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Started by upstream project "BIOFORMATS-test-repo" build number 65 originally caused by: Started by upstream project "Trigger" build number 72 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins7526418679109948756.sh + '[' scanr = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_9775_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 02:19:42,789 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:19:42,790 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 02:19:42,790 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:19:42,791 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:19:42,791 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:19:42,792 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:19:42,792 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:19:42,792 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:19:42,793 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:19:42,793 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:19:42,793 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:19:42,794 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:19:42,952 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:19:42,952 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:19:42,977 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:19:42,977 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:19:42,983 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:19:42,983 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:19:42,983 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:19:42,983 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:19:42,983 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 02:19:42,984 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 02:19:42,984 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 191 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-05-16 02:19:42,993] [main] java.version = 21 [testng] 02:19:42,996 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:19:42,996 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:19:43,036 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-16_02-19-43.log] [testng] 02:19:43,038 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-05-16 02:19:43,039] [main] testng.directory = /data [testng] [2024-05-16 02:19:43,039] [main] testng.configDirectory = /config [testng] [2024-05-16 02:19:43,048] [main] testng.multiplier = 1.0 [testng] [2024-05-16 02:19:43,048] [main] testng.in-memory = false [testng] [2024-05-16 02:19:43,048] [main] testng.allow-missing = false [testng] [2024-05-16 02:19:43,048] [main] user.language = en [testng] [2024-05-16 02:19:43,048] [main] user.country = ${user.country} [testng] [2024-05-16 02:19:43,048] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-05-16 02:25:08,033] [main] ---------------------------------------- [testng] [2024-05-16 02:25:08,033] [main] Total files: 2169 [testng] [2024-05-16 02:25:08,034] [main] Scan time: 324.984 s (149 ms/file) [testng] [2024-05-16 02:25:08,035] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-05-16 02:42:37,437] [pool-1-thread-1] Initializing /data/christian/example/experiment_descriptor.xml: [testng] 02:42:37,438 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:42:37,438 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:42:37,439 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-16_02-42-37.log] [testng] 02:42:37,440 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38b720d4 - End of configuration. [testng] [2024-05-16 02:42:37,623] [pool-1-thread-12] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml: [testng] 02:42:37,624 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:42:37,624 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:42:37,625 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-16_02-42-37.log] [testng] 02:42:37,625 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6fdb0be0 - End of configuration. [testng] [2024-05-16 02:44:22,185] [pool-1-thread-11] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml: [testng] 02:44:22,186 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:44:22,186 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:44:22,188 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-16_02-44-22.log] [testng] 02:44:22,189 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4537863e - End of configuration. [testng] [2024-05-16 02:47:04,340] [pool-1-thread-10] Initializing /data/embl/Maik_001/experiment_descriptor.xml: [testng] 02:47:04,341 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:47:04,341 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:47:04,343 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-16_02-47-04.log] [testng] 02:47:04,343 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1995b358 - End of configuration. [testng] [2024-05-16 02:47:12,603] [pool-1-thread-9] Initializing /data/ruben/plate_002/experiment_descriptor.xml: [testng] 02:47:12,603 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:47:12,603 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:47:12,604 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-16_02-47-12.log] [testng] 02:47:12,604 |-INFO in ch.qos.logback.core.sift.SiftProcessor@559edb09 - End of configuration. [testng] [2024-05-16 02:47:16,032] [pool-1-thread-8] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml: [testng] 02:47:16,032 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:47:16,032 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:47:16,033 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-16_02-47-16.log] [testng] 02:47:16,034 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4ded36c3 - End of configuration. [testng] [2024-05-16 02:47:20,993] [pool-1-thread-7] Initializing /data/ruben/20100827_004/experiment_descriptor.xml: [testng] 02:47:20,993 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:47:20,993 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:47:20,994 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-16_02-47-20.log] [testng] 02:47:20,995 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5cd5fa79 - End of configuration. [testng] [2024-05-16 02:48:38,351] [pool-1-thread-6] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml: [testng] 02:48:38,352 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:48:38,352 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:48:38,352 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-16_02-48-38.log] [testng] 02:48:38,353 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f93751 - End of configuration. [testng] [2024-05-16 02:48:55,490] [pool-1-thread-5] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml: [testng] 02:48:55,491 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:48:55,491 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:48:55,493 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-16_02-48-55.log] [testng] 02:48:55,493 |-INFO in ch.qos.logback.core.sift.SiftProcessor@473e2494 - End of configuration. [testng] [2024-05-16 02:50:40,085] [pool-1-thread-4] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml: [testng] 02:50:40,085 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:50:40,086 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:50:40,087 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-16_02-50-40.log] [testng] 02:50:40,088 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79a4a18a - End of configuration. [testng] [2024-05-16 02:51:55,864] [pool-1-thread-3] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml: [testng] 02:51:55,864 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:51:55,864 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:51:55,866 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-16_02-51-55.log] [testng] 02:51:55,866 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a6edaaf - End of configuration. [testng] [2024-05-16 02:52:27,254] [pool-1-thread-2] Initializing /data/juergen/Experiment/experiment_descriptor.xml: [testng] 02:52:27,254 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:52:27,254 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:52:27,256 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-16_02-52-27.log] [testng] 02:52:27,256 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2aee526f - End of configuration. [testng] [2024-05-16 02:52:29,888] [pool-1-thread-1] Initializing /data/nadine/experiment_descriptor.xml: [testng] [2024-05-16 02:52:30,416] [pool-1-thread-2] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml: [testng] [2024-05-16 02:53:33,667] [pool-1-thread-1] Initializing /data/gideon/experiment_descriptor.xml: [testng] [2024-05-16 02:54:16,064] [pool-1-thread-8] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml: [testng] [2024-05-16 02:55:34,034] [pool-1-thread-10] 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: 42 minutes 28 seconds Finished: SUCCESS