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Started by upstream project "BIOFORMATS-test-repo" build number 277 originally caused by: Started by upstream project "Trigger" build number 298 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8 [BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins8599647796976797708.sh + '[' scanr = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_43741_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] WARNING: An illegal reflective access operation has occurred [testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket [testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener [testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [testng] WARNING: All illegal access operations will be denied in a future release [testng] File leak detector installed [testng] 03:13:43,287 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:13:43,289 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 03:13:43,289 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:13:43,290 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:13:43,290 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:13:43,291 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:13:43,291 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 03:13:43,291 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:13:43,292 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:13:43,292 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:13:43,292 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:13:43,293 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:13:43,462 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:13:43,462 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:13:43,484 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:13:43,484 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:13:43,490 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:13:43,490 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:13:43,490 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:13:43,491 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:13:43,491 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 03:13:43,492 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 03:13:43,492 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 200 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-03 03:13:43,501] [main] java.version = 11.0.16 [testng] 03:13:43,504 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:13:43,504 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:13:43,547 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-03_03-13-43.log] [testng] 03:13:43,549 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-12-03 03:13:43,551] [main] testng.directory = /data [testng] [2024-12-03 03:13:43,551] [main] testng.configDirectory = /config [testng] [2024-12-03 03:13:43,561] [main] testng.multiplier = 1.0 [testng] [2024-12-03 03:13:43,562] [main] testng.in-memory = false [testng] [2024-12-03 03:13:43,563] [main] testng.allow-missing = false [testng] [2024-12-03 03:13:43,563] [main] user.language = en [testng] [2024-12-03 03:13:43,563] [main] user.country = ${user.country} [testng] [2024-12-03 03:13:43,563] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-03 03:19:49,293] [main] ---------------------------------------- [testng] [2024-12-03 03:19:49,294] [main] Total files: 2169 [testng] [2024-12-03 03:19:49,294] [main] Scan time: 365.73 s (168 ms/file) [testng] [2024-12-03 03:19:49,294] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-03 03:38:45,425] [pool-1-thread-1] Initializing /data/embl/Maik_001/experiment_descriptor.xml: [testng] 03:38:45,426 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:38:45,426 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:38:45,428 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-03_03-38-45.log] [testng] 03:38:45,429 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d007708 - End of configuration. [testng] [2024-12-03 03:38:57,002] [pool-1-thread-12] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml: [testng] 03:38:57,002 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:38:57,002 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:38:57,004 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-03_03-38-57.log] [testng] 03:38:57,004 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b8f3ad - End of configuration. [testng] [2024-12-03 03:42:09,223] [pool-1-thread-11] Initializing /data/ruben/20100827_004/experiment_descriptor.xml: [testng] 03:42:09,224 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:42:09,224 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:42:09,225 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-03_03-42-09.log] [testng] 03:42:09,225 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d284a8f - End of configuration. [testng] [2024-12-03 03:43:24,378] [pool-1-thread-10] Initializing /data/gideon/experiment_descriptor.xml: [testng] 03:43:24,379 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:43:24,379 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:43:24,380 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-03_03-43-24.log] [testng] 03:43:24,381 |-INFO in ch.qos.logback.core.sift.SiftProcessor@c52538f - End of configuration. [testng] [2024-12-03 03:44:00,033] [pool-1-thread-9] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml: [testng] 03:44:00,033 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:44:00,033 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:44:00,034 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-03_03-44-00.log] [testng] 03:44:00,034 |-INFO in ch.qos.logback.core.sift.SiftProcessor@42ee55a - End of configuration. [testng] [2024-12-03 03:45:06,477] [pool-1-thread-8] Initializing /data/juergen/Experiment/experiment_descriptor.xml: [testng] 03:45:06,478 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:45:06,478 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:45:06,478 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-03_03-45-06.log] [testng] 03:45:06,479 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13bf279d - End of configuration. [testng] [2024-12-03 03:45:07,487] [pool-1-thread-7] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml: [testng] 03:45:07,488 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:45:07,488 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:45:07,489 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-03_03-45-07.log] [testng] 03:45:07,489 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4953dce9 - End of configuration. [testng] [2024-12-03 03:45:44,983] [pool-1-thread-6] Initializing /data/nadine/experiment_descriptor.xml: [testng] 03:45:44,983 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:45:44,983 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:45:44,984 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-03_03-45-44.log] [testng] 03:45:44,984 |-INFO in ch.qos.logback.core.sift.SiftProcessor@189924ac - End of configuration. [testng] [2024-12-03 03:45:46,152] [pool-1-thread-5] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml: [testng] 03:45:46,153 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:45:46,153 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:45:46,153 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-03_03-45-46.log] [testng] 03:45:46,154 |-INFO in ch.qos.logback.core.sift.SiftProcessor@51474f3a - End of configuration. [testng] [2024-12-03 03:47:01,064] [pool-1-thread-4] Initializing /data/christian/example/experiment_descriptor.xml: [testng] 03:47:01,064 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:47:01,065 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:47:01,066 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-03_03-47-01.log] [testng] 03:47:01,066 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18b8d6a5 - End of configuration. [testng] [2024-12-03 03:47:01,940] [pool-1-thread-3] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml: [testng] 03:47:01,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:47:01,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:47:01,941 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-03_03-47-01.log] [testng] 03:47:01,941 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ec9bda6 - End of configuration. [testng] [2024-12-03 03:47:07,442] [pool-1-thread-2] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml: [testng] 03:47:07,442 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:47:07,442 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:47:07,443 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-03_03-47-07.log] [testng] 03:47:07,443 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f036cd3 - End of configuration. [testng] [2024-12-03 03:47:59,872] [pool-1-thread-4] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml: [testng] [2024-12-03 03:51:14,122] [pool-1-thread-8] Initializing /data/ruben/plate_002/experiment_descriptor.xml: [testng] [2024-12-03 03:51:28,671] [pool-1-thread-6] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml: [testng] [2024-12-03 03:56:14,560] [pool-1-thread-8] Initializing /data/ruben/161009test2/151009_001/experiment_descriptor.xml: [testng] [2024-12-03 03:59:35,586] [pool-1-thread-3] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml: [testng] 05:07:05,412 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 05:07:05,412 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:07:05,413 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-03_05-07-05.log] [testng] 05:07:05,414 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ddba18f - End of configuration. [testng] 05:08:01,161 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 05:08:01,161 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:08:01,163 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-03_05-08-01.log] [testng] 05:08:01,163 |-INFO in ch.qos.logback.core.sift.SiftProcessor@62a23fda - End of configuration. [testng] 05:08:09,614 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 05:08:09,614 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:08:09,615 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-03_05-08-09.log] [testng] 05:08:09,616 |-INFO in ch.qos.logback.core.sift.SiftProcessor@664ec0da - End of configuration. [testng] 05:09:31,301 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 05:09:31,301 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:09:31,302 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-03_05-09-31.log] [testng] 05:09:31,302 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3266dc6 - End of configuration. [testng] 05:15:42,209 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 05:15:42,209 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:15:42,210 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-03_05-15-42.log] [testng] 05:15:42,211 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a8b30a3 - 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: 122 minutes 3 seconds Finished: SUCCESS