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Started by upstream project "BIOFORMATS-test-repo" build number 241 originally caused by: Started by upstream project "Trigger" build number 266 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/jenkins5733751126326212904.sh + '[' scanr = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_37966_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 test-automated: [testng] File leak detector installed [testng] 02:55:39,779 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:55:39,781 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 02:55:39,781 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:55:39,782 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:55:39,782 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:55:39,782 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:55:39,782 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:55:39,782 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:55:39,783 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:55:39,783 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:55:39,783 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:55:39,783 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:55:40,014 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:55:40,014 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:55:40,042 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:55:40,042 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:55:40,050 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:55:40,050 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:55:40,050 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:55:40,050 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:55:40,051 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 02:55:40,051 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 02:55:40,051 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 268 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-01 02:55:40,061] [main] java.version = 1.8.0_342 [testng] 02:55:40,065 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:55:40,065 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:55:40,111 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-01_02-55-40.log] [testng] 02:55:40,113 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-11-01 02:55:40,115] [main] testng.directory = /data [testng] [2024-11-01 02:55:40,115] [main] testng.configDirectory = /config [testng] [2024-11-01 02:55:40,127] [main] testng.multiplier = 1.0 [testng] [2024-11-01 02:55:40,127] [main] testng.in-memory = false [testng] [2024-11-01 02:55:40,128] [main] testng.allow-missing = false [testng] [2024-11-01 02:55:40,128] [main] user.language = en [testng] [2024-11-01 02:55:40,128] [main] user.country = ${user.country} [testng] [2024-11-01 02:55:40,128] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-11-01 03:00:13,252] [main] ---------------------------------------- [testng] [2024-11-01 03:00:13,253] [main] Total files: 2169 [testng] [2024-11-01 03:00:13,253] [main] Scan time: 273.124 s (125 ms/file) [testng] [2024-11-01 03:00:13,253] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-01 03:17:43,037] [pool-1-thread-1] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml: [testng] 03:17:43,038 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:17:43,038 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:17:43,039 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-01_03-17-43.log] [testng] 03:17:43,039 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56e69187 - End of configuration. [testng] [2024-11-01 03:19:40,213] [pool-1-thread-12] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml: [testng] 03:19:40,213 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:19:40,213 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:19:40,215 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-01_03-19-40.log] [testng] 03:19:40,215 |-INFO in ch.qos.logback.core.sift.SiftProcessor@312c4b1e - End of configuration. [testng] [2024-11-01 03:19:47,117] [pool-1-thread-11] Initializing /data/ruben/20100827_004/experiment_descriptor.xml: [testng] 03:19:47,118 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:19:47,118 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:19:47,119 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-01_03-19-47.log] [testng] 03:19:47,119 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9f44ae3 - End of configuration. [testng] [2024-11-01 03:21:17,163] [pool-1-thread-10] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml: [testng] 03:21:17,163 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:21:17,164 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:21:17,164 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-01_03-21-17.log] [testng] 03:21:17,165 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5486510e - End of configuration. [testng] [2024-11-01 03:21:28,832] [pool-1-thread-9] Initializing /data/gideon/experiment_descriptor.xml: [testng] 03:21:28,832 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:21:28,832 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:21:28,833 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-01_03-21-28.log] [testng] 03:21:28,833 |-INFO in ch.qos.logback.core.sift.SiftProcessor@42e03df8 - End of configuration. [testng] [2024-11-01 03:21:51,465] [pool-1-thread-8] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml: [testng] 03:21:51,465 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:21:51,465 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:21:51,466 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-01_03-21-51.log] [testng] 03:21:51,467 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18c23057 - End of configuration. [testng] [2024-11-01 03:22:30,722] [pool-1-thread-7] Initializing /data/ruben/plate_002/experiment_descriptor.xml: [testng] 03:22:30,722 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:22:30,722 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:22:30,723 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-01_03-22-30.log] [testng] 03:22:30,723 |-INFO in ch.qos.logback.core.sift.SiftProcessor@dd9f651 - End of configuration. [testng] [2024-11-01 03:22:33,201] [pool-1-thread-6] Initializing /data/embl/Maik_001/experiment_descriptor.xml: [testng] 03:22:33,202 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:22:33,202 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:22:33,202 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-01_03-22-33.log] [testng] 03:22:33,203 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3af49ceb - End of configuration. [testng] [2024-11-01 03:22:38,466] [pool-1-thread-5] Initializing /data/christian/example/experiment_descriptor.xml: [testng] 03:22:38,466 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:22:38,466 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:22:38,468 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-01_03-22-38.log] [testng] 03:22:38,468 |-INFO in ch.qos.logback.core.sift.SiftProcessor@786e052e - End of configuration. [testng] [2024-11-01 03:22:39,277] [pool-1-thread-4] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml: [testng] 03:22:39,277 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:22:39,278 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:22:39,278 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-01_03-22-39.log] [testng] 03:22:39,278 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71a7f219 - End of configuration. [testng] [2024-11-01 03:23:14,361] [pool-1-thread-3] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml: [testng] 03:23:14,362 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:23:14,362 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:23:14,363 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-01_03-23-14.log] [testng] 03:23:14,365 |-INFO in ch.qos.logback.core.sift.SiftProcessor@28ca078d - End of configuration. [testng] [2024-11-01 03:23:49,543] [pool-1-thread-2] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml: [testng] 03:23:49,543 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:23:49,543 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:23:49,545 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-01_03-23-49.log] [testng] 03:23:49,545 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b1bd579 - End of configuration. [testng] [2024-11-01 03:25:57,422] [pool-1-thread-5] Initializing /data/ruben/161009test2/151009_001/experiment_descriptor.xml: [testng] [2024-11-01 03:28:45,887] [pool-1-thread-7] Initializing /data/juergen/Experiment/experiment_descriptor.xml: [testng] [2024-11-01 03:29:16,006] [pool-1-thread-7] Initializing /data/nadine/experiment_descriptor.xml: [testng] [2024-11-01 03:29:53,372] [pool-1-thread-7] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml: [testng] [2024-11-01 03:33:26,299] [pool-1-thread-12] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml: [testng] 04:40:00,402 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 04:40:00,402 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:40:00,403 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-01_04-40-00.log] [testng] 04:40:00,403 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f388188 - End of configuration. [testng] 04:40:52,403 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 04:40:52,403 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:40:52,405 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-01_04-40-52.log] [testng] 04:40:52,405 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1656ef00 - End of configuration. [testng] 04:42:38,393 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 04:42:38,393 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:42:38,395 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-01_04-42-38.log] [testng] 04:42:38,395 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e11cf8d - End of configuration. [testng] 04:44:51,022 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 04:44:51,022 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:44:51,023 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-01_04-44-51.log] [testng] 04:44:51,023 |-INFO in ch.qos.logback.core.sift.SiftProcessor@382ebbba - End of configuration. [testng] 04:49:32,581 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 04:49:32,581 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:49:32,582 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-01_04-49-32.log] [testng] 04:49:32,582 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3bd710f8 - 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: 113 minutes 55 seconds Finished: SUCCESS