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Started by upstream project "BIOFORMATS-test-repo" build number 300 originally caused by: Started by upstream project "Trigger" build number 322 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/jenkins5271478997656174747.sh + '[' cellh5 = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_47421_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 test-automated: [testng] File leak detector installed [testng] 00:29:30,629 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:29:30,631 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 00:29:30,631 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:29:30,632 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:29:30,632 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:29:30,632 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:29:30,633 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:29:30,633 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:29:30,633 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:29:30,633 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:29:30,634 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:29:30,634 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:29:30,893 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:29:30,894 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:29:30,930 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:29:30,930 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:29:30,942 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:29:30,942 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:29:30,942 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:29:30,943 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:29:30,943 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 00:29:30,944 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 00:29:30,944 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 311 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-27 00:29:30,956] [main] java.version = 1.8.0_342 [testng] 00:29:30,961 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:29:30,961 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:31,018 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-27_00-29-30.log] [testng] 00:29:31,019 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-12-27 00:29:31,021] [main] testng.directory = /data [testng] [2024-12-27 00:29:31,022] [main] testng.configDirectory = /config [testng] [2024-12-27 00:29:31,034] [main] testng.multiplier = 1.0 [testng] [2024-12-27 00:29:31,035] [main] testng.in-memory = false [testng] [2024-12-27 00:29:31,035] [main] testng.allow-missing = false [testng] [2024-12-27 00:29:31,035] [main] user.language = en [testng] [2024-12-27 00:29:31,035] [main] user.country = ${user.country} [testng] [2024-12-27 00:29:31,035] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-12-27 00:29:31,894] [main] ---------------------------------------- [testng] [2024-12-27 00:29:31,894] [main] Total files: 11 [testng] [2024-12-27 00:29:31,894] [main] Scan time: 0.859 s (78 ms/file) [testng] [2024-12-27 00:29:31,894] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 10 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-27 00:34:04,002] [pool-1-thread-1] Initializing /data/public/samples/full/0039.ch5: [testng] 00:34:04,003 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:34:04,003 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:04,004 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-27_00-34-04.log] [testng] 00:34:04,005 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76f38684 - End of configuration. [testng] [2024-12-27 00:34:04,639] [pool-1-thread-10] Initializing /data/public/idr0013/00001_01.ch5: [testng] 00:34:04,639 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:34:04,639 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:04,640 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-27_00-34-04.log] [testng] 00:34:04,641 |-INFO in ch.qos.logback.core.sift.SiftProcessor@11e8944f - End of configuration. [testng] [2024-12-27 00:34:05,365] [pool-1-thread-9] Initializing /data/public/samples/full/0042.ch5: [testng] 00:34:05,365 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:34:05,365 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:05,366 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-27_00-34-05.log] [testng] 00:34:05,366 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6afab3d - End of configuration. [testng] [2024-12-27 00:34:05,949] [pool-1-thread-8] Initializing /data/public/samples/full/0037.ch5: [testng] 00:34:05,950 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:34:05,950 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:05,950 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-27_00-34-05.log] [testng] 00:34:05,951 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71c75587 - End of configuration. [testng] [2024-12-27 00:34:06,426] [pool-1-thread-7] Initializing /data/public/samples/full/0046.ch5: [testng] 00:34:06,426 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:34:06,426 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:06,427 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-27_00-34-06.log] [testng] 00:34:06,427 |-INFO in ch.qos.logback.core.sift.SiftProcessor@c37887f - End of configuration. [testng] [2024-12-27 00:34:06,883] [pool-1-thread-6] Initializing /data/public/samples/full/0013.ch5: [testng] 00:34:06,883 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:34:06,883 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:06,884 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-27_00-34-06.log] [testng] 00:34:06,884 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c56c6f - End of configuration. [testng] [2024-12-27 00:34:07,558] [pool-1-thread-5] Initializing /data/public/samples/reduced/0038.ch5: [testng] 00:34:07,559 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:34:07,559 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:07,561 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-27_00-34-07.log] [testng] 00:34:07,561 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2e8572f8 - End of configuration. [testng] [2024-12-27 00:34:08,127] [pool-1-thread-4] Initializing /data/public/samples/full/0041.ch5: [testng] 00:34:08,127 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:34:08,128 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:08,128 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-27_00-34-08.log] [testng] 00:34:08,129 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d7822a8 - End of configuration. [testng] [2024-12-27 00:34:08,745] [pool-1-thread-3] Initializing /data/public/samples/full/0040.ch5: [testng] 00:34:08,745 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:34:08,745 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:08,746 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-27_00-34-08.log] [testng] 00:34:08,746 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2fef6682 - End of configuration. [testng] [2024-12-27 00:34:09,211] [pool-1-thread-2] Initializing /data/public/samples/full/0045.ch5: [testng] 00:34:09,211 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:34:09,211 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:09,212 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-27_00-34-09.log] [testng] 00:34:09,212 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d5748b7 - 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: 24 minutes 56 seconds Finished: SUCCESS