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Started by upstream project "BIOFORMATS-test-repo" build number 129 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4 [BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins4909733947001467714.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_20169_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] 13:53:16,704 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 13:53:16,706 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 13:53:16,706 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 13:53:16,707 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 13:53:16,707 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 13:53:16,708 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 13:53:16,708 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 13:53:16,708 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 13:53:16,708 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 13:53:16,709 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 13:53:16,709 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 13:53:16,709 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 13:53:16,951 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 13:53:16,951 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 13:53:16,981 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 13:53:16,981 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 13:53:16,992 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 13:53:16,992 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 13:53:16,992 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 13:53:16,993 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 13:53:16,993 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 13:53:16,994 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 13:53:16,994 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 286 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-22 13:53:17,004] [main] java.version = 1.8.0_342 [testng] 13:53:17,008 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 13:53:17,008 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:53:17,056 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-22_13-53-17.log] [testng] 13:53:17,058 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-07-22 13:53:17,060] [main] testng.directory = /data [testng] [2024-07-22 13:53:17,060] [main] testng.configDirectory = /config [testng] [2024-07-22 13:53:17,072] [main] testng.multiplier = 1.0 [testng] [2024-07-22 13:53:17,073] [main] testng.in-memory = false [testng] [2024-07-22 13:53:17,073] [main] testng.allow-missing = false [testng] [2024-07-22 13:53:17,073] [main] user.language = fr [testng] [2024-07-22 13:53:17,073] [main] user.country = FR [testng] [2024-07-22 13:53:17,073] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-07-22 13:53:17,675] [main] ---------------------------------------- [testng] [2024-07-22 13:53:17,676] [main] Total files: 15 [testng] [2024-07-22 13:53:17,676] [main] Scan time: 0.602 s (40 ms/file) [testng] [2024-07-22 13:53:17,676] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 12 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-22 13:53:18,877] [pool-1-thread-1] Initializing /data/jeremy/Hiv_spikes.am: [testng] 13:53:18,878 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 13:53:18,878 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:53:18,879 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-22_13-53-18.log] [testng] 13:53:18,879 |-INFO in ch.qos.logback.core.sift.SiftProcessor@507a7975 - End of configuration. [testng] [2024-07-22 13:53:18,907] [pool-1-thread-12] Initializing /data/public/imagesc-50585/BF_CheckAmira.am: [testng] 13:53:18,907 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 13:53:18,907 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:53:18,908 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-22_13-53-18.log] [testng] 13:53:18,909 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d1204c3 - End of configuration. [testng] [2024-07-22 13:53:18,923] [pool-1-thread-11] Initializing /data/johannes/template.grey: [testng] 13:53:18,923 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 13:53:18,923 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:53:18,924 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-22_13-53-18.log] [testng] 13:53:18,924 |-INFO in ch.qos.logback.core.sift.SiftProcessor@29b3a47f - End of configuration. [testng] [2024-07-22 13:53:18,968] [pool-1-thread-10] Initializing /data/ilya/test.am: [testng] 13:53:18,968 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 13:53:18,968 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:53:18,969 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-22_13-53-18.log] [testng] 13:53:18,969 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7cba96a2 - End of configuration. [testng] [2024-07-22 13:53:19,004] [pool-1-thread-9] Initializing /data/jeremy/Virus_Membrane7-screenshot.PNG: [testng] 13:53:19,004 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 13:53:19,004 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:53:19,005 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-22_13-53-19.log] [testng] 13:53:19,005 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36e4deb9 - End of configuration. [testng] [2024-07-22 13:53:19,009] [pool-1-thread-8] Initializing /data/public/imagesc-50585/BF_Check.tif: [testng] 13:53:19,009 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 13:53:19,009 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:53:19,010 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-22_13-53-19.log] [testng] 13:53:19,010 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f41ada2 - End of configuration. [testng] [2024-07-22 13:53:19,035] [pool-1-thread-7] Initializing /data/public/ignacio/test.am: [testng] 13:53:19,035 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 13:53:19,035 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:53:19,036 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-22_13-53-19.log] [testng] 13:53:19,036 |-INFO in ch.qos.logback.core.sift.SiftProcessor@55260ff0 - End of configuration. [testng] [2024-07-22 13:53:19,049] [pool-1-thread-6] Initializing /data/public/imagesc-50585/BF_CheckMIB.am: [testng] 13:53:19,049 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 13:53:19,049 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:53:19,050 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-22_13-53-19.log] [testng] 13:53:19,050 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f96191f - End of configuration. [testng] [2024-07-22 13:53:19,060] [pool-1-thread-5] Initializing /data/johannes/template.labels: [testng] 13:53:19,060 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 13:53:19,061 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:53:19,061 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-22_13-53-19.log] [testng] 13:53:19,061 |-INFO in ch.qos.logback.core.sift.SiftProcessor@545e4e34 - End of configuration. [testng] [2024-07-22 13:53:19,072] [pool-1-thread-4] Initializing /data/jcb/201108088/Haberman-Fig4A-original.am: [testng] 13:53:19,072 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 13:53:19,072 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:53:19,073 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-22_13-53-19.log] [testng] 13:53:19,073 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a3510df - End of configuration. [testng] [2024-07-22 13:53:19,100] [pool-1-thread-3] Initializing /data/samples/emptykey/test.am: [testng] 13:53:19,101 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 13:53:19,101 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:53:19,102 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-22_13-53-19.log] [testng] 13:53:19,102 |-INFO in ch.qos.logback.core.sift.SiftProcessor@164150b - End of configuration. [testng] [2024-07-22 13:53:19,113] [pool-1-thread-2] Initializing /data/jeremy/Virus_Membrane7.am: [testng] 13:53:19,113 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 13:53:19,113 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:53:19,114 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-22_13-53-19.log] [testng] 13:53:19,114 |-INFO in ch.qos.logback.core.sift.SiftProcessor@418bd941 - 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: 11 seconds Finished: SUCCESS