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Started by upstream project "BIOFORMATS-test-repo" build number 225 originally caused by: Started by user devspace 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/jenkins1554956435633812061.sh + '[' minc = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_35503_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 15:15:46,978 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 15:15:46,979 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 15:15:46,980 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 15:15:46,980 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 15:15:46,981 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 15:15:46,981 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 15:15:46,981 |-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] 15:15:46,981 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 15:15:46,982 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 15:15:46,982 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 15:15:46,983 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 15:15:46,983 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 15:15:47,131 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 15:15:47,131 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 15:15:47,155 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 15:15:47,155 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 15:15:47,161 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 15:15:47,161 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 15:15:47,161 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 15:15:47,161 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 15:15:47,161 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 15:15:47,162 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 15:15:47,162 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 180 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-17 15:15:47,171] [main] java.version = 21 [testng] 15:15:47,174 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 15:15:47,174 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:15:47,213 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-17_15-15-47.log] [testng] 15:15:47,214 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-10-17 15:15:47,215] [main] testng.directory = /data [testng] [2024-10-17 15:15:47,216] [main] testng.configDirectory = /config [testng] [2024-10-17 15:15:47,224] [main] testng.multiplier = 1.0 [testng] [2024-10-17 15:15:47,224] [main] testng.in-memory = false [testng] [2024-10-17 15:15:47,224] [main] testng.allow-missing = false [testng] [2024-10-17 15:15:47,224] [main] user.language = en [testng] [2024-10-17 15:15:47,224] [main] user.country = ${user.country} [testng] [2024-10-17 15:15:47,224] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-17 15:15:47,854] [main] ---------------------------------------- [testng] [2024-10-17 15:15:47,855] [main] Total files: 15 [testng] [2024-10-17 15:15:47,855] [main] Scan time: 0.629 s (41 ms/file) [testng] [2024-10-17 15:15:47,855] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 15 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-17 15:16:39,040] [pool-1-thread-1] Initializing /data/samples/ICBM/icbm_template_zero.75mm.mnc: [testng] 15:16:39,040 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 15:16:39,041 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:16:39,042 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-17_15-16-39.log] [testng] 15:16:39,042 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3af916c0 - End of configuration. [testng] [2024-10-17 15:16:41,463] [pool-1-thread-12] Initializing /data/samples/ICBM/icbm_atlas_cerebellum_avg_53_mask_1mm.mnc: [testng] 15:16:41,464 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 15:16:41,464 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:16:41,465 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-17_15-16-41.log] [testng] 15:16:41,465 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f9630d6 - End of configuration. [testng] [2024-10-17 15:16:44,148] [pool-1-thread-11] Initializing /data/samples/ICBM/icbm_template_zero.50mm.mnc: [testng] 15:16:44,148 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 15:16:44,148 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:16:44,149 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-17_15-16-44.log] [testng] 15:16:44,150 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7bb840f1 - End of configuration. [testng] [2024-10-17 15:16:46,824] [pool-1-thread-10] Initializing /data/samples/ICBM/icbm_template_3.00mm.mnc: [testng] 15:16:46,825 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 15:16:46,825 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:16:46,825 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-17_15-16-46.log] [testng] 15:16:46,826 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6cb40df3 - End of configuration. [testng] [2024-10-17 15:16:48,696] [pool-1-thread-9] Initializing /data/samples/ICBM/icbm_template_6.00mm.mnc: [testng] 15:16:48,696 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 15:16:48,696 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:16:48,697 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-17_15-16-48.log] [testng] 15:16:48,697 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9377794 - End of configuration. [testng] [2024-10-17 15:16:51,271] [pool-1-thread-8] Initializing /data/bigbrain/full16_400um_2009b_sym.mnc: [testng] 15:16:51,272 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 15:16:51,272 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:16:51,272 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-17_15-16-51.log] [testng] 15:16:51,273 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6ac7d5fa - End of configuration. [testng] [2024-10-17 15:16:56,053] [pool-1-thread-7] Initializing /data/qa-17215/IBSR01.mnc: [testng] 15:16:56,053 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 15:16:56,053 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:16:56,054 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-17_15-16-56.log] [testng] 15:16:56,055 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ab602f6 - End of configuration. [testng] [2024-10-17 15:16:58,460] [pool-1-thread-6] Initializing /data/samples/N3/average_305_mask_1mm.mnc: [testng] 15:16:58,461 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 15:16:58,461 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:16:58,461 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-17_15-16-58.log] [testng] 15:16:58,462 |-INFO in ch.qos.logback.core.sift.SiftProcessor@461efbec - End of configuration. [testng] [2024-10-17 15:17:00,473] [pool-1-thread-5] Initializing /data/samples/ICBM/icbm_template_2.00mm.mnc: [testng] 15:17:00,473 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 15:17:00,473 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:17:00,474 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-17_15-17-00.log] [testng] 15:17:00,474 |-INFO in ch.qos.logback.core.sift.SiftProcessor@11a3343d - End of configuration. [testng] [2024-10-17 15:17:02,921] [pool-1-thread-4] Initializing /data/daren/test_32bit_float.mnc: [testng] 15:17:02,921 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 15:17:02,922 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:17:02,922 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-17_15-17-02.log] [testng] 15:17:02,922 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8f932b5 - End of configuration. [testng] [2024-10-17 15:17:06,006] [pool-1-thread-3] Initializing /data/bigbrain/pm6479o.mnc: [testng] 15:17:06,007 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 15:17:06,007 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:17:06,007 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-17_15-17-06.log] [testng] 15:17:06,008 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b344155 - End of configuration. [testng] [2024-10-17 15:17:08,931] [pool-1-thread-2] Initializing /data/bigbrain/8-bit_full_400um_2009b_sym.mnc: [testng] 15:17:08,931 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 15:17:08,931 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:17:08,932 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-17_15-17-08.log] [testng] 15:17:08,932 |-INFO in ch.qos.logback.core.sift.SiftProcessor@212ece15 - End of configuration. BUILD SUCCESSFUL Total time: 2 minutes 10 seconds Finished: SUCCESS