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Started by upstream project "BIOFORMATS-test-repo" build number 228 originally caused by: Started by upstream project "Trigger" build number 253 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/jenkins796438217947405404.sh + '[' minc = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_35779_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] 02:28:44,331 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:28:44,333 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 02:28:44,333 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:28:44,333 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:28:44,334 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:28:44,334 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:28:44,335 |-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] 02:28:44,335 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:28:44,335 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:28:44,336 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:28:44,336 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:28:44,336 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:28:44,521 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:28:44,521 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:28:44,544 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:28:44,544 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:28:44,550 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:28:44,550 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:28:44,550 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:28:44,550 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:28:44,550 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 02:28:44,551 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 02:28:44,551 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 216 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-19 02:28:44,560] [main] java.version = 11.0.16 [testng] 02:28:44,563 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:28:44,563 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:28:44,606 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-19_02-28-44.log] [testng] 02:28:44,608 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-10-19 02:28:44,610] [main] testng.directory = /data [testng] [2024-10-19 02:28:44,610] [main] testng.configDirectory = /config [testng] [2024-10-19 02:28:44,620] [main] testng.multiplier = 1.0 [testng] [2024-10-19 02:28:44,621] [main] testng.in-memory = false [testng] [2024-10-19 02:28:44,622] [main] testng.allow-missing = false [testng] [2024-10-19 02:28:44,622] [main] user.language = en [testng] [2024-10-19 02:28:44,622] [main] user.country = ${user.country} [testng] [2024-10-19 02:28:44,622] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-19 02:28:45,218] [main] ---------------------------------------- [testng] [2024-10-19 02:28:45,218] [main] Total files: 15 [testng] [2024-10-19 02:28:45,219] [main] Scan time: 0.596 s (39 ms/file) [testng] [2024-10-19 02:28:45,219] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 15 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-19 02:28:57,635] [pool-1-thread-1] Initializing /data/samples/ICBM/icbm_template_6.00mm.mnc: [testng] 02:28:57,636 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:28:57,636 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:28:57,638 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-19_02-28-57.log] [testng] 02:28:57,638 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f1258a0 - End of configuration. [testng] [2024-10-19 02:28:58,014] [pool-1-thread-12] Initializing /data/samples/ICBM/icbm_template_zero.50mm.mnc: [testng] 02:28:58,014 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:28:58,014 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:28:58,015 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-19_02-28-58.log] [testng] 02:28:58,016 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2265455f - End of configuration. [testng] [2024-10-19 02:28:58,495] [pool-1-thread-11] Initializing /data/samples/ICBM/icbm_atlas_cerebellum_avg_53_mask_1mm.mnc: [testng] 02:28:58,495 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:28:58,495 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:28:58,496 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-19_02-28-58.log] [testng] 02:28:58,496 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d55d0f8 - End of configuration. [testng] [2024-10-19 02:28:58,869] [pool-1-thread-10] Initializing /data/samples/ICBM/icbm_template_4.00mm.mnc: [testng] 02:28:58,870 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:28:58,870 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:28:58,870 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-19_02-28-58.log] [testng] 02:28:58,871 |-INFO in ch.qos.logback.core.sift.SiftProcessor@668f85f5 - End of configuration. [testng] [2024-10-19 02:28:59,217] [pool-1-thread-9] Initializing /data/samples/ICBM/icbm_template_one.00mm.mnc: [testng] 02:28:59,217 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:28:59,218 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:28:59,218 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-19_02-28-59.log] [testng] 02:28:59,219 |-INFO in ch.qos.logback.core.sift.SiftProcessor@52363fd4 - End of configuration. [testng] [2024-10-19 02:28:59,749] [pool-1-thread-8] Initializing /data/samples/ICBM/icbm_template_one.50mm.mnc: [testng] 02:28:59,749 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:28:59,750 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:28:59,750 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-19_02-28-59.log] [testng] 02:28:59,751 |-INFO in ch.qos.logback.core.sift.SiftProcessor@342759c1 - End of configuration. [testng] [2024-10-19 02:29:00,071] [pool-1-thread-7] Initializing /data/samples/ICBM/icbm_template_2.00mm.mnc: [testng] 02:29:00,072 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:29:00,072 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:29:00,073 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-19_02-29-00.log] [testng] 02:29:00,073 |-INFO in ch.qos.logback.core.sift.SiftProcessor@306a986 - End of configuration. [testng] [2024-10-19 02:29:00,439] [pool-1-thread-6] Initializing /data/samples/ICBM/icbm_template_zero.75mm.mnc: [testng] 02:29:00,439 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:29:00,439 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:29:00,439 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-19_02-29-00.log] [testng] 02:29:00,440 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18f65f9d - End of configuration. [testng] [2024-10-19 02:29:00,799] [pool-1-thread-5] Initializing /data/bigbrain/pm6479o.mnc: [testng] 02:29:00,799 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:29:00,799 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:29:00,800 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-19_02-29-00.log] [testng] 02:29:00,800 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d99ecf - End of configuration. [testng] [2024-10-19 02:29:01,782] [pool-1-thread-4] Initializing /data/samples/ICBM/icbm_template_3.00mm.mnc: [testng] 02:29:01,782 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:29:01,782 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:29:01,783 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-19_02-29-01.log] [testng] 02:29:01,783 |-INFO in ch.qos.logback.core.sift.SiftProcessor@25df6ff8 - End of configuration. [testng] [2024-10-19 02:29:02,139] [pool-1-thread-3] Initializing /data/qa-17215/IBSR01.mnc: [testng] 02:29:02,139 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:29:02,139 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:29:02,140 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-19_02-29-02.log] [testng] 02:29:02,140 |-INFO in ch.qos.logback.core.sift.SiftProcessor@273496f2 - End of configuration. [testng] [2024-10-19 02:29:02,626] [pool-1-thread-2] Initializing /data/samples/N3/average_305_mask_1mm.mnc: [testng] 02:29:02,626 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:29:02,626 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:29:02,627 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-19_02-29-02.log] [testng] 02:29:02,627 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1cb62117 - End of configuration. BUILD SUCCESSFUL Total time: 47 seconds Finished: SUCCESS