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Started by upstream project "BIOFORMATS-test-repo" build number 76 originally caused by: Started by upstream project "Trigger" build number 84 originally caused by: Started by timer 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/jenkins10650461902913293024.sh + '[' scanr = 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_11579_merge_ci -v /uod/idr/repos/curated/scanr:/data -v /uod/idr-scratch/merge-ci/curated/scanr:/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] 02:23:52,801 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:23:52,803 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 02:23:52,803 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:23:52,804 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:23:52,804 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:23:52,804 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:23:52,805 |-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] 02:23:52,805 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:23:52,806 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:23:52,806 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:23:52,806 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:23:52,806 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:23:53,079 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:23:53,079 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:23:53,119 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:23:53,119 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:23:53,134 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:23:53,134 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:23:53,134 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:23:53,135 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:23:53,135 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 02:23:53,136 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 02:23:53,136 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 331 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-05-27 02:23:53,150] [main] java.version = 1.8.0_342 [testng] 02:23:53,153 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:23:53,154 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:23:53,206 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-27_02-23-53.log] [testng] 02:23:53,209 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-05-27 02:23:53,211] [main] testng.directory = /data [testng] [2024-05-27 02:23:53,211] [main] testng.configDirectory = /config [testng] [2024-05-27 02:23:53,224] [main] testng.multiplier = 1.0 [testng] [2024-05-27 02:23:53,225] [main] testng.in-memory = false [testng] [2024-05-27 02:23:53,225] [main] testng.allow-missing = false [testng] [2024-05-27 02:23:53,225] [main] user.language = fr [testng] [2024-05-27 02:23:53,225] [main] user.country = FR [testng] [2024-05-27 02:23:53,225] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-05-27 02:30:30,209] [main] ---------------------------------------- [testng] [2024-05-27 02:30:30,209] [main] Total files: 2169 [testng] [2024-05-27 02:30:30,210] [main] Scan time: 396.984 s (183 ms/file) [testng] [2024-05-27 02:30:30,210] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-05-27 02:48:52,682] [pool-1-thread-1] Initializing /data/juergen/Experiment/experiment_descriptor.xml: [testng] 02:48:52,683 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:48:52,683 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:48:52,684 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-27_02-48-52.log] [testng] 02:48:52,685 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4eaadaa4 - End of configuration. [testng] [2024-05-27 02:48:52,938] [pool-1-thread-12] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml: [testng] 02:48:52,938 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:48:52,938 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:48:52,939 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-27_02-48-52.log] [testng] 02:48:52,940 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68b60108 - End of configuration. [testng] [2024-05-27 02:51:43,477] [pool-1-thread-11] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml: [testng] 02:51:43,478 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:51:43,478 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:51:43,479 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-27_02-51-43.log] [testng] 02:51:43,480 |-INFO in ch.qos.logback.core.sift.SiftProcessor@153291a7 - End of configuration. [testng] [2024-05-27 02:51:43,765] [pool-1-thread-10] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml: [testng] 02:51:43,765 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:51:43,765 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:51:43,766 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-27_02-51-43.log] [testng] 02:51:43,767 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b2909e - End of configuration. [testng] [2024-05-27 02:51:44,098] [pool-1-thread-9] Initializing /data/ruben/plate_002/experiment_descriptor.xml: [testng] 02:51:44,099 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:51:44,099 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:51:44,100 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-27_02-51-44.log] [testng] 02:51:44,100 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ca1db79 - End of configuration. [testng] [2024-05-27 02:51:44,179] [pool-1-thread-8] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml: [testng] 02:51:44,179 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:51:44,179 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:51:44,180 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-27_02-51-44.log] [testng] 02:51:44,180 |-INFO in ch.qos.logback.core.sift.SiftProcessor@23efb800 - End of configuration. [testng] [2024-05-27 02:53:00,773] [pool-1-thread-7] Initializing /data/embl/Maik_001/experiment_descriptor.xml: [testng] 02:53:00,773 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:53:00,774 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:53:00,775 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-27_02-53-00.log] [testng] 02:53:00,776 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f927d6a - End of configuration. [testng] [2024-05-27 02:53:10,520] [pool-1-thread-6] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml: [testng] 02:53:10,521 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:53:10,521 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:53:10,521 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-27_02-53-10.log] [testng] 02:53:10,522 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68160474 - End of configuration. [testng] [2024-05-27 02:53:45,600] [pool-1-thread-5] Initializing /data/gideon/experiment_descriptor.xml: [testng] 02:53:45,601 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:53:45,601 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:53:45,602 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-27_02-53-45.log] [testng] 02:53:45,602 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e9ad8d7 - End of configuration. [testng] [2024-05-27 02:54:18,350] [pool-1-thread-4] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml: [testng] 02:54:18,350 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:54:18,350 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:54:18,352 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-27_02-54-18.log] [testng] 02:54:18,352 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d7d0dd - End of configuration. [testng] [2024-05-27 02:55:19,441] [pool-1-thread-3] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml: [testng] 02:55:19,441 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:55:19,441 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:55:19,442 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-27_02-55-19.log] [testng] 02:55:19,443 |-INFO in ch.qos.logback.core.sift.SiftProcessor@46a4292d - End of configuration. [testng] [2024-05-27 02:55:36,869] [pool-1-thread-2] Initializing /data/ruben/20100827_004/experiment_descriptor.xml: [testng] 02:55:36,870 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:55:36,870 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:55:36,871 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-27_02-55-36.log] [testng] 02:55:36,872 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d1bba7 - End of configuration. [testng] [2024-05-27 02:57:43,858] [pool-1-thread-1] Initializing /data/nadine/experiment_descriptor.xml: [testng] [2024-05-27 02:57:46,975] [pool-1-thread-1] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml: [testng] [2024-05-27 02:58:51,664] [pool-1-thread-10] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml: [testng] [2024-05-27 03:00:35,072] [pool-1-thread-7] Initializing /data/christian/example/experiment_descriptor.xml: [testng] [2024-05-27 03:00:36,608] [pool-1-thread-7] Initializing /data/ruben/161009test2/151009_001/experiment_descriptor.xml: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 901, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 44 minutes 11 seconds Finished: SUCCESS