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Started by upstream project "BIOFORMATS-test-repo" build number 242 originally caused by: Started by upstream project "Trigger" build number 267 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/jenkins8075497989696144332.sh + '[' scanr = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_38130_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] 03:10:01,294 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:10:01,295 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 03:10:01,295 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:10:01,296 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:10:01,297 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:10:01,297 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:10:01,298 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 03:10:01,298 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:10:01,298 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:10:01,299 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:10:01,299 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:10:01,299 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:10:01,479 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:10:01,479 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:10:01,504 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:10:01,504 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:10:01,511 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:10:01,511 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:10:01,511 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:10:01,512 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:10:01,512 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 03:10:01,513 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 03:10:01,513 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 215 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-02 03:10:01,524] [main] java.version = 11.0.16 [testng] 03:10:01,527 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:10:01,527 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:10:01,575 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-02_03-10-01.log] [testng] 03:10:01,577 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-11-02 03:10:01,579] [main] testng.directory = /data [testng] [2024-11-02 03:10:01,579] [main] testng.configDirectory = /config [testng] [2024-11-02 03:10:01,590] [main] testng.multiplier = 1.0 [testng] [2024-11-02 03:10:01,591] [main] testng.in-memory = false [testng] [2024-11-02 03:10:01,591] [main] testng.allow-missing = false [testng] [2024-11-02 03:10:01,591] [main] user.language = en [testng] [2024-11-02 03:10:01,591] [main] user.country = ${user.country} [testng] [2024-11-02 03:10:01,591] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-02 03:14:15,092] [main] ---------------------------------------- [testng] [2024-11-02 03:14:15,092] [main] Total files: 2169 [testng] [2024-11-02 03:14:15,093] [main] Scan time: 253.5 s (116 ms/file) [testng] [2024-11-02 03:14:15,093] [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 03:31:33,844] [pool-1-thread-1] Initializing /data/embl/Maik_001/experiment_descriptor.xml: [testng] 03:31:33,845 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:31:33,845 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:31:33,847 |-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_03-31-33.log] [testng] 03:31:33,848 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14b12fa1 - End of configuration. [testng] [2024-11-02 03:31:39,471] [pool-1-thread-12] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml: [testng] 03:31:39,472 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:31:39,472 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:31:39,473 |-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_03-31-39.log] [testng] 03:31:39,473 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ba8322d - End of configuration. [testng] [2024-11-02 03:33:44,347] [pool-1-thread-11] Initializing /data/ruben/20100827_004/experiment_descriptor.xml: [testng] 03:33:44,347 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:33:44,347 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:33:44,348 |-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_03-33-44.log] [testng] 03:33:44,349 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1c46c072 - End of configuration. [testng] [2024-11-02 03:34:57,526] [pool-1-thread-10] Initializing /data/gideon/experiment_descriptor.xml: [testng] 03:34:57,527 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:34:57,527 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:34:57,528 |-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_03-34-57.log] [testng] 03:34:57,528 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a74b669 - End of configuration. [testng] [2024-11-02 03:35:17,965] [pool-1-thread-9] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml: [testng] 03:35:17,966 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:35:17,966 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:35:17,967 |-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_03-35-17.log] [testng] 03:35:17,967 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34088f86 - End of configuration. [testng] [2024-11-02 03:35:57,077] [pool-1-thread-8] Initializing /data/juergen/Experiment/experiment_descriptor.xml: [testng] 03:35:57,077 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:35:57,077 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:35:57,078 |-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_03-35-57.log] [testng] 03:35:57,078 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2aa673c1 - End of configuration. [testng] [2024-11-02 03:35:57,841] [pool-1-thread-7] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml: [testng] 03:35:57,841 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:35:57,842 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:35:57,842 |-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_03-35-57.log] [testng] 03:35:57,843 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d1adb37 - End of configuration. [testng] [2024-11-02 03:36:28,656] [pool-1-thread-6] Initializing /data/nadine/experiment_descriptor.xml: [testng] 03:36:28,657 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:36:28,657 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:36:28,658 |-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_03-36-28.log] [testng] 03:36:28,658 |-INFO in ch.qos.logback.core.sift.SiftProcessor@563aaf01 - End of configuration. [testng] [2024-11-02 03:36:29,425] [pool-1-thread-5] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml: [testng] 03:36:29,426 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:36:29,426 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:36:29,426 |-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_03-36-29.log] [testng] 03:36:29,427 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b0306c0 - End of configuration. [testng] [2024-11-02 03:37:12,379] [pool-1-thread-4] Initializing /data/christian/example/experiment_descriptor.xml: [testng] 03:37:12,380 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:37:12,380 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:37:12,381 |-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_03-37-12.log] [testng] 03:37:12,381 |-INFO in ch.qos.logback.core.sift.SiftProcessor@11e418e4 - End of configuration. [testng] [2024-11-02 03:37:13,293] [pool-1-thread-3] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml: [testng] 03:37:13,293 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:37:13,293 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:37:13,294 |-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_03-37-13.log] [testng] 03:37:13,295 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2eb1f6bb - End of configuration. [testng] [2024-11-02 03:37:19,487] [pool-1-thread-2] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml: [testng] 03:37:19,487 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:37:19,487 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:37:19,488 |-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_03-37-19.log] [testng] 03:37:19,488 |-INFO in ch.qos.logback.core.sift.SiftProcessor@279516f7 - End of configuration. [testng] [2024-11-02 03:37:56,127] [pool-1-thread-4] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml: [testng] [2024-11-02 03:39:57,205] [pool-1-thread-8] Initializing /data/ruben/plate_002/experiment_descriptor.xml: [testng] [2024-11-02 03:40:08,845] [pool-1-thread-6] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml: [testng] [2024-11-02 03:43:20,855] [pool-1-thread-8] Initializing /data/ruben/161009test2/151009_001/experiment_descriptor.xml: [testng] [2024-11-02 03:46:20,302] [pool-1-thread-1] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml: [testng] 04:52:59,074 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 04:52:59,074 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:52:59,075 |-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_04-52-59.log] [testng] 04:52:59,076 |-INFO in ch.qos.logback.core.sift.SiftProcessor@46ff1c3b - End of configuration. [testng] 04:53:55,052 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 04:53:55,052 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:53:55,054 |-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_04-53-55.log] [testng] 04:53:55,055 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66aef41 - End of configuration. [testng] 04:54:10,561 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 04:54:10,561 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:54:10,563 |-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_04-54-10.log] [testng] 04:54:10,564 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3904b8f1 - End of configuration. [testng] 04:55:39,085 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 04:55:39,085 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:55:39,086 |-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_04-55-39.log] [testng] 04:55:39,087 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3272c3a5 - End of configuration. [testng] 05:01:37,714 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 05:01:37,714 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:01:37,715 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-02_05-01-37.log] [testng] 05:01:37,715 |-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: 111 minutes 39 seconds Finished: SUCCESS