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Started by upstream project "BIOFORMATS-test-repo" build number 38 originally caused by: Started by upstream project "Trigger" build number 44 originally caused by: Started by user devspace 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/jenkins17650874529615743408.sh + '[' scanr = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_5346_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] 10:08:40,767 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 10:08:40,769 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 10:08:40,769 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 10:08:40,770 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 10:08:40,770 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 10:08:40,770 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 10:08:40,770 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 10:08:40,770 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 10:08:40,771 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 10:08:40,771 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 10:08:40,771 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 10:08:40,772 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 10:08:41,011 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 10:08:41,011 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 10:08:41,041 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 10:08:41,041 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 10:08:41,049 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 10:08:41,049 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 10:08:41,050 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 10:08:41,050 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 10:08:41,050 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 10:08:41,051 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 10:08:41,051 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 280 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-04-19 10:08:41,061] [main] java.version = 1.8.0_342 [testng] 10:08:41,065 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 10:08:41,065 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:08:41,111 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-19_10-08-41.log] [testng] 10:08:41,113 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-04-19 10:08:41,115] [main] testng.directory = /data [testng] [2024-04-19 10:08:41,115] [main] testng.configDirectory = /config [testng] [2024-04-19 10:08:41,128] [main] testng.multiplier = 1.0 [testng] [2024-04-19 10:08:41,129] [main] testng.in-memory = false [testng] [2024-04-19 10:08:41,129] [main] testng.allow-missing = false [testng] [2024-04-19 10:08:41,129] [main] user.language = en [testng] [2024-04-19 10:08:41,129] [main] user.country = ${user.country} [testng] [2024-04-19 10:08:41,129] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-04-19 10:13:38,502] [main] ---------------------------------------- [testng] [2024-04-19 10:13:38,503] [main] Total files: 2169 [testng] [2024-04-19 10:13:38,503] [main] Scan time: 297.373 s (137 ms/file) [testng] [2024-04-19 10:13:38,503] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-04-19 10:31:49,002] [pool-1-thread-1] Initializing /data/ruben/161009test2/151009_001/experiment_descriptor.xml: [testng] 10:31:49,002 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 10:31:49,002 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:31:49,003 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-19_10-31-49.log] [testng] 10:31:49,004 |-INFO in ch.qos.logback.core.sift.SiftProcessor@253d1299 - End of configuration. [testng] [2024-04-19 10:35:08,276] [pool-1-thread-12] Initializing /data/ruben/plate_002/experiment_descriptor.xml: [testng] 10:35:08,277 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 10:35:08,277 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:35:08,280 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-19_10-35-08.log] [testng] 10:35:08,280 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3cc6b479 - End of configuration. [testng] [2024-04-19 10:35:08,375] [pool-1-thread-11] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml: [testng] 10:35:08,375 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 10:35:08,376 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:35:08,376 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-19_10-35-08.log] [testng] 10:35:08,377 |-INFO in ch.qos.logback.core.sift.SiftProcessor@464caae9 - End of configuration. [testng] [2024-04-19 10:36:20,786] [pool-1-thread-10] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml: [testng] 10:36:20,786 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 10:36:20,787 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:36:20,788 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-19_10-36-20.log] [testng] 10:36:20,788 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2872b4d5 - End of configuration. [testng] [2024-04-19 10:37:34,172] [pool-1-thread-9] Initializing /data/juergen/Experiment/experiment_descriptor.xml: [testng] 10:37:34,173 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 10:37:34,173 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:37:34,174 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-19_10-37-34.log] [testng] 10:37:34,175 |-INFO in ch.qos.logback.core.sift.SiftProcessor@17a63d67 - End of configuration. [testng] [2024-04-19 10:37:34,438] [pool-1-thread-8] Initializing /data/nadine/experiment_descriptor.xml: [testng] 10:37:34,438 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 10:37:34,438 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:37:34,439 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-19_10-37-34.log] [testng] 10:37:34,439 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d7fcf05 - End of configuration. [testng] [2024-04-19 10:37:34,868] [pool-1-thread-7] Initializing /data/embl/Maik_001/experiment_descriptor.xml: [testng] 10:37:34,868 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 10:37:34,868 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:37:34,869 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-19_10-37-34.log] [testng] 10:37:34,869 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f8adbf8 - End of configuration. [testng] [2024-04-19 10:37:44,577] [pool-1-thread-6] Initializing /data/christian/example/experiment_descriptor.xml: [testng] 10:37:44,577 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 10:37:44,577 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:37:44,579 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-19_10-37-44.log] [testng] 10:37:44,579 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b27d2c5 - End of configuration. [testng] [2024-04-19 10:37:44,684] [pool-1-thread-5] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml: [testng] 10:37:44,685 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 10:37:44,685 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:37:44,685 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-19_10-37-44.log] [testng] 10:37:44,686 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ed85a00 - End of configuration. [testng] [2024-04-19 10:39:27,081] [pool-1-thread-4] Initializing /data/gideon/experiment_descriptor.xml: [testng] 10:39:27,082 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 10:39:27,082 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:39:27,083 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-19_10-39-27.log] [testng] 10:39:27,084 |-INFO in ch.qos.logback.core.sift.SiftProcessor@622bb131 - End of configuration. [testng] [2024-04-19 10:40:01,746] [pool-1-thread-3] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml: [testng] 10:40:01,747 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 10:40:01,747 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:40:01,749 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-19_10-40-01.log] [testng] 10:40:01,750 |-INFO in ch.qos.logback.core.sift.SiftProcessor@394011ed - End of configuration. [testng] [2024-04-19 10:40:05,676] [pool-1-thread-2] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml: [testng] 10:40:05,677 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 10:40:05,677 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:40:05,677 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-19_10-40-05.log] [testng] 10:40:05,678 |-INFO in ch.qos.logback.core.sift.SiftProcessor@42146051 - End of configuration. [testng] [2024-04-19 10:40:10,092] [pool-1-thread-6] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml: [testng] [2024-04-19 10:43:49,181] [pool-1-thread-8] Initializing /data/ruben/20100827_004/experiment_descriptor.xml: [testng] [2024-04-19 10:46:40,736] [pool-1-thread-9] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml: [testng] [2024-04-19 10:47:10,250] [pool-1-thread-3] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml: [testng] [2024-04-19 10:48:45,222] [pool-1-thread-12] Initializing /data/ruben/TestPlate_Mock_01_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: 44 minutes 45 seconds Finished: SUCCESS