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Started by upstream project "BIOFORMATS-test-repo" build number 23 originally caused by: Started by upstream project "Trigger" build number 26 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/jenkins10625747991469474238.sh + '[' scanr = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_2886_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] 02:18:22,848 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:18:22,850 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 02:18:22,850 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:18:22,852 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:18:22,852 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:18:22,852 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:18:22,853 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:18:22,853 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:18:22,853 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:18:22,854 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:18:22,854 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:18:22,854 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:18:23,093 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:18:23,094 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:18:23,122 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:18:23,122 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:18:23,135 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:18:23,135 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:18:23,135 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:18:23,136 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:18:23,136 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 02:18:23,137 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 02:18:23,137 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 284 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-04-05 02:18:23,150] [main] java.version = 1.8.0_342 [testng] 02:18:23,155 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:18:23,155 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:18:23,204 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-05_02-18-23.log] [testng] 02:18:23,206 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-04-05 02:18:23,208] [main] testng.directory = /data [testng] [2024-04-05 02:18:23,208] [main] testng.configDirectory = /config [testng] [2024-04-05 02:18:23,222] [main] testng.multiplier = 1.0 [testng] [2024-04-05 02:18:23,222] [main] testng.in-memory = false [testng] [2024-04-05 02:18:23,222] [main] testng.allow-missing = false [testng] [2024-04-05 02:18:23,222] [main] user.language = en [testng] [2024-04-05 02:18:23,222] [main] user.country = ${user.country} [testng] [2024-04-05 02:18:23,222] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-04-05 02:23:57,571] [main] ---------------------------------------- [testng] [2024-04-05 02:23:57,572] [main] Total files: 2169 [testng] [2024-04-05 02:23:57,572] [main] Scan time: 334.349 s (154 ms/file) [testng] [2024-04-05 02:23:57,573] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-04-05 02:41:37,759] [pool-1-thread-1] Initializing /data/ruben/161009test2/151009_001/experiment_descriptor.xml: [testng] 02:41:37,760 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:41:37,760 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:41:37,761 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-05_02-41-37.log] [testng] 02:41:37,762 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65e22a7a - End of configuration. [testng] [2024-04-05 02:44:31,202] [pool-1-thread-12] Initializing /data/ruben/plate_002/experiment_descriptor.xml: [testng] 02:44:31,202 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:44:31,202 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:44:31,204 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-05_02-44-31.log] [testng] 02:44:31,205 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d1bba7 - End of configuration. [testng] [2024-04-05 02:44:31,314] [pool-1-thread-11] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml: [testng] 02:44:31,315 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:44:31,315 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:44:31,315 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-05_02-44-31.log] [testng] 02:44:31,316 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5dd9fee7 - End of configuration. [testng] [2024-04-05 02:45:45,027] [pool-1-thread-10] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml: [testng] 02:45:45,028 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:45:45,028 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:45:45,029 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-05_02-45-45.log] [testng] 02:45:45,029 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48884e02 - End of configuration. [testng] [2024-04-05 02:46:56,393] [pool-1-thread-9] Initializing /data/juergen/Experiment/experiment_descriptor.xml: [testng] 02:46:56,393 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:46:56,393 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:46:56,394 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-05_02-46-56.log] [testng] 02:46:56,395 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d84ebaf - End of configuration. [testng] [2024-04-05 02:46:56,763] [pool-1-thread-8] Initializing /data/nadine/experiment_descriptor.xml: [testng] 02:46:56,763 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:46:56,763 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:46:56,764 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-05_02-46-56.log] [testng] 02:46:56,764 |-INFO in ch.qos.logback.core.sift.SiftProcessor@24ce8ae5 - End of configuration. [testng] [2024-04-05 02:46:57,154] [pool-1-thread-7] Initializing /data/embl/Maik_001/experiment_descriptor.xml: [testng] 02:46:57,154 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:46:57,154 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:46:57,155 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-05_02-46-57.log] [testng] 02:46:57,155 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2cf4e258 - End of configuration. [testng] [2024-04-05 02:47:05,514] [pool-1-thread-6] Initializing /data/christian/example/experiment_descriptor.xml: [testng] 02:47:05,515 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:47:05,515 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:47:05,516 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-05_02-47-05.log] [testng] 02:47:05,516 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6eeb840c - End of configuration. [testng] [2024-04-05 02:47:05,661] [pool-1-thread-5] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml: [testng] 02:47:05,661 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:47:05,661 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:47:05,661 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-05_02-47-05.log] [testng] 02:47:05,662 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66a47fcb - End of configuration. [testng] [2024-04-05 02:48:50,865] [pool-1-thread-4] Initializing /data/gideon/experiment_descriptor.xml: [testng] 02:48:50,865 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:48:50,865 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:48:50,866 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-05_02-48-50.log] [testng] 02:48:50,867 |-INFO in ch.qos.logback.core.sift.SiftProcessor@62049387 - End of configuration. [testng] [2024-04-05 02:49:24,813] [pool-1-thread-3] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml: [testng] 02:49:24,814 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:49:24,814 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:49:24,817 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-05_02-49-24.log] [testng] 02:49:24,818 |-INFO in ch.qos.logback.core.sift.SiftProcessor@92288ad - End of configuration. [testng] [2024-04-05 02:49:33,666] [pool-1-thread-2] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml: [testng] 02:49:33,666 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:49:33,666 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:49:33,668 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-05_02-49-33.log] [testng] 02:49:33,668 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2d5727d1 - End of configuration. [testng] [2024-04-05 02:50:49,436] [pool-1-thread-6] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml: [testng] [2024-04-05 02:54:15,194] [pool-1-thread-8] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml: [testng] [2024-04-05 02:54:49,219] [pool-1-thread-9] Initializing /data/ruben/20100827_004/experiment_descriptor.xml: [testng] [2024-04-05 02:57:18,733] [pool-1-thread-3] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml: [testng] [2024-04-05 02:58:58,129] [pool-1-thread-7] Initializing /data/ruben/TestPlate_Mock_01_001/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: 45 minutes 17 seconds Finished: SUCCESS