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Started by upstream project "BIOFORMATS-test-repo" build number 221 originally caused by: Started by upstream project "Trigger" build number 248 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@6 [BIOFORMATS-test-folder@6] $ /bin/bash -xe /tmp/jenkins18271333956291374525.sh + '[' minc = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_35096_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] 05:06:45,645 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 05:06:45,647 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 05:06:45,647 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 05:06:45,648 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 05:06:45,648 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 05:06:45,649 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 05:06:45,649 |-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] 05:06:45,649 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 05:06:45,650 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 05:06:45,651 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 05:06:45,651 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 05:06:45,651 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 05:06:45,828 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 05:06:45,828 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 05:06:45,852 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 05:06:45,852 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 05:06:45,857 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 05:06:45,857 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 05:06:45,858 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 05:06:45,858 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 05:06:45,858 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 05:06:45,859 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 05:06:45,859 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 209 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-15 05:06:45,869] [main] java.version = 11.0.16 [testng] 05:06:45,872 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 05:06:45,872 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:06:45,915 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-15_05-06-45.log] [testng] 05:06:45,917 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-10-15 05:06:45,919] [main] testng.directory = /data [testng] [2024-10-15 05:06:45,919] [main] testng.configDirectory = /config [testng] [2024-10-15 05:06:45,929] [main] testng.multiplier = 1.0 [testng] [2024-10-15 05:06:45,931] [main] testng.in-memory = false [testng] [2024-10-15 05:06:45,931] [main] testng.allow-missing = false [testng] [2024-10-15 05:06:45,931] [main] user.language = en [testng] [2024-10-15 05:06:45,931] [main] user.country = ${user.country} [testng] [2024-10-15 05:06:45,931] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-15 05:06:47,418] [main] ---------------------------------------- [testng] [2024-10-15 05:06:47,419] [main] Total files: 15 [testng] [2024-10-15 05:06:47,419] [main] Scan time: 1.487 s (99 ms/file) [testng] [2024-10-15 05:06:47,419] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 15 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-15 05:07:04,019] [pool-1-thread-1] Initializing /data/samples/ICBM/icbm_template_6.00mm.mnc: [testng] 05:07:04,019 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 05:07:04,020 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:07:04,021 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-15_05-07-04.log] [testng] 05:07:04,022 |-INFO in ch.qos.logback.core.sift.SiftProcessor@212d0bdc - End of configuration. [testng] [2024-10-15 05:07:04,610] [pool-1-thread-12] Initializing /data/samples/ICBM/icbm_template_zero.50mm.mnc: [testng] 05:07:04,610 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 05:07:04,610 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:07:04,611 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-15_05-07-04.log] [testng] 05:07:04,612 |-INFO in ch.qos.logback.core.sift.SiftProcessor@29880d7 - End of configuration. [testng] [2024-10-15 05:07:05,336] [pool-1-thread-11] Initializing /data/samples/ICBM/icbm_atlas_cerebellum_avg_53_mask_1mm.mnc: [testng] 05:07:05,336 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 05:07:05,336 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:07:05,337 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-15_05-07-05.log] [testng] 05:07:05,337 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e368dca - End of configuration. [testng] [2024-10-15 05:07:05,889] [pool-1-thread-10] Initializing /data/samples/ICBM/icbm_template_4.00mm.mnc: [testng] 05:07:05,889 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 05:07:05,889 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:07:05,889 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-15_05-07-05.log] [testng] 05:07:05,890 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3683c75 - End of configuration. [testng] [2024-10-15 05:07:06,340] [pool-1-thread-9] Initializing /data/samples/ICBM/icbm_template_one.00mm.mnc: [testng] 05:07:06,340 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 05:07:06,340 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:07:06,341 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-15_05-07-06.log] [testng] 05:07:06,341 |-INFO in ch.qos.logback.core.sift.SiftProcessor@16be17a8 - End of configuration. [testng] [2024-10-15 05:07:06,915] [pool-1-thread-8] Initializing /data/samples/ICBM/icbm_template_one.50mm.mnc: [testng] 05:07:06,915 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 05:07:06,915 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:07:06,916 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-15_05-07-06.log] [testng] 05:07:06,916 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4314352d - End of configuration. [testng] [2024-10-15 05:07:07,835] [pool-1-thread-7] Initializing /data/samples/ICBM/icbm_template_2.00mm.mnc: [testng] 05:07:07,835 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 05:07:07,835 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:07:07,836 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-15_05-07-07.log] [testng] 05:07:07,836 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4193a0e2 - End of configuration. [testng] [2024-10-15 05:07:08,719] [pool-1-thread-6] Initializing /data/samples/ICBM/icbm_template_zero.75mm.mnc: [testng] 05:07:08,720 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 05:07:08,720 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:07:08,720 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-15_05-07-08.log] [testng] 05:07:08,721 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1fb5311d - End of configuration. [testng] [2024-10-15 05:07:09,310] [pool-1-thread-5] Initializing /data/bigbrain/pm6479o.mnc: [testng] 05:07:09,310 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 05:07:09,310 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:07:09,311 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-15_05-07-09.log] [testng] 05:07:09,311 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2762e327 - End of configuration. [testng] [2024-10-15 05:07:10,926] [pool-1-thread-4] Initializing /data/samples/ICBM/icbm_template_3.00mm.mnc: [testng] 05:07:10,927 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 05:07:10,927 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:07:10,927 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-15_05-07-10.log] [testng] 05:07:10,928 |-INFO in ch.qos.logback.core.sift.SiftProcessor@127c3b52 - End of configuration. [testng] [2024-10-15 05:07:11,582] [pool-1-thread-3] Initializing /data/qa-17215/IBSR01.mnc: [testng] 05:07:11,582 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 05:07:11,582 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:07:11,582 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-15_05-07-11.log] [testng] 05:07:11,583 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5022dafe - End of configuration. [testng] [2024-10-15 05:07:12,433] [pool-1-thread-2] Initializing /data/samples/N3/average_305_mask_1mm.mnc: [testng] 05:07:12,434 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 05:07:12,434 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:07:12,435 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-15_05-07-12.log] [testng] 05:07:12,435 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e6de53b - End of configuration. BUILD SUCCESSFUL Total time: 59 seconds Finished: SUCCESS