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Started by upstream project "BIOFORMATS-test-repo" build number 83 originally caused by: Started by upstream project "Trigger" build number 93 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/jenkins4867991083055300134.sh + '[' metaxpress = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_12641_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] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket [testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket [testng] File leak detector installed [testng] 01:27:34,194 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:27:34,195 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 01:27:34,195 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:27:34,196 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:27:34,197 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:27:34,197 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:27:34,197 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:27:34,197 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:27:34,198 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:27:34,198 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:27:34,199 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:27:34,199 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:27:34,378 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:27:34,378 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:27:34,403 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:27:34,403 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:27:34,409 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:27:34,410 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:27:34,410 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:27:34,410 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:27:34,410 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 01:27:34,411 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 01:27:34,412 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 214 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-06-05 01:27:34,423] [main] java.version = 17.0.2 [testng] 01:27:34,427 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:27:34,428 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:27:34,485 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-05_01-27-34.log] [testng] 01:27:34,487 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-06-05 01:27:34,491] [main] testng.directory = /data [testng] [2024-06-05 01:27:34,491] [main] testng.configDirectory = /config [testng] [2024-06-05 01:27:34,505] [main] testng.multiplier = 1.0 [testng] [2024-06-05 01:27:34,506] [main] testng.in-memory = false [testng] [2024-06-05 01:27:34,506] [main] testng.allow-missing = false [testng] [2024-06-05 01:27:34,506] [main] user.language = en [testng] [2024-06-05 01:27:34,506] [main] user.country = ${user.country} [testng] [2024-06-05 01:27:34,507] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-06-05 01:35:24,189] [main] ---------------------------------------- [testng] [2024-06-05 01:35:24,190] [main] Total files: 1231 [testng] [2024-06-05 01:35:24,190] [main] Scan time: 469.682 s (381 ms/file) [testng] [2024-06-05 01:35:24,191] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 10 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-06-05 01:40:04,345] [pool-1-thread-1] Initializing /data/samples/multi-z/2011-04-19-plate-1.HTD: [testng] 01:40:04,346 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:40:04,346 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:04,347 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-05_01-40-04.log] [testng] 01:40:04,348 |-INFO in ch.qos.logback.core.sift.SiftProcessor@461d0f5a - End of configuration. [testng] [2024-06-05 01:40:05,502] [pool-1-thread-10] Initializing /data/samples/single-site-test/single-site.HTD: [testng] 01:40:05,502 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:40:05,502 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:05,503 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-05_01-40-05.log] [testng] 01:40:05,504 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5fcd3d28 - End of configuration. [testng] [2024-06-05 01:40:05,594] [pool-1-thread-9] Initializing /data/public/idr0006/plate 11001_Plate_136/TimePoint_1/plate 11001.HTD: [testng] 01:40:05,594 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:40:05,594 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:05,595 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-05_01-40-05.log] [testng] 01:40:05,596 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5fa2a816 - End of configuration. [testng] [2024-06-05 01:40:22,371] [pool-1-thread-8] Initializing /data/qa-4207/NSC.HTD: [testng] 01:40:22,371 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:40:22,372 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:22,373 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-05_01-40-22.log] [testng] 01:40:22,374 |-INFO in ch.qos.logback.core.sift.SiftProcessor@755a2696 - End of configuration. [testng] [2024-06-05 01:40:22,888] [pool-1-thread-7] Initializing /data/samples/multi-channel-test/multi-channel.HTD: [testng] 01:40:22,889 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:40:22,889 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:22,890 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-05_01-40-22.log] [testng] 01:40:22,890 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ed67e5e - End of configuration. [testng] [2024-06-05 01:40:22,973] [pool-1-thread-6] Initializing /data/samples/multi-channel-missing-corner/multi-channel.HTD: [testng] 01:40:22,973 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:40:22,973 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:22,974 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-05_01-40-22.log] [testng] 01:40:22,974 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36e07125 - End of configuration. [testng] [2024-06-05 01:40:23,584] [pool-1-thread-5] Initializing /data/public/idr0081/BSF018292-1A/BSF018292-1A.HTD: [testng] 01:40:23,585 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:40:23,585 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:23,586 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-05_01-40-23.log] [testng] 01:40:23,586 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43599b04 - End of configuration. [testng] [2024-06-05 01:40:25,568] [pool-1-thread-4] Initializing /data/public/idr0005/Primary_001/2011-04-19-plate-1.HTD: [testng] 01:40:25,569 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:40:25,569 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:25,570 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-05_01-40-25.log] [testng] 01:40:25,570 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e4cb806 - End of configuration. [testng] [2024-06-05 01:40:27,021] [pool-1-thread-3] Initializing /data/public/idr0008/Plate10_Actinome1/Act1_Plate10-SP-A8.HTD: [testng] 01:40:27,022 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:40:27,022 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:27,023 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-05_01-40-27.log] [testng] 01:40:27,023 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5738580c - End of configuration. [testng] [2024-06-05 01:40:35,143] [pool-1-thread-2] Initializing /data/samples/thumb-test/2011-04-19-plate-1.HTD: [testng] 01:40:35,143 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:40:35,143 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:35,144 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-05_01-40-35.log] [testng] 01:40:35,144 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4072c9f2 - 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 21 seconds Finished: SUCCESS