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Started by upstream project "BIOFORMATS-test-repo" build number 3 originally caused by: Started by upstream project "Trigger" build number 4 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9 [BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins8250185594568169450.sh + '[' specs = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_325_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 [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] 00:25:23,418 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:25:23,420 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 00:25:23,420 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:25:23,421 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:25:23,422 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:25:23,422 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:25:23,422 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:25:23,422 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:25:23,423 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:25:23,424 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:25:23,424 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:25:23,424 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:25:23,629 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:25:23,629 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:25:23,659 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:25:23,660 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:25:23,667 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:25:23,667 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:25:23,668 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:25:23,668 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:25:23,668 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 00:25:23,669 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 00:25:23,669 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 246 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-16 00:25:23,682] [main] java.version = 11.0.16 [testng] 00:25:23,686 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:25:23,686 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:25:23,728 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-16_00-25-23.log] [testng] 00:25:23,730 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-03-16 00:25:23,732] [main] testng.directory = /data [testng] [2024-03-16 00:25:23,732] [main] testng.configDirectory = /config [testng] [2024-03-16 00:25:23,742] [main] testng.multiplier = 1.0 [testng] [2024-03-16 00:25:23,743] [main] testng.in-memory = false [testng] [2024-03-16 00:25:23,743] [main] testng.allow-missing = false [testng] [2024-03-16 00:25:23,743] [main] user.language = en [testng] [2024-03-16 00:25:23,743] [main] user.country = ${user.country} [testng] [2024-03-16 00:25:23,743] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-03-16 00:26:04,083] [main] ---------------------------------------- [testng] [2024-03-16 00:26:04,083] [main] Total files: 226 [testng] [2024-03-16 00:26:04,084] [main] Scan time: 40.34 s (178 ms/file) [testng] [2024-03-16 00:26:04,084] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 28 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-16 00:27:06,862] [pool-1-thread-1] Initializing /data/fluoview/Sample_XYZ.TIF: [testng] 00:27:06,862 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:27:06,864 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:06,867 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-16_00-27-06.log] [testng] 00:27:06,868 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38e2f593 - End of configuration. [testng] [2024-03-16 00:27:07,134] [pool-1-thread-12] Initializing /data/iplab/Color Histology.IPL: [testng] 00:27:07,135 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:27:07,135 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:07,136 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-16_00-27-07.log] [testng] 00:27:07,136 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a300a80 - End of configuration. [testng] [2024-03-16 00:27:07,174] [pool-1-thread-11] Initializing /data/fluoview/Sample_TwoCH.TIF: [testng] 00:27:07,174 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:27:07,174 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:07,175 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-16_00-27-07.log] [testng] 00:27:07,175 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4161d894 - End of configuration. [testng] [2024-03-16 00:27:07,587] [pool-1-thread-10] Initializing /data/iplab/Chromosomes.IPL: [testng] 00:27:07,587 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:27:07,587 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:07,588 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-16_00-27-07.log] [testng] 00:27:07,588 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e883053 - End of configuration. [testng] [2024-03-16 00:27:07,609] [pool-1-thread-9] Initializing /data/iplab/Blend_Fitc.IPL: [testng] 00:27:07,609 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:27:07,609 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:07,610 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-16_00-27-07.log] [testng] 00:27:07,610 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ba92753 - End of configuration. [testng] [2024-03-16 00:27:07,633] [pool-1-thread-8] Initializing /data/fluoview/sample_labled_XYZCh.tif: [testng] 00:27:07,633 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:27:07,633 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:07,634 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-16_00-27-07.log] [testng] 00:27:07,634 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5068b96f - End of configuration. [testng] [2024-03-16 00:27:07,745] [pool-1-thread-7] Initializing /data/zeiss_lsm/X-Y-Z-T-Ch-Tile--MultiTrack-1.lsm: [testng] 00:27:07,746 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:27:07,746 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:07,746 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-16_00-27-07.log] [testng] 00:27:07,747 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f0da17 - End of configuration. [testng] [2024-03-16 00:27:08,260] [pool-1-thread-6] Initializing /data/gatan/ImageReader2003/ImageReaderTest/TestFiles/Test.dm3: [testng] 00:27:08,260 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:27:08,260 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:08,261 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-16_00-27-08.log] [testng] 00:27:08,262 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6cb6e7eb - End of configuration. [testng] [2024-03-16 00:27:08,323] [pool-1-thread-5] Initializing /data/iplab/Blend_DIC.IPL: [testng] 00:27:08,323 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:27:08,323 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:08,324 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-16_00-27-08.log] [testng] 00:27:08,324 |-INFO in ch.qos.logback.core.sift.SiftProcessor@102ebc8c - End of configuration. [testng] [2024-03-16 00:27:08,372] [pool-1-thread-4] Initializing /data/iplab/10x Blood and Bacteria.IPL: [testng] 00:27:08,373 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:27:08,373 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:08,373 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-16_00-27-08.log] [testng] 00:27:08,374 |-INFO in ch.qos.logback.core.sift.SiftProcessor@330d4d34 - End of configuration. [testng] [2024-03-16 00:27:08,442] [pool-1-thread-3] Initializing /data/fluoview/sample_labled_XYZTCh.tif: [testng] 00:27:08,443 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:27:08,443 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:08,443 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-16_00-27-08.log] [testng] 00:27:08,444 |-INFO in ch.qos.logback.core.sift.SiftProcessor@54fe9db0 - End of configuration. [testng] [2024-03-16 00:27:08,672] [pool-1-thread-2] Initializing /data/fluoview/sample_labled_XYTCh.tif: [testng] 00:27:08,673 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:27:08,673 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:08,673 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-16_00-27-08.log] [testng] 00:27:08,674 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2c1a9a74 - End of configuration. [testng] [2024-03-16 00:27:11,010] [pool-1-thread-12] Initializing /data/fluoview/SpineAnimation.tif: [testng] [2024-03-16 00:27:11,129] [pool-1-thread-10] Initializing /data/fluoview/SpineAnimation.avi: [testng] [2024-03-16 00:27:11,239] [pool-1-thread-6] Initializing /data/iplab/Blend_Dapi.IPL: [testng] [2024-03-16 00:27:11,271] [pool-1-thread-5] Initializing /data/zeiss_lsm/X-Y-Z-T-Ch-Tile-1.lsm: [testng] [2024-03-16 00:27:11,515] [pool-1-thread-9] Initializing /data/iplab/16Bit XRay.IPL: [testng] [2024-03-16 00:27:11,541] [pool-1-thread-4] Initializing /data/fluoview/Sample_XT.tif: [testng] [2024-03-16 00:27:12,050] [pool-1-thread-8] Initializing /data/iplab/3t3 Cell.IPL: [testng] [2024-03-16 00:27:12,099] [pool-1-thread-2] Initializing /data/fluoview/Sample_XYT.TIF: [testng] [2024-03-16 00:27:12,330] [pool-1-thread-3] Initializing /data/gatan/ImageReader2003/ImageReaderTest/TestFiles/test3.dm3: [testng] [2024-03-16 00:27:12,376] [pool-1-thread-1] Initializing /data/iplab/Actin.IPL: [testng] [2024-03-16 00:27:12,410] [pool-1-thread-11] Initializing /data/gatan/ImageReader2003/ImageReaderTest/TestFiles/Test2.dm3: [testng] [2024-03-16 00:27:12,924] [pool-1-thread-9] Initializing /data/iplab/Blend_Final.IPL: [testng] [2024-03-16 00:27:13,037] [pool-1-thread-6] Initializing /data/iplab/Blend_Tritc.IPL: [testng] [2024-03-16 00:27:13,400] [pool-1-thread-8] Initializing /data/zeiss_lsm/X-Y-Z-T-Ch-Tile-2.lsm: [testng] [2024-03-16 00:27:13,636] [pool-1-thread-1] Initializing /data/fluoview/Sample_ThreeCH.TIF: [testng] [2024-03-16 00:27:13,911] [pool-1-thread-11] 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: 1 minute 57 seconds Finished: SUCCESS