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Started by upstream project "BIOFORMATS-test-repo" build number 221 originally caused by: Started by upstream project "Trigger" build number 248 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8 [BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins2793643679248581298.sh + '[' cellomics = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_35128_merge_ci -v /uod/idr/repos/curated/cellomics:/data -v /uod/idr-scratch/merge-ci/curated/cellomics:/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] WARNING: An illegal reflective access operation has occurred [testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket [testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener [testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [testng] WARNING: All illegal access operations will be denied in a future release [testng] File leak detector installed [testng] 06:57:41,589 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 06:57:41,591 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 06:57:41,591 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 06:57:41,592 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 06:57:41,592 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 06:57:41,592 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 06:57:41,593 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 06:57:41,593 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 06:57:41,593 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 06:57:41,594 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 06:57:41,594 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 06:57:41,594 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 06:57:41,767 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 06:57:41,768 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 06:57:41,791 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 06:57:41,791 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 06:57:41,796 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 06:57:41,796 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 06:57:41,797 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 06:57:41,797 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 06:57:41,797 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 06:57:41,798 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 06:57:41,798 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 205 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-15 06:57:41,807] [main] java.version = 11.0.16 [testng] 06:57:41,810 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 06:57:41,810 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:57:41,853 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-15_06-57-41.log] [testng] 06:57:41,854 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-10-15 06:57:41,856] [main] testng.directory = /data [testng] [2024-10-15 06:57:41,856] [main] testng.configDirectory = /config [testng] [2024-10-15 06:57:41,866] [main] testng.multiplier = 1.0 [testng] [2024-10-15 06:57:41,867] [main] testng.in-memory = false [testng] [2024-10-15 06:57:41,868] [main] testng.allow-missing = false [testng] [2024-10-15 06:57:41,868] [main] user.language = en [testng] [2024-10-15 06:57:41,868] [main] user.country = ${user.country} [testng] [2024-10-15 06:57:41,868] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-15 06:58:54,654] [main] ---------------------------------------- [testng] [2024-10-15 06:58:54,654] [main] Total files: 2539 [testng] [2024-10-15 06:58:54,655] [main] Scan time: 72.786 s (28 ms/file) [testng] [2024-10-15 06:58:54,655] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-15 06:59:44,977] [pool-1-thread-1] Initializing /data/harri/MFGTMP-PC_111018140003/MFGTMP-PC_111018140003_E04f00d0.C01: [testng] 06:59:44,978 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 06:59:44,978 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:59:44,980 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-15_06-59-44.log] [testng] 06:59:44,980 |-INFO in ch.qos.logback.core.sift.SiftProcessor@289ce6c3 - End of configuration. [testng] [2024-10-15 06:59:45,769] [pool-1-thread-12] Initializing /data/omar/FB03f00o1.C01: [testng] 06:59:45,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 06:59:45,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:59:45,770 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-15_06-59-45.log] [testng] 06:59:45,770 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b531779 - End of configuration. [testng] [2024-10-15 06:59:46,287] [pool-1-thread-11] Initializing /data/samples/different-field-count/plate_B03f00d0.C01: [testng] 06:59:46,287 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 06:59:46,287 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:59:46,288 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-15_06-59-46.log] [testng] 06:59:46,288 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40215639 - End of configuration. [testng] [2024-10-15 06:59:46,822] [pool-1-thread-10] Initializing /data/qa-7352/test/MFGTMP-PC_130509120002_B02f00o1.C01: [testng] 06:59:46,822 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 06:59:46,822 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:59:46,823 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-15_06-59-46.log] [testng] 06:59:46,823 |-INFO in ch.qos.logback.core.sift.SiftProcessor@93d1b98 - End of configuration. [testng] [2024-10-15 06:59:47,453] [pool-1-thread-9] Initializing /data/qa-21720/AS_09125_050117190001_A14f00d0.DIB: [testng] 06:59:47,454 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 06:59:47,454 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:59:47,454 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-15_06-59-47.log] [testng] 06:59:47,455 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e800c9f - End of configuration. [testng] [2024-10-15 06:59:48,097] [pool-1-thread-8] Initializing /data/omar/FB03f00o2.C01: [testng] 06:59:48,097 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 06:59:48,097 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:59:48,098 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-15_06-59-48.log] [testng] 06:59:48,098 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13e8abbb - End of configuration. [testng] [2024-10-15 06:59:48,864] [pool-1-thread-7] Initializing /data/johannes/MFGTMP_081128200001_A02f239d1.C01: [testng] 06:59:48,865 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 06:59:48,865 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:59:48,865 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-15_06-59-48.log] [testng] 06:59:48,866 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37ba8f6a - End of configuration. [testng] [2024-10-15 06:59:49,617] [pool-1-thread-6] Initializing /data/samples/sparse-plate/plate_E03f00d0.C01: [testng] 06:59:49,617 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 06:59:49,617 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:59:49,618 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-15_06-59-49.log] [testng] 06:59:49,618 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2bce9cdc - End of configuration. [testng] [2024-10-15 06:59:50,366] [pool-1-thread-5] Initializing /data/qa-7352/test/MFGTMP-PC_130509120002_B02f00d0.C01: [testng] 06:59:50,366 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 06:59:50,366 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:59:50,367 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-15_06-59-50.log] [testng] 06:59:50,368 |-INFO in ch.qos.logback.core.sift.SiftProcessor@67b535aa - End of configuration. [testng] [2024-10-15 06:59:51,250] [pool-1-thread-4] Initializing /data/lee/AS_09125_050116030001_D03f00d0.DIB: [testng] 06:59:51,251 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 06:59:51,251 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:59:51,251 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-15_06-59-51.log] [testng] 06:59:51,252 |-INFO in ch.qos.logback.core.sift.SiftProcessor@47e3378c - End of configuration. [testng] [2024-10-15 06:59:51,973] [pool-1-thread-3] Initializing /data/omar/FB03f00d1.C01: [testng] 06:59:51,973 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 06:59:51,973 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:59:51,973 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-15_06-59-51.log] [testng] 06:59:51,974 |-INFO in ch.qos.logback.core.sift.SiftProcessor@145c1f58 - End of configuration. [testng] [2024-10-15 06:59:52,658] [pool-1-thread-2] Initializing /data/lee/icd002235_090127090001_a01f00d1.c01: [testng] 06:59:52,658 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 06:59:52,658 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:59:52,659 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-15_06-59-52.log] [testng] 06:59:52,659 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4fa3eb9b - End of configuration. [testng] [2024-10-15 06:59:59,138] [pool-1-thread-4] Initializing /data/omar/FB03f00d0.C01: [testng] [2024-10-15 07:00:04,573] [pool-1-thread-2] Initializing /data/public/BBBC001/AS_09125_050118150001_A03f00d0.DIB: [testng] [2024-10-15 07:00:05,771] [pool-1-thread-7] Initializing /data/omar/FB03f03o2.DIB: [testng] [2024-10-15 07:00:06,973] [pool-1-thread-3] Initializing /data/johannes/MFGTMP_081222130005_E07f00d0.C01: [testng] [2024-10-15 07:00:07,814] [pool-1-thread-8] Initializing /data/samples/plate-size/plate_B03f00d0.C01: time="2024-10-15T06:00:37Z" level=error msg="error waiting for container: unexpected EOF" Build step 'Execute shell' marked build as failure Finished: FAILURE