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Started by upstream project "BIOFORMATS-test-repo" build number 235 originally caused by: Started by upstream project "Trigger" build number 260 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8 [BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins9829800263019693449.sh + '[' scanr = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_36982_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] 04:13:36,068 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 04:13:36,070 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 04:13:36,070 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 04:13:36,071 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 04:13:36,071 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 04:13:36,071 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 04:13:36,072 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 04:13:36,072 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 04:13:36,072 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 04:13:36,073 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 04:13:36,073 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 04:13:36,074 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 04:13:36,247 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 04:13:36,247 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 04:13:36,269 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 04:13:36,269 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 04:13:36,275 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 04:13:36,275 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 04:13:36,275 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 04:13:36,275 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 04:13:36,275 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 04:13:36,276 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 04:13:36,276 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 204 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-26 04:13:36,285] [main] java.version = 11.0.16 [testng] 04:13:36,289 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 04:13:36,289 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:13:36,332 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-26_04-13-36.log] [testng] 04:13:36,334 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-10-26 04:13:36,336] [main] testng.directory = /data [testng] [2024-10-26 04:13:36,336] [main] testng.configDirectory = /config [testng] [2024-10-26 04:13:36,347] [main] testng.multiplier = 1.0 [testng] [2024-10-26 04:13:36,348] [main] testng.in-memory = false [testng] [2024-10-26 04:13:36,348] [main] testng.allow-missing = false [testng] [2024-10-26 04:13:36,349] [main] user.language = en [testng] [2024-10-26 04:13:36,349] [main] user.country = ${user.country} [testng] [2024-10-26 04:13:36,349] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-26 04:19:42,008] [main] ---------------------------------------- [testng] [2024-10-26 04:19:42,009] [main] Total files: 2169 [testng] [2024-10-26 04:19:42,009] [main] Scan time: 365.659 s (168 ms/file) [testng] [2024-10-26 04:19:42,009] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-26 04:39:24,640] [pool-1-thread-1] Initializing /data/embl/Maik_001/experiment_descriptor.xml: [testng] 04:39:24,641 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 04:39:24,641 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:39:24,643 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-26_04-39-24.log] [testng] 04:39:24,643 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a132caf - End of configuration. [testng] [2024-10-26 04:39:33,926] [pool-1-thread-12] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml: [testng] 04:39:33,926 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 04:39:33,926 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:39:33,927 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-26_04-39-33.log] [testng] 04:39:33,927 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a52244e - End of configuration. [testng] [2024-10-26 04:42:43,593] [pool-1-thread-11] Initializing /data/ruben/20100827_004/experiment_descriptor.xml: [testng] 04:42:43,593 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 04:42:43,593 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:42:43,594 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-26_04-42-43.log] [testng] 04:42:43,595 |-INFO in ch.qos.logback.core.sift.SiftProcessor@41178ab4 - End of configuration. [testng] [2024-10-26 04:44:04,238] [pool-1-thread-10] Initializing /data/gideon/experiment_descriptor.xml: [testng] 04:44:04,238 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 04:44:04,239 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:44:04,240 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-26_04-44-04.log] [testng] 04:44:04,241 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38ee54b7 - End of configuration. [testng] [2024-10-26 04:44:41,120] [pool-1-thread-9] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml: [testng] 04:44:41,120 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 04:44:41,120 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:44:41,121 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-26_04-44-41.log] [testng] 04:44:41,121 |-INFO in ch.qos.logback.core.sift.SiftProcessor@961e7fe - End of configuration. [testng] [2024-10-26 04:45:45,158] [pool-1-thread-8] Initializing /data/juergen/Experiment/experiment_descriptor.xml: [testng] 04:45:45,158 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 04:45:45,159 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:45:45,159 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-26_04-45-45.log] [testng] 04:45:45,160 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7dcb0f3e - End of configuration. [testng] [2024-10-26 04:45:45,986] [pool-1-thread-7] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml: [testng] 04:45:45,986 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 04:45:45,986 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:45:45,987 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-26_04-45-45.log] [testng] 04:45:45,987 |-INFO in ch.qos.logback.core.sift.SiftProcessor@33348217 - End of configuration. [testng] [2024-10-26 04:46:17,088] [pool-1-thread-6] Initializing /data/nadine/experiment_descriptor.xml: [testng] 04:46:17,088 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 04:46:17,088 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:46:17,090 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-26_04-46-17.log] [testng] 04:46:17,090 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21499625 - End of configuration. [testng] [2024-10-26 04:46:18,053] [pool-1-thread-5] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml: [testng] 04:46:18,053 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 04:46:18,053 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:46:18,053 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-26_04-46-18.log] [testng] 04:46:18,054 |-INFO in ch.qos.logback.core.sift.SiftProcessor@401f56b8 - End of configuration. [testng] [2024-10-26 04:47:27,496] [pool-1-thread-4] Initializing /data/christian/example/experiment_descriptor.xml: [testng] 04:47:27,497 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 04:47:27,497 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:47:27,498 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-26_04-47-27.log] [testng] 04:47:27,498 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7d2bd40a - End of configuration. [testng] [2024-10-26 04:47:28,296] [pool-1-thread-3] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml: [testng] 04:47:28,296 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 04:47:28,296 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:47:28,296 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-26_04-47-28.log] [testng] 04:47:28,297 |-INFO in ch.qos.logback.core.sift.SiftProcessor@170b84df - End of configuration. [testng] [2024-10-26 04:47:33,363] [pool-1-thread-2] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml: [testng] 04:47:33,364 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 04:47:33,364 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:47:33,364 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-26_04-47-33.log] [testng] 04:47:33,365 |-INFO in ch.qos.logback.core.sift.SiftProcessor@b621704 - End of configuration. [testng] [2024-10-26 04:48:28,604] [pool-1-thread-4] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml: [testng] [2024-10-26 04:52:00,049] [pool-1-thread-8] Initializing /data/ruben/plate_002/experiment_descriptor.xml: [testng] [2024-10-26 04:52:15,380] [pool-1-thread-6] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml: [testng] [2024-10-26 04:57:07,964] [pool-1-thread-8] Initializing /data/ruben/161009test2/151009_001/experiment_descriptor.xml: [testng] [2024-10-26 05:01:15,112] [pool-1-thread-3] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml: [testng] 06:04:11,178 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 06:04:11,179 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:04:11,180 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-26_06-04-11.log] [testng] 06:04:11,180 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43401dad - End of configuration. [testng] 06:04:21,778 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 06:04:21,778 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:04:21,780 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-26_06-04-21.log] [testng] 06:04:21,780 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f3344f5 - End of configuration. [testng] 06:05:22,871 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 06:05:22,871 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:05:22,872 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-26_06-05-22.log] [testng] 06:05:22,873 |-INFO in ch.qos.logback.core.sift.SiftProcessor@364b1b47 - End of configuration. [testng] 06:06:28,614 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 06:06:28,614 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:06:28,615 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-26_06-06-28.log] [testng] 06:06:28,615 |-INFO in ch.qos.logback.core.sift.SiftProcessor@664783ab - End of configuration. [testng] 06:11:49,215 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 06:11:49,215 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:11:49,216 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-26_06-11-49.log] [testng] 06:11:49,216 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a8b30a3 - 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: 118 minutes 16 seconds Finished: SUCCESS