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Started by upstream project "BIOFORMATS-test-repo" build number 237 originally caused by: Started by upstream project "Trigger" build number 262 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/jenkins14777017869655510868.sh + '[' scanr = slidebook ']' ++ date +%u + '[' 1 -le 1 ']' + DOCKER_ARGS='-Dtestng.memory=15g -Dtestng.threadCount=12 -Duser.language=fr -Duser.country=FR' + sudo docker run --rm --name BIOFORMATS-test-folder_37310_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 -Duser.language=fr -Duser.country=FR 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] 03:02:20,508 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:02:20,510 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 03:02:20,510 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:02:20,511 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:02:20,511 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:02:20,511 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:02:20,512 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 03:02:20,512 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:02:20,512 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:02:20,512 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:02:20,513 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:02:20,513 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:02:20,739 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:02:20,739 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:02:20,767 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:02:20,767 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:02:20,775 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:02:20,775 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:02:20,775 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:02:20,776 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:02:20,776 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 03:02:20,777 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 03:02:20,777 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 265 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-28 03:02:20,786] [main] java.version = 1.8.0_342 [testng] 03:02:20,790 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:02:20,790 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:02:20,834 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-28_03-02-20.log] [testng] 03:02:20,836 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-10-28 03:02:20,838] [main] testng.directory = /data [testng] [2024-10-28 03:02:20,838] [main] testng.configDirectory = /config [testng] [2024-10-28 03:02:20,850] [main] testng.multiplier = 1.0 [testng] [2024-10-28 03:02:20,850] [main] testng.in-memory = false [testng] [2024-10-28 03:02:20,850] [main] testng.allow-missing = false [testng] [2024-10-28 03:02:20,850] [main] user.language = fr [testng] [2024-10-28 03:02:20,850] [main] user.country = FR [testng] [2024-10-28 03:02:20,850] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-10-28 03:07:44,256] [main] ---------------------------------------- [testng] [2024-10-28 03:07:44,256] [main] Total files: 2169 [testng] [2024-10-28 03:07:44,256] [main] Scan time: 323.406 s (149 ms/file) [testng] [2024-10-28 03:07:44,256] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-28 03:28:58,761] [pool-1-thread-1] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml: [testng] 03:28:58,762 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:28:58,762 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:28:58,763 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-28_03-28-58.log] [testng] 03:28:58,763 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3627bbb - End of configuration. [testng] [2024-10-28 03:30:56,839] [pool-1-thread-12] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml: [testng] 03:30:56,839 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:30:56,839 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:30:56,840 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-28_03-30-56.log] [testng] 03:30:56,841 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2647d9b4 - End of configuration. [testng] [2024-10-28 03:31:02,366] [pool-1-thread-11] Initializing /data/ruben/20100827_004/experiment_descriptor.xml: [testng] 03:31:02,367 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:31:02,367 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:31:02,368 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-28_03-31-02.log] [testng] 03:31:02,369 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b6a2a65 - End of configuration. [testng] [2024-10-28 03:32:18,150] [pool-1-thread-10] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml: [testng] 03:32:18,150 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:32:18,150 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:32:18,151 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-28_03-32-18.log] [testng] 03:32:18,151 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4de358b9 - End of configuration. [testng] [2024-10-28 03:32:28,984] [pool-1-thread-9] Initializing /data/gideon/experiment_descriptor.xml: [testng] 03:32:28,984 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:32:28,984 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:32:28,985 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-28_03-32-28.log] [testng] 03:32:28,986 |-INFO in ch.qos.logback.core.sift.SiftProcessor@41fdce3c - End of configuration. [testng] [2024-10-28 03:33:03,729] [pool-1-thread-8] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml: [testng] 03:33:03,730 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:33:03,730 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:33:03,730 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-28_03-33-03.log] [testng] 03:33:03,731 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71c501a7 - End of configuration. [testng] [2024-10-28 03:34:04,189] [pool-1-thread-7] Initializing /data/ruben/plate_002/experiment_descriptor.xml: [testng] 03:34:04,190 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:34:04,190 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:34:04,191 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-28_03-34-04.log] [testng] 03:34:04,192 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3eae470a - End of configuration. [testng] [2024-10-28 03:34:06,635] [pool-1-thread-6] Initializing /data/embl/Maik_001/experiment_descriptor.xml: [testng] 03:34:06,635 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:34:06,635 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:34:06,636 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-28_03-34-06.log] [testng] 03:34:06,637 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1c7d09e5 - End of configuration. [testng] [2024-10-28 03:34:15,786] [pool-1-thread-5] Initializing /data/christian/example/experiment_descriptor.xml: [testng] 03:34:15,787 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:34:15,787 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:34:15,787 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-28_03-34-15.log] [testng] 03:34:15,788 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2c991a1 - End of configuration. [testng] [2024-10-28 03:34:16,637] [pool-1-thread-4] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml: [testng] 03:34:16,637 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:34:16,637 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:34:16,638 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-28_03-34-16.log] [testng] 03:34:16,638 |-INFO in ch.qos.logback.core.sift.SiftProcessor@74e2267b - End of configuration. [testng] [2024-10-28 03:34:51,085] [pool-1-thread-3] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml: [testng] 03:34:51,085 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:34:51,086 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:34:51,086 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-28_03-34-51.log] [testng] 03:34:51,087 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e3b5562 - End of configuration. [testng] [2024-10-28 03:35:30,589] [pool-1-thread-2] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml: [testng] 03:35:30,589 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:35:30,589 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:35:30,590 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-28_03-35-30.log] [testng] 03:35:30,590 |-INFO in ch.qos.logback.core.sift.SiftProcessor@508f11b9 - End of configuration. [testng] [2024-10-28 03:37:27,579] [pool-1-thread-5] Initializing /data/ruben/161009test2/151009_001/experiment_descriptor.xml: [testng] [2024-10-28 03:40:37,758] [pool-1-thread-7] Initializing /data/juergen/Experiment/experiment_descriptor.xml: [testng] [2024-10-28 03:41:09,102] [pool-1-thread-7] Initializing /data/nadine/experiment_descriptor.xml: [testng] [2024-10-28 03:41:50,687] [pool-1-thread-7] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml: [testng] [2024-10-28 03:46:16,838] [pool-1-thread-12] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml: [testng] 04:48:21,521 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 04:48:21,522 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:48:21,522 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-28_04-48-21.log] [testng] 04:48:21,523 |-INFO in ch.qos.logback.core.sift.SiftProcessor@52e01e0a - End of configuration. [testng] 04:49:00,588 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 04:49:00,588 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:49:00,590 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-28_04-49-00.log] [testng] 04:49:00,590 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f8c1418 - End of configuration. [testng] 04:50:53,134 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 04:50:53,134 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:50:53,135 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-28_04-50-53.log] [testng] 04:50:53,136 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f1f61ff - End of configuration. [testng] 04:53:04,598 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 04:53:04,598 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:53:04,599 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-28_04-53-04.log] [testng] 04:53:04,600 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4888752c - End of configuration. [testng] 04:58:27,422 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 04:58:27,422 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:58:27,423 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-28_04-58-27.log] [testng] 04:58:27,423 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3bd710f8 - 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: 116 minutes 11 seconds Finished: SUCCESS