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Started by upstream project "BIOFORMATS-test-repo" build number 264 originally caused by: Started by upstream project "Trigger" build number 287 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8 [BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins13851536574027875247.sh + '[' amira = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_41636_merge_ci -v /uod/idr/repos/curated/amira:/data -v /uod/idr-scratch/merge-ci/curated/amira:/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 test-automated: [testng] File leak detector installed [testng] 00:29:31,246 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:29:31,248 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 00:29:31,248 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:29:31,249 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:29:31,249 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:29:31,249 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:29:31,250 |-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] 00:29:31,250 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:29:31,250 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:29:31,250 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:29:31,250 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:29:31,251 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:29:31,487 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:29:31,487 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:29:31,518 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:29:31,518 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:29:31,526 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:29:31,526 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:29:31,526 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:29:31,527 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:29:31,527 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 00:29:31,528 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 00:29:31,528 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 278 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-22 00:29:31,538] [main] java.version = 1.8.0_342 [testng] 00:29:31,543 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:29:31,543 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:31,595 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-22_00-29-31.log] [testng] 00:29:31,596 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-11-22 00:29:31,598] [main] testng.directory = /data [testng] [2024-11-22 00:29:31,599] [main] testng.configDirectory = /config [testng] [2024-11-22 00:29:31,611] [main] testng.multiplier = 1.0 [testng] [2024-11-22 00:29:31,611] [main] testng.in-memory = false [testng] [2024-11-22 00:29:31,611] [main] testng.allow-missing = false [testng] [2024-11-22 00:29:31,611] [main] user.language = en [testng] [2024-11-22 00:29:31,611] [main] user.country = ${user.country} [testng] [2024-11-22 00:29:31,611] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-11-22 00:29:36,525] [main] ---------------------------------------- [testng] [2024-11-22 00:29:36,526] [main] Total files: 15 [testng] [2024-11-22 00:29:36,526] [main] Scan time: 4.913 s (327 ms/file) [testng] [2024-11-22 00:29:36,526] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 12 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-22 00:29:47,085] [pool-1-thread-1] Initializing /data/ilya/test.am: [testng] 00:29:47,085 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:29:47,085 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:47,086 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-22_00-29-47.log] [testng] 00:29:47,087 |-INFO in ch.qos.logback.core.sift.SiftProcessor@453907dd - End of configuration. [testng] [2024-11-22 00:29:47,593] [pool-1-thread-12] Initializing /data/jeremy/Virus_Membrane7.am: [testng] 00:29:47,593 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:29:47,593 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:47,594 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-22_00-29-47.log] [testng] 00:29:47,595 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e98b4a1 - End of configuration. [testng] [2024-11-22 00:29:48,146] [pool-1-thread-11] Initializing /data/jeremy/Virus_Membrane7-screenshot.PNG: [testng] 00:29:48,146 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:29:48,146 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:48,147 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-22_00-29-48.log] [testng] 00:29:48,147 |-INFO in ch.qos.logback.core.sift.SiftProcessor@51cfd1f6 - End of configuration. [testng] [2024-11-22 00:29:48,185] [pool-1-thread-10] Initializing /data/johannes/template.labels: [testng] 00:29:48,185 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:29:48,185 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:48,186 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-22_00-29-48.log] [testng] 00:29:48,187 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43d108ff - End of configuration. [testng] [2024-11-22 00:29:48,662] [pool-1-thread-9] Initializing /data/jcb/201108088/Haberman-Fig4A-original.am: [testng] 00:29:48,662 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:29:48,662 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:48,663 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-22_00-29-48.log] [testng] 00:29:48,663 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2e711d35 - End of configuration. [testng] [2024-11-22 00:29:49,146] [pool-1-thread-8] Initializing /data/public/imagesc-50585/BF_Check.tif: [testng] 00:29:49,146 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:29:49,146 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:49,147 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-22_00-29-49.log] [testng] 00:29:49,147 |-INFO in ch.qos.logback.core.sift.SiftProcessor@49774d52 - End of configuration. [testng] [2024-11-22 00:29:50,264] [pool-1-thread-7] Initializing /data/public/ignacio/test.am: [testng] 00:29:50,264 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:29:50,264 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:50,265 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-22_00-29-50.log] [testng] 00:29:50,265 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10f4640b - End of configuration. [testng] [2024-11-22 00:29:50,748] [pool-1-thread-6] Initializing /data/jeremy/Hiv_spikes.am: [testng] 00:29:50,748 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:29:50,748 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:50,749 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-22_00-29-50.log] [testng] 00:29:50,749 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6ca9b5d4 - End of configuration. [testng] [2024-11-22 00:29:51,228] [pool-1-thread-5] Initializing /data/public/imagesc-50585/BF_CheckMIB.am: [testng] 00:29:51,228 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:29:51,228 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:51,229 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-22_00-29-51.log] [testng] 00:29:51,230 |-INFO in ch.qos.logback.core.sift.SiftProcessor@74d7db63 - End of configuration. [testng] [2024-11-22 00:29:51,720] [pool-1-thread-4] Initializing /data/samples/emptykey/test.am: [testng] 00:29:51,721 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:29:51,721 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:51,722 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-22_00-29-51.log] [testng] 00:29:51,722 |-INFO in ch.qos.logback.core.sift.SiftProcessor@542f888a - End of configuration. [testng] [2024-11-22 00:29:52,205] [pool-1-thread-3] Initializing /data/public/imagesc-50585/BF_CheckAmira.am: [testng] 00:29:52,205 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:29:52,205 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:52,206 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-22_00-29-52.log] [testng] 00:29:52,206 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f500507 - End of configuration. [testng] [2024-11-22 00:29:52,700] [pool-1-thread-2] Initializing /data/johannes/template.grey: [testng] 00:29:52,700 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:29:52,700 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:52,701 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-22_00-29-52.log] [testng] 00:29:52,701 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f63b4d1 - End of configuration. [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 636, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 32 seconds Finished: SUCCESS