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Started by upstream project "BIOFORMATS-test-repo" build number 7 originally caused by: Started by upstream project "Trigger" build number 10 originally caused by: Started by timer 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/jenkins5936887842988076059.sh + '[' scanr = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_1069_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. [javac] 4 warnings 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] 07:51:15,895 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 07:51:15,896 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 07:51:15,896 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 07:51:15,897 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 07:51:15,898 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 07:51:15,898 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 07:51:15,898 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 07:51:15,898 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 07:51:15,899 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 07:51:15,899 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 07:51:15,900 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 07:51:15,900 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 07:51:16,071 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 07:51:16,071 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 07:51:16,099 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 07:51:16,099 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 07:51:16,106 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 07:51:16,106 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 07:51:16,106 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 07:51:16,107 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 07:51:16,107 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 07:51:16,107 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 07:51:16,108 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 209 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-21 07:51:16,117] [main] java.version = 21 [testng] 07:51:16,121 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 07:51:16,121 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:51:16,165 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-21_07-51-16.log] [testng] 07:51:16,166 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-03-21 07:51:16,168] [main] testng.directory = /data [testng] [2024-03-21 07:51:16,168] [main] testng.configDirectory = /config [testng] [2024-03-21 07:51:16,177] [main] testng.multiplier = 1.0 [testng] [2024-03-21 07:51:16,178] [main] testng.in-memory = false [testng] [2024-03-21 07:51:16,178] [main] testng.allow-missing = false [testng] [2024-03-21 07:51:16,178] [main] user.language = en [testng] [2024-03-21 07:51:16,178] [main] user.country = ${user.country} [testng] [2024-03-21 07:51:16,178] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-03-21 07:55:21,150] [main] ---------------------------------------- [testng] [2024-03-21 07:55:21,150] [main] Total files: 2169 [testng] [2024-03-21 07:55:21,150] [main] Scan time: 244.972 s (112 ms/file) [testng] [2024-03-21 07:55:21,151] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-21 08:18:58,984] [pool-1-thread-1] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml: [testng] 08:18:58,985 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 08:18:58,985 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:18:58,987 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-21_08-18-58.log] [testng] 08:18:58,988 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a8c2d7c - End of configuration. [testng] [2024-03-21 08:19:20,691] [pool-1-thread-12] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml: [testng] 08:19:20,691 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 08:19:20,691 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:19:20,692 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-21_08-19-20.log] [testng] 08:19:20,693 |-INFO in ch.qos.logback.core.sift.SiftProcessor@113be424 - End of configuration. [testng] [2024-03-21 08:21:28,248] [pool-1-thread-11] Initializing /data/ruben/161009test2/151009_001/experiment_descriptor.xml: [testng] 08:21:28,248 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 08:21:28,249 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:21:28,251 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-21_08-21-28.log] [testng] 08:21:28,251 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14e967e8 - End of configuration. [testng] [2024-03-21 08:25:13,575] [pool-1-thread-10] Initializing /data/nadine/experiment_descriptor.xml: [testng] 08:25:13,575 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 08:25:13,575 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:25:13,577 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-21_08-25-13.log] [testng] 08:25:13,577 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4894a29a - End of configuration. [testng] [2024-03-21 08:25:14,417] [pool-1-thread-9] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml: [testng] 08:25:14,417 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 08:25:14,417 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:25:14,418 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-21_08-25-14.log] [testng] 08:25:14,419 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6718173a - End of configuration. [testng] [2024-03-21 08:25:17,182] [pool-1-thread-8] Initializing /data/ruben/20100827_004/experiment_descriptor.xml: [testng] 08:25:17,182 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 08:25:17,182 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:25:17,183 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-21_08-25-17.log] [testng] 08:25:17,184 |-INFO in ch.qos.logback.core.sift.SiftProcessor@51b7fbfa - End of configuration. [testng] [2024-03-21 08:27:11,424] [pool-1-thread-7] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml: [testng] 08:27:11,424 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 08:27:11,425 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:27:11,427 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-21_08-27-11.log] [testng] 08:27:11,427 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d431695 - End of configuration. [testng] [2024-03-21 08:28:31,095] [pool-1-thread-6] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml: [testng] 08:28:31,095 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 08:28:31,096 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:28:31,097 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-21_08-28-31.log] [testng] 08:28:31,097 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3be774f1 - End of configuration. [testng] [2024-03-21 08:28:46,749] [pool-1-thread-5] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml: [testng] 08:28:46,750 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 08:28:46,750 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:28:46,752 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-21_08-28-46.log] [testng] 08:28:46,753 |-INFO in ch.qos.logback.core.sift.SiftProcessor@712c9e82 - End of configuration. [testng] [2024-03-21 08:30:02,823] [pool-1-thread-4] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml: [testng] 08:30:02,823 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 08:30:02,823 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:30:02,825 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-21_08-30-02.log] [testng] 08:30:02,825 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57cc9fff - End of configuration. [testng] [2024-03-21 08:33:36,871] [pool-1-thread-3] Initializing /data/ruben/plate_002/experiment_descriptor.xml: [testng] 08:33:36,872 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 08:33:36,872 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:33:36,873 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-21_08-33-36.log] [testng] 08:33:36,874 |-INFO in ch.qos.logback.core.sift.SiftProcessor@373b5721 - End of configuration. [testng] [2024-03-21 08:33:40,382] [pool-1-thread-2] Initializing /data/embl/Maik_001/experiment_descriptor.xml: [testng] 08:33:40,382 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 08:33:40,382 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:33:40,384 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-21_08-33-40.log] [testng] 08:33:40,384 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5dea054e - End of configuration. [testng] [2024-03-21 08:34:02,276] [pool-1-thread-10] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml: [testng] [2024-03-21 08:35:44,155] [pool-1-thread-3] Initializing /data/christian/example/experiment_descriptor.xml: [testng] [2024-03-21 08:35:52,491] [pool-1-thread-3] Initializing /data/gideon/experiment_descriptor.xml: [testng] [2024-03-21 08:37:18,692] [pool-1-thread-9] Initializing /data/juergen/Experiment/experiment_descriptor.xml: [testng] [2024-03-21 08:37:28,636] [pool-1-thread-2] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml: [testng] 09:18:41,469 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 09:18:41,469 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:18:41,470 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-21_09-18-41.log] [testng] 09:18:41,470 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14e9eace - End of configuration. [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 901, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 87 minutes 29 seconds Finished: SUCCESS