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Started by upstream project "BIOFORMATS-test-repo" build number 275 originally caused by: Started by upstream project "Trigger" build number 296 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@7 [BIOFORMATS-test-folder@7] $ /bin/bash -xe /tmp/jenkins2241856430611496535.sh + '[' zip = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_43309_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] 00:26:20,248 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:26:20,249 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 00:26:20,249 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:26:20,250 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:26:20,251 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:26:20,251 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:26:20,251 |-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] 00:26:20,251 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:26:20,252 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:26:20,252 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:26:20,252 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:26:20,253 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:26:20,424 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:26:20,424 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:26:20,447 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:26:20,448 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:26:20,454 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:26:20,454 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:26:20,454 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:26:20,454 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:26:20,454 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 00:26:20,455 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 00:26:20,455 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 203 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-01 00:26:20,465] [main] java.version = 17.0.2 [testng] 00:26:20,468 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:26:20,469 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:26:20,511 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-01_00-26-20.log] [testng] 00:26:20,512 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-12-01 00:26:20,514] [main] testng.directory = /data [testng] [2024-12-01 00:26:20,515] [main] testng.configDirectory = /config [testng] [2024-12-01 00:26:20,523] [main] testng.multiplier = 1.0 [testng] [2024-12-01 00:26:20,524] [main] testng.in-memory = false [testng] [2024-12-01 00:26:20,524] [main] testng.allow-missing = false [testng] [2024-12-01 00:26:20,525] [main] user.language = en [testng] [2024-12-01 00:26:20,525] [main] user.country = ${user.country} [testng] [2024-12-01 00:26:20,525] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-01 00:26:21,500] [main] ---------------------------------------- [testng] [2024-12-01 00:26:21,500] [main] Total files: 22 [testng] [2024-12-01 00:26:21,500] [main] Scan time: 0.975 s (44 ms/file) [testng] [2024-12-01 00:26:21,500] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 22 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-01 00:28:11,800] [pool-1-thread-1] Initializing /data/imagej/fat-cells.zip: [testng] 00:28:11,800 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:28:11,801 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:28:11,802 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-01_00-28-11.log] [testng] 00:28:11,802 |-INFO in ch.qos.logback.core.sift.SiftProcessor@479b0181 - End of configuration. [testng] [2024-12-01 00:28:16,396] [pool-1-thread-12] Initializing /data/imagej/gel-electrophoresis.zip: [testng] 00:28:16,396 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:28:16,396 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:28:16,397 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-01_00-28-16.log] [testng] 00:28:16,397 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4fcb720b - End of configuration. [testng] [2024-12-01 00:28:19,922] [pool-1-thread-11] Initializing /data/imagej/3D_Chromosome.zip: [testng] 00:28:19,922 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:28:19,923 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:28:19,924 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-01_00-28-19.log] [testng] 00:28:19,925 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14905b4d - End of configuration. [testng] [2024-12-01 00:28:22,666] [pool-1-thread-10] Initializing /data/imagej/xrays.zip: [testng] 00:28:22,666 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:28:22,666 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:28:22,667 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-01_00-28-22.log] [testng] 00:28:22,667 |-INFO in ch.qos.logback.core.sift.SiftProcessor@524de17f - End of configuration. [testng] [2024-12-01 00:28:24,769] [pool-1-thread-9] Initializing /data/imagej/flybrain.zip: [testng] 00:28:24,770 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:28:24,770 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:28:24,770 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-01_00-28-24.log] [testng] 00:28:24,771 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32f860d - End of configuration. [testng] [2024-12-01 00:28:34,271] [pool-1-thread-8] Initializing /data/imagej/m51.zip: [testng] 00:28:34,271 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:28:34,271 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:28:34,272 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-01_00-28-34.log] [testng] 00:28:34,272 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6057f525 - End of configuration. [testng] [2024-12-01 00:28:35,983] [pool-1-thread-7] Initializing /data/imagej/se3.zip: [testng] 00:28:35,983 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:28:35,983 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:28:35,983 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-01_00-28-35.log] [testng] 00:28:35,984 |-INFO in ch.qos.logback.core.sift.SiftProcessor@51efdebe - End of configuration. [testng] [2024-12-01 00:28:43,562] [pool-1-thread-6] Initializing /data/imagej/cheetah_256_8.tif.zip: [testng] 00:28:43,563 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:28:43,563 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:28:43,564 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-01_00-28-43.log] [testng] 00:28:43,564 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b2c2862 - End of configuration. [testng] [2024-12-01 00:28:46,244] [pool-1-thread-5] Initializing /data/imagej/Rat_Hippocampal_Neuron.zip: [testng] 00:28:46,244 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:28:46,244 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:28:46,245 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-01_00-28-46.log] [testng] 00:28:46,245 |-INFO in ch.qos.logback.core.sift.SiftProcessor@196ae177 - End of configuration. [testng] [2024-12-01 00:28:49,790] [pool-1-thread-4] Initializing /data/imagej/RatBrain.zip: [testng] 00:28:49,791 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:28:49,791 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:28:49,791 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-01_00-28-49.log] [testng] 00:28:49,792 |-INFO in ch.qos.logback.core.sift.SiftProcessor@58fdbaaf - End of configuration. [testng] [2024-12-01 00:28:52,026] [pool-1-thread-3] Initializing /data/imagej/4D-Stack(256x256x20x10).zip: [testng] 00:28:52,026 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:28:52,026 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:28:52,027 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-01_00-28-52.log] [testng] 00:28:52,027 |-INFO in ch.qos.logback.core.sift.SiftProcessor@44859c38 - End of configuration. [testng] [2024-12-01 00:29:02,466] [pool-1-thread-2] Initializing /data/imagej/hela-cells.zip: [testng] 00:29:02,466 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:29:02,466 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:02,467 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-01_00-29-02.log] [testng] 00:29:02,467 |-INFO in ch.qos.logback.core.sift.SiftProcessor@88b8aa - End of configuration. [testng] [2024-12-01 00:29:28,040] [pool-1-thread-10] Initializing /data/samples/bat-cochlea-volume.zip: [testng] [2024-12-01 00:29:31,824] [pool-1-thread-8] Initializing /data/imagej/Rat_Hippocampal_Neuron2.zip: [testng] [2024-12-01 00:29:41,006] [pool-1-thread-4] Initializing /data/imagej/confocal-stack.zip: [testng] [2024-12-01 00:29:51,418] [pool-1-thread-6] Initializing /data/imagej/scala-media.zip: [testng] [2024-12-01 00:29:54,224] [pool-1-thread-11] Initializing /data/samples/sdub.zip: [testng] [2024-12-01 00:30:06,855] [pool-1-thread-11] Initializing /data/imagej/mri-stack.zip: [testng] [2024-12-01 00:30:12,656] [pool-1-thread-2] Initializing /data/imagej/blood-brain-barrier.zip: [testng] [2024-12-01 00:30:27,202] [pool-1-thread-6] Initializing /data/imagej/watershed-animation.zip: [testng] [2024-12-01 00:30:32,692] [pool-1-thread-12] Initializing /data/imagej/FluorescentCells.zip: [testng] [2024-12-01 00:30:35,073] [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 16 seconds Finished: SUCCESS