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Started by upstream project "BIOFORMATS-test-repo" build number 308 originally caused by: Started by upstream project "Trigger" build number 330 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/jenkins16307284298592061362.sh + '[' zip = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_48740_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] 00:28:39,663 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:28:39,664 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 00:28:39,664 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:28:39,665 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:28:39,666 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:28:39,666 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:28:39,667 |-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] 00:28:39,667 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:28:39,667 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:28:39,668 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:28:39,668 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:28:39,668 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:28:39,850 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:28:39,850 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:28:39,874 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:28:39,874 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:28:39,880 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:28:39,880 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:28:39,880 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:28:39,881 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:28:39,881 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 00:28:39,882 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 00:28:39,882 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 215 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-01-04 00:28:39,891] [main] java.version = 11.0.16 [testng] 00:28:39,894 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:28:39,894 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:28:39,938 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-01-04_00-28-39.log] [testng] 00:28:39,939 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2025-01-04 00:28:39,941] [main] testng.directory = /data [testng] [2025-01-04 00:28:39,942] [main] testng.configDirectory = /config [testng] [2025-01-04 00:28:39,951] [main] testng.multiplier = 1.0 [testng] [2025-01-04 00:28:39,952] [main] testng.in-memory = false [testng] [2025-01-04 00:28:39,953] [main] testng.allow-missing = false [testng] [2025-01-04 00:28:39,953] [main] user.language = en [testng] [2025-01-04 00:28:39,953] [main] user.country = ${user.country} [testng] [2025-01-04 00:28:39,953] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-01-04 00:28:40,582] [main] ---------------------------------------- [testng] [2025-01-04 00:28:40,583] [main] Total files: 22 [testng] [2025-01-04 00:28:40,583] [main] Scan time: 0.629 s (28 ms/file) [testng] [2025-01-04 00:28:40,583] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 22 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-01-04 00:30:37,447] [pool-1-thread-1] Initializing /data/imagej/confocal-series.zip: [testng] 00:30:37,448 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:30:37,448 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:37,450 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-01-04_00-30-37.log] [testng] 00:30:37,450 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6978fffb - End of configuration. [testng] [2025-01-04 00:30:45,119] [pool-1-thread-12] Initializing /data/imagej/xrays.zip: [testng] 00:30:45,120 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:30:45,120 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:45,121 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-01-04_00-30-45.log] [testng] 00:30:45,121 |-INFO in ch.qos.logback.core.sift.SiftProcessor@240c3835 - End of configuration. [testng] [2025-01-04 00:30:46,796] [pool-1-thread-11] Initializing /data/imagej/fat-cells.zip: [testng] 00:30:46,796 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:30:46,796 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:46,797 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-01-04_00-30-46.log] [testng] 00:30:46,797 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35503e90 - End of configuration. [testng] [2025-01-04 00:30:52,124] [pool-1-thread-10] Initializing /data/imagej/confocal-stack.zip: [testng] 00:30:52,125 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:30:52,125 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:52,125 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-01-04_00-30-52.log] [testng] 00:30:52,126 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14a5bd6b - End of configuration. [testng] [2025-01-04 00:31:07,068] [pool-1-thread-9] Initializing /data/imagej/Rat_Hippocampal_Neuron.zip: [testng] 00:31:07,068 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:31:07,068 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:31:07,069 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-01-04_00-31-07.log] [testng] 00:31:07,070 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a7a40ff - End of configuration. [testng] [2025-01-04 00:31:11,171] [pool-1-thread-8] Initializing /data/imagej/m51.zip: [testng] 00:31:11,171 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:31:11,171 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:31:11,171 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-01-04_00-31-11.log] [testng] 00:31:11,172 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56c0c053 - End of configuration. [testng] [2025-01-04 00:31:12,875] [pool-1-thread-7] Initializing /data/imagej/cheetah_256_8.tif.zip: [testng] 00:31:12,875 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:31:12,875 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:31:12,876 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-01-04_00-31-12.log] [testng] 00:31:12,876 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e77f532 - End of configuration. [testng] [2025-01-04 00:31:17,099] [pool-1-thread-6] Initializing /data/imagej/Rat_Hippocampal_Neuron2.zip: [testng] 00:31:17,099 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:31:17,100 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:31:17,100 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-01-04_00-31-17.log] [testng] 00:31:17,101 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6fa03425 - End of configuration. [testng] [2025-01-04 00:31:21,545] [pool-1-thread-5] Initializing /data/imagej/flybrain.zip: [testng] 00:31:21,545 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:31:21,545 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:31:21,546 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-01-04_00-31-21.log] [testng] 00:31:21,546 |-INFO in ch.qos.logback.core.sift.SiftProcessor@24b82369 - End of configuration. [testng] [2025-01-04 00:31:30,827] [pool-1-thread-4] Initializing /data/imagej/RatBrain.zip: [testng] 00:31:30,827 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:31:30,827 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:31:30,828 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-01-04_00-31-30.log] [testng] 00:31:30,828 |-INFO in ch.qos.logback.core.sift.SiftProcessor@185dbddc - End of configuration. [testng] [2025-01-04 00:31:34,834] [pool-1-thread-3] Initializing /data/imagej/3D_Chromosome.zip: [testng] 00:31:34,834 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:31:34,835 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:31:34,836 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-01-04_00-31-34.log] [testng] 00:31:34,836 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e27117c - End of configuration. [testng] [2025-01-04 00:31:37,405] [pool-1-thread-2] Initializing /data/imagej/se3.zip: [testng] 00:31:37,405 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:31:37,405 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:31:37,406 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-01-04_00-31-37.log] [testng] 00:31:37,406 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7bea5deb - End of configuration. [testng] [2025-01-04 00:32:14,107] [pool-1-thread-8] Initializing /data/samples/sdub.zip: [testng] [2025-01-04 00:32:14,956] [pool-1-thread-12] Initializing /data/imagej/scala-media.zip: [testng] [2025-01-04 00:32:24,682] [pool-1-thread-4] Initializing /data/imagej/watershed-animation.zip: [testng] [2025-01-04 00:32:27,660] [pool-1-thread-3] Initializing /data/imagej/gel-electrophoresis.zip: [testng] [2025-01-04 00:32:33,590] [pool-1-thread-7] Initializing /data/imagej/hela-cells.zip: [testng] [2025-01-04 00:32:44,736] [pool-1-thread-8] Initializing /data/samples/bat-cochlea-volume.zip: [testng] [2025-01-04 00:32:56,557] [pool-1-thread-12] Initializing /data/imagej/FluorescentCells.zip: [testng] [2025-01-04 00:33:01,670] [pool-1-thread-4] Initializing /data/imagej/4D-Stack(256x256x20x10).zip: [testng] [2025-01-04 00:33:13,874] [pool-1-thread-9] Initializing /data/imagej/blood-brain-barrier.zip: [testng] [2025-01-04 00:33:22,465] [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: 8 minutes 45 seconds Finished: SUCCESS