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Started by upstream project "BIOFORMATS-test-repo" build number 107 originally caused by: Started by upstream project "Trigger" build number 119 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9 [BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins6399330023276950764.sh + '[' cellomics = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_16641_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] 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] 02:10:34,454 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:10:34,456 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 02:10:34,456 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:10:34,457 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:10:34,458 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:10:34,458 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:10:34,458 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:10:34,458 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:10:34,459 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:10:34,459 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:10:34,460 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:10:34,460 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:10:34,658 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:10:34,658 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:10:34,684 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:10:34,684 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:10:34,691 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:10:34,691 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:10:34,691 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:10:34,692 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:10:34,692 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 02:10:34,693 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 02:10:34,693 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 234 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-06-30 02:10:34,702] [main] java.version = 17.0.2 [testng] 02:10:34,705 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:10:34,706 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:10:34,758 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-30_02-10-34.log] [testng] 02:10:34,760 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-06-30 02:10:34,762] [main] testng.directory = /data [testng] [2024-06-30 02:10:34,762] [main] testng.configDirectory = /config [testng] [2024-06-30 02:10:34,775] [main] testng.multiplier = 1.0 [testng] [2024-06-30 02:10:34,776] [main] testng.in-memory = false [testng] [2024-06-30 02:10:34,777] [main] testng.allow-missing = false [testng] [2024-06-30 02:10:34,777] [main] user.language = en [testng] [2024-06-30 02:10:34,777] [main] user.country = ${user.country} [testng] [2024-06-30 02:10:34,777] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-06-30 02:10:45,112] [main] ---------------------------------------- [testng] [2024-06-30 02:10:45,112] [main] Total files: 2539 [testng] [2024-06-30 02:10:45,112] [main] Scan time: 10.335 s (4 ms/file) [testng] [2024-06-30 02:10:45,112] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-06-30 02:10:47,130] [pool-1-thread-1] Initializing /data/harri/MFGTMP-PC_111018140003/MFGTMP-PC_111018140003_E04f00d0.C01: [testng] 02:10:47,131 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:10:47,132 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:10:47,134 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-30_02-10-47.log] [testng] 02:10:47,134 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3063c111 - End of configuration. [testng] [2024-06-30 02:10:47,318] [pool-1-thread-12] Initializing /data/omar/FB03f00d0.C01: [testng] 02:10:47,319 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:10:47,319 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:10:47,324 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-30_02-10-47.log] [testng] 02:10:47,325 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3424afd6 - End of configuration. [testng] [2024-06-30 02:10:47,371] [pool-1-thread-11] Initializing /data/qa-21720/AS_09125_050117190001_A14f00d0.DIB: [testng] 02:10:47,372 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:10:47,372 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:10:47,373 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-30_02-10-47.log] [testng] 02:10:47,374 |-INFO in ch.qos.logback.core.sift.SiftProcessor@525738bb - End of configuration. [testng] [2024-06-30 02:10:47,416] [pool-1-thread-10] Initializing /data/omar/FB03f00o2.C01: [testng] 02:10:47,417 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:10:47,417 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:10:47,418 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-30_02-10-47.log] [testng] 02:10:47,419 |-INFO in ch.qos.logback.core.sift.SiftProcessor@58ffd31b - End of configuration. [testng] [2024-06-30 02:10:47,445] [pool-1-thread-9] Initializing /data/samples/different-field-count/plate_B03f00d0.C01: [testng] 02:10:47,446 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:10:47,446 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:10:47,447 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-30_02-10-47.log] [testng] 02:10:47,448 |-INFO in ch.qos.logback.core.sift.SiftProcessor@70640e51 - End of configuration. [testng] [2024-06-30 02:10:47,505] [pool-1-thread-8] Initializing /data/omar/FB03f03o2.DIB: [testng] 02:10:47,506 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:10:47,506 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:10:47,508 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-30_02-10-47.log] [testng] 02:10:47,508 |-INFO in ch.qos.logback.core.sift.SiftProcessor@41a3a0af - End of configuration. [testng] [2024-06-30 02:10:47,538] [pool-1-thread-7] Initializing /data/omar/FB03f00o1.C01: [testng] 02:10:47,539 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:10:47,539 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:10:47,540 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-30_02-10-47.log] [testng] 02:10:47,541 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76786538 - End of configuration. [testng] [2024-06-30 02:10:47,566] [pool-1-thread-6] Initializing /data/qa-7352/test/MFGTMP-PC_130509120002_B02f00o1.C01: [testng] 02:10:47,567 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:10:47,567 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:10:47,571 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-30_02-10-47.log] [testng] 02:10:47,572 |-INFO in ch.qos.logback.core.sift.SiftProcessor@441db5af - End of configuration. [testng] [2024-06-30 02:10:47,722] [pool-1-thread-5] Initializing /data/omar/FB03f00d1.C01: [testng] 02:10:47,722 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:10:47,722 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:10:47,723 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-30_02-10-47.log] [testng] 02:10:47,723 |-INFO in ch.qos.logback.core.sift.SiftProcessor@74675abb - End of configuration. [testng] [2024-06-30 02:10:47,767] [pool-1-thread-4] Initializing /data/samples/plate-size/plate_B03f00d0.C01: [testng] 02:10:47,768 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:10:47,768 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:10:47,769 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-30_02-10-47.log] [testng] 02:10:47,769 |-INFO in ch.qos.logback.core.sift.SiftProcessor@191a9d77 - End of configuration. [testng] [2024-06-30 02:10:47,819] [pool-1-thread-3] Initializing /data/samples/sparse-plate/plate_E03f00d0.C01: [testng] 02:10:47,820 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:10:47,820 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:10:47,821 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-30_02-10-47.log] [testng] 02:10:47,822 |-INFO in ch.qos.logback.core.sift.SiftProcessor@17fa9f4f - End of configuration. [testng] [2024-06-30 02:10:47,885] [pool-1-thread-2] Initializing /data/lee/AS_09125_050116030001_D03f00d0.DIB: [testng] 02:10:47,885 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:10:47,885 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:10:47,887 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-30_02-10-47.log] [testng] 02:10:47,888 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5deb8caa - End of configuration. [testng] [2024-06-30 02:10:50,122] [pool-1-thread-2] Initializing /data/lee/icd002235_090127090001_a01f00d1.c01: [testng] [2024-06-30 02:10:50,139] [pool-1-thread-7] Initializing /data/johannes/MFGTMP_081222130005_E07f00d0.C01: [testng] [2024-06-30 02:10:50,152] [pool-1-thread-8] Initializing /data/qa-7352/test/MFGTMP-PC_130509120002_B02f00d0.C01: [testng] [2024-06-30 02:10:50,348] [pool-1-thread-12] Initializing /data/johannes/MFGTMP_081128200001_A02f239d1.C01: [testng] [2024-06-30 02:10:50,380] [pool-1-thread-5] Initializing /data/public/BBBC001/AS_09125_050118150001_A03f00d0.DIB: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 901, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 4 minutes 36 seconds Finished: SUCCESS