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Started by upstream project "BIOFORMATS-test-repo" build number 25 originally caused by: Started by upstream project "Trigger" build number 28 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/jenkins16918229390933519653.sh + '[' nrrd = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_3199_merge_ci -v /uod/idr/repos/curated/nrrd:/data -v /uod/idr-scratch/merge-ci/curated/nrrd:/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] 02:15:27,912 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:15:27,915 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 02:15:27,915 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:15:27,917 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:15:27,918 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:15:27,919 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:15:27,919 |-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] 02:15:27,919 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:15:27,920 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:15:27,921 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:15:27,921 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:15:27,922 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:15:28,127 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:15:28,127 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:15:28,153 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:15:28,153 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:15:28,160 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:15:28,160 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:15:28,160 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:15:28,160 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:15:28,161 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 02:15:28,163 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 02:15:28,163 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 243 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-04-06 02:15:28,174] [main] java.version = 11.0.16 [testng] 02:15:28,177 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:15:28,178 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:15:28,225 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-06_02-15-28.log] [testng] 02:15:28,227 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-04-06 02:15:28,229] [main] testng.directory = /data [testng] [2024-04-06 02:15:28,229] [main] testng.configDirectory = /config [testng] [2024-04-06 02:15:28,239] [main] testng.multiplier = 1.0 [testng] [2024-04-06 02:15:28,241] [main] testng.in-memory = false [testng] [2024-04-06 02:15:28,241] [main] testng.allow-missing = false [testng] [2024-04-06 02:15:28,241] [main] user.language = en [testng] [2024-04-06 02:15:28,241] [main] user.country = ${user.country} [testng] [2024-04-06 02:15:28,241] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-04-06 02:17:11,429] [main] ---------------------------------------- [testng] [2024-04-06 02:17:11,429] [main] Total files: 14 [testng] [2024-04-06 02:17:11,429] [main] Scan time: 103.188 s (7370 ms/file) [testng] [2024-04-06 02:17:11,429] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 10 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-04-06 02:17:12,660] [pool-1-thread-1] Initializing /data/public/glencoe/version4/dt-helix.nhdr: [testng] 02:17:12,661 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:17:12,662 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:17:12,664 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-06_02-17-12.log] [testng] 02:17:12,665 |-INFO in ch.qos.logback.core.sift.SiftProcessor@132661a5 - End of configuration. [testng] [2024-04-06 02:17:12,694] [pool-1-thread-10] Initializing /data/public/glencoe/gzip/dt-helix.nrrd.gz: [testng] 02:17:12,695 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:17:12,695 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:17:12,696 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-06_02-17-12.log] [testng] 02:17:12,697 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4197096d - End of configuration. [testng] [2024-04-06 02:17:12,842] [pool-1-thread-9] Initializing /data/public/gordon/dt-helix.nhdr: [testng] 02:17:12,843 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:17:12,844 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:17:12,845 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-06_02-17-12.log] [testng] 02:17:12,846 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6faa7f8d - End of configuration. [testng] [2024-04-06 02:17:12,881] [pool-1-thread-8] Initializing /data/public/gordon/gk2-rcc-mask.nhdr: [testng] 02:17:12,881 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:17:12,882 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:17:12,884 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-06_02-17-12.log] [testng] 02:17:12,885 |-INFO in ch.qos.logback.core.sift.SiftProcessor@322defc9 - End of configuration. [testng] [2024-04-06 02:17:12,937] [pool-1-thread-7] Initializing /data/public/gordon/gk2-rcc-mask2.nhdr: [testng] 02:17:12,938 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:17:12,938 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:17:12,939 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-06_02-17-12.log] [testng] 02:17:12,940 |-INFO in ch.qos.logback.core.sift.SiftProcessor@b0ecf2b - End of configuration. [testng] [2024-04-06 02:17:12,973] [pool-1-thread-6] Initializing /data/greg/average-goodbrains-warp40-5_e1e-2.PIC.gz.nhdr: [testng] 02:17:12,974 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:17:12,974 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:17:12,975 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-06_02-17-12.log] [testng] 02:17:12,976 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66451f6b - End of configuration. [testng] [2024-04-06 02:17:13,013] [pool-1-thread-5] Initializing /data/greg/average-goodbrains-warp40-5_e1e-2.am.nrrd: [testng] 02:17:13,014 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:17:13,014 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:17:13,016 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-06_02-17-13.log] [testng] 02:17:13,017 |-INFO in ch.qos.logback.core.sift.SiftProcessor@15196867 - End of configuration. [testng] [2024-04-06 02:17:13,174] [pool-1-thread-4] Initializing /data/greg/average-goodbrains-warp40-5_e1e-2.PIC.nhdr: [testng] 02:17:13,175 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:17:13,175 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:17:13,176 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-06_02-17-13.log] [testng] 02:17:13,177 |-INFO in ch.qos.logback.core.sift.SiftProcessor@15c5039c - End of configuration. [testng] [2024-04-06 02:17:13,208] [pool-1-thread-3] Initializing /data/carlos/big4DImage.nrrd: [testng] 02:17:13,208 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:17:13,209 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:17:13,210 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-06_02-17-13.log] [testng] 02:17:13,211 |-INFO in ch.qos.logback.core.sift.SiftProcessor@310ebc6e - End of configuration. [testng] [2024-04-06 02:17:13,329] [pool-1-thread-2] Initializing /data/public/midas/01011-dwi.nhdr: [testng] 02:17:13,330 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:17:13,330 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:17:13,331 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-06_02-17-13.log] [testng] 02:17:13,332 |-INFO in ch.qos.logback.core.sift.SiftProcessor@bacff6e - 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: 3 minutes 33 seconds Finished: SUCCESS