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Started by upstream project "BIOFORMATS-test-repo" build number 259 originally caused by: Started by upstream project "Trigger" build number 283 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/jenkins14870593445132480311.sh + '[' specs = slidebook ']' ++ date +%u + '[' 1 -le 1 ']' + DOCKER_ARGS='-Dtestng.memory=15g -Dtestng.threadCount=12 -Duser.language=fr -Duser.country=FR' + sudo docker run --rm --name BIOFORMATS-test-folder_40819_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 -Duser.language=fr -Duser.country=FR 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] 00:29:18,681 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:29:18,683 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 00:29:18,683 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:29:18,685 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:29:18,685 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:29:18,685 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:29:18,685 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:29:18,685 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:29:18,686 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:29:18,686 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:29:18,686 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:29:18,686 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:29:18,939 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:29:18,939 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:29:18,970 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:29:18,970 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:29:18,980 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:29:18,980 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:29:18,980 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:29:18,980 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:29:18,981 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 00:29:18,981 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 00:29:18,982 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 296 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-18 00:29:18,992] [main] java.version = 1.8.0_342 [testng] 00:29:18,996 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:29:18,996 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:19,046 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-18_00-29-19.log] [testng] 00:29:19,048 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-11-18 00:29:19,050] [main] testng.directory = /data [testng] [2024-11-18 00:29:19,050] [main] testng.configDirectory = /config [testng] [2024-11-18 00:29:19,064] [main] testng.multiplier = 1.0 [testng] [2024-11-18 00:29:19,064] [main] testng.in-memory = false [testng] [2024-11-18 00:29:19,064] [main] testng.allow-missing = false [testng] [2024-11-18 00:29:19,064] [main] user.language = fr [testng] [2024-11-18 00:29:19,064] [main] user.country = FR [testng] [2024-11-18 00:29:19,064] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-11-18 00:31:52,023] [main] ---------------------------------------- [testng] [2024-11-18 00:31:52,023] [main] Total files: 226 [testng] [2024-11-18 00:31:52,023] [main] Scan time: 152.959 s (676 ms/file) [testng] [2024-11-18 00:31:52,023] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 28 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-18 00:33:12,966] [pool-1-thread-1] Initializing /data/iplab/Blend_Fitc.IPL: [testng] 00:33:12,967 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:33:12,967 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:12,968 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-18_00-33-12.log] [testng] 00:33:12,969 |-INFO in ch.qos.logback.core.sift.SiftProcessor@70c74c1f - End of configuration. [testng] [2024-11-18 00:33:13,009] [pool-1-thread-12] Initializing /data/fluoview/sample_labled_XYZTCh.tif: [testng] 00:33:13,009 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:33:13,009 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:13,010 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-18_00-33-13.log] [testng] 00:33:13,010 |-INFO in ch.qos.logback.core.sift.SiftProcessor@272b4d14 - End of configuration. [testng] [2024-11-18 00:33:13,227] [pool-1-thread-11] Initializing /data/fluoview/Sample_XT.tif: [testng] 00:33:13,227 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:33:13,227 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:13,228 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-18_00-33-13.log] [testng] 00:33:13,228 |-INFO in ch.qos.logback.core.sift.SiftProcessor@763073ec - End of configuration. [testng] [2024-11-18 00:33:13,408] [pool-1-thread-10] Initializing /data/gatan/ImageReader2003/ImageReaderTest/TestFiles/test3.dm3: [testng] 00:33:13,408 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:33:13,408 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:13,409 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-18_00-33-13.log] [testng] 00:33:13,409 |-INFO in ch.qos.logback.core.sift.SiftProcessor@429b32ce - End of configuration. [testng] [2024-11-18 00:33:13,454] [pool-1-thread-9] Initializing /data/fluoview/Sample_ThreeCH.TIF: [testng] 00:33:13,454 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:33:13,454 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:13,455 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-18_00-33-13.log] [testng] 00:33:13,455 |-INFO in ch.qos.logback.core.sift.SiftProcessor@23c53687 - End of configuration. [testng] [2024-11-18 00:33:13,617] [pool-1-thread-8] Initializing /data/fluoview/sample_labled_XYZCh.tif: [testng] 00:33:13,617 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:33:13,617 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:13,618 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-18_00-33-13.log] [testng] 00:33:13,618 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2e84c03a - End of configuration. [testng] [2024-11-18 00:33:13,794] [pool-1-thread-7] Initializing /data/iplab/Blend_Final.IPL: [testng] 00:33:13,795 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:33:13,795 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:13,795 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-18_00-33-13.log] [testng] 00:33:13,796 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f498a55 - End of configuration. [testng] [2024-11-18 00:33:13,822] [pool-1-thread-6] Initializing /data/fluoview/Sample_XYT.TIF: [testng] 00:33:13,822 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:33:13,822 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:13,823 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-18_00-33-13.log] [testng] 00:33:13,823 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b9d7e78 - End of configuration. [testng] [2024-11-18 00:33:13,991] [pool-1-thread-5] Initializing /data/gatan/ImageReader2003/ImageReaderTest/TestFiles/Test2.dm3: [testng] 00:33:13,991 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:33:13,991 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:13,992 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-18_00-33-13.log] [testng] 00:33:13,993 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71814e7 - End of configuration. [testng] [2024-11-18 00:33:14,032] [pool-1-thread-4] Initializing /data/iplab/10x Blood and Bacteria.IPL: [testng] 00:33:14,032 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:33:14,032 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:14,033 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-18_00-33-14.log] [testng] 00:33:14,033 |-INFO in ch.qos.logback.core.sift.SiftProcessor@c75831 - End of configuration. [testng] [2024-11-18 00:33:14,062] [pool-1-thread-3] Initializing /data/fluoview/Sample_XYZ.TIF: [testng] 00:33:14,063 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:33:14,063 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:14,063 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-18_00-33-14.log] [testng] 00:33:14,064 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f88c6a7 - End of configuration. [testng] [2024-11-18 00:33:14,232] [pool-1-thread-2] Initializing /data/zeiss_lsm/X-Y-Z-T-Ch-Tile--MultiTrack-1.lsm: [testng] 00:33:14,233 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:33:14,233 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:14,233 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-18_00-33-14.log] [testng] 00:33:14,234 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3736daa9 - End of configuration. [testng] [2024-11-18 00:33:16,795] [pool-1-thread-1] Initializing /data/zeiss_lsm/X-Y-Z-T-Ch-Tile-2.lsm: [testng] [2024-11-18 00:33:17,021] [pool-1-thread-5] Initializing /data/gatan/ImageReader2003/ImageReaderTest/TestFiles/Test.dm3: [testng] [2024-11-18 00:33:17,065] [pool-1-thread-10] Initializing /data/iplab/Blend_Tritc.IPL: [testng] [2024-11-18 00:33:17,097] [pool-1-thread-7] Initializing /data/fluoview/Sample_TwoCH.TIF: [testng] [2024-11-18 00:33:17,401] [pool-1-thread-4] Initializing /data/zeiss_lsm/X-Y-Z-T-Ch-Tile-1.lsm: [testng] [2024-11-18 00:33:18,374] [pool-1-thread-8] Initializing /data/fluoview/SpineAnimation.avi: [testng] [2024-11-18 00:33:18,471] [pool-1-thread-12] Initializing /data/iplab/Chromosomes.IPL: [testng] [2024-11-18 00:33:18,513] [pool-1-thread-6] Initializing /data/iplab/Blend_Dapi.IPL: [testng] [2024-11-18 00:33:18,709] [pool-1-thread-3] Initializing /data/iplab/Color Histology.IPL: [testng] [2024-11-18 00:33:18,958] [pool-1-thread-10] Initializing /data/fluoview/SpineAnimation.tif: [testng] [2024-11-18 00:33:19,294] [pool-1-thread-5] Initializing /data/iplab/Actin.IPL: [testng] [2024-11-18 00:33:19,342] [pool-1-thread-11] Initializing /data/iplab/3t3 Cell.IPL: [testng] [2024-11-18 00:33:19,393] [pool-1-thread-9] Initializing /data/fluoview/sample_labled_XYTCh.tif: [testng] [2024-11-18 00:33:20,164] [pool-1-thread-3] Initializing /data/iplab/Blend_DIC.IPL: [testng] [2024-11-18 00:33:20,209] [pool-1-thread-12] Initializing /data/iplab/Color Image.IPL: [testng] [2024-11-18 00:33:20,324] [pool-1-thread-6] Initializing /data/iplab/16Bit XRay.IPL: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1484, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 4 minutes 7 seconds Finished: SUCCESS