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Started by upstream project "BIOFORMATS-test-repo" build number 304 originally caused by: Started by upstream project "Trigger" build number 326 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@7 [BIOFORMATS-test-folder@7] $ /bin/bash -xe /tmp/jenkins9636811256563154072.sh + '[' zip = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_48080_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] 00:42:15,274 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:42:15,276 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 00:42:15,276 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:42:15,277 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:42:15,278 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:42:15,278 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:42:15,279 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:42:15,279 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:42:15,279 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:42:15,280 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:42:15,280 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:42:15,280 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:42:15,461 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:42:15,461 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:42:15,486 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:42:15,486 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:42:15,492 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:42:15,492 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:42:15,492 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:42:15,492 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:42:15,492 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 00:42:15,493 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 00:42:15,493 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 214 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-31 00:42:15,502] [main] java.version = 11.0.16 [testng] 00:42:15,506 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:42:15,506 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:15,550 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-31_00-42-15.log] [testng] 00:42:15,551 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-12-31 00:42:15,553] [main] testng.directory = /data [testng] [2024-12-31 00:42:15,553] [main] testng.configDirectory = /config [testng] [2024-12-31 00:42:15,564] [main] testng.multiplier = 1.0 [testng] [2024-12-31 00:42:15,565] [main] testng.in-memory = false [testng] [2024-12-31 00:42:15,565] [main] testng.allow-missing = false [testng] [2024-12-31 00:42:15,565] [main] user.language = en [testng] [2024-12-31 00:42:15,565] [main] user.country = ${user.country} [testng] [2024-12-31 00:42:15,565] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-31 00:42:16,704] [main] ---------------------------------------- [testng] [2024-12-31 00:42:16,705] [main] Total files: 22 [testng] [2024-12-31 00:42:16,705] [main] Scan time: 1.139 s (51 ms/file) [testng] [2024-12-31 00:42:16,705] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 22 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-31 00:44:55,732] [pool-1-thread-1] Initializing /data/imagej/confocal-series.zip: [testng] 00:44:55,733 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:44:55,733 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:44:55,735 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-31_00-44-55.log] [testng] 00:44:55,735 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b9d3341 - End of configuration. [testng] [2024-12-31 00:45:05,177] [pool-1-thread-12] Initializing /data/imagej/xrays.zip: [testng] 00:45:05,177 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:45:05,178 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:45:05,179 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-31_00-45-05.log] [testng] 00:45:05,180 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12b45d9a - End of configuration. [testng] [2024-12-31 00:45:07,810] [pool-1-thread-11] Initializing /data/imagej/fat-cells.zip: [testng] 00:45:07,810 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:45:07,811 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:45:07,811 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-31_00-45-07.log] [testng] 00:45:07,812 |-INFO in ch.qos.logback.core.sift.SiftProcessor@880b141 - End of configuration. [testng] [2024-12-31 00:45:14,378] [pool-1-thread-10] Initializing /data/imagej/confocal-stack.zip: [testng] 00:45:14,378 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:45:14,378 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:45:14,379 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-31_00-45-14.log] [testng] 00:45:14,379 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35503e90 - End of configuration. [testng] [2024-12-31 00:45:28,018] [pool-1-thread-9] Initializing /data/imagej/Rat_Hippocampal_Neuron.zip: [testng] 00:45:28,018 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:45:28,018 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:45:28,019 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-31_00-45-28.log] [testng] 00:45:28,019 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1919ec54 - End of configuration. [testng] [2024-12-31 00:45:33,577] [pool-1-thread-8] Initializing /data/imagej/m51.zip: [testng] 00:45:33,578 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:45:33,578 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:45:33,578 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-31_00-45-33.log] [testng] 00:45:33,579 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a6fc8dd - End of configuration. [testng] [2024-12-31 00:45:38,139] [pool-1-thread-7] Initializing /data/imagej/cheetah_256_8.tif.zip: [testng] 00:45:38,139 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:45:38,139 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:45:38,140 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-31_00-45-38.log] [testng] 00:45:38,140 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36f276ed - End of configuration. [testng] [2024-12-31 00:45:42,568] [pool-1-thread-6] Initializing /data/imagej/Rat_Hippocampal_Neuron2.zip: [testng] 00:45:42,568 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:45:42,568 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:45:42,569 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-31_00-45-42.log] [testng] 00:45:42,569 |-INFO in ch.qos.logback.core.sift.SiftProcessor@17189322 - End of configuration. [testng] [2024-12-31 00:45:47,856] [pool-1-thread-5] Initializing /data/imagej/flybrain.zip: [testng] 00:45:47,856 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:45:47,857 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:45:47,857 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-31_00-45-47.log] [testng] 00:45:47,857 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e9d855 - End of configuration. [testng] [2024-12-31 00:46:01,992] [pool-1-thread-4] Initializing /data/imagej/RatBrain.zip: [testng] 00:46:01,992 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:46:01,992 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:46:01,993 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-31_00-46-01.log] [testng] 00:46:01,993 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35e646e1 - End of configuration. [testng] [2024-12-31 00:46:05,916] [pool-1-thread-3] Initializing /data/imagej/3D_Chromosome.zip: [testng] 00:46:05,916 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:46:05,916 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:46:05,917 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-31_00-46-05.log] [testng] 00:46:05,917 |-INFO in ch.qos.logback.core.sift.SiftProcessor@124b54a8 - End of configuration. [testng] [2024-12-31 00:46:09,612] [pool-1-thread-2] Initializing /data/imagej/se3.zip: [testng] 00:46:09,612 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:46:09,612 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:46:09,613 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-31_00-46-09.log] [testng] 00:46:09,613 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34408473 - End of configuration. [testng] [2024-12-31 00:47:05,274] [pool-1-thread-8] Initializing /data/samples/sdub.zip: [testng] [2024-12-31 00:47:06,370] [pool-1-thread-12] Initializing /data/imagej/scala-media.zip: [testng] [2024-12-31 00:47:19,574] [pool-1-thread-3] Initializing /data/imagej/watershed-animation.zip: [testng] [2024-12-31 00:47:23,450] [pool-1-thread-4] Initializing /data/imagej/gel-electrophoresis.zip: [testng] [2024-12-31 00:47:33,643] [pool-1-thread-8] Initializing /data/imagej/hela-cells.zip: [testng] [2024-12-31 00:47:38,900] [pool-1-thread-7] Initializing /data/samples/bat-cochlea-volume.zip: [testng] [2024-12-31 00:48:03,271] [pool-1-thread-12] Initializing /data/imagej/FluorescentCells.zip: [testng] [2024-12-31 00:48:15,082] [pool-1-thread-9] Initializing /data/imagej/4D-Stack(256x256x20x10).zip: [testng] [2024-12-31 00:48:27,034] [pool-1-thread-3] Initializing /data/imagej/blood-brain-barrier.zip: [testng] [2024-12-31 00:48:40,080] [pool-1-thread-6] Initializing /data/imagej/mri-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: 11 minutes 0 seconds Finished: SUCCESS