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Started by upstream project "BIOFORMATS-test-repo" build number 258 originally caused by: Started by upstream project "Trigger" build number 282 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4 [BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins3306692764652141581.sh + '[' zip = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_40650_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] 00:26:59,714 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:26:59,715 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 00:26:59,715 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:26:59,716 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:26:59,717 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:26:59,717 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:26:59,718 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:26:59,718 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:26:59,718 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:26:59,718 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:26:59,719 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:26:59,719 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:26:59,881 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:26:59,881 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:26:59,902 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:26:59,902 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:26:59,907 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:26:59,908 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:26:59,908 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:26:59,908 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:26:59,908 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 00:26:59,909 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 00:26:59,909 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 191 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-17 00:26:59,917] [main] java.version = 17.0.2 [testng] 00:26:59,920 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:26:59,920 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:26:59,959 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-17_00-26-59.log] [testng] 00:26:59,960 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-11-17 00:26:59,962] [main] testng.directory = /data [testng] [2024-11-17 00:26:59,962] [main] testng.configDirectory = /config [testng] [2024-11-17 00:26:59,970] [main] testng.multiplier = 1.0 [testng] [2024-11-17 00:26:59,971] [main] testng.in-memory = false [testng] [2024-11-17 00:26:59,971] [main] testng.allow-missing = false [testng] [2024-11-17 00:26:59,971] [main] user.language = en [testng] [2024-11-17 00:26:59,971] [main] user.country = ${user.country} [testng] [2024-11-17 00:26:59,972] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-17 00:27:00,542] [main] ---------------------------------------- [testng] [2024-11-17 00:27:00,543] [main] Total files: 22 [testng] [2024-11-17 00:27:00,543] [main] Scan time: 0.57 s (25 ms/file) [testng] [2024-11-17 00:27:00,543] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 22 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-17 00:28:51,865] [pool-1-thread-1] Initializing /data/imagej/fat-cells.zip: [testng] 00:28:51,866 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:28:51,866 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:28:51,867 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-17_00-28-51.log] [testng] 00:28:51,868 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3804373c - End of configuration. [testng] [2024-11-17 00:28:56,921] [pool-1-thread-12] Initializing /data/imagej/gel-electrophoresis.zip: [testng] 00:28:56,922 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:28:56,922 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:28:56,923 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-17_00-28-56.log] [testng] 00:28:56,923 |-INFO in ch.qos.logback.core.sift.SiftProcessor@436c8730 - End of configuration. [testng] [2024-11-17 00:29:00,563] [pool-1-thread-11] Initializing /data/imagej/3D_Chromosome.zip: [testng] 00:29:00,564 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:29:00,564 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:00,564 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-17_00-29-00.log] [testng] 00:29:00,565 |-INFO in ch.qos.logback.core.sift.SiftProcessor@602431cf - End of configuration. [testng] [2024-11-17 00:29:03,524] [pool-1-thread-10] Initializing /data/imagej/xrays.zip: [testng] 00:29:03,524 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:29:03,524 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:03,525 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-17_00-29-03.log] [testng] 00:29:03,526 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ee4d5 - End of configuration. [testng] [2024-11-17 00:29:05,552] [pool-1-thread-9] Initializing /data/imagej/flybrain.zip: [testng] 00:29:05,553 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:29:05,553 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:05,553 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-17_00-29-05.log] [testng] 00:29:05,554 |-INFO in ch.qos.logback.core.sift.SiftProcessor@67fbeca0 - End of configuration. [testng] [2024-11-17 00:29:15,332] [pool-1-thread-8] Initializing /data/imagej/m51.zip: [testng] 00:29:15,332 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:29:15,332 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:15,333 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-17_00-29-15.log] [testng] 00:29:15,334 |-INFO in ch.qos.logback.core.sift.SiftProcessor@44042792 - End of configuration. [testng] [2024-11-17 00:29:17,374] [pool-1-thread-7] Initializing /data/imagej/se3.zip: [testng] 00:29:17,375 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:29:17,375 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:17,376 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-17_00-29-17.log] [testng] 00:29:17,376 |-INFO in ch.qos.logback.core.sift.SiftProcessor@b45ebd0 - End of configuration. [testng] [2024-11-17 00:29:25,234] [pool-1-thread-6] Initializing /data/imagej/cheetah_256_8.tif.zip: [testng] 00:29:25,235 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:29:25,235 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:25,235 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-17_00-29-25.log] [testng] 00:29:25,236 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6b297a01 - End of configuration. [testng] [2024-11-17 00:29:28,158] [pool-1-thread-5] Initializing /data/imagej/Rat_Hippocampal_Neuron.zip: [testng] 00:29:28,158 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:29:28,158 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:28,159 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-17_00-29-28.log] [testng] 00:29:28,159 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3641c20 - End of configuration. [testng] [2024-11-17 00:29:33,979] [pool-1-thread-4] Initializing /data/imagej/RatBrain.zip: [testng] 00:29:33,979 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:29:33,979 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:33,980 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-17_00-29-33.log] [testng] 00:29:33,981 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4fe7b522 - End of configuration. [testng] [2024-11-17 00:29:37,876] [pool-1-thread-3] Initializing /data/imagej/4D-Stack(256x256x20x10).zip: [testng] 00:29:37,876 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:29:37,876 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:37,877 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-17_00-29-37.log] [testng] 00:29:37,877 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6156bc8f - End of configuration. [testng] [2024-11-17 00:29:46,560] [pool-1-thread-2] Initializing /data/imagej/hela-cells.zip: [testng] 00:29:46,560 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:29:46,560 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:46,561 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-17_00-29-46.log] [testng] 00:29:46,561 |-INFO in ch.qos.logback.core.sift.SiftProcessor@606b1490 - End of configuration. [testng] [2024-11-17 00:30:13,352] [pool-1-thread-10] Initializing /data/samples/bat-cochlea-volume.zip: [testng] [2024-11-17 00:30:17,075] [pool-1-thread-8] Initializing /data/imagej/Rat_Hippocampal_Neuron2.zip: [testng] [2024-11-17 00:30:26,521] [pool-1-thread-4] Initializing /data/imagej/confocal-stack.zip: [testng] [2024-11-17 00:30:37,117] [pool-1-thread-6] Initializing /data/imagej/scala-media.zip: [testng] [2024-11-17 00:30:39,896] [pool-1-thread-11] Initializing /data/samples/sdub.zip: [testng] [2024-11-17 00:30:52,983] [pool-1-thread-11] Initializing /data/imagej/mri-stack.zip: [testng] [2024-11-17 00:30:58,736] [pool-1-thread-2] Initializing /data/imagej/blood-brain-barrier.zip: [testng] [2024-11-17 00:31:14,823] [pool-1-thread-6] Initializing /data/imagej/watershed-animation.zip: [testng] [2024-11-17 00:31:21,395] [pool-1-thread-12] Initializing /data/imagej/FluorescentCells.zip: [testng] [2024-11-17 00:31:23,943] [pool-1-thread-5] Initializing /data/imagej/confocal-series.zip: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1166, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 8 minutes 25 seconds Finished: SUCCESS