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Started by upstream project "BIOFORMATS-test-repo" build number 273 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@10 [BIOFORMATS-test-folder@10] $ /bin/bash -xe /tmp/jenkins17568538632854159395.sh + '[' specs = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_42986_merge_ci -v /uod/idr/repos/curated/specs:/data -v /uod/idr-scratch/merge-ci/curated/specs:/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] 07:06:11,449 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 07:06:11,450 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 07:06:11,450 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 07:06:11,451 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 07:06:11,452 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 07:06:11,452 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 07:06:11,452 |-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] 07:06:11,452 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 07:06:11,453 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 07:06:11,453 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 07:06:11,453 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 07:06:11,453 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 07:06:11,678 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 07:06:11,678 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 07:06:11,707 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 07:06:11,707 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 07:06:11,715 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 07:06:11,715 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 07:06:11,715 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 07:06:11,716 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 07:06:11,716 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 07:06:11,717 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 07:06:11,717 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 264 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-29 07:06:11,726] [main] java.version = 1.8.0_342 [testng] 07:06:11,730 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 07:06:11,730 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:06:11,775 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-29_07-06-11.log] [testng] 07:06:11,776 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-11-29 07:06:11,778] [main] testng.directory = /data [testng] [2024-11-29 07:06:11,778] [main] testng.configDirectory = /config [testng] [2024-11-29 07:06:11,790] [main] testng.multiplier = 1.0 [testng] [2024-11-29 07:06:11,791] [main] testng.in-memory = false [testng] [2024-11-29 07:06:11,791] [main] testng.allow-missing = false [testng] [2024-11-29 07:06:11,791] [main] user.language = en [testng] [2024-11-29 07:06:11,791] [main] user.country = ${user.country} [testng] [2024-11-29 07:06:11,791] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-11-29 07:11:26,165] [main] ---------------------------------------- [testng] [2024-11-29 07:11:26,165] [main] Total files: 226 [testng] [2024-11-29 07:11:26,166] [main] Scan time: 314.374 s (1391 ms/file) [testng] [2024-11-29 07:11:26,166] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 28 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-29 07:15:06,605] [pool-1-thread-1] Initializing /data/iplab/Blend_Fitc.IPL: [testng] 07:15:06,606 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 07:15:06,606 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:15:06,607 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-29_07-15-06.log] [testng] 07:15:06,608 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ee8f2d7 - End of configuration. [testng] [2024-11-29 07:15:06,783] [pool-1-thread-12] Initializing /data/fluoview/sample_labled_XYZTCh.tif: [testng] 07:15:06,783 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 07:15:06,783 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:15:06,784 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-29_07-15-06.log] [testng] 07:15:06,785 |-INFO in ch.qos.logback.core.sift.SiftProcessor@633836a7 - End of configuration. [testng] [2024-11-29 07:15:07,947] [pool-1-thread-11] Initializing /data/fluoview/Sample_XT.tif: [testng] 07:15:07,947 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 07:15:07,947 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:15:07,948 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-29_07-15-07.log] [testng] 07:15:07,948 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c3cb327 - End of configuration. [testng] [2024-11-29 07:15:08,550] [pool-1-thread-10] Initializing /data/gatan/ImageReader2003/ImageReaderTest/TestFiles/test3.dm3: [testng] 07:15:08,551 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 07:15:08,551 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:15:08,551 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-29_07-15-08.log] [testng] 07:15:08,552 |-INFO in ch.qos.logback.core.sift.SiftProcessor@301e9e2a - End of configuration. [testng] [2024-11-29 07:15:08,699] [pool-1-thread-9] Initializing /data/fluoview/Sample_ThreeCH.TIF: [testng] 07:15:08,699 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 07:15:08,699 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:15:08,699 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-29_07-15-08.log] [testng] 07:15:08,700 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ca80ad9 - End of configuration. [testng] [2024-11-29 07:15:09,139] [pool-1-thread-8] Initializing /data/fluoview/sample_labled_XYZCh.tif: [testng] 07:15:09,139 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 07:15:09,139 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:15:09,140 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-29_07-15-09.log] [testng] 07:15:09,141 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1c7b26fa - End of configuration. [testng] [2024-11-29 07:15:09,523] [pool-1-thread-7] Initializing /data/iplab/Blend_Final.IPL: [testng] 07:15:09,523 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 07:15:09,523 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:15:09,524 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-29_07-15-09.log] [testng] 07:15:09,524 |-INFO in ch.qos.logback.core.sift.SiftProcessor@72808297 - End of configuration. [testng] [2024-11-29 07:15:09,588] [pool-1-thread-6] Initializing /data/fluoview/Sample_XYT.TIF: [testng] 07:15:09,588 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 07:15:09,589 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:15:09,589 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-29_07-15-09.log] [testng] 07:15:09,590 |-INFO in ch.qos.logback.core.sift.SiftProcessor@777607c - End of configuration. [testng] [2024-11-29 07:15:10,013] [pool-1-thread-5] Initializing /data/gatan/ImageReader2003/ImageReaderTest/TestFiles/Test2.dm3: [testng] 07:15:10,013 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 07:15:10,013 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:15:10,014 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-29_07-15-10.log] [testng] 07:15:10,014 |-INFO in ch.qos.logback.core.sift.SiftProcessor@53855c44 - End of configuration. [testng] [2024-11-29 07:15:10,155] [pool-1-thread-4] Initializing /data/iplab/10x Blood and Bacteria.IPL: [testng] 07:15:10,156 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 07:15:10,156 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:15:10,156 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-29_07-15-10.log] [testng] 07:15:10,157 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f1745bf - End of configuration. [testng] [2024-11-29 07:15:10,267] [pool-1-thread-3] Initializing /data/fluoview/Sample_XYZ.TIF: [testng] 07:15:10,267 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 07:15:10,267 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:15:10,268 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-29_07-15-10.log] [testng] 07:15:10,269 |-INFO in ch.qos.logback.core.sift.SiftProcessor@472dfcb1 - End of configuration. [testng] [2024-11-29 07:15:10,745] [pool-1-thread-2] Initializing /data/zeiss_lsm/X-Y-Z-T-Ch-Tile--MultiTrack-1.lsm: [testng] 07:15:10,745 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 07:15:10,746 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:15:10,746 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-29_07-15-10.log] [testng] 07:15:10,747 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48b57759 - End of configuration. [testng] [2024-11-29 07:15:14,352] [pool-1-thread-7] Initializing /data/zeiss_lsm/X-Y-Z-T-Ch-Tile-2.lsm: [testng] [2024-11-29 07:15:14,914] [pool-1-thread-1] Initializing /data/gatan/ImageReader2003/ImageReaderTest/TestFiles/Test.dm3: [testng] [2024-11-29 07:15:15,028] [pool-1-thread-4] Initializing /data/iplab/Blend_Tritc.IPL: [testng] [2024-11-29 07:15:15,104] [pool-1-thread-10] Initializing /data/fluoview/Sample_TwoCH.TIF: [testng] [2024-11-29 07:15:15,972] [pool-1-thread-5] Initializing /data/zeiss_lsm/X-Y-Z-T-Ch-Tile-1.lsm: [testng] [2024-11-29 07:15:19,099] [pool-1-thread-4] Initializing /data/fluoview/SpineAnimation.avi: [testng] [2024-11-29 07:15:19,677] [pool-1-thread-1] Initializing /data/iplab/Blend_Dapi.IPL: [testng] [2024-11-29 07:15:20,437] [pool-1-thread-12] Initializing /data/iplab/Chromosomes.IPL: [testng] [2024-11-29 07:15:20,601] [pool-1-thread-3] Initializing /data/iplab/Actin.IPL: [testng] [2024-11-29 07:15:20,765] [pool-1-thread-6] Initializing /data/fluoview/SpineAnimation.tif: [testng] [2024-11-29 07:15:21,412] [pool-1-thread-8] Initializing /data/iplab/Color Histology.IPL: [testng] [2024-11-29 07:15:21,588] [pool-1-thread-11] Initializing /data/fluoview/sample_labled_XYTCh.tif: [testng] [2024-11-29 07:15:22,725] [pool-1-thread-9] Initializing /data/iplab/3t3 Cell.IPL: [testng] [2024-11-29 07:15:23,707] [pool-1-thread-3] Initializing /data/iplab/Blend_DIC.IPL: [testng] [2024-11-29 07:15:23,882] [pool-1-thread-8] Initializing /data/iplab/16Bit XRay.IPL: [testng] [2024-11-29 07:15:24,023] [pool-1-thread-12] Initializing /data/iplab/Color Image.IPL: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1484, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 9 minutes 20 seconds Finished: SUCCESS