /data/public/idr0048/astroP65.xml, /data/public/samples/HisYFP-SPIM.h5, /data/public/samples/HisYFP-SPIM.xml, /data/public/samples/drosophila.h5, /data/public/samples/drosophila.xml] [testng] The tests failed. BUILD FAILED /bio-formats-build/bioformats/components/test-suite/build.xml:270: if=failedTest Total time: 7 seconds Build step 'Execute shell' marked build as failure Finished: FAILURE