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Started by upstream project "BIOFORMATS-test-repo" build number 89 originally caused by: Started by upstream project "Trigger" build number 100 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/jenkins13017741151252174445.sh + '[' imaris = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_13702_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] 02:14:44,628 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:14:44,629 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 02:14:44,629 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:14:44,630 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:14:44,631 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:14:44,631 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:14:44,632 |-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] 02:14:44,632 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:14:44,632 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:14:44,633 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:14:44,633 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:14:44,633 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:14:44,826 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:14:44,826 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:14:44,849 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:14:44,849 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:14:44,855 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:14:44,855 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:14:44,855 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:14:44,856 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:14:44,856 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 02:14:44,857 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 02:14:44,857 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 225 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-06-11 02:14:44,867] [main] java.version = 11.0.16 [testng] 02:14:44,870 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:14:44,870 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:14:44,913 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-11_02-14-44.log] [testng] 02:14:44,915 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-06-11 02:14:44,917] [main] testng.directory = /data [testng] [2024-06-11 02:14:44,917] [main] testng.configDirectory = /config [testng] [2024-06-11 02:14:44,928] [main] testng.multiplier = 1.0 [testng] [2024-06-11 02:14:44,929] [main] testng.in-memory = false [testng] [2024-06-11 02:14:44,929] [main] testng.allow-missing = false [testng] [2024-06-11 02:14:44,929] [main] user.language = en [testng] [2024-06-11 02:14:44,930] [main] user.country = ${user.country} [testng] [2024-06-11 02:14:44,930] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-06-11 02:14:52,099] [main] ---------------------------------------- [testng] [2024-06-11 02:14:52,099] [main] Total files: 67 [testng] [2024-06-11 02:14:52,099] [main] Scan time: 7.169 s (107 ms/file) [testng] [2024-06-11 02:14:52,099] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-06-11 02:15:14,546] [pool-1-thread-1] Initializing /data/public/davemason/Convallaria_3C_3T_35Z_confocal_IMS3.ims: [testng] 02:15:14,547 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:15:14,547 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:15:14,549 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-11_02-15-14.log] [testng] 02:15:14,549 |-INFO in ch.qos.logback.core.sift.SiftProcessor@52316745 - End of configuration. [testng] [2024-06-11 02:15:14,583] [pool-1-thread-12] Initializing /data/generated/10-31_E_t0007.ims: [testng] 02:15:14,584 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:15:14,584 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:15:14,585 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-11_02-15-14.log] [testng] 02:15:14,586 |-INFO in ch.qos.logback.core.sift.SiftProcessor@431b1293 - End of configuration. [testng] [2024-06-11 02:15:14,601] [pool-1-thread-11] Initializing /data/generated/10-31_E_t0001.ims: [testng] 02:15:14,602 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:15:14,602 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:15:14,603 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-11_02-15-14.log] [testng] 02:15:14,603 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34cb6ced - End of configuration. [testng] [2024-06-11 02:15:14,616] [pool-1-thread-10] Initializing /data/public/davemason/Convallaria_3C_10T_confocal.ims: [testng] 02:15:14,616 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:15:14,616 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:15:14,617 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-11_02-15-14.log] [testng] 02:15:14,618 |-INFO in ch.qos.logback.core.sift.SiftProcessor@25d387c7 - End of configuration. [testng] [2024-06-11 02:15:14,657] [pool-1-thread-9] Initializing /data/generated/10-31_E_t0009.ims: [testng] 02:15:14,657 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:15:14,657 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:15:14,658 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-11_02-15-14.log] [testng] 02:15:14,658 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3dbf1ca5 - End of configuration. [testng] [2024-06-11 02:15:14,670] [pool-1-thread-8] Initializing /data/generated/mri-stack-original.ims: [testng] 02:15:14,670 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:15:14,670 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:15:14,671 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-11_02-15-14.log] [testng] 02:15:14,671 |-INFO in ch.qos.logback.core.sift.SiftProcessor@df79610 - End of configuration. [testng] [2024-06-11 02:15:14,682] [pool-1-thread-7] Initializing /data/jason/imaris_5_5_demoimages/PtK2Cell.ims: [testng] 02:15:14,682 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:15:14,682 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:15:14,683 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-11_02-15-14.log] [testng] 02:15:14,683 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66a013f3 - End of configuration. [testng] [2024-06-11 02:15:14,714] [pool-1-thread-6] Initializing /data/oliver/Stack2_8Bit.ims: [testng] 02:15:14,715 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:15:14,715 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:15:14,715 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-11_02-15-14.log] [testng] 02:15:14,716 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57081e10 - End of configuration. [testng] [2024-06-11 02:15:14,761] [pool-1-thread-5] Initializing /data/qa-17522/2016-12-14_08.43.34_Sample Prefix_WAINWRIGHT James_Protocol.ims: [testng] 02:15:14,761 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:15:14,761 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:15:14,762 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-11_02-15-14.log] [testng] 02:15:14,762 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7bcf3bab - End of configuration. [testng] [2024-06-11 02:15:20,625] [pool-1-thread-4] Initializing /data/jcb/fig 6B GFP-AP-2d.ims: [testng] 02:15:20,626 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:15:20,626 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:15:20,627 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-11_02-15-20.log] [testng] 02:15:20,627 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d29fe38 - End of configuration. [testng] [2024-06-11 02:15:20,668] [pool-1-thread-3] Initializing /data/public/davemason/Convallaria_3C_3T_2x2grid_confocal.ims: [testng] 02:15:20,668 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:15:20,668 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:15:20,669 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-11_02-15-20.log] [testng] 02:15:20,670 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3bb451a2 - End of configuration. [testng] [2024-06-11 02:15:20,728] [pool-1-thread-2] Initializing /data/jake/p75Cherry M2 010-3~B.ims: [testng] 02:15:20,729 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:15:20,729 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:15:20,729 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-11_02-15-20.log] [testng] 02:15:20,730 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a35ee0c - End of configuration. BUILD SUCCESSFUL Total time: 1 minute 33 seconds Finished: SUCCESS