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Started by upstream project "BIOFORMATS-test-repo" build number 133 originally caused by: Started by upstream project "Trigger" build number 153 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@6 [BIOFORMATS-test-folder@6] $ /bin/bash -xe /tmp/jenkins845599669138538983.sh + '[' scanr = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_20927_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 test-automated: [testng] File leak detector installed [testng] 02:26:25,436 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:26:25,438 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 02:26:25,438 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:26:25,439 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:26:25,439 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:26:25,440 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:26:25,440 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:26:25,440 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:26:25,441 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:26:25,441 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:26:25,441 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:26:25,441 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:26:25,684 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:26:25,684 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:26:25,714 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:26:25,714 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:26:25,723 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:26:25,724 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:26:25,724 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:26:25,724 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:26:25,724 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 02:26:25,725 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 02:26:25,725 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 284 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-26 02:26:25,736] [main] java.version = 1.8.0_342 [testng] 02:26:25,740 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:26:25,740 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:26:25,788 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-26_02-26-25.log] [testng] 02:26:25,790 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-07-26 02:26:25,792] [main] testng.directory = /data [testng] [2024-07-26 02:26:25,792] [main] testng.configDirectory = /config [testng] [2024-07-26 02:26:25,806] [main] testng.multiplier = 1.0 [testng] [2024-07-26 02:26:25,807] [main] testng.in-memory = false [testng] [2024-07-26 02:26:25,807] [main] testng.allow-missing = false [testng] [2024-07-26 02:26:25,807] [main] user.language = en [testng] [2024-07-26 02:26:25,807] [main] user.country = ${user.country} [testng] [2024-07-26 02:26:25,807] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-07-26 02:31:42,016] [main] ---------------------------------------- [testng] [2024-07-26 02:31:42,016] [main] Total files: 2169 [testng] [2024-07-26 02:31:42,016] [main] Scan time: 316.209 s (145 ms/file) [testng] [2024-07-26 02:31:42,017] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-26 02:50:01,899] [pool-1-thread-1] Initializing /data/juergen/Experiment/experiment_descriptor.xml: [testng] 02:50:01,900 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:50:01,900 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:50:01,901 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-26_02-50-01.log] [testng] 02:50:01,902 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14cbbdc2 - End of configuration. [testng] [2024-07-26 02:50:02,240] [pool-1-thread-12] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml: [testng] 02:50:02,240 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:50:02,240 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:50:02,241 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-26_02-50-02.log] [testng] 02:50:02,241 |-INFO in ch.qos.logback.core.sift.SiftProcessor@23fbd4f3 - End of configuration. [testng] [2024-07-26 02:52:37,311] [pool-1-thread-11] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml: [testng] 02:52:37,312 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:52:37,312 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:52:37,313 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-26_02-52-37.log] [testng] 02:52:37,314 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4df38951 - End of configuration. [testng] [2024-07-26 02:52:37,641] [pool-1-thread-10] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml: [testng] 02:52:37,641 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:52:37,641 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:52:37,642 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-26_02-52-37.log] [testng] 02:52:37,643 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f1aca17 - End of configuration. [testng] [2024-07-26 02:52:37,837] [pool-1-thread-9] Initializing /data/ruben/plate_002/experiment_descriptor.xml: [testng] 02:52:37,837 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:52:37,837 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:52:37,838 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-26_02-52-37.log] [testng] 02:52:37,838 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7471d0f0 - End of configuration. [testng] [2024-07-26 02:52:37,937] [pool-1-thread-8] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml: [testng] 02:52:37,938 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:52:37,938 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:52:37,939 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-26_02-52-37.log] [testng] 02:52:37,939 |-INFO in ch.qos.logback.core.sift.SiftProcessor@39fd4899 - End of configuration. [testng] [2024-07-26 02:54:13,437] [pool-1-thread-7] Initializing /data/embl/Maik_001/experiment_descriptor.xml: [testng] 02:54:13,438 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:54:13,438 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:54:13,440 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-26_02-54-13.log] [testng] 02:54:13,440 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d52fbd3 - End of configuration. [testng] [2024-07-26 02:54:20,892] [pool-1-thread-6] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml: [testng] 02:54:20,893 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:54:20,893 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:54:20,894 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-26_02-54-20.log] [testng] 02:54:20,895 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2876ea10 - End of configuration. [testng] [2024-07-26 02:55:03,627] [pool-1-thread-5] Initializing /data/gideon/experiment_descriptor.xml: [testng] 02:55:03,627 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:55:03,628 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:55:03,629 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-26_02-55-03.log] [testng] 02:55:03,630 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7745e9de - End of configuration. [testng] [2024-07-26 02:55:36,395] [pool-1-thread-4] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml: [testng] 02:55:36,396 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:55:36,396 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:55:36,397 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-26_02-55-36.log] [testng] 02:55:36,398 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3215d59 - End of configuration. [testng] [2024-07-26 02:56:56,463] [pool-1-thread-3] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml: [testng] 02:56:56,463 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:56:56,463 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:56:56,464 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-26_02-56-56.log] [testng] 02:56:56,465 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a7ac853 - End of configuration. [testng] [2024-07-26 02:57:17,300] [pool-1-thread-2] Initializing /data/ruben/20100827_004/experiment_descriptor.xml: [testng] 02:57:17,300 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:57:17,301 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:57:17,302 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-26_02-57-17.log] [testng] 02:57:17,303 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4fc5e3a2 - End of configuration. [testng] [2024-07-26 02:59:53,092] [pool-1-thread-1] Initializing /data/nadine/experiment_descriptor.xml: [testng] [2024-07-26 02:59:55,368] [pool-1-thread-1] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml: [testng] [2024-07-26 03:01:23,596] [pool-1-thread-10] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml: [testng] [2024-07-26 03:03:15,128] [pool-1-thread-9] Initializing /data/christian/example/experiment_descriptor.xml: [testng] [2024-07-26 03:03:16,837] [pool-1-thread-9] Initializing /data/ruben/161009test2/151009_001/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: 45 minutes 10 seconds Finished: SUCCESS