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Started by upstream project "BIOFORMATS-test-repo" build number 101 originally caused by: Started by upstream project "Trigger" build number 112 originally caused by: Started by timer 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/jenkins1644673003432329382.sh + '[' zip = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_15575_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] 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] 01:21:39,292 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:21:39,293 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 01:21:39,293 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:21:39,294 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:21:39,295 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:21:39,295 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:21:39,295 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:21:39,295 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:21:39,296 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:21:39,296 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:21:39,296 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:21:39,297 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:21:39,472 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:21:39,472 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:21:39,496 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:21:39,497 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:21:39,505 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:21:39,506 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:21:39,506 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:21:39,507 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:21:39,507 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 01:21:39,508 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 01:21:39,508 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 212 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-06-23 01:21:39,518] [main] java.version = 17.0.2 [testng] 01:21:39,522 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:21:39,522 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:39,570 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-23_01-21-39.log] [testng] 01:21:39,572 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-06-23 01:21:39,574] [main] testng.directory = /data [testng] [2024-06-23 01:21:39,575] [main] testng.configDirectory = /config [testng] [2024-06-23 01:21:39,586] [main] testng.multiplier = 1.0 [testng] [2024-06-23 01:21:39,587] [main] testng.in-memory = false [testng] [2024-06-23 01:21:39,587] [main] testng.allow-missing = false [testng] [2024-06-23 01:21:39,588] [main] user.language = en [testng] [2024-06-23 01:21:39,588] [main] user.country = ${user.country} [testng] [2024-06-23 01:21:39,588] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-06-23 01:21:39,964] [main] ---------------------------------------- [testng] [2024-06-23 01:21:39,964] [main] Total files: 22 [testng] [2024-06-23 01:21:39,964] [main] Scan time: 0.376 s (17 ms/file) [testng] [2024-06-23 01:21:39,965] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 22 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-06-23 01:22:21,394] [pool-1-thread-1] Initializing /data/imagej/4D-Stack(256x256x20x10).zip: [testng] 01:22:21,395 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:22:21,395 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:21,396 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-23_01-22-21.log] [testng] 01:22:21,396 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2efb79a8 - End of configuration. [testng] [2024-06-23 01:22:27,565] [pool-1-thread-12] Initializing /data/imagej/fat-cells.zip: [testng] 01:22:27,565 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:22:27,565 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:27,566 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-23_01-22-27.log] [testng] 01:22:27,567 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f36bc1b - End of configuration. [testng] [2024-06-23 01:22:30,207] [pool-1-thread-11] Initializing /data/imagej/FluorescentCells.zip: [testng] 01:22:30,207 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:22:30,207 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:30,208 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-23_01-22-30.log] [testng] 01:22:30,208 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3904cf8e - End of configuration. [testng] [2024-06-23 01:22:30,579] [pool-1-thread-10] Initializing /data/imagej/Rat_Hippocampal_Neuron2.zip: [testng] 01:22:30,579 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:22:30,579 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:30,580 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-23_01-22-30.log] [testng] 01:22:30,580 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5382ff34 - End of configuration. [testng] [2024-06-23 01:22:31,698] [pool-1-thread-9] Initializing /data/imagej/xrays.zip: [testng] 01:22:31,698 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:22:31,698 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:31,699 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-23_01-22-31.log] [testng] 01:22:31,699 |-INFO in ch.qos.logback.core.sift.SiftProcessor@19b57930 - End of configuration. [testng] [2024-06-23 01:22:31,792] [pool-1-thread-8] Initializing /data/imagej/confocal-series.zip: [testng] 01:22:31,793 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:22:31,793 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:31,793 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-23_01-22-31.log] [testng] 01:22:31,794 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e883053 - End of configuration. [testng] [2024-06-23 01:22:35,178] [pool-1-thread-7] Initializing /data/imagej/watershed-animation.zip: [testng] 01:22:35,178 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:22:35,178 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:35,179 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-23_01-22-35.log] [testng] 01:22:35,180 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6f31f68d - End of configuration. [testng] [2024-06-23 01:22:35,372] [pool-1-thread-6] Initializing /data/imagej/scala-media.zip: [testng] 01:22:35,372 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:22:35,372 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:35,373 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-23_01-22-35.log] [testng] 01:22:35,373 |-INFO in ch.qos.logback.core.sift.SiftProcessor@183b1266 - End of configuration. [testng] [2024-06-23 01:22:35,479] [pool-1-thread-5] Initializing /data/imagej/m51.zip: [testng] 01:22:35,479 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:22:35,479 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:35,480 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-23_01-22-35.log] [testng] 01:22:35,480 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3bd11776 - End of configuration. [testng] [2024-06-23 01:22:35,608] [pool-1-thread-4] Initializing /data/imagej/Rat_Hippocampal_Neuron.zip: [testng] 01:22:35,608 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:22:35,609 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:35,610 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-23_01-22-35.log] [testng] 01:22:35,611 |-INFO in ch.qos.logback.core.sift.SiftProcessor@54adffce - End of configuration. [testng] [2024-06-23 01:22:36,705] [pool-1-thread-3] Initializing /data/imagej/hela-cells.zip: [testng] 01:22:36,705 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:22:36,705 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:36,706 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-23_01-22-36.log] [testng] 01:22:36,706 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c1c7cae - End of configuration. [testng] [2024-06-23 01:22:37,479] [pool-1-thread-2] Initializing /data/samples/bat-cochlea-volume.zip: [testng] 01:22:37,479 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:22:37,479 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:37,480 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-23_01-22-37.log] [testng] 01:22:37,480 |-INFO in ch.qos.logback.core.sift.SiftProcessor@58130b5f - End of configuration. [testng] [2024-06-23 01:22:40,621] [pool-1-thread-6] Initializing /data/imagej/RatBrain.zip: [testng] [2024-06-23 01:22:40,853] [pool-1-thread-9] Initializing /data/imagej/flybrain.zip: [testng] [2024-06-23 01:22:46,203] [pool-1-thread-5] Initializing /data/imagej/3D_Chromosome.zip: [testng] [2024-06-23 01:22:48,336] [pool-1-thread-7] Initializing /data/imagej/cheetah_256_8.tif.zip: [testng] [2024-06-23 01:22:48,902] [pool-1-thread-11] Initializing /data/imagej/gel-electrophoresis.zip: [testng] [2024-06-23 01:22:52,473] [pool-1-thread-6] Initializing /data/imagej/se3.zip: [testng] [2024-06-23 01:22:56,565] [pool-1-thread-7] Initializing /data/samples/sdub.zip: [testng] [2024-06-23 01:23:00,410] [pool-1-thread-5] Initializing /data/imagej/blood-brain-barrier.zip: [testng] [2024-06-23 01:23:06,746] [pool-1-thread-2] Initializing /data/imagej/mri-stack.zip: [testng] [2024-06-23 01:23:08,978] [pool-1-thread-7] Initializing /data/imagej/confocal-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 43 seconds Finished: SUCCESS