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Started by upstream project "BIOFORMATS-test-repo" build number 225 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@10 [BIOFORMATS-test-folder@10] $ /bin/bash -xe /tmp/jenkins13492683807218577398.sh + '[' zip = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_35453_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 11:18:09,004 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 11:18:09,005 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 11:18:09,005 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:18:09,006 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:18:09,007 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 11:18:09,007 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 11:18:09,007 |-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] 11:18:09,007 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:18:09,008 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:18:09,008 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 11:18:09,009 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 11:18:09,009 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 11:18:09,164 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 11:18:09,164 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 11:18:09,189 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 11:18:09,189 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 11:18:09,195 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 11:18:09,195 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 11:18:09,195 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 11:18:09,196 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 11:18:09,196 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 11:18:09,196 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 11:18:09,197 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 189 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-17 11:18:09,205] [main] java.version = 21 [testng] 11:18:09,208 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 11:18:09,208 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:18:09,249 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-17_11-18-09.log] [testng] 11:18:09,250 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-10-17 11:18:09,252] [main] testng.directory = /data [testng] [2024-10-17 11:18:09,252] [main] testng.configDirectory = /config [testng] [2024-10-17 11:18:09,261] [main] testng.multiplier = 1.0 [testng] [2024-10-17 11:18:09,261] [main] testng.in-memory = false [testng] [2024-10-17 11:18:09,261] [main] testng.allow-missing = false [testng] [2024-10-17 11:18:09,261] [main] user.language = en [testng] [2024-10-17 11:18:09,261] [main] user.country = ${user.country} [testng] [2024-10-17 11:18:09,261] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-17 11:18:09,855] [main] ---------------------------------------- [testng] [2024-10-17 11:18:09,855] [main] Total files: 22 [testng] [2024-10-17 11:18:09,855] [main] Scan time: 0.594 s (27 ms/file) [testng] [2024-10-17 11:18:09,855] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 22 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-17 11:26:58,942] [pool-1-thread-1] Initializing /data/imagej/m51.zip: [testng] 11:26:58,943 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 11:26:58,943 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:26:58,944 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-17_11-26-58.log] [testng] 11:26:58,944 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6460ebb7 - End of configuration. [testng] [2024-10-17 11:27:11,273] [pool-1-thread-12] Initializing /data/imagej/cheetah_256_8.tif.zip: [testng] 11:27:11,273 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 11:27:11,273 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:27:11,274 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-17_11-27-11.log] [testng] 11:27:11,274 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22bea41 - End of configuration. [testng] [2024-10-17 11:27:29,790] [pool-1-thread-11] Initializing /data/imagej/watershed-animation.zip: [testng] 11:27:29,791 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 11:27:29,791 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:27:29,791 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-17_11-27-29.log] [testng] 11:27:29,792 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3324e708 - End of configuration. [testng] [2024-10-17 11:27:53,473] [pool-1-thread-10] Initializing /data/imagej/hela-cells.zip: [testng] 11:27:53,473 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 11:27:53,473 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:27:53,474 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-17_11-27-53.log] [testng] 11:27:53,474 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2734bdb4 - End of configuration. [testng] [2024-10-17 11:28:14,736] [pool-1-thread-9] Initializing /data/imagej/fat-cells.zip: [testng] 11:28:14,736 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 11:28:14,736 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:28:14,737 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-17_11-28-14.log] [testng] 11:28:14,737 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22260f7f - End of configuration. [testng] [2024-10-17 11:28:35,802] [pool-1-thread-8] Initializing /data/samples/bat-cochlea-volume.zip: [testng] 11:28:35,802 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 11:28:35,802 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:28:35,804 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-17_11-28-35.log] [testng] 11:28:35,804 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b33f7f4 - End of configuration. [testng] [2024-10-17 11:28:56,420] [pool-1-thread-7] Initializing /data/imagej/gel-electrophoresis.zip: [testng] 11:28:56,420 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 11:28:56,420 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:28:56,421 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-17_11-28-56.log] [testng] 11:28:56,422 |-INFO in ch.qos.logback.core.sift.SiftProcessor@24a990a9 - End of configuration. [testng] [2024-10-17 11:29:11,387] [pool-1-thread-6] Initializing /data/imagej/blood-brain-barrier.zip: [testng] 11:29:11,387 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 11:29:11,387 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:29:11,388 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-17_11-29-11.log] [testng] 11:29:11,389 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20df9bd1 - End of configuration. [testng] [2024-10-17 11:30:03,701] [pool-1-thread-5] Initializing /data/imagej/scala-media.zip: [testng] 11:30:03,702 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 11:30:03,702 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:30:03,703 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-17_11-30-03.log] [testng] 11:30:03,703 |-INFO in ch.qos.logback.core.sift.SiftProcessor@233264b8 - End of configuration. [testng] [2024-10-17 11:30:19,506] [pool-1-thread-4] Initializing /data/imagej/4D-Stack(256x256x20x10).zip: [testng] 11:30:19,506 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 11:30:19,507 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:30:19,507 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-17_11-30-19.log] [testng] 11:30:19,508 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6718173a - End of configuration. [testng] [2024-10-17 11:30:52,581] [pool-1-thread-3] Initializing /data/imagej/se3.zip: [testng] 11:30:52,582 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 11:30:52,582 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:30:52,583 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-17_11-30-52.log] [testng] 11:30:52,583 |-INFO in ch.qos.logback.core.sift.SiftProcessor@11afd562 - End of configuration. [testng] [2024-10-17 11:31:21,758] [pool-1-thread-2] Initializing /data/imagej/xrays.zip: [testng] 11:31:21,759 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 11:31:21,759 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:31:21,760 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-17_11-31-21.log] [testng] 11:31:21,760 |-INFO in ch.qos.logback.core.sift.SiftProcessor@51b7fbfa - End of configuration. [testng] [2024-10-17 11:34:36,611] [pool-1-thread-1] Initializing /data/samples/sdub.zip: [testng] [2024-10-17 11:34:49,097] [pool-1-thread-2] Initializing /data/imagej/Rat_Hippocampal_Neuron.zip: [testng] [2024-10-17 11:37:06,575] [pool-1-thread-11] Initializing /data/imagej/confocal-series.zip: [testng] [2024-10-17 11:37:43,387] [pool-1-thread-5] Initializing /data/imagej/3D_Chromosome.zip: [testng] [2024-10-17 11:38:34,069] [pool-1-thread-1] Initializing /data/imagej/flybrain.zip: [testng] [2024-10-17 11:39:16,686] [pool-1-thread-7] Initializing /data/imagej/RatBrain.zip: [testng] [2024-10-17 11:39:32,344] [pool-1-thread-12] Initializing /data/imagej/Rat_Hippocampal_Neuron2.zip: [testng] [2024-10-17 11:39:58,323] [pool-1-thread-10] Initializing /data/imagej/mri-stack.zip: [testng] [2024-10-17 11:40:13,632] [pool-1-thread-8] Initializing /data/imagej/FluorescentCells.zip: [testng] [2024-10-17 11:40:57,571] [pool-1-thread-9] 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: 34 minutes 41 seconds Finished: SUCCESS