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Started by upstream project "BIOFORMATS-test-repo" build number 129 originally caused by: Started by user devspace 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/jenkins6598189789683070675.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_20167_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] 13:53:03,516 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 13:53:03,518 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 13:53:03,518 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 13:53:03,519 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 13:53:03,519 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 13:53:03,519 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 13:53:03,520 |-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] 13:53:03,520 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 13:53:03,520 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 13:53:03,520 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 13:53:03,520 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 13:53:03,521 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 13:53:03,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 13:53:03,770 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 13:53:03,802 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 13:53:03,802 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 13:53:03,813 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 13:53:03,813 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 13:53:03,813 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 13:53:03,814 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 13:53:03,814 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 13:53:03,815 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 13:53:03,815 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 295 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-22 13:53:03,826] [main] java.version = 1.8.0_342 [testng] 13:53:03,830 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 13:53:03,830 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:53:03,890 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-22_13-53-03.log] [testng] 13:53:03,892 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-07-22 13:53:03,894] [main] testng.directory = /data [testng] [2024-07-22 13:53:03,895] [main] testng.configDirectory = /config [testng] [2024-07-22 13:53:03,911] [main] testng.multiplier = 1.0 [testng] [2024-07-22 13:53:03,911] [main] testng.in-memory = false [testng] [2024-07-22 13:53:03,911] [main] testng.allow-missing = false [testng] [2024-07-22 13:53:03,911] [main] user.language = fr [testng] [2024-07-22 13:53:03,911] [main] user.country = FR [testng] [2024-07-22 13:53:03,911] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-07-22 13:53:04,394] [main] ---------------------------------------- [testng] [2024-07-22 13:53:04,395] [main] Total files: 22 [testng] [2024-07-22 13:53:04,395] [main] Scan time: 0.483 s (21 ms/file) [testng] [2024-07-22 13:53:04,395] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 22 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-22 13:53:50,655] [pool-1-thread-1] Initializing /data/imagej/gel-electrophoresis.zip: [testng] 13:53:50,656 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 13:53:50,656 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:53:50,657 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-22_13-53-50.log] [testng] 13:53:50,658 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a46ddda - End of configuration. [testng] [2024-07-22 13:53:52,343] [pool-1-thread-12] Initializing /data/imagej/scala-media.zip: [testng] 13:53:52,343 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 13:53:52,343 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:53:52,344 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-22_13-53-52.log] [testng] 13:53:52,345 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50b207d2 - End of configuration. [testng] [2024-07-22 13:53:52,458] [pool-1-thread-11] Initializing /data/imagej/xrays.zip: [testng] 13:53:52,458 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 13:53:52,458 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:53:52,459 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-22_13-53-52.log] [testng] 13:53:52,459 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7116d13d - End of configuration. [testng] [2024-07-22 13:53:52,574] [pool-1-thread-10] Initializing /data/imagej/RatBrain.zip: [testng] 13:53:52,574 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 13:53:52,574 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:53:52,575 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-22_13-53-52.log] [testng] 13:53:52,575 |-INFO in ch.qos.logback.core.sift.SiftProcessor@30a05f70 - End of configuration. [testng] [2024-07-22 13:53:52,813] [pool-1-thread-9] Initializing /data/imagej/flybrain.zip: [testng] 13:53:52,814 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 13:53:52,814 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:53:52,814 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-22_13-53-52.log] [testng] 13:53:52,815 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e0f403 - End of configuration. [testng] [2024-07-22 13:53:58,075] [pool-1-thread-8] Initializing /data/samples/sdub.zip: [testng] 13:53:58,075 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 13:53:58,075 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:53:58,076 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-22_13-53-58.log] [testng] 13:53:58,076 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5be07624 - End of configuration. [testng] [2024-07-22 13:53:58,625] [pool-1-thread-7] Initializing /data/imagej/fat-cells.zip: [testng] 13:53:58,625 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 13:53:58,625 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:53:58,626 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-22_13-53-58.log] [testng] 13:53:58,627 |-INFO in ch.qos.logback.core.sift.SiftProcessor@49df87b5 - End of configuration. [testng] [2024-07-22 13:54:02,155] [pool-1-thread-6] Initializing /data/imagej/FluorescentCells.zip: [testng] 13:54:02,156 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 13:54:02,156 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:54:02,157 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-22_13-54-02.log] [testng] 13:54:02,157 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7bc6ef9b - End of configuration. [testng] [2024-07-22 13:54:02,417] [pool-1-thread-5] Initializing /data/imagej/Rat_Hippocampal_Neuron2.zip: [testng] 13:54:02,417 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 13:54:02,417 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:54:02,418 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-22_13-54-02.log] [testng] 13:54:02,418 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50452390 - End of configuration. [testng] [2024-07-22 13:54:04,023] [pool-1-thread-4] Initializing /data/imagej/4D-Stack(256x256x20x10).zip: [testng] 13:54:04,023 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 13:54:04,023 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:54:04,024 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-22_13-54-04.log] [testng] 13:54:04,024 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35253f65 - End of configuration. [testng] [2024-07-22 13:54:10,219] [pool-1-thread-3] Initializing /data/imagej/se3.zip: [testng] 13:54:10,219 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 13:54:10,219 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:54:10,220 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-22_13-54-10.log] [testng] 13:54:10,220 |-INFO in ch.qos.logback.core.sift.SiftProcessor@774922d - End of configuration. [testng] [2024-07-22 13:54:14,390] [pool-1-thread-2] Initializing /data/imagej/mri-stack.zip: [testng] 13:54:14,390 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 13:54:14,390 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:54:14,391 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-22_13-54-14.log] [testng] 13:54:14,391 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2128ed53 - End of configuration. [testng] [2024-07-22 13:54:16,844] [pool-1-thread-11] Initializing /data/imagej/Rat_Hippocampal_Neuron.zip: [testng] [2024-07-22 13:54:18,329] [pool-1-thread-12] Initializing /data/imagej/blood-brain-barrier.zip: [testng] [2024-07-22 13:54:28,728] [pool-1-thread-10] Initializing /data/imagej/confocal-stack.zip: [testng] [2024-07-22 13:54:37,993] [pool-1-thread-6] Initializing /data/imagej/hela-cells.zip: [testng] [2024-07-22 13:54:39,076] [pool-1-thread-2] Initializing /data/imagej/watershed-animation.zip: [testng] [2024-07-22 13:54:41,153] [pool-1-thread-2] Initializing /data/imagej/3D_Chromosome.zip: [testng] [2024-07-22 13:54:41,578] [pool-1-thread-8] Initializing /data/imagej/m51.zip: [testng] [2024-07-22 13:54:43,488] [pool-1-thread-8] Initializing /data/imagej/confocal-series.zip: [testng] [2024-07-22 13:54:53,575] [pool-1-thread-2] Initializing /data/samples/bat-cochlea-volume.zip: [testng] [2024-07-22 13:55:09,664] [pool-1-thread-5] Initializing /data/imagej/cheetah_256_8.tif.zip: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1166, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 7 minutes 10 seconds Finished: SUCCESS