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Started by upstream project "BIOFORMATS-test-repo" build number 7 originally caused by: Started by upstream project "Trigger" build number 10 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/jenkins6406233351834983636.sh + '[' minc = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_1026_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. [javac] 4 warnings test-automated: [testng] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket [testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket [testng] File leak detector installed [testng] 00:54:50,412 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:54:50,413 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 00:54:50,413 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:54:50,414 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:54:50,415 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:54:50,415 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:54:50,415 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:54:50,415 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:54:50,416 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:54:50,416 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:54:50,417 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:54:50,417 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:54:50,594 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:54:50,594 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:54:50,621 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:54:50,621 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:54:50,628 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:54:50,628 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:54:50,628 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:54:50,629 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:54:50,629 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 00:54:50,630 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 00:54:50,630 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 214 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-21 00:54:50,639] [main] java.version = 21 [testng] 00:54:50,643 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:54:50,643 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:54:50,687 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-21_00-54-50.log] [testng] 00:54:50,688 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-03-21 00:54:50,690] [main] testng.directory = /data [testng] [2024-03-21 00:54:50,690] [main] testng.configDirectory = /config [testng] [2024-03-21 00:54:50,700] [main] testng.multiplier = 1.0 [testng] [2024-03-21 00:54:50,701] [main] testng.in-memory = false [testng] [2024-03-21 00:54:50,701] [main] testng.allow-missing = false [testng] [2024-03-21 00:54:50,701] [main] user.language = en [testng] [2024-03-21 00:54:50,701] [main] user.country = ${user.country} [testng] [2024-03-21 00:54:50,701] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-03-21 00:54:51,103] [main] ---------------------------------------- [testng] [2024-03-21 00:54:51,103] [main] Total files: 15 [testng] [2024-03-21 00:54:51,103] [main] Scan time: 0.401 s (26 ms/file) [testng] [2024-03-21 00:54:51,104] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 15 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-21 00:55:01,510] [pool-1-thread-1] Initializing /data/samples/ICBM/icbm_template_3.00mm.mnc: [testng] 00:55:01,511 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:55:01,511 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:01,513 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-21_00-55-01.log] [testng] 00:55:01,514 |-INFO in ch.qos.logback.core.sift.SiftProcessor@729db567 - End of configuration. [testng] [2024-03-21 00:55:01,567] [pool-1-thread-12] Initializing /data/samples/ICBM/icbm_template_6.00mm.mnc: [testng] 00:55:01,567 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:55:01,567 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:01,568 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-21_00-55-01.log] [testng] 00:55:01,569 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5724c9e9 - End of configuration. [testng] [2024-03-21 00:55:01,600] [pool-1-thread-11] Initializing /data/bigbrain/pm6479o.mnc: [testng] 00:55:01,600 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:55:01,600 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:01,601 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-21_00-55-01.log] [testng] 00:55:01,602 |-INFO in ch.qos.logback.core.sift.SiftProcessor@53a2efb8 - End of configuration. [testng] [2024-03-21 00:55:02,319] [pool-1-thread-10] Initializing /data/samples/N3/average_305_mask_1mm.mnc: [testng] 00:55:02,319 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:55:02,319 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:02,320 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-21_00-55-02.log] [testng] 00:55:02,321 |-INFO in ch.qos.logback.core.sift.SiftProcessor@347f05e6 - End of configuration. [testng] [2024-03-21 00:55:02,416] [pool-1-thread-9] Initializing /data/qa-17215/IBSR01.mnc: [testng] 00:55:02,417 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:55:02,417 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:02,418 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-21_00-55-02.log] [testng] 00:55:02,418 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75045dc1 - End of configuration. [testng] [2024-03-21 00:55:02,590] [pool-1-thread-8] Initializing /data/samples/ICBM/icbm_template_2.00mm.mnc: [testng] 00:55:02,590 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:55:02,590 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:02,592 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-21_00-55-02.log] [testng] 00:55:02,592 |-INFO in ch.qos.logback.core.sift.SiftProcessor@52aecc65 - End of configuration. [testng] [2024-03-21 00:55:02,617] [pool-1-thread-7] Initializing /data/bigbrain/full16_400um_2009b_sym.mnc: [testng] 00:55:02,617 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:55:02,617 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:02,618 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-21_00-55-02.log] [testng] 00:55:02,618 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21db6e1d - End of configuration. [testng] [2024-03-21 00:55:04,750] [pool-1-thread-6] Initializing /data/samples/ICBM/icbm_template_one.00mm.mnc: [testng] 00:55:04,750 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:55:04,750 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:04,751 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-21_00-55-04.log] [testng] 00:55:04,752 |-INFO in ch.qos.logback.core.sift.SiftProcessor@488940c - End of configuration. [testng] [2024-03-21 00:55:04,778] [pool-1-thread-5] Initializing /data/samples/ICBM/icbm_template_zero.50mm.mnc: [testng] 00:55:04,778 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:55:04,778 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:04,779 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-21_00-55-04.log] [testng] 00:55:04,779 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8752ccd - End of configuration. [testng] [2024-03-21 00:55:04,876] [pool-1-thread-4] Initializing /data/samples/ICBM/icbm_template_4.00mm.mnc: [testng] 00:55:04,877 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:55:04,877 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:04,877 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-21_00-55-04.log] [testng] 00:55:04,878 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10368886 - End of configuration. [testng] [2024-03-21 00:55:04,890] [pool-1-thread-3] Initializing /data/samples/ICBM/icbm_atlas_cerebellum_avg_53_mask_1mm.mnc: [testng] 00:55:04,890 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:55:04,890 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:04,891 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-21_00-55-04.log] [testng] 00:55:04,891 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5213f438 - End of configuration. [testng] [2024-03-21 00:55:04,928] [pool-1-thread-2] Initializing /data/samples/ICBM/icbm_template_zero.75mm.mnc: [testng] 00:55:04,929 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:55:04,929 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:04,930 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-21_00-55-04.log] [testng] 00:55:04,930 |-INFO in ch.qos.logback.core.sift.SiftProcessor@29c692b1 - End of configuration. BUILD SUCCESSFUL Total time: 33 seconds Finished: SUCCESS