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Started by upstream project "BIOFORMATS-test-repo" build number 33 originally caused by: Started by upstream project "Trigger" build number 37 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/jenkins4331321796050171249.sh + '[' scanr = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_4526_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 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] 02:14:18,097 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:14:18,098 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 02:14:18,098 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:14:18,100 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:14:18,101 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:14:18,101 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:14:18,102 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:14:18,102 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:14:18,103 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:14:18,104 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:14:18,104 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:14:18,105 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:14:18,382 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:14:18,383 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:14:18,427 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:14:18,427 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:14:18,442 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:14:18,443 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:14:18,443 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:14:18,444 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:14:18,444 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 02:14:18,446 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 02:14:18,446 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 343 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-04-14 02:14:18,468] [main] java.version = 17.0.2 [testng] 02:14:18,475 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:14:18,475 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:14:18,541 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-14_02-14-18.log] [testng] 02:14:18,553 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-04-14 02:14:18,572] [main] testng.directory = /data [testng] [2024-04-14 02:14:18,573] [main] testng.configDirectory = /config [testng] [2024-04-14 02:14:18,583] [main] testng.multiplier = 1.0 [testng] [2024-04-14 02:14:18,585] [main] testng.in-memory = false [testng] [2024-04-14 02:14:18,585] [main] testng.allow-missing = false [testng] [2024-04-14 02:14:18,585] [main] user.language = en [testng] [2024-04-14 02:14:18,585] [main] user.country = ${user.country} [testng] [2024-04-14 02:14:18,585] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-04-14 02:19:39,448] [main] ---------------------------------------- [testng] [2024-04-14 02:19:39,448] [main] Total files: 2169 [testng] [2024-04-14 02:19:39,448] [main] Scan time: 320.862 s (147 ms/file) [testng] [2024-04-14 02:19:39,448] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-04-14 02:37:34,096] [pool-1-thread-1] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml: [testng] 02:37:34,096 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:37:34,097 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:37:34,098 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-14_02-37-34.log] [testng] 02:37:34,098 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57d06e46 - End of configuration. [testng] [2024-04-14 02:37:34,452] [pool-1-thread-12] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml: [testng] 02:37:34,452 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:37:34,452 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:37:34,453 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-14_02-37-34.log] [testng] 02:37:34,453 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2cd1cbcc - End of configuration. [testng] [2024-04-14 02:39:31,275] [pool-1-thread-11] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml: [testng] 02:39:31,276 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:39:31,276 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:39:31,278 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-14_02-39-31.log] [testng] 02:39:31,279 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f24f1c7 - End of configuration. [testng] [2024-04-14 02:39:32,533] [pool-1-thread-10] Initializing /data/ruben/20100827_004/experiment_descriptor.xml: [testng] 02:39:32,533 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:39:32,534 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:39:32,535 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-14_02-39-32.log] [testng] 02:39:32,535 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2c9cc5d7 - End of configuration. [testng] [2024-04-14 02:40:13,404] [pool-1-thread-9] Initializing /data/juergen/Experiment/experiment_descriptor.xml: [testng] 02:40:13,405 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:40:13,405 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:13,406 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-14_02-40-13.log] [testng] 02:40:13,406 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f8a7185 - End of configuration. [testng] [2024-04-14 02:40:13,727] [pool-1-thread-8] Initializing /data/nadine/experiment_descriptor.xml: [testng] 02:40:13,727 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:40:13,727 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:13,728 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-14_02-40-13.log] [testng] 02:40:13,728 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9c27da4 - End of configuration. [testng] [2024-04-14 02:40:14,130] [pool-1-thread-7] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml: [testng] 02:40:14,131 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:40:14,131 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:14,132 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-14_02-40-14.log] [testng] 02:40:14,132 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ee20634 - End of configuration. [testng] [2024-04-14 02:42:05,339] [pool-1-thread-6] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml: [testng] 02:42:05,339 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:42:05,340 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:42:05,341 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-14_02-42-05.log] [testng] 02:42:05,341 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e213dfd - End of configuration. [testng] [2024-04-14 02:43:13,483] [pool-1-thread-5] Initializing /data/gideon/experiment_descriptor.xml: [testng] 02:43:13,484 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:43:13,484 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:43:13,485 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-14_02-43-13.log] [testng] 02:43:13,486 |-INFO in ch.qos.logback.core.sift.SiftProcessor@310f2c99 - End of configuration. [testng] [2024-04-14 02:43:49,643] [pool-1-thread-4] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml: [testng] 02:43:49,644 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:43:49,644 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:43:49,646 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-14_02-43-49.log] [testng] 02:43:49,647 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f8c89ad - End of configuration. [testng] [2024-04-14 02:44:21,617] [pool-1-thread-3] Initializing /data/christian/example/experiment_descriptor.xml: [testng] 02:44:21,618 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:44:21,618 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:44:21,619 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-14_02-44-21.log] [testng] 02:44:21,620 |-INFO in ch.qos.logback.core.sift.SiftProcessor@33b4dd5e - End of configuration. [testng] [2024-04-14 02:44:21,793] [pool-1-thread-2] Initializing /data/ruben/161009test2/151009_001/experiment_descriptor.xml: [testng] 02:44:21,794 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:44:21,794 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:44:21,795 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-14_02-44-21.log] [testng] 02:44:21,796 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22616914 - End of configuration. [testng] [2024-04-14 02:48:19,140] [pool-1-thread-3] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml: [testng] [2024-04-14 02:48:40,082] [pool-1-thread-8] Initializing /data/embl/Maik_001/experiment_descriptor.xml: [testng] [2024-04-14 02:48:50,537] [pool-1-thread-9] Initializing /data/ruben/plate_002/experiment_descriptor.xml: [testng] [2024-04-14 02:48:56,910] [pool-1-thread-1] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml: [testng] [2024-04-14 02:50:31,998] [pool-1-thread-9] Initializing /data/ruben/161009test2/151009_002/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: 42 minutes 42 seconds Finished: SUCCESS