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Started by upstream project "BIOFORMATS-test-repo" build number 364 originally caused by: Started by upstream project "Trigger" build number 390 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/jenkins14405050311846811291.sh + '[' cellomics = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_58067_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] 02:49:04,889 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 02:49:04,891 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - No custom configurators were discovered as a service. [testng] 02:49:04,891 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:49:04,892 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:49:04,892 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:49:04,892 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:49:04,893 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:49:04,893 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:49:04,893 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:49:04,894 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:49:04,894 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:49:04,894 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:49:05,058 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:49:05,058 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:49:05,079 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:49:05,079 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:49:05,084 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:49:05,084 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:49:05,084 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:49:05,085 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:49:05,085 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@65c7a252 - End of configuration. [testng] 02:49:05,085 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@38cee291 - Registering current configuration as safe fallback point [testng] 02:49:05,085 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 192 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-04 02:49:05,094] [main] java.version = 11.0.16 [testng] 02:49:05,097 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:49:05,097 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:49:05,139 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-04_02-49-05.log] [testng] 02:49:05,140 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13d73f29 - End of configuration. [testng] [2025-03-04 02:49:05,142] [main] testng.directory = /data [testng] [2025-03-04 02:49:05,143] [main] testng.configDirectory = /config [testng] [2025-03-04 02:49:05,152] [main] testng.multiplier = 1.0 [testng] [2025-03-04 02:49:05,154] [main] testng.in-memory = false [testng] [2025-03-04 02:49:05,154] [main] testng.allow-missing = false [testng] [2025-03-04 02:49:05,154] [main] user.language = en [testng] [2025-03-04 02:49:05,154] [main] user.country = ${user.country} [testng] [2025-03-04 02:49:05,154] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-03-04 02:49:30,390] [main] ---------------------------------------- [testng] [2025-03-04 02:49:30,391] [main] Total files: 2539 [testng] [2025-03-04 02:49:30,391] [main] Scan time: 25.236 s (9 ms/file) [testng] [2025-03-04 02:49:30,391] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-04 02:49:50,311] [pool-1-thread-1] Initializing /data/harri/MFGTMP-PC_111018140003/MFGTMP-PC_111018140003_E04f00d0.C01: [testng] 02:49:50,312 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:49:50,312 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:49:50,314 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-04_02-49-50.log] [testng] 02:49:50,314 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d6d8928 - End of configuration. [testng] [2025-03-04 02:49:50,690] [pool-1-thread-12] Initializing /data/lee/icd002235_090127090001_a01f00d1.c01: [testng] 02:49:50,690 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:49:50,690 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:49:50,691 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-04_02-49-50.log] [testng] 02:49:50,692 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6fd52919 - End of configuration. [testng] [2025-03-04 02:49:50,976] [pool-1-thread-11] Initializing /data/samples/sparse-plate/plate_E03f00d0.C01: [testng] 02:49:50,977 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:49:50,977 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:49:50,978 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-04_02-49-50.log] [testng] 02:49:50,978 |-INFO in ch.qos.logback.core.sift.SiftProcessor@261e4ae3 - End of configuration. [testng] [2025-03-04 02:49:51,295] [pool-1-thread-10] Initializing /data/johannes/MFGTMP_081222130005_E07f00d0.C01: [testng] 02:49:51,295 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:49:51,295 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:49:51,295 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-04_02-49-51.log] [testng] 02:49:51,296 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6bf75dbe - End of configuration. [testng] [2025-03-04 02:49:51,585] [pool-1-thread-9] Initializing /data/johannes/MFGTMP_081128200001_A02f239d1.C01: [testng] 02:49:51,585 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:49:51,585 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:49:51,586 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-04_02-49-51.log] [testng] 02:49:51,586 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7890d7b0 - End of configuration. [testng] [2025-03-04 02:49:51,910] [pool-1-thread-8] Initializing /data/omar/FB03f03o2.DIB: [testng] 02:49:51,910 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:49:51,910 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:49:51,910 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-04_02-49-51.log] [testng] 02:49:51,911 |-INFO in ch.qos.logback.core.sift.SiftProcessor@29f6bc17 - End of configuration. [testng] [2025-03-04 02:49:52,178] [pool-1-thread-7] Initializing /data/lee/AS_09125_050116030001_D03f00d0.DIB: [testng] 02:49:52,178 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:49:52,178 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:49:52,179 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-04_02-49-52.log] [testng] 02:49:52,179 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1362e2ab - End of configuration. [testng] [2025-03-04 02:49:52,433] [pool-1-thread-6] Initializing /data/qa-21720/AS_09125_050117190001_A14f00d0.DIB: [testng] 02:49:52,433 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:49:52,433 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:49:52,434 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-04_02-49-52.log] [testng] 02:49:52,434 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f207649 - End of configuration. [testng] [2025-03-04 02:49:52,696] [pool-1-thread-5] Initializing /data/omar/FB03f00d1.C01: [testng] 02:49:52,696 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:49:52,696 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:49:52,697 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-04_02-49-52.log] [testng] 02:49:52,697 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2d3126aa - End of configuration. [testng] [2025-03-04 02:49:52,985] [pool-1-thread-4] Initializing /data/samples/different-field-count/plate_B03f00d0.C01: [testng] 02:49:52,985 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:49:52,985 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:49:52,986 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-04_02-49-52.log] [testng] 02:49:52,986 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3cc61d5c - End of configuration. [testng] [2025-03-04 02:49:53,253] [pool-1-thread-3] Initializing /data/qa-7352/test/MFGTMP-PC_130509120002_B02f00d0.C01: [testng] 02:49:53,253 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:49:53,253 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:49:53,254 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-04_02-49-53.log] [testng] 02:49:53,254 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2aea48b7 - End of configuration. [testng] [2025-03-04 02:49:53,646] [pool-1-thread-2] Initializing /data/omar/FB03f00o2.C01: [testng] 02:49:53,646 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:49:53,646 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:49:53,647 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-04_02-49-53.log] [testng] 02:49:53,647 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1998f9fd - End of configuration. [testng] [2025-03-04 02:49:57,277] [pool-1-thread-7] Initializing /data/omar/FB03f00o1.C01: [testng] [2025-03-04 02:49:57,628] [pool-1-thread-8] Initializing /data/samples/plate-size/plate_B03f00d0.C01: [testng] [2025-03-04 02:49:59,985] [pool-1-thread-12] Initializing /data/omar/FB03f00d0.C01: [testng] [2025-03-04 02:50:00,576] [pool-1-thread-10] Initializing /data/qa-7352/test/MFGTMP-PC_130509120002_B02f00o1.C01: [testng] [2025-03-04 02:50:00,973] [pool-1-thread-2] 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: 33 minutes 2 seconds Finished: SUCCESS