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Started by upstream project "BIOFORMATS-test-repo" build number 214 originally caused by: Started by upstream project "Trigger" build number 241 originally caused by: Started by user devspace 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/jenkins10646287015091099188.sh + '[' zip = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_33950_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] WARNING: An illegal reflective access operation has occurred [testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket [testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener [testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [testng] WARNING: All illegal access operations will be denied in a future release [testng] File leak detector installed [testng] 08:48:50,320 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 08:48:50,322 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 08:48:50,322 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 08:48:50,323 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 08:48:50,323 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 08:48:50,324 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 08:48:50,324 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 08:48:50,324 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 08:48:50,324 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 08:48:50,325 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 08:48:50,325 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 08:48:50,326 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 08:48:50,488 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 08:48:50,488 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 08:48:50,509 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 08:48:50,510 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 08:48:50,515 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 08:48:50,515 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 08:48:50,515 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 08:48:50,516 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 08:48:50,516 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 08:48:50,516 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 08:48:50,517 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 193 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-08 08:48:50,525] [main] java.version = 11.0.16 [testng] 08:48:50,528 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 08:48:50,528 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:48:50,568 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-08_08-48-50.log] [testng] 08:48:50,570 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-10-08 08:48:50,572] [main] testng.directory = /data [testng] [2024-10-08 08:48:50,572] [main] testng.configDirectory = /config [testng] [2024-10-08 08:48:50,582] [main] testng.multiplier = 1.0 [testng] [2024-10-08 08:48:50,583] [main] testng.in-memory = false [testng] [2024-10-08 08:48:50,583] [main] testng.allow-missing = false [testng] [2024-10-08 08:48:50,583] [main] user.language = en [testng] [2024-10-08 08:48:50,583] [main] user.country = ${user.country} [testng] [2024-10-08 08:48:50,583] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-08 08:48:51,552] [main] ---------------------------------------- [testng] [2024-10-08 08:48:51,553] [main] Total files: 22 [testng] [2024-10-08 08:48:51,553] [main] Scan time: 0.969 s (44 ms/file) [testng] [2024-10-08 08:48:51,553] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 22 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-08 08:51:05,563] [pool-1-thread-1] Initializing /data/imagej/blood-brain-barrier.zip: [testng] 08:51:05,564 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 08:51:05,564 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:51:05,565 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-08_08-51-05.log] [testng] 08:51:05,566 |-INFO in ch.qos.logback.core.sift.SiftProcessor@17d2d1e0 - End of configuration. [testng] [2024-10-08 08:51:17,922] [pool-1-thread-12] Initializing /data/imagej/confocal-series.zip: [testng] 08:51:17,922 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 08:51:17,922 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:51:17,923 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-08_08-51-17.log] [testng] 08:51:17,923 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ef89e71 - End of configuration. [testng] [2024-10-08 08:51:26,977] [pool-1-thread-11] Initializing /data/imagej/m51.zip: [testng] 08:51:26,977 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 08:51:26,977 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:51:26,978 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-08_08-51-26.log] [testng] 08:51:26,978 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4603a93f - End of configuration. [testng] [2024-10-08 08:51:29,483] [pool-1-thread-10] Initializing /data/imagej/xrays.zip: [testng] 08:51:29,484 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 08:51:29,484 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:51:29,484 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-08_08-51-29.log] [testng] 08:51:29,485 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f0afb5 - End of configuration. [testng] [2024-10-08 08:51:31,981] [pool-1-thread-9] Initializing /data/imagej/se3.zip: [testng] 08:51:31,981 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 08:51:31,982 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:51:31,982 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-08_08-51-31.log] [testng] 08:51:31,982 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b2c04b3 - End of configuration. [testng] [2024-10-08 08:51:41,412] [pool-1-thread-8] Initializing /data/imagej/mri-stack.zip: [testng] 08:51:41,413 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 08:51:41,413 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:51:41,414 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-08_08-51-41.log] [testng] 08:51:41,414 |-INFO in ch.qos.logback.core.sift.SiftProcessor@24819205 - End of configuration. [testng] [2024-10-08 08:51:44,605] [pool-1-thread-7] Initializing /data/imagej/RatBrain.zip: [testng] 08:51:44,605 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 08:51:44,605 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:51:44,606 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-08_08-51-44.log] [testng] 08:51:44,606 |-INFO in ch.qos.logback.core.sift.SiftProcessor@28b95d44 - End of configuration. [testng] [2024-10-08 08:51:48,846] [pool-1-thread-6] Initializing /data/imagej/scala-media.zip: [testng] 08:51:48,846 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 08:51:48,846 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:51:48,847 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-08_08-51-48.log] [testng] 08:51:48,847 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4a088d82 - End of configuration. [testng] [2024-10-08 08:51:51,958] [pool-1-thread-5] Initializing /data/imagej/3D_Chromosome.zip: [testng] 08:51:51,958 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 08:51:51,959 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:51:51,959 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-08_08-51-51.log] [testng] 08:51:51,959 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38aad0e - End of configuration. [testng] [2024-10-08 08:51:55,564] [pool-1-thread-4] Initializing /data/imagej/gel-electrophoresis.zip: [testng] 08:51:55,564 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 08:51:55,564 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:51:55,565 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-08_08-51-55.log] [testng] 08:51:55,566 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35e6aa83 - End of configuration. [testng] [2024-10-08 08:51:59,673] [pool-1-thread-3] Initializing /data/imagej/flybrain.zip: [testng] 08:51:59,673 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 08:51:59,673 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:51:59,674 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-08_08-51-59.log] [testng] 08:51:59,674 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56db8742 - End of configuration. [testng] [2024-10-08 08:52:10,041] [pool-1-thread-2] Initializing /data/imagej/hela-cells.zip: [testng] 08:52:10,041 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 08:52:10,041 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:52:10,042 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-08_08-52-10.log] [testng] 08:52:10,043 |-INFO in ch.qos.logback.core.sift.SiftProcessor@372932f4 - End of configuration. [testng] [2024-10-08 08:52:48,202] [pool-1-thread-11] Initializing /data/samples/bat-cochlea-volume.zip: [testng] [2024-10-08 08:52:53,927] [pool-1-thread-10] Initializing /data/imagej/fat-cells.zip: [testng] [2024-10-08 08:53:00,017] [pool-1-thread-6] Initializing /data/imagej/Rat_Hippocampal_Neuron2.zip: [testng] [2024-10-08 08:53:05,648] [pool-1-thread-8] Initializing /data/imagej/cheetah_256_8.tif.zip: [testng] [2024-10-08 08:53:09,746] [pool-1-thread-5] Initializing /data/imagej/FluorescentCells.zip: [testng] [2024-10-08 08:53:13,163] [pool-1-thread-7] Initializing /data/imagej/4D-Stack(256x256x20x10).zip: [testng] [2024-10-08 08:53:49,296] [pool-1-thread-2] Initializing /data/imagej/confocal-stack.zip: [testng] [2024-10-08 08:54:13,964] [pool-1-thread-4] Initializing /data/imagej/watershed-animation.zip: [testng] [2024-10-08 08:54:27,180] [pool-1-thread-5] Initializing /data/samples/sdub.zip: [testng] [2024-10-08 08:54:30,010] [pool-1-thread-8] Initializing /data/imagej/Rat_Hippocampal_Neuron.zip: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1166, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 10 minutes 17 seconds Finished: SUCCESS