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Started by upstream project "BIOFORMATS-test-repo" build number 367 originally caused by: Started by upstream project "Trigger" build number 393 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4 [BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins8887587200444657711.sh + '[' incell = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_58578_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 test-automated: [testng] File leak detector installed [testng] 07:02:55,675 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 07:02:55,677 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - No custom configurators were discovered as a service. [testng] 07:02:55,677 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 07:02:55,678 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 07:02:55,678 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 07:02:55,679 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 07:02:55,679 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 07:02:55,679 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 07:02:55,679 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 07:02:55,680 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 07:02:55,680 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 07:02:55,680 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 07:02:55,912 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 07:02:55,912 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 07:02:55,942 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 07:02:55,942 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 07:02:55,951 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 07:02:55,951 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 07:02:55,951 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 07:02:55,951 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 07:02:55,951 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@63355449 - End of configuration. [testng] 07:02:55,952 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48ae9b55 - Registering current configuration as safe fallback point [testng] 07:02:55,952 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 273 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-07 07:02:55,962] [main] java.version = 1.8.0_342 [testng] 07:02:55,966 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 07:02:55,966 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:02:56,011 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-07_07-02-55.log] [testng] 07:02:56,013 |-INFO in ch.qos.logback.core.sift.SiftProcessor@765d7657 - End of configuration. [testng] [2025-03-07 07:02:56,015] [main] testng.directory = /data [testng] [2025-03-07 07:02:56,015] [main] testng.configDirectory = /config [testng] [2025-03-07 07:02:56,029] [main] testng.multiplier = 1.0 [testng] [2025-03-07 07:02:56,029] [main] testng.in-memory = false [testng] [2025-03-07 07:02:56,029] [main] testng.allow-missing = false [testng] [2025-03-07 07:02:56,029] [main] user.language = en [testng] [2025-03-07 07:02:56,029] [main] user.country = ${user.country} [testng] [2025-03-07 07:02:56,029] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2025-03-07 08:44:14,563] [main] ---------------------------------------- [testng] [2025-03-07 08:44:14,563] [main] Total files: 8203 [testng] [2025-03-07 08:44:14,563] [main] Scan time: 6078.533 s (741 ms/file) [testng] [2025-03-07 08:44:14,563] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 30 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-07 10:09:48,342] [pool-1-thread-1] Initializing /data/karsten/gabriele_-1_2/~gabriele_-1_2.xdce: [testng] 10:09:48,342 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 10:09:48,343 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:09:48,343 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-07_10-09-48.log] [testng] 10:09:48,344 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57556878 - End of configuration. [testng] [2025-03-07 10:09:59,424] [pool-1-thread-12] Initializing /data/frans/incell_25juni2009/ANALYZE files/plaat HR 38/excel output file/HCT116_HR2009.97.038/HCT116_HR2009.97.038.xdce: [testng] 10:09:59,424 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 10:09:59,424 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:09:59,426 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-07_10-09-59.log] [testng] 10:09:59,426 |-INFO in ch.qos.logback.core.sift.SiftProcessor@136ed2c7 - End of configuration. [testng] [2025-03-07 10:10:17,724] [pool-1-thread-11] Initializing /data/damir/20x Z1 16fields Gr Rd DAPI Cy5_140610-3_fix_2.xdce: [testng] 10:10:17,724 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 10:10:17,724 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:10:17,725 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-07_10-10-17.log] [testng] 10:10:17,725 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5afd1245 - End of configuration. [testng] [2025-03-07 10:10:34,654] [pool-1-thread-10] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_IM/2009_97_238_IM/2009_97_238_IM.xdce: [testng] 10:10:34,654 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 10:10:34,654 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:10:34,655 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-07_10-10-34.log] [testng] 10:10:34,655 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6f3dbb84 - End of configuration. [testng] [2025-03-07 10:10:49,469] [pool-1-thread-9] Initializing /data/public/INMAC384-DAPI-CM-eGFP_59224_1/INMAC384-DAPI-CM-eGFP_59224_1.xdce: [testng] 10:10:49,470 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 10:10:49,470 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:10:49,470 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-07_10-10-49.log] [testng] 10:10:49,470 |-INFO in ch.qos.logback.core.sift.SiftProcessor@782894e - End of configuration. [testng] [2025-03-07 10:11:03,966] [pool-1-thread-8] Initializing /data/qa-4122/KJH YFPPML 2000_A-101061_1.xdce: [testng] 10:11:03,967 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 10:11:03,967 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:11:03,967 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-07_10-11-03.log] [testng] 10:11:03,968 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5703549 - End of configuration. [testng] [2025-03-07 10:11:17,361] [pool-1-thread-7] Initializing /data/frans/im dataset/PC3_ER2009.97.180_IM.xdce: [testng] 10:11:17,361 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 10:11:17,361 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:11:17,362 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-07_10-11-17.log] [testng] 10:11:17,362 |-INFO in ch.qos.logback.core.sift.SiftProcessor@62b24a90 - End of configuration. [testng] [2025-03-07 10:11:31,980] [pool-1-thread-6] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_Tif/ER2009_97_239_TIFF/PC3_ER2009.97.239.xdce: [testng] 10:11:31,980 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 10:11:31,981 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:11:31,981 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-07_10-11-31.log] [testng] 10:11:31,982 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6bf2e7eb - End of configuration. [testng] [2025-03-07 10:11:49,846] [pool-1-thread-5] Initializing /data/public/INMAC384-DAPI-CM-eGFP_59223_1/INMAC384-DAPI-CM-eGFP_59223_1.xdce: [testng] 10:11:49,846 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 10:11:49,846 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:11:49,847 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-07_10-11-49.log] [testng] 10:11:49,847 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6aa07 - End of configuration. [testng] [2025-03-07 10:12:09,563] [pool-1-thread-4] Initializing /data/samples/variable-field-count/test.xdce: [testng] 10:12:09,563 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 10:12:09,563 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:12:09,564 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-07_10-12-09.log] [testng] 10:12:09,565 |-INFO in ch.qos.logback.core.sift.SiftProcessor@354f63ce - End of configuration. [testng] [2025-03-07 10:12:21,431] [pool-1-thread-3] Initializing /data/michael/Single plane no flatfield corr/2007.10.17.17.04.55.xdce: [testng] 10:12:21,431 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 10:12:21,431 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:12:21,432 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-07_10-12-21.log] [testng] 10:12:21,432 |-INFO in ch.qos.logback.core.sift.SiftProcessor@513622aa - End of configuration. [testng] [2025-03-07 10:12:37,154] [pool-1-thread-2] Initializing /data/public/zenodo-14777242/Training_Demo_1.xdce: [testng] 10:12:37,154 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 10:12:37,154 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:12:37,155 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-07_10-12-37.log] [testng] 10:12:37,155 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d68012d - End of configuration. [testng] [2025-03-07 10:15:45,723] [pool-1-thread-8] Initializing /data/samples/images_number_mismatch/test.xdce: [testng] [2025-03-07 10:21:47,693] [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] [2025-03-07 10:24:26,630] [pool-1-thread-8] Initializing /data/michael/firstStack/2007.07.05.17.33.35.xdce: [testng] [2025-03-07 10:28:02,371] [pool-1-thread-11] Initializing /data/brian/livecell/H2b10xtrial.xdce: [testng] [2025-03-07 11:13:59,121] [pool-1-thread-1] Initializing /data/brian/2Hour10x/H2b2Hour10x5fields.xdce: [testng] 12:34:07,757 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 12:34:07,757 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:34:07,758 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-07_12-34-07.log] [testng] 12:34:07,758 |-INFO in ch.qos.logback.core.sift.SiftProcessor@74581ad2 - End of configuration. [testng] [2025-03-07 12:45:48,928] [pool-1-thread-3] Initializing /data/michael/2007.08.02.16.43.24/2007.08.02.16.43.24.xdce: [testng] 12:56:25,805 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 12:56:25,806 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:56:25,808 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-07_12-56-25.log] [testng] 12:56:25,809 |-INFO in ch.qos.logback.core.sift.SiftProcessor@676dd4a8 - End of configuration. [testng] [2025-03-07 13:00:06,528] [pool-1-thread-8] Initializing /data/michael/Z Sections with flatfield corr/2007.10.17.17.13.59.xdce: [testng] 14:13:51,552 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 14:13:51,552 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:13:51,553 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-07_14-13-51.log] [testng] 14:13:51,554 |-INFO in ch.qos.logback.core.sift.SiftProcessor@392ee66c - End of configuration. [testng] [2025-03-07 14:17:20,975] [pool-1-thread-2] Initializing /data/frans/incell_25juni2009/ANALYZE files/plaat HR37/excel output file/HCT116_HR2009.97.037/HCT116_HR2009.97.037.xdce: [testng] 20:01:48,776 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 20:01:48,776 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 20:01:48,777 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-07_20-01-48.log] [testng] 20:01:48,777 |-INFO in ch.qos.logback.core.sift.SiftProcessor@322dcd61 - End of configuration. [testng] [2025-03-07 20:12:38,675] [pool-1-thread-10] 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] 20:24:24,334 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 20:24:24,334 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 20:24:24,335 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-07_20-24-24.log] [testng] 20:24:24,335 |-INFO in ch.qos.logback.core.sift.SiftProcessor@61f20f45 - End of configuration. [testng] [2025-03-07 20:37:37,819] [pool-1-thread-7] Initializing /data/brian/Proper Dark Images/2007.11.12.13.37.27.xdce: [testng] [2025-03-07 21:01:34,745] [pool-1-thread-7] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_IM/2009_97_239_IM/2009_97_239_IM.xdce: Build was aborted Calling Pipeline was cancelled Finished: ABORTED