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Started by upstream project "BIOFORMATS-test-repo" build number 305 originally caused by: Started by upstream project "Trigger" build number 327 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5 [BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins12954015344259889766.sh + '[' scanr = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_48349_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] 03:31:32,352 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:31:32,353 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 03:31:32,353 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:31:32,354 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:31:32,354 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:31:32,355 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:31:32,355 |-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] 03:31:32,355 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:31:32,355 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:31:32,356 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:31:32,356 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:31:32,356 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:31:32,524 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:31:32,524 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:31:32,547 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:31:32,547 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:31:32,553 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:31:32,553 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:31:32,553 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:31:32,553 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:31:32,554 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 03:31:32,554 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 03:31:32,554 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 199 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-01-01 03:31:32,563] [main] java.version = 17.0.2 [testng] 03:31:32,567 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:31:32,567 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:31:32,609 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-01-01_03-31-32.log] [testng] 03:31:32,610 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2025-01-01 03:31:32,612] [main] testng.directory = /data [testng] [2025-01-01 03:31:32,612] [main] testng.configDirectory = /config [testng] [2025-01-01 03:31:32,621] [main] testng.multiplier = 1.0 [testng] [2025-01-01 03:31:32,622] [main] testng.in-memory = false [testng] [2025-01-01 03:31:32,622] [main] testng.allow-missing = false [testng] [2025-01-01 03:31:32,622] [main] user.language = en [testng] [2025-01-01 03:31:32,622] [main] user.country = ${user.country} [testng] [2025-01-01 03:31:32,622] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-01-01 03:36:12,692] [main] ---------------------------------------- [testng] [2025-01-01 03:36:12,693] [main] Total files: 2169 [testng] [2025-01-01 03:36:12,693] [main] Scan time: 280.07 s (129 ms/file) [testng] [2025-01-01 03:36:12,693] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-01-01 03:56:33,051] [pool-1-thread-1] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml: [testng] 03:56:33,052 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:56:33,052 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:56:33,053 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-01-01_03-56-33.log] [testng] 03:56:33,053 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4ba0e340 - End of configuration. [testng] [2025-01-01 03:58:11,177] [pool-1-thread-12] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml: [testng] 03:58:11,178 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:58:11,178 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:58:11,179 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-01-01_03-58-11.log] [testng] 03:58:11,179 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7cf788aa - End of configuration. [testng] [2025-01-01 03:58:18,410] [pool-1-thread-11] Initializing /data/ruben/20100827_004/experiment_descriptor.xml: [testng] 03:58:18,410 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:58:18,410 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:58:18,411 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-01-01_03-58-18.log] [testng] 03:58:18,411 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ad0ef37 - End of configuration. [testng] [2025-01-01 03:59:33,830] [pool-1-thread-10] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml: [testng] 03:59:33,830 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:59:33,831 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:59:33,831 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-01-01_03-59-33.log] [testng] 03:59:33,832 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f06a2b2 - End of configuration. [testng] [2025-01-01 03:59:50,824] [pool-1-thread-9] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml: [testng] 03:59:50,824 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:59:50,824 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:59:50,825 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-01-01_03-59-50.log] [testng] 03:59:50,825 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1145df01 - End of configuration. [testng] [2025-01-01 04:01:05,307] [pool-1-thread-8] Initializing /data/nadine/experiment_descriptor.xml: [testng] 04:01:05,307 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 04:01:05,307 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:01:05,309 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-01-01_04-01-05.log] [testng] 04:01:05,309 |-INFO in ch.qos.logback.core.sift.SiftProcessor@613cff18 - End of configuration. [testng] [2025-01-01 04:01:06,577] [pool-1-thread-7] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml: [testng] 04:01:06,578 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 04:01:06,578 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:01:06,579 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-01-01_04-01-06.log] [testng] 04:01:06,579 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a0aca3e - End of configuration. [testng] [2025-01-01 04:01:17,631] [pool-1-thread-6] Initializing /data/ruben/161009test2/151009_001/experiment_descriptor.xml: [testng] 04:01:17,631 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 04:01:17,631 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:01:17,632 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-01-01_04-01-17.log] [testng] 04:01:17,633 |-INFO in ch.qos.logback.core.sift.SiftProcessor@217af219 - End of configuration. [testng] [2025-01-01 04:04:04,893] [pool-1-thread-5] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml: [testng] 04:04:04,894 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 04:04:04,894 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:04:04,895 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-01-01_04-04-04.log] [testng] 04:04:04,896 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c6546f3 - End of configuration. [testng] [2025-01-01 04:04:37,222] [pool-1-thread-4] Initializing /data/ruben/plate_002/experiment_descriptor.xml: [testng] 04:04:37,222 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 04:04:37,222 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:04:37,222 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-01-01_04-04-37.log] [testng] 04:04:37,223 |-INFO in ch.qos.logback.core.sift.SiftProcessor@55318f3d - End of configuration. [testng] [2025-01-01 04:04:39,227] [pool-1-thread-3] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml: [testng] 04:04:39,227 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 04:04:39,227 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:04:39,228 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-01-01_04-04-39.log] [testng] 04:04:39,229 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57159334 - End of configuration. [testng] [2025-01-01 04:07:29,149] [pool-1-thread-2] Initializing /data/christian/example/experiment_descriptor.xml: [testng] 04:07:29,150 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 04:07:29,150 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:07:29,151 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-01-01_04-07-29.log] [testng] 04:07:29,151 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68338ff1 - End of configuration. [testng] [2025-01-01 04:07:50,397] [pool-1-thread-2] Initializing /data/embl/Maik_001/experiment_descriptor.xml: [testng] [2025-01-01 04:08:16,059] [pool-1-thread-8] Initializing /data/gideon/experiment_descriptor.xml: [testng] [2025-01-01 04:11:04,756] [pool-1-thread-4] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml: [testng] [2025-01-01 04:16:01,194] [pool-1-thread-12] Initializing /data/juergen/Experiment/experiment_descriptor.xml: [testng] [2025-01-01 04:16:33,342] [pool-1-thread-2] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml: [testng] 05:23:08,794 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 05:23:08,794 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:23:08,795 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-01-01_05-23-08.log] [testng] 05:23:08,796 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1db04ad9 - End of configuration. [testng] 05:23:23,115 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 05:23:23,115 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:23:23,117 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-01-01_05-23-23.log] [testng] 05:23:23,117 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2bad8307 - End of configuration. [testng] 05:26:15,975 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 05:26:15,975 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:26:15,977 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-01-01_05-26-15.log] [testng] 05:26:15,977 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c24d0f0 - End of configuration. [testng] 05:27:24,865 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 05:27:24,865 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:27:24,866 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-01-01_05-27-24.log] [testng] 05:27:24,866 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ef334e4 - End of configuration. [testng] 05:32:45,573 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 05:32:45,574 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:32:45,574 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-01-01_05-32-45.log] [testng] 05:32:45,575 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e4d2e2d - 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: 121 minutes 18 seconds Finished: SUCCESS