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Started by upstream project "BIOFORMATS-test-repo" build number 388 originally caused by: Started by upstream project "Trigger" build number 411 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@16 [BIOFORMATS-test-folder@16] $ /bin/bash -xe /tmp/jenkins15278566618464167714.sh + '[' zip = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_61344_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] 00:23:53,575 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 00:23:53,577 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - No custom configurators were discovered as a service. [testng] 00:23:53,577 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:23:53,578 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:23:53,579 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:23:53,579 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:23:53,580 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:23:53,580 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:23:53,580 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:23:53,581 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:23:53,582 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:23:53,582 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:23:53,789 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:23:53,789 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:23:53,814 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:23:53,814 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:23:53,820 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:23:53,820 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:23:53,820 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:23:53,821 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:23:53,821 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@3f6f6701 - End of configuration. [testng] 00:23:53,822 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@4f80542f - Registering current configuration as safe fallback point [testng] 00:23:53,822 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 242 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-23 00:23:53,832] [main] java.version = 17.0.2 [testng] 00:23:53,835 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:23:53,836 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:53,887 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-23_00-23-53.log] [testng] 00:23:53,888 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14bdbc74 - End of configuration. [testng] [2025-03-23 00:23:53,891] [main] testng.directory = /data [testng] [2025-03-23 00:23:53,891] [main] testng.configDirectory = /config [testng] [2025-03-23 00:23:53,902] [main] testng.multiplier = 1.0 [testng] [2025-03-23 00:23:53,903] [main] testng.in-memory = false [testng] [2025-03-23 00:23:53,903] [main] testng.allow-missing = false [testng] [2025-03-23 00:23:53,904] [main] user.language = en [testng] [2025-03-23 00:23:53,904] [main] user.country = ${user.country} [testng] [2025-03-23 00:23:53,904] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-03-23 00:23:54,387] [main] ---------------------------------------- [testng] [2025-03-23 00:23:54,387] [main] Total files: 22 [testng] [2025-03-23 00:23:54,388] [main] Scan time: 0.483 s (21 ms/file) [testng] [2025-03-23 00:23:54,388] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 22 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-23 00:29:30,724] [pool-1-thread-1] Initializing /data/imagej/fat-cells.zip: [testng] 00:29:30,724 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:29:30,724 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:30,726 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-23_00-29-30.log] [testng] 00:29:30,726 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75475f7a - End of configuration. [testng] [2025-03-23 00:29:43,251] [pool-1-thread-12] Initializing /data/imagej/gel-electrophoresis.zip: [testng] 00:29:43,251 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:29:43,251 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:43,252 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-23_00-29-43.log] [testng] 00:29:43,253 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78bd2ab7 - End of configuration. [testng] [2025-03-23 00:29:54,123] [pool-1-thread-11] Initializing /data/imagej/3D_Chromosome.zip: [testng] 00:29:54,123 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:29:54,123 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:54,124 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-23_00-29-54.log] [testng] 00:29:54,124 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b13bd2 - End of configuration. [testng] [2025-03-23 00:30:02,122] [pool-1-thread-10] Initializing /data/imagej/xrays.zip: [testng] 00:30:02,122 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:30:02,123 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:02,124 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-23_00-30-02.log] [testng] 00:30:02,125 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c6dc7be - End of configuration. [testng] [2025-03-23 00:30:07,191] [pool-1-thread-9] Initializing /data/imagej/flybrain.zip: [testng] 00:30:07,191 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:30:07,191 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:07,192 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-23_00-30-07.log] [testng] 00:30:07,192 |-INFO in ch.qos.logback.core.sift.SiftProcessor@26f5dea8 - End of configuration. [testng] [2025-03-23 00:30:24,092] [pool-1-thread-8] Initializing /data/imagej/m51.zip: [testng] 00:30:24,092 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:30:24,092 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:24,093 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-23_00-30-24.log] [testng] 00:30:24,093 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12e898bc - End of configuration. [testng] [2025-03-23 00:30:31,668] [pool-1-thread-7] Initializing /data/imagej/se3.zip: [testng] 00:30:31,668 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:30:31,668 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:31,669 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-23_00-30-31.log] [testng] 00:30:31,670 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a002f1 - End of configuration. [testng] [2025-03-23 00:30:51,584] [pool-1-thread-6] Initializing /data/imagej/cheetah_256_8.tif.zip: [testng] 00:30:51,584 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:30:51,584 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:51,585 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-23_00-30-51.log] [testng] 00:30:51,585 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4aa773fa - End of configuration. [testng] [2025-03-23 00:30:59,503] [pool-1-thread-5] Initializing /data/imagej/Rat_Hippocampal_Neuron.zip: [testng] 00:30:59,503 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:30:59,503 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:59,504 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-23_00-30-59.log] [testng] 00:30:59,504 |-INFO in ch.qos.logback.core.sift.SiftProcessor@51efdebe - End of configuration. [testng] [2025-03-23 00:31:08,861] [pool-1-thread-4] Initializing /data/imagej/RatBrain.zip: [testng] 00:31:08,861 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:31:08,861 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:31:08,862 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-23_00-31-08.log] [testng] 00:31:08,862 |-INFO in ch.qos.logback.core.sift.SiftProcessor@275be4c1 - End of configuration. [testng] [2025-03-23 00:31:15,773] [pool-1-thread-3] Initializing /data/imagej/4D-Stack(256x256x20x10).zip: [testng] 00:31:15,773 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:31:15,773 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:31:15,774 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-23_00-31-15.log] [testng] 00:31:15,774 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6ddc5575 - End of configuration. [testng] [2025-03-23 00:31:41,409] [pool-1-thread-2] Initializing /data/imagej/hela-cells.zip: [testng] 00:31:41,409 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:31:41,409 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:31:41,409 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-23_00-31-41.log] [testng] 00:31:41,410 |-INFO in ch.qos.logback.core.sift.SiftProcessor@139e39f9 - End of configuration. [testng] [2025-03-23 00:33:22,512] [pool-1-thread-8] Initializing /data/samples/bat-cochlea-volume.zip: [testng] [2025-03-23 00:33:41,515] [pool-1-thread-10] Initializing /data/imagej/Rat_Hippocampal_Neuron2.zip: [testng] [2025-03-23 00:34:13,342] [pool-1-thread-11] Initializing /data/imagej/confocal-stack.zip: [testng] [2025-03-23 00:34:45,838] [pool-1-thread-4] Initializing /data/imagej/scala-media.zip: [testng] [2025-03-23 00:35:23,334] [pool-1-thread-12] Initializing /data/samples/sdub.zip: [testng] [2025-03-23 00:35:26,977] [pool-1-thread-2] Initializing /data/imagej/mri-stack.zip: [testng] [2025-03-23 00:35:40,881] [pool-1-thread-6] Initializing /data/imagej/blood-brain-barrier.zip: [testng] [2025-03-23 00:36:19,827] [pool-1-thread-5] Initializing /data/imagej/watershed-animation.zip: [testng] [2025-03-23 00:36:50,425] [pool-1-thread-12] Initializing /data/imagej/FluorescentCells.zip: [testng] [2025-03-23 00:37:01,065] [pool-1-thread-1] 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: 19 minutes 52 seconds Finished: SUCCESS