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Started by upstream project "BIOFORMATS-test-repo" build number 59 originally caused by: Started by upstream project "Trigger" build number 66 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4 [BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins1163635701383430920.sh + '[' scanr = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_8791_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] 02:22:56,888 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:22:56,890 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 02:22:56,890 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:22:56,893 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:22:56,893 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:22:56,893 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:22:56,893 |-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] 02:22:56,893 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:22:56,894 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:22:56,894 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:22:56,894 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:22:56,895 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:22:57,279 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:22:57,280 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:22:57,340 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:22:57,341 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:22:57,400 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:22:57,400 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:22:57,400 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:22:57,401 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:22:57,401 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 02:22:57,403 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 02:22:57,403 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 509 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-05-10 02:22:57,419] [main] java.version = 1.8.0_342 [testng] 02:22:57,426 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:22:57,427 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:22:57,548 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-10_02-22-57.log] [testng] 02:22:57,551 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-05-10 02:22:57,575] [main] testng.directory = /data [testng] [2024-05-10 02:22:57,575] [main] testng.configDirectory = /config [testng] [2024-05-10 02:22:57,662] [main] testng.multiplier = 1.0 [testng] [2024-05-10 02:22:57,662] [main] testng.in-memory = false [testng] [2024-05-10 02:22:57,663] [main] testng.allow-missing = false [testng] [2024-05-10 02:22:57,663] [main] user.language = en [testng] [2024-05-10 02:22:57,663] [main] user.country = ${user.country} [testng] [2024-05-10 02:22:57,663] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-05-10 02:27:57,641] [main] ---------------------------------------- [testng] [2024-05-10 02:27:57,642] [main] Total files: 2169 [testng] [2024-05-10 02:27:57,642] [main] Scan time: 299.978 s (138 ms/file) [testng] [2024-05-10 02:27:57,642] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-05-10 02:46:45,816] [pool-1-thread-1] Initializing /data/juergen/Experiment/experiment_descriptor.xml: [testng] 02:46:45,817 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:46:45,817 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:46:45,818 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-10_02-46-45.log] [testng] 02:46:45,818 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d7be8f4 - End of configuration. [testng] [2024-05-10 02:46:45,862] [pool-1-thread-12] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml: [testng] 02:46:45,862 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:46:45,862 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:46:45,863 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-10_02-46-45.log] [testng] 02:46:45,863 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e5f2ad0 - End of configuration. [testng] [2024-05-10 02:46:48,349] [pool-1-thread-11] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml: [testng] 02:46:48,350 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:46:48,350 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:46:48,350 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-10_02-46-48.log] [testng] 02:46:48,351 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65bfed6f - End of configuration. [testng] [2024-05-10 02:46:48,606] [pool-1-thread-10] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml: [testng] 02:46:48,606 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:46:48,606 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:46:48,607 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-10_02-46-48.log] [testng] 02:46:48,607 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4274238f - End of configuration. [testng] [2024-05-10 02:46:48,745] [pool-1-thread-9] Initializing /data/ruben/plate_002/experiment_descriptor.xml: [testng] 02:46:48,745 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:46:48,745 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:46:48,746 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-10_02-46-48.log] [testng] 02:46:48,746 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12fa3795 - End of configuration. [testng] [2024-05-10 02:46:48,812] [pool-1-thread-8] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml: [testng] 02:46:48,812 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:46:48,812 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:46:48,813 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-10_02-46-48.log] [testng] 02:46:48,813 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66a95b7c - End of configuration. [testng] [2024-05-10 02:48:18,039] [pool-1-thread-7] Initializing /data/embl/Maik_001/experiment_descriptor.xml: [testng] 02:48:18,039 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:48:18,039 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:48:18,040 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-10_02-48-18.log] [testng] 02:48:18,041 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1194c0e - End of configuration. [testng] [2024-05-10 02:48:27,186] [pool-1-thread-6] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml: [testng] 02:48:27,187 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:48:27,187 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:48:27,188 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-10_02-48-27.log] [testng] 02:48:27,188 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c2e984a - End of configuration. [testng] [2024-05-10 02:48:28,089] [pool-1-thread-5] Initializing /data/gideon/experiment_descriptor.xml: [testng] 02:48:28,090 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:48:28,090 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:48:28,090 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-10_02-48-28.log] [testng] 02:48:28,090 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c882da3 - End of configuration. [testng] [2024-05-10 02:49:02,808] [pool-1-thread-4] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml: [testng] 02:49:02,808 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:49:02,808 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:49:02,809 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-10_02-49-02.log] [testng] 02:49:02,810 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2982b34e - End of configuration. [testng] [2024-05-10 02:50:05,674] [pool-1-thread-3] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml: [testng] 02:50:05,674 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:50:05,675 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:50:05,676 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-10_02-50-05.log] [testng] 02:50:05,676 |-INFO in ch.qos.logback.core.sift.SiftProcessor@55dc60d3 - End of configuration. [testng] [2024-05-10 02:50:06,030] [pool-1-thread-2] Initializing /data/ruben/20100827_004/experiment_descriptor.xml: [testng] 02:50:06,030 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:50:06,030 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:50:06,030 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-10_02-50-06.log] [testng] 02:50:06,031 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2d527a0c - End of configuration. [testng] [2024-05-10 02:50:11,084] [pool-1-thread-1] Initializing /data/nadine/experiment_descriptor.xml: [testng] [2024-05-10 02:50:13,368] [pool-1-thread-1] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml: [testng] [2024-05-10 02:50:20,041] [pool-1-thread-10] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml: [testng] [2024-05-10 02:51:59,773] [pool-1-thread-9] Initializing /data/christian/example/experiment_descriptor.xml: [testng] [2024-05-10 02:52:01,233] [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: 34 minutes 18 seconds Finished: SUCCESS