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Started by upstream project "BIOFORMATS-test-repo" build number 290 originally caused by: Started by upstream project "Trigger" build number 309 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/jenkins7120749898852957319.sh + '[' specs = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_45776_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] 00:36:17,828 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:36:17,830 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 00:36:17,830 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:36:17,831 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:36:17,832 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:36:17,832 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:36:17,832 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:36:17,832 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:36:17,833 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:36:17,833 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:36:17,834 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:36:17,834 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:36:18,007 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:36:18,007 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:36:18,030 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:36:18,030 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:36:18,036 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:36:18,036 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:36:18,036 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:36:18,036 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:36:18,037 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 00:36:18,037 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 00:36:18,037 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 204 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-14 00:36:18,046] [main] java.version = 11.0.16 [testng] 00:36:18,050 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:36:18,050 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:18,093 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-14_00-36-18.log] [testng] 00:36:18,095 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-12-14 00:36:18,097] [main] testng.directory = /data [testng] [2024-12-14 00:36:18,097] [main] testng.configDirectory = /config [testng] [2024-12-14 00:36:18,107] [main] testng.multiplier = 1.0 [testng] [2024-12-14 00:36:18,108] [main] testng.in-memory = false [testng] [2024-12-14 00:36:18,108] [main] testng.allow-missing = false [testng] [2024-12-14 00:36:18,108] [main] user.language = en [testng] [2024-12-14 00:36:18,108] [main] user.country = ${user.country} [testng] [2024-12-14 00:36:18,108] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-14 00:45:26,211] [main] ---------------------------------------- [testng] [2024-12-14 00:45:26,211] [main] Total files: 226 [testng] [2024-12-14 00:45:26,211] [main] Scan time: 548.102 s (2425 ms/file) [testng] [2024-12-14 00:45:26,211] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 28 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-14 00:53:33,229] [pool-1-thread-1] Initializing /data/fluoview/Sample_XT.tif: [testng] 00:53:33,230 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:53:33,230 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:53:33,232 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-14_00-53-33.log] [testng] 00:53:33,232 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5592829e - End of configuration. [testng] [2024-12-14 00:53:34,821] [pool-1-thread-12] Initializing /data/iplab/Blend_DIC.IPL: [testng] 00:53:34,821 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:53:34,821 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:53:34,823 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-14_00-53-34.log] [testng] 00:53:34,823 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13e8abbb - End of configuration. [testng] [2024-12-14 00:53:34,999] [pool-1-thread-11] Initializing /data/iplab/Color Histology.IPL: [testng] 00:53:34,999 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:53:35,000 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:53:35,000 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-14_00-53-35.log] [testng] 00:53:35,001 |-INFO in ch.qos.logback.core.sift.SiftProcessor@51efdebe - End of configuration. [testng] [2024-12-14 00:53:35,181] [pool-1-thread-10] Initializing /data/iplab/Color Image.IPL: [testng] 00:53:35,181 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:53:35,181 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:53:35,182 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-14_00-53-35.log] [testng] 00:53:35,183 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a87b0b0 - End of configuration. [testng] [2024-12-14 00:53:35,359] [pool-1-thread-9] Initializing /data/iplab/Chromosomes.IPL: [testng] 00:53:35,359 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:53:35,360 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:53:35,360 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-14_00-53-35.log] [testng] 00:53:35,361 |-INFO in ch.qos.logback.core.sift.SiftProcessor@196ae177 - End of configuration. [testng] [2024-12-14 00:53:35,529] [pool-1-thread-8] Initializing /data/gatan/ImageReader2003/ImageReaderTest/TestFiles/Test2.dm3: [testng] 00:53:35,529 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:53:35,529 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:53:35,529 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-14_00-53-35.log] [testng] 00:53:35,530 |-INFO in ch.qos.logback.core.sift.SiftProcessor@58fdbaaf - End of configuration. [testng] [2024-12-14 00:53:35,867] [pool-1-thread-7] Initializing /data/fluoview/sample_labled_XYZTCh.tif: [testng] 00:53:35,867 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:53:35,867 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:53:35,867 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-14_00-53-35.log] [testng] 00:53:35,868 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f4d841e - End of configuration. [testng] [2024-12-14 00:53:38,731] [pool-1-thread-6] Initializing /data/iplab/16Bit XRay.IPL: [testng] 00:53:38,732 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:53:38,732 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:53:38,732 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-14_00-53-38.log] [testng] 00:53:38,733 |-INFO in ch.qos.logback.core.sift.SiftProcessor@b45ebd0 - End of configuration. [testng] [2024-12-14 00:53:38,958] [pool-1-thread-5] Initializing /data/iplab/Blend_Fitc.IPL: [testng] 00:53:38,958 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:53:38,958 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:53:38,959 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-14_00-53-38.log] [testng] 00:53:38,959 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6b07284d - End of configuration. [testng] [2024-12-14 00:53:39,185] [pool-1-thread-4] Initializing /data/fluoview/SpineAnimation.tif: [testng] 00:53:39,186 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:53:39,186 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:53:39,187 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-14_00-53-39.log] [testng] 00:53:39,199 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4286258b - End of configuration. [testng] [2024-12-14 00:53:40,745] [pool-1-thread-3] Initializing /data/zeiss_lsm/X-Y-Z-T-Ch-Tile--MultiTrack-1.lsm: [testng] 00:53:40,745 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:53:40,745 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:53:40,746 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-14_00-53-40.log] [testng] 00:53:40,746 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6b933cb - End of configuration. [testng] [2024-12-14 00:53:41,832] [pool-1-thread-2] Initializing /data/iplab/Blend_Tritc.IPL: [testng] 00:53:41,833 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:53:41,833 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:53:41,833 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-14_00-53-41.log] [testng] 00:53:41,834 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75615228 - End of configuration. [testng] [2024-12-14 00:53:46,027] [pool-1-thread-10] Initializing /data/gatan/ImageReader2003/ImageReaderTest/TestFiles/test3.dm3: [testng] [2024-12-14 00:53:46,606] [pool-1-thread-8] Initializing /data/fluoview/Sample_TwoCH.TIF: [testng] [2024-12-14 00:53:48,319] [pool-1-thread-9] Initializing /data/fluoview/Sample_XYZ.TIF: [testng] [2024-12-14 00:53:50,561] [pool-1-thread-6] Initializing /data/iplab/Blend_Final.IPL: [testng] [2024-12-14 00:53:51,016] [pool-1-thread-11] Initializing /data/fluoview/sample_labled_XYTCh.tif: [testng] [2024-12-14 00:53:53,120] [pool-1-thread-12] Initializing /data/iplab/3t3 Cell.IPL: [testng] [2024-12-14 00:53:53,612] [pool-1-thread-5] Initializing /data/fluoview/Sample_XYT.TIF: [testng] [2024-12-14 00:53:54,832] [pool-1-thread-2] Initializing /data/zeiss_lsm/X-Y-Z-T-Ch-Tile-1.lsm: [testng] [2024-12-14 00:53:59,264] [pool-1-thread-12] Initializing /data/fluoview/Sample_ThreeCH.TIF: [testng] [2024-12-14 00:54:01,339] [pool-1-thread-6] Initializing /data/fluoview/SpineAnimation.avi: [testng] [2024-12-14 00:54:02,071] [pool-1-thread-10] Initializing /data/fluoview/sample_labled_XYZCh.tif: [testng] [2024-12-14 00:54:04,380] [pool-1-thread-4] Initializing /data/iplab/Blend_Dapi.IPL: [testng] [2024-12-14 00:54:04,784] [pool-1-thread-7] Initializing /data/zeiss_lsm/X-Y-Z-T-Ch-Tile-2.lsm: [testng] [2024-12-14 00:54:07,162] [pool-1-thread-1] Initializing /data/gatan/ImageReader2003/ImageReaderTest/TestFiles/Test.dm3: [testng] [2024-12-14 00:54:10,235] [pool-1-thread-4] Initializing /data/iplab/Actin.IPL: [testng] [2024-12-14 00:54:10,618] [pool-1-thread-6] Initializing /data/iplab/10x Blood and Bacteria.IPL: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1484, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 18 minutes 11 seconds Finished: SUCCESS