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Started by upstream project "BIOFORMATS-test-repo" build number 204 originally caused by: Started by upstream project "Trigger" build number 230 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/jenkins9087953389820903173.sh + '[' scanr = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_32414_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] 1 warning 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] 03:30:56,161 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:30:56,162 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 03:30:56,162 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:30:56,163 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:30:56,164 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:30:56,164 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:30:56,165 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 03:30:56,165 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:30:56,165 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:30:56,166 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:30:56,166 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:30:56,166 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:30:56,368 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:30:56,368 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:30:56,392 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:30:56,392 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:30:56,398 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:30:56,398 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:30:56,398 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:30:56,399 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:30:56,399 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 03:30:56,399 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 03:30:56,399 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 234 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-09-29 03:30:56,410] [main] java.version = 17.0.2 [testng] 03:30:56,413 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:30:56,413 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:30:56,458 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-29_03-30-56.log] [testng] 03:30:56,459 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-09-29 03:30:56,461] [main] testng.directory = /data [testng] [2024-09-29 03:30:56,462] [main] testng.configDirectory = /config [testng] [2024-09-29 03:30:56,471] [main] testng.multiplier = 1.0 [testng] [2024-09-29 03:30:56,472] [main] testng.in-memory = false [testng] [2024-09-29 03:30:56,472] [main] testng.allow-missing = false [testng] [2024-09-29 03:30:56,472] [main] user.language = en [testng] [2024-09-29 03:30:56,472] [main] user.country = ${user.country} [testng] [2024-09-29 03:30:56,472] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-09-29 03:37:09,967] [main] ---------------------------------------- [testng] [2024-09-29 03:37:09,967] [main] Total files: 2169 [testng] [2024-09-29 03:37:09,968] [main] Scan time: 373.494 s (172 ms/file) [testng] [2024-09-29 03:37:09,968] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-09-29 03:56:17,401] [pool-1-thread-1] Initializing /data/embl/Maik_001/experiment_descriptor.xml: [testng] 03:56:17,402 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:56:17,402 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:56:17,403 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-09-29_03-56-17.log] [testng] 03:56:17,404 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d3e96b0 - End of configuration. [testng] [2024-09-29 03:56:26,071] [pool-1-thread-12] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml: [testng] 03:56:26,071 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:56:26,072 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:56:26,073 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-09-29_03-56-26.log] [testng] 03:56:26,073 |-INFO in ch.qos.logback.core.sift.SiftProcessor@55896030 - End of configuration. [testng] [2024-09-29 03:59:05,945] [pool-1-thread-11] Initializing /data/ruben/161009test2/151009_001/experiment_descriptor.xml: [testng] 03:59:05,946 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:59:05,946 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:59:05,947 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-09-29_03-59-05.log] [testng] 03:59:05,948 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d6b8a81 - End of configuration. [testng] [2024-09-29 04:00:49,862] [pool-1-thread-10] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml: [testng] 04:00:49,863 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 04:00:49,863 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:00:49,864 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-09-29_04-00-49.log] [testng] 04:00:49,865 |-INFO in ch.qos.logback.core.sift.SiftProcessor@fedb565 - End of configuration. [testng] [2024-09-29 04:01:05,070] [pool-1-thread-9] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml: [testng] 04:01:05,071 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 04:01:05,071 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:01:05,072 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-09-29_04-01-05.log] [testng] 04:01:05,072 |-INFO in ch.qos.logback.core.sift.SiftProcessor@62389fb6 - End of configuration. [testng] [2024-09-29 04:01:29,116] [pool-1-thread-8] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml: [testng] 04:01:29,116 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 04:01:29,117 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:01:29,118 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-09-29_04-01-29.log] [testng] 04:01:29,118 |-INFO in ch.qos.logback.core.sift.SiftProcessor@189bf79d - End of configuration. [testng] [2024-09-29 04:02:08,831] [pool-1-thread-7] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml: [testng] 04:02:08,832 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 04:02:08,832 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:02:08,833 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-09-29_04-02-08.log] [testng] 04:02:08,834 |-INFO in ch.qos.logback.core.sift.SiftProcessor@686787ad - End of configuration. [testng] [2024-09-29 04:02:16,557] [pool-1-thread-6] Initializing /data/juergen/Experiment/experiment_descriptor.xml: [testng] 04:02:16,558 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 04:02:16,558 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:02:16,558 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-09-29_04-02-16.log] [testng] 04:02:16,559 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35e0638d - End of configuration. [testng] [2024-09-29 04:02:17,254] [pool-1-thread-5] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml: [testng] 04:02:17,255 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 04:02:17,255 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:02:17,255 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-09-29_04-02-17.log] [testng] 04:02:17,256 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12e898bc - End of configuration. [testng] [2024-09-29 04:03:33,750] [pool-1-thread-4] Initializing /data/christian/example/experiment_descriptor.xml: [testng] 04:03:33,750 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 04:03:33,750 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:03:33,752 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-09-29_04-03-33.log] [testng] 04:03:33,752 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35dffa3d - End of configuration. [testng] [2024-09-29 04:03:34,368] [pool-1-thread-3] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml: [testng] 04:03:34,368 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 04:03:34,368 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:03:34,369 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-09-29_04-03-34.log] [testng] 04:03:34,369 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7aa4b958 - End of configuration. [testng] [2024-09-29 04:04:35,692] [pool-1-thread-2] Initializing /data/nadine/experiment_descriptor.xml: [testng] 04:04:35,692 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 04:04:35,693 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:04:35,694 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-09-29_04-04-35.log] [testng] 04:04:35,694 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a002f1 - End of configuration. [testng] [2024-09-29 04:04:58,884] [pool-1-thread-4] Initializing /data/ruben/20100827_004/experiment_descriptor.xml: [testng] [2024-09-29 04:06:21,744] [pool-1-thread-6] Initializing /data/gideon/experiment_descriptor.xml: [testng] [2024-09-29 04:07:10,626] [pool-1-thread-2] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml: [testng] [2024-09-29 04:11:09,949] [pool-1-thread-1] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml: [testng] [2024-09-29 04:15:23,302] [pool-1-thread-2] Initializing /data/ruben/plate_002/experiment_descriptor.xml: [testng] 05:08:40,689 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 05:08:40,689 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:08:40,691 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-09-29_05-08-40.log] [testng] 05:08:40,692 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2294060b - End of configuration. [testng] 05:08:41,106 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 05:08:41,106 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:08:41,108 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-09-29_05-08-41.log] [testng] 05:08:41,108 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7d960a25 - End of configuration. [testng] 05:10:58,936 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 05:10:58,936 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:10:58,937 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-09-29_05-10-58.log] [testng] 05:10:58,938 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48684dcd - End of configuration. [testng] 05:19:10,616 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 05:19:10,617 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:19:10,618 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-29_05-19-10.log] [testng] 05:19:10,618 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5615f2ac - End of configuration. [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 901, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 108 minutes 19 seconds Finished: SUCCESS