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Started by upstream project "BIOFORMATS-test-repo" build number 222 originally caused by: Started by upstream project "Trigger" build number 249 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5 [BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins1171551104218131259.sh + '[' zip = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_35210_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] 01:35:29,921 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:35:29,922 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 01:35:29,922 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:35:29,923 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:35:29,923 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:35:29,923 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:35:29,924 |-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] 01:35:29,924 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:35:29,924 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:35:29,925 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:35:29,925 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:35:29,925 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:35:30,078 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:35:30,078 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:35:30,099 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:35:30,099 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:35:30,104 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:35:30,104 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:35:30,104 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:35:30,105 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:35:30,105 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 01:35:30,106 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 01:35:30,106 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 182 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-16 01:35:30,114] [main] java.version = 17.0.2 [testng] 01:35:30,117 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:35:30,117 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:35:30,156 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-16_01-35-30.log] [testng] 01:35:30,157 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-10-16 01:35:30,159] [main] testng.directory = /data [testng] [2024-10-16 01:35:30,159] [main] testng.configDirectory = /config [testng] [2024-10-16 01:35:30,167] [main] testng.multiplier = 1.0 [testng] [2024-10-16 01:35:30,168] [main] testng.in-memory = false [testng] [2024-10-16 01:35:30,168] [main] testng.allow-missing = false [testng] [2024-10-16 01:35:30,168] [main] user.language = en [testng] [2024-10-16 01:35:30,168] [main] user.country = ${user.country} [testng] [2024-10-16 01:35:30,168] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-16 01:35:30,667] [main] ---------------------------------------- [testng] [2024-10-16 01:35:30,667] [main] Total files: 22 [testng] [2024-10-16 01:35:30,667] [main] Scan time: 0.499 s (22 ms/file) [testng] [2024-10-16 01:35:30,667] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 22 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-16 01:47:20,427] [pool-1-thread-1] Initializing /data/imagej/fat-cells.zip: [testng] 01:47:20,427 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:47:20,427 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:47:20,428 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-16_01-47-20.log] [testng] 01:47:20,429 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36d29b7a - End of configuration. [testng] [2024-10-16 01:47:44,198] [pool-1-thread-12] Initializing /data/imagej/gel-electrophoresis.zip: [testng] 01:47:44,199 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:47:44,199 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:47:44,200 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-16_01-47-44.log] [testng] 01:47:44,200 |-INFO in ch.qos.logback.core.sift.SiftProcessor@340030bc - End of configuration. [testng] [2024-10-16 01:48:03,759] [pool-1-thread-11] Initializing /data/imagej/3D_Chromosome.zip: [testng] 01:48:03,759 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:48:03,759 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:03,760 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-16_01-48-03.log] [testng] 01:48:03,760 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56af8fea - End of configuration. [testng] [2024-10-16 01:48:23,253] [pool-1-thread-10] Initializing /data/imagej/xrays.zip: [testng] 01:48:23,253 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:48:23,253 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:23,254 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-16_01-48-23.log] [testng] 01:48:23,254 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f07fc19 - End of configuration. [testng] [2024-10-16 01:48:40,072] [pool-1-thread-9] Initializing /data/imagej/flybrain.zip: [testng] 01:48:40,072 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:48:40,072 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:40,072 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-16_01-48-40.log] [testng] 01:48:40,073 |-INFO in ch.qos.logback.core.sift.SiftProcessor@602431cf - End of configuration. [testng] [2024-10-16 01:49:25,511] [pool-1-thread-8] Initializing /data/imagej/m51.zip: [testng] 01:49:25,511 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:49:25,511 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:49:25,512 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-16_01-49-25.log] [testng] 01:49:25,512 |-INFO in ch.qos.logback.core.sift.SiftProcessor@139e39f9 - End of configuration. [testng] [2024-10-16 01:49:40,134] [pool-1-thread-7] Initializing /data/imagej/se3.zip: [testng] 01:49:40,134 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:49:40,134 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:49:40,135 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-16_01-49-40.log] [testng] 01:49:40,135 |-INFO in ch.qos.logback.core.sift.SiftProcessor@196ae177 - End of configuration. [testng] [2024-10-16 01:50:27,079] [pool-1-thread-6] Initializing /data/imagej/cheetah_256_8.tif.zip: [testng] 01:50:27,079 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:50:27,079 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:50:27,080 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-16_01-50-27.log] [testng] 01:50:27,081 |-INFO in ch.qos.logback.core.sift.SiftProcessor@240da70a - End of configuration. [testng] [2024-10-16 01:50:59,428] [pool-1-thread-5] Initializing /data/imagej/Rat_Hippocampal_Neuron.zip: [testng] 01:50:59,428 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:50:59,428 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:50:59,429 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-16_01-50-59.log] [testng] 01:50:59,429 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f85131 - End of configuration. [testng] [2024-10-16 01:51:26,359] [pool-1-thread-4] Initializing /data/imagej/RatBrain.zip: [testng] 01:51:26,359 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:51:26,359 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:51:26,360 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-16_01-51-26.log] [testng] 01:51:26,360 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2858bf4a - End of configuration. [testng] [2024-10-16 01:51:48,068] [pool-1-thread-3] Initializing /data/imagej/4D-Stack(256x256x20x10).zip: [testng] 01:51:48,068 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:51:48,068 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:51:48,069 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-16_01-51-48.log] [testng] 01:51:48,069 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6899e5dd - End of configuration. [testng] [2024-10-16 01:52:38,086] [pool-1-thread-2] Initializing /data/imagej/hela-cells.zip: [testng] 01:52:38,087 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:52:38,087 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:52:38,088 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-16_01-52-38.log] [testng] 01:52:38,088 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40fc9a9e - End of configuration. [testng] [2024-10-16 01:57:35,228] [pool-1-thread-8] Initializing /data/samples/bat-cochlea-volume.zip: [testng] [2024-10-16 01:58:25,783] [pool-1-thread-10] Initializing /data/imagej/Rat_Hippocampal_Neuron2.zip: [testng] [2024-10-16 01:59:40,274] [pool-1-thread-11] Initializing /data/imagej/confocal-stack.zip: [testng] [2024-10-16 02:00:36,472] [pool-1-thread-12] Initializing /data/imagej/scala-media.zip: [testng] [2024-10-16 02:01:12,207] [pool-1-thread-4] Initializing /data/samples/sdub.zip: [testng] [2024-10-16 02:01:19,401] [pool-1-thread-2] Initializing /data/imagej/mri-stack.zip: [testng] [2024-10-16 02:01:49,665] [pool-1-thread-6] Initializing /data/imagej/blood-brain-barrier.zip: [testng] [2024-10-16 02:03:45,226] [pool-1-thread-1] Initializing /data/imagej/watershed-animation.zip: [testng] [2024-10-16 02:04:07,564] [pool-1-thread-5] Initializing /data/imagej/FluorescentCells.zip: [testng] [2024-10-16 02:05:13,113] [pool-1-thread-4] 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: 42 minutes 10 seconds Finished: SUCCESS