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Started by upstream project "BIOFORMATS-test-repo" build number 243 originally caused by: Started by user devspace 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/jenkins8673984915046251848.sh + '[' zip = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_38190_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] 14:02:40,056 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 14:02:40,058 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 14:02:40,058 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 14:02:40,060 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 14:02:40,060 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 14:02:40,061 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 14:02:40,061 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 14:02:40,061 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 14:02:40,062 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 14:02:40,062 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 14:02:40,063 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 14:02:40,063 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 14:02:40,257 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 14:02:40,257 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 14:02:40,284 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 14:02:40,284 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 14:02:40,291 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 14:02:40,291 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 14:02:40,291 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 14:02:40,292 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 14:02:40,292 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 14:02:40,292 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 14:02:40,293 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 230 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-02 14:02:40,302] [main] java.version = 11.0.16 [testng] 14:02:40,306 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 14:02:40,306 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:02:40,351 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-02_14-02-40.log] [testng] 14:02:40,353 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-11-02 14:02:40,355] [main] testng.directory = /data [testng] [2024-11-02 14:02:40,356] [main] testng.configDirectory = /config [testng] [2024-11-02 14:02:40,367] [main] testng.multiplier = 1.0 [testng] [2024-11-02 14:02:40,368] [main] testng.in-memory = false [testng] [2024-11-02 14:02:40,368] [main] testng.allow-missing = false [testng] [2024-11-02 14:02:40,368] [main] user.language = en [testng] [2024-11-02 14:02:40,368] [main] user.country = ${user.country} [testng] [2024-11-02 14:02:40,369] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-02 14:02:40,951] [main] ---------------------------------------- [testng] [2024-11-02 14:02:40,951] [main] Total files: 22 [testng] [2024-11-02 14:02:40,952] [main] Scan time: 0.582 s (26 ms/file) [testng] [2024-11-02 14:02:40,952] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 22 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-02 14:04:56,023] [pool-1-thread-1] Initializing /data/imagej/blood-brain-barrier.zip: [testng] 14:04:56,023 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 14:04:56,024 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:04:56,025 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-02_14-04-56.log] [testng] 14:04:56,026 |-INFO in ch.qos.logback.core.sift.SiftProcessor@122dcc67 - End of configuration. [testng] [2024-11-02 14:05:08,092] [pool-1-thread-12] Initializing /data/imagej/confocal-series.zip: [testng] 14:05:08,092 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 14:05:08,092 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:05:08,093 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-02_14-05-08.log] [testng] 14:05:08,094 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21bb88d9 - End of configuration. [testng] [2024-11-02 14:05:15,927] [pool-1-thread-11] Initializing /data/imagej/m51.zip: [testng] 14:05:15,927 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 14:05:15,927 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:05:15,928 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-02_14-05-15.log] [testng] 14:05:15,928 |-INFO in ch.qos.logback.core.sift.SiftProcessor@58d90431 - End of configuration. [testng] [2024-11-02 14:05:17,971] [pool-1-thread-10] Initializing /data/imagej/xrays.zip: [testng] 14:05:17,971 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 14:05:17,971 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:05:17,972 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-02_14-05-17.log] [testng] 14:05:17,972 |-INFO in ch.qos.logback.core.sift.SiftProcessor@28f981ce - End of configuration. [testng] [2024-11-02 14:05:19,881] [pool-1-thread-9] Initializing /data/imagej/se3.zip: [testng] 14:05:19,881 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 14:05:19,881 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:05:19,882 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-02_14-05-19.log] [testng] 14:05:19,882 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e1ec5a3 - End of configuration. [testng] [2024-11-02 14:05:27,897] [pool-1-thread-8] Initializing /data/imagej/mri-stack.zip: [testng] 14:05:27,897 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 14:05:27,897 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:05:27,898 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-02_14-05-27.log] [testng] 14:05:27,899 |-INFO in ch.qos.logback.core.sift.SiftProcessor@72ca7894 - End of configuration. [testng] [2024-11-02 14:05:30,389] [pool-1-thread-7] Initializing /data/imagej/RatBrain.zip: [testng] 14:05:30,389 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 14:05:30,389 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:05:30,390 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-02_14-05-30.log] [testng] 14:05:30,390 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4537863e - End of configuration. [testng] [2024-11-02 14:05:33,208] [pool-1-thread-6] Initializing /data/imagej/scala-media.zip: [testng] 14:05:33,209 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 14:05:33,209 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:05:33,209 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-02_14-05-33.log] [testng] 14:05:33,210 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56db8742 - End of configuration. [testng] [2024-11-02 14:05:35,702] [pool-1-thread-5] Initializing /data/imagej/3D_Chromosome.zip: [testng] 14:05:35,702 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 14:05:35,702 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:05:35,702 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-02_14-05-35.log] [testng] 14:05:35,703 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3929702b - End of configuration. [testng] [2024-11-02 14:05:38,360] [pool-1-thread-4] Initializing /data/imagej/gel-electrophoresis.zip: [testng] 14:05:38,360 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 14:05:38,360 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:05:38,361 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-02_14-05-38.log] [testng] 14:05:38,361 |-INFO in ch.qos.logback.core.sift.SiftProcessor@39455cc8 - End of configuration. [testng] [2024-11-02 14:05:41,872] [pool-1-thread-3] Initializing /data/imagej/flybrain.zip: [testng] 14:05:41,872 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 14:05:41,872 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:05:41,873 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-02_14-05-41.log] [testng] 14:05:41,873 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c0015ab - End of configuration. [testng] [2024-11-02 14:05:51,018] [pool-1-thread-2] Initializing /data/imagej/hela-cells.zip: [testng] 14:05:51,018 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 14:05:51,018 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:05:51,019 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-02_14-05-51.log] [testng] 14:05:51,019 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c3b43c4 - End of configuration. [testng] [2024-11-02 14:06:21,440] [pool-1-thread-11] Initializing /data/samples/bat-cochlea-volume.zip: [testng] [2024-11-02 14:06:25,684] [pool-1-thread-10] Initializing /data/imagej/fat-cells.zip: [testng] [2024-11-02 14:06:30,495] [pool-1-thread-6] Initializing /data/imagej/Rat_Hippocampal_Neuron2.zip: [testng] [2024-11-02 14:06:34,896] [pool-1-thread-8] Initializing /data/imagej/cheetah_256_8.tif.zip: [testng] [2024-11-02 14:06:39,386] [pool-1-thread-7] Initializing /data/imagej/4D-Stack(256x256x20x10).zip: [testng] [2024-11-02 14:06:50,132] [pool-1-thread-5] Initializing /data/imagej/FluorescentCells.zip: [testng] [2024-11-02 14:07:07,745] [pool-1-thread-2] Initializing /data/imagej/confocal-stack.zip: [testng] [2024-11-02 14:07:36,496] [pool-1-thread-4] Initializing /data/imagej/watershed-animation.zip: [testng] [2024-11-02 14:07:45,747] [pool-1-thread-5] Initializing /data/samples/sdub.zip: [testng] [2024-11-02 14:07:47,112] [pool-1-thread-8] Initializing /data/imagej/Rat_Hippocampal_Neuron.zip: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1166, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 9 minutes 17 seconds Finished: SUCCESS