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Started by upstream project "BIOFORMATS-test-repo" build number 130 originally caused by: Started by upstream project "Trigger" build number 147 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5 [BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins7962905088747515577.sh + '[' specs = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_20336_merge_ci -v /uod/idr/repos/curated/specs:/data -v /uod/idr-scratch/merge-ci/curated/specs:/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] 11:16:23,346 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 11:16:23,347 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 11:16:23,347 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:16:23,348 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:16:23,349 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 11:16:23,349 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 11:16:23,350 |-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] 11:16:23,350 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:16:23,350 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:16:23,351 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 11:16:23,351 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 11:16:23,351 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 11:16:23,549 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 11:16:23,549 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 11:16:23,576 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 11:16:23,576 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 11:16:23,582 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 11:16:23,582 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 11:16:23,583 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 11:16:23,583 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 11:16:23,584 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 11:16:23,584 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 11:16:23,584 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 234 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-23 11:16:23,594] [main] java.version = 11.0.16 [testng] 11:16:23,597 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 11:16:23,598 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:16:23,648 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-23_11-16-23.log] [testng] 11:16:23,650 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-07-23 11:16:23,654] [main] testng.directory = /data [testng] [2024-07-23 11:16:23,654] [main] testng.configDirectory = /config [testng] [2024-07-23 11:16:23,668] [main] testng.multiplier = 1.0 [testng] [2024-07-23 11:16:23,669] [main] testng.in-memory = false [testng] [2024-07-23 11:16:23,669] [main] testng.allow-missing = false [testng] [2024-07-23 11:16:23,669] [main] user.language = en [testng] [2024-07-23 11:16:23,670] [main] user.country = ${user.country} [testng] [2024-07-23 11:16:23,670] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-07-23 11:16:36,139] [main] ---------------------------------------- [testng] [2024-07-23 11:16:36,139] [main] Total files: 226 [testng] [2024-07-23 11:16:36,139] [main] Scan time: 12.469 s (55 ms/file) [testng] [2024-07-23 11:16:36,139] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 28 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-23 11:16:41,702] [pool-1-thread-1] Initializing /data/fluoview/Sample_XYZ.TIF: [testng] 11:16:41,702 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 11:16:41,703 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:16:41,704 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-23_11-16-41.log] [testng] 11:16:41,705 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e42b13d - End of configuration. [testng] [2024-07-23 11:16:41,760] [pool-1-thread-12] Initializing /data/iplab/Color Histology.IPL: [testng] 11:16:41,760 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 11:16:41,760 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:16:41,761 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-23_11-16-41.log] [testng] 11:16:41,762 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c070f00 - End of configuration. [testng] [2024-07-23 11:16:41,769] [pool-1-thread-11] Initializing /data/fluoview/Sample_TwoCH.TIF: [testng] 11:16:41,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 11:16:41,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:16:41,769 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-23_11-16-41.log] [testng] 11:16:41,770 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65792977 - End of configuration. [testng] [2024-07-23 11:16:41,812] [pool-1-thread-10] Initializing /data/iplab/Chromosomes.IPL: [testng] 11:16:41,812 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 11:16:41,812 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:16:41,813 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-23_11-16-41.log] [testng] 11:16:41,813 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6b59bfe8 - End of configuration. [testng] [2024-07-23 11:16:41,820] [pool-1-thread-9] Initializing /data/iplab/Blend_Fitc.IPL: [testng] 11:16:41,820 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 11:16:41,820 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:16:41,821 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-23_11-16-41.log] [testng] 11:16:41,821 |-INFO in ch.qos.logback.core.sift.SiftProcessor@500fb382 - End of configuration. [testng] [2024-07-23 11:16:41,831] [pool-1-thread-8] Initializing /data/fluoview/sample_labled_XYZCh.tif: [testng] 11:16:41,832 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 11:16:41,832 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:16:41,839 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-23_11-16-41.log] [testng] 11:16:41,839 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a7b5593 - End of configuration. [testng] [2024-07-23 11:16:41,878] [pool-1-thread-7] Initializing /data/zeiss_lsm/X-Y-Z-T-Ch-Tile--MultiTrack-1.lsm: [testng] 11:16:41,878 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 11:16:41,878 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:16:41,879 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-23_11-16-41.log] [testng] 11:16:41,880 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c28bd54 - End of configuration. [testng] [2024-07-23 11:16:41,971] [pool-1-thread-6] Initializing /data/gatan/ImageReader2003/ImageReaderTest/TestFiles/Test.dm3: [testng] 11:16:41,971 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 11:16:41,971 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:16:41,972 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-23_11-16-41.log] [testng] 11:16:41,972 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2084c319 - End of configuration. [testng] [2024-07-23 11:16:41,984] [pool-1-thread-5] Initializing /data/iplab/Blend_DIC.IPL: [testng] 11:16:41,984 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 11:16:41,984 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:16:41,985 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-23_11-16-41.log] [testng] 11:16:41,985 |-INFO in ch.qos.logback.core.sift.SiftProcessor@262f9fe8 - End of configuration. [testng] [2024-07-23 11:16:41,993] [pool-1-thread-4] Initializing /data/iplab/10x Blood and Bacteria.IPL: [testng] 11:16:41,994 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 11:16:41,994 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:16:41,994 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-23_11-16-41.log] [testng] 11:16:41,995 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7bf40750 - End of configuration. [testng] [2024-07-23 11:16:42,004] [pool-1-thread-3] Initializing /data/fluoview/sample_labled_XYZTCh.tif: [testng] 11:16:42,004 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 11:16:42,004 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:16:42,005 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-23_11-16-42.log] [testng] 11:16:42,015 |-INFO in ch.qos.logback.core.sift.SiftProcessor@30eed605 - End of configuration. [testng] [2024-07-23 11:16:42,040] [pool-1-thread-2] Initializing /data/fluoview/sample_labled_XYTCh.tif: [testng] 11:16:42,040 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 11:16:42,040 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:16:42,041 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-23_11-16-42.log] [testng] 11:16:42,041 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a38c728 - End of configuration. [testng] [2024-07-23 11:16:44,665] [pool-1-thread-10] Initializing /data/fluoview/SpineAnimation.tif: [testng] [2024-07-23 11:16:44,715] [pool-1-thread-6] Initializing /data/iplab/Actin.IPL: [testng] [2024-07-23 11:16:44,722] [pool-1-thread-12] Initializing /data/gatan/ImageReader2003/ImageReaderTest/TestFiles/Test2.dm3: [testng] [2024-07-23 11:16:44,746] [pool-1-thread-9] Initializing /data/fluoview/Sample_XYT.TIF: [testng] [2024-07-23 11:16:44,809] [pool-1-thread-5] Initializing /data/gatan/ImageReader2003/ImageReaderTest/TestFiles/test3.dm3: [testng] [2024-07-23 11:16:44,817] [pool-1-thread-2] Initializing /data/iplab/3t3 Cell.IPL: [testng] [2024-07-23 11:16:44,823] [pool-1-thread-4] Initializing /data/fluoview/SpineAnimation.avi: [testng] [2024-07-23 11:16:44,840] [pool-1-thread-8] Initializing /data/iplab/Blend_Dapi.IPL: [testng] [2024-07-23 11:16:44,851] [pool-1-thread-3] Initializing /data/zeiss_lsm/X-Y-Z-T-Ch-Tile-1.lsm: [testng] [2024-07-23 11:16:44,929] [pool-1-thread-1] Initializing /data/iplab/16Bit XRay.IPL: [testng] [2024-07-23 11:16:44,936] [pool-1-thread-11] Initializing /data/fluoview/Sample_XT.tif: [testng] [2024-07-23 11:16:45,463] [pool-1-thread-2] Initializing /data/iplab/Blend_Final.IPL: [testng] [2024-07-23 11:16:45,504] [pool-1-thread-6] Initializing /data/iplab/Blend_Tritc.IPL: [testng] [2024-07-23 11:16:45,581] [pool-1-thread-1] Initializing /data/zeiss_lsm/X-Y-Z-T-Ch-Tile-2.lsm: [testng] [2024-07-23 11:16:45,776] [pool-1-thread-5] Initializing /data/fluoview/Sample_ThreeCH.TIF: [testng] [2024-07-23 11:16:45,875] [pool-1-thread-12] Initializing /data/iplab/Color Image.IPL: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1484, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 28 seconds Finished: SUCCESS