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Started by upstream project "BIOFORMATS-test-repo" build number 105 originally caused by: Started by upstream project "Trigger" build number 117 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8 [BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins1958141408891456642.sh + '[' scanr = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_16335_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] 02:29:47,859 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:29:47,861 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 02:29:47,861 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:29:47,862 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:29:47,862 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:29:47,862 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:29:47,863 |-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] 02:29:47,863 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:29:47,863 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:29:47,864 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:29:47,864 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:29:47,864 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:29:48,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:29:48,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:29:48,245 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:29:48,245 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:29:48,256 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:29:48,256 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:29:48,256 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:29:48,257 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:29:48,257 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 02:29:48,258 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 02:29:48,258 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 395 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-06-28 02:29:48,269] [main] java.version = 1.8.0_342 [testng] 02:29:48,273 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:29:48,273 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:29:48,325 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-28_02-29-48.log] [testng] 02:29:48,327 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-06-28 02:29:48,329] [main] testng.directory = /data [testng] [2024-06-28 02:29:48,330] [main] testng.configDirectory = /config [testng] [2024-06-28 02:29:48,343] [main] testng.multiplier = 1.0 [testng] [2024-06-28 02:29:48,344] [main] testng.in-memory = false [testng] [2024-06-28 02:29:48,344] [main] testng.allow-missing = false [testng] [2024-06-28 02:29:48,344] [main] user.language = en [testng] [2024-06-28 02:29:48,344] [main] user.country = ${user.country} [testng] [2024-06-28 02:29:48,344] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-06-28 02:35:40,170] [main] ---------------------------------------- [testng] [2024-06-28 02:35:40,171] [main] Total files: 2169 [testng] [2024-06-28 02:35:40,171] [main] Scan time: 351.826 s (162 ms/file) [testng] [2024-06-28 02:35:40,172] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-06-28 02:53:47,978] [pool-1-thread-1] Initializing /data/juergen/Experiment/experiment_descriptor.xml: [testng] 02:53:47,979 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:53:47,979 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:53:47,980 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-28_02-53-47.log] [testng] 02:53:47,981 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4639214b - End of configuration. [testng] [2024-06-28 02:53:48,064] [pool-1-thread-12] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml: [testng] 02:53:48,065 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:53:48,065 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:53:48,065 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-28_02-53-48.log] [testng] 02:53:48,066 |-INFO in ch.qos.logback.core.sift.SiftProcessor@659f4cf8 - End of configuration. [testng] [2024-06-28 02:53:50,995] [pool-1-thread-11] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml: [testng] 02:53:50,996 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:53:50,996 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:53:50,997 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-28_02-53-50.log] [testng] 02:53:50,997 |-INFO in ch.qos.logback.core.sift.SiftProcessor@58dc1f94 - End of configuration. [testng] [2024-06-28 02:53:51,255] [pool-1-thread-10] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml: [testng] 02:53:51,256 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:53:51,256 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:53:51,257 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-28_02-53-51.log] [testng] 02:53:51,257 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ff4480d - End of configuration. [testng] [2024-06-28 02:53:51,403] [pool-1-thread-9] Initializing /data/ruben/plate_002/experiment_descriptor.xml: [testng] 02:53:51,403 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:53:51,403 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:53:51,404 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-28_02-53-51.log] [testng] 02:53:51,404 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d86a7cb - End of configuration. [testng] [2024-06-28 02:53:51,470] [pool-1-thread-8] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml: [testng] 02:53:51,470 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:53:51,470 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:53:51,470 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-28_02-53-51.log] [testng] 02:53:51,471 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22ca8094 - End of configuration. [testng] [2024-06-28 02:53:54,026] [pool-1-thread-7] Initializing /data/embl/Maik_001/experiment_descriptor.xml: [testng] 02:53:54,026 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:53:54,027 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:53:54,027 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-28_02-53-54.log] [testng] 02:53:54,028 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35ed1447 - End of configuration. [testng] [2024-06-28 02:53:54,154] [pool-1-thread-6] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml: [testng] 02:53:54,154 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:53:54,154 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:53:54,155 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-28_02-53-54.log] [testng] 02:53:54,155 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ab59af3 - End of configuration. [testng] [2024-06-28 02:53:55,502] [pool-1-thread-5] Initializing /data/gideon/experiment_descriptor.xml: [testng] 02:53:55,502 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:53:55,502 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:53:55,503 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-28_02-53-55.log] [testng] 02:53:55,503 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3157acbe - End of configuration. [testng] [2024-06-28 02:53:56,056] [pool-1-thread-4] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml: [testng] 02:53:56,056 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:53:56,056 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:53:56,057 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-28_02-53-56.log] [testng] 02:53:56,057 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c676d36 - End of configuration. [testng] [2024-06-28 02:53:57,091] [pool-1-thread-3] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml: [testng] 02:53:57,091 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:53:57,091 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:53:57,092 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-28_02-53-57.log] [testng] 02:53:57,092 |-INFO in ch.qos.logback.core.sift.SiftProcessor@29fd32ca - End of configuration. [testng] [2024-06-28 02:53:57,555] [pool-1-thread-2] Initializing /data/ruben/20100827_004/experiment_descriptor.xml: [testng] 02:53:57,555 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:53:57,555 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:53:57,556 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-28_02-53-57.log] [testng] 02:53:57,556 |-INFO in ch.qos.logback.core.sift.SiftProcessor@54bc09e0 - End of configuration. [testng] [2024-06-28 02:54:03,369] [pool-1-thread-1] Initializing /data/nadine/experiment_descriptor.xml: [testng] [2024-06-28 02:54:06,173] [pool-1-thread-1] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml: [testng] [2024-06-28 02:54:14,364] [pool-1-thread-10] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml: [testng] [2024-06-28 02:54:23,120] [pool-1-thread-9] Initializing /data/christian/example/experiment_descriptor.xml: [testng] [2024-06-28 02:54:24,541] [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: 30 minutes 2 seconds Finished: SUCCESS