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Started by upstream project "BIOFORMATS-test-repo" build number 96 originally caused by: Started by upstream project "Trigger" build number 107 originally caused by: Started by timer 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/jenkins8628320947370366633.sh + '[' imaris = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_14850_merge_ci -v /uod/idr/repos/curated/imaris:/data -v /uod/idr-scratch/merge-ci/curated/imaris:/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] 02:15:26,856 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:15:26,858 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 02:15:26,858 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:15:26,859 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:15:26,859 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:15:26,860 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:15:26,860 |-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] 02:15:26,860 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:15:26,860 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:15:26,861 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:15:26,861 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:15:26,862 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:15:27,044 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:15:27,044 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:15:27,071 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:15:27,071 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:15:27,080 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:15:27,080 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:15:27,080 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:15:27,081 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:15:27,081 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 02:15:27,082 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 02:15:27,082 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 222 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-06-18 02:15:27,093] [main] java.version = 11.0.16 [testng] 02:15:27,097 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:15:27,097 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:15:27,147 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-18_02-15-27.log] [testng] 02:15:27,149 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-06-18 02:15:27,152] [main] testng.directory = /data [testng] [2024-06-18 02:15:27,152] [main] testng.configDirectory = /config [testng] [2024-06-18 02:15:27,162] [main] testng.multiplier = 1.0 [testng] [2024-06-18 02:15:27,164] [main] testng.in-memory = false [testng] [2024-06-18 02:15:27,164] [main] testng.allow-missing = false [testng] [2024-06-18 02:15:27,164] [main] user.language = en [testng] [2024-06-18 02:15:27,164] [main] user.country = ${user.country} [testng] [2024-06-18 02:15:27,164] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-06-18 02:15:34,962] [main] ---------------------------------------- [testng] [2024-06-18 02:15:34,962] [main] Total files: 67 [testng] [2024-06-18 02:15:34,962] [main] Scan time: 7.798 s (116 ms/file) [testng] [2024-06-18 02:15:34,962] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-06-18 02:16:03,580] [pool-1-thread-1] Initializing /data/public/davemason/Convallaria_3C_3T_35Z_confocal_IMS3.ims: [testng] 02:16:03,581 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:16:03,581 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:03,583 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-18_02-16-03.log] [testng] 02:16:03,584 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ec5d2d - End of configuration. [testng] [2024-06-18 02:16:03,635] [pool-1-thread-12] Initializing /data/generated/10-31_E_t0007.ims: [testng] 02:16:03,635 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:16:03,635 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:03,637 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-18_02-16-03.log] [testng] 02:16:03,637 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3211c824 - End of configuration. [testng] [2024-06-18 02:16:03,659] [pool-1-thread-11] Initializing /data/generated/10-31_E_t0001.ims: [testng] 02:16:03,659 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:16:03,659 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:03,660 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-18_02-16-03.log] [testng] 02:16:03,660 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2c22bebb - End of configuration. [testng] [2024-06-18 02:16:03,677] [pool-1-thread-10] Initializing /data/public/davemason/Convallaria_3C_10T_confocal.ims: [testng] 02:16:03,677 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:16:03,677 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:03,678 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-18_02-16-03.log] [testng] 02:16:03,678 |-INFO in ch.qos.logback.core.sift.SiftProcessor@cb32175 - End of configuration. [testng] [2024-06-18 02:16:03,720] [pool-1-thread-9] Initializing /data/generated/10-31_E_t0009.ims: [testng] 02:16:03,721 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:16:03,721 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:03,722 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-18_02-16-03.log] [testng] 02:16:03,722 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c3c9a0b - End of configuration. [testng] [2024-06-18 02:16:03,743] [pool-1-thread-8] Initializing /data/generated/mri-stack-original.ims: [testng] 02:16:03,743 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:16:03,743 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:03,744 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-18_02-16-03.log] [testng] 02:16:03,745 |-INFO in ch.qos.logback.core.sift.SiftProcessor@17c6285f - End of configuration. [testng] [2024-06-18 02:16:03,760] [pool-1-thread-7] Initializing /data/jason/imaris_5_5_demoimages/PtK2Cell.ims: [testng] 02:16:03,760 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:16:03,760 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:03,761 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-18_02-16-03.log] [testng] 02:16:03,761 |-INFO in ch.qos.logback.core.sift.SiftProcessor@72d19d3b - End of configuration. [testng] [2024-06-18 02:16:03,798] [pool-1-thread-6] Initializing /data/oliver/Stack2_8Bit.ims: [testng] 02:16:03,798 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:16:03,799 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:03,799 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-18_02-16-03.log] [testng] 02:16:03,800 |-INFO in ch.qos.logback.core.sift.SiftProcessor@294ac656 - End of configuration. [testng] [2024-06-18 02:16:03,839] [pool-1-thread-5] Initializing /data/qa-17522/2016-12-14_08.43.34_Sample Prefix_WAINWRIGHT James_Protocol.ims: [testng] 02:16:03,840 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:16:03,840 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:03,841 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-18_02-16-03.log] [testng] 02:16:03,841 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7d78a2a8 - End of configuration. [testng] [2024-06-18 02:16:09,233] [pool-1-thread-4] Initializing /data/jcb/fig 6B GFP-AP-2d.ims: [testng] 02:16:09,233 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:16:09,233 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:09,235 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-18_02-16-09.log] [testng] 02:16:09,235 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f810e45 - End of configuration. [testng] [2024-06-18 02:16:09,299] [pool-1-thread-3] Initializing /data/public/davemason/Convallaria_3C_3T_2x2grid_confocal.ims: [testng] 02:16:09,299 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:16:09,299 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:09,300 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-18_02-16-09.log] [testng] 02:16:09,300 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b471354 - End of configuration. [testng] [2024-06-18 02:16:09,370] [pool-1-thread-2] Initializing /data/jake/p75Cherry M2 010-3~B.ims: [testng] 02:16:09,370 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:16:09,370 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:09,371 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-18_02-16-09.log] [testng] 02:16:09,371 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6922ebcd - End of configuration. BUILD SUCCESSFUL Total time: 2 minutes 39 seconds Finished: SUCCESS