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Started by upstream project "BIOFORMATS-test-repo" build number 2 originally caused by: Started by upstream project "Trigger" build number 3 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/jenkins10068047795855379572.sh + '[' zip = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_156_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 test-automated: [testng] File leak detector installed [testng] 00:22:25,687 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:22:25,688 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 00:22:25,688 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:22:25,689 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:22:25,689 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:22:25,689 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:22:25,690 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:22:25,690 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:22:25,690 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:22:25,690 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:22:25,691 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:22:25,691 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:22:25,904 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:22:25,904 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:22:25,930 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:22:25,931 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:22:25,938 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:22:25,938 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:22:25,938 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:22:25,939 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:22:25,939 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 00:22:25,940 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 00:22:25,940 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 250 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-15 00:22:25,949] [main] java.version = 1.8.0_342 [testng] 00:22:25,952 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:22:25,952 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:26,002 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-15_00-22-25.log] [testng] 00:22:26,004 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-03-15 00:22:26,005] [main] testng.directory = /data [testng] [2024-03-15 00:22:26,006] [main] testng.configDirectory = /config [testng] [2024-03-15 00:22:26,018] [main] testng.multiplier = 1.0 [testng] [2024-03-15 00:22:26,018] [main] testng.in-memory = false [testng] [2024-03-15 00:22:26,018] [main] testng.allow-missing = false [testng] [2024-03-15 00:22:26,018] [main] user.language = en [testng] [2024-03-15 00:22:26,018] [main] user.country = ${user.country} [testng] [2024-03-15 00:22:26,018] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-03-15 00:22:26,417] [main] ---------------------------------------- [testng] [2024-03-15 00:22:26,417] [main] Total files: 22 [testng] [2024-03-15 00:22:26,417] [main] Scan time: 0.399 s (18 ms/file) [testng] [2024-03-15 00:22:26,417] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 22 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-15 00:23:28,136] [pool-1-thread-1] Initializing /data/imagej/3D_Chromosome.zip: [testng] 00:23:28,136 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:23:28,137 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:28,137 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-15_00-23-28.log] [testng] 00:23:28,138 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b931d94 - End of configuration. [testng] [2024-03-15 00:23:28,786] [pool-1-thread-12] Initializing /data/imagej/watershed-animation.zip: [testng] 00:23:28,787 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:23:28,787 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:28,788 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-15_00-23-28.log] [testng] 00:23:28,788 |-INFO in ch.qos.logback.core.sift.SiftProcessor@104cf393 - End of configuration. [testng] [2024-03-15 00:23:29,172] [pool-1-thread-11] Initializing /data/imagej/scala-media.zip: [testng] 00:23:29,172 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:23:29,172 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:29,173 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-15_00-23-29.log] [testng] 00:23:29,173 |-INFO in ch.qos.logback.core.sift.SiftProcessor@354c97a8 - End of configuration. [testng] [2024-03-15 00:23:29,575] [pool-1-thread-10] Initializing /data/imagej/cheetah_256_8.tif.zip: [testng] 00:23:29,575 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:23:29,575 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:29,576 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-15_00-23-29.log] [testng] 00:23:29,576 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6591f60a - End of configuration. [testng] [2024-03-15 00:23:30,163] [pool-1-thread-9] Initializing /data/imagej/mri-stack.zip: [testng] 00:23:30,163 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:23:30,163 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:30,164 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-15_00-23-30.log] [testng] 00:23:30,164 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6989bc3a - End of configuration. [testng] [2024-03-15 00:23:30,653] [pool-1-thread-8] Initializing /data/imagej/blood-brain-barrier.zip: [testng] 00:23:30,653 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:23:30,653 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:30,654 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-15_00-23-30.log] [testng] 00:23:30,654 |-INFO in ch.qos.logback.core.sift.SiftProcessor@33d8d87 - End of configuration. [testng] [2024-03-15 00:23:36,322] [pool-1-thread-7] Initializing /data/imagej/Rat_Hippocampal_Neuron.zip: [testng] 00:23:36,322 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:23:36,322 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:36,323 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-15_00-23-36.log] [testng] 00:23:36,323 |-INFO in ch.qos.logback.core.sift.SiftProcessor@77980339 - End of configuration. [testng] [2024-03-15 00:23:37,690] [pool-1-thread-6] Initializing /data/imagej/m51.zip: [testng] 00:23:37,691 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:23:37,691 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:37,691 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-15_00-23-37.log] [testng] 00:23:37,692 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27335f8e - End of configuration. [testng] [2024-03-15 00:23:37,908] [pool-1-thread-5] Initializing /data/imagej/se3.zip: [testng] 00:23:37,908 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:23:37,908 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:37,909 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-15_00-23-37.log] [testng] 00:23:37,909 |-INFO in ch.qos.logback.core.sift.SiftProcessor@776bd811 - End of configuration. [testng] [2024-03-15 00:23:41,945] [pool-1-thread-4] Initializing /data/imagej/hela-cells.zip: [testng] 00:23:41,945 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:23:41,945 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:41,946 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-15_00-23-41.log] [testng] 00:23:41,946 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2597045a - End of configuration. [testng] [2024-03-15 00:23:42,893] [pool-1-thread-3] Initializing /data/imagej/FluorescentCells.zip: [testng] 00:23:42,894 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:23:42,894 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:42,894 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-15_00-23-42.log] [testng] 00:23:42,895 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2695e169 - End of configuration. [testng] [2024-03-15 00:23:43,219] [pool-1-thread-2] Initializing /data/imagej/4D-Stack(256x256x20x10).zip: [testng] 00:23:43,219 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:23:43,220 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:43,220 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-15_00-23-43.log] [testng] 00:23:43,221 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a3700e5 - End of configuration. [testng] [2024-03-15 00:23:54,689] [pool-1-thread-6] Initializing /data/samples/sdub.zip: [testng] [2024-03-15 00:23:55,284] [pool-1-thread-11] Initializing /data/imagej/gel-electrophoresis.zip: [testng] [2024-03-15 00:23:58,802] [pool-1-thread-12] Initializing /data/imagej/confocal-stack.zip: [testng] [2024-03-15 00:24:08,235] [pool-1-thread-10] Initializing /data/samples/bat-cochlea-volume.zip: [testng] [2024-03-15 00:24:09,966] [pool-1-thread-3] Initializing /data/imagej/RatBrain.zip: [testng] [2024-03-15 00:24:10,614] [pool-1-thread-9] Initializing /data/imagej/fat-cells.zip: [testng] [2024-03-15 00:24:14,784] [pool-1-thread-6] Initializing /data/imagej/flybrain.zip: [testng] [2024-03-15 00:24:20,583] [pool-1-thread-1] Initializing /data/imagej/xrays.zip: [testng] [2024-03-15 00:24:23,762] [pool-1-thread-3] Initializing /data/imagej/Rat_Hippocampal_Neuron2.zip: [testng] [2024-03-15 00:24:25,881] [pool-1-thread-1] 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: 6 minutes 54 seconds Finished: SUCCESS