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Started by upstream project "BIOFORMATS-test-repo" build number 371 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins5854043922329664691.sh + '[' amira = slidebook ']' ++ date +%u + '[' 1 -le 1 ']' + DOCKER_ARGS='-Dtestng.memory=15g -Dtestng.threadCount=12 -Duser.language=fr -Duser.country=FR' + sudo docker run --rm --name BIOFORMATS-test-folder_58984_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 -Duser.language=fr -Duser.country=FR 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 test-automated: [testng] File leak detector installed [testng] 11:45:16,441 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 11:45:16,443 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - No custom configurators were discovered as a service. [testng] 11:45:16,443 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:45:16,444 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:45:16,444 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 11:45:16,445 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 11:45:16,445 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 11:45:16,445 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:45:16,445 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:45:16,446 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 11:45:16,446 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 11:45:16,446 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 11:45:16,682 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 11:45:16,682 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 11:45:16,712 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 11:45:16,712 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 11:45:16,720 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 11:45:16,720 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 11:45:16,720 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 11:45:16,720 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 11:45:16,721 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@63355449 - End of configuration. [testng] 11:45:16,721 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48ae9b55 - Registering current configuration as safe fallback point [testng] 11:45:16,721 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 276 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-10 11:45:16,731] [main] java.version = 1.8.0_342 [testng] 11:45:16,734 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 11:45:16,734 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:45:16,777 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-10_11-45-16.log] [testng] 11:45:16,779 |-INFO in ch.qos.logback.core.sift.SiftProcessor@765d7657 - End of configuration. [testng] [2025-03-10 11:45:16,780] [main] testng.directory = /data [testng] [2025-03-10 11:45:16,781] [main] testng.configDirectory = /config [testng] [2025-03-10 11:45:16,792] [main] testng.multiplier = 1.0 [testng] [2025-03-10 11:45:16,793] [main] testng.in-memory = false [testng] [2025-03-10 11:45:16,793] [main] testng.allow-missing = false [testng] [2025-03-10 11:45:16,793] [main] user.language = fr [testng] [2025-03-10 11:45:16,793] [main] user.country = FR [testng] [2025-03-10 11:45:16,793] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2025-03-10 11:45:21,252] [main] ---------------------------------------- [testng] [2025-03-10 11:45:21,252] [main] Total files: 15 [testng] [2025-03-10 11:45:21,253] [main] Scan time: 4.459 s (297 ms/file) [testng] [2025-03-10 11:45:21,253] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 12 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-10 11:45:30,384] [pool-1-thread-1] Initializing /data/jeremy/Hiv_spikes.am: [testng] 11:45:30,384 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 11:45:30,384 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:45:30,385 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-10_11-45-30.log] [testng] 11:45:30,385 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50418ba6 - End of configuration. [testng] [2025-03-10 11:45:31,045] [pool-1-thread-12] Initializing /data/johannes/template.labels: [testng] 11:45:31,045 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 11:45:31,046 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:45:31,047 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-10_11-45-31.log] [testng] 11:45:31,047 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d39ee1 - End of configuration. [testng] [2025-03-10 11:45:31,696] [pool-1-thread-11] Initializing /data/johannes/template.grey: [testng] 11:45:31,697 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 11:45:31,697 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:45:31,697 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-10_11-45-31.log] [testng] 11:45:31,698 |-INFO in ch.qos.logback.core.sift.SiftProcessor@338d7ae0 - End of configuration. [testng] [2025-03-10 11:45:32,330] [pool-1-thread-10] Initializing /data/public/imagesc-50585/BF_Check.tif: [testng] 11:45:32,330 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 11:45:32,330 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:45:32,331 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-10_11-45-32.log] [testng] 11:45:32,331 |-INFO in ch.qos.logback.core.sift.SiftProcessor@49774d52 - End of configuration. [testng] [2025-03-10 11:45:33,558] [pool-1-thread-9] Initializing /data/jcb/201108088/Haberman-Fig4A-original.am: [testng] 11:45:33,559 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 11:45:33,559 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:45:33,559 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-10_11-45-33.log] [testng] 11:45:33,560 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10f4640b - End of configuration. [testng] [2025-03-10 11:45:33,907] [pool-1-thread-8] Initializing /data/jeremy/Virus_Membrane7-screenshot.PNG: [testng] 11:45:33,907 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 11:45:33,907 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:45:33,908 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-10_11-45-33.log] [testng] 11:45:33,908 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6ca9b5d4 - End of configuration. [testng] [2025-03-10 11:45:33,936] [pool-1-thread-7] Initializing /data/public/imagesc-50585/BF_CheckMIB.am: [testng] 11:45:33,936 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 11:45:33,936 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:45:33,937 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-10_11-45-33.log] [testng] 11:45:33,937 |-INFO in ch.qos.logback.core.sift.SiftProcessor@74d7db63 - End of configuration. [testng] [2025-03-10 11:45:34,285] [pool-1-thread-6] Initializing /data/public/imagesc-50585/BF_CheckAmira.am: [testng] 11:45:34,285 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 11:45:34,285 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:45:34,286 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-10_11-45-34.log] [testng] 11:45:34,286 |-INFO in ch.qos.logback.core.sift.SiftProcessor@542f888a - End of configuration. [testng] [2025-03-10 11:45:34,653] [pool-1-thread-5] Initializing /data/jeremy/Virus_Membrane7.am: [testng] 11:45:34,654 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 11:45:34,654 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:45:34,654 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-10_11-45-34.log] [testng] 11:45:34,655 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7d6d71fb - End of configuration. [testng] [2025-03-10 11:45:35,014] [pool-1-thread-4] Initializing /data/ilya/test.am: [testng] 11:45:35,015 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 11:45:35,015 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:45:35,015 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-10_11-45-35.log] [testng] 11:45:35,016 |-INFO in ch.qos.logback.core.sift.SiftProcessor@b1271b0 - End of configuration. [testng] [2025-03-10 11:45:35,392] [pool-1-thread-3] Initializing /data/samples/emptykey/test.am: [testng] 11:45:35,392 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 11:45:35,392 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:45:35,393 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-10_11-45-35.log] [testng] 11:45:35,393 |-INFO in ch.qos.logback.core.sift.SiftProcessor@59c19573 - End of configuration. [testng] [2025-03-10 11:45:35,829] [pool-1-thread-2] Initializing /data/public/ignacio/test.am: [testng] 11:45:35,829 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 11:45:35,829 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:45:35,830 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-10_11-45-35.log] [testng] 11:45:35,830 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7df234ca - 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: 30 seconds Finished: SUCCESS