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Started by upstream project "BIOFORMATS-test-repo" build number 309 originally caused by: Started by upstream project "Trigger" build number 331 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins14277920125780431568.sh + '[' scanr = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_49009_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] 03:28:21,208 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:28:21,209 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 03:28:21,209 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:28:21,210 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:28:21,210 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:28:21,210 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:28:21,211 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 03:28:21,211 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:28:21,211 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:28:21,212 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:28:21,212 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:28:21,212 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:28:21,370 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:28:21,370 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:28:21,392 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:28:21,392 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:28:21,397 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:28:21,397 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:28:21,397 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:28:21,398 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:28:21,398 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 03:28:21,399 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 03:28:21,399 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 188 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-01-05 03:28:21,407] [main] java.version = 17.0.2 [testng] 03:28:21,410 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:28:21,411 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:28:21,451 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-01-05_03-28-21.log] [testng] 03:28:21,452 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2025-01-05 03:28:21,454] [main] testng.directory = /data [testng] [2025-01-05 03:28:21,454] [main] testng.configDirectory = /config [testng] [2025-01-05 03:28:21,463] [main] testng.multiplier = 1.0 [testng] [2025-01-05 03:28:21,463] [main] testng.in-memory = false [testng] [2025-01-05 03:28:21,463] [main] testng.allow-missing = false [testng] [2025-01-05 03:28:21,464] [main] user.language = en [testng] [2025-01-05 03:28:21,464] [main] user.country = ${user.country} [testng] [2025-01-05 03:28:21,464] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-01-05 03:33:15,782] [main] ---------------------------------------- [testng] [2025-01-05 03:33:15,783] [main] Total files: 2169 [testng] [2025-01-05 03:33:15,783] [main] Scan time: 294.318 s (135 ms/file) [testng] [2025-01-05 03:33:15,783] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-01-05 03:51:49,462] [pool-1-thread-1] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml: [testng] 03:51:49,463 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:51:49,463 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:51:49,464 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-01-05_03-51-49.log] [testng] 03:51:49,464 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6985c9ed - End of configuration. [testng] [2025-01-05 03:53:06,720] [pool-1-thread-12] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml: [testng] 03:53:06,720 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:53:06,720 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:53:06,722 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-01-05_03-53-06.log] [testng] 03:53:06,723 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ee5cc3c - End of configuration. [testng] [2025-01-05 03:53:11,041] [pool-1-thread-11] Initializing /data/ruben/20100827_004/experiment_descriptor.xml: [testng] 03:53:11,041 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:53:11,041 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:53:11,042 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-01-05_03-53-11.log] [testng] 03:53:11,043 |-INFO in ch.qos.logback.core.sift.SiftProcessor@753ed5f9 - End of configuration. [testng] [2025-01-05 03:54:17,512] [pool-1-thread-10] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml: [testng] 03:54:17,512 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:54:17,512 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:54:17,514 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-01-05_03-54-17.log] [testng] 03:54:17,514 |-INFO in ch.qos.logback.core.sift.SiftProcessor@61f8351 - End of configuration. [testng] [2025-01-05 03:54:31,363] [pool-1-thread-9] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml: [testng] 03:54:31,363 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:54:31,363 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:54:31,363 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-01-05_03-54-31.log] [testng] 03:54:31,364 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68338ff1 - End of configuration. [testng] [2025-01-05 03:55:39,603] [pool-1-thread-8] Initializing /data/nadine/experiment_descriptor.xml: [testng] 03:55:39,603 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:55:39,603 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:55:39,604 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-01-05_03-55-39.log] [testng] 03:55:39,604 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ef5ebb9 - End of configuration. [testng] [2025-01-05 03:55:40,768] [pool-1-thread-7] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml: [testng] 03:55:40,768 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:55:40,768 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:55:40,769 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-01-05_03-55-40.log] [testng] 03:55:40,769 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4ebc06b4 - End of configuration. [testng] [2025-01-05 03:55:49,884] [pool-1-thread-6] Initializing /data/ruben/161009test2/151009_001/experiment_descriptor.xml: [testng] 03:55:49,884 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:55:49,884 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:55:49,885 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-01-05_03-55-49.log] [testng] 03:55:49,886 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c91519d - End of configuration. [testng] [2025-01-05 03:57:19,529] [pool-1-thread-5] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml: [testng] 03:57:19,529 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:57:19,529 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:57:19,530 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-01-05_03-57-19.log] [testng] 03:57:19,530 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8f0cf82 - End of configuration. [testng] [2025-01-05 03:57:50,218] [pool-1-thread-4] Initializing /data/ruben/plate_002/experiment_descriptor.xml: [testng] 03:57:50,219 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:57:50,219 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:57:50,219 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-01-05_03-57-50.log] [testng] 03:57:50,220 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8b1fe32 - End of configuration. [testng] [2025-01-05 03:57:52,347] [pool-1-thread-3] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml: [testng] 03:57:52,347 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:57:52,347 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:57:52,348 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-01-05_03-57-52.log] [testng] 03:57:52,348 |-INFO in ch.qos.logback.core.sift.SiftProcessor@54be2924 - End of configuration. [testng] [2025-01-05 04:00:18,647] [pool-1-thread-2] Initializing /data/christian/example/experiment_descriptor.xml: [testng] 04:00:18,648 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 04:00:18,648 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:00:18,649 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-01-05_04-00-18.log] [testng] 04:00:18,649 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7447d428 - End of configuration. [testng] [2025-01-05 04:00:38,184] [pool-1-thread-2] Initializing /data/embl/Maik_001/experiment_descriptor.xml: [testng] [2025-01-05 04:01:03,453] [pool-1-thread-8] Initializing /data/gideon/experiment_descriptor.xml: [testng] [2025-01-05 04:03:21,616] [pool-1-thread-4] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml: [testng] [2025-01-05 04:08:04,791] [pool-1-thread-12] Initializing /data/juergen/Experiment/experiment_descriptor.xml: [testng] [2025-01-05 04:08:40,537] [pool-1-thread-12] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml: [testng] 05:14:18,981 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 05:14:18,981 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:14:18,982 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-01-05_05-14-18.log] [testng] 05:14:18,983 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20848764 - End of configuration. [testng] 05:14:20,608 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 05:14:20,608 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:14:20,610 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-01-05_05-14-20.log] [testng] 05:14:20,610 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60256db6 - End of configuration. [testng] 05:17:17,947 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 05:17:17,947 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:17:17,949 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-01-05_05-17-17.log] [testng] 05:17:17,949 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4dd8cc5c - End of configuration. [testng] 05:18:35,712 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 05:18:35,712 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:18:35,713 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-01-05_05-18-35.log] [testng] 05:18:35,713 |-INFO in ch.qos.logback.core.sift.SiftProcessor@103169c1 - End of configuration. [testng] 05:23:50,090 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 05:23:50,091 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:23:50,092 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-01-05_05-23-50.log] [testng] 05:23:50,092 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e4d2e2d - 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: 115 minutes 33 seconds Finished: SUCCESS