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Started by upstream project "BIOFORMATS-test-repo" build number 239 originally caused by: Started by upstream project "Trigger" build number 264 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/jenkins12582104740456932682.sh + '[' specs = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_37539_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] 00:35:04,979 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:35:04,980 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 00:35:04,980 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:35:04,981 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:35:04,981 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:35:04,982 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:35:04,982 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:35:04,982 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:35:04,982 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:35:04,983 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:35:04,983 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:35:04,983 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:35:05,132 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:35:05,133 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:35:05,152 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:35:05,152 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:35:05,157 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:35:05,157 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:35:05,157 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:35:05,158 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:35:05,158 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 00:35:05,158 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 00:35:05,159 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 177 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-30 00:35:05,166] [main] java.version = 17.0.2 [testng] 00:35:05,169 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:35:05,169 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:05,207 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-30_00-35-05.log] [testng] 00:35:05,208 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-10-30 00:35:05,210] [main] testng.directory = /data [testng] [2024-10-30 00:35:05,210] [main] testng.configDirectory = /config [testng] [2024-10-30 00:35:05,218] [main] testng.multiplier = 1.0 [testng] [2024-10-30 00:35:05,219] [main] testng.in-memory = false [testng] [2024-10-30 00:35:05,219] [main] testng.allow-missing = false [testng] [2024-10-30 00:35:05,219] [main] user.language = en [testng] [2024-10-30 00:35:05,219] [main] user.country = ${user.country} [testng] [2024-10-30 00:35:05,219] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-30 00:40:29,956] [main] ---------------------------------------- [testng] [2024-10-30 00:40:29,957] [main] Total files: 226 [testng] [2024-10-30 00:40:29,957] [main] Scan time: 324.737 s (1436 ms/file) [testng] [2024-10-30 00:40:29,957] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 28 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-30 00:42:05,581] [pool-1-thread-1] Initializing /data/fluoview/SpineAnimation.tif: [testng] 00:42:05,581 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:42:05,581 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:05,583 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-30_00-42-05.log] [testng] 00:42:05,583 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6dcaa96a - End of configuration. [testng] [2024-10-30 00:42:05,931] [pool-1-thread-12] Initializing /data/fluoview/Sample_XYZ.TIF: [testng] 00:42:05,932 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:42:05,932 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:05,933 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-30_00-42-05.log] [testng] 00:42:05,933 |-INFO in ch.qos.logback.core.sift.SiftProcessor@58bea10d - End of configuration. [testng] [2024-10-30 00:42:06,152] [pool-1-thread-11] Initializing /data/gatan/ImageReader2003/ImageReaderTest/TestFiles/Test2.dm3: [testng] 00:42:06,152 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:42:06,152 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:06,153 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-30_00-42-06.log] [testng] 00:42:06,153 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c0a7017 - End of configuration. [testng] [2024-10-30 00:42:06,206] [pool-1-thread-10] Initializing /data/iplab/Blend_Dapi.IPL: [testng] 00:42:06,206 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:42:06,206 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:06,207 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-30_00-42-06.log] [testng] 00:42:06,207 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d0405b4 - End of configuration. [testng] [2024-10-30 00:42:06,239] [pool-1-thread-9] Initializing /data/iplab/Blend_Fitc.IPL: [testng] 00:42:06,239 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:42:06,239 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:06,240 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-30_00-42-06.log] [testng] 00:42:06,240 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1bd4e928 - End of configuration. [testng] [2024-10-30 00:42:06,274] [pool-1-thread-8] Initializing /data/zeiss_lsm/X-Y-Z-T-Ch-Tile-2.lsm: [testng] 00:42:06,274 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:42:06,274 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:06,275 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-30_00-42-06.log] [testng] 00:42:06,275 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18349045 - End of configuration. [testng] [2024-10-30 00:42:06,539] [pool-1-thread-7] Initializing /data/iplab/Color Histology.IPL: [testng] 00:42:06,540 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:42:06,540 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:06,540 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-30_00-42-06.log] [testng] 00:42:06,541 |-INFO in ch.qos.logback.core.sift.SiftProcessor@19a19720 - End of configuration. [testng] [2024-10-30 00:42:06,586] [pool-1-thread-6] Initializing /data/iplab/Blend_Final.IPL: [testng] 00:42:06,586 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:42:06,586 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:06,587 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-30_00-42-06.log] [testng] 00:42:06,588 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3bc9ab94 - End of configuration. [testng] [2024-10-30 00:42:06,625] [pool-1-thread-5] Initializing /data/fluoview/Sample_XT.tif: [testng] 00:42:06,626 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:42:06,626 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:06,626 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-30_00-42-06.log] [testng] 00:42:06,627 |-INFO in ch.qos.logback.core.sift.SiftProcessor@64482366 - End of configuration. [testng] [2024-10-30 00:42:06,866] [pool-1-thread-4] Initializing /data/iplab/Blend_DIC.IPL: [testng] 00:42:06,866 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:42:06,866 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:06,867 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-30_00-42-06.log] [testng] 00:42:06,867 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c425b87 - End of configuration. [testng] [2024-10-30 00:42:06,909] [pool-1-thread-3] Initializing /data/fluoview/sample_labled_XYTCh.tif: [testng] 00:42:06,909 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:42:06,909 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:06,910 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-30_00-42-06.log] [testng] 00:42:06,910 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36adcaa0 - End of configuration. [testng] [2024-10-30 00:42:07,363] [pool-1-thread-2] Initializing /data/iplab/16Bit XRay.IPL: [testng] 00:42:07,363 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:42:07,363 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:07,364 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-30_00-42-07.log] [testng] 00:42:07,364 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71b5cb66 - End of configuration. [testng] [2024-10-30 00:42:10,164] [pool-1-thread-7] Initializing /data/iplab/Actin.IPL: [testng] [2024-10-30 00:42:10,240] [pool-1-thread-2] Initializing /data/fluoview/Sample_XYT.TIF: [testng] [2024-10-30 00:42:10,543] [pool-1-thread-6] Initializing /data/zeiss_lsm/X-Y-Z-T-Ch-Tile--MultiTrack-1.lsm: [testng] [2024-10-30 00:42:10,882] [pool-1-thread-9] Initializing /data/iplab/3t3 Cell.IPL: [testng] [2024-10-30 00:42:10,967] [pool-1-thread-10] Initializing /data/fluoview/SpineAnimation.avi: [testng] [2024-10-30 00:42:11,116] [pool-1-thread-4] Initializing /data/iplab/Color Image.IPL: [testng] [2024-10-30 00:42:11,186] [pool-1-thread-11] Initializing /data/gatan/ImageReader2003/ImageReaderTest/TestFiles/test3.dm3: [testng] [2024-10-30 00:42:11,705] [pool-1-thread-1] Initializing /data/fluoview/Sample_TwoCH.TIF: [testng] [2024-10-30 00:42:12,229] [pool-1-thread-12] Initializing /data/iplab/10x Blood and Bacteria.IPL: [testng] [2024-10-30 00:42:12,335] [pool-1-thread-3] Initializing /data/iplab/Chromosomes.IPL: [testng] [2024-10-30 00:42:12,879] [pool-1-thread-5] Initializing /data/iplab/Blend_Tritc.IPL: [testng] [2024-10-30 00:42:12,951] [pool-1-thread-7] Initializing /data/fluoview/sample_labled_XYZTCh.tif: [testng] [2024-10-30 00:42:13,269] [pool-1-thread-4] Initializing /data/zeiss_lsm/X-Y-Z-T-Ch-Tile-1.lsm: [testng] [2024-10-30 00:42:13,715] [pool-1-thread-11] Initializing /data/fluoview/Sample_ThreeCH.TIF: [testng] [2024-10-30 00:42:14,097] [pool-1-thread-9] Initializing /data/fluoview/sample_labled_XYZCh.tif: [testng] [2024-10-30 00:42:14,624] [pool-1-thread-10] Initializing /data/gatan/ImageReader2003/ImageReaderTest/TestFiles/Test.dm3: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1484, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 7 minutes 54 seconds Finished: SUCCESS