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Started by upstream project "BIOFORMATS-test-repo" build number 53 originally caused by: Started by upstream project "Trigger" build number 60 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8 [BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins3359932669502775842.sh + '[' zip = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_7703_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] 01:22:55,303 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:22:55,304 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 01:22:55,304 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:22:55,305 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:22:55,306 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:22:55,306 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:22:55,307 |-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] 01:22:55,307 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:22:55,307 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:22:55,308 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:22:55,308 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:22:55,308 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:22:55,482 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:22:55,482 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:22:55,506 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:22:55,506 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:22:55,512 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:22:55,512 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:22:55,512 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:22:55,512 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:22:55,512 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 01:22:55,513 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 01:22:55,513 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 206 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-05-04 01:22:55,523] [main] java.version = 11.0.16 [testng] 01:22:55,526 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:22:55,526 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:55,570 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-04_01-22-55.log] [testng] 01:22:55,572 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-05-04 01:22:55,574] [main] testng.directory = /data [testng] [2024-05-04 01:22:55,574] [main] testng.configDirectory = /config [testng] [2024-05-04 01:22:55,585] [main] testng.multiplier = 1.0 [testng] [2024-05-04 01:22:55,586] [main] testng.in-memory = false [testng] [2024-05-04 01:22:55,586] [main] testng.allow-missing = false [testng] [2024-05-04 01:22:55,586] [main] user.language = en [testng] [2024-05-04 01:22:55,586] [main] user.country = ${user.country} [testng] [2024-05-04 01:22:55,586] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-05-04 01:22:55,979] [main] ---------------------------------------- [testng] [2024-05-04 01:22:55,979] [main] Total files: 22 [testng] [2024-05-04 01:22:55,979] [main] Scan time: 0.391 s (17 ms/file) [testng] [2024-05-04 01:22:55,979] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 22 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-05-04 01:23:37,409] [pool-1-thread-1] Initializing /data/imagej/confocal-series.zip: [testng] 01:23:37,410 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:23:37,410 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:37,412 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-04_01-23-37.log] [testng] 01:23:37,412 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6b595a77 - End of configuration. [testng] [2024-05-04 01:23:40,746] [pool-1-thread-12] Initializing /data/imagej/xrays.zip: [testng] 01:23:40,746 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:23:40,746 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:40,748 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-04_01-23-40.log] [testng] 01:23:40,748 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2aeb11bb - End of configuration. [testng] [2024-05-04 01:23:40,850] [pool-1-thread-11] Initializing /data/imagej/fat-cells.zip: [testng] 01:23:40,850 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:23:40,850 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:40,851 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-04_01-23-40.log] [testng] 01:23:40,852 |-INFO in ch.qos.logback.core.sift.SiftProcessor@167a4d23 - End of configuration. [testng] [2024-05-04 01:23:43,430] [pool-1-thread-10] Initializing /data/imagej/confocal-stack.zip: [testng] 01:23:43,430 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:23:43,430 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:43,431 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-04_01-23-43.log] [testng] 01:23:43,431 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a1148bb - End of configuration. [testng] [2024-05-04 01:23:49,910] [pool-1-thread-9] Initializing /data/imagej/Rat_Hippocampal_Neuron.zip: [testng] 01:23:49,911 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:23:49,911 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:49,912 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-04_01-23-49.log] [testng] 01:23:49,912 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a56bb7b - End of configuration. [testng] [2024-05-04 01:23:50,943] [pool-1-thread-8] Initializing /data/imagej/m51.zip: [testng] 01:23:50,943 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:23:50,943 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:50,944 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-04_01-23-50.log] [testng] 01:23:50,944 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d816635 - End of configuration. [testng] [2024-05-04 01:23:51,037] [pool-1-thread-7] Initializing /data/imagej/cheetah_256_8.tif.zip: [testng] 01:23:51,037 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:23:51,037 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:51,038 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-04_01-23-51.log] [testng] 01:23:51,039 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c37c7e8 - End of configuration. [testng] [2024-05-04 01:23:51,207] [pool-1-thread-6] Initializing /data/imagej/Rat_Hippocampal_Neuron2.zip: [testng] 01:23:51,207 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:23:51,207 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:51,208 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-04_01-23-51.log] [testng] 01:23:51,208 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ae6d0cc - End of configuration. [testng] [2024-05-04 01:23:52,266] [pool-1-thread-5] Initializing /data/imagej/flybrain.zip: [testng] 01:23:52,266 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:23:52,266 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:52,267 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-04_01-23-52.log] [testng] 01:23:52,267 |-INFO in ch.qos.logback.core.sift.SiftProcessor@437ddcf1 - End of configuration. [testng] [2024-05-04 01:23:56,399] [pool-1-thread-4] Initializing /data/imagej/RatBrain.zip: [testng] 01:23:56,400 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:23:56,400 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:56,401 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-04_01-23-56.log] [testng] 01:23:56,401 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e4a8f3b - End of configuration. [testng] [2024-05-04 01:23:56,604] [pool-1-thread-3] Initializing /data/imagej/3D_Chromosome.zip: [testng] 01:23:56,604 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:23:56,604 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:56,605 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-04_01-23-56.log] [testng] 01:23:56,605 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c1e0a2d - End of configuration. [testng] [2024-05-04 01:23:56,948] [pool-1-thread-2] Initializing /data/imagej/se3.zip: [testng] 01:23:56,948 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:23:56,948 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:56,949 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-04_01-23-56.log] [testng] 01:23:56,949 |-INFO in ch.qos.logback.core.sift.SiftProcessor@381b06ff - End of configuration. [testng] [2024-05-04 01:24:02,570] [pool-1-thread-12] Initializing /data/samples/sdub.zip: [testng] [2024-05-04 01:24:03,047] [pool-1-thread-8] Initializing /data/imagej/scala-media.zip: [testng] [2024-05-04 01:24:03,914] [pool-1-thread-7] Initializing /data/imagej/watershed-animation.zip: [testng] [2024-05-04 01:24:04,084] [pool-1-thread-4] Initializing /data/imagej/gel-electrophoresis.zip: [testng] [2024-05-04 01:24:06,088] [pool-1-thread-8] Initializing /data/imagej/hela-cells.zip: [testng] [2024-05-04 01:24:07,449] [pool-1-thread-7] Initializing /data/samples/bat-cochlea-volume.zip: [testng] [2024-05-04 01:24:09,847] [pool-1-thread-3] Initializing /data/imagej/FluorescentCells.zip: [testng] [2024-05-04 01:24:10,213] [pool-1-thread-12] Initializing /data/imagej/4D-Stack(256x256x20x10).zip: [testng] [2024-05-04 01:24:17,257] [pool-1-thread-3] Initializing /data/imagej/blood-brain-barrier.zip: [testng] [2024-05-04 01:24:30,079] [pool-1-thread-7] 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 25 seconds Finished: SUCCESS