Started by upstream project "BIOFORMATS-test-repo" build number 86
originally caused by:
Started by upstream project "Trigger" build number 97
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/jenkins13541295019721768799.sh
+ '[' cellomics = slidebook ']'
++ date +%u
+ '[' 6 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_13197_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] 02:16:48,520 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 02:16:48,521 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service.
[testng] 02:16:48,521 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:16:48,522 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:16:48,523 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 02:16:48,523 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 02:16:48,524 |-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] 02:16:48,524 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:16:48,524 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:16:48,525 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 02:16:48,525 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 02:16:48,525 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 02:16:48,698 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 02:16:48,698 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 02:16:48,720 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 02:16:48,720 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 02:16:48,726 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 02:16:48,726 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 02:16:48,726 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 02:16:48,727 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 02:16:48,727 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration.
[testng] 02:16:48,728 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point
[testng] 02:16:48,728 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 204 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-06-08 02:16:48,737] [main] java.version = 11.0.16
[testng] 02:16:48,740 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 02:16:48,741 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:16:48,783 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-08_02-16-48.log]
[testng] 02:16:48,785 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration.
[testng] [2024-06-08 02:16:48,787] [main] testng.directory = /data
[testng] [2024-06-08 02:16:48,787] [main] testng.configDirectory = /config
[testng] [2024-06-08 02:16:48,797] [main] testng.multiplier = 1.0
[testng] [2024-06-08 02:16:48,798] [main] testng.in-memory = false
[testng] [2024-06-08 02:16:48,799] [main] testng.allow-missing = false
[testng] [2024-06-08 02:16:48,799] [main] user.language = en
[testng] [2024-06-08 02:16:48,799] [main] user.country = ${user.country}
[testng] [2024-06-08 02:16:48,799] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-06-08 02:16:58,208] [main] ----------------------------------------
[testng] [2024-06-08 02:16:58,209] [main] Total files: 2539
[testng] [2024-06-08 02:16:58,209] [main] Scan time: 9.409 s (3 ms/file)
[testng] [2024-06-08 02:16:58,209] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 17 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-06-08 02:17:00,444] [pool-1-thread-1] Initializing /data/lee/AS_09125_050116030001_D03f00d0.DIB:
[testng] 02:17:00,445 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 02:17:00,445 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:17:00,447 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-08_02-17-00.log]
[testng] 02:17:00,448 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c5507d2 - End of configuration.
[testng] [2024-06-08 02:17:00,477] [pool-1-thread-12] Initializing /data/public/BBBC001/AS_09125_050118150001_A03f00d0.DIB:
[testng] 02:17:00,477 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 02:17:00,477 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:17:00,478 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-08_02-17-00.log]
[testng] 02:17:00,478 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3bd11776 - End of configuration.
[testng] [2024-06-08 02:17:00,495] [pool-1-thread-11] Initializing /data/omar/FB03f00o1.C01:
[testng] 02:17:00,496 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 02:17:00,496 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:17:00,496 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-08_02-17-00.log]
[testng] 02:17:00,497 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5076499b - End of configuration.
[testng] [2024-06-08 02:17:00,520] [pool-1-thread-10] Initializing /data/omar/FB03f00d0.C01:
[testng] 02:17:00,520 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 02:17:00,520 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:17:00,521 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-08_02-17-00.log]
[testng] 02:17:00,521 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75084d66 - End of configuration.
[testng] [2024-06-08 02:17:00,562] [pool-1-thread-9] Initializing /data/lee/icd002235_090127090001_a01f00d1.c01:
[testng] 02:17:00,562 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 02:17:00,562 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:17:00,563 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-08_02-17-00.log]
[testng] 02:17:00,564 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66bdfd84 - End of configuration.
[testng] [2024-06-08 02:17:00,588] [pool-1-thread-8] Initializing /data/qa-7352/test/MFGTMP-PC_130509120002_B02f00d0.C01:
[testng] 02:17:00,588 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 02:17:00,588 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:17:00,589 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-08_02-17-00.log]
[testng] 02:17:00,589 |-INFO in ch.qos.logback.core.sift.SiftProcessor@316ac66a - End of configuration.
[testng] [2024-06-08 02:17:00,751] [pool-1-thread-7] Initializing /data/omar/FB03f00d1.C01:
[testng] 02:17:00,752 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 02:17:00,752 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:17:00,752 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-08_02-17-00.log]
[testng] 02:17:00,753 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35fe2a4b - End of configuration.
[testng] [2024-06-08 02:17:00,794] [pool-1-thread-6] Initializing /data/johannes/MFGTMP_081128200001_A02f239d1.C01:
[testng] 02:17:00,794 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 02:17:00,794 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:17:00,795 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-08_02-17-00.log]
[testng] 02:17:00,795 |-INFO in ch.qos.logback.core.sift.SiftProcessor@23ce541e - End of configuration.
[testng] [2024-06-08 02:17:00,835] [pool-1-thread-5] Initializing /data/samples/different-field-count/plate_B03f00d0.C01:
[testng] 02:17:00,835 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 02:17:00,835 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:17:00,836 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-08_02-17-00.log]
[testng] 02:17:00,837 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2c1a9a74 - End of configuration.
[testng] [2024-06-08 02:17:00,882] [pool-1-thread-4] Initializing /data/omar/FB03f03o2.DIB:
[testng] 02:17:00,883 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 02:17:00,883 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:17:00,883 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-08_02-17-00.log]
[testng] 02:17:00,884 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6cbcfc18 - End of configuration.
[testng] [2024-06-08 02:17:00,905] [pool-1-thread-3] Initializing /data/samples/plate-size/plate_B03f00d0.C01:
[testng] 02:17:00,905 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 02:17:00,906 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:17:00,906 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-08_02-17-00.log]
[testng] 02:17:00,906 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43767748 - End of configuration.
[testng] [2024-06-08 02:17:00,947] [pool-1-thread-2] Initializing /data/qa-21720/AS_09125_050117190001_A14f00d0.DIB:
[testng] 02:17:00,947 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 02:17:00,947 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:17:00,948 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-08_02-17-00.log]
[testng] 02:17:00,948 |-INFO in ch.qos.logback.core.sift.SiftProcessor@533d5656 - End of configuration.
[testng] [2024-06-08 02:17:02,801] [pool-1-thread-1] Initializing /data/harri/MFGTMP-PC_111018140003/MFGTMP-PC_111018140003_E04f00d0.C01:
[testng] [2024-06-08 02:17:02,880] [pool-1-thread-4] Initializing /data/qa-7352/test/MFGTMP-PC_130509120002_B02f00o1.C01:
[testng] [2024-06-08 02:17:02,955] [pool-1-thread-10] Initializing /data/johannes/MFGTMP_081222130005_E07f00d0.C01:
[testng] [2024-06-08 02:17:02,972] [pool-1-thread-12] Initializing /data/samples/sparse-plate/plate_E03f00d0.C01:
[testng] [2024-06-08 02:17:03,009] [pool-1-thread-7] Initializing /data/omar/FB03f00o2.C01:
[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 20 seconds
Finished: SUCCESS