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Started by upstream project "BIOFORMATS-test-repo" build number 116 originally caused by: Started by upstream project "Trigger" build number 133 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5 [BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins10481249099565748325.sh + '[' specs = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_18040_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] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket [testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket [testng] File leak detector installed [testng] 01:24:05,169 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:24:05,170 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 01:24:05,170 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:24:05,171 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:24:05,172 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:24:05,172 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:24:05,172 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:24:05,172 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:24:05,173 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:24:05,174 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:24:05,174 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:24:05,174 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:24:05,363 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:24:05,363 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:24:05,394 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:24:05,394 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:24:05,402 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:24:05,402 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:24:05,402 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:24:05,403 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:24:05,403 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 01:24:05,404 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 01:24:05,404 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 231 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-10 01:24:05,415] [main] java.version = 17.0.2 [testng] 01:24:05,419 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:24:05,419 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:05,480 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-10_01-24-05.log] [testng] 01:24:05,483 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-07-10 01:24:05,486] [main] testng.directory = /data [testng] [2024-07-10 01:24:05,486] [main] testng.configDirectory = /config [testng] [2024-07-10 01:24:05,500] [main] testng.multiplier = 1.0 [testng] [2024-07-10 01:24:05,501] [main] testng.in-memory = false [testng] [2024-07-10 01:24:05,502] [main] testng.allow-missing = false [testng] [2024-07-10 01:24:05,502] [main] user.language = en [testng] [2024-07-10 01:24:05,502] [main] user.country = ${user.country} [testng] [2024-07-10 01:24:05,502] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-07-10 01:24:19,210] [main] ---------------------------------------- [testng] [2024-07-10 01:24:19,210] [main] Total files: 226 [testng] [2024-07-10 01:24:19,210] [main] Scan time: 13.708 s (60 ms/file) [testng] [2024-07-10 01:24:19,211] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 28 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-10 01:24:26,938] [pool-1-thread-1] Initializing /data/iplab/Blend_DIC.IPL: [testng] 01:24:26,938 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:24:26,938 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:26,939 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-10_01-24-26.log] [testng] 01:24:26,940 |-INFO in ch.qos.logback.core.sift.SiftProcessor@67c7c96f - End of configuration. [testng] [2024-07-10 01:24:26,964] [pool-1-thread-12] Initializing /data/fluoview/Sample_TwoCH.TIF: [testng] 01:24:26,964 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:24:26,964 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:26,966 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-10_01-24-26.log] [testng] 01:24:26,966 |-INFO in ch.qos.logback.core.sift.SiftProcessor@727a1e7a - End of configuration. [testng] [2024-07-10 01:24:27,015] [pool-1-thread-11] Initializing /data/zeiss_lsm/X-Y-Z-T-Ch-Tile-2.lsm: [testng] 01:24:27,016 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:24:27,016 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:27,017 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-10_01-24-27.log] [testng] 01:24:27,017 |-INFO in ch.qos.logback.core.sift.SiftProcessor@51ee79a3 - End of configuration. [testng] [2024-07-10 01:24:27,108] [pool-1-thread-10] Initializing /data/iplab/3t3 Cell.IPL: [testng] 01:24:27,108 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:24:27,109 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:27,109 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-10_01-24-27.log] [testng] 01:24:27,110 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7685806e - End of configuration. [testng] [2024-07-10 01:24:27,116] [pool-1-thread-9] Initializing /data/fluoview/sample_labled_XYTCh.tif: [testng] 01:24:27,116 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:24:27,116 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:27,117 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-10_01-24-27.log] [testng] 01:24:27,117 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e1a0082 - End of configuration. [testng] [2024-07-10 01:24:27,136] [pool-1-thread-8] Initializing /data/fluoview/SpineAnimation.tif: [testng] 01:24:27,137 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:24:27,137 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:27,138 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-10_01-24-27.log] [testng] 01:24:27,138 |-INFO in ch.qos.logback.core.sift.SiftProcessor@58ca5b26 - End of configuration. [testng] [2024-07-10 01:24:27,175] [pool-1-thread-7] Initializing /data/iplab/Chromosomes.IPL: [testng] 01:24:27,175 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:24:27,175 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:27,176 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-10_01-24-27.log] [testng] 01:24:27,176 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ad6c9be - End of configuration. [testng] [2024-07-10 01:24:27,181] [pool-1-thread-6] Initializing /data/fluoview/sample_labled_XYZTCh.tif: [testng] 01:24:27,181 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:24:27,181 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:27,182 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-10_01-24-27.log] [testng] 01:24:27,182 |-INFO in ch.qos.logback.core.sift.SiftProcessor@52a734d1 - End of configuration. [testng] [2024-07-10 01:24:27,210] [pool-1-thread-5] Initializing /data/fluoview/SpineAnimation.avi: [testng] 01:24:27,210 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:24:27,211 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:27,211 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-10_01-24-27.log] [testng] 01:24:27,212 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6ce942fc - End of configuration. [testng] [2024-07-10 01:24:27,224] [pool-1-thread-4] Initializing /data/iplab/10x Blood and Bacteria.IPL: [testng] 01:24:27,224 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:24:27,224 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:27,225 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-10_01-24-27.log] [testng] 01:24:27,225 |-INFO in ch.qos.logback.core.sift.SiftProcessor@736f2edb - End of configuration. [testng] [2024-07-10 01:24:27,249] [pool-1-thread-3] Initializing /data/iplab/Blend_Dapi.IPL: [testng] 01:24:27,249 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:24:27,249 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:27,250 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-10_01-24-27.log] [testng] 01:24:27,251 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27761594 - End of configuration. [testng] [2024-07-10 01:24:27,262] [pool-1-thread-2] Initializing /data/zeiss_lsm/X-Y-Z-T-Ch-Tile--MultiTrack-1.lsm: [testng] 01:24:27,262 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:24:27,262 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:27,263 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-10_01-24-27.log] [testng] 01:24:27,264 |-INFO in ch.qos.logback.core.sift.SiftProcessor@134e6961 - End of configuration. [testng] [2024-07-10 01:24:28,900] [pool-1-thread-10] Initializing /data/iplab/Color Histology.IPL: [testng] [2024-07-10 01:24:28,906] [pool-1-thread-7] Initializing /data/fluoview/Sample_ThreeCH.TIF: [testng] [2024-07-10 01:24:28,939] [pool-1-thread-9] Initializing /data/iplab/Color Image.IPL: [testng] [2024-07-10 01:24:28,947] [pool-1-thread-5] Initializing /data/gatan/ImageReader2003/ImageReaderTest/TestFiles/test3.dm3: [testng] [2024-07-10 01:24:28,956] [pool-1-thread-3] Initializing /data/fluoview/Sample_XYT.TIF: [testng] [2024-07-10 01:24:28,989] [pool-1-thread-1] Initializing /data/iplab/16Bit XRay.IPL: [testng] [2024-07-10 01:24:28,996] [pool-1-thread-6] Initializing /data/fluoview/sample_labled_XYZCh.tif: [testng] [2024-07-10 01:24:29,021] [pool-1-thread-4] Initializing /data/zeiss_lsm/X-Y-Z-T-Ch-Tile-1.lsm: [testng] [2024-07-10 01:24:29,086] [pool-1-thread-8] Initializing /data/iplab/Actin.IPL: [testng] [2024-07-10 01:24:29,092] [pool-1-thread-12] Initializing /data/fluoview/Sample_XT.tif: [testng] [2024-07-10 01:24:29,423] [pool-1-thread-8] Initializing /data/iplab/Blend_Fitc.IPL: [testng] [2024-07-10 01:24:29,431] [pool-1-thread-9] Initializing /data/fluoview/Sample_XYZ.TIF: [testng] [2024-07-10 01:24:29,487] [pool-1-thread-10] Initializing /data/gatan/ImageReader2003/ImageReaderTest/TestFiles/Test.dm3: [testng] [2024-07-10 01:24:29,546] [pool-1-thread-1] Initializing /data/gatan/ImageReader2003/ImageReaderTest/TestFiles/Test2.dm3: [testng] [2024-07-10 01:24:29,557] [pool-1-thread-5] Initializing /data/iplab/Blend_Final.IPL: [testng] [2024-07-10 01:24:29,722] [pool-1-thread-6] Initializing /data/iplab/Blend_Tritc.IPL: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1484, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 28 seconds Finished: SUCCESS