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Started by upstream project "BIOFORMATS-test-repo" build number 398 originally caused by: Started by upstream project "Trigger" build number 484 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@18 [BIOFORMATS-test-folder@18] $ /bin/bash -xe /tmp/jenkins469361615911410817.sh + '[' zip = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_62817_merge_ci -v /uod/idr/repos/curated/zip:/data -v /uod/idr-scratch/merge-ci/curated/zip:/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] 01:33:11,357 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 01:33:11,358 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - No custom configurators were discovered as a service. [testng] 01:33:11,358 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:33:11,359 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:33:11,360 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:33:11,360 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:33:11,360 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:33:11,360 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:33:11,361 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:33:11,361 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:33:11,362 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:33:11,362 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:33:11,515 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:33:11,516 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:33:11,536 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:33:11,536 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:33:11,541 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:33:11,541 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:33:11,541 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:33:11,542 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:33:11,542 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@3f6f6701 - End of configuration. [testng] 01:33:11,543 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@4f80542f - Registering current configuration as safe fallback point [testng] 01:33:11,543 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 182 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-05-18 01:33:11,551] [main] java.version = 17.0.2 [testng] 01:33:11,554 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:33:11,554 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:33:11,592 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-05-18_01-33-11.log] [testng] 01:33:11,594 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14bdbc74 - End of configuration. [testng] [2025-05-18 01:33:11,596] [main] testng.directory = /data [testng] [2025-05-18 01:33:11,596] [main] testng.configDirectory = /config [testng] [2025-05-18 01:33:11,604] [main] testng.multiplier = 1.0 [testng] [2025-05-18 01:33:11,605] [main] testng.in-memory = false [testng] [2025-05-18 01:33:11,605] [main] testng.allow-missing = false [testng] [2025-05-18 01:33:11,605] [main] user.language = en [testng] [2025-05-18 01:33:11,605] [main] user.country = ${user.country} [testng] [2025-05-18 01:33:11,605] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-05-18 01:33:13,295] [main] ---------------------------------------- [testng] [2025-05-18 01:33:13,295] [main] Total files: 22 [testng] [2025-05-18 01:33:13,296] [main] Scan time: 1.69 s (76 ms/file) [testng] [2025-05-18 01:33:13,296] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 22 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-05-18 01:58:53,438] [pool-1-thread-1] Initializing /data/imagej/fat-cells.zip: [testng] 01:58:53,438 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:58:53,438 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:58:53,439 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-05-18_01-58-53.log] [testng] 01:58:53,440 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b1bf022 - End of configuration. [testng] [2025-05-18 01:59:34,907] [pool-1-thread-12] Initializing /data/imagej/gel-electrophoresis.zip: [testng] 01:59:34,907 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:59:34,907 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:59:34,908 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-05-18_01-59-34.log] [testng] 01:59:34,908 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37c5d91d - End of configuration. [testng] [2025-05-18 02:00:08,215] [pool-1-thread-11] Initializing /data/imagej/3D_Chromosome.zip: [testng] 02:00:08,215 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:00:08,215 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:00:08,216 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-05-18_02-00-08.log] [testng] 02:00:08,216 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6b46adb0 - End of configuration. [testng] [2025-05-18 02:00:55,044] [pool-1-thread-10] Initializing /data/imagej/xrays.zip: [testng] 02:00:55,044 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:00:55,044 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:00:55,044 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-05-18_02-00-55.log] [testng] 02:00:55,045 |-INFO in ch.qos.logback.core.sift.SiftProcessor@16f76c02 - End of configuration. [testng] [2025-05-18 02:01:23,187] [pool-1-thread-9] Initializing /data/imagej/flybrain.zip: [testng] 02:01:23,187 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:01:23,187 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:01:23,188 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-05-18_02-01-23.log] [testng] 02:01:23,188 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ede508b - End of configuration. [testng] [2025-05-18 02:03:15,307] [pool-1-thread-8] Initializing /data/imagej/m51.zip: [testng] 02:03:15,307 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:03:15,307 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:03:15,308 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-05-18_02-03-15.log] [testng] 02:03:15,308 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d06df06 - End of configuration. [testng] [2025-05-18 02:03:53,505] [pool-1-thread-7] Initializing /data/imagej/se3.zip: [testng] 02:03:53,505 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:03:53,505 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:03:53,506 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-05-18_02-03-53.log] [testng] 02:03:53,506 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6424595d - End of configuration. [testng] [2025-05-18 02:05:04,270] [pool-1-thread-6] Initializing /data/imagej/cheetah_256_8.tif.zip: [testng] 02:05:04,270 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:05:04,270 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:05:04,271 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-05-18_02-05-04.log] [testng] 02:05:04,271 |-INFO in ch.qos.logback.core.sift.SiftProcessor@780a43ec - End of configuration. [testng] [2025-05-18 02:06:47,222] [pool-1-thread-5] Initializing /data/imagej/Rat_Hippocampal_Neuron.zip: [testng] 02:06:47,223 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:06:47,223 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:06:47,223 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-05-18_02-06-47.log] [testng] 02:06:47,224 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b67495b - End of configuration. [testng] [2025-05-18 02:08:44,998] [pool-1-thread-4] Initializing /data/imagej/RatBrain.zip: [testng] 02:08:44,998 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:08:44,998 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:08:44,998 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-05-18_02-08-44.log] [testng] 02:08:44,999 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7afdf47e - End of configuration. [testng] [2025-05-18 02:09:43,021] [pool-1-thread-3] Initializing /data/imagej/4D-Stack(256x256x20x10).zip: [testng] 02:09:43,021 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:09:43,021 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:09:43,021 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-05-18_02-09-43.log] [testng] 02:09:43,022 |-INFO in ch.qos.logback.core.sift.SiftProcessor@52bc526f - End of configuration. [testng] [2025-05-18 02:12:28,113] [pool-1-thread-2] Initializing /data/imagej/hela-cells.zip: [testng] 02:12:28,113 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:12:28,113 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:12:28,114 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-05-18_02-12-28.log] [testng] 02:12:28,114 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d39d781 - End of configuration. [testng] [2025-05-18 02:29:30,579] [pool-1-thread-8] Initializing /data/samples/bat-cochlea-volume.zip: [testng] [2025-05-18 02:31:45,728] [pool-1-thread-10] Initializing /data/imagej/Rat_Hippocampal_Neuron2.zip: [testng] [2025-05-18 02:35:38,171] [pool-1-thread-12] Initializing /data/imagej/confocal-stack.zip: [testng] [2025-05-18 02:39:55,474] [pool-1-thread-11] Initializing /data/imagej/scala-media.zip: [testng] [2025-05-18 02:42:16,644] [pool-1-thread-4] Initializing /data/samples/sdub.zip: [testng] [2025-05-18 02:42:40,125] [pool-1-thread-2] Initializing /data/imagej/mri-stack.zip: [testng] [2025-05-18 02:47:09,303] [pool-1-thread-1] Initializing /data/imagej/blood-brain-barrier.zip: [testng] [2025-05-18 02:51:05,159] [pool-1-thread-6] Initializing /data/imagej/watershed-animation.zip: [testng] [2025-05-18 02:52:50,293] [pool-1-thread-5] Initializing /data/imagej/FluorescentCells.zip: [testng] [2025-05-18 02:57:00,304] [pool-1-thread-4] Initializing /data/imagej/confocal-series.zip: [testng] 03:41:18,122 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:41:18,122 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:41:18,123 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-05-18_03-41-18.log] [testng] 03:41:18,123 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32b46831 - End of configuration. [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1166, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 128 minutes 9 seconds Finished: SUCCESS