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Started by upstream project "BIOFORMATS-test-repo" build number 97 originally caused by: Started by upstream project "Trigger" build number 108 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/jenkins16524133617610658187.sh + '[' scanr = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_15023_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] 02:20:47,234 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:20:47,235 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 02:20:47,235 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:20:47,236 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:20:47,237 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:20:47,237 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:20:47,237 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:20:47,237 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:20:47,238 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:20:47,238 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:20:47,238 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:20:47,239 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:20:47,410 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:20:47,410 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:20:47,433 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:20:47,434 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:20:47,439 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:20:47,439 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:20:47,440 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:20:47,440 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:20:47,440 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 02:20:47,441 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 02:20:47,441 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 203 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-06-19 02:20:47,451] [main] java.version = 17.0.2 [testng] 02:20:47,454 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:20:47,454 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:47,498 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-19_02-20-47.log] [testng] 02:20:47,499 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-06-19 02:20:47,502] [main] testng.directory = /data [testng] [2024-06-19 02:20:47,502] [main] testng.configDirectory = /config [testng] [2024-06-19 02:20:47,510] [main] testng.multiplier = 1.0 [testng] [2024-06-19 02:20:47,511] [main] testng.in-memory = false [testng] [2024-06-19 02:20:47,511] [main] testng.allow-missing = false [testng] [2024-06-19 02:20:47,511] [main] user.language = en [testng] [2024-06-19 02:20:47,512] [main] user.country = ${user.country} [testng] [2024-06-19 02:20:47,512] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-06-19 02:26:02,132] [main] ---------------------------------------- [testng] [2024-06-19 02:26:02,133] [main] Total files: 2169 [testng] [2024-06-19 02:26:02,133] [main] Scan time: 314.62 s (145 ms/file) [testng] [2024-06-19 02:26:02,133] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-06-19 02:42:48,406] [pool-1-thread-1] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml: [testng] 02:42:48,407 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:42:48,407 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:42:48,408 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-19_02-42-48.log] [testng] 02:42:48,408 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57e3355b - End of configuration. [testng] [2024-06-19 02:44:02,367] [pool-1-thread-12] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml: [testng] 02:44:02,368 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:44:02,368 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:44:02,369 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-19_02-44-02.log] [testng] 02:44:02,369 |-INFO in ch.qos.logback.core.sift.SiftProcessor@444d1f58 - End of configuration. [testng] [2024-06-19 02:44:02,623] [pool-1-thread-11] Initializing /data/ruben/plate_002/experiment_descriptor.xml: [testng] 02:44:02,623 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:44:02,623 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:44:02,624 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-19_02-44-02.log] [testng] 02:44:02,624 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6b933cb - End of configuration. [testng] [2024-06-19 02:44:02,685] [pool-1-thread-10] Initializing /data/nadine/experiment_descriptor.xml: [testng] 02:44:02,685 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:44:02,685 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:44:02,686 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-19_02-44-02.log] [testng] 02:44:02,686 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a15d87 - End of configuration. [testng] [2024-06-19 02:44:03,064] [pool-1-thread-9] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml: [testng] 02:44:03,064 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:44:03,064 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:44:03,065 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-19_02-44-03.log] [testng] 02:44:03,066 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7211b1de - End of configuration. [testng] [2024-06-19 02:44:36,607] [pool-1-thread-8] Initializing /data/embl/Maik_001/experiment_descriptor.xml: [testng] 02:44:36,608 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:44:36,609 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:44:36,611 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-19_02-44-36.log] [testng] 02:44:36,612 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e6535fe - End of configuration. [testng] [2024-06-19 02:44:42,231] [pool-1-thread-7] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml: [testng] 02:44:42,232 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:44:42,232 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:44:42,235 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-19_02-44-42.log] [testng] 02:44:42,236 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75615228 - End of configuration. [testng] [2024-06-19 02:45:35,628] [pool-1-thread-6] Initializing /data/ruben/161009test2/151009_001/experiment_descriptor.xml: [testng] 02:45:35,629 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:45:35,629 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:45:35,630 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-19_02-45-35.log] [testng] 02:45:35,631 |-INFO in ch.qos.logback.core.sift.SiftProcessor@bce76b3 - End of configuration. [testng] [2024-06-19 02:48:12,466] [pool-1-thread-5] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml: [testng] 02:48:12,467 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:48:12,467 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:48:12,469 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-19_02-48-12.log] [testng] 02:48:12,470 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3cbb3301 - End of configuration. [testng] [2024-06-19 02:48:54,336] [pool-1-thread-4] Initializing /data/gideon/experiment_descriptor.xml: [testng] 02:48:54,336 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:48:54,336 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:48:54,338 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-19_02-48-54.log] [testng] 02:48:54,338 |-INFO in ch.qos.logback.core.sift.SiftProcessor@63cda7e6 - End of configuration. [testng] [2024-06-19 02:49:27,515] [pool-1-thread-3] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml: [testng] 02:49:27,515 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:49:27,515 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:49:27,516 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-19_02-49-27.log] [testng] 02:49:27,517 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5394169b - End of configuration. [testng] [2024-06-19 02:49:28,536] [pool-1-thread-2] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml: [testng] 02:49:28,537 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:49:28,537 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:49:28,538 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-19_02-49-28.log] [testng] 02:49:28,538 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3100407b - End of configuration. [testng] [2024-06-19 02:51:05,265] [pool-1-thread-10] Initializing /data/juergen/Experiment/experiment_descriptor.xml: [testng] [2024-06-19 02:51:08,663] [pool-1-thread-10] Initializing /data/christian/example/experiment_descriptor.xml: [testng] [2024-06-19 02:51:10,718] [pool-1-thread-10] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml: [testng] [2024-06-19 02:52:49,931] [pool-1-thread-8] Initializing /data/ruben/20100827_004/experiment_descriptor.xml: [testng] [2024-06-19 02:52:53,839] [pool-1-thread-11] Initializing /data/ruben/280809_8wellLT_008/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: 37 minutes 43 seconds Finished: SUCCESS