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Started by upstream project "BIOFORMATS-test-repo" build number 181 originally caused by: Started by upstream project "Trigger" build number 202 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@6 [BIOFORMATS-test-folder@6] $ /bin/bash -xe /tmp/jenkins13112368238659795908.sh + '[' zip = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_28538_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] 06:56:36,964 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 06:56:36,966 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 06:56:36,966 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 06:56:36,967 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 06:56:36,968 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 06:56:36,968 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 06:56:36,969 |-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] 06:56:36,969 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 06:56:36,969 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 06:56:36,970 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 06:56:36,971 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 06:56:36,971 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 06:56:37,190 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 06:56:37,190 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 06:56:37,222 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 06:56:37,222 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 06:56:37,230 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 06:56:37,231 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 06:56:37,231 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 06:56:37,231 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 06:56:37,231 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 06:56:37,233 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 06:56:37,233 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 264 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-09-10 06:56:37,247] [main] java.version = 11.0.16 [testng] 06:56:37,252 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 06:56:37,252 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:56:37,317 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-10_06-56-37.log] [testng] 06:56:37,319 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-09-10 06:56:37,323] [main] testng.directory = /data [testng] [2024-09-10 06:56:37,323] [main] testng.configDirectory = /config [testng] [2024-09-10 06:56:37,338] [main] testng.multiplier = 1.0 [testng] [2024-09-10 06:56:37,340] [main] testng.in-memory = false [testng] [2024-09-10 06:56:37,341] [main] testng.allow-missing = false [testng] [2024-09-10 06:56:37,341] [main] user.language = en [testng] [2024-09-10 06:56:37,341] [main] user.country = ${user.country} [testng] [2024-09-10 06:56:37,341] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-09-10 06:56:37,917] [main] ---------------------------------------- [testng] [2024-09-10 06:56:37,917] [main] Total files: 22 [testng] [2024-09-10 06:56:37,917] [main] Scan time: 0.576 s (26 ms/file) [testng] [2024-09-10 06:56:37,917] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 22 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-09-10 06:57:23,386] [pool-1-thread-1] Initializing /data/imagej/blood-brain-barrier.zip: [testng] 06:57:23,386 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 06:57:23,387 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:57:23,389 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-09-10_06-57-23.log] [testng] 06:57:23,389 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65ee9e6d - End of configuration. [testng] [2024-09-10 06:57:28,103] [pool-1-thread-12] Initializing /data/imagej/confocal-series.zip: [testng] 06:57:28,103 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 06:57:28,103 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:57:28,104 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-09-10_06-57-28.log] [testng] 06:57:28,105 |-INFO in ch.qos.logback.core.sift.SiftProcessor@372932f4 - End of configuration. [testng] [2024-09-10 06:57:31,674] [pool-1-thread-11] Initializing /data/imagej/m51.zip: [testng] 06:57:31,674 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 06:57:31,674 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:57:31,675 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-09-10_06-57-31.log] [testng] 06:57:31,675 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c0015ab - End of configuration. [testng] [2024-09-10 06:57:31,801] [pool-1-thread-10] Initializing /data/imagej/xrays.zip: [testng] 06:57:31,801 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 06:57:31,801 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:57:31,802 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-09-10_06-57-31.log] [testng] 06:57:31,803 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3aace575 - End of configuration. [testng] [2024-09-10 06:57:31,930] [pool-1-thread-9] Initializing /data/imagej/se3.zip: [testng] 06:57:31,930 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 06:57:31,930 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:57:31,931 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-09-10_06-57-31.log] [testng] 06:57:31,931 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e60e8ec - End of configuration. [testng] [2024-09-10 06:57:35,481] [pool-1-thread-8] Initializing /data/imagej/mri-stack.zip: [testng] 06:57:35,482 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 06:57:35,482 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:57:35,482 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-09-10_06-57-35.log] [testng] 06:57:35,483 |-INFO in ch.qos.logback.core.sift.SiftProcessor@648de2ba - End of configuration. [testng] [2024-09-10 06:57:35,754] [pool-1-thread-7] Initializing /data/imagej/RatBrain.zip: [testng] 06:57:35,754 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 06:57:35,754 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:57:35,755 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-09-10_06-57-35.log] [testng] 06:57:35,755 |-INFO in ch.qos.logback.core.sift.SiftProcessor@51d48b07 - End of configuration. [testng] [2024-09-10 06:57:35,989] [pool-1-thread-6] Initializing /data/imagej/scala-media.zip: [testng] 06:57:35,989 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 06:57:35,989 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:57:35,990 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-09-10_06-57-35.log] [testng] 06:57:35,990 |-INFO in ch.qos.logback.core.sift.SiftProcessor@393b56c9 - End of configuration. [testng] [2024-09-10 06:57:36,160] [pool-1-thread-5] Initializing /data/imagej/3D_Chromosome.zip: [testng] 06:57:36,161 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 06:57:36,161 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:57:36,161 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-09-10_06-57-36.log] [testng] 06:57:36,162 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a1148bb - End of configuration. [testng] [2024-09-10 06:57:36,535] [pool-1-thread-4] Initializing /data/imagej/gel-electrophoresis.zip: [testng] 06:57:36,535 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 06:57:36,535 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:57:36,536 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-09-10_06-57-36.log] [testng] 06:57:36,536 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6655f3c2 - End of configuration. [testng] [2024-09-10 06:57:37,929] [pool-1-thread-3] Initializing /data/imagej/flybrain.zip: [testng] 06:57:37,929 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 06:57:37,929 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:57:37,930 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-09-10_06-57-37.log] [testng] 06:57:37,931 |-INFO in ch.qos.logback.core.sift.SiftProcessor@26791810 - End of configuration. [testng] [2024-09-10 06:57:42,345] [pool-1-thread-2] Initializing /data/imagej/hela-cells.zip: [testng] 06:57:42,345 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 06:57:42,345 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:57:42,346 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-09-10_06-57-42.log] [testng] 06:57:42,346 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ccbad38 - End of configuration. [testng] [2024-09-10 06:57:45,874] [pool-1-thread-10] Initializing /data/samples/bat-cochlea-volume.zip: [testng] [2024-09-10 06:57:46,579] [pool-1-thread-6] Initializing /data/imagej/Rat_Hippocampal_Neuron2.zip: [testng] [2024-09-10 06:57:47,753] [pool-1-thread-11] Initializing /data/imagej/fat-cells.zip: [testng] [2024-09-10 06:57:51,061] [pool-1-thread-7] Initializing /data/imagej/cheetah_256_8.tif.zip: [testng] [2024-09-10 06:57:52,848] [pool-1-thread-8] Initializing /data/imagej/4D-Stack(256x256x20x10).zip: [testng] [2024-09-10 06:57:59,453] [pool-1-thread-5] Initializing /data/imagej/FluorescentCells.zip: [testng] [2024-09-10 06:58:00,246] [pool-1-thread-7] Initializing /data/imagej/confocal-stack.zip: [testng] [2024-09-10 06:58:09,601] [pool-1-thread-5] Initializing /data/imagej/watershed-animation.zip: [testng] [2024-09-10 06:58:12,508] [pool-1-thread-5] Initializing /data/samples/sdub.zip: [testng] [2024-09-10 06:58:13,681] [pool-1-thread-10] Initializing /data/imagej/Rat_Hippocampal_Neuron.zip: time="2024-09-10T06:00:26Z" level=error msg="error waiting for container: unexpected EOF" Build step 'Execute shell' marked build as failure Finished: FAILURE