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Started by upstream project "BIOFORMATS-test-repo" build number 93 originally caused by: Started by upstream project "Trigger" build number 104 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/jenkins11925816057606998933.sh + '[' zip = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_14263_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] 01:22:10,268 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:22:10,270 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 01:22:10,270 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:22:10,271 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:22:10,272 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:22:10,272 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:22:10,273 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:22:10,273 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:22:10,273 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:22:10,274 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:22:10,274 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:22:10,274 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:22:10,473 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:22:10,473 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:22:10,501 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:22:10,501 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:22:10,508 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:22:10,508 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:22:10,508 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:22:10,508 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:22:10,509 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 01:22:10,509 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 01:22:10,510 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 237 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-06-15 01:22:10,520] [main] java.version = 11.0.16 [testng] 01:22:10,525 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:22:10,525 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:10,575 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-15_01-22-10.log] [testng] 01:22:10,577 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-06-15 01:22:10,580] [main] testng.directory = /data [testng] [2024-06-15 01:22:10,580] [main] testng.configDirectory = /config [testng] [2024-06-15 01:22:10,594] [main] testng.multiplier = 1.0 [testng] [2024-06-15 01:22:10,595] [main] testng.in-memory = false [testng] [2024-06-15 01:22:10,596] [main] testng.allow-missing = false [testng] [2024-06-15 01:22:10,596] [main] user.language = en [testng] [2024-06-15 01:22:10,596] [main] user.country = ${user.country} [testng] [2024-06-15 01:22:10,596] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-06-15 01:22:11,062] [main] ---------------------------------------- [testng] [2024-06-15 01:22:11,062] [main] Total files: 22 [testng] [2024-06-15 01:22:11,062] [main] Scan time: 0.466 s (21 ms/file) [testng] [2024-06-15 01:22:11,062] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 22 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-06-15 01:22:57,062] [pool-1-thread-1] Initializing /data/imagej/confocal-series.zip: [testng] 01:22:57,062 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:22:57,063 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:57,065 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-15_01-22-57.log] [testng] 01:22:57,066 |-INFO in ch.qos.logback.core.sift.SiftProcessor@77e73294 - End of configuration. [testng] [2024-06-15 01:23:00,418] [pool-1-thread-12] Initializing /data/imagej/xrays.zip: [testng] 01:23:00,419 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:23:00,419 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:00,420 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-15_01-23-00.log] [testng] 01:23:00,420 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a30a3b6 - End of configuration. [testng] [2024-06-15 01:23:00,527] [pool-1-thread-11] Initializing /data/imagej/fat-cells.zip: [testng] 01:23:00,527 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:23:00,527 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:00,528 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-15_01-23-00.log] [testng] 01:23:00,528 |-INFO in ch.qos.logback.core.sift.SiftProcessor@29ad6434 - End of configuration. [testng] [2024-06-15 01:23:02,792] [pool-1-thread-10] Initializing /data/imagej/confocal-stack.zip: [testng] 01:23:02,792 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:23:02,792 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:02,793 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-15_01-23-02.log] [testng] 01:23:02,793 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5aa0721d - End of configuration. [testng] [2024-06-15 01:23:09,217] [pool-1-thread-9] Initializing /data/imagej/Rat_Hippocampal_Neuron.zip: [testng] 01:23:09,217 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:23:09,218 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:09,218 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-15_01-23-09.log] [testng] 01:23:09,219 |-INFO in ch.qos.logback.core.sift.SiftProcessor@121c8b03 - End of configuration. [testng] [2024-06-15 01:23:10,373] [pool-1-thread-8] Initializing /data/imagej/m51.zip: [testng] 01:23:10,374 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:23:10,374 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:10,377 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-15_01-23-10.log] [testng] 01:23:10,378 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5aa96d36 - End of configuration. [testng] [2024-06-15 01:23:10,482] [pool-1-thread-7] Initializing /data/imagej/cheetah_256_8.tif.zip: [testng] 01:23:10,482 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:23:10,482 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:10,483 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-15_01-23-10.log] [testng] 01:23:10,483 |-INFO in ch.qos.logback.core.sift.SiftProcessor@15042d07 - End of configuration. [testng] [2024-06-15 01:23:10,662] [pool-1-thread-6] Initializing /data/imagej/Rat_Hippocampal_Neuron2.zip: [testng] 01:23:10,663 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:23:10,663 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:10,664 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-15_01-23-10.log] [testng] 01:23:10,664 |-INFO in ch.qos.logback.core.sift.SiftProcessor@72df112a - End of configuration. [testng] [2024-06-15 01:23:11,646] [pool-1-thread-5] Initializing /data/imagej/flybrain.zip: [testng] 01:23:11,646 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:23:11,647 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:11,647 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-15_01-23-11.log] [testng] 01:23:11,648 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c7bde09 - End of configuration. [testng] [2024-06-15 01:23:16,322] [pool-1-thread-4] Initializing /data/imagej/RatBrain.zip: [testng] 01:23:16,323 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:23:16,323 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:16,324 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-15_01-23-16.log] [testng] 01:23:16,324 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b31582d - End of configuration. [testng] [2024-06-15 01:23:16,648] [pool-1-thread-3] Initializing /data/imagej/3D_Chromosome.zip: [testng] 01:23:16,648 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:23:16,648 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:16,649 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-15_01-23-16.log] [testng] 01:23:16,649 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5bd4979a - End of configuration. [testng] [2024-06-15 01:23:17,091] [pool-1-thread-2] Initializing /data/imagej/se3.zip: [testng] 01:23:17,092 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:23:17,092 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:17,092 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-15_01-23-17.log] [testng] 01:23:17,093 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b529531 - End of configuration. [testng] [2024-06-15 01:23:22,957] [pool-1-thread-8] Initializing /data/samples/sdub.zip: [testng] [2024-06-15 01:23:23,405] [pool-1-thread-12] Initializing /data/imagej/watershed-animation.zip: [testng] [2024-06-15 01:23:23,507] [pool-1-thread-7] Initializing /data/imagej/scala-media.zip: [testng] [2024-06-15 01:23:23,600] [pool-1-thread-4] Initializing /data/imagej/gel-electrophoresis.zip: [testng] [2024-06-15 01:23:26,532] [pool-1-thread-7] Initializing /data/imagej/hela-cells.zip: [testng] [2024-06-15 01:23:27,924] [pool-1-thread-12] Initializing /data/samples/bat-cochlea-volume.zip: [testng] [2024-06-15 01:23:29,731] [pool-1-thread-3] Initializing /data/imagej/FluorescentCells.zip: [testng] [2024-06-15 01:23:31,834] [pool-1-thread-8] Initializing /data/imagej/4D-Stack(256x256x20x10).zip: [testng] [2024-06-15 01:23:40,031] [pool-1-thread-3] Initializing /data/imagej/blood-brain-barrier.zip: [testng] [2024-06-15 01:23:51,734] [pool-1-thread-12] Initializing /data/imagej/mri-stack.zip: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1166, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 5 minutes 34 seconds Finished: SUCCESS