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Started by upstream project "BIOFORMATS-test-repo" build number 259 originally caused by: Started by upstream project "Trigger" build number 283 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5 [BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins8622994555003237540.sh + '[' zip = slidebook ']' ++ date +%u + '[' 1 -le 1 ']' + DOCKER_ARGS='-Dtestng.memory=15g -Dtestng.threadCount=12 -Duser.language=fr -Duser.country=FR' + sudo docker run --rm --name BIOFORMATS-test-folder_40814_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 -Duser.language=fr -Duser.country=FR 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] 00:27:35,335 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:27:35,337 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 00:27:35,338 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:27:35,339 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:27:35,339 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:27:35,339 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:27:35,339 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:27:35,339 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:27:35,340 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:27:35,340 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:27:35,340 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:27:35,341 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:27:35,584 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:27:35,584 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:27:35,612 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:27:35,612 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:27:35,620 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:27:35,620 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:27:35,620 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:27:35,621 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:27:35,621 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 00:27:35,622 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 00:27:35,622 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 282 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-18 00:27:35,632] [main] java.version = 1.8.0_342 [testng] 00:27:35,635 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:27:35,635 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:35,680 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-18_00-27-35.log] [testng] 00:27:35,682 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-11-18 00:27:35,684] [main] testng.directory = /data [testng] [2024-11-18 00:27:35,684] [main] testng.configDirectory = /config [testng] [2024-11-18 00:27:35,695] [main] testng.multiplier = 1.0 [testng] [2024-11-18 00:27:35,696] [main] testng.in-memory = false [testng] [2024-11-18 00:27:35,696] [main] testng.allow-missing = false [testng] [2024-11-18 00:27:35,696] [main] user.language = fr [testng] [2024-11-18 00:27:35,696] [main] user.country = FR [testng] [2024-11-18 00:27:35,696] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-11-18 00:27:36,320] [main] ---------------------------------------- [testng] [2024-11-18 00:27:36,320] [main] Total files: 22 [testng] [2024-11-18 00:27:36,320] [main] Scan time: 0.624 s (28 ms/file) [testng] [2024-11-18 00:27:36,320] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 22 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-18 00:29:27,119] [pool-1-thread-1] Initializing /data/samples/sdub.zip: [testng] 00:29:27,120 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:29:27,120 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:27,121 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-18_00-29-27.log] [testng] 00:29:27,121 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3aec143a - End of configuration. [testng] [2024-11-18 00:29:28,580] [pool-1-thread-12] Initializing /data/imagej/mri-stack.zip: [testng] 00:29:28,581 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:29:28,581 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:28,582 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-18_00-29-28.log] [testng] 00:29:28,582 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b20de5e - End of configuration. [testng] [2024-11-18 00:29:33,810] [pool-1-thread-11] Initializing /data/imagej/hela-cells.zip: [testng] 00:29:33,810 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:29:33,810 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:33,811 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-18_00-29-33.log] [testng] 00:29:33,811 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c2cae6a - End of configuration. [testng] [2024-11-18 00:29:37,240] [pool-1-thread-10] Initializing /data/imagej/watershed-animation.zip: [testng] 00:29:37,240 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:29:37,241 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:37,241 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-18_00-29-37.log] [testng] 00:29:37,242 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36dc19ae - End of configuration. [testng] [2024-11-18 00:29:39,623] [pool-1-thread-9] Initializing /data/imagej/4D-Stack(256x256x20x10).zip: [testng] 00:29:39,624 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:29:39,624 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:39,624 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-18_00-29-39.log] [testng] 00:29:39,624 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1fe2283 - End of configuration. [testng] [2024-11-18 00:29:51,361] [pool-1-thread-8] Initializing /data/imagej/gel-electrophoresis.zip: [testng] 00:29:51,361 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:29:51,361 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:51,361 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-18_00-29-51.log] [testng] 00:29:51,362 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1eed4bea - End of configuration. [testng] [2024-11-18 00:29:54,900] [pool-1-thread-7] Initializing /data/imagej/cheetah_256_8.tif.zip: [testng] 00:29:54,900 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:29:54,900 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:54,901 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-18_00-29-54.log] [testng] 00:29:54,901 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14d012fc - End of configuration. [testng] [2024-11-18 00:29:57,839] [pool-1-thread-6] Initializing /data/imagej/xrays.zip: [testng] 00:29:57,839 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:29:57,839 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:57,840 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-18_00-29-57.log] [testng] 00:29:57,840 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76866051 - End of configuration. [testng] [2024-11-18 00:29:59,544] [pool-1-thread-5] Initializing /data/imagej/confocal-stack.zip: [testng] 00:29:59,544 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:29:59,544 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:59,545 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-18_00-29-59.log] [testng] 00:29:59,545 |-INFO in ch.qos.logback.core.sift.SiftProcessor@295e6498 - End of configuration. [testng] [2024-11-18 00:30:11,570] [pool-1-thread-4] Initializing /data/imagej/FluorescentCells.zip: [testng] 00:30:11,571 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:30:11,571 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:11,572 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-18_00-30-11.log] [testng] 00:30:11,572 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d88a41f - End of configuration. [testng] [2024-11-18 00:30:13,978] [pool-1-thread-3] Initializing /data/imagej/fat-cells.zip: [testng] 00:30:13,978 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:30:13,978 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:13,978 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-18_00-30-13.log] [testng] 00:30:13,979 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36ed5905 - End of configuration. [testng] [2024-11-18 00:30:18,373] [pool-1-thread-2] Initializing /data/imagej/Rat_Hippocampal_Neuron2.zip: [testng] 00:30:18,374 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:30:18,374 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:18,375 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-18_00-30-18.log] [testng] 00:30:18,376 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f4cbd34 - End of configuration. [testng] [2024-11-18 00:30:36,389] [pool-1-thread-1] Initializing /data/imagej/se3.zip: [testng] [2024-11-18 00:30:52,331] [pool-1-thread-6] Initializing /data/imagej/RatBrain.zip: [testng] [2024-11-18 00:30:57,111] [pool-1-thread-10] Initializing /data/imagej/blood-brain-barrier.zip: [testng] [2024-11-18 00:31:11,447] [pool-1-thread-12] Initializing /data/imagej/Rat_Hippocampal_Neuron.zip: [testng] [2024-11-18 00:31:15,660] [pool-1-thread-7] Initializing /data/imagej/scala-media.zip: [testng] [2024-11-18 00:31:17,781] [pool-1-thread-4] Initializing /data/imagej/confocal-series.zip: [testng] [2024-11-18 00:31:37,762] [pool-1-thread-11] Initializing /data/imagej/3D_Chromosome.zip: [testng] [2024-11-18 00:31:41,830] [pool-1-thread-6] Initializing /data/imagej/flybrain.zip: [testng] [2024-11-18 00:31:50,428] [pool-1-thread-2] Initializing /data/imagej/m51.zip: [testng] [2024-11-18 00:31:53,753] [pool-1-thread-7] Initializing /data/samples/bat-cochlea-volume.zip: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1166, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 8 minutes 46 seconds Finished: SUCCESS