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Started by upstream project "BIOFORMATS-test-repo" build number 260 originally caused by: Started by upstream project "Trigger" build number 284 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins13339505719629946623.sh + '[' nrrd = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_41067_merge_ci -v /uod/idr/repos/curated/nrrd:/data -v /uod/idr-scratch/merge-ci/curated/nrrd:/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] 02:44:55,343 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:44:55,345 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 02:44:55,345 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:44:55,346 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:44:55,347 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:44:55,347 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:44:55,347 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:44:55,347 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:44:55,348 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:44:55,349 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:44:55,349 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:44:55,349 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:44:55,515 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:44:55,515 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:44:55,537 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:44:55,537 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:44:55,543 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:44:55,543 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:44:55,543 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:44:55,543 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:44:55,543 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 02:44:55,544 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 02:44:55,544 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 196 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-19 02:44:55,553] [main] java.version = 11.0.16 [testng] 02:44:55,556 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:44:55,556 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:44:55,598 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-19_02-44-55.log] [testng] 02:44:55,599 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-11-19 02:44:55,601] [main] testng.directory = /data [testng] [2024-11-19 02:44:55,601] [main] testng.configDirectory = /config [testng] [2024-11-19 02:44:55,611] [main] testng.multiplier = 1.0 [testng] [2024-11-19 02:44:55,612] [main] testng.in-memory = false [testng] [2024-11-19 02:44:55,612] [main] testng.allow-missing = false [testng] [2024-11-19 02:44:55,612] [main] user.language = en [testng] [2024-11-19 02:44:55,612] [main] user.country = ${user.country} [testng] [2024-11-19 02:44:55,612] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-19 02:46:43,005] [main] ---------------------------------------- [testng] [2024-11-19 02:46:43,006] [main] Total files: 14 [testng] [2024-11-19 02:46:43,006] [main] Scan time: 107.392 s (7670 ms/file) [testng] [2024-11-19 02:46:43,006] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 10 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-19 02:46:49,112] [pool-1-thread-1] Initializing /data/greg/average-goodbrains-warp40-5_e1e-2.am.nrrd: [testng] 02:46:49,113 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:46:49,113 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:46:49,115 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-19_02-46-49.log] [testng] 02:46:49,115 |-INFO in ch.qos.logback.core.sift.SiftProcessor@54ae3410 - End of configuration. [testng] [2024-11-19 02:46:49,508] [pool-1-thread-10] Initializing /data/public/gordon/dt-helix.nhdr: [testng] 02:46:49,509 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:46:49,509 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:46:49,509 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-19_02-46-49.log] [testng] 02:46:49,510 |-INFO in ch.qos.logback.core.sift.SiftProcessor@605b712d - End of configuration. [testng] [2024-11-19 02:46:49,706] [pool-1-thread-9] Initializing /data/public/gordon/gk2-rcc-mask.nhdr: [testng] 02:46:49,706 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:46:49,706 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:46:49,707 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-19_02-46-49.log] [testng] 02:46:49,707 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79170391 - End of configuration. [testng] [2024-11-19 02:46:49,893] [pool-1-thread-8] Initializing /data/public/glencoe/gzip/dt-helix.nrrd.gz: [testng] 02:46:49,893 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:46:49,893 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:46:49,894 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-19_02-46-49.log] [testng] 02:46:49,894 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50b15497 - End of configuration. [testng] [2024-11-19 02:46:50,320] [pool-1-thread-7] Initializing /data/public/glencoe/version4/dt-helix.nhdr: [testng] 02:46:50,320 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:46:50,320 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:46:50,321 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-19_02-46-50.log] [testng] 02:46:50,322 |-INFO in ch.qos.logback.core.sift.SiftProcessor@141fc1fc - End of configuration. [testng] [2024-11-19 02:46:50,502] [pool-1-thread-6] Initializing /data/greg/average-goodbrains-warp40-5_e1e-2.PIC.gz.nhdr: [testng] 02:46:50,502 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:46:50,502 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:46:50,503 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-19_02-46-50.log] [testng] 02:46:50,503 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7230887c - End of configuration. [testng] [2024-11-19 02:46:50,665] [pool-1-thread-5] Initializing /data/public/midas/01011-dwi.nhdr: [testng] 02:46:50,665 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:46:50,665 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:46:50,666 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-19_02-46-50.log] [testng] 02:46:50,666 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e6cf46b - End of configuration. [testng] [2024-11-19 02:46:50,846] [pool-1-thread-4] Initializing /data/carlos/big4DImage.nrrd: [testng] 02:46:50,846 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:46:50,847 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:46:50,847 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-19_02-46-50.log] [testng] 02:46:50,847 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12b9e56c - End of configuration. [testng] [2024-11-19 02:46:51,057] [pool-1-thread-3] Initializing /data/public/gordon/gk2-rcc-mask2.nhdr: [testng] 02:46:51,057 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:46:51,057 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:46:51,058 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-19_02-46-51.log] [testng] 02:46:51,058 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d585696 - End of configuration. [testng] [2024-11-19 02:46:51,240] [pool-1-thread-2] Initializing /data/greg/average-goodbrains-warp40-5_e1e-2.PIC.nhdr: [testng] 02:46:51,241 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:46:51,241 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:46:51,241 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-19_02-46-51.log] [testng] 02:46:51,242 |-INFO in ch.qos.logback.core.sift.SiftProcessor@240cd427 - End of configuration. [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 530, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 3 minutes 41 seconds Finished: SUCCESS