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Started by upstream project "BIOFORMATS-test-repo" build number 236 originally caused by: Started by upstream project "Trigger" build number 261 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins15670417279581599057.sh + '[' minc = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_37092_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 [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] 01:32:22,497 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:32:22,499 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 01:32:22,499 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:32:22,500 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:32:22,500 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:32:22,500 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:32:22,501 |-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] 01:32:22,501 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:32:22,501 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:32:22,502 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:32:22,502 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:32:22,502 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:32:22,671 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:32:22,671 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:32:22,693 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:32:22,693 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:32:22,699 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:32:22,699 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:32:22,699 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:32:22,700 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:32:22,700 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 01:32:22,701 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 01:32:22,701 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 200 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-27 01:32:22,710] [main] java.version = 17.0.2 [testng] 01:32:22,713 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:32:22,713 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:32:22,753 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-27_01-32-22.log] [testng] 01:32:22,755 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-10-27 01:32:22,757] [main] testng.directory = /data [testng] [2024-10-27 01:32:22,757] [main] testng.configDirectory = /config [testng] [2024-10-27 01:32:22,766] [main] testng.multiplier = 1.0 [testng] [2024-10-27 01:32:22,767] [main] testng.in-memory = false [testng] [2024-10-27 01:32:22,767] [main] testng.allow-missing = false [testng] [2024-10-27 01:32:22,767] [main] user.language = en [testng] [2024-10-27 01:32:22,767] [main] user.country = ${user.country} [testng] [2024-10-27 01:32:22,767] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-27 01:32:23,708] [main] ---------------------------------------- [testng] [2024-10-27 01:32:23,708] [main] Total files: 15 [testng] [2024-10-27 01:32:23,708] [main] Scan time: 0.941 s (62 ms/file) [testng] [2024-10-27 01:32:23,708] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 15 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-27 01:32:38,068] [pool-1-thread-1] Initializing /data/samples/ICBM/icbm_template_2.00mm.mnc: [testng] 01:32:38,069 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:32:38,069 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:32:38,070 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-27_01-32-38.log] [testng] 01:32:38,071 |-INFO in ch.qos.logback.core.sift.SiftProcessor@61aa20b3 - End of configuration. [testng] [2024-10-27 01:32:38,362] [pool-1-thread-12] Initializing /data/bigbrain/8-bit_full_400um_2009b_sym.mnc: [testng] 01:32:38,363 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:32:38,363 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:32:38,363 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-27_01-32-38.log] [testng] 01:32:38,364 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14c16d0f - End of configuration. [testng] [2024-10-27 01:32:39,767] [pool-1-thread-11] Initializing /data/qa-17215/IBSR01.mnc: [testng] 01:32:39,768 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:32:39,768 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:32:39,768 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-27_01-32-39.log] [testng] 01:32:39,769 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f4a2f18 - End of configuration. [testng] [2024-10-27 01:32:40,237] [pool-1-thread-10] Initializing /data/samples/ICBM/icbm_template_4.00mm.mnc: [testng] 01:32:40,238 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:32:40,238 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:32:40,238 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-27_01-32-40.log] [testng] 01:32:40,239 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d7a4e84 - End of configuration. [testng] [2024-10-27 01:32:40,554] [pool-1-thread-9] Initializing /data/bigbrain/pm6479o.mnc: [testng] 01:32:40,554 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:32:40,554 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:32:40,555 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-27_01-32-40.log] [testng] 01:32:40,555 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f0908 - End of configuration. [testng] [2024-10-27 01:32:41,734] [pool-1-thread-8] Initializing /data/samples/ICBM/icbm_template_zero.50mm.mnc: [testng] 01:32:41,735 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:32:41,735 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:32:41,735 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-27_01-32-41.log] [testng] 01:32:41,736 |-INFO in ch.qos.logback.core.sift.SiftProcessor@fb15d2e - End of configuration. [testng] [2024-10-27 01:32:42,444] [pool-1-thread-7] Initializing /data/samples/ICBM/icbm_atlas_cerebellum_avg_53_mask_1mm.mnc: [testng] 01:32:42,444 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:32:42,444 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:32:42,445 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-27_01-32-42.log] [testng] 01:32:42,445 |-INFO in ch.qos.logback.core.sift.SiftProcessor@28aaf059 - End of configuration. [testng] [2024-10-27 01:32:42,877] [pool-1-thread-6] Initializing /data/samples/ICBM/icbm_template_one.50mm.mnc: [testng] 01:32:42,877 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:32:42,877 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:32:42,878 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-27_01-32-42.log] [testng] 01:32:42,879 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2be6ed7a - End of configuration. [testng] [2024-10-27 01:32:43,256] [pool-1-thread-5] Initializing /data/samples/ICBM/icbm_template_3.00mm.mnc: [testng] 01:32:43,256 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:32:43,256 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:32:43,257 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-27_01-32-43.log] [testng] 01:32:43,257 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ae44ede - End of configuration. [testng] [2024-10-27 01:32:43,670] [pool-1-thread-4] Initializing /data/samples/N3/average_305_mask_1mm.mnc: [testng] 01:32:43,670 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:32:43,670 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:32:43,671 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-27_01-32-43.log] [testng] 01:32:43,672 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d88d6f5 - End of configuration. [testng] [2024-10-27 01:32:44,139] [pool-1-thread-3] Initializing /data/samples/ICBM/icbm_template_zero.75mm.mnc: [testng] 01:32:44,140 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:32:44,140 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:32:44,141 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-27_01-32-44.log] [testng] 01:32:44,141 |-INFO in ch.qos.logback.core.sift.SiftProcessor@15a83e5d - End of configuration. [testng] [2024-10-27 01:32:44,628] [pool-1-thread-2] Initializing /data/samples/ICBM/icbm_template_6.00mm.mnc: [testng] 01:32:44,629 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:32:44,629 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:32:44,630 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-27_01-32-44.log] [testng] 01:32:44,630 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13d0b6da - End of configuration. BUILD SUCCESSFUL Total time: 50 seconds Finished: SUCCESS