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Started by upstream project "BIOFORMATS-test-repo" build number 280 originally caused by: Started by upstream project "Trigger" build number 300 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@2 [BIOFORMATS-test-folder@2] $ /bin/bash -xe /tmp/jenkins12249862148246793746.sh + '[' incell = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_44227_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 03:43:34,357 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:43:34,358 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 03:43:34,358 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:43:34,359 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:43:34,359 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:43:34,360 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:43:34,360 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 03:43:34,360 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:43:34,361 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:43:34,361 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:43:34,361 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:43:34,362 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:43:34,522 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:43:34,522 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:43:34,548 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:43:34,548 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:43:34,554 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:43:34,555 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:43:34,555 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:43:34,555 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:43:34,555 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 03:43:34,556 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 03:43:34,556 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 196 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-05 03:43:34,565] [main] java.version = 21 [testng] 03:43:34,569 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:43:34,569 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:43:34,611 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-05_03-43-34.log] [testng] 03:43:34,612 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-12-05 03:43:34,614] [main] testng.directory = /data [testng] [2024-12-05 03:43:34,614] [main] testng.configDirectory = /config [testng] [2024-12-05 03:43:34,623] [main] testng.multiplier = 1.0 [testng] [2024-12-05 03:43:34,623] [main] testng.in-memory = false [testng] [2024-12-05 03:43:34,623] [main] testng.allow-missing = false [testng] [2024-12-05 03:43:34,623] [main] user.language = en [testng] [2024-12-05 03:43:34,624] [main] user.country = ${user.country} [testng] [2024-12-05 03:43:34,624] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-05 04:12:07,689] [main] ---------------------------------------- [testng] [2024-12-05 04:12:07,689] [main] Total files: 4190 [testng] [2024-12-05 04:12:07,690] [main] Scan time: 1713.065 s (408 ms/file) [testng] [2024-12-05 04:12:07,690] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 27 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-05 04:14:05,704] [pool-1-thread-1] Initializing /data/frans/incell_25juni2009/ANALYZE files/plaat HR37/excel output file/HCT116_HR2009.97.037/HCT116_HR2009.97.037.xdce: [testng] 04:14:05,704 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 04:14:05,704 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:14:05,706 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-05_04-14-05.log] [testng] 04:14:05,706 |-INFO in ch.qos.logback.core.sift.SiftProcessor@30743ca1 - End of configuration. [testng] [2024-12-05 04:14:07,539] [pool-1-thread-12] 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] 04:14:07,539 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 04:14:07,539 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:14:07,540 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-05_04-14-07.log] [testng] 04:14:07,540 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d82a8d4 - End of configuration. [testng] [2024-12-05 04:14:07,958] [pool-1-thread-11] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_IM/2009_97_239_IM/2009_97_239_IM.xdce: [testng] 04:14:07,958 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 04:14:07,959 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:14:07,960 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-05_04-14-07.log] [testng] 04:14:07,960 |-INFO in ch.qos.logback.core.sift.SiftProcessor@603fe20a - End of configuration. [testng] [2024-12-05 04:14:08,846] [pool-1-thread-10] Initializing /data/qa-4122/KJH YFPPML 2000_A-101061_1.xdce: [testng] 04:14:08,846 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 04:14:08,846 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:14:08,847 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-05_04-14-08.log] [testng] 04:14:08,847 |-INFO in ch.qos.logback.core.sift.SiftProcessor@243b1e06 - End of configuration. [testng] [2024-12-05 04:14:09,314] [pool-1-thread-9] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_Tif/ER2009_97_239_TIFF/PC3_ER2009.97.239.xdce: [testng] 04:14:09,314 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 04:14:09,314 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:14:09,315 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-05_04-14-09.log] [testng] 04:14:09,315 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e979c51 - End of configuration. [testng] [2024-12-05 04:14:10,479] [pool-1-thread-8] 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] 04:14:10,479 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 04:14:10,479 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:14:10,480 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-05_04-14-10.log] [testng] 04:14:10,480 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57e31b15 - End of configuration. [testng] [2024-12-05 04:14:12,143] [pool-1-thread-7] Initializing /data/michael/2007.08.02.16.43.24/2007.08.02.16.43.24.xdce: [testng] 04:14:12,144 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 04:14:12,144 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:14:12,145 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-05_04-14-12.log] [testng] 04:14:12,145 |-INFO in ch.qos.logback.core.sift.SiftProcessor@52da22fa - End of configuration. [testng] [2024-12-05 04:14:12,663] [pool-1-thread-6] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_Tif/ER2009_97_240_TIFF/PC3_ER2009.97.240(ok).xdce: [testng] 04:14:12,663 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 04:14:12,663 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:14:12,663 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-05_04-14-12.log] [testng] 04:14:12,664 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6fe7a740 - End of configuration. [testng] [2024-12-05 04:14:14,025] [pool-1-thread-5] Initializing /data/michael/Single plane no flatfield corr/2007.10.17.17.04.55.xdce: [testng] 04:14:14,026 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 04:14:14,026 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:14:14,027 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-05_04-14-14.log] [testng] 04:14:14,027 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4003a3a7 - End of configuration. [testng] [2024-12-05 04:14:14,855] [pool-1-thread-4] Initializing /data/public/INMAC384-DAPI-CM-eGFP_59223_1/INMAC384-DAPI-CM-eGFP_59223_1.xdce: [testng] 04:14:14,856 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 04:14:14,856 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:14:14,856 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-05_04-14-14.log] [testng] 04:14:14,857 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ee7218e - End of configuration. [testng] [2024-12-05 04:14:15,798] [pool-1-thread-3] Initializing /data/karsten/gabriele_-1_2/~gabriele_-1_2.xdce: [testng] 04:14:15,798 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 04:14:15,798 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:14:15,799 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-05_04-14-15.log] [testng] 04:14:15,799 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5162d575 - End of configuration. [testng] [2024-12-05 04:14:16,587] [pool-1-thread-2] Initializing /data/michael/firstStack/2007.07.05.17.33.35.xdce: [testng] 04:14:16,587 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 04:14:16,587 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:14:16,588 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-05_04-14-16.log] [testng] 04:14:16,588 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e220c54 - End of configuration. [testng] [2024-12-05 04:15:53,056] [pool-1-thread-10] Initializing /data/public/INMAC384-DAPI-CM-eGFP_59224_1/INMAC384-DAPI-CM-eGFP_59224_1.xdce: [testng] [2024-12-05 04:17:49,022] [pool-1-thread-3] Initializing /data/brian/H2Blivecell20x/H2Blivecell20x.xdce: [testng] [2024-12-05 04:19:19,101] [pool-1-thread-2] Initializing /data/brian/livecell/H2b10xtrial.xdce: [testng] [2024-12-05 04:19:53,767] [pool-1-thread-5] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_Tif/ER2009_97_238_TIFF/PC3_ER2009.97.238.xdce: [testng] [2024-12-05 04:31:47,406] [pool-1-thread-7] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_IM/2009_97_238_IM/2009_97_238_IM.xdce: [testng] [2024-12-05 04:32:18,985] [pool-1-thread-11] Initializing /data/samples/variable-field-count/test.xdce: [testng] [2024-12-05 04:32:56,859] [pool-1-thread-11] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_IM/2009_97_240_IM/2009_97_240_IM.xdce: [testng] [2024-12-05 04:51:19,776] [pool-1-thread-8] Initializing /data/michael/Z Sections with flatfield corr/2007.10.17.17.13.59.xdce: [testng] [2024-12-05 04:52:21,712] [pool-1-thread-7] Initializing /data/karsten/gabriele_-1_2/gabriele_-1_2.xdce: [testng] [2024-12-05 04:53:49,395] [pool-1-thread-11] Initializing /data/brian/Proper Dark Images/2007.11.12.13.37.27.xdce: [testng] [2024-12-05 04:54:48,539] [pool-1-thread-11] Initializing /data/samples/images_number_mismatch/test.xdce: [testng] [2024-12-05 04:55:05,901] [pool-1-thread-1] Initializing /data/brian/2Hour10x/H2b2Hour10x5fields.xdce: [testng] [2024-12-05 04:55:13,883] [pool-1-thread-9] Initializing /data/frans/im dataset/PC3_ER2009.97.180_IM.xdce: [testng] [2024-12-05 04:55:15,871] [pool-1-thread-6] Initializing /data/damir/20x Z1 16fields Gr Rd DAPI Cy5_140610-3_fix_2.xdce: [testng] [2024-12-05 04:55:38,647] [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] 05:26:28,216 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 05:26:28,216 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:26:28,218 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-05_05-26-28.log] [testng] 05:26:28,218 |-INFO in ch.qos.logback.core.sift.SiftProcessor@47dc5366 - End of configuration. [testng] 05:59:30,258 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 05:59:30,259 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:59:30,260 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-05_05-59-30.log] [testng] 05:59:30,260 |-INFO in ch.qos.logback.core.sift.SiftProcessor@249d5324 - End of configuration. [testng] 06:03:55,502 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 06:03:55,502 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:03:55,503 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-05_06-03-55.log] [testng] 06:03:55,504 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3878046c - End of configuration. [testng] 06:12:04,484 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 06:12:04,484 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:12:04,485 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-05_06-12-04.log] [testng] 06:12:04,485 |-INFO in ch.qos.logback.core.sift.SiftProcessor@16286b4e - End of configuration. [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1431, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 148 minutes 33 seconds Finished: SUCCESS