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Started by upstream project "BIOFORMATS-test-repo" build number 4 originally caused by: Started by upstream project "Trigger" build number 5 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@2 [BIOFORMATS-test-folder@2] $ /bin/bash -xe /tmp/jenkins14392370320892421743.sh + '[' zip = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_484_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] 00:22:53,851 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:22:53,852 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 00:22:53,852 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:22:53,853 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:22:53,854 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:22:53,854 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:22:53,854 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:22:53,854 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:22:53,855 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:22:53,855 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:22:53,855 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:22:53,856 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:22:54,040 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:22:54,040 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:22:54,062 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:22:54,062 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:22:54,068 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:22:54,068 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:22:54,069 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:22:54,069 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:22:54,069 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 00:22:54,070 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 00:22:54,070 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 215 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-17 00:22:54,079] [main] java.version = 17.0.2 [testng] 00:22:54,083 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:22:54,083 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:54,129 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-17_00-22-54.log] [testng] 00:22:54,131 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-03-17 00:22:54,133] [main] testng.directory = /data [testng] [2024-03-17 00:22:54,133] [main] testng.configDirectory = /config [testng] [2024-03-17 00:22:54,142] [main] testng.multiplier = 1.0 [testng] [2024-03-17 00:22:54,142] [main] testng.in-memory = false [testng] [2024-03-17 00:22:54,143] [main] testng.allow-missing = false [testng] [2024-03-17 00:22:54,143] [main] user.language = en [testng] [2024-03-17 00:22:54,143] [main] user.country = ${user.country} [testng] [2024-03-17 00:22:54,143] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-03-17 00:22:54,488] [main] ---------------------------------------- [testng] [2024-03-17 00:22:54,488] [main] Total files: 22 [testng] [2024-03-17 00:22:54,488] [main] Scan time: 0.345 s (15 ms/file) [testng] [2024-03-17 00:22:54,488] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 22 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-17 00:24:04,874] [pool-1-thread-1] Initializing /data/imagej/4D-Stack(256x256x20x10).zip: [testng] 00:24:04,875 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:24:04,875 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:24:04,876 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-17_00-24-04.log] [testng] 00:24:04,876 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3714301e - End of configuration. [testng] [2024-03-17 00:24:11,699] [pool-1-thread-12] Initializing /data/imagej/fat-cells.zip: [testng] 00:24:11,699 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:24:11,699 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:24:11,700 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-17_00-24-11.log] [testng] 00:24:11,700 |-INFO in ch.qos.logback.core.sift.SiftProcessor@139e39f9 - End of configuration. [testng] [2024-03-17 00:24:15,455] [pool-1-thread-11] Initializing /data/imagej/FluorescentCells.zip: [testng] 00:24:15,455 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:24:15,455 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:24:15,457 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-17_00-24-15.log] [testng] 00:24:15,457 |-INFO in ch.qos.logback.core.sift.SiftProcessor@72db820e - End of configuration. [testng] [2024-03-17 00:24:16,911] [pool-1-thread-10] Initializing /data/imagej/Rat_Hippocampal_Neuron2.zip: [testng] 00:24:16,911 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:24:16,911 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:24:16,912 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-17_00-24-16.log] [testng] 00:24:16,912 |-INFO in ch.qos.logback.core.sift.SiftProcessor@49b5e6bb - End of configuration. [testng] [2024-03-17 00:24:18,880] [pool-1-thread-9] Initializing /data/imagej/xrays.zip: [testng] 00:24:18,880 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:24:18,880 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:24:18,880 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-17_00-24-18.log] [testng] 00:24:18,881 |-INFO in ch.qos.logback.core.sift.SiftProcessor@481ffd45 - End of configuration. [testng] [2024-03-17 00:24:19,466] [pool-1-thread-8] Initializing /data/imagej/confocal-series.zip: [testng] 00:24:19,467 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:24:19,467 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:24:19,468 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-17_00-24-19.log] [testng] 00:24:19,468 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e883053 - End of configuration. [testng] [2024-03-17 00:24:24,292] [pool-1-thread-7] Initializing /data/imagej/watershed-animation.zip: [testng] 00:24:24,292 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:24:24,292 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:24:24,293 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-17_00-24-24.log] [testng] 00:24:24,293 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c2eaf8f - End of configuration. [testng] [2024-03-17 00:24:25,213] [pool-1-thread-6] Initializing /data/imagej/scala-media.zip: [testng] 00:24:25,213 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:24:25,213 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:24:25,214 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-17_00-24-25.log] [testng] 00:24:25,214 |-INFO in ch.qos.logback.core.sift.SiftProcessor@509f50f - End of configuration. [testng] [2024-03-17 00:24:26,138] [pool-1-thread-5] Initializing /data/imagej/m51.zip: [testng] 00:24:26,138 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:24:26,138 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:24:26,139 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-17_00-24-26.log] [testng] 00:24:26,139 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4644f4c5 - End of configuration. [testng] [2024-03-17 00:24:26,796] [pool-1-thread-4] Initializing /data/imagej/Rat_Hippocampal_Neuron.zip: [testng] 00:24:26,796 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:24:26,796 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:24:26,797 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-17_00-24-26.log] [testng] 00:24:26,797 |-INFO in ch.qos.logback.core.sift.SiftProcessor@487e20d9 - End of configuration. [testng] [2024-03-17 00:24:28,756] [pool-1-thread-3] Initializing /data/imagej/hela-cells.zip: [testng] 00:24:28,756 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:24:28,756 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:24:28,757 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-17_00-24-28.log] [testng] 00:24:28,757 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5076499b - End of configuration. [testng] [2024-03-17 00:24:30,480] [pool-1-thread-2] Initializing /data/samples/bat-cochlea-volume.zip: [testng] 00:24:30,480 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:24:30,480 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:24:30,481 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-17_00-24-30.log] [testng] 00:24:30,481 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75084d66 - End of configuration. [testng] [2024-03-17 00:24:40,546] [pool-1-thread-9] Initializing /data/imagej/RatBrain.zip: [testng] [2024-03-17 00:24:41,542] [pool-1-thread-5] Initializing /data/imagej/flybrain.zip: [testng] [2024-03-17 00:24:47,107] [pool-1-thread-6] Initializing /data/imagej/3D_Chromosome.zip: [testng] [2024-03-17 00:24:48,863] [pool-1-thread-7] Initializing /data/imagej/cheetah_256_8.tif.zip: [testng] [2024-03-17 00:24:52,508] [pool-1-thread-11] Initializing /data/imagej/gel-electrophoresis.zip: [testng] [2024-03-17 00:24:55,984] [pool-1-thread-9] Initializing /data/imagej/se3.zip: [testng] [2024-03-17 00:25:05,078] [pool-1-thread-7] Initializing /data/samples/sdub.zip: [testng] [2024-03-17 00:25:08,054] [pool-1-thread-6] Initializing /data/imagej/blood-brain-barrier.zip: [testng] [2024-03-17 00:25:13,685] [pool-1-thread-3] Initializing /data/imagej/mri-stack.zip: [testng] [2024-03-17 00:25:14,301] [pool-1-thread-2] 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: 6 minutes 42 seconds Finished: SUCCESS