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Started by upstream project "BIOFORMATS-test-repo" build number 113 originally caused by: Started by upstream project "Trigger" build number 126 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/jenkins12010018051588066788.sh + '[' metaxpress = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_17561_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] 01:28:39,433 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:28:39,434 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 01:28:39,434 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:28:39,435 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:28:39,436 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:28:39,436 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:28:39,437 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:28:39,437 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:28:39,437 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:28:39,438 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:28:39,438 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:28:39,439 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:28:39,696 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:28:39,696 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:28:39,723 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:28:39,723 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:28:39,730 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:28:39,730 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:28:39,730 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:28:39,731 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:28:39,731 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 01:28:39,732 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 01:28:39,732 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 295 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-06 01:28:39,743] [main] java.version = 11.0.16 [testng] 01:28:39,747 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:28:39,747 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:28:39,795 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-06_01-28-39.log] [testng] 01:28:39,797 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-07-06 01:28:39,800] [main] testng.directory = /data [testng] [2024-07-06 01:28:39,800] [main] testng.configDirectory = /config [testng] [2024-07-06 01:28:39,811] [main] testng.multiplier = 1.0 [testng] [2024-07-06 01:28:39,813] [main] testng.in-memory = false [testng] [2024-07-06 01:28:39,813] [main] testng.allow-missing = false [testng] [2024-07-06 01:28:39,813] [main] user.language = en [testng] [2024-07-06 01:28:39,813] [main] user.country = ${user.country} [testng] [2024-07-06 01:28:39,813] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-07-06 01:35:36,270] [main] ---------------------------------------- [testng] [2024-07-06 01:35:36,271] [main] Total files: 1231 [testng] [2024-07-06 01:35:36,271] [main] Scan time: 416.457 s (338 ms/file) [testng] [2024-07-06 01:35:36,272] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 10 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-06 01:40:03,617] [pool-1-thread-1] Initializing /data/samples/multi-z/2011-04-19-plate-1.HTD: [testng] 01:40:03,617 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:40:03,618 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:03,620 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-06_01-40-03.log] [testng] 01:40:03,620 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43c0f458 - End of configuration. [testng] [2024-07-06 01:40:04,769] [pool-1-thread-10] Initializing /data/samples/thumb-test/2011-04-19-plate-1.HTD: [testng] 01:40:04,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:40:04,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:04,770 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-06_01-40-04.log] [testng] 01:40:04,770 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5431765e - End of configuration. [testng] [2024-07-06 01:40:05,927] [pool-1-thread-9] Initializing /data/public/idr0081/BSF018292-1A/BSF018292-1A.HTD: [testng] 01:40:05,927 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:40:05,927 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:05,927 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-06_01-40-05.log] [testng] 01:40:05,928 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f38462d - End of configuration. [testng] [2024-07-06 01:40:07,832] [pool-1-thread-8] Initializing /data/samples/multi-channel-test/multi-channel.HTD: [testng] 01:40:07,832 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:40:07,832 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:07,833 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-06_01-40-07.log] [testng] 01:40:07,833 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f99b84c - End of configuration. [testng] [2024-07-06 01:40:07,907] [pool-1-thread-7] Initializing /data/samples/multi-channel-missing-corner/multi-channel.HTD: [testng] 01:40:07,907 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:40:07,907 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:07,908 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-06_01-40-07.log] [testng] 01:40:07,908 |-INFO in ch.qos.logback.core.sift.SiftProcessor@15360893 - End of configuration. [testng] [2024-07-06 01:40:08,424] [pool-1-thread-6] Initializing /data/samples/single-site-test/single-site.HTD: [testng] 01:40:08,424 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:40:08,424 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:08,425 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-06_01-40-08.log] [testng] 01:40:08,425 |-INFO in ch.qos.logback.core.sift.SiftProcessor@283fec70 - End of configuration. [testng] [2024-07-06 01:40:08,550] [pool-1-thread-5] Initializing /data/public/idr0006/plate 11001_Plate_136/TimePoint_1/plate 11001.HTD: [testng] 01:40:08,550 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:40:08,550 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:08,551 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-06_01-40-08.log] [testng] 01:40:08,551 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4eb3d248 - End of configuration. [testng] [2024-07-06 01:40:26,987] [pool-1-thread-4] Initializing /data/public/idr0005/Primary_001/2011-04-19-plate-1.HTD: [testng] 01:40:26,987 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:40:26,988 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:26,988 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-06_01-40-26.log] [testng] 01:40:26,989 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f4c8578 - End of configuration. [testng] [2024-07-06 01:40:28,766] [pool-1-thread-3] Initializing /data/qa-4207/NSC.HTD: [testng] 01:40:28,766 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:40:28,766 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:28,766 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-06_01-40-28.log] [testng] 01:40:28,767 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ac758f9 - End of configuration. [testng] [2024-07-06 01:40:29,258] [pool-1-thread-2] Initializing /data/public/idr0008/Plate10_Actinome1/Act1_Plate10-SP-A8.HTD: [testng] 01:40:29,258 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:40:29,258 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:29,259 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-06_01-40-29.log] [testng] 01:40:29,260 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4a998f97 - 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: 31 minutes 23 seconds Finished: SUCCESS