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Started by upstream project "BIOFORMATS-test-repo" build number 271 originally caused by: Started by upstream project "Trigger" build number 293 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/jenkins1535874646211706586.sh + '[' specs = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_42658_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. [javac] 4 warnings 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] 00:30:34,347 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:30:34,348 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 00:30:34,348 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:30:34,349 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:30:34,350 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:30:34,350 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:30:34,350 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:30:34,350 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:30:34,351 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:30:34,352 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:30:34,352 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:30:34,352 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:30:34,514 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:30:34,514 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:30:34,538 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:30:34,538 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:30:34,545 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:30:34,545 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:30:34,545 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:30:34,545 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:30:34,545 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 00:30:34,546 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 00:30:34,546 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 195 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-28 00:30:34,555] [main] java.version = 21 [testng] 00:30:34,558 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:30:34,558 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:34,599 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-28_00-30-34.log] [testng] 00:30:34,600 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-11-28 00:30:34,602] [main] testng.directory = /data [testng] [2024-11-28 00:30:34,602] [main] testng.configDirectory = /config [testng] [2024-11-28 00:30:34,610] [main] testng.multiplier = 1.0 [testng] [2024-11-28 00:30:34,611] [main] testng.in-memory = false [testng] [2024-11-28 00:30:34,611] [main] testng.allow-missing = false [testng] [2024-11-28 00:30:34,611] [main] user.language = en [testng] [2024-11-28 00:30:34,611] [main] user.country = ${user.country} [testng] [2024-11-28 00:30:34,611] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-28 00:36:24,539] [main] ---------------------------------------- [testng] [2024-11-28 00:36:24,539] [main] Total files: 226 [testng] [2024-11-28 00:36:24,539] [main] Scan time: 349.928 s (1548 ms/file) [testng] [2024-11-28 00:36:24,539] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 28 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-28 00:40:05,592] [pool-1-thread-1] Initializing /data/fluoview/Sample_XYT.TIF: [testng] 00:40:05,593 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:40:05,593 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:40:05,594 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-28_00-40-05.log] [testng] 00:40:05,594 |-INFO in ch.qos.logback.core.sift.SiftProcessor@72aac2f8 - End of configuration. [testng] [2024-11-28 00:40:06,073] [pool-1-thread-12] Initializing /data/iplab/3t3 Cell.IPL: [testng] 00:40:06,073 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:40:06,073 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:40:06,074 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-28_00-40-06.log] [testng] 00:40:06,074 |-INFO in ch.qos.logback.core.sift.SiftProcessor@77ad8440 - End of configuration. [testng] [2024-11-28 00:40:06,152] [pool-1-thread-11] Initializing /data/iplab/Blend_Final.IPL: [testng] 00:40:06,152 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:40:06,152 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:40:06,153 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-28_00-40-06.log] [testng] 00:40:06,153 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e21092d - End of configuration. [testng] [2024-11-28 00:40:06,225] [pool-1-thread-10] Initializing /data/zeiss_lsm/X-Y-Z-T-Ch-Tile--MultiTrack-1.lsm: [testng] 00:40:06,225 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:40:06,225 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:40:06,226 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-28_00-40-06.log] [testng] 00:40:06,226 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e353dd - End of configuration. [testng] [2024-11-28 00:40:06,679] [pool-1-thread-9] Initializing /data/iplab/Color Image.IPL: [testng] 00:40:06,679 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:40:06,680 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:40:06,680 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-28_00-40-06.log] [testng] 00:40:06,681 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22c27c61 - End of configuration. [testng] [2024-11-28 00:40:06,767] [pool-1-thread-8] Initializing /data/zeiss_lsm/X-Y-Z-T-Ch-Tile-1.lsm: [testng] 00:40:06,767 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:40:06,767 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:40:06,768 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-28_00-40-06.log] [testng] 00:40:06,768 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35dffa3d - End of configuration. [testng] [2024-11-28 00:40:07,212] [pool-1-thread-7] Initializing /data/iplab/Blend_DIC.IPL: [testng] 00:40:07,213 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:40:07,213 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:40:07,213 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-28_00-40-07.log] [testng] 00:40:07,214 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a002f1 - End of configuration. [testng] [2024-11-28 00:40:07,294] [pool-1-thread-6] Initializing /data/iplab/Blend_Dapi.IPL: [testng] 00:40:07,294 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:40:07,294 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:40:07,295 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-28_00-40-07.log] [testng] 00:40:07,295 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4fcb720b - End of configuration. [testng] [2024-11-28 00:40:07,364] [pool-1-thread-5] Initializing /data/iplab/16Bit XRay.IPL: [testng] 00:40:07,364 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:40:07,364 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:40:07,365 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-28_00-40-07.log] [testng] 00:40:07,365 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14905b4d - End of configuration. [testng] [2024-11-28 00:40:07,433] [pool-1-thread-4] Initializing /data/iplab/Actin.IPL: [testng] 00:40:07,433 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:40:07,433 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:40:07,433 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-28_00-40-07.log] [testng] 00:40:07,434 |-INFO in ch.qos.logback.core.sift.SiftProcessor@524de17f - End of configuration. [testng] [2024-11-28 00:40:07,503] [pool-1-thread-3] Initializing /data/gatan/ImageReader2003/ImageReaderTest/TestFiles/test3.dm3: [testng] 00:40:07,503 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:40:07,503 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:40:07,504 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-28_00-40-07.log] [testng] 00:40:07,504 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79714da3 - End of configuration. [testng] [2024-11-28 00:40:07,616] [pool-1-thread-2] Initializing /data/zeiss_lsm/X-Y-Z-T-Ch-Tile-2.lsm: [testng] 00:40:07,616 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:40:07,616 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:40:07,617 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-28_00-40-07.log] [testng] 00:40:07,617 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35d0197e - End of configuration. [testng] [2024-11-28 00:40:10,631] [pool-1-thread-5] Initializing /data/fluoview/Sample_XYZ.TIF: [testng] [2024-11-28 00:40:10,951] [pool-1-thread-9] Initializing /data/fluoview/sample_labled_XYZCh.tif: [testng] [2024-11-28 00:40:11,306] [pool-1-thread-12] Initializing /data/iplab/Chromosomes.IPL: [testng] [2024-11-28 00:40:11,360] [pool-1-thread-4] Initializing /data/gatan/ImageReader2003/ImageReaderTest/TestFiles/Test2.dm3: [testng] [2024-11-28 00:40:11,436] [pool-1-thread-11] Initializing /data/fluoview/sample_labled_XYZTCh.tif: [testng] [2024-11-28 00:40:11,765] [pool-1-thread-7] Initializing /data/iplab/10x Blood and Bacteria.IPL: [testng] [2024-11-28 00:40:11,817] [pool-1-thread-3] Initializing /data/iplab/Blend_Tritc.IPL: [testng] [2024-11-28 00:40:11,869] [pool-1-thread-6] Initializing /data/iplab/Color Histology.IPL: [testng] [2024-11-28 00:40:13,422] [pool-1-thread-12] Initializing /data/iplab/Blend_Fitc.IPL: [testng] [2024-11-28 00:40:13,536] [pool-1-thread-6] Initializing /data/fluoview/Sample_XT.tif: [testng] [2024-11-28 00:40:14,034] [pool-1-thread-7] Initializing /data/fluoview/Sample_TwoCH.TIF: [testng] [2024-11-28 00:40:14,599] [pool-1-thread-4] Initializing /data/fluoview/sample_labled_XYTCh.tif: [testng] [2024-11-28 00:40:14,927] [pool-1-thread-1] Initializing /data/fluoview/SpineAnimation.tif: [testng] [2024-11-28 00:40:15,241] [pool-1-thread-3] Initializing /data/fluoview/Sample_ThreeCH.TIF: [testng] [2024-11-28 00:40:16,305] [pool-1-thread-12] Initializing /data/gatan/ImageReader2003/ImageReaderTest/TestFiles/Test.dm3: [testng] [2024-11-28 00:40:17,899] [pool-1-thread-9] Initializing /data/fluoview/SpineAnimation.avi: [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 49 seconds Finished: SUCCESS