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Started by upstream project "BIOFORMATS-test-repo" build number 201 originally caused by: Started by upstream project "Trigger" build number 226 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/jenkins6319647306074854662.sh + '[' zip = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_31818_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. [javac] 4 warnings test-automated: [testng] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket [testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket [testng] File leak detector installed [testng] 12:14:10,073 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 12:14:10,074 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 12:14:10,074 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 12:14:10,075 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 12:14:10,076 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 12:14:10,076 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 12:14:10,076 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 12:14:10,076 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 12:14:10,077 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 12:14:10,077 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 12:14:10,078 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 12:14:10,078 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 12:14:10,241 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 12:14:10,242 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 12:14:10,267 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 12:14:10,268 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 12:14:10,274 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 12:14:10,274 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 12:14:10,274 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 12:14:10,275 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 12:14:10,275 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 12:14:10,276 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 12:14:10,276 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 199 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-09-26 12:14:10,286] [main] java.version = 21 [testng] 12:14:10,289 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 12:14:10,289 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:14:10,330 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-26_12-14-10.log] [testng] 12:14:10,331 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-09-26 12:14:10,333] [main] testng.directory = /data [testng] [2024-09-26 12:14:10,333] [main] testng.configDirectory = /config [testng] [2024-09-26 12:14:10,342] [main] testng.multiplier = 1.0 [testng] [2024-09-26 12:14:10,342] [main] testng.in-memory = false [testng] [2024-09-26 12:14:10,342] [main] testng.allow-missing = false [testng] [2024-09-26 12:14:10,343] [main] user.language = en [testng] [2024-09-26 12:14:10,343] [main] user.country = ${user.country} [testng] [2024-09-26 12:14:10,343] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-09-26 12:14:10,784] [main] ---------------------------------------- [testng] [2024-09-26 12:14:10,784] [main] Total files: 22 [testng] [2024-09-26 12:14:10,784] [main] Scan time: 0.441 s (20 ms/file) [testng] [2024-09-26 12:14:10,785] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 22 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-09-26 12:16:00,430] [pool-1-thread-1] Initializing /data/imagej/Rat_Hippocampal_Neuron.zip: [testng] 12:16:00,430 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 12:16:00,430 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:16:00,432 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-09-26_12-16-00.log] [testng] 12:16:00,432 |-INFO in ch.qos.logback.core.sift.SiftProcessor@67e2af77 - End of configuration. [testng] [2024-09-26 12:16:08,895] [pool-1-thread-12] Initializing /data/imagej/watershed-animation.zip: [testng] 12:16:08,896 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 12:16:08,896 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:16:08,897 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-09-26_12-16-08.log] [testng] 12:16:08,897 |-INFO in ch.qos.logback.core.sift.SiftProcessor@289b666f - End of configuration. [testng] [2024-09-26 12:16:10,930] [pool-1-thread-11] Initializing /data/imagej/cheetah_256_8.tif.zip: [testng] 12:16:10,931 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 12:16:10,931 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:16:10,931 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-09-26_12-16-10.log] [testng] 12:16:10,932 |-INFO in ch.qos.logback.core.sift.SiftProcessor@124b54a8 - End of configuration. [testng] [2024-09-26 12:16:13,734] [pool-1-thread-10] Initializing /data/imagej/Rat_Hippocampal_Neuron2.zip: [testng] 12:16:13,734 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 12:16:13,734 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:16:13,735 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-09-26_12-16-13.log] [testng] 12:16:13,736 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2e5c83f0 - End of configuration. [testng] [2024-09-26 12:16:18,343] [pool-1-thread-9] Initializing /data/imagej/mri-stack.zip: [testng] 12:16:18,343 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 12:16:18,343 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:16:18,345 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-09-26_12-16-18.log] [testng] 12:16:18,345 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7676f92a - End of configuration. [testng] [2024-09-26 12:16:20,751] [pool-1-thread-8] Initializing /data/imagej/gel-electrophoresis.zip: [testng] 12:16:20,751 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 12:16:20,751 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:16:20,752 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-09-26_12-16-20.log] [testng] 12:16:20,752 |-INFO in ch.qos.logback.core.sift.SiftProcessor@72ab1e71 - End of configuration. [testng] [2024-09-26 12:16:24,277] [pool-1-thread-7] Initializing /data/imagej/3D_Chromosome.zip: [testng] 12:16:24,278 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 12:16:24,278 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:16:24,278 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-09-26_12-16-24.log] [testng] 12:16:24,279 |-INFO in ch.qos.logback.core.sift.SiftProcessor@373b5721 - End of configuration. [testng] [2024-09-26 12:16:26,646] [pool-1-thread-6] Initializing /data/imagej/hela-cells.zip: [testng] 12:16:26,646 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 12:16:26,646 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:16:26,647 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-09-26_12-16-26.log] [testng] 12:16:26,647 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a30a3b6 - End of configuration. [testng] [2024-09-26 12:16:30,058] [pool-1-thread-5] Initializing /data/imagej/FluorescentCells.zip: [testng] 12:16:30,059 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 12:16:30,059 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:16:30,059 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-09-26_12-16-30.log] [testng] 12:16:30,060 |-INFO in ch.qos.logback.core.sift.SiftProcessor@309cd7df - End of configuration. [testng] [2024-09-26 12:16:32,882] [pool-1-thread-4] Initializing /data/imagej/flybrain.zip: [testng] 12:16:32,883 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 12:16:32,883 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:16:32,883 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-09-26_12-16-32.log] [testng] 12:16:32,884 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7980cd53 - End of configuration. [testng] [2024-09-26 12:16:43,544] [pool-1-thread-3] Initializing /data/imagej/4D-Stack(256x256x20x10).zip: [testng] 12:16:43,544 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 12:16:43,544 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:16:43,545 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-09-26_12-16-43.log] [testng] 12:16:43,545 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1dd80ae9 - End of configuration. [testng] [2024-09-26 12:16:53,878] [pool-1-thread-2] Initializing /data/imagej/xrays.zip: [testng] 12:16:53,878 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 12:16:53,879 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:16:53,880 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-09-26_12-16-53.log] [testng] 12:16:53,880 |-INFO in ch.qos.logback.core.sift.SiftProcessor@45749ad8 - End of configuration. [testng] [2024-09-26 12:17:17,206] [pool-1-thread-2] Initializing /data/imagej/confocal-series.zip: [testng] [2024-09-26 12:17:29,573] [pool-1-thread-12] Initializing /data/samples/bat-cochlea-volume.zip: [testng] [2024-09-26 12:17:34,826] [pool-1-thread-9] Initializing /data/imagej/RatBrain.zip: [testng] [2024-09-26 12:17:36,871] [pool-1-thread-5] Initializing /data/imagej/confocal-stack.zip: [testng] [2024-09-26 12:17:47,911] [pool-1-thread-11] Initializing /data/imagej/scala-media.zip: [testng] [2024-09-26 12:17:48,987] [pool-1-thread-7] Initializing /data/imagej/m51.zip: [testng] [2024-09-26 12:18:05,517] [pool-1-thread-6] Initializing /data/imagej/blood-brain-barrier.zip: [testng] [2024-09-26 12:18:15,215] [pool-1-thread-7] Initializing /data/imagej/se3.zip: [testng] [2024-09-26 12:18:23,467] [pool-1-thread-11] Initializing /data/samples/sdub.zip: [testng] [2024-09-26 12:18:24,200] [pool-1-thread-9] Initializing /data/imagej/fat-cells.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 52 seconds Finished: SUCCESS