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Started by upstream project "BIOFORMATS-test-repo" build number 264 originally caused by: Started by upstream project "Trigger" build number 287 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@6 [BIOFORMATS-test-folder@6] $ /bin/bash -xe /tmp/jenkins2646781666394623042.sh + '[' scanr = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_41738_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] 04:07:44,466 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 04:07:44,467 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 04:07:44,467 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 04:07:44,468 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 04:07:44,469 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 04:07:44,469 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 04:07:44,469 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 04:07:44,469 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 04:07:44,470 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 04:07:44,470 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 04:07:44,470 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 04:07:44,470 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 04:07:44,698 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 04:07:44,699 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 04:07:44,726 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 04:07:44,727 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 04:07:44,735 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 04:07:44,735 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 04:07:44,735 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 04:07:44,735 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 04:07:44,735 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 04:07:44,736 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 04:07:44,736 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 266 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-22 04:07:44,746] [main] java.version = 1.8.0_342 [testng] 04:07:44,750 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 04:07:44,750 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:07:44,795 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-22_04-07-44.log] [testng] 04:07:44,796 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-11-22 04:07:44,798] [main] testng.directory = /data [testng] [2024-11-22 04:07:44,799] [main] testng.configDirectory = /config [testng] [2024-11-22 04:07:44,811] [main] testng.multiplier = 1.0 [testng] [2024-11-22 04:07:44,811] [main] testng.in-memory = false [testng] [2024-11-22 04:07:44,811] [main] testng.allow-missing = false [testng] [2024-11-22 04:07:44,811] [main] user.language = en [testng] [2024-11-22 04:07:44,811] [main] user.country = ${user.country} [testng] [2024-11-22 04:07:44,811] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-11-22 04:11:58,051] [main] ---------------------------------------- [testng] [2024-11-22 04:11:58,052] [main] Total files: 2169 [testng] [2024-11-22 04:11:58,052] [main] Scan time: 253.24 s (116 ms/file) [testng] [2024-11-22 04:11:58,052] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-22 04:33:15,136] [pool-1-thread-1] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml: [testng] 04:33:15,136 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 04:33:15,136 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:33:15,137 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-22_04-33-15.log] [testng] 04:33:15,138 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6980379f - End of configuration. [testng] [2024-11-22 04:36:05,147] [pool-1-thread-12] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml: [testng] 04:36:05,147 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 04:36:05,148 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:36:05,149 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-22_04-36-05.log] [testng] 04:36:05,149 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2d1135be - End of configuration. [testng] [2024-11-22 04:36:14,139] [pool-1-thread-11] Initializing /data/ruben/20100827_004/experiment_descriptor.xml: [testng] 04:36:14,140 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 04:36:14,140 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:36:14,141 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-22_04-36-14.log] [testng] 04:36:14,142 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4ccf94dd - End of configuration. [testng] [2024-11-22 04:38:19,679] [pool-1-thread-10] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml: [testng] 04:38:19,680 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 04:38:19,680 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:38:19,681 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-22_04-38-19.log] [testng] 04:38:19,681 |-INFO in ch.qos.logback.core.sift.SiftProcessor@576f3991 - End of configuration. [testng] [2024-11-22 04:38:34,240] [pool-1-thread-9] Initializing /data/gideon/experiment_descriptor.xml: [testng] 04:38:34,241 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 04:38:34,241 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:38:34,241 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-22_04-38-34.log] [testng] 04:38:34,242 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56a1afd2 - End of configuration. [testng] [2024-11-22 04:39:03,120] [pool-1-thread-8] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml: [testng] 04:39:03,120 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 04:39:03,120 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:39:03,121 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-22_04-39-03.log] [testng] 04:39:03,121 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68188a13 - End of configuration. [testng] [2024-11-22 04:39:57,101] [pool-1-thread-7] Initializing /data/ruben/plate_002/experiment_descriptor.xml: [testng] 04:39:57,101 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 04:39:57,101 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:39:57,102 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-22_04-39-57.log] [testng] 04:39:57,102 |-INFO in ch.qos.logback.core.sift.SiftProcessor@30e024a3 - End of configuration. [testng] [2024-11-22 04:40:01,011] [pool-1-thread-6] Initializing /data/embl/Maik_001/experiment_descriptor.xml: [testng] 04:40:01,011 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 04:40:01,011 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:40:01,012 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-22_04-40-01.log] [testng] 04:40:01,012 |-INFO in ch.qos.logback.core.sift.SiftProcessor@606ca299 - End of configuration. [testng] [2024-11-22 04:40:10,228] [pool-1-thread-5] Initializing /data/christian/example/experiment_descriptor.xml: [testng] 04:40:10,228 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 04:40:10,228 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:40:10,229 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-22_04-40-10.log] [testng] 04:40:10,229 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a63d06a - End of configuration. [testng] [2024-11-22 04:40:11,447] [pool-1-thread-4] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml: [testng] 04:40:11,447 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 04:40:11,447 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:40:11,448 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-22_04-40-11.log] [testng] 04:40:11,448 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b1903f5 - End of configuration. [testng] [2024-11-22 04:41:15,384] [pool-1-thread-3] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml: [testng] 04:41:15,384 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 04:41:15,385 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:41:15,385 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-22_04-41-15.log] [testng] 04:41:15,386 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d084fff - End of configuration. [testng] [2024-11-22 04:42:05,231] [pool-1-thread-2] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml: [testng] 04:42:05,232 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 04:42:05,232 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:42:05,232 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-22_04-42-05.log] [testng] 04:42:05,233 |-INFO in ch.qos.logback.core.sift.SiftProcessor@167d5c83 - End of configuration. [testng] [2024-11-22 04:45:00,422] [pool-1-thread-5] Initializing /data/ruben/161009test2/151009_001/experiment_descriptor.xml: [testng] [2024-11-22 04:49:53,625] [pool-1-thread-7] Initializing /data/juergen/Experiment/experiment_descriptor.xml: [testng] [2024-11-22 04:50:48,858] [pool-1-thread-7] Initializing /data/nadine/experiment_descriptor.xml: [testng] [2024-11-22 04:51:55,312] [pool-1-thread-7] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml: [testng] [2024-11-22 04:57:50,445] [pool-1-thread-12] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml: [testng] 05:48:48,011 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 05:48:48,011 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:48:48,012 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-22_05-48-48.log] [testng] 05:48:48,012 |-INFO in ch.qos.logback.core.sift.SiftProcessor@62b36a52 - End of configuration. [testng] 05:49:12,453 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 05:49:12,453 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:49:12,455 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-22_05-49-12.log] [testng] 05:49:12,456 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6f69b5dd - End of configuration. [testng] 06:30:18,677 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 06:30:18,677 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:30:18,679 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-22_06-30-18.log] [testng] 06:30:18,680 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ac73e7c - End of configuration. [testng] 06:42:43,490 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 06:42:43,490 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:42:43,491 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-22_06-42-43.log] [testng] 06:42:43,492 |-INFO in ch.qos.logback.core.sift.SiftProcessor@206ef2f4 - End of configuration. [testng] 06:43:20,192 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 06:43:20,192 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:43:20,192 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-22_06-43-20.log] [testng] 06:43:20,193 |-INFO in ch.qos.logback.core.sift.SiftProcessor@579343d8 - End of configuration. [testng] 06:45:51,885 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 06:45:51,885 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:45:51,885 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-22_06-45-51.log] [testng] 06:45:51,886 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48d49518 - End of configuration. [testng] 06:49:22,518 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 06:49:22,518 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:49:22,518 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-22_06-49-22.log] [testng] 06:49:22,519 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6fe4ec92 - End of configuration. [testng] 06:56:21,452 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 06:56:21,452 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:56:21,453 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-22_06-56-21.log] [testng] 06:56:21,454 |-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: 168 minutes 39 seconds Finished: SUCCESS