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Started by upstream project "BIOFORMATS-test-repo" build number 270 originally caused by: Started by user devspace 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/jenkins15576333731204330860.sh + '[' amira = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_42620_merge_ci -v /uod/idr/repos/curated/amira:/data -v /uod/idr-scratch/merge-ci/curated/amira:/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] 11:39:48,427 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 11:39:48,428 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 11:39:48,428 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:39:48,429 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:39:48,429 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 11:39:48,429 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 11:39:48,430 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 11:39:48,430 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:39:48,430 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:39:48,431 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 11:39:48,431 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 11:39:48,431 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 11:39:48,591 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 11:39:48,591 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 11:39:48,615 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 11:39:48,615 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 11:39:48,621 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 11:39:48,621 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 11:39:48,621 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 11:39:48,622 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 11:39:48,622 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 11:39:48,623 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 11:39:48,623 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 193 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-27 11:39:48,632] [main] java.version = 17.0.2 [testng] 11:39:48,636 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 11:39:48,636 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:39:48,677 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-27_11-39-48.log] [testng] 11:39:48,678 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-11-27 11:39:48,680] [main] testng.directory = /data [testng] [2024-11-27 11:39:48,681] [main] testng.configDirectory = /config [testng] [2024-11-27 11:39:48,689] [main] testng.multiplier = 1.0 [testng] [2024-11-27 11:39:48,690] [main] testng.in-memory = false [testng] [2024-11-27 11:39:48,690] [main] testng.allow-missing = false [testng] [2024-11-27 11:39:48,691] [main] user.language = en [testng] [2024-11-27 11:39:48,691] [main] user.country = ${user.country} [testng] [2024-11-27 11:39:48,691] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-27 11:39:53,707] [main] ---------------------------------------- [testng] [2024-11-27 11:39:53,707] [main] Total files: 15 [testng] [2024-11-27 11:39:53,707] [main] Scan time: 5.016 s (334 ms/file) [testng] [2024-11-27 11:39:53,707] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 12 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-27 11:40:09,862] [pool-1-thread-1] Initializing /data/public/imagesc-50585/BF_CheckAmira.am: [testng] 11:40:09,862 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 11:40:09,862 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:40:09,863 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-27_11-40-09.log] [testng] 11:40:09,864 |-INFO in ch.qos.logback.core.sift.SiftProcessor@44f140b0 - End of configuration. [testng] [2024-11-27 11:40:10,406] [pool-1-thread-12] Initializing /data/jcb/201108088/Haberman-Fig4A-original.am: [testng] 11:40:10,406 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 11:40:10,406 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:40:10,407 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-27_11-40-10.log] [testng] 11:40:10,407 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ddafda5 - End of configuration. [testng] [2024-11-27 11:40:11,380] [pool-1-thread-11] Initializing /data/johannes/template.labels: [testng] 11:40:11,380 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 11:40:11,380 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:40:11,381 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-27_11-40-11.log] [testng] 11:40:11,381 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f042255 - End of configuration. [testng] [2024-11-27 11:40:12,409] [pool-1-thread-10] Initializing /data/samples/emptykey/test.am: [testng] 11:40:12,409 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 11:40:12,409 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:40:12,409 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-27_11-40-12.log] [testng] 11:40:12,410 |-INFO in ch.qos.logback.core.sift.SiftProcessor@44b7b736 - End of configuration. [testng] [2024-11-27 11:40:13,216] [pool-1-thread-9] Initializing /data/public/ignacio/test.am: [testng] 11:40:13,217 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 11:40:13,217 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:40:13,217 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-27_11-40-13.log] [testng] 11:40:13,218 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2858bf4a - End of configuration. [testng] [2024-11-27 11:40:13,756] [pool-1-thread-8] Initializing /data/johannes/template.grey: [testng] 11:40:13,756 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 11:40:13,756 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:40:13,757 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-27_11-40-13.log] [testng] 11:40:13,758 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5394169b - End of configuration. [testng] [2024-11-27 11:40:14,419] [pool-1-thread-7] Initializing /data/public/imagesc-50585/BF_CheckMIB.am: [testng] 11:40:14,419 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 11:40:14,419 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:40:14,420 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-27_11-40-14.log] [testng] 11:40:14,420 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6971659a - End of configuration. [testng] [2024-11-27 11:40:14,974] [pool-1-thread-6] Initializing /data/jeremy/Hiv_spikes.am: [testng] 11:40:14,975 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 11:40:14,975 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:40:14,975 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-27_11-40-14.log] [testng] 11:40:14,976 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ccd0ddd - End of configuration. [testng] [2024-11-27 11:40:15,509] [pool-1-thread-5] Initializing /data/ilya/test.am: [testng] 11:40:15,509 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 11:40:15,510 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:40:15,510 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-27_11-40-15.log] [testng] 11:40:15,511 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8f068e2 - End of configuration. [testng] [2024-11-27 11:40:16,208] [pool-1-thread-4] Initializing /data/public/imagesc-50585/BF_Check.tif: [testng] 11:40:16,208 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 11:40:16,208 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:40:16,209 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-27_11-40-16.log] [testng] 11:40:16,209 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3fee6804 - End of configuration. [testng] [2024-11-27 11:40:17,694] [pool-1-thread-3] Initializing /data/jeremy/Virus_Membrane7.am: [testng] 11:40:17,694 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 11:40:17,694 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:40:17,695 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-27_11-40-17.log] [testng] 11:40:17,695 |-INFO in ch.qos.logback.core.sift.SiftProcessor@42be334b - End of configuration. [testng] [2024-11-27 11:40:18,234] [pool-1-thread-2] Initializing /data/jeremy/Virus_Membrane7-screenshot.PNG: [testng] 11:40:18,234 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 11:40:18,234 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:40:18,235 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-27_11-40-18.log] [testng] 11:40:18,235 |-INFO in ch.qos.logback.core.sift.SiftProcessor@404dde5 - End of configuration. [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 636, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 41 seconds Finished: SUCCESS