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Started by upstream project "BIOFORMATS-test-repo" build number 78 originally caused by: Started by upstream project "Trigger" build number 86 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@2 [BIOFORMATS-test-folder@2] $ /bin/bash -xe /tmp/jenkins5549235360167409387.sh + '[' zip = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_11803_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] 01:22:41,378 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:22:41,380 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 01:22:41,380 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:22:41,381 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:22:41,381 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:22:41,381 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:22:41,382 |-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] 01:22:41,382 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:22:41,382 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:22:41,383 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:22:41,383 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:22:41,383 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:22:41,541 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:22:41,541 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:22:41,562 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:22:41,563 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:22:41,568 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:22:41,568 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:22:41,568 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:22:41,569 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:22:41,569 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 01:22:41,569 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 01:22:41,569 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 187 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-05-29 01:22:41,578] [main] java.version = 17.0.2 [testng] 01:22:41,581 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:22:41,581 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:41,626 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-29_01-22-41.log] [testng] 01:22:41,627 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-05-29 01:22:41,629] [main] testng.directory = /data [testng] [2024-05-29 01:22:41,629] [main] testng.configDirectory = /config [testng] [2024-05-29 01:22:41,638] [main] testng.multiplier = 1.0 [testng] [2024-05-29 01:22:41,639] [main] testng.in-memory = false [testng] [2024-05-29 01:22:41,639] [main] testng.allow-missing = false [testng] [2024-05-29 01:22:41,639] [main] user.language = en [testng] [2024-05-29 01:22:41,639] [main] user.country = ${user.country} [testng] [2024-05-29 01:22:41,639] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-05-29 01:22:42,009] [main] ---------------------------------------- [testng] [2024-05-29 01:22:42,009] [main] Total files: 22 [testng] [2024-05-29 01:22:42,010] [main] Scan time: 0.37 s (16 ms/file) [testng] [2024-05-29 01:22:42,010] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 22 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-05-29 01:23:21,428] [pool-1-thread-1] Initializing /data/imagej/4D-Stack(256x256x20x10).zip: [testng] 01:23:21,429 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:23:21,429 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:21,430 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-29_01-23-21.log] [testng] 01:23:21,430 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e732da7 - End of configuration. [testng] [2024-05-29 01:23:26,867] [pool-1-thread-12] Initializing /data/imagej/fat-cells.zip: [testng] 01:23:26,867 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:23:26,868 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:26,869 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-29_01-23-26.log] [testng] 01:23:26,869 |-INFO in ch.qos.logback.core.sift.SiftProcessor@196ae177 - End of configuration. [testng] [2024-05-29 01:23:29,443] [pool-1-thread-11] Initializing /data/imagej/FluorescentCells.zip: [testng] 01:23:29,443 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:23:29,443 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:29,445 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-29_01-23-29.log] [testng] 01:23:29,446 |-INFO in ch.qos.logback.core.sift.SiftProcessor@88b8aa - End of configuration. [testng] [2024-05-29 01:23:29,751] [pool-1-thread-10] Initializing /data/imagej/Rat_Hippocampal_Neuron2.zip: [testng] 01:23:29,751 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:23:29,751 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:29,752 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-29_01-23-29.log] [testng] 01:23:29,752 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5382ff34 - End of configuration. [testng] [2024-05-29 01:23:30,958] [pool-1-thread-9] Initializing /data/imagej/xrays.zip: [testng] 01:23:30,958 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:23:30,958 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:30,959 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-29_01-23-30.log] [testng] 01:23:30,959 |-INFO in ch.qos.logback.core.sift.SiftProcessor@73486367 - End of configuration. [testng] [2024-05-29 01:23:31,072] [pool-1-thread-8] Initializing /data/imagej/confocal-series.zip: [testng] 01:23:31,073 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:23:31,073 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:31,073 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-29_01-23-31.log] [testng] 01:23:31,074 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1190531a - End of configuration. [testng] [2024-05-29 01:23:34,540] [pool-1-thread-7] Initializing /data/imagej/watershed-animation.zip: [testng] 01:23:34,540 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:23:34,541 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:34,541 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-29_01-23-34.log] [testng] 01:23:34,542 |-INFO in ch.qos.logback.core.sift.SiftProcessor@509f50f - End of configuration. [testng] [2024-05-29 01:23:34,711] [pool-1-thread-6] Initializing /data/imagej/scala-media.zip: [testng] 01:23:34,711 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:23:34,711 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:34,712 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-29_01-23-34.log] [testng] 01:23:34,712 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5890eee9 - End of configuration. [testng] [2024-05-29 01:23:34,823] [pool-1-thread-5] Initializing /data/imagej/m51.zip: [testng] 01:23:34,823 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:23:34,823 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:34,824 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-29_01-23-34.log] [testng] 01:23:34,825 |-INFO in ch.qos.logback.core.sift.SiftProcessor@54469fd3 - End of configuration. [testng] [2024-05-29 01:23:34,968] [pool-1-thread-4] Initializing /data/imagej/Rat_Hippocampal_Neuron.zip: [testng] 01:23:34,968 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:23:34,969 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:34,969 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-29_01-23-34.log] [testng] 01:23:34,969 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2d73cd79 - End of configuration. [testng] [2024-05-29 01:23:36,019] [pool-1-thread-3] Initializing /data/imagej/hela-cells.zip: [testng] 01:23:36,019 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:23:36,019 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:36,020 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-29_01-23-36.log] [testng] 01:23:36,020 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2dc9bf62 - End of configuration. [testng] [2024-05-29 01:23:36,748] [pool-1-thread-2] Initializing /data/samples/bat-cochlea-volume.zip: [testng] 01:23:36,748 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:23:36,749 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:36,749 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-29_01-23-36.log] [testng] 01:23:36,750 |-INFO in ch.qos.logback.core.sift.SiftProcessor@319f3339 - End of configuration. [testng] [2024-05-29 01:23:39,845] [pool-1-thread-6] Initializing /data/imagej/RatBrain.zip: [testng] [2024-05-29 01:23:40,053] [pool-1-thread-9] Initializing /data/imagej/flybrain.zip: [testng] [2024-05-29 01:23:45,051] [pool-1-thread-5] Initializing /data/imagej/3D_Chromosome.zip: [testng] [2024-05-29 01:23:46,875] [pool-1-thread-7] Initializing /data/imagej/cheetah_256_8.tif.zip: [testng] [2024-05-29 01:23:47,794] [pool-1-thread-11] Initializing /data/imagej/gel-electrophoresis.zip: [testng] [2024-05-29 01:23:51,182] [pool-1-thread-6] Initializing /data/imagej/se3.zip: [testng] [2024-05-29 01:23:55,513] [pool-1-thread-7] Initializing /data/samples/sdub.zip: [testng] [2024-05-29 01:23:59,430] [pool-1-thread-5] Initializing /data/imagej/blood-brain-barrier.zip: [testng] [2024-05-29 01:24:07,264] [pool-1-thread-2] Initializing /data/imagej/mri-stack.zip: [testng] [2024-05-29 01:24:07,607] [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 45 seconds Finished: SUCCESS