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Started by upstream project "BIOFORMATS-test-repo" build number 235 originally caused by: Started by upstream project "Trigger" build number 260 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9 [BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins16382474626470241748.sh + '[' minc = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_36928_merge_ci -v /uod/idr/repos/curated/minc:/data -v /uod/idr-scratch/merge-ci/curated/minc:/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] 02:38:52,178 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:38:52,180 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 02:38:52,180 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:38:52,181 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:38:52,182 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:38:52,182 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:38:52,183 |-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] 02:38:52,183 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:38:52,184 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:38:52,184 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:38:52,185 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:38:52,185 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:38:52,373 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:38:52,373 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:38:52,396 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:38:52,396 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:38:52,402 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:38:52,402 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:38:52,402 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:38:52,402 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:38:52,402 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 02:38:52,403 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 02:38:52,403 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 219 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-26 02:38:52,412] [main] java.version = 11.0.16 [testng] 02:38:52,416 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:38:52,416 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:38:52,458 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-26_02-38-52.log] [testng] 02:38:52,460 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-10-26 02:38:52,462] [main] testng.directory = /data [testng] [2024-10-26 02:38:52,462] [main] testng.configDirectory = /config [testng] [2024-10-26 02:38:52,473] [main] testng.multiplier = 1.0 [testng] [2024-10-26 02:38:52,475] [main] testng.in-memory = false [testng] [2024-10-26 02:38:52,475] [main] testng.allow-missing = false [testng] [2024-10-26 02:38:52,475] [main] user.language = en [testng] [2024-10-26 02:38:52,475] [main] user.country = ${user.country} [testng] [2024-10-26 02:38:52,475] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-26 02:38:53,497] [main] ---------------------------------------- [testng] [2024-10-26 02:38:53,497] [main] Total files: 15 [testng] [2024-10-26 02:38:53,497] [main] Scan time: 1.022 s (68 ms/file) [testng] [2024-10-26 02:38:53,497] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 15 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-26 02:39:06,353] [pool-1-thread-1] Initializing /data/samples/ICBM/icbm_template_6.00mm.mnc: [testng] 02:39:06,354 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:39:06,354 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:39:06,356 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-26_02-39-06.log] [testng] 02:39:06,357 |-INFO in ch.qos.logback.core.sift.SiftProcessor@799f519a - End of configuration. [testng] [2024-10-26 02:39:06,734] [pool-1-thread-12] Initializing /data/samples/ICBM/icbm_template_zero.50mm.mnc: [testng] 02:39:06,734 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:39:06,734 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:39:06,735 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-26_02-39-06.log] [testng] 02:39:06,735 |-INFO in ch.qos.logback.core.sift.SiftProcessor@69a08c7a - End of configuration. [testng] [2024-10-26 02:39:07,226] [pool-1-thread-11] Initializing /data/samples/ICBM/icbm_atlas_cerebellum_avg_53_mask_1mm.mnc: [testng] 02:39:07,226 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:39:07,226 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:39:07,227 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-26_02-39-07.log] [testng] 02:39:07,228 |-INFO in ch.qos.logback.core.sift.SiftProcessor@bd54769 - End of configuration. [testng] [2024-10-26 02:39:07,711] [pool-1-thread-10] Initializing /data/samples/ICBM/icbm_template_4.00mm.mnc: [testng] 02:39:07,711 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:39:07,711 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:39:07,711 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-26_02-39-07.log] [testng] 02:39:07,712 |-INFO in ch.qos.logback.core.sift.SiftProcessor@195bd13f - End of configuration. [testng] [2024-10-26 02:39:08,050] [pool-1-thread-9] Initializing /data/samples/ICBM/icbm_template_one.00mm.mnc: [testng] 02:39:08,050 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:39:08,050 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:39:08,051 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-26_02-39-08.log] [testng] 02:39:08,051 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3379e0c6 - End of configuration. [testng] [2024-10-26 02:39:08,404] [pool-1-thread-8] Initializing /data/samples/ICBM/icbm_template_one.50mm.mnc: [testng] 02:39:08,404 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:39:08,404 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:39:08,405 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-26_02-39-08.log] [testng] 02:39:08,405 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c9d8ea8 - End of configuration. [testng] [2024-10-26 02:39:08,752] [pool-1-thread-7] Initializing /data/samples/ICBM/icbm_template_2.00mm.mnc: [testng] 02:39:08,752 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:39:08,752 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:39:08,753 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-26_02-39-08.log] [testng] 02:39:08,753 |-INFO in ch.qos.logback.core.sift.SiftProcessor@708aa825 - End of configuration. [testng] [2024-10-26 02:39:09,223] [pool-1-thread-6] Initializing /data/samples/ICBM/icbm_template_zero.75mm.mnc: [testng] 02:39:09,223 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:39:09,223 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:39:09,223 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-26_02-39-09.log] [testng] 02:39:09,224 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ff78578 - End of configuration. [testng] [2024-10-26 02:39:09,613] [pool-1-thread-5] Initializing /data/bigbrain/pm6479o.mnc: [testng] 02:39:09,613 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:39:09,613 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:39:09,614 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-26_02-39-09.log] [testng] 02:39:09,614 |-INFO in ch.qos.logback.core.sift.SiftProcessor@259ffa85 - End of configuration. [testng] [2024-10-26 02:39:10,615] [pool-1-thread-4] Initializing /data/samples/ICBM/icbm_template_3.00mm.mnc: [testng] 02:39:10,615 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:39:10,615 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:39:10,616 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-26_02-39-10.log] [testng] 02:39:10,616 |-INFO in ch.qos.logback.core.sift.SiftProcessor@b0589d5 - End of configuration. [testng] [2024-10-26 02:39:11,113] [pool-1-thread-3] Initializing /data/qa-17215/IBSR01.mnc: [testng] 02:39:11,113 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:39:11,113 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:39:11,114 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-26_02-39-11.log] [testng] 02:39:11,114 |-INFO in ch.qos.logback.core.sift.SiftProcessor@632b5381 - End of configuration. [testng] [2024-10-26 02:39:11,600] [pool-1-thread-2] Initializing /data/samples/N3/average_305_mask_1mm.mnc: [testng] 02:39:11,600 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:39:11,600 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:39:11,601 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-26_02-39-11.log] [testng] 02:39:11,601 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b1dc6be - End of configuration. BUILD SUCCESSFUL Total time: 54 seconds Finished: SUCCESS