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Started by upstream project "BIOFORMATS-test-repo" build number 229 originally caused by: Started by upstream project "Trigger" build number 254 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@7 [BIOFORMATS-test-folder@7] $ /bin/bash -xe /tmp/jenkins8173011320034091062.sh + '[' scanr = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_35997_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] 03:47:49,974 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:47:49,975 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 03:47:49,975 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:47:49,976 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:47:49,976 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:47:49,976 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:47:49,977 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 03:47:49,977 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:47:49,977 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:47:49,978 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:47:49,978 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:47:49,978 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:47:50,136 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:47:50,136 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:47:50,157 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:47:50,157 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:47:50,163 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:47:50,163 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:47:50,163 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:47:50,163 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:47:50,163 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 03:47:50,164 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 03:47:50,164 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 187 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-20 03:47:50,173] [main] java.version = 17.0.2 [testng] 03:47:50,175 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:47:50,175 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:47:50,215 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-20_03-47-50.log] [testng] 03:47:50,216 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-10-20 03:47:50,218] [main] testng.directory = /data [testng] [2024-10-20 03:47:50,218] [main] testng.configDirectory = /config [testng] [2024-10-20 03:47:50,226] [main] testng.multiplier = 1.0 [testng] [2024-10-20 03:47:50,227] [main] testng.in-memory = false [testng] [2024-10-20 03:47:50,227] [main] testng.allow-missing = false [testng] [2024-10-20 03:47:50,227] [main] user.language = en [testng] [2024-10-20 03:47:50,227] [main] user.country = ${user.country} [testng] [2024-10-20 03:47:50,228] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-20 03:52:50,287] [main] ---------------------------------------- [testng] [2024-10-20 03:52:50,287] [main] Total files: 2169 [testng] [2024-10-20 03:52:50,287] [main] Scan time: 300.059 s (138 ms/file) [testng] [2024-10-20 03:52:50,288] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-20 04:10:13,697] [pool-1-thread-1] Initializing /data/christian/example/experiment_descriptor.xml: [testng] 04:10:13,697 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 04:10:13,697 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:10:13,699 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-20_04-10-13.log] [testng] 04:10:13,699 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75e86f38 - End of configuration. [testng] [2024-10-20 04:10:14,548] [pool-1-thread-12] Initializing /data/gideon/experiment_descriptor.xml: [testng] 04:10:14,549 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 04:10:14,549 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:10:14,550 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-20_04-10-14.log] [testng] 04:10:14,550 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6273f06a - End of configuration. [testng] [2024-10-20 04:10:33,207] [pool-1-thread-11] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml: [testng] 04:10:33,208 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 04:10:33,208 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:10:33,209 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-20_04-10-33.log] [testng] 04:10:33,209 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8364c3c - End of configuration. [testng] [2024-10-20 04:11:02,855] [pool-1-thread-10] Initializing /data/nadine/experiment_descriptor.xml: [testng] 04:11:02,856 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 04:11:02,856 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:11:02,857 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-20_04-11-02.log] [testng] 04:11:02,858 |-INFO in ch.qos.logback.core.sift.SiftProcessor@41a97571 - End of configuration. [testng] [2024-10-20 04:11:03,675] [pool-1-thread-9] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml: [testng] 04:11:03,676 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 04:11:03,676 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:11:03,677 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-20_04-11-03.log] [testng] 04:11:03,677 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6eee67c0 - End of configuration. [testng] [2024-10-20 04:11:12,862] [pool-1-thread-8] Initializing /data/juergen/Experiment/experiment_descriptor.xml: [testng] 04:11:12,862 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 04:11:12,862 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:11:12,863 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-20_04-11-12.log] [testng] 04:11:12,863 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c31bd20 - End of configuration. [testng] [2024-10-20 04:11:13,759] [pool-1-thread-7] Initializing /data/ruben/20100827_004/experiment_descriptor.xml: [testng] 04:11:13,760 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 04:11:13,760 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:11:13,760 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-20_04-11-13.log] [testng] 04:11:13,761 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43ee698f - End of configuration. [testng] [2024-10-20 04:12:26,506] [pool-1-thread-6] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml: [testng] 04:12:26,506 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 04:12:26,506 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:12:26,508 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-20_04-12-26.log] [testng] 04:12:26,508 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22c27c61 - End of configuration. [testng] [2024-10-20 04:14:06,239] [pool-1-thread-5] Initializing /data/ruben/plate_002/experiment_descriptor.xml: [testng] 04:14:06,239 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 04:14:06,240 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:14:06,241 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-20_04-14-06.log] [testng] 04:14:06,241 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2c0ac1f7 - End of configuration. [testng] [2024-10-20 04:14:08,774] [pool-1-thread-4] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml: [testng] 04:14:08,774 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 04:14:08,774 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:14:08,775 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-20_04-14-08.log] [testng] 04:14:08,775 |-INFO in ch.qos.logback.core.sift.SiftProcessor@763c82e3 - End of configuration. [testng] [2024-10-20 04:14:22,982] [pool-1-thread-3] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml: [testng] 04:14:22,983 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 04:14:22,983 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:14:22,983 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-20_04-14-22.log] [testng] 04:14:22,984 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b13bd2 - End of configuration. [testng] [2024-10-20 04:16:02,025] [pool-1-thread-2] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml: [testng] 04:16:02,025 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 04:16:02,025 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:16:02,027 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-20_04-16-02.log] [testng] 04:16:02,027 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c6dc7be - End of configuration. [testng] [2024-10-20 04:16:56,005] [pool-1-thread-1] Initializing /data/ruben/161009test2/151009_001/experiment_descriptor.xml: [testng] [2024-10-20 04:18:43,323] [pool-1-thread-8] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml: [testng] [2024-10-20 04:19:24,041] [pool-1-thread-10] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml: [testng] [2024-10-20 04:21:57,464] [pool-1-thread-5] Initializing /data/embl/Maik_001/experiment_descriptor.xml: [testng] [2024-10-20 04:29:26,666] [pool-1-thread-5] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml: [testng] 05:25:42,718 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 05:25:42,718 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:25:42,720 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-20_05-25-42.log] [testng] 05:25:42,720 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d994789 - End of configuration. [testng] 05:26:00,977 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 05:26:00,977 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:26:00,979 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-20_05-26-00.log] [testng] 05:26:00,979 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4dae089c - End of configuration. [testng] 05:26:52,271 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 05:26:52,271 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:26:52,273 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-20_05-26-52.log] [testng] 05:26:52,273 |-INFO in ch.qos.logback.core.sift.SiftProcessor@55836c3e - End of configuration. [testng] 05:27:33,698 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 05:27:33,698 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:27:33,699 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-20_05-27-33.log] [testng] 05:27:33,699 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e213a1c - End of configuration. [testng] 05:33:04,118 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 05:33:04,118 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:33:04,119 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-20_05-33-04.log] [testng] 05:33:04,120 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d449860 - 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: 105 minutes 17 seconds Finished: SUCCESS