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Started by upstream project "BIOFORMATS-test-repo" build number 332 originally caused by: Started by upstream project "Trigger" build number 355 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5 [BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins5927054989227557870.sh + '[' incell = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_52803_merge_ci -v /uod/idr/repos/curated/incell:/data -v /uod/idr-scratch/merge-ci/curated/incell:/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] 1 warning 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] 02:57:14,138 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 02:57:14,139 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - No custom configurators were discovered as a service. [testng] 02:57:14,139 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:57:14,140 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:57:14,141 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:57:14,141 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:57:14,141 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:57:14,141 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:57:14,142 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:57:14,142 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:57:14,142 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:57:14,143 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:57:14,300 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:57:14,301 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:57:14,323 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:57:14,323 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:57:14,328 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:57:14,328 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:57:14,328 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:57:14,329 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:57:14,329 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@3f6f6701 - End of configuration. [testng] 02:57:14,329 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@4f80542f - Registering current configuration as safe fallback point [testng] 02:57:14,329 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 187 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-01-29 02:57:14,338] [main] java.version = 17.0.2 [testng] 02:57:14,341 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:57:14,341 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:57:14,380 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-01-29_02-57-14.log] [testng] 02:57:14,382 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14bdbc74 - End of configuration. [testng] [2025-01-29 02:57:14,384] [main] testng.directory = /data [testng] [2025-01-29 02:57:14,384] [main] testng.configDirectory = /config [testng] [2025-01-29 02:57:14,392] [main] testng.multiplier = 1.0 [testng] [2025-01-29 02:57:14,393] [main] testng.in-memory = false [testng] [2025-01-29 02:57:14,393] [main] testng.allow-missing = false [testng] [2025-01-29 02:57:14,393] [main] user.language = en [testng] [2025-01-29 02:57:14,393] [main] user.country = ${user.country} [testng] [2025-01-29 02:57:14,394] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-01-29 03:19:13,483] [main] ---------------------------------------- [testng] [2025-01-29 03:19:13,483] [main] Total files: 4190 [testng] [2025-01-29 03:19:13,483] [main] Scan time: 1319.089 s (314 ms/file) [testng] [2025-01-29 03:19:13,484] [main] ---------------------------------------- [testng] [2025-01-29 03:19:23,588] [main] setId("/data/brian/Proper Dark Images/2007.11.12.13.37.27.xdce") failed [testng] java.lang.NullPointerException: Cannot invoke "java.lang.Boolean.booleanValue()" because "this.doZ" is null [testng] at loci.formats.in.InCellReader$MinimalInCellHandler.startElement(InCellReader.java:925) [testng] at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) [testng] at org.apache.xerces.parsers.AbstractXMLDocumentParser.emptyElement(Unknown Source) [testng] at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanStartElement(Unknown Source) [testng] at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source) [testng] at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) [testng] at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) [testng] at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) [testng] at org.apache.xerces.parsers.XMLParser.parse(Unknown Source) [testng] at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source) [testng] at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source) [testng] at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source) [testng] at java.xml/javax.xml.parsers.SAXParser.parse(SAXParser.java:197) [testng] at loci.common.xml.XMLTools.parseXML(XMLTools.java:551) [testng] at loci.common.xml.XMLTools.parseXML(XMLTools.java:533) [testng] at loci.formats.in.InCellReader.initFile(InCellReader.java:380) [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.NativeMethodAccessorImpl.invoke0(Native Method) [testng] at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) [testng] at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) [testng] at java.base/java.lang.reflect.Method.invoke(Method.java:568) [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$DefaultTestRunnerFactory.newTestRunner(SuiteRunner.java:522) [testng] at org.testng.SuiteRunner.init(SuiteRunner.java:157) [testng] at org.testng.SuiteRunner.<init>(SuiteRunner.java:111) [testng] at org.testng.TestNG.createSuiteRunner(TestNG.java:1273) [testng] at org.testng.TestNG.createSuiteRunners(TestNG.java:1260) [testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1114) [testng] at org.testng.TestNG.run(TestNG.java:1031) [testng] at org.testng.TestNG.privateMain(TestNG.java:1338) [testng] at org.testng.TestNG.main(TestNG.java:1307) [testng] [2025-01-29 03:19:55,067] [main] setId("/data/michael/Z Sections with flatfield corr/2007.10.17.17.13.59.xdce") failed [testng] java.lang.NullPointerException: Cannot invoke "java.lang.Boolean.booleanValue()" because "this.doZ" is null [testng] at loci.formats.in.InCellReader$MinimalInCellHandler.startElement(InCellReader.java:925) [testng] at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) [testng] at org.apache.xerces.parsers.AbstractXMLDocumentParser.emptyElement(Unknown Source) [testng] at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanStartElement(Unknown Source) [testng] at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source) [testng] at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) [testng] at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) [testng] at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) [testng] at org.apache.xerces.parsers.XMLParser.parse(Unknown Source) [testng] at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source) [testng] at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source) [testng] at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source) [testng] at java.xml/javax.xml.parsers.SAXParser.parse(SAXParser.java:197) [testng] at loci.common.xml.XMLTools.parseXML(XMLTools.java:551) [testng] at loci.common.xml.XMLTools.parseXML(XMLTools.java:533) [testng] at loci.formats.in.InCellReader.initFile(InCellReader.java:380) [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.NativeMethodAccessorImpl.invoke0(Native Method) [testng] at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) [testng] at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) [testng] at java.base/java.lang.reflect.Method.invoke(Method.java:568) [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$DefaultTestRunnerFactory.newTestRunner(SuiteRunner.java:522) [testng] at org.testng.SuiteRunner.init(SuiteRunner.java:157) [testng] at org.testng.SuiteRunner.<init>(SuiteRunner.java:111) [testng] at org.testng.TestNG.createSuiteRunner(TestNG.java:1273) [testng] at org.testng.TestNG.createSuiteRunners(TestNG.java:1260) [testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1114) [testng] at org.testng.TestNG.run(TestNG.java:1031) [testng] at org.testng.TestNG.privateMain(TestNG.java:1338) [testng] at org.testng.TestNG.main(TestNG.java:1307) [testng] [2025-01-29 03:19:55,291] [main] setId("/data/michael/firstStack/2007.07.05.17.33.35.xdce") failed [testng] java.lang.NullPointerException: Cannot invoke "java.lang.Boolean.booleanValue()" because "this.doZ" is null [testng] at loci.formats.in.InCellReader$MinimalInCellHandler.startElement(InCellReader.java:925) [testng] at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) [testng] at org.apache.xerces.parsers.AbstractXMLDocumentParser.emptyElement(Unknown Source) [testng] at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanStartElement(Unknown Source) [testng] at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source) [testng] at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) [testng] at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) [testng] at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) [testng] at org.apache.xerces.parsers.XMLParser.parse(Unknown Source) [testng] at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source) [testng] at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source) [testng] at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source) [testng] at java.xml/javax.xml.parsers.SAXParser.parse(SAXParser.java:197) [testng] at loci.common.xml.XMLTools.parseXML(XMLTools.java:551) [testng] at loci.common.xml.XMLTools.parseXML(XMLTools.java:533) [testng] at loci.formats.in.InCellReader.initFile(InCellReader.java:380) [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.NativeMethodAccessorImpl.invoke0(Native Method) [testng] at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) [testng] at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) [testng] at java.base/java.lang.reflect.Method.invoke(Method.java:568) [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] [2025-01-29 03:20:18,216] [main] setId failed on [/data/brian/Proper Dark Images/2007.11.12.13.37.27.xdce, /data/michael/Z Sections with flatfield corr/2007.10.17.17.13.59.xdce, /data/michael/firstStack/2007.07.05.17.33.35.xdce] [testng] [TestNG] [Error] [testng] The factory method class loci.tests.testng.FormatReaderTestFactory.createInstances() threw an exception [testng] The tests failed. BUILD FAILED /bio-formats-build/bioformats/components/test-suite/build.xml:270: if=failedTest Total time: 23 minutes 6 seconds Build step 'Execute shell' marked build as failure Finished: FAILURE