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Started by upstream project "BIOFORMATS-test-repo" build number 387 originally caused by: Started by upstream project "Trigger" build number 410 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@11 [BIOFORMATS-test-folder@11] $ /bin/bash -xe /tmp/jenkins15777015826286461854.sh + '[' zip = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_61179_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] WARNING: An illegal reflective access operation has occurred [testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket [testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener [testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [testng] WARNING: All illegal access operations will be denied in a future release [testng] File leak detector installed [testng] 00:27:07,389 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 00:27:07,391 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - No custom configurators were discovered as a service. [testng] 00:27:07,391 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:27:07,392 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:27:07,393 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:27:07,393 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:27:07,394 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:27:07,394 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:27:07,394 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:27:07,395 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:27:07,395 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:27:07,396 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:27:07,588 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:27:07,588 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:27:07,613 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:27:07,613 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:27:07,620 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:27:07,620 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:27:07,620 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:27:07,621 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:27:07,621 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@65c7a252 - End of configuration. [testng] 00:27:07,622 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@38cee291 - Registering current configuration as safe fallback point [testng] 00:27:07,622 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 228 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-22 00:27:07,632] [main] java.version = 11.0.16 [testng] 00:27:07,635 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:27:07,635 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:07,681 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-22_00-27-07.log] [testng] 00:27:07,683 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13d73f29 - End of configuration. [testng] [2025-03-22 00:27:07,685] [main] testng.directory = /data [testng] [2025-03-22 00:27:07,685] [main] testng.configDirectory = /config [testng] [2025-03-22 00:27:07,695] [main] testng.multiplier = 1.0 [testng] [2025-03-22 00:27:07,697] [main] testng.in-memory = false [testng] [2025-03-22 00:27:07,697] [main] testng.allow-missing = false [testng] [2025-03-22 00:27:07,697] [main] user.language = en [testng] [2025-03-22 00:27:07,698] [main] user.country = ${user.country} [testng] [2025-03-22 00:27:07,698] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-03-22 00:27:08,231] [main] ---------------------------------------- [testng] [2025-03-22 00:27:08,231] [main] Total files: 22 [testng] [2025-03-22 00:27:08,231] [main] Scan time: 0.533 s (24 ms/file) [testng] [2025-03-22 00:27:08,231] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 22 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-22 00:31:47,549] [pool-1-thread-1] Initializing /data/imagej/hela-cells.zip: [testng] 00:31:47,550 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:31:47,550 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:31:47,551 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-22_00-31-47.log] [testng] 00:31:47,552 |-INFO in ch.qos.logback.core.sift.SiftProcessor@84605d6 - End of configuration. [testng] [2025-03-22 00:31:56,125] [pool-1-thread-12] Initializing /data/imagej/Rat_Hippocampal_Neuron.zip: [testng] 00:31:56,125 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:31:56,125 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:31:56,126 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-22_00-31-56.log] [testng] 00:31:56,127 |-INFO in ch.qos.logback.core.sift.SiftProcessor@358e1a56 - End of configuration. [testng] [2025-03-22 00:32:06,235] [pool-1-thread-11] Initializing /data/imagej/4D-Stack(256x256x20x10).zip: [testng] 00:32:06,236 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:32:06,236 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:32:06,236 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-22_00-32-06.log] [testng] 00:32:06,237 |-INFO in ch.qos.logback.core.sift.SiftProcessor@411b8130 - End of configuration. [testng] [2025-03-22 00:32:30,728] [pool-1-thread-10] Initializing /data/imagej/m51.zip: [testng] 00:32:30,728 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:32:30,728 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:32:30,728 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-22_00-32-30.log] [testng] 00:32:30,729 |-INFO in ch.qos.logback.core.sift.SiftProcessor@310e1db0 - End of configuration. [testng] [2025-03-22 00:32:36,770] [pool-1-thread-9] Initializing /data/imagej/confocal-stack.zip: [testng] 00:32:36,770 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:32:36,770 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:32:36,770 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-22_00-32-36.log] [testng] 00:32:36,771 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50edd8b4 - End of configuration. [testng] [2025-03-22 00:32:56,825] [pool-1-thread-8] Initializing /data/imagej/xrays.zip: [testng] 00:32:56,825 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:32:56,825 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:32:56,826 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-22_00-32-56.log] [testng] 00:32:56,826 |-INFO in ch.qos.logback.core.sift.SiftProcessor@67bfe4eb - End of configuration. [testng] [2025-03-22 00:33:01,866] [pool-1-thread-7] Initializing /data/imagej/gel-electrophoresis.zip: [testng] 00:33:01,866 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:33:01,866 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:01,867 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-22_00-33-01.log] [testng] 00:33:01,867 |-INFO in ch.qos.logback.core.sift.SiftProcessor@520bea7c - End of configuration. [testng] [2025-03-22 00:33:10,876] [pool-1-thread-6] Initializing /data/imagej/fat-cells.zip: [testng] 00:33:10,877 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:33:10,877 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:10,877 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-22_00-33-10.log] [testng] 00:33:10,878 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56db8742 - End of configuration. [testng] [2025-03-22 00:33:20,725] [pool-1-thread-5] Initializing /data/imagej/3D_Chromosome.zip: [testng] 00:33:20,726 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:33:20,726 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:20,726 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-22_00-33-20.log] [testng] 00:33:20,727 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7055fa48 - End of configuration. [testng] [2025-03-22 00:33:28,215] [pool-1-thread-4] Initializing /data/imagej/scala-media.zip: [testng] 00:33:28,215 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:33:28,215 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:28,216 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-22_00-33-28.log] [testng] 00:33:28,216 |-INFO in ch.qos.logback.core.sift.SiftProcessor@178a1e09 - End of configuration. [testng] [2025-03-22 00:33:35,545] [pool-1-thread-3] Initializing /data/imagej/confocal-series.zip: [testng] 00:33:35,545 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:33:35,545 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:35,546 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-22_00-33-35.log] [testng] 00:33:35,546 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79869d92 - End of configuration. [testng] [2025-03-22 00:33:53,394] [pool-1-thread-2] Initializing /data/imagej/Rat_Hippocampal_Neuron2.zip: [testng] 00:33:53,394 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:33:53,394 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:53,395 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-22_00-33-53.log] [testng] 00:33:53,395 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f861faf - End of configuration. [testng] [2025-03-22 00:35:10,962] [pool-1-thread-10] Initializing /data/imagej/mri-stack.zip: [testng] [2025-03-22 00:35:20,260] [pool-1-thread-8] Initializing /data/samples/sdub.zip: [testng] [2025-03-22 00:35:43,557] [pool-1-thread-4] Initializing /data/imagej/se3.zip: [testng] [2025-03-22 00:36:01,659] [pool-1-thread-5] Initializing /data/imagej/watershed-animation.zip: [testng] [2025-03-22 00:36:18,947] [pool-1-thread-8] Initializing /data/imagej/FluorescentCells.zip: [testng] [2025-03-22 00:36:37,258] [pool-1-thread-1] Initializing /data/imagej/RatBrain.zip: [testng] [2025-03-22 00:36:58,703] [pool-1-thread-7] Initializing /data/imagej/cheetah_256_8.tif.zip: [testng] [2025-03-22 00:37:25,133] [pool-1-thread-12] Initializing /data/imagej/blood-brain-barrier.zip: [testng] [2025-03-22 00:37:48,974] [pool-1-thread-10] Initializing /data/imagej/flybrain.zip: [testng] [2025-03-22 00:38:11,489] [pool-1-thread-2] Initializing /data/samples/bat-cochlea-volume.zip: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1166, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 18 minutes 2 seconds Finished: SUCCESS