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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@2 [BIOFORMATS-test-folder@2] $ /bin/bash -xe /tmp/jenkins11031074802861638357.sh + '[' analyze = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_47016_merge_ci -v /uod/idr/repos/curated/analyze:/data -v /uod/idr-scratch/merge-ci/curated/analyze:/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] 03:41:45,466 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:41:45,468 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 03:41:45,468 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:41:45,469 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:41:45,469 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:41:45,469 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:41:45,470 |-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] 03:41:45,470 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:41:45,470 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:41:45,470 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:41:45,471 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:41:45,471 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:41:45,692 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:41:45,692 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:41:45,719 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:41:45,719 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:41:45,727 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:41:45,727 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:41:45,727 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:41:45,728 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:41:45,728 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 03:41:45,729 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 03:41:45,729 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 259 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-24 03:41:45,738] [main] java.version = 1.8.0_342 [testng] 03:41:45,742 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:41:45,742 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:41:45,786 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-24_03-41-45.log] [testng] 03:41:45,788 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-12-24 03:41:45,790] [main] testng.directory = /data [testng] [2024-12-24 03:41:45,790] [main] testng.configDirectory = /config [testng] [2024-12-24 03:41:45,802] [main] testng.multiplier = 1.0 [testng] [2024-12-24 03:41:45,802] [main] testng.in-memory = false [testng] [2024-12-24 03:41:45,802] [main] testng.allow-missing = false [testng] [2024-12-24 03:41:45,802] [main] user.language = en [testng] [2024-12-24 03:41:45,802] [main] user.country = ${user.country} [testng] [2024-12-24 03:41:45,802] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-12-24 03:41:54,144] [main] ---------------------------------------- [testng] [2024-12-24 03:41:54,144] [main] Total files: 21 [testng] [2024-12-24 03:41:54,145] [main] Scan time: 8.342 s (397 ms/file) [testng] [2024-12-24 03:41:54,145] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 21 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-24 03:42:04,023] [pool-1-thread-1] Initializing /data/frans/ch2bet.hdr: [testng] 03:42:04,023 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:42:04,023 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:42:04,024 |-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_03-42-04.log] [testng] 03:42:04,025 |-INFO in ch.qos.logback.core.sift.SiftProcessor@64e7845d - End of configuration. [testng] [2024-12-24 03:42:04,492] [pool-1-thread-12] Initializing /data/frans/Test Files for Frans/200-PLA_sansBD_spmT_0005.hdr: [testng] 03:42:04,492 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:42:04,492 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:42:04,493 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-24_03-42-04.log] [testng] 03:42:04,494 |-INFO in ch.qos.logback.core.sift.SiftProcessor@29fac680 - End of configuration. [testng] [2024-12-24 03:42:04,878] [pool-1-thread-11] Initializing /data/frans/CT_WHOLE.hdr: [testng] 03:42:04,879 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:42:04,879 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:42:04,879 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-24_03-42-04.log] [testng] 03:42:04,880 |-INFO in ch.qos.logback.core.sift.SiftProcessor@39c1f8e6 - End of configuration. [testng] [2024-12-24 03:42:05,289] [pool-1-thread-10] Initializing /data/frans/MR_SEGBRAIN.hdr: [testng] 03:42:05,289 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:42:05,289 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:42:05,290 |-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_03-42-05.log] [testng] 03:42:05,290 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1816330a - End of configuration. [testng] [2024-12-24 03:42:05,724] [pool-1-thread-9] Initializing /data/frans/Test Files for Frans/F005_1002_MF_SCAN1_stat_brain_fdg_JJ_Volume_Corrected.hdr: [testng] 03:42:05,724 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:42:05,724 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:42:05,724 |-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_03-42-05.log] [testng] 03:42:05,725 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e8baa8a - End of configuration. [testng] [2024-12-24 03:42:06,139] [pool-1-thread-8] Initializing /data/frans/CT_FOOT.hdr: [testng] 03:42:06,140 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:42:06,140 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:42:06,140 |-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_03-42-06.log] [testng] 03:42:06,141 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7cd70a5f - End of configuration. [testng] [2024-12-24 03:42:06,566] [pool-1-thread-7] Initializing /data/frans/CT_KNEE.hdr: [testng] 03:42:06,567 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:42:06,567 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:42:06,567 |-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_03-42-06.log] [testng] 03:42:06,568 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56f78f24 - End of configuration. [testng] [2024-12-24 03:42:06,971] [pool-1-thread-6] Initializing /data/frans/CT_APERT.hdr: [testng] 03:42:06,971 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:42:06,971 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:42:06,972 |-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_03-42-06.log] [testng] 03:42:06,972 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4322e9ef - End of configuration. [testng] [2024-12-24 03:42:07,369] [pool-1-thread-5] Initializing /data/frans/betmask.hdr: [testng] 03:42:07,369 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:42:07,369 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:42:07,370 |-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_03-42-07.log] [testng] 03:42:07,370 |-INFO in ch.qos.logback.core.sift.SiftProcessor@fab7a6a - End of configuration. [testng] [2024-12-24 03:42:07,788] [pool-1-thread-4] Initializing /data/frans/CT_HAND.hdr: [testng] 03:42:07,788 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:42:07,788 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:42:07,789 |-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_03-42-07.log] [testng] 03:42:07,789 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a30d2fe - End of configuration. [testng] [2024-12-24 03:42:08,220] [pool-1-thread-3] Initializing /data/frans/Test Files for Frans/1002-sag-transform-box-est_flip-ord.hdr: [testng] 03:42:08,220 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:42:08,220 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:42:08,221 |-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_03-42-08.log] [testng] 03:42:08,238 |-INFO in ch.qos.logback.core.sift.SiftProcessor@15eb5812 - End of configuration. [testng] [2024-12-24 03:42:08,640] [pool-1-thread-2] Initializing /data/frans/m000-MR_CHEST.gif: [testng] 03:42:08,640 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:42:08,640 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:42:08,641 |-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_03-42-08.log] [testng] 03:42:08,641 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12133707 - End of configuration. [testng] [2024-12-24 03:42:11,409] [pool-1-thread-2] Initializing /data/frans/Test Files for Frans/PLA-zm2-16mm_1002_MF_V1.hdr: [testng] [2024-12-24 03:42:15,953] [pool-1-thread-5] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1.img.hdr: [testng] [2024-12-24 03:42:16,444] [pool-1-thread-12] Initializing /data/frans/MR_CHEST.hdr: [testng] [2024-12-24 03:42:16,844] [pool-1-thread-9] Initializing /data/frans/CT_CHEST.hdr: [testng] [2024-12-24 03:42:17,266] [pool-1-thread-10] Initializing /data/frans/brodmann.hdr: [testng] [2024-12-24 03:42:17,725] [pool-1-thread-7] Initializing /data/frans/CT_CRANI.hdr: [testng] [2024-12-24 03:42:18,124] [pool-1-thread-11] Initializing /data/frans/ch2.hdr: [testng] [2024-12-24 03:42:18,529] [pool-1-thread-4] Initializing /data/frans/Test Files for Frans/06-101-mask-40pc2dil.hdr: [testng] [2024-12-24 03:42:18,955] [pool-1-thread-8] Initializing /data/frans/aal.hdr: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1113, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 49 seconds Finished: SUCCESS