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Started by upstream project "BIOFORMATS-test-repo" build number 243 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4 [BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins6227524382854183889.sh + '[' scanr = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_38294_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] 16:27:10,522 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 16:27:10,523 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 16:27:10,523 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 16:27:10,524 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 16:27:10,525 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 16:27:10,525 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 16:27:10,525 |-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] 16:27:10,525 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 16:27:10,526 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 16:27:10,526 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 16:27:10,527 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 16:27:10,527 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 16:27:10,691 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 16:27:10,691 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 16:27:10,713 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 16:27:10,713 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 16:27:10,719 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 16:27:10,719 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 16:27:10,719 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 16:27:10,719 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 16:27:10,719 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 16:27:10,720 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 16:27:10,720 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 194 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-02 16:27:10,729] [main] java.version = 11.0.16 [testng] 16:27:10,732 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 16:27:10,732 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:27:10,774 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-02_16-27-10.log] [testng] 16:27:10,775 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-11-02 16:27:10,777] [main] testng.directory = /data [testng] [2024-11-02 16:27:10,778] [main] testng.configDirectory = /config [testng] [2024-11-02 16:27:10,787] [main] testng.multiplier = 1.0 [testng] [2024-11-02 16:27:10,789] [main] testng.in-memory = false [testng] [2024-11-02 16:27:10,789] [main] testng.allow-missing = false [testng] [2024-11-02 16:27:10,789] [main] user.language = en [testng] [2024-11-02 16:27:10,789] [main] user.country = ${user.country} [testng] [2024-11-02 16:27:10,789] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-02 16:31:29,228] [main] ---------------------------------------- [testng] [2024-11-02 16:31:29,228] [main] Total files: 2169 [testng] [2024-11-02 16:31:29,228] [main] Scan time: 258.439 s (119 ms/file) [testng] [2024-11-02 16:31:29,229] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-02 16:52:14,453] [pool-1-thread-1] Initializing /data/embl/Maik_001/experiment_descriptor.xml: [testng] 16:52:14,454 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 16:52:14,454 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:52:14,457 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-02_16-52-14.log] [testng] 16:52:14,457 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56d4a352 - End of configuration. [testng] [2024-11-02 16:52:20,753] [pool-1-thread-12] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml: [testng] 16:52:20,753 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 16:52:20,753 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:52:20,754 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-02_16-52-20.log] [testng] 16:52:20,755 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c0a7e95 - End of configuration. [testng] [2024-11-02 16:54:05,889] [pool-1-thread-11] Initializing /data/ruben/20100827_004/experiment_descriptor.xml: [testng] 16:54:05,889 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 16:54:05,889 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:54:05,890 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-02_16-54-05.log] [testng] 16:54:05,890 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4768974f - End of configuration. [testng] [2024-11-02 16:55:18,411] [pool-1-thread-10] Initializing /data/gideon/experiment_descriptor.xml: [testng] 16:55:18,412 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 16:55:18,412 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:55:18,413 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-02_16-55-18.log] [testng] 16:55:18,413 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40b25c13 - End of configuration. [testng] [2024-11-02 16:55:39,889] [pool-1-thread-9] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml: [testng] 16:55:39,889 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 16:55:39,890 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:55:39,890 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-02_16-55-39.log] [testng] 16:55:39,891 |-INFO in ch.qos.logback.core.sift.SiftProcessor@409b93f2 - End of configuration. [testng] [2024-11-02 16:56:14,664] [pool-1-thread-8] Initializing /data/juergen/Experiment/experiment_descriptor.xml: [testng] 16:56:14,664 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 16:56:14,665 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:56:14,665 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-02_16-56-14.log] [testng] 16:56:14,666 |-INFO in ch.qos.logback.core.sift.SiftProcessor@673cd323 - End of configuration. [testng] [2024-11-02 16:56:15,518] [pool-1-thread-7] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml: [testng] 16:56:15,518 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 16:56:15,518 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:56:15,519 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-02_16-56-15.log] [testng] 16:56:15,519 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a1156eb - End of configuration. [testng] [2024-11-02 16:56:48,654] [pool-1-thread-6] Initializing /data/nadine/experiment_descriptor.xml: [testng] 16:56:48,655 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 16:56:48,655 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:56:48,655 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-02_16-56-48.log] [testng] 16:56:48,656 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4947175f - End of configuration. [testng] [2024-11-02 16:56:49,702] [pool-1-thread-5] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml: [testng] 16:56:49,702 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 16:56:49,702 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:56:49,703 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-02_16-56-49.log] [testng] 16:56:49,703 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38f4915e - End of configuration. [testng] [2024-11-02 16:57:36,308] [pool-1-thread-4] Initializing /data/christian/example/experiment_descriptor.xml: [testng] 16:57:36,309 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 16:57:36,309 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:57:36,310 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-02_16-57-36.log] [testng] 16:57:36,310 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34b37611 - End of configuration. [testng] [2024-11-02 16:57:37,344] [pool-1-thread-3] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml: [testng] 16:57:37,345 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 16:57:37,345 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:57:37,345 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-02_16-57-37.log] [testng] 16:57:37,345 |-INFO in ch.qos.logback.core.sift.SiftProcessor@542f888a - End of configuration. [testng] [2024-11-02 16:57:43,156] [pool-1-thread-2] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml: [testng] 16:57:43,156 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 16:57:43,156 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:57:43,157 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-02_16-57-43.log] [testng] 16:57:43,157 |-INFO in ch.qos.logback.core.sift.SiftProcessor@224ebe5 - End of configuration. [testng] [2024-11-02 16:58:29,720] [pool-1-thread-4] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml: [testng] [2024-11-02 17:00:44,495] [pool-1-thread-8] Initializing /data/ruben/plate_002/experiment_descriptor.xml: [testng] [2024-11-02 17:00:58,943] [pool-1-thread-6] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml: [testng] [2024-11-02 17:04:23,483] [pool-1-thread-8] Initializing /data/ruben/161009test2/151009_001/experiment_descriptor.xml: [testng] [2024-11-02 17:07:10,152] [pool-1-thread-3] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml: [testng] 18:10:13,254 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 18:10:13,254 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 18:10:13,255 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-02_18-10-13.log] [testng] 18:10:13,255 |-INFO in ch.qos.logback.core.sift.SiftProcessor@24aba141 - End of configuration. [testng] 18:10:49,163 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 18:10:49,163 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 18:10:49,165 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-02_18-10-49.log] [testng] 18:10:49,166 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c6eda50 - End of configuration. [testng] 18:11:12,814 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 18:11:12,814 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 18:11:12,816 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-02_18-11-12.log] [testng] 18:11:12,816 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3bac373b - End of configuration. [testng] 18:12:29,379 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 18:12:29,379 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 18:12:29,380 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-02_18-12-29.log] [testng] 18:12:29,380 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2e94ad55 - End of configuration. [testng] 18:17:57,355 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 18:17:57,355 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 18:17:57,356 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-02_18-17-57.log] [testng] 18:17:57,357 |-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: 110 minutes 50 seconds Finished: SUCCESS