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Started by upstream project "BIOFORMATS-test-repo" build number 271 originally caused by: Started by upstream project "Trigger" build number 293 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9 [BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins10153311169348704993.sh + '[' zip = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_42653_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 00:27:28,548 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:27:28,549 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 00:27:28,549 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:27:28,550 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:27:28,551 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:27:28,551 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:27:28,551 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:27:28,551 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:27:28,552 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:27:28,552 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:27:28,553 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:27:28,553 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:27:28,704 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:27:28,705 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:27:28,731 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:27:28,731 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:27:28,737 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:27:28,737 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:27:28,737 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:27:28,738 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:27:28,738 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 00:27:28,738 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 00:27:28,739 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 187 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-28 00:27:28,747] [main] java.version = 21 [testng] 00:27:28,750 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:27:28,750 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:28,791 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-28_00-27-28.log] [testng] 00:27:28,792 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-11-28 00:27:28,794] [main] testng.directory = /data [testng] [2024-11-28 00:27:28,794] [main] testng.configDirectory = /config [testng] [2024-11-28 00:27:28,802] [main] testng.multiplier = 1.0 [testng] [2024-11-28 00:27:28,803] [main] testng.in-memory = false [testng] [2024-11-28 00:27:28,803] [main] testng.allow-missing = false [testng] [2024-11-28 00:27:28,803] [main] user.language = en [testng] [2024-11-28 00:27:28,803] [main] user.country = ${user.country} [testng] [2024-11-28 00:27:28,803] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-28 00:27:29,240] [main] ---------------------------------------- [testng] [2024-11-28 00:27:29,240] [main] Total files: 22 [testng] [2024-11-28 00:27:29,240] [main] Scan time: 0.437 s (19 ms/file) [testng] [2024-11-28 00:27:29,241] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 22 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-28 00:30:15,250] [pool-1-thread-1] Initializing /data/imagej/m51.zip: [testng] 00:30:15,251 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:30:15,251 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:15,252 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-28_00-30-15.log] [testng] 00:30:15,253 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e73b355 - End of configuration. [testng] [2024-11-28 00:30:18,353] [pool-1-thread-12] Initializing /data/imagej/cheetah_256_8.tif.zip: [testng] 00:30:18,353 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:30:18,353 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:18,354 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-28_00-30-18.log] [testng] 00:30:18,354 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56c0c053 - End of configuration. [testng] [2024-11-28 00:30:23,502] [pool-1-thread-11] Initializing /data/imagej/watershed-animation.zip: [testng] 00:30:23,502 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:30:23,502 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:23,503 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-28_00-30-23.log] [testng] 00:30:23,503 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34d8a34 - End of configuration. [testng] [2024-11-28 00:30:27,419] [pool-1-thread-10] Initializing /data/imagej/hela-cells.zip: [testng] 00:30:27,419 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:30:27,420 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:27,421 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-28_00-30-27.log] [testng] 00:30:27,421 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e27117c - End of configuration. [testng] [2024-11-28 00:30:32,707] [pool-1-thread-9] Initializing /data/imagej/fat-cells.zip: [testng] 00:30:32,707 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:30:32,707 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:32,708 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-28_00-30-32.log] [testng] 00:30:32,708 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e9d855 - End of configuration. [testng] [2024-11-28 00:30:40,225] [pool-1-thread-8] Initializing /data/samples/bat-cochlea-volume.zip: [testng] 00:30:40,225 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:30:40,225 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:40,226 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-28_00-30-40.log] [testng] 00:30:40,227 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a7fdfad - End of configuration. [testng] [2024-11-28 00:30:46,233] [pool-1-thread-7] Initializing /data/imagej/gel-electrophoresis.zip: [testng] 00:30:46,233 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:30:46,233 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:46,234 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-28_00-30-46.log] [testng] 00:30:46,234 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36b1fce1 - End of configuration. [testng] [2024-11-28 00:30:51,750] [pool-1-thread-6] Initializing /data/imagej/blood-brain-barrier.zip: [testng] 00:30:51,750 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:30:51,750 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:51,751 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-28_00-30-51.log] [testng] 00:30:51,752 |-INFO in ch.qos.logback.core.sift.SiftProcessor@628a96a4 - End of configuration. [testng] [2024-11-28 00:31:07,434] [pool-1-thread-5] Initializing /data/imagej/scala-media.zip: [testng] 00:31:07,434 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:31:07,434 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:31:07,435 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-28_00-31-07.log] [testng] 00:31:07,436 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78a0342e - End of configuration. [testng] [2024-11-28 00:31:10,768] [pool-1-thread-4] Initializing /data/imagej/4D-Stack(256x256x20x10).zip: [testng] 00:31:10,768 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:31:10,768 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:31:10,769 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-28_00-31-10.log] [testng] 00:31:10,769 |-INFO in ch.qos.logback.core.sift.SiftProcessor@59e87e0e - End of configuration. [testng] [2024-11-28 00:31:24,080] [pool-1-thread-3] Initializing /data/imagej/se3.zip: [testng] 00:31:24,080 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:31:24,081 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:31:24,081 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-28_00-31-24.log] [testng] 00:31:24,082 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e280321 - End of configuration. [testng] [2024-11-28 00:31:35,157] [pool-1-thread-2] Initializing /data/imagej/xrays.zip: [testng] 00:31:35,157 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:31:35,157 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:31:35,158 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-28_00-31-35.log] [testng] 00:31:35,159 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14e967e8 - End of configuration. [testng] [2024-11-28 00:32:21,145] [pool-1-thread-1] Initializing /data/samples/sdub.zip: [testng] [2024-11-28 00:32:22,808] [pool-1-thread-2] Initializing /data/imagej/Rat_Hippocampal_Neuron.zip: [testng] [2024-11-28 00:32:38,139] [pool-1-thread-5] Initializing /data/imagej/confocal-series.zip: [testng] [2024-11-28 00:32:51,807] [pool-1-thread-11] Initializing /data/imagej/3D_Chromosome.zip: [testng] [2024-11-28 00:33:07,968] [pool-1-thread-12] Initializing /data/imagej/flybrain.zip: [testng] [2024-11-28 00:33:24,579] [pool-1-thread-1] Initializing /data/imagej/RatBrain.zip: [testng] [2024-11-28 00:33:44,901] [pool-1-thread-10] Initializing /data/imagej/Rat_Hippocampal_Neuron2.zip: [testng] [2024-11-28 00:34:01,064] [pool-1-thread-7] Initializing /data/imagej/mri-stack.zip: [testng] [2024-11-28 00:34:15,957] [pool-1-thread-8] Initializing /data/imagej/FluorescentCells.zip: [testng] [2024-11-28 00:34:32,090] [pool-1-thread-11] 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: 13 minutes 36 seconds Finished: SUCCESS