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Started by upstream project "BIOFORMATS-test-repo" build number 41 originally caused by: Started by upstream project "Trigger" build number 47 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4 [BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins14530621000520743651.sh + '[' cellworx = slidebook ']' ++ date +%u + '[' 1 -le 1 ']' + DOCKER_ARGS='-Dtestng.memory=15g -Dtestng.threadCount=12 -Duser.language=fr -Duser.country=FR' + sudo docker run --rm --name BIOFORMATS-test-folder_5748_merge_ci -v /uod/idr/repos/curated/cellworx:/data -v /uod/idr-scratch/merge-ci/curated/cellworx:/config snoopycrimecop/bioformats:merge_ci -Dtestng.memory=15g -Dtestng.threadCount=12 -Duser.language=fr -Duser.country=FR 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 test-automated: [testng] File leak detector installed [testng] 01:28:47,519 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:28:47,521 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 01:28:47,521 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:28:47,522 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:28:47,522 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:28:47,522 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:28:47,522 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:28:47,522 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:28:47,523 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:28:47,523 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:28:47,523 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:28:47,523 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:28:47,755 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:28:47,755 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:28:47,785 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:28:47,785 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:28:47,794 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:28:47,795 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:28:47,795 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:28:47,795 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:28:47,795 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 01:28:47,796 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 01:28:47,796 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 273 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-04-22 01:28:47,807] [main] java.version = 1.8.0_342 [testng] 01:28:47,811 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:28:47,811 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:28:47,856 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-22_01-28-47.log] [testng] 01:28:47,858 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-04-22 01:28:47,860] [main] testng.directory = /data [testng] [2024-04-22 01:28:47,860] [main] testng.configDirectory = /config [testng] [2024-04-22 01:28:47,872] [main] testng.multiplier = 1.0 [testng] [2024-04-22 01:28:47,873] [main] testng.in-memory = false [testng] [2024-04-22 01:28:47,873] [main] testng.allow-missing = false [testng] [2024-04-22 01:28:47,873] [main] user.language = fr [testng] [2024-04-22 01:28:47,873] [main] user.country = FR [testng] [2024-04-22 01:28:47,873] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-04-22 01:29:36,086] [main] ---------------------------------------- [testng] [2024-04-22 01:29:36,087] [main] Total files: 4 [testng] [2024-04-22 01:29:36,087] [main] Scan time: 48.213 s (12053 ms/file) [testng] [2024-04-22 01:29:36,087] [main] ---------------------------------------- [testng] [2024-04-22 01:29:41,523] [main] setId("/data/hms/184A1-225/184A1-225.HTD") failed [testng] java.lang.NullPointerException: Length: Length cannot be constructed with a null value. [testng] at ome.units.quantity.Length.<init>(Length.java:66) [testng] at loci.formats.in.CellWorxReader.parseWellLogFile(CellWorxReader.java:788) [testng] at loci.formats.in.CellWorxReader.populateMetadata(CellWorxReader.java:545) [testng] at loci.formats.in.CellWorxReader.initFile(CellWorxReader.java:310) [testng] at loci.formats.FormatReader.setId(FormatReader.java:1480) [testng] at loci.formats.ImageReader.setId(ImageReader.java:865) [testng] at loci.tests.testng.FormatReaderTestFactory.createInstances(FormatReaderTestFactory.java:251) [testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) [testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) [testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) [testng] at java.lang.reflect.Method.invoke(Method.java:498) [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] [2024-04-22 01:29:44,758] [main] setId("/data/hms/96-well-sample-dataset/PNL_Representative_Data_Set_96_Well/PNL_Representative_Data_Set_96_Well.HTD") failed [testng] java.lang.NullPointerException: Length: Length cannot be constructed with a null value. [testng] at ome.units.quantity.Length.<init>(Length.java:66) [testng] at loci.formats.in.CellWorxReader.parseWellLogFile(CellWorxReader.java:788) [testng] at loci.formats.in.CellWorxReader.populateMetadata(CellWorxReader.java:545) [testng] at loci.formats.in.CellWorxReader.initFile(CellWorxReader.java:310) [testng] at loci.formats.FormatReader.setId(FormatReader.java:1480) [testng] at loci.formats.ImageReader.setId(ImageReader.java:865) [testng] at loci.tests.testng.FormatReaderTestFactory.createInstances(FormatReaderTestFactory.java:251) [testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) [testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) [testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) [testng] at java.lang.reflect.Method.invoke(Method.java:498) [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] [2024-04-22 01:29:46,663] [main] setId("/data/hms/plate1/plate1.HTD") failed [testng] java.lang.NullPointerException: Length: Length cannot be constructed with a null value. [testng] at ome.units.quantity.Length.<init>(Length.java:66) [testng] at loci.formats.in.CellWorxReader.parseWellLogFile(CellWorxReader.java:788) [testng] at loci.formats.in.CellWorxReader.populateMetadata(CellWorxReader.java:545) [testng] at loci.formats.in.CellWorxReader.initFile(CellWorxReader.java:310) [testng] at loci.formats.FormatReader.setId(FormatReader.java:1480) [testng] at loci.formats.ImageReader.setId(ImageReader.java:865) [testng] at loci.tests.testng.FormatReaderTestFactory.createInstances(FormatReaderTestFactory.java:251) [testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) [testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) [testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) [testng] at java.lang.reflect.Method.invoke(Method.java:498) [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] [2024-04-22 01:29:50,723] [main] setId("/data/pki/SKMEL28_10K_1.HTD") failed [testng] java.lang.NullPointerException: Length: Length cannot be constructed with a null value. [testng] at ome.units.quantity.Length.<init>(Length.java:66) [testng] at loci.formats.in.CellWorxReader.parseWellLogFile(CellWorxReader.java:788) [testng] at loci.formats.in.CellWorxReader.populateMetadata(CellWorxReader.java:545) [testng] at loci.formats.in.CellWorxReader.initFile(CellWorxReader.java:310) [testng] at loci.formats.FormatReader.setId(FormatReader.java:1480) [testng] at loci.formats.ImageReader.setId(ImageReader.java:865) [testng] at loci.tests.testng.FormatReaderTestFactory.createInstances(FormatReaderTestFactory.java:251) [testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) [testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) [testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) [testng] at java.lang.reflect.Method.invoke(Method.java:498) [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] [2024-04-22 01:29:50,733] [main] setId failed on [/data/hms/184A1-225/184A1-225.HTD, /data/hms/96-well-sample-dataset/PNL_Representative_Data_Set_96_Well/PNL_Representative_Data_Set_96_Well.HTD, /data/hms/plate1/plate1.HTD, /data/pki/SKMEL28_10K_1.HTD] [testng] The tests failed. BUILD FAILED /bio-formats-build/bioformats/components/test-suite/build.xml:270: if=failedTest Total time: 1 minute 8 seconds Build step 'Execute shell' marked build as failure Finished: FAILURE