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Started by user devspace
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder
[BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins13932504504883115922.sh
+ '[' cellomics = slidebook ']'
++ date +%u
+ '[' 3 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_42629_merge_ci -v /uod/idr/repos/curated/cellomics:/data -v /uod/idr-scratch/merge-ci/curated/cellomics:/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] 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] 11:55:33,893 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
   [testng] 11:55:33,894 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service.
   [testng] 11:55:33,894 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
   [testng] 11:55:33,895 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
   [testng] 11:55:33,895 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
   [testng] 11:55:33,896 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
   [testng] 11:55:33,896 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
   [testng] 11:55:33,896 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
   [testng] 11:55:33,896 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
   [testng] 11:55:33,897 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
   [testng] 11:55:33,897 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
   [testng] 11:55:33,897 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
   [testng] 11:55:34,048 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
   [testng] 11:55:34,048 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
   [testng] 11:55:34,068 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
   [testng] 11:55:34,068 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
   [testng] 11:55:34,073 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
   [testng] 11:55:34,073 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
   [testng] 11:55:34,073 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
   [testng] 11:55:34,073 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
   [testng] 11:55:34,073 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration.
   [testng] 11:55:34,074 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point
   [testng] 11:55:34,074 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 178 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
   [testng] [2024-11-27 11:55:34,082] [main] java.version = 17.0.2
   [testng] 11:55:34,085 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
   [testng] 11:55:34,085 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 11:55:34,125 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-27_11-55-34.log]
   [testng] 11:55:34,126 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration.
   [testng] [2024-11-27 11:55:34,127] [main] testng.directory = /data
   [testng] [2024-11-27 11:55:34,128] [main] testng.configDirectory = /config
   [testng] [2024-11-27 11:55:34,136] [main] testng.multiplier = 1.0
   [testng] [2024-11-27 11:55:34,136] [main] testng.in-memory = false
   [testng] [2024-11-27 11:55:34,136] [main] testng.allow-missing = false
   [testng] [2024-11-27 11:55:34,137] [main] user.language = en
   [testng] [2024-11-27 11:55:34,137] [main] user.country = ${user.country}
   [testng] [2024-11-27 11:55:34,137] [main] Maximum heap size = 15360 MB
   [testng] Scanning for files...
   [testng] [2024-11-27 11:55:48,117] [main] ----------------------------------------
   [testng] [2024-11-27 11:55:48,117] [main] Total files: 2539
   [testng] [2024-11-27 11:55:48,117] [main] Scan time: 13.98 s (5 ms/file)
   [testng] [2024-11-27 11:55:48,118] [main] ----------------------------------------
   [testng] Building list of tests...
   [testng] Ready to test 17 files
   [testng] [TestNG] Running:
   [testng]   Bio-Formats software test suite
   [testng] 
   [testng] [2024-11-27 11:55:51,425] [pool-1-thread-1] Initializing /data/samples/sparse-plate/plate_E03f00d0.C01: 
   [testng] 11:55:51,426 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
   [testng] 11:55:51,426 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 11:55:51,427 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-27_11-55-51.log]
   [testng] 11:55:51,427 |-INFO in ch.qos.logback.core.sift.SiftProcessor@365154b8 - End of configuration.
   [testng] [2024-11-27 11:55:51,491] [pool-1-thread-12] Initializing /data/samples/plate-size/plate_B03f00d0.C01: 
   [testng] 11:55:51,491 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
   [testng] 11:55:51,491 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 11:55:51,492 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-27_11-55-51.log]
   [testng] 11:55:51,493 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1c8c8230 - End of configuration.
   [testng] [2024-11-27 11:55:51,549] [pool-1-thread-11] Initializing /data/omar/FB03f03o2.DIB: 
   [testng] 11:55:51,549 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
   [testng] 11:55:51,549 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 11:55:51,550 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-27_11-55-51.log]
   [testng] 11:55:51,550 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78ea91b5 - End of configuration.
   [testng] [2024-11-27 11:55:51,581] [pool-1-thread-10] Initializing /data/omar/FB03f00o2.C01: 
   [testng] 11:55:51,582 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
   [testng] 11:55:51,582 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 11:55:51,582 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-27_11-55-51.log]
   [testng] 11:55:51,583 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e4a8f3b - End of configuration.
   [testng] [2024-11-27 11:55:51,627] [pool-1-thread-9] Initializing /data/qa-7352/test/MFGTMP-PC_130509120002_B02f00o1.C01: 
   [testng] 11:55:51,627 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
   [testng] 11:55:51,628 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 11:55:51,629 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-27_11-55-51.log]
   [testng] 11:55:51,629 |-INFO in ch.qos.logback.core.sift.SiftProcessor@c793665 - End of configuration.
   [testng] [2024-11-27 11:55:51,775] [pool-1-thread-8] Initializing /data/harri/MFGTMP-PC_111018140003/MFGTMP-PC_111018140003_E04f00d0.C01: 
   [testng] 11:55:51,775 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
   [testng] 11:55:51,775 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 11:55:51,782 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-27_11-55-51.log]
   [testng] 11:55:51,783 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6475b136 - End of configuration.
   [testng] [2024-11-27 11:55:51,884] [pool-1-thread-7] Initializing /data/lee/AS_09125_050116030001_D03f00d0.DIB: 
   [testng] 11:55:51,884 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
   [testng] 11:55:51,884 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 11:55:51,885 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-27_11-55-51.log]
   [testng] 11:55:51,885 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5bd4979a - End of configuration.
   [testng] [2024-11-27 11:55:51,918] [pool-1-thread-6] Initializing /data/qa-21720/AS_09125_050117190001_A14f00d0.DIB: 
   [testng] 11:55:51,918 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
   [testng] 11:55:51,918 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 11:55:51,919 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-27_11-55-51.log]
   [testng] 11:55:51,919 |-INFO in ch.qos.logback.core.sift.SiftProcessor@63e0483 - End of configuration.
   [testng] [2024-11-27 11:55:51,950] [pool-1-thread-5] Initializing /data/public/BBBC001/AS_09125_050118150001_A03f00d0.DIB: 
   [testng] 11:55:51,950 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
   [testng] 11:55:51,950 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 11:55:51,951 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-27_11-55-51.log]
   [testng] 11:55:51,951 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6522fb08 - End of configuration.
   [testng] [2024-11-27 11:55:51,994] [pool-1-thread-4] Initializing /data/johannes/MFGTMP_081222130005_E07f00d0.C01: 
   [testng] 11:55:51,995 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
   [testng] 11:55:51,995 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 11:55:51,995 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-27_11-55-51.log]
   [testng] 11:55:51,995 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b529531 - End of configuration.
   [testng] [2024-11-27 11:55:52,047] [pool-1-thread-3] Initializing /data/lee/icd002235_090127090001_a01f00d1.c01: 
   [testng] 11:55:52,048 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
   [testng] 11:55:52,048 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 11:55:52,048 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-27_11-55-52.log]
   [testng] 11:55:52,049 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d6b7360 - End of configuration.
   [testng] [2024-11-27 11:55:52,090] [pool-1-thread-2] Initializing /data/omar/FB03f00d0.C01: 
   [testng] 11:55:52,091 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
   [testng] 11:55:52,091 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 11:55:52,091 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-27_11-55-52.log]
   [testng] 11:55:52,092 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e1e360c - End of configuration.
   [testng] [2024-11-27 11:55:54,287] [pool-1-thread-7] Initializing /data/qa-7352/test/MFGTMP-PC_130509120002_B02f00d0.C01: 
   [testng] [2024-11-27 11:55:54,484] [pool-1-thread-11] Initializing /data/samples/different-field-count/plate_B03f00d0.C01: 
   [testng] [2024-11-27 11:55:55,068] [pool-1-thread-3] Initializing /data/johannes/MFGTMP_081128200001_A02f239d1.C01: 
   [testng] [2024-11-27 11:55:55,202] [pool-1-thread-4] Initializing /data/omar/FB03f00d1.C01: 
   [testng] [2024-11-27 11:55:55,346] [pool-1-thread-10] Initializing /data/omar/FB03f00o1.C01: 
   [testng] 
   [testng] ===============================================
   [testng] Bio-Formats software test suite
   [testng] Total tests run: 901, Failures: 0, Skips: 0
   [testng] ===============================================
   [testng] 

BUILD SUCCESSFUL
Total time: 5 minutes 55 seconds
Finished: SUCCESS