Skip to content

Console Output

Started by upstream project "BIOFORMATS-test-repo" build number 53
originally caused by:
 Started by upstream project "Trigger" build number 60
 originally caused by:
  Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8
[BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins11660247340896689478.sh
+ '[' cellomics = slidebook ']'
++ date +%u
+ '[' 6 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_7785_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] 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] 02:16:08,378 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
   [testng] 02:16:08,382 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service.
   [testng] 02:16:08,382 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
   [testng] 02:16:08,384 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
   [testng] 02:16:08,385 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
   [testng] 02:16:08,385 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
   [testng] 02:16:08,386 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
   [testng] 02:16:08,386 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
   [testng] 02:16:08,387 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
   [testng] 02:16:08,388 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
   [testng] 02:16:08,389 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
   [testng] 02:16:08,389 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
   [testng] 02:16:08,685 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
   [testng] 02:16:08,686 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
   [testng] 02:16:08,720 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
   [testng] 02:16:08,720 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
   [testng] 02:16:08,727 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
   [testng] 02:16:08,728 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
   [testng] 02:16:08,728 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
   [testng] 02:16:08,728 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
   [testng] 02:16:08,729 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration.
   [testng] 02:16:08,729 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point
   [testng] 02:16:08,730 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 342 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
   [testng] [2024-05-04 02:16:08,740] [main] java.version = 11.0.16
   [testng] 02:16:08,744 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
   [testng] 02:16:08,744 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 02:16:08,793 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-04_02-16-08.log]
   [testng] 02:16:08,795 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration.
   [testng] [2024-05-04 02:16:08,797] [main] testng.directory = /data
   [testng] [2024-05-04 02:16:08,797] [main] testng.configDirectory = /config
   [testng] [2024-05-04 02:16:08,809] [main] testng.multiplier = 1.0
   [testng] [2024-05-04 02:16:08,811] [main] testng.in-memory = false
   [testng] [2024-05-04 02:16:08,811] [main] testng.allow-missing = false
   [testng] [2024-05-04 02:16:08,811] [main] user.language = en
   [testng] [2024-05-04 02:16:08,811] [main] user.country = ${user.country}
   [testng] [2024-05-04 02:16:08,811] [main] Maximum heap size = 15360 MB
   [testng] Scanning for files...
   [testng] [2024-05-04 02:16:18,327] [main] ----------------------------------------
   [testng] [2024-05-04 02:16:18,327] [main] Total files: 2539
   [testng] [2024-05-04 02:16:18,328] [main] Scan time: 9.516 s (3 ms/file)
   [testng] [2024-05-04 02:16:18,328] [main] ----------------------------------------
   [testng] Building list of tests...
   [testng] Ready to test 17 files
   [testng] [TestNG] Running:
   [testng]   Bio-Formats software test suite
   [testng] 
   [testng] [2024-05-04 02:16:20,827] [pool-1-thread-1] Initializing /data/omar/FB03f00d0.C01: 
   [testng] 02:16:20,828 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
   [testng] 02:16:20,828 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 02:16:20,830 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-04_02-16-20.log]
   [testng] 02:16:20,830 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2c8e92a5 - End of configuration.
   [testng] [2024-05-04 02:16:20,872] [pool-1-thread-12] Initializing /data/qa-7352/test/MFGTMP-PC_130509120002_B02f00d0.C01: 
   [testng] 02:16:20,872 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
   [testng] 02:16:20,872 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 02:16:20,873 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-04_02-16-20.log]
   [testng] 02:16:20,874 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b40e4ec - End of configuration.
   [testng] [2024-05-04 02:16:21,037] [pool-1-thread-11] Initializing /data/lee/icd002235_090127090001_a01f00d1.c01: 
   [testng] 02:16:21,038 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
   [testng] 02:16:21,038 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 02:16:21,038 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-04_02-16-21.log]
   [testng] 02:16:21,039 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4917ba06 - End of configuration.
   [testng] [2024-05-04 02:16:21,055] [pool-1-thread-10] Initializing /data/johannes/MFGTMP_081128200001_A02f239d1.C01: 
   [testng] 02:16:21,056 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
   [testng] 02:16:21,056 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 02:16:21,057 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-04_02-16-21.log]
   [testng] 02:16:21,057 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6bbd8a9e - End of configuration.
   [testng] [2024-05-04 02:16:21,089] [pool-1-thread-9] Initializing /data/samples/sparse-plate/plate_E03f00d0.C01: 
   [testng] 02:16:21,090 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
   [testng] 02:16:21,090 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 02:16:21,090 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-04_02-16-21.log]
   [testng] 02:16:21,090 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e21ad8d - End of configuration.
   [testng] [2024-05-04 02:16:21,123] [pool-1-thread-8] Initializing /data/qa-7352/test/MFGTMP-PC_130509120002_B02f00o1.C01: 
   [testng] 02:16:21,123 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
   [testng] 02:16:21,124 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 02:16:21,124 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-04_02-16-21.log]
   [testng] 02:16:21,124 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d3f9a20 - End of configuration.
   [testng] [2024-05-04 02:16:21,240] [pool-1-thread-7] Initializing /data/omar/FB03f00d1.C01: 
   [testng] 02:16:21,240 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
   [testng] 02:16:21,240 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 02:16:21,241 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-04_02-16-21.log]
   [testng] 02:16:21,241 |-INFO in ch.qos.logback.core.sift.SiftProcessor@55f1fee7 - End of configuration.
   [testng] [2024-05-04 02:16:21,293] [pool-1-thread-6] Initializing /data/harri/MFGTMP-PC_111018140003/MFGTMP-PC_111018140003_E04f00d0.C01: 
   [testng] 02:16:21,293 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
   [testng] 02:16:21,293 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 02:16:21,294 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-04_02-16-21.log]
   [testng] 02:16:21,294 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ea509bb - End of configuration.
   [testng] [2024-05-04 02:16:21,415] [pool-1-thread-5] Initializing /data/omar/FB03f00o2.C01: 
   [testng] 02:16:21,415 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
   [testng] 02:16:21,415 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 02:16:21,416 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-04_02-16-21.log]
   [testng] 02:16:21,416 |-INFO in ch.qos.logback.core.sift.SiftProcessor@42fc01b6 - End of configuration.
   [testng] [2024-05-04 02:16:21,434] [pool-1-thread-4] Initializing /data/lee/AS_09125_050116030001_D03f00d0.DIB: 
   [testng] 02:16:21,435 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
   [testng] 02:16:21,435 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 02:16:21,435 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-04_02-16-21.log]
   [testng] 02:16:21,436 |-INFO in ch.qos.logback.core.sift.SiftProcessor@378dfbbd - End of configuration.
   [testng] [2024-05-04 02:16:21,454] [pool-1-thread-3] Initializing /data/qa-21720/AS_09125_050117190001_A14f00d0.DIB: 
   [testng] 02:16:21,454 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
   [testng] 02:16:21,454 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 02:16:21,455 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-04_02-16-21.log]
   [testng] 02:16:21,456 |-INFO in ch.qos.logback.core.sift.SiftProcessor@755533c1 - End of configuration.
   [testng] [2024-05-04 02:16:21,473] [pool-1-thread-2] Initializing /data/omar/FB03f03o2.DIB: 
   [testng] 02:16:21,474 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
   [testng] 02:16:21,474 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 02:16:21,475 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-04_02-16-21.log]
   [testng] 02:16:21,475 |-INFO in ch.qos.logback.core.sift.SiftProcessor@53cc4861 - End of configuration.
   [testng] [2024-05-04 02:16:23,341] [pool-1-thread-4] Initializing /data/johannes/MFGTMP_081222130005_E07f00d0.C01: 
   [testng] [2024-05-04 02:16:23,356] [pool-1-thread-2] Initializing /data/omar/FB03f00o1.C01: 
   [testng] [2024-05-04 02:16:23,375] [pool-1-thread-10] Initializing /data/samples/different-field-count/plate_B03f00d0.C01: 
   [testng] [2024-05-04 02:16:23,414] [pool-1-thread-1] Initializing /data/samples/plate-size/plate_B03f00d0.C01: 
   [testng] [2024-05-04 02:16:23,460] [pool-1-thread-5] Initializing /data/public/BBBC001/AS_09125_050118150001_A03f00d0.DIB: 
   [testng] 
   [testng] ===============================================
   [testng] Bio-Formats software test suite
   [testng] Total tests run: 901, Failures: 0, Skips: 0
   [testng] ===============================================
   [testng] 

BUILD SUCCESSFUL
Total time: 4 minutes 29 seconds
Finished: SUCCESS