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Started by upstream project "BIOFORMATS-test-repo" build number 3 originally caused by: Started by upstream project "Trigger" build number 4 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins4810200829725695635.sh + '[' metaxpress = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_338_merge_ci -v /uod/idr/repos/curated/metaxpress:/data -v /uod/idr-scratch/merge-ci/curated/metaxpress:/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] 00:30:51,378 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:30:51,380 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 00:30:51,380 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:30:51,381 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:30:51,381 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:30:51,382 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:30:51,382 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:30:51,382 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:30:51,382 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:30:51,383 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:30:51,383 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:30:51,384 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:30:51,578 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:30:51,579 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:30:51,605 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:30:51,605 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:30:51,611 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:30:51,611 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:30:51,611 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:30:51,612 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:30:51,612 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 00:30:51,613 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 00:30:51,613 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 231 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-16 00:30:51,623] [main] java.version = 11.0.16 [testng] 00:30:51,626 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:30:51,627 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:51,675 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-16_00-30-51.log] [testng] 00:30:51,677 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-03-16 00:30:51,679] [main] testng.directory = /data [testng] [2024-03-16 00:30:51,680] [main] testng.configDirectory = /config [testng] [2024-03-16 00:30:51,692] [main] testng.multiplier = 1.0 [testng] [2024-03-16 00:30:51,694] [main] testng.in-memory = false [testng] [2024-03-16 00:30:51,694] [main] testng.allow-missing = false [testng] [2024-03-16 00:30:51,694] [main] user.language = en [testng] [2024-03-16 00:30:51,694] [main] user.country = ${user.country} [testng] [2024-03-16 00:30:51,694] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-03-16 00:37:35,730] [main] ---------------------------------------- [testng] [2024-03-16 00:37:35,731] [main] Total files: 1231 [testng] [2024-03-16 00:37:35,731] [main] Scan time: 404.036 s (328 ms/file) [testng] [2024-03-16 00:37:35,731] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 10 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-16 00:43:06,621] [pool-1-thread-1] Initializing /data/samples/multi-channel-test/multi-channel.HTD: [testng] 00:43:06,623 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:43:06,623 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:43:06,625 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-16_00-43-06.log] [testng] 00:43:06,626 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5de2ed73 - End of configuration. [testng] [2024-03-16 00:43:07,195] [pool-1-thread-10] Initializing /data/samples/multi-channel-missing-corner/multi-channel.HTD: [testng] 00:43:07,195 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:43:07,195 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:43:07,196 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-16_00-43-07.log] [testng] 00:43:07,196 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5968f422 - End of configuration. [testng] [2024-03-16 00:43:08,971] [pool-1-thread-9] Initializing /data/public/idr0006/plate 11001_Plate_136/TimePoint_1/plate 11001.HTD: [testng] 00:43:08,972 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:43:08,972 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:43:08,973 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-16_00-43-08.log] [testng] 00:43:08,973 |-INFO in ch.qos.logback.core.sift.SiftProcessor@11816e27 - End of configuration. [testng] [2024-03-16 00:44:11,920] [pool-1-thread-8] Initializing /data/samples/single-site-test/single-site.HTD: [testng] 00:44:11,921 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:44:11,921 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:44:11,923 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-16_00-44-11.log] [testng] 00:44:11,924 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a746735 - End of configuration. [testng] [2024-03-16 00:44:12,972] [pool-1-thread-7] Initializing /data/public/idr0005/Primary_001/2011-04-19-plate-1.HTD: [testng] 00:44:12,972 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:44:12,972 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:44:12,973 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-16_00-44-12.log] [testng] 00:44:12,973 |-INFO in ch.qos.logback.core.sift.SiftProcessor@948aecf - End of configuration. [testng] [2024-03-16 00:44:20,463] [pool-1-thread-6] Initializing /data/samples/thumb-test/2011-04-19-plate-1.HTD: [testng] 00:44:20,463 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:44:20,463 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:44:20,464 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-16_00-44-20.log] [testng] 00:44:20,464 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f428320 - End of configuration. [testng] [2024-03-16 00:44:26,534] [pool-1-thread-5] Initializing /data/public/idr0008/Plate10_Actinome1/Act1_Plate10-SP-A8.HTD: [testng] 00:44:26,535 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:44:26,535 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:44:26,536 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-16_00-44-26.log] [testng] 00:44:26,536 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18b9d0dc - End of configuration. [testng] [2024-03-16 00:44:57,241] [pool-1-thread-4] Initializing /data/samples/multi-z/2011-04-19-plate-1.HTD: [testng] 00:44:57,241 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:44:57,241 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:44:57,242 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-16_00-44-57.log] [testng] 00:44:57,243 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79ab01e - End of configuration. [testng] [2024-03-16 00:45:05,406] [pool-1-thread-3] Initializing /data/qa-4207/NSC.HTD: [testng] 00:45:05,407 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:45:05,407 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:45:05,408 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-16_00-45-05.log] [testng] 00:45:05,408 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3241e8a0 - End of configuration. [testng] [2024-03-16 00:45:06,138] [pool-1-thread-2] Initializing /data/public/idr0081/BSF018292-1A/BSF018292-1A.HTD: [testng] 00:45:06,138 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:45:06,138 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:45:06,139 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-16_00-45-06.log] [testng] 00:45:06,139 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1c078e95 - End of configuration. [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 530, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 38 minutes 31 seconds Finished: SUCCESS