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Started by upstream project "BIOFORMATS-test-repo" build number 294 originally caused by: Started by upstream project "Trigger" build number 313 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/jenkins16540352071139776805.sh + '[' zip = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_46429_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] 00:36:48,906 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:36:48,907 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 00:36:48,907 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:36:48,908 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:36:48,909 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:36:48,909 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:36:48,909 |-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] 00:36:48,909 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:36:48,910 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:36:48,911 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:36:48,911 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:36:48,911 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:36:49,087 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:36:49,087 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:36:49,111 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:36:49,112 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:36:49,117 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:36:49,117 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:36:49,117 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:36:49,118 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:36:49,118 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 00:36:49,119 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 00:36:49,119 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 209 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-18 00:36:49,130] [main] java.version = 17.0.2 [testng] 00:36:49,133 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:36:49,133 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:49,181 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-18_00-36-49.log] [testng] 00:36:49,183 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-12-18 00:36:49,185] [main] testng.directory = /data [testng] [2024-12-18 00:36:49,185] [main] testng.configDirectory = /config [testng] [2024-12-18 00:36:49,194] [main] testng.multiplier = 1.0 [testng] [2024-12-18 00:36:49,195] [main] testng.in-memory = false [testng] [2024-12-18 00:36:49,195] [main] testng.allow-missing = false [testng] [2024-12-18 00:36:49,195] [main] user.language = en [testng] [2024-12-18 00:36:49,195] [main] user.country = ${user.country} [testng] [2024-12-18 00:36:49,195] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-18 00:37:01,027] [main] ---------------------------------------- [testng] [2024-12-18 00:37:01,027] [main] Total files: 22 [testng] [2024-12-18 00:37:01,027] [main] Scan time: 11.832 s (537 ms/file) [testng] [2024-12-18 00:37:01,027] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 22 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-18 00:42:49,649] [pool-1-thread-1] Initializing /data/imagej/4D-Stack(256x256x20x10).zip: [testng] 00:42:49,649 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:42:49,649 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:49,651 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-18_00-42-49.log] [testng] 00:42:49,651 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18724774 - End of configuration. [testng] [2024-12-18 00:43:30,590] [pool-1-thread-12] Initializing /data/imagej/fat-cells.zip: [testng] 00:43:30,591 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:43:30,591 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:43:30,591 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-18_00-43-30.log] [testng] 00:43:30,592 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6273f06a - End of configuration. [testng] [2024-12-18 00:43:53,579] [pool-1-thread-11] Initializing /data/imagej/FluorescentCells.zip: [testng] 00:43:53,580 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:43:53,580 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:43:53,580 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-18_00-43-53.log] [testng] 00:43:53,581 |-INFO in ch.qos.logback.core.sift.SiftProcessor@41ac9d44 - End of configuration. [testng] [2024-12-18 00:44:09,529] [pool-1-thread-10] Initializing /data/imagej/Rat_Hippocampal_Neuron2.zip: [testng] 00:44:09,529 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:44:09,529 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:44:09,530 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-18_00-44-09.log] [testng] 00:44:09,530 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e353dd - End of configuration. [testng] [2024-12-18 00:44:23,341] [pool-1-thread-9] Initializing /data/imagej/xrays.zip: [testng] 00:44:23,341 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:44:23,341 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:44:23,342 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-18_00-44-23.log] [testng] 00:44:23,342 |-INFO in ch.qos.logback.core.sift.SiftProcessor@84bc4d2 - End of configuration. [testng] [2024-12-18 00:44:29,927] [pool-1-thread-8] Initializing /data/imagej/confocal-series.zip: [testng] 00:44:29,928 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:44:29,928 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:44:29,928 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-18_00-44-29.log] [testng] 00:44:29,929 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37e05dad - End of configuration. [testng] [2024-12-18 00:44:53,019] [pool-1-thread-7] Initializing /data/imagej/watershed-animation.zip: [testng] 00:44:53,020 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:44:53,020 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:44:53,020 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-18_00-44-53.log] [testng] 00:44:53,021 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5000dd6c - End of configuration. [testng] [2024-12-18 00:45:01,599] [pool-1-thread-6] Initializing /data/imagej/scala-media.zip: [testng] 00:45:01,599 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:45:01,600 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:45:01,600 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-18_00-45-01.log] [testng] 00:45:01,600 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e8cafe4 - End of configuration. [testng] [2024-12-18 00:45:09,335] [pool-1-thread-5] Initializing /data/imagej/m51.zip: [testng] 00:45:09,335 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:45:09,335 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:45:09,336 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-18_00-45-09.log] [testng] 00:45:09,336 |-INFO in ch.qos.logback.core.sift.SiftProcessor@61caa8d7 - End of configuration. [testng] [2024-12-18 00:45:14,538] [pool-1-thread-4] Initializing /data/imagej/Rat_Hippocampal_Neuron.zip: [testng] 00:45:14,538 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:45:14,538 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:45:14,539 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-18_00-45-14.log] [testng] 00:45:14,539 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b531779 - End of configuration. [testng] [2024-12-18 00:45:32,961] [pool-1-thread-3] Initializing /data/imagej/hela-cells.zip: [testng] 00:45:32,961 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:45:32,961 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:45:32,962 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-18_00-45-32.log] [testng] 00:45:32,962 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e8584b3 - End of configuration. [testng] [2024-12-18 00:45:49,113] [pool-1-thread-2] Initializing /data/samples/bat-cochlea-volume.zip: [testng] 00:45:49,113 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:45:49,113 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:45:49,114 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-18_00-45-49.log] [testng] 00:45:49,114 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40215639 - End of configuration. [testng] [2024-12-18 00:48:16,663] [pool-1-thread-9] Initializing /data/imagej/RatBrain.zip: [testng] [2024-12-18 00:48:25,000] [pool-1-thread-5] Initializing /data/imagej/flybrain.zip: [testng] [2024-12-18 00:49:03,419] [pool-1-thread-7] Initializing /data/imagej/3D_Chromosome.zip: [testng] [2024-12-18 00:49:21,175] [pool-1-thread-6] Initializing /data/imagej/cheetah_256_8.tif.zip: [testng] [2024-12-18 00:49:47,814] [pool-1-thread-11] Initializing /data/imagej/gel-electrophoresis.zip: [testng] [2024-12-18 00:50:56,949] [pool-1-thread-3] Initializing /data/imagej/se3.zip: [testng] [2024-12-18 00:52:12,859] [pool-1-thread-12] Initializing /data/samples/sdub.zip: [testng] [2024-12-18 00:52:20,576] [pool-1-thread-2] Initializing /data/imagej/blood-brain-barrier.zip: [testng] [2024-12-18 00:53:09,324] [pool-1-thread-10] Initializing /data/imagej/mri-stack.zip: [testng] [2024-12-18 00:53:25,308] [pool-1-thread-4] 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: 24 minutes 2 seconds Finished: SUCCESS