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Started by upstream project "BIOFORMATS-test-repo" build number 213 originally caused by: Started by upstream project "Trigger" build number 240 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9 [BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins13731473541977791276.sh + '[' metaxpress = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_33804_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] 06:24:42,228 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 06:24:42,230 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 06:24:42,230 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 06:24:42,231 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 06:24:42,232 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 06:24:42,232 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 06:24:42,233 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 06:24:42,233 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 06:24:42,233 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 06:24:42,234 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 06:24:42,234 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 06:24:42,234 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 06:24:42,408 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 06:24:42,408 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 06:24:42,430 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 06:24:42,430 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 06:24:42,436 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 06:24:42,436 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 06:24:42,436 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 06:24:42,436 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 06:24:42,436 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 06:24:42,437 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 06:24:42,437 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 204 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-08 06:24:42,446] [main] java.version = 11.0.16 [testng] 06:24:42,449 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 06:24:42,449 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:24:42,491 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-08_06-24-42.log] [testng] 06:24:42,492 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-10-08 06:24:42,494] [main] testng.directory = /data [testng] [2024-10-08 06:24:42,495] [main] testng.configDirectory = /config [testng] [2024-10-08 06:24:42,504] [main] testng.multiplier = 1.0 [testng] [2024-10-08 06:24:42,505] [main] testng.in-memory = false [testng] [2024-10-08 06:24:42,506] [main] testng.allow-missing = false [testng] [2024-10-08 06:24:42,506] [main] user.language = en [testng] [2024-10-08 06:24:42,506] [main] user.country = ${user.country} [testng] [2024-10-08 06:24:42,506] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-08 06:31:21,320] [main] ---------------------------------------- [testng] [2024-10-08 06:31:21,321] [main] Total files: 1231 [testng] [2024-10-08 06:31:21,321] [main] Scan time: 398.814 s (323 ms/file) [testng] [2024-10-08 06:31:21,321] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 10 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-08 06:35:43,663] [pool-1-thread-1] Initializing /data/public/idr0081/BSF018292-1A/BSF018292-1A.HTD: [testng] 06:35:43,664 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 06:35:43,664 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:35:43,666 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-08_06-35-43.log] [testng] 06:35:43,666 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60e62394 - End of configuration. [testng] [2024-10-08 06:35:59,942] [pool-1-thread-10] Initializing /data/samples/multi-z/2011-04-19-plate-1.HTD: [testng] 06:35:59,942 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 06:35:59,942 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:35:59,943 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-08_06-35-59.log] [testng] 06:35:59,943 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c8e1f3d - End of configuration. [testng] [2024-10-08 06:36:13,187] [pool-1-thread-9] Initializing /data/samples/multi-channel-missing-corner/multi-channel.HTD: [testng] 06:36:13,187 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 06:36:13,187 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:36:13,188 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-08_06-36-13.log] [testng] 06:36:13,189 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57bbdc7 - End of configuration. [testng] [2024-10-08 06:36:14,393] [pool-1-thread-8] Initializing /data/public/idr0005/Primary_001/2011-04-19-plate-1.HTD: [testng] 06:36:14,393 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 06:36:14,393 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:36:14,394 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-08_06-36-14.log] [testng] 06:36:14,394 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71fbea43 - End of configuration. [testng] [2024-10-08 06:36:28,930] [pool-1-thread-7] Initializing /data/samples/multi-channel-test/multi-channel.HTD: [testng] 06:36:28,931 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 06:36:28,931 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:36:28,932 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-08_06-36-28.log] [testng] 06:36:28,932 |-INFO in ch.qos.logback.core.sift.SiftProcessor@428dc2ff - End of configuration. [testng] [2024-10-08 06:36:29,909] [pool-1-thread-6] Initializing /data/public/idr0008/Plate10_Actinome1/Act1_Plate10-SP-A8.HTD: [testng] 06:36:29,909 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 06:36:29,909 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:36:29,910 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-08_06-36-29.log] [testng] 06:36:29,910 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2acbe81c - End of configuration. [testng] [2024-10-08 06:37:34,241] [pool-1-thread-5] Initializing /data/qa-4207/NSC.HTD: [testng] 06:37:34,241 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 06:37:34,241 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:37:34,242 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-08_06-37-34.log] [testng] 06:37:34,243 |-INFO in ch.qos.logback.core.sift.SiftProcessor@465a3923 - End of configuration. [testng] [2024-10-08 06:37:35,389] [pool-1-thread-4] Initializing /data/samples/single-site-test/single-site.HTD: [testng] 06:37:35,389 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 06:37:35,389 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:37:35,389 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-08_06-37-35.log] [testng] 06:37:35,390 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6457dbdd - End of configuration. [testng] [2024-10-08 06:37:37,393] [pool-1-thread-3] Initializing /data/public/idr0006/plate 11001_Plate_136/TimePoint_1/plate 11001.HTD: [testng] 06:37:37,393 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 06:37:37,394 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:37:37,394 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-08_06-37-37.log] [testng] 06:37:37,395 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4fcb4766 - End of configuration. [testng] [2024-10-08 06:39:04,757] [pool-1-thread-2] Initializing /data/samples/thumb-test/2011-04-19-plate-1.HTD: [testng] 06:39:04,758 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 06:39:04,758 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:39:04,758 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-08_06-39-04.log] [testng] 06:39:04,759 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6cc158e3 - End of configuration. time="2024-10-08T06:01:38Z" level=error msg="error waiting for container: unexpected EOF" Build step 'Execute shell' marked build as failure Finished: FAILURE