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Started by upstream project "BIOFORMATS-test-repo" build number 37 originally caused by: Started by upstream project "Trigger" build number 42 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@6 [BIOFORMATS-test-folder@6] $ /bin/bash -xe /tmp/jenkins17789279914614468136.sh + '[' incell = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_5176_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. [javac] 4 warnings 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] 02:11:09,395 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:11:09,396 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 02:11:09,396 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:11:09,397 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:11:09,398 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:11:09,398 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:11:09,399 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:11:09,399 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:11:09,399 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:11:09,400 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:11:09,400 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:11:09,400 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:11:09,561 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:11:09,561 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:11:09,586 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:11:09,586 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:11:09,593 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:11:09,593 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:11:09,593 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:11:09,594 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:11:09,594 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 02:11:09,595 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 02:11:09,595 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 196 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-04-18 02:11:09,604] [main] java.version = 21 [testng] 02:11:09,607 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:11:09,607 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:11:09,650 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-18_02-11-09.log] [testng] 02:11:09,652 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-04-18 02:11:09,668] [main] testng.directory = /data [testng] [2024-04-18 02:11:09,669] [main] testng.configDirectory = /config [testng] [2024-04-18 02:11:09,690] [main] testng.multiplier = 1.0 [testng] [2024-04-18 02:11:09,691] [main] testng.in-memory = false [testng] [2024-04-18 02:11:09,691] [main] testng.allow-missing = false [testng] [2024-04-18 02:11:09,691] [main] user.language = en [testng] [2024-04-18 02:11:09,691] [main] user.country = ${user.country} [testng] [2024-04-18 02:11:09,691] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-04-18 02:17:21,818] [main] ---------------------------------------- [testng] [2024-04-18 02:17:21,819] [main] Total files: 4190 [testng] [2024-04-18 02:17:21,819] [main] Scan time: 372.127 s (88 ms/file) [testng] [2024-04-18 02:17:21,820] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 27 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-04-18 02:17:41,812] [pool-1-thread-1] Initializing /data/brian/H2Blivecell20x/H2Blivecell20x.xdce: [testng] 02:17:41,813 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:17:41,813 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:17:41,815 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-18_02-17-41.log] [testng] 02:17:41,815 |-INFO in ch.qos.logback.core.sift.SiftProcessor@535be53e - End of configuration. [testng] [2024-04-18 02:17:42,650] [pool-1-thread-12] Initializing /data/michael/2007.08.02.16.43.24/2007.08.02.16.43.24.xdce: [testng] 02:17:42,650 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:17:42,650 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:17:42,652 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-18_02-17-42.log] [testng] 02:17:42,652 |-INFO in ch.qos.logback.core.sift.SiftProcessor@b5716ba - End of configuration. [testng] [2024-04-18 02:17:42,805] [pool-1-thread-11] Initializing /data/frans/incell_25juni2009/ANALYZE files/plaat HR 38/excel output file/HCT116_HR2009.97.038/HCT116_HR2009.97.038.xdce: [testng] 02:17:42,805 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:17:42,806 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:17:42,807 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-18_02-17-42.log] [testng] 02:17:42,807 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c87b23d - End of configuration. [testng] [2024-04-18 02:17:43,037] [pool-1-thread-10] Initializing /data/public/INMAC384-DAPI-CM-eGFP_59224_1/INMAC384-DAPI-CM-eGFP_59224_1.xdce: [testng] 02:17:43,037 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:17:43,037 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:17:43,039 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-18_02-17-43.log] [testng] 02:17:43,039 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fd6b38 - End of configuration. [testng] [2024-04-18 02:17:43,668] [pool-1-thread-9] Initializing /data/brian/2Hour10x/H2b2Hour10x5fields.xdce: [testng] 02:17:43,668 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:17:43,668 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:17:43,670 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-18_02-17-43.log] [testng] 02:17:43,671 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8199a49 - End of configuration. [testng] [2024-04-18 02:17:44,446] [pool-1-thread-8] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_IM/2009_97_239_IM/2009_97_239_IM.xdce: [testng] 02:17:44,447 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:17:44,447 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:17:44,449 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-18_02-17-44.log] [testng] 02:17:44,449 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66a62904 - End of configuration. [testng] [2024-04-18 02:17:44,551] [pool-1-thread-7] Initializing /data/frans/incell_25juni2009/ANALYZE files/plaat HR 38/txt en XML output file/HCT116_HR2009.97.038/HCT116_HR2009.97.038.xdce: [testng] 02:17:44,551 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:17:44,551 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:17:44,552 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-18_02-17-44.log] [testng] 02:17:44,553 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f0b4dfa - End of configuration. [testng] [2024-04-18 02:17:44,838] [pool-1-thread-6] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_IM/2009_97_240_IM/2009_97_240_IM.xdce: [testng] 02:17:44,838 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:17:44,838 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:17:44,839 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-18_02-17-44.log] [testng] 02:17:44,840 |-INFO in ch.qos.logback.core.sift.SiftProcessor@58edbc99 - End of configuration. [testng] [2024-04-18 02:17:44,935] [pool-1-thread-5] Initializing /data/samples/images_number_mismatch/test.xdce: [testng] 02:17:44,936 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:17:44,936 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:17:44,937 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-18_02-17-44.log] [testng] 02:17:44,938 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66ad4cae - End of configuration. [testng] [2024-04-18 02:17:45,018] [pool-1-thread-4] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_Tif/ER2009_97_240_TIFF/PC3_ER2009.97.240(ok).xdce: [testng] 02:17:45,019 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:17:45,019 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:17:45,020 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-18_02-17-45.log] [testng] 02:17:45,020 |-INFO in ch.qos.logback.core.sift.SiftProcessor@29c23297 - End of configuration. [testng] [2024-04-18 02:17:45,296] [pool-1-thread-3] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_IM/2009_97_238_IM/2009_97_238_IM.xdce: [testng] 02:17:45,297 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:17:45,297 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:17:45,297 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-18_02-17-45.log] [testng] 02:17:45,298 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3caf129b - End of configuration. [testng] [2024-04-18 02:17:45,396] [pool-1-thread-2] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_Tif/ER2009_97_239_TIFF/PC3_ER2009.97.239.xdce: [testng] 02:17:45,396 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:17:45,396 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:17:45,398 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-18_02-17-45.log] [testng] 02:17:45,398 |-INFO in ch.qos.logback.core.sift.SiftProcessor@134e6b50 - End of configuration. [testng] [2024-04-18 02:17:58,856] [pool-1-thread-5] Initializing /data/public/INMAC384-DAPI-CM-eGFP_59223_1/INMAC384-DAPI-CM-eGFP_59223_1.xdce: [testng] [2024-04-18 02:19:09,755] [pool-1-thread-12] Initializing /data/brian/livecell/H2b10xtrial.xdce: [testng] [2024-04-18 02:19:35,775] [pool-1-thread-3] Initializing /data/karsten/gabriele_-1_2/~gabriele_-1_2.xdce: [testng] [2024-04-18 02:19:39,182] [pool-1-thread-6] Initializing /data/qa-4122/KJH YFPPML 2000_A-101061_1.xdce: [testng] [2024-04-18 02:19:39,274] [pool-1-thread-8] Initializing /data/karsten/gabriele_-1_2/gabriele_-1_2.xdce: [testng] [2024-04-18 02:20:08,511] [pool-1-thread-7] Initializing /data/frans/im dataset/PC3_ER2009.97.180_IM.xdce: [testng] [2024-04-18 02:20:09,169] [pool-1-thread-11] Initializing /data/brian/Proper Dark Images/2007.11.12.13.37.27.xdce: [testng] [2024-04-18 02:20:11,128] [pool-1-thread-11] Initializing /data/michael/Z Sections with flatfield corr/2007.10.17.17.13.59.xdce: [testng] [2024-04-18 02:20:13,374] [pool-1-thread-3] Initializing /data/damir/20x Z1 16fields Gr Rd DAPI Cy5_140610-3_fix_2.xdce: [testng] [2024-04-18 02:20:18,840] [pool-1-thread-8] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_Tif/ER2009_97_238_TIFF/PC3_ER2009.97.238.xdce: [testng] [2024-04-18 02:20:24,543] [pool-1-thread-4] Initializing /data/frans/incell_25juni2009/ANALYZE files/plaat HR37/excel output file/HCT116_HR2009.97.037/HCT116_HR2009.97.037.xdce: [testng] [2024-04-18 02:20:25,294] [pool-1-thread-2] Initializing /data/michael/firstStack/2007.07.05.17.33.35.xdce: [testng] [2024-04-18 02:20:39,837] [pool-1-thread-2] Initializing /data/samples/variable-field-count/test.xdce: [testng] [2024-04-18 02:20:50,742] [pool-1-thread-2] Initializing /data/public/idr0017/2011-11-17_X-Man_LOPAC_X01_LP_S01_1/2011-11-17 X-Man LOPAC_X03_LP_S01_1.xdce: [testng] [2024-04-18 02:21:08,913] [pool-1-thread-11] Initializing /data/michael/Single plane no flatfield corr/2007.10.17.17.04.55.xdce: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1431, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 39 minutes 38 seconds Finished: SUCCESS