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Started by upstream project "BIOFORMATS-test-repo" build number 3 originally caused by: Started by upstream project "Trigger" build number 4 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/jenkins4061565436252027587.sh + '[' cellomics = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_402_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] 01:31:30,454 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:31:30,456 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 01:31:30,456 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:31:30,457 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:31:30,457 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:31:30,457 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:31:30,458 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:31:30,458 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:31:30,458 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:31:30,459 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:31:30,459 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:31:30,459 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:31:30,631 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:31:30,631 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:31:30,652 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:31:30,653 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:31:30,658 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:31:30,658 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:31:30,658 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:31:30,659 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:31:30,659 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 01:31:30,660 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 01:31:30,660 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 202 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-16 01:31:30,669] [main] java.version = 11.0.16 [testng] 01:31:30,672 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:31:30,672 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:31:30,714 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-16_01-31-30.log] [testng] 01:31:30,716 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-03-16 01:31:30,718] [main] testng.directory = /data [testng] [2024-03-16 01:31:30,718] [main] testng.configDirectory = /config [testng] [2024-03-16 01:31:30,728] [main] testng.multiplier = 1.0 [testng] [2024-03-16 01:31:30,729] [main] testng.in-memory = false [testng] [2024-03-16 01:31:30,730] [main] testng.allow-missing = false [testng] [2024-03-16 01:31:30,730] [main] user.language = en [testng] [2024-03-16 01:31:30,730] [main] user.country = ${user.country} [testng] [2024-03-16 01:31:30,730] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-03-16 01:31:46,180] [main] ---------------------------------------- [testng] [2024-03-16 01:31:46,181] [main] Total files: 2539 [testng] [2024-03-16 01:31:46,181] [main] Scan time: 15.45 s (6 ms/file) [testng] [2024-03-16 01:31:46,181] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-16 01:31:56,904] [pool-1-thread-1] Initializing /data/lee/AS_09125_050116030001_D03f00d0.DIB: [testng] 01:31:56,905 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:31:56,905 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:31:56,907 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-16_01-31-56.log] [testng] 01:31:56,908 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7145957c - End of configuration. [testng] [2024-03-16 01:31:57,080] [pool-1-thread-12] Initializing /data/public/BBBC001/AS_09125_050118150001_A03f00d0.DIB: [testng] 01:31:57,080 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:31:57,080 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:31:57,081 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-16_01-31-57.log] [testng] 01:31:57,081 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d1eaea3 - End of configuration. [testng] [2024-03-16 01:31:57,206] [pool-1-thread-11] Initializing /data/omar/FB03f00o1.C01: [testng] 01:31:57,206 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:31:57,206 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:31:57,207 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-16_01-31-57.log] [testng] 01:31:57,208 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10ddc54a - End of configuration. [testng] [2024-03-16 01:31:57,340] [pool-1-thread-10] Initializing /data/omar/FB03f00d0.C01: [testng] 01:31:57,340 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:31:57,340 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:31:57,340 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-16_01-31-57.log] [testng] 01:31:57,341 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6bfbb9e1 - End of configuration. [testng] [2024-03-16 01:31:57,468] [pool-1-thread-9] Initializing /data/lee/icd002235_090127090001_a01f00d1.c01: [testng] 01:31:57,468 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:31:57,468 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:31:57,468 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-16_01-31-57.log] [testng] 01:31:57,469 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56f83690 - End of configuration. [testng] [2024-03-16 01:31:57,624] [pool-1-thread-8] Initializing /data/qa-7352/test/MFGTMP-PC_130509120002_B02f00d0.C01: [testng] 01:31:57,624 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:31:57,624 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:31:57,625 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-16_01-31-57.log] [testng] 01:31:57,626 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1cb74978 - End of configuration. [testng] [2024-03-16 01:31:57,890] [pool-1-thread-7] Initializing /data/omar/FB03f00d1.C01: [testng] 01:31:57,890 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:31:57,890 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:31:57,892 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-16_01-31-57.log] [testng] 01:31:57,892 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1dc24ef9 - End of configuration. [testng] [2024-03-16 01:31:58,076] [pool-1-thread-6] Initializing /data/johannes/MFGTMP_081128200001_A02f239d1.C01: [testng] 01:31:58,077 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:31:58,077 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:31:58,078 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-16_01-31-58.log] [testng] 01:31:58,079 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d654a70 - End of configuration. [testng] [2024-03-16 01:31:58,241] [pool-1-thread-5] Initializing /data/samples/different-field-count/plate_B03f00d0.C01: [testng] 01:31:58,242 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:31:58,242 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:31:58,242 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-16_01-31-58.log] [testng] 01:31:58,243 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48ef9df7 - End of configuration. [testng] [2024-03-16 01:31:58,375] [pool-1-thread-4] Initializing /data/omar/FB03f03o2.DIB: [testng] 01:31:58,375 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:31:58,375 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:31:58,376 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-16_01-31-58.log] [testng] 01:31:58,376 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3206a7c8 - End of configuration. [testng] [2024-03-16 01:31:58,484] [pool-1-thread-3] Initializing /data/samples/plate-size/plate_B03f00d0.C01: [testng] 01:31:58,484 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:31:58,485 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:31:58,485 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-16_01-31-58.log] [testng] 01:31:58,486 |-INFO in ch.qos.logback.core.sift.SiftProcessor@30a776f0 - End of configuration. [testng] [2024-03-16 01:31:58,698] [pool-1-thread-2] Initializing /data/qa-21720/AS_09125_050117190001_A14f00d0.DIB: [testng] 01:31:58,698 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:31:58,698 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:31:58,699 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-16_01-31-58.log] [testng] 01:31:58,700 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22616914 - End of configuration. [testng] [2024-03-16 01:32:01,148] [pool-1-thread-1] Initializing /data/harri/MFGTMP-PC_111018140003/MFGTMP-PC_111018140003_E04f00d0.C01: [testng] [2024-03-16 01:32:01,452] [pool-1-thread-4] Initializing /data/omar/FB03f00o2.C01: [testng] [2024-03-16 01:32:02,133] [pool-1-thread-9] Initializing /data/samples/sparse-plate/plate_E03f00d0.C01: [testng] [2024-03-16 01:32:02,638] [pool-1-thread-11] Initializing /data/johannes/MFGTMP_081222130005_E07f00d0.C01: [testng] [2024-03-16 01:32:02,846] [pool-1-thread-6] Initializing /data/qa-7352/test/MFGTMP-PC_130509120002_B02f00o1.C01: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 901, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 11 minutes 53 seconds Finished: SUCCESS