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Started by upstream project "BIOFORMATS-test-repo" build number 127 originally caused by: Started by upstream project "Trigger" build number 144 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@7 [BIOFORMATS-test-folder@7] $ /bin/bash -xe /tmp/jenkins16402062295671504541.sh + '[' imaris = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_19934_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] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket [testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket [testng] File leak detector installed [testng] 02:13:18,604 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:13:18,605 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 02:13:18,605 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:13:18,606 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:13:18,606 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:13:18,607 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:13:18,607 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:13:18,607 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:13:18,607 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:13:18,608 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:13:18,608 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:13:18,608 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:13:18,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:13:18,770 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:13:18,793 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:13:18,793 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:13:18,799 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:13:18,799 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:13:18,799 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:13:18,800 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:13:18,800 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 02:13:18,800 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 02:13:18,800 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 193 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-21 02:13:18,809] [main] java.version = 17.0.2 [testng] 02:13:18,813 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:13:18,813 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:18,853 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-21_02-13-18.log] [testng] 02:13:18,855 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-07-21 02:13:18,857] [main] testng.directory = /data [testng] [2024-07-21 02:13:18,857] [main] testng.configDirectory = /config [testng] [2024-07-21 02:13:18,866] [main] testng.multiplier = 1.0 [testng] [2024-07-21 02:13:18,867] [main] testng.in-memory = false [testng] [2024-07-21 02:13:18,867] [main] testng.allow-missing = false [testng] [2024-07-21 02:13:18,867] [main] user.language = en [testng] [2024-07-21 02:13:18,867] [main] user.country = ${user.country} [testng] [2024-07-21 02:13:18,867] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-07-21 02:13:27,553] [main] ---------------------------------------- [testng] [2024-07-21 02:13:27,553] [main] Total files: 68 [testng] [2024-07-21 02:13:27,553] [main] Scan time: 8.686 s (127 ms/file) [testng] [2024-07-21 02:13:27,553] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 60 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-21 02:13:51,560] [pool-1-thread-1] Initializing /data/public/eliana/retina_large.ims: [testng] 02:13:51,561 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:13:51,561 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:51,562 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-21_02-13-51.log] [testng] 02:13:51,562 |-INFO in ch.qos.logback.core.sift.SiftProcessor@739d6656 - End of configuration. [testng] [2024-07-21 02:13:51,595] [pool-1-thread-12] Initializing /data/gh-4193/24-5-9_RSV+AfumMscar+CFW_40x Stack_deconvolved.ims: [testng] 02:13:51,595 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:13:51,595 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:51,596 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-21_02-13-51.log] [testng] 02:13:51,597 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b3aa4ef - End of configuration. [testng] [2024-07-21 02:13:51,623] [pool-1-thread-11] Initializing /data/public/davemason/Convallaria_3C_3T_2x2grid_confocal.ims: [testng] 02:13:51,623 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:13:51,623 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:51,624 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-21_02-13-51.log] [testng] 02:13:51,624 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6dabc21c - End of configuration. [testng] [2024-07-21 02:13:51,657] [pool-1-thread-10] Initializing /data/kay/Imaris503_test_Kay.ims: [testng] 02:13:51,657 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:13:51,657 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:51,658 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-21_02-13-51.log] [testng] 02:13:51,659 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b15269c - End of configuration. [testng] [2024-07-21 02:13:51,681] [pool-1-thread-9] Initializing /data/public/davemason/Convallaria_3C_3T_35Z_confocal_deconvolved_IMS3.ims: [testng] 02:13:51,681 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:13:51,681 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:51,682 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-21_02-13-51.log] [testng] 02:13:51,682 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6fcacfc2 - End of configuration. [testng] [2024-07-21 02:13:51,709] [pool-1-thread-8] Initializing /data/generated/10-31_E_t0006.ims: [testng] 02:13:51,709 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:13:51,710 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:51,710 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-21_02-13-51.log] [testng] 02:13:51,711 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4461365b - End of configuration. [testng] [2024-07-21 02:13:51,745] [pool-1-thread-7] Initializing /data/oliver/Stack2_u16Bit.ims: [testng] 02:13:51,745 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:13:51,745 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:51,746 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-21_02-13-51.log] [testng] 02:13:51,746 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5260a8b - End of configuration. [testng] [2024-07-21 02:13:51,779] [pool-1-thread-6] Initializing /data/generated/10-31_E_t0013.ims: [testng] 02:13:51,780 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:13:51,780 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:51,781 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-21_02-13-51.log] [testng] 02:13:51,781 |-INFO in ch.qos.logback.core.sift.SiftProcessor@245814c0 - End of configuration. [testng] [2024-07-21 02:13:51,796] [pool-1-thread-5] Initializing /data/jason/imaris_5_5_demoimages/HeLaCell.ims: [testng] 02:13:51,796 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:13:51,797 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:51,797 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-21_02-13-51.log] [testng] 02:13:51,798 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e35f24a - End of configuration. [testng] [2024-07-21 02:13:51,834] [pool-1-thread-4] Initializing /data/qa-8019/wrong_num_dimensions.ims: [testng] 02:13:51,834 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:13:51,834 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:51,835 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-21_02-13-51.log] [testng] 02:13:51,835 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f2b66c7 - End of configuration. [testng] [2024-07-21 02:13:51,882] [pool-1-thread-3] Initializing /data/jason/imaris_5_5_demoimages/SwimmingAlgae.ims: [testng] 02:13:51,882 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:13:51,882 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:51,883 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-21_02-13-51.log] [testng] 02:13:51,884 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b94360b - End of configuration. [testng] [2024-07-21 02:13:51,969] [pool-1-thread-2] Initializing /data/public/davemason/Convallaria_3C_1T_2x2grid_confocal.ims: [testng] 02:13:51,969 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:13:51,969 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:51,970 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-21_02-13-51.log] [testng] 02:13:51,970 |-INFO in ch.qos.logback.core.sift.SiftProcessor@295b69ee - End of configuration. BUILD SUCCESSFUL Total time: 1 minute 32 seconds Finished: SUCCESS