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Started by upstream project "BIOFORMATS-test-repo" build number 297 originally caused by: Started by upstream project "Trigger" build number 319 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4 [BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins8864136860042439611.sh + '[' nrrd = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_47014_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] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-mdbtools/5.3.4-SNAPSHOT/maven-metadata.xml [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/metakit/5.3.8-SNAPSHOT/maven-metadata.xml [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-poi/5.3.10-SNAPSHOT/maven-metadata.xml [resolver:resolve] Resolving artifacts [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-mdbtools/5.3.4-SNAPSHOT/maven-metadata.xml [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/metakit/5.3.8-SNAPSHOT/maven-metadata.xml [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-poi/5.3.10-SNAPSHOT/maven-metadata.xml compile-tests: [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-mdbtools/5.3.4-SNAPSHOT/maven-metadata.xml [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/metakit/5.3.8-SNAPSHOT/maven-metadata.xml [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-poi/5.3.10-SNAPSHOT/maven-metadata.xml [resolver:resolve] Resolving artifacts [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-mdbtools/5.3.4-SNAPSHOT/maven-metadata.xml [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/metakit/5.3.8-SNAPSHOT/maven-metadata.xml [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-poi/5.3.10-SNAPSHOT/maven-metadata.xml [javac] Compiling 1 source file to /bio-formats-build/bioformats/components/test-suite/test test-automated: [testng] File leak detector installed [testng] 03:41:26,948 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:41:26,950 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 03:41:26,950 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:41:26,950 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:41:26,951 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:41:26,951 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:41:26,951 |-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] 03:41:26,951 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:41:26,952 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:41:26,952 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:41:26,952 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:41:26,952 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:41:27,165 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:41:27,165 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:41:27,190 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:41:27,190 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:41:27,198 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:41:27,198 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:41:27,198 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:41:27,198 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:41:27,198 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 03:41:27,199 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 03:41:27,199 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 247 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-24 03:41:27,208] [main] java.version = 1.8.0_342 [testng] 03:41:27,211 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:41:27,211 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:41:27,253 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-24_03-41-27.log] [testng] 03:41:27,254 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-12-24 03:41:27,256] [main] testng.directory = /data [testng] [2024-12-24 03:41:27,256] [main] testng.configDirectory = /config [testng] [2024-12-24 03:41:27,267] [main] testng.multiplier = 1.0 [testng] [2024-12-24 03:41:27,267] [main] testng.in-memory = false [testng] [2024-12-24 03:41:27,267] [main] testng.allow-missing = false [testng] [2024-12-24 03:41:27,268] [main] user.language = en [testng] [2024-12-24 03:41:27,268] [main] user.country = ${user.country} [testng] [2024-12-24 03:41:27,268] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-12-24 03:43:23,329] [main] ---------------------------------------- [testng] [2024-12-24 03:43:23,329] [main] Total files: 14 [testng] [2024-12-24 03:43:23,329] [main] Scan time: 116.061 s (8290 ms/file) [testng] [2024-12-24 03:43:23,329] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 10 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-24 03:43:31,727] [pool-1-thread-1] Initializing /data/greg/average-goodbrains-warp40-5_e1e-2.PIC.nhdr: [testng] 03:43:31,728 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:43:31,728 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:43:31,728 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-24_03-43-31.log] [testng] 03:43:31,729 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d76ea91 - End of configuration. [testng] [2024-12-24 03:43:32,099] [pool-1-thread-10] Initializing /data/public/midas/01011-dwi.nhdr: [testng] 03:43:32,099 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:43:32,099 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:43:32,100 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-24_03-43-32.log] [testng] 03:43:32,100 |-INFO in ch.qos.logback.core.sift.SiftProcessor@166742d - End of configuration. [testng] [2024-12-24 03:43:32,483] [pool-1-thread-9] Initializing /data/public/glencoe/gzip/dt-helix.nrrd.gz: [testng] 03:43:32,483 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:43:32,483 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:43:32,484 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-24_03-43-32.log] [testng] 03:43:32,484 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d6a012e - End of configuration. [testng] [2024-12-24 03:43:33,354] [pool-1-thread-8] Initializing /data/public/gordon/gk2-rcc-mask2.nhdr: [testng] 03:43:33,354 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:43:33,354 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:43:33,355 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-24_03-43-33.log] [testng] 03:43:33,355 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2fd3c18f - End of configuration. [testng] [2024-12-24 03:43:33,748] [pool-1-thread-7] Initializing /data/carlos/big4DImage.nrrd: [testng] 03:43:33,748 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:43:33,748 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:43:33,749 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-24_03-43-33.log] [testng] 03:43:33,749 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ac99820 - End of configuration. [testng] [2024-12-24 03:43:34,155] [pool-1-thread-6] Initializing /data/public/glencoe/version4/dt-helix.nhdr: [testng] 03:43:34,155 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:43:34,155 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:43:34,156 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-24_03-43-34.log] [testng] 03:43:34,156 |-INFO in ch.qos.logback.core.sift.SiftProcessor@253bb622 - End of configuration. [testng] [2024-12-24 03:43:34,599] [pool-1-thread-5] Initializing /data/greg/average-goodbrains-warp40-5_e1e-2.am.nrrd: [testng] 03:43:34,599 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:43:34,600 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:43:34,600 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-24_03-43-34.log] [testng] 03:43:34,600 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f46765 - End of configuration. [testng] [2024-12-24 03:43:35,054] [pool-1-thread-4] Initializing /data/greg/average-goodbrains-warp40-5_e1e-2.PIC.gz.nhdr: [testng] 03:43:35,054 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:43:35,054 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:43:35,055 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-24_03-43-35.log] [testng] 03:43:35,055 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ad3190c - End of configuration. [testng] [2024-12-24 03:43:35,466] [pool-1-thread-3] Initializing /data/public/gordon/gk2-rcc-mask.nhdr: [testng] 03:43:35,466 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:43:35,466 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:43:35,467 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-24_03-43-35.log] [testng] 03:43:35,467 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d5e7b18 - End of configuration. [testng] [2024-12-24 03:43:35,897] [pool-1-thread-2] Initializing /data/public/gordon/dt-helix.nhdr: [testng] 03:43:35,897 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:43:35,897 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:43:35,898 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-24_03-43-35.log] [testng] 03:43:35,898 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6ac53ca1 - 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: 4 minutes 13 seconds Finished: SUCCESS