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Started by upstream project "BIOFORMATS-test-repo" build number 299 originally caused by: Started by upstream project "Trigger" build number 321 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/jenkins13377016471460779639.sh + '[' zip = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_47255_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 00:30:29,189 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:30:29,190 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 00:30:29,190 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:30:29,191 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:30:29,192 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:30:29,192 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:30:29,192 |-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] 00:30:29,192 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:30:29,193 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:30:29,193 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:30:29,194 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:30:29,194 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:30:29,360 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:30:29,360 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:30:29,385 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:30:29,385 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:30:29,392 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:30:29,392 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:30:29,392 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:30:29,392 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:30:29,393 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 00:30:29,393 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 00:30:29,393 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 200 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-26 00:30:29,402] [main] java.version = 21 [testng] 00:30:29,405 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:30:29,405 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:29,447 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-26_00-30-29.log] [testng] 00:30:29,448 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-12-26 00:30:29,450] [main] testng.directory = /data [testng] [2024-12-26 00:30:29,450] [main] testng.configDirectory = /config [testng] [2024-12-26 00:30:29,459] [main] testng.multiplier = 1.0 [testng] [2024-12-26 00:30:29,460] [main] testng.in-memory = false [testng] [2024-12-26 00:30:29,460] [main] testng.allow-missing = false [testng] [2024-12-26 00:30:29,460] [main] user.language = en [testng] [2024-12-26 00:30:29,460] [main] user.country = ${user.country} [testng] [2024-12-26 00:30:29,460] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-26 00:30:30,011] [main] ---------------------------------------- [testng] [2024-12-26 00:30:30,011] [main] Total files: 22 [testng] [2024-12-26 00:30:30,011] [main] Scan time: 0.551 s (25 ms/file) [testng] [2024-12-26 00:30:30,012] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 22 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-26 00:33:10,512] [pool-1-thread-1] Initializing /data/imagej/Rat_Hippocampal_Neuron2.zip: [testng] 00:33:10,512 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:33:10,512 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:10,514 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-26_00-33-10.log] [testng] 00:33:10,514 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e0ce540 - End of configuration. [testng] [2024-12-26 00:33:16,530] [pool-1-thread-12] Initializing /data/samples/sdub.zip: [testng] 00:33:16,530 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:33:16,530 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:16,531 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-26_00-33-16.log] [testng] 00:33:16,531 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7fccf415 - End of configuration. [testng] [2024-12-26 00:33:17,492] [pool-1-thread-11] Initializing /data/imagej/confocal-stack.zip: [testng] 00:33:17,492 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:33:17,492 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:17,493 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-26_00-33-17.log] [testng] 00:33:17,493 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3929702b - End of configuration. [testng] [2024-12-26 00:33:32,965] [pool-1-thread-10] Initializing /data/imagej/Rat_Hippocampal_Neuron.zip: [testng] 00:33:32,965 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:33:32,965 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:32,966 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-26_00-33-32.log] [testng] 00:33:32,967 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a7a40ff - End of configuration. [testng] [2024-12-26 00:33:38,620] [pool-1-thread-9] Initializing /data/imagej/4D-Stack(256x256x20x10).zip: [testng] 00:33:38,620 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:33:38,620 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:38,621 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-26_00-33-38.log] [testng] 00:33:38,621 |-INFO in ch.qos.logback.core.sift.SiftProcessor@358869f5 - End of configuration. [testng] [2024-12-26 00:33:54,647] [pool-1-thread-8] Initializing /data/imagej/flybrain.zip: [testng] 00:33:54,648 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:33:54,648 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:54,648 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-26_00-33-54.log] [testng] 00:33:54,649 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2555b67b - End of configuration. [testng] [2024-12-26 00:34:08,745] [pool-1-thread-7] Initializing /data/imagej/RatBrain.zip: [testng] 00:34:08,745 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:34:08,745 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:08,746 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-26_00-34-08.log] [testng] 00:34:08,746 |-INFO in ch.qos.logback.core.sift.SiftProcessor@648de2ba - End of configuration. [testng] [2024-12-26 00:34:13,363] [pool-1-thread-6] Initializing /data/imagej/cheetah_256_8.tif.zip: [testng] 00:34:13,363 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:34:13,363 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:13,363 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-26_00-34-13.log] [testng] 00:34:13,364 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7af252af - End of configuration. [testng] [2024-12-26 00:34:18,558] [pool-1-thread-5] Initializing /data/imagej/confocal-series.zip: [testng] 00:34:18,558 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:34:18,558 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:18,559 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-26_00-34-18.log] [testng] 00:34:18,559 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36338337 - End of configuration. [testng] [2024-12-26 00:34:29,040] [pool-1-thread-4] Initializing /data/samples/bat-cochlea-volume.zip: [testng] 00:34:29,040 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:34:29,040 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:29,041 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-26_00-34-29.log] [testng] 00:34:29,041 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2aeb11bb - End of configuration. [testng] [2024-12-26 00:34:34,456] [pool-1-thread-3] Initializing /data/imagej/fat-cells.zip: [testng] 00:34:34,457 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:34:34,457 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:34,458 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-26_00-34-34.log] [testng] 00:34:34,458 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c015497 - End of configuration. [testng] [2024-12-26 00:34:40,950] [pool-1-thread-2] Initializing /data/imagej/hela-cells.zip: [testng] 00:34:40,950 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:34:40,951 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:40,951 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-26_00-34-40.log] [testng] 00:34:40,951 |-INFO in ch.qos.logback.core.sift.SiftProcessor@77c64ad4 - End of configuration. [testng] [2024-12-26 00:35:01,794] [pool-1-thread-12] Initializing /data/imagej/m51.zip: [testng] [2024-12-26 00:35:33,311] [pool-1-thread-7] Initializing /data/imagej/scala-media.zip: [testng] [2024-12-26 00:35:39,550] [pool-1-thread-12] Initializing /data/imagej/se3.zip: [testng] [2024-12-26 00:35:49,913] [pool-1-thread-6] Initializing /data/imagej/gel-electrophoresis.zip: [testng] [2024-12-26 00:36:14,968] [pool-1-thread-2] Initializing /data/imagej/watershed-animation.zip: [testng] [2024-12-26 00:36:20,456] [pool-1-thread-4] Initializing /data/imagej/mri-stack.zip: [testng] [2024-12-26 00:36:26,806] [pool-1-thread-7] Initializing /data/imagej/FluorescentCells.zip: [testng] [2024-12-26 00:36:30,897] [pool-1-thread-10] Initializing /data/imagej/blood-brain-barrier.zip: [testng] [2024-12-26 00:36:42,383] [pool-1-thread-1] Initializing /data/imagej/xrays.zip: [testng] [2024-12-26 00:37:07,167] [pool-1-thread-2] Initializing /data/imagej/3D_Chromosome.zip: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1166, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 11 minutes 39 seconds Finished: SUCCESS