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Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins3277383266140366794.sh + '[' cellh5 = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_35428_merge_ci -v /uod/idr/repos/curated/cellh5:/data -v /uod/idr-scratch/merge-ci/curated/cellh5:/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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. [javac] 4 warnings 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] 09:55:03,205 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 09:55:03,206 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 09:55:03,206 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 09:55:03,207 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 09:55:03,208 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 09:55:03,208 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 09:55:03,208 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 09:55:03,208 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 09:55:03,209 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 09:55:03,209 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 09:55:03,210 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 09:55:03,210 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 09:55:03,368 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 09:55:03,369 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 09:55:03,394 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 09:55:03,394 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 09:55:03,400 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 09:55:03,400 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 09:55:03,401 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 09:55:03,401 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 09:55:03,401 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 09:55:03,402 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 09:55:03,402 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 193 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-17 09:55:03,411] [main] java.version = 21 [testng] 09:55:03,414 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 09:55:03,414 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:55:03,455 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-17_09-55-03.log] [testng] 09:55:03,456 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-10-17 09:55:03,457] [main] testng.directory = /data [testng] [2024-10-17 09:55:03,458] [main] testng.configDirectory = /config [testng] [2024-10-17 09:55:03,466] [main] testng.multiplier = 1.0 [testng] [2024-10-17 09:55:03,467] [main] testng.in-memory = false [testng] [2024-10-17 09:55:03,467] [main] testng.allow-missing = false [testng] [2024-10-17 09:55:03,467] [main] user.language = en [testng] [2024-10-17 09:55:03,467] [main] user.country = ${user.country} [testng] [2024-10-17 09:55:03,467] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-17 09:55:04,122] [main] ---------------------------------------- [testng] [2024-10-17 09:55:04,122] [main] Total files: 11 [testng] [2024-10-17 09:55:04,122] [main] Scan time: 0.655 s (59 ms/file) [testng] [2024-10-17 09:55:04,122] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 10 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-17 09:59:55,129] [pool-1-thread-1] Initializing /data/public/samples/full/0040.ch5: [testng] 09:59:55,129 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 09:59:55,130 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:59:55,131 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-17_09-59-55.log] [testng] 09:59:55,131 |-INFO in ch.qos.logback.core.sift.SiftProcessor@765657e4 - End of configuration. [testng] [2024-10-17 09:59:55,505] [pool-1-thread-10] Initializing /data/public/samples/full/0045.ch5: [testng] 09:59:55,505 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 09:59:55,505 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:59:55,506 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-17_09-59-55.log] [testng] 09:59:55,506 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c03d633 - End of configuration. [testng] [2024-10-17 09:59:55,906] [pool-1-thread-9] Initializing /data/public/samples/full/0039.ch5: [testng] 09:59:55,906 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 09:59:55,906 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:59:55,907 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-17_09-59-55.log] [testng] 09:59:55,907 |-INFO in ch.qos.logback.core.sift.SiftProcessor@116317bb - End of configuration. [testng] [2024-10-17 09:59:56,331] [pool-1-thread-8] Initializing /data/public/samples/reduced/0038.ch5: [testng] 09:59:56,331 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 09:59:56,331 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:59:56,332 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-17_09-59-56.log] [testng] 09:59:56,333 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3fd112a6 - End of configuration. [testng] [2024-10-17 09:59:56,769] [pool-1-thread-7] Initializing /data/public/samples/full/0013.ch5: [testng] 09:59:56,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 09:59:56,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:59:56,769 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-17_09-59-56.log] [testng] 09:59:56,770 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79d65223 - End of configuration. [testng] [2024-10-17 09:59:57,176] [pool-1-thread-6] Initializing /data/public/samples/full/0037.ch5: [testng] 09:59:57,176 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 09:59:57,176 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:59:57,177 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-17_09-59-57.log] [testng] 09:59:57,177 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1648c01f - End of configuration. [testng] [2024-10-17 09:59:57,529] [pool-1-thread-5] Initializing /data/public/idr0013/00001_01.ch5: [testng] 09:59:57,530 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 09:59:57,530 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:59:57,530 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-17_09-59-57.log] [testng] 09:59:57,531 |-INFO in ch.qos.logback.core.sift.SiftProcessor@64974386 - End of configuration. [testng] [2024-10-17 09:59:57,708] [pool-1-thread-4] Initializing /data/public/samples/full/0046.ch5: [testng] 09:59:57,709 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 09:59:57,709 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:59:57,709 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-17_09-59-57.log] [testng] 09:59:57,710 |-INFO in ch.qos.logback.core.sift.SiftProcessor@173bc0ff - End of configuration. [testng] [2024-10-17 09:59:57,852] [pool-1-thread-3] Initializing /data/public/samples/full/0042.ch5: [testng] 09:59:57,852 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 09:59:57,852 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:59:57,853 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-17_09-59-57.log] [testng] 09:59:57,853 |-INFO in ch.qos.logback.core.sift.SiftProcessor@bbf61ef - End of configuration. [testng] [2024-10-17 09:59:58,162] [pool-1-thread-2] Initializing /data/public/samples/full/0041.ch5: [testng] 09:59:58,162 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 09:59:58,162 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:59:58,163 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-17_09-59-58.log] [testng] 09:59:58,163 |-INFO in ch.qos.logback.core.sift.SiftProcessor@685c143 - End of configuration. [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 530, Failures: 0, Skips: 10 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 19 minutes 32 seconds Finished: SUCCESS