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Started by upstream project "BIOFORMATS-test-repo" build number 263 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins7800166717645866937.sh + '[' zip = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_41470_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. [javac] 4 warnings test-automated: [testng] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket [testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket [testng] File leak detector installed [testng] 15:32:36,432 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 15:32:36,433 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 15:32:36,433 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 15:32:36,434 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 15:32:36,434 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 15:32:36,435 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 15:32:36,435 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 15:32:36,435 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 15:32:36,436 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 15:32:36,436 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 15:32:36,436 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 15:32:36,437 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 15:32:36,587 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 15:32:36,587 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 15:32:36,610 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 15:32:36,610 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 15:32:36,616 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 15:32:36,616 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 15:32:36,616 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 15:32:36,617 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 15:32:36,617 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 15:32:36,618 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 15:32:36,618 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 182 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-21 15:32:36,626] [main] java.version = 21 [testng] 15:32:36,629 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 15:32:36,629 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:32:36,669 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-21_15-32-36.log] [testng] 15:32:36,670 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-11-21 15:32:36,671] [main] testng.directory = /data [testng] [2024-11-21 15:32:36,672] [main] testng.configDirectory = /config [testng] [2024-11-21 15:32:36,680] [main] testng.multiplier = 1.0 [testng] [2024-11-21 15:32:36,681] [main] testng.in-memory = false [testng] [2024-11-21 15:32:36,681] [main] testng.allow-missing = false [testng] [2024-11-21 15:32:36,681] [main] user.language = en [testng] [2024-11-21 15:32:36,681] [main] user.country = ${user.country} [testng] [2024-11-21 15:32:36,681] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-21 15:32:37,229] [main] ---------------------------------------- [testng] [2024-11-21 15:32:37,229] [main] Total files: 22 [testng] [2024-11-21 15:32:37,230] [main] Scan time: 0.548 s (24 ms/file) [testng] [2024-11-21 15:32:37,230] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 22 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-21 15:35:57,745] [pool-1-thread-1] Initializing /data/imagej/m51.zip: [testng] 15:35:57,746 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 15:35:57,746 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:35:57,747 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-21_15-35-57.log] [testng] 15:35:57,747 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6460ebb7 - End of configuration. [testng] [2024-11-21 15:36:00,645] [pool-1-thread-12] Initializing /data/imagej/cheetah_256_8.tif.zip: [testng] 15:36:00,646 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 15:36:00,646 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:36:00,647 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-21_15-36-00.log] [testng] 15:36:00,647 |-INFO in ch.qos.logback.core.sift.SiftProcessor@790ef9ee - End of configuration. [testng] [2024-11-21 15:36:06,725] [pool-1-thread-11] Initializing /data/imagej/watershed-animation.zip: [testng] 15:36:06,725 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 15:36:06,725 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:36:06,726 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-21_15-36-06.log] [testng] 15:36:06,726 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12e241f9 - End of configuration. [testng] [2024-11-21 15:36:12,657] [pool-1-thread-10] Initializing /data/imagej/hela-cells.zip: [testng] 15:36:12,657 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 15:36:12,657 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:36:12,658 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-21_15-36-12.log] [testng] 15:36:12,658 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38a1d97f - End of configuration. [testng] [2024-11-21 15:36:20,126] [pool-1-thread-9] Initializing /data/imagej/fat-cells.zip: [testng] 15:36:20,126 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 15:36:20,126 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:36:20,126 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-21_15-36-20.log] [testng] 15:36:20,127 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7bd9bf62 - End of configuration. [testng] [2024-11-21 15:36:27,857] [pool-1-thread-8] Initializing /data/samples/bat-cochlea-volume.zip: [testng] 15:36:27,857 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 15:36:27,857 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:36:27,857 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-21_15-36-27.log] [testng] 15:36:27,858 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d1f8608 - End of configuration. [testng] [2024-11-21 15:36:34,777] [pool-1-thread-7] Initializing /data/imagej/gel-electrophoresis.zip: [testng] 15:36:34,778 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 15:36:34,778 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:36:34,778 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-21_15-36-34.log] [testng] 15:36:34,779 |-INFO in ch.qos.logback.core.sift.SiftProcessor@59e87e0e - End of configuration. [testng] [2024-11-21 15:36:40,157] [pool-1-thread-6] Initializing /data/imagej/blood-brain-barrier.zip: [testng] 15:36:40,157 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 15:36:40,157 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:36:40,158 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-21_15-36-40.log] [testng] 15:36:40,158 |-INFO in ch.qos.logback.core.sift.SiftProcessor@24a990a9 - End of configuration. [testng] [2024-11-21 15:36:55,372] [pool-1-thread-5] Initializing /data/imagej/scala-media.zip: [testng] 15:36:55,372 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 15:36:55,372 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:36:55,373 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-21_15-36-55.log] [testng] 15:36:55,373 |-INFO in ch.qos.logback.core.sift.SiftProcessor@233264b8 - End of configuration. [testng] [2024-11-21 15:36:59,009] [pool-1-thread-4] Initializing /data/imagej/4D-Stack(256x256x20x10).zip: [testng] 15:36:59,009 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 15:36:59,009 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:36:59,010 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-21_15-36-59.log] [testng] 15:36:59,010 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6718173a - End of configuration. [testng] [2024-11-21 15:37:13,676] [pool-1-thread-3] Initializing /data/imagej/se3.zip: [testng] 15:37:13,676 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 15:37:13,676 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:37:13,677 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-21_15-37-13.log] [testng] 15:37:13,677 |-INFO in ch.qos.logback.core.sift.SiftProcessor@11afd562 - End of configuration. [testng] [2024-11-21 15:37:24,842] [pool-1-thread-2] Initializing /data/imagej/xrays.zip: [testng] 15:37:24,843 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 15:37:24,843 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:37:24,843 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-21_15-37-24.log] [testng] 15:37:24,844 |-INFO in ch.qos.logback.core.sift.SiftProcessor@51b7fbfa - End of configuration. [testng] [2024-11-21 15:38:09,531] [pool-1-thread-2] Initializing /data/samples/sdub.zip: [testng] [2024-11-21 15:38:10,725] [pool-1-thread-1] Initializing /data/imagej/Rat_Hippocampal_Neuron.zip: [testng] [2024-11-21 15:38:21,379] [pool-1-thread-11] Initializing /data/imagej/confocal-series.zip: [testng] [2024-11-21 15:38:32,027] [pool-1-thread-5] Initializing /data/imagej/3D_Chromosome.zip: [testng] [2024-11-21 15:38:43,623] [pool-1-thread-12] Initializing /data/imagej/flybrain.zip: [testng] [2024-11-21 15:38:58,422] [pool-1-thread-2] Initializing /data/imagej/RatBrain.zip: [testng] [2024-11-21 15:39:14,890] [pool-1-thread-10] Initializing /data/imagej/Rat_Hippocampal_Neuron2.zip: [testng] [2024-11-21 15:39:27,954] [pool-1-thread-8] Initializing /data/imagej/mri-stack.zip: [testng] [2024-11-21 15:39:45,426] [pool-1-thread-7] Initializing /data/imagej/FluorescentCells.zip: [testng] [2024-11-21 15:39:55,336] [pool-1-thread-5] Initializing /data/imagej/confocal-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: 14 minutes 23 seconds Finished: SUCCESS