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Started by upstream project "BIOFORMATS-test-repo" build number 295 originally caused by: Started by upstream project "Trigger" build number 314 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@2 [BIOFORMATS-test-folder@2] $ /bin/bash -xe /tmp/jenkins13676919546143293474.sh + '[' scanr = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_46698_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. [javac] 4 warnings test-automated: [testng] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket [testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket [testng] File leak detector installed [testng] 03:42:29,518 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:42:29,520 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 03:42:29,520 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:42:29,521 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:42:29,521 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:42:29,522 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:42:29,522 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 03:42:29,522 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:42:29,522 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:42:29,523 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:42:29,523 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:42:29,524 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:42:29,691 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:42:29,691 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:42:29,717 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:42:29,717 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:42:29,724 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:42:29,724 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:42:29,724 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:42:29,724 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:42:29,725 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 03:42:29,725 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 03:42:29,725 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 203 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-19 03:42:29,735] [main] java.version = 21 [testng] 03:42:29,738 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:42:29,738 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:42:29,783 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-19_03-42-29.log] [testng] 03:42:29,784 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-12-19 03:42:29,786] [main] testng.directory = /data [testng] [2024-12-19 03:42:29,786] [main] testng.configDirectory = /config [testng] [2024-12-19 03:42:29,795] [main] testng.multiplier = 1.0 [testng] [2024-12-19 03:42:29,795] [main] testng.in-memory = false [testng] [2024-12-19 03:42:29,795] [main] testng.allow-missing = false [testng] [2024-12-19 03:42:29,795] [main] user.language = en [testng] [2024-12-19 03:42:29,796] [main] user.country = ${user.country} [testng] [2024-12-19 03:42:29,796] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-19 03:46:57,272] [main] ---------------------------------------- [testng] [2024-12-19 03:46:57,272] [main] Total files: 2169 [testng] [2024-12-19 03:46:57,272] [main] Scan time: 267.476 s (123 ms/file) [testng] [2024-12-19 03:46:57,273] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-19 04:13:27,015] [pool-1-thread-1] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml: [testng] 04:13:27,016 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 04:13:27,016 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:13:27,017 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-19_04-13-27.log] [testng] 04:13:27,017 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2af4368f - End of configuration. [testng] [2024-12-19 04:16:29,399] [pool-1-thread-12] Initializing /data/ruben/20100827_004/experiment_descriptor.xml: [testng] 04:16:29,399 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 04:16:29,399 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:16:29,401 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-19_04-16-29.log] [testng] 04:16:29,401 |-INFO in ch.qos.logback.core.sift.SiftProcessor@69a8198a - End of configuration. [testng] [2024-12-19 04:19:47,194] [pool-1-thread-11] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml: [testng] 04:19:47,194 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 04:19:47,194 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:19:47,195 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-19_04-19-47.log] [testng] 04:19:47,196 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6de21855 - End of configuration. [testng] [2024-12-19 04:20:18,668] [pool-1-thread-10] Initializing /data/christian/example/experiment_descriptor.xml: [testng] 04:20:18,668 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 04:20:18,668 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:20:18,670 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-19_04-20-18.log] [testng] 04:20:18,670 |-INFO in ch.qos.logback.core.sift.SiftProcessor@533d5656 - End of configuration. [testng] [2024-12-19 04:20:20,441] [pool-1-thread-9] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml: [testng] 04:20:20,441 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 04:20:20,441 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:20:20,442 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-19_04-20-20.log] [testng] 04:20:20,442 |-INFO in ch.qos.logback.core.sift.SiftProcessor@24fe875f - End of configuration. [testng] [2024-12-19 04:21:48,408] [pool-1-thread-8] Initializing /data/gideon/experiment_descriptor.xml: [testng] 04:21:48,408 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 04:21:48,409 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:21:48,410 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-19_04-21-48.log] [testng] 04:21:48,411 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4cb4b556 - End of configuration. [testng] [2024-12-19 04:22:42,110] [pool-1-thread-7] Initializing /data/nadine/experiment_descriptor.xml: [testng] 04:22:42,110 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 04:22:42,110 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:22:42,111 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-19_04-22-42.log] [testng] 04:22:42,111 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e480bb4 - End of configuration. [testng] [2024-12-19 04:22:44,051] [pool-1-thread-6] Initializing /data/embl/Maik_001/experiment_descriptor.xml: [testng] 04:22:44,052 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 04:22:44,052 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:22:44,052 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-19_04-22-44.log] [testng] 04:22:44,053 |-INFO in ch.qos.logback.core.sift.SiftProcessor@136436c8 - End of configuration. [testng] [2024-12-19 04:22:56,449] [pool-1-thread-5] Initializing /data/ruben/161009test2/151009_001/experiment_descriptor.xml: [testng] 04:22:56,449 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 04:22:56,449 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:22:56,449 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-19_04-22-56.log] [testng] 04:22:56,450 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b46a36f - End of configuration. [testng] [2024-12-19 04:27:07,017] [pool-1-thread-4] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml: [testng] 04:27:07,018 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 04:27:07,018 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:27:07,019 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-19_04-27-07.log] [testng] 04:27:07,019 |-INFO in ch.qos.logback.core.sift.SiftProcessor@626501d4 - End of configuration. [testng] [2024-12-19 04:27:29,353] [pool-1-thread-3] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml: [testng] 04:27:29,354 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 04:27:29,354 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:27:29,354 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-19_04-27-29.log] [testng] 04:27:29,355 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c8b9033 - End of configuration. [testng] [2024-12-19 04:32:20,914] [pool-1-thread-2] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml: [testng] 04:32:20,915 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 04:32:20,915 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:32:20,916 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-19_04-32-20.log] [testng] 04:32:20,916 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6b99d60f - End of configuration. [testng] [2024-12-19 04:37:18,075] [pool-1-thread-10] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml: [testng] [2024-12-19 04:39:47,708] [pool-1-thread-7] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml: [testng] [2024-12-19 04:52:13,162] [pool-1-thread-6] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml: [testng] [2024-12-19 04:57:13,141] [pool-1-thread-7] Initializing /data/juergen/Experiment/experiment_descriptor.xml: [testng] [2024-12-19 04:58:19,130] [pool-1-thread-7] Initializing /data/ruben/plate_002/experiment_descriptor.xml: [testng] 06:08:35,549 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 06:08:35,549 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:08:35,550 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-19_06-08-35.log] [testng] 06:08:35,550 |-INFO in ch.qos.logback.core.sift.SiftProcessor@381c7839 - End of configuration. [testng] 06:12:23,538 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 06:12:23,538 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:12:23,539 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-19_06-12-23.log] [testng] 06:12:23,539 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2958aff2 - End of configuration. [testng] 06:53:24,319 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 06:53:24,319 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:53:24,320 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-19_06-53-24.log] [testng] 06:53:24,320 |-INFO in ch.qos.logback.core.sift.SiftProcessor@61c5a66a - End of configuration. [testng] 07:07:10,049 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 07:07:10,049 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:07:10,050 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-19_07-07-10.log] [testng] 07:07:10,051 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36f46a6f - End of configuration. [testng] 07:07:12,458 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 07:07:12,458 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:07:12,458 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-19_07-07-12.log] [testng] 07:07:12,459 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a72db14 - End of configuration. [testng] 07:11:55,151 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 07:11:55,151 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:11:55,151 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-19_07-11-55.log] [testng] 07:11:55,152 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d2be01c - End of configuration. [testng] 07:11:57,782 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 07:11:57,782 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:11:57,782 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-19_07-11-57.log] [testng] 07:11:57,783 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a2b729b - End of configuration. [testng] 07:21:20,645 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 07:21:20,645 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:21:20,645 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-19_07-21-20.log] [testng] 07:21:20,646 |-INFO in ch.qos.logback.core.sift.SiftProcessor@fbf59af - 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: 218 minutes 54 seconds Finished: SUCCESS