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Started by upstream project "BIOFORMATS-test-repo" build number 273 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9 [BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins7053211045476082132.sh + '[' minc = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_43031_merge_ci -v /uod/idr/repos/curated/minc:/data -v /uod/idr-scratch/merge-ci/curated/minc:/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] 08:22:04,190 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 08:22:04,192 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 08:22:04,192 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 08:22:04,193 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 08:22:04,193 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 08:22:04,193 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 08:22:04,194 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 08:22:04,194 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 08:22:04,194 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 08:22:04,194 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 08:22:04,195 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 08:22:04,195 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 08:22:04,433 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 08:22:04,433 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 08:22:04,463 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 08:22:04,463 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 08:22:04,472 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 08:22:04,473 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 08:22:04,473 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 08:22:04,473 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 08:22:04,473 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 08:22:04,474 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 08:22:04,474 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 280 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-29 08:22:04,485] [main] java.version = 1.8.0_342 [testng] 08:22:04,489 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 08:22:04,489 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:22:04,537 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-29_08-22-04.log] [testng] 08:22:04,539 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-11-29 08:22:04,541] [main] testng.directory = /data [testng] [2024-11-29 08:22:04,542] [main] testng.configDirectory = /config [testng] [2024-11-29 08:22:04,554] [main] testng.multiplier = 1.0 [testng] [2024-11-29 08:22:04,555] [main] testng.in-memory = false [testng] [2024-11-29 08:22:04,555] [main] testng.allow-missing = false [testng] [2024-11-29 08:22:04,555] [main] user.language = en [testng] [2024-11-29 08:22:04,555] [main] user.country = ${user.country} [testng] [2024-11-29 08:22:04,555] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-11-29 08:22:05,201] [main] ---------------------------------------- [testng] [2024-11-29 08:22:05,201] [main] Total files: 15 [testng] [2024-11-29 08:22:05,201] [main] Scan time: 0.646 s (43 ms/file) [testng] [2024-11-29 08:22:05,201] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 15 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-29 08:22:19,146] [pool-1-thread-1] Initializing /data/bigbrain/full16_400um_2009b_sym.mnc: [testng] 08:22:19,147 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 08:22:19,147 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:22:19,149 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-29_08-22-19.log] [testng] 08:22:20,212 |-INFO in ch.qos.logback.core.sift.SiftProcessor@31e95639 - End of configuration. [testng] [2024-11-29 08:22:23,152] [pool-1-thread-12] Initializing /data/samples/ICBM/icbm_template_6.00mm.mnc: [testng] 08:22:23,153 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 08:22:23,153 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:22:23,154 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-29_08-22-23.log] [testng] 08:22:23,154 |-INFO in ch.qos.logback.core.sift.SiftProcessor@132d9fd7 - End of configuration. [testng] [2024-11-29 08:22:23,634] [pool-1-thread-11] Initializing /data/daren/test_32bit_float.mnc: [testng] 08:22:23,634 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 08:22:23,635 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:22:23,635 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-29_08-22-23.log] [testng] 08:22:23,636 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3459daec - End of configuration. [testng] [2024-11-29 08:22:24,358] [pool-1-thread-10] Initializing /data/samples/ICBM/icbm_template_2.00mm.mnc: [testng] 08:22:24,358 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 08:22:24,358 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:22:24,358 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-29_08-22-24.log] [testng] 08:22:24,359 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e5cab41 - End of configuration. [testng] [2024-11-29 08:22:24,823] [pool-1-thread-9] Initializing /data/samples/ICBM/icbm_template_3.00mm.mnc: [testng] 08:22:24,823 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 08:22:24,823 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:22:24,824 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-29_08-22-24.log] [testng] 08:22:24,824 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4082eb51 - End of configuration. [testng] [2024-11-29 08:22:25,300] [pool-1-thread-8] Initializing /data/samples/ICBM/icbm_template_4.00mm.mnc: [testng] 08:22:25,300 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 08:22:25,300 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:22:25,301 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-29_08-22-25.log] [testng] 08:22:25,301 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57463cb6 - End of configuration. [testng] [2024-11-29 08:22:25,752] [pool-1-thread-7] Initializing /data/qa-17215/IBSR01.mnc: [testng] 08:22:25,752 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 08:22:25,752 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:22:25,753 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-29_08-22-25.log] [testng] 08:22:25,753 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36c39a5 - End of configuration. [testng] [2024-11-29 08:22:26,305] [pool-1-thread-6] Initializing /data/bigbrain/pm6479o.mnc: [testng] 08:22:26,305 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 08:22:26,305 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:22:26,306 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-29_08-22-26.log] [testng] 08:22:26,306 |-INFO in ch.qos.logback.core.sift.SiftProcessor@24219f46 - End of configuration. [testng] [2024-11-29 08:22:27,275] [pool-1-thread-5] Initializing /data/samples/N3/average_305_mask_1mm.mnc: [testng] 08:22:27,275 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 08:22:27,275 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:22:27,276 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-29_08-22-27.log] [testng] 08:22:27,276 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5bc1ff52 - End of configuration. [testng] [2024-11-29 08:22:27,793] [pool-1-thread-4] Initializing /data/samples/ICBM/icbm_template_one.00mm.mnc: [testng] 08:22:27,793 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 08:22:27,793 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:22:27,794 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-29_08-22-27.log] [testng] 08:22:27,794 |-INFO in ch.qos.logback.core.sift.SiftProcessor@548de449 - End of configuration. [testng] [2024-11-29 08:22:28,307] [pool-1-thread-3] Initializing /data/samples/ICBM/icbm_template_zero.50mm.mnc: [testng] 08:22:28,307 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 08:22:28,307 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:22:28,308 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-29_08-22-28.log] [testng] 08:22:28,308 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3331067e - End of configuration. [testng] [2024-11-29 08:22:28,867] [pool-1-thread-2] Initializing /data/bigbrain/8-bit_full_400um_2009b_sym.mnc: [testng] 08:22:28,867 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 08:22:28,867 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:22:28,868 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-29_08-22-28.log] [testng] 08:22:28,868 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f427e93 - End of configuration. BUILD SUCCESSFUL Total time: 51 seconds Finished: SUCCESS