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Started by upstream project "BIOFORMATS-test-repo" build number 122 originally caused by: Started by upstream project "Trigger" build number 139 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/jenkins6211877789639502008.sh + '[' scanr = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_19123_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] WARNING: An illegal reflective access operation has occurred [testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket [testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener [testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [testng] WARNING: All illegal access operations will be denied in a future release [testng] File leak detector installed [testng] 02:17:13,598 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:17:13,600 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 02:17:13,600 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:17:13,601 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:17:13,601 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:17:13,602 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:17:13,602 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:17:13,602 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:17:13,603 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:17:13,603 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:17:13,603 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:17:13,604 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:17:13,785 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:17:13,785 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:17:13,810 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:17:13,810 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:17:13,816 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:17:13,817 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:17:13,817 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:17:13,817 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:17:13,817 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 02:17:13,818 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 02:17:13,819 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 216 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-16 02:17:13,828] [main] java.version = 11.0.16 [testng] 02:17:13,832 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:17:13,832 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:17:13,879 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-16_02-17-13.log] [testng] 02:17:13,881 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-07-16 02:17:13,883] [main] testng.directory = /data [testng] [2024-07-16 02:17:13,884] [main] testng.configDirectory = /config [testng] [2024-07-16 02:17:13,894] [main] testng.multiplier = 1.0 [testng] [2024-07-16 02:17:13,895] [main] testng.in-memory = false [testng] [2024-07-16 02:17:13,895] [main] testng.allow-missing = false [testng] [2024-07-16 02:17:13,895] [main] user.language = en [testng] [2024-07-16 02:17:13,896] [main] user.country = ${user.country} [testng] [2024-07-16 02:17:13,896] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-07-16 02:21:56,501] [main] ---------------------------------------- [testng] [2024-07-16 02:21:56,502] [main] Total files: 2169 [testng] [2024-07-16 02:21:56,502] [main] Scan time: 282.605 s (130 ms/file) [testng] [2024-07-16 02:21:56,503] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-16 02:41:05,240] [pool-1-thread-1] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml: [testng] 02:41:05,240 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:41:05,241 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:41:05,242 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-16_02-41-05.log] [testng] 02:41:05,243 |-INFO in ch.qos.logback.core.sift.SiftProcessor@141e302d - End of configuration. [testng] [2024-07-16 02:41:31,955] [pool-1-thread-12] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml: [testng] 02:41:31,956 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:41:31,956 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:41:31,957 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-16_02-41-31.log] [testng] 02:41:31,957 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38e4ca8f - End of configuration. [testng] [2024-07-16 02:41:32,243] [pool-1-thread-11] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml: [testng] 02:41:32,244 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:41:32,244 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:41:32,244 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-16_02-41-32.log] [testng] 02:41:32,245 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8ec5a70 - End of configuration. [testng] [2024-07-16 02:42:48,694] [pool-1-thread-10] Initializing /data/christian/example/experiment_descriptor.xml: [testng] 02:42:48,695 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:42:48,695 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:42:48,696 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-16_02-42-48.log] [testng] 02:42:48,696 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4187c481 - End of configuration. [testng] [2024-07-16 02:42:48,863] [pool-1-thread-9] Initializing /data/embl/Maik_001/experiment_descriptor.xml: [testng] 02:42:48,863 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:42:48,863 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:42:48,864 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-16_02-42-48.log] [testng] 02:42:48,864 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ec3efc - End of configuration. [testng] [2024-07-16 02:42:58,219] [pool-1-thread-8] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml: [testng] 02:42:58,219 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:42:58,219 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:42:58,220 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-16_02-42-58.log] [testng] 02:42:58,221 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50275152 - End of configuration. [testng] [2024-07-16 02:44:49,474] [pool-1-thread-7] Initializing /data/gideon/experiment_descriptor.xml: [testng] 02:44:49,474 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:44:49,474 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:44:49,475 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-16_02-44-49.log] [testng] 02:44:49,476 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d2d21f2 - End of configuration. [testng] [2024-07-16 02:45:26,498] [pool-1-thread-6] Initializing /data/ruben/20100827_004/experiment_descriptor.xml: [testng] 02:45:26,498 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:45:26,499 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:45:26,500 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-16_02-45-26.log] [testng] 02:45:26,500 |-INFO in ch.qos.logback.core.sift.SiftProcessor@136c64b6 - End of configuration. [testng] [2024-07-16 02:45:28,620] [pool-1-thread-5] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml: [testng] 02:45:28,620 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:45:28,620 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:45:28,621 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-16_02-45-28.log] [testng] 02:45:28,621 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ed7bc45 - End of configuration. [testng] [2024-07-16 02:48:34,034] [pool-1-thread-4] Initializing /data/nadine/experiment_descriptor.xml: [testng] 02:48:34,034 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:48:34,034 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:48:34,035 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-16_02-48-34.log] [testng] 02:48:34,036 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68ecb7c7 - End of configuration. [testng] [2024-07-16 02:48:34,427] [pool-1-thread-3] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml: [testng] 02:48:34,428 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:48:34,428 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:48:34,429 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-16_02-48-34.log] [testng] 02:48:34,429 |-INFO in ch.qos.logback.core.sift.SiftProcessor@719ce509 - End of configuration. [testng] [2024-07-16 02:49:43,339] [pool-1-thread-2] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml: [testng] 02:49:43,339 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:49:43,340 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:49:43,341 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-16_02-49-43.log] [testng] 02:49:43,341 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36afaec9 - End of configuration. [testng] [2024-07-16 02:49:46,653] [pool-1-thread-10] Initializing /data/juergen/Experiment/experiment_descriptor.xml: [testng] [2024-07-16 02:49:46,842] [pool-1-thread-4] Initializing /data/ruben/plate_002/experiment_descriptor.xml: [testng] [2024-07-16 02:49:49,527] [pool-1-thread-10] Initializing /data/ruben/161009test2/151009_001/experiment_descriptor.xml: [testng] [2024-07-16 02:53:23,824] [pool-1-thread-2] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml: [testng] [2024-07-16 02:55:38,722] [pool-1-thread-9] Initializing /data/ruben/scanr_no_labels/Peter/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: 43 minutes 7 seconds Finished: SUCCESS