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Started by upstream project "BIOFORMATS-test-repo" build number 314 originally caused by: Started by upstream project "Trigger" build number 336 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5 [BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins17988604039252675422.sh + '[' scanr = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_49834_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] 04:03:53,426 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 04:03:53,428 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 04:03:53,428 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 04:03:53,430 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 04:03:53,430 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 04:03:53,430 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 04:03:53,430 |-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] 04:03:53,430 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 04:03:53,431 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 04:03:53,431 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 04:03:53,431 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 04:03:53,431 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 04:03:53,675 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 04:03:53,675 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 04:03:53,717 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 04:03:53,717 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 04:03:53,730 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 04:03:53,730 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 04:03:53,730 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 04:03:53,731 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 04:03:53,731 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 04:03:53,732 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 04:03:53,733 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 302 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-01-10 04:03:53,748] [main] java.version = 1.8.0_342 [testng] 04:03:53,753 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 04:03:53,753 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:03:53,818 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-01-10_04-03-53.log] [testng] 04:03:53,820 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2025-01-10 04:03:53,822] [main] testng.directory = /data [testng] [2025-01-10 04:03:53,823] [main] testng.configDirectory = /config [testng] [2025-01-10 04:03:53,836] [main] testng.multiplier = 1.0 [testng] [2025-01-10 04:03:53,837] [main] testng.in-memory = false [testng] [2025-01-10 04:03:53,837] [main] testng.allow-missing = false [testng] [2025-01-10 04:03:53,837] [main] user.language = en [testng] [2025-01-10 04:03:53,837] [main] user.country = ${user.country} [testng] [2025-01-10 04:03:53,837] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2025-01-10 04:08:21,060] [main] ---------------------------------------- [testng] [2025-01-10 04:08:21,061] [main] Total files: 2169 [testng] [2025-01-10 04:08:21,061] [main] Scan time: 267.223 s (123 ms/file) [testng] [2025-01-10 04:08:21,062] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-01-10 04:24:27,789] [pool-1-thread-1] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml: [testng] 04:24:27,789 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 04:24:27,789 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:24:27,790 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-01-10_04-24-27.log] [testng] 04:24:27,791 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e7a327b - End of configuration. [testng] [2025-01-10 04:24:40,889] [pool-1-thread-12] Initializing /data/christian/example/experiment_descriptor.xml: [testng] 04:24:40,889 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 04:24:40,889 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:24:40,890 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-01-10_04-24-40.log] [testng] 04:24:40,890 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a5b967a - End of configuration. [testng] [2025-01-10 04:24:41,747] [pool-1-thread-11] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml: [testng] 04:24:41,747 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 04:24:41,747 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:24:41,748 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-01-10_04-24-41.log] [testng] 04:24:41,749 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9a52645 - End of configuration. [testng] [2025-01-10 04:25:15,411] [pool-1-thread-10] Initializing /data/ruben/plate_002/experiment_descriptor.xml: [testng] 04:25:15,411 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 04:25:15,411 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:25:15,413 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-01-10_04-25-15.log] [testng] 04:25:15,413 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e7ff0d6 - End of configuration. [testng] [2025-01-10 04:25:17,866] [pool-1-thread-9] Initializing /data/ruben/161009test2/151009_001/experiment_descriptor.xml: [testng] 04:25:17,866 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 04:25:17,866 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:25:17,866 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-01-10_04-25-17.log] [testng] 04:25:17,867 |-INFO in ch.qos.logback.core.sift.SiftProcessor@769f3269 - End of configuration. [testng] [2025-01-10 04:26:55,838] [pool-1-thread-8] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml: [testng] 04:26:55,838 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 04:26:55,838 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:26:55,839 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-01-10_04-26-55.log] [testng] 04:26:55,839 |-INFO in ch.qos.logback.core.sift.SiftProcessor@64c4c6e0 - End of configuration. [testng] [2025-01-10 04:28:48,086] [pool-1-thread-7] Initializing /data/embl/Maik_001/experiment_descriptor.xml: [testng] 04:28:48,086 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 04:28:48,086 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:28:48,087 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-01-10_04-28-48.log] [testng] 04:28:48,087 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75e10445 - End of configuration. [testng] [2025-01-10 04:28:53,100] [pool-1-thread-6] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml: [testng] 04:28:53,100 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 04:28:53,100 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:28:53,101 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-01-10_04-28-53.log] [testng] 04:28:53,101 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1df3e162 - End of configuration. [testng] [2025-01-10 04:30:42,756] [pool-1-thread-5] Initializing /data/juergen/Experiment/experiment_descriptor.xml: [testng] 04:30:42,756 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 04:30:42,756 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:30:42,758 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-01-10_04-30-42.log] [testng] 04:30:42,758 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71c4d65a - End of configuration. [testng] [2025-01-10 04:30:43,568] [pool-1-thread-4] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml: [testng] 04:30:43,568 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 04:30:43,568 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:30:43,569 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-01-10_04-30-43.log] [testng] 04:30:43,569 |-INFO in ch.qos.logback.core.sift.SiftProcessor@277c0c6c - End of configuration. [testng] [2025-01-10 04:32:06,705] [pool-1-thread-3] Initializing /data/gideon/experiment_descriptor.xml: [testng] 04:32:06,705 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 04:32:06,705 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:32:06,706 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-01-10_04-32-06.log] [testng] 04:32:06,706 |-INFO in ch.qos.logback.core.sift.SiftProcessor@b066a48 - End of configuration. [testng] [2025-01-10 04:32:21,360] [pool-1-thread-2] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml: [testng] 04:32:21,360 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 04:32:21,360 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:32:21,361 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-01-10_04-32-21.log] [testng] 04:32:21,361 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27111f70 - End of configuration. [testng] [2025-01-10 04:32:48,594] [pool-1-thread-12] Initializing /data/ruben/20100827_004/experiment_descriptor.xml: [testng] [2025-01-10 04:34:17,253] [pool-1-thread-5] Initializing /data/nadine/experiment_descriptor.xml: [testng] [2025-01-10 04:34:55,009] [pool-1-thread-5] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml: [testng] [2025-01-10 04:35:58,786] [pool-1-thread-10] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml: [testng] [2025-01-10 04:39:35,323] [pool-1-thread-7] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml: [testng] 05:47:52,064 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 05:47:52,064 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:47:52,065 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-01-10_05-47-52.log] [testng] 05:47:52,066 |-INFO in ch.qos.logback.core.sift.SiftProcessor@710de88b - End of configuration. [testng] 05:47:52,242 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 05:47:52,242 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:47:52,244 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-01-10_05-47-52.log] [testng] 05:47:52,245 |-INFO in ch.qos.logback.core.sift.SiftProcessor@31c17e12 - End of configuration. [testng] 05:50:14,885 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 05:50:14,885 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:50:14,887 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-01-10_05-50-14.log] [testng] 05:50:14,887 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5941944b - End of configuration. [testng] 05:50:17,987 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 05:50:17,987 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:50:17,988 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-01-10_05-50-17.log] [testng] 05:50:17,988 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f56352d - End of configuration. [testng] 05:56:27,020 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 05:56:27,020 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:56:27,021 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-01-10_05-56-27.log] [testng] 05:56:27,022 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c6e3c25 - 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: 112 minutes 38 seconds Finished: SUCCESS