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Started by upstream project "BIOFORMATS-test-repo" build number 130 originally caused by: Started by upstream project "Trigger" build number 147 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins2969033673684976274.sh + '[' zip = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_20331_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] 11:14:40,175 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 11:14:40,177 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 11:14:40,177 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:14:40,179 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:14:40,180 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 11:14:40,180 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 11:14:40,181 |-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] 11:14:40,181 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:14:40,181 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:14:40,182 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 11:14:40,183 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 11:14:40,183 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 11:14:40,351 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 11:14:40,352 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 11:14:40,376 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 11:14:40,376 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 11:14:40,382 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 11:14:40,383 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 11:14:40,383 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 11:14:40,383 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 11:14:40,383 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 11:14:40,384 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 11:14:40,384 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 203 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-23 11:14:40,393] [main] java.version = 11.0.16 [testng] 11:14:40,397 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 11:14:40,397 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:14:40,445 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-23_11-14-40.log] [testng] 11:14:40,447 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-07-23 11:14:40,450] [main] testng.directory = /data [testng] [2024-07-23 11:14:40,450] [main] testng.configDirectory = /config [testng] [2024-07-23 11:14:40,465] [main] testng.multiplier = 1.0 [testng] [2024-07-23 11:14:40,467] [main] testng.in-memory = false [testng] [2024-07-23 11:14:40,467] [main] testng.allow-missing = false [testng] [2024-07-23 11:14:40,467] [main] user.language = en [testng] [2024-07-23 11:14:40,467] [main] user.country = ${user.country} [testng] [2024-07-23 11:14:40,467] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-07-23 11:14:40,984] [main] ---------------------------------------- [testng] [2024-07-23 11:14:40,984] [main] Total files: 22 [testng] [2024-07-23 11:14:40,984] [main] Scan time: 0.517 s (23 ms/file) [testng] [2024-07-23 11:14:40,984] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 22 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-23 11:15:21,004] [pool-1-thread-1] Initializing /data/imagej/confocal-series.zip: [testng] 11:15:21,004 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 11:15:21,005 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:15:21,006 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-23_11-15-21.log] [testng] 11:15:21,007 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ebfe744 - End of configuration. [testng] [2024-07-23 11:15:24,079] [pool-1-thread-12] Initializing /data/imagej/xrays.zip: [testng] 11:15:24,080 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 11:15:24,080 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:15:24,081 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-23_11-15-24.log] [testng] 11:15:24,082 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38a1d97f - End of configuration. [testng] [2024-07-23 11:15:24,174] [pool-1-thread-11] Initializing /data/imagej/fat-cells.zip: [testng] 11:15:24,174 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 11:15:24,175 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:15:24,175 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-23_11-15-24.log] [testng] 11:15:24,175 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5eae2cd8 - End of configuration. [testng] [2024-07-23 11:15:26,254] [pool-1-thread-10] Initializing /data/imagej/confocal-stack.zip: [testng] 11:15:26,255 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 11:15:26,255 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:15:26,255 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-23_11-15-26.log] [testng] 11:15:26,256 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7bd9bf62 - End of configuration. [testng] [2024-07-23 11:15:32,454] [pool-1-thread-9] Initializing /data/imagej/Rat_Hippocampal_Neuron.zip: [testng] 11:15:32,455 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 11:15:32,455 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:15:32,456 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-23_11-15-32.log] [testng] 11:15:32,456 |-INFO in ch.qos.logback.core.sift.SiftProcessor@23e587c6 - End of configuration. [testng] [2024-07-23 11:15:33,606] [pool-1-thread-8] Initializing /data/imagej/m51.zip: [testng] 11:15:33,606 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 11:15:33,606 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:15:33,607 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-23_11-15-33.log] [testng] 11:15:33,607 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76a2c23a - End of configuration. [testng] [2024-07-23 11:15:33,720] [pool-1-thread-7] Initializing /data/imagej/cheetah_256_8.tif.zip: [testng] 11:15:33,720 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 11:15:33,721 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:15:33,722 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-23_11-15-33.log] [testng] 11:15:33,722 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78a0342e - End of configuration. [testng] [2024-07-23 11:15:33,936] [pool-1-thread-6] Initializing /data/imagej/Rat_Hippocampal_Neuron2.zip: [testng] 11:15:33,937 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 11:15:33,937 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:15:33,938 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-23_11-15-33.log] [testng] 11:15:33,938 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40def581 - End of configuration. [testng] [2024-07-23 11:15:35,078] [pool-1-thread-5] Initializing /data/imagej/flybrain.zip: [testng] 11:15:35,078 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 11:15:35,078 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:15:35,079 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-23_11-15-35.log] [testng] 11:15:35,079 |-INFO in ch.qos.logback.core.sift.SiftProcessor@77294ace - End of configuration. [testng] [2024-07-23 11:15:40,293] [pool-1-thread-4] Initializing /data/imagej/RatBrain.zip: [testng] 11:15:40,293 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 11:15:40,293 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:15:40,294 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-23_11-15-40.log] [testng] 11:15:40,295 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ce66f7d - End of configuration. [testng] [2024-07-23 11:15:40,481] [pool-1-thread-3] Initializing /data/imagej/3D_Chromosome.zip: [testng] 11:15:40,481 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 11:15:40,481 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:15:40,482 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-23_11-15-40.log] [testng] 11:15:40,482 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3607e50d - End of configuration. [testng] [2024-07-23 11:15:40,826] [pool-1-thread-2] Initializing /data/imagej/se3.zip: [testng] 11:15:40,826 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 11:15:40,826 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:15:40,827 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-23_11-15-40.log] [testng] 11:15:40,827 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3285db32 - End of configuration. [testng] [2024-07-23 11:15:46,262] [pool-1-thread-12] Initializing /data/samples/sdub.zip: [testng] [2024-07-23 11:15:46,701] [pool-1-thread-8] Initializing /data/imagej/scala-media.zip: [testng] [2024-07-23 11:15:47,205] [pool-1-thread-7] Initializing /data/imagej/watershed-animation.zip: [testng] [2024-07-23 11:15:47,585] [pool-1-thread-4] Initializing /data/imagej/gel-electrophoresis.zip: [testng] [2024-07-23 11:15:49,782] [pool-1-thread-8] Initializing /data/imagej/hela-cells.zip: [testng] [2024-07-23 11:15:51,138] [pool-1-thread-7] Initializing /data/samples/bat-cochlea-volume.zip: [testng] [2024-07-23 11:15:54,336] [pool-1-thread-3] Initializing /data/imagej/FluorescentCells.zip: [testng] [2024-07-23 11:15:54,981] [pool-1-thread-12] Initializing /data/imagej/4D-Stack(256x256x20x10).zip: [testng] [2024-07-23 11:16:04,396] [pool-1-thread-3] Initializing /data/imagej/blood-brain-barrier.zip: [testng] [2024-07-23 11:16:15,695] [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 36 seconds Finished: SUCCESS