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Started by upstream project "BIOFORMATS-test-repo" build number 227 originally caused by: Started by upstream project "Trigger" build number 252 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins10546589227560957222.sh + '[' minc = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_35615_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] 10:39:55,556 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 10:39:55,558 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 10:39:55,558 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 10:39:55,559 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 10:39:55,559 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 10:39:55,559 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 10:39:55,559 |-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] 10:39:55,559 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 10:39:55,560 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 10:39:55,560 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 10:39:55,560 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 10:39:55,560 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 10:39:55,802 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 10:39:55,802 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 10:39:55,832 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 10:39:55,832 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 10:39:55,842 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 10:39:55,842 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 10:39:55,842 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 10:39:55,842 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 10:39:55,843 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 10:39:55,843 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 10:39:55,843 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 283 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-18 10:39:55,855] [main] java.version = 1.8.0_342 [testng] 10:39:55,859 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 10:39:55,859 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:39:55,909 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-18_10-39-55.log] [testng] 10:39:55,910 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-10-18 10:39:55,913] [main] testng.directory = /data [testng] [2024-10-18 10:39:55,913] [main] testng.configDirectory = /config [testng] [2024-10-18 10:39:55,927] [main] testng.multiplier = 1.0 [testng] [2024-10-18 10:39:55,927] [main] testng.in-memory = false [testng] [2024-10-18 10:39:55,927] [main] testng.allow-missing = false [testng] [2024-10-18 10:39:55,927] [main] user.language = en [testng] [2024-10-18 10:39:55,927] [main] user.country = ${user.country} [testng] [2024-10-18 10:39:55,928] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-10-18 10:39:56,591] [main] ---------------------------------------- [testng] [2024-10-18 10:39:56,592] [main] Total files: 15 [testng] [2024-10-18 10:39:56,592] [main] Scan time: 0.663 s (44 ms/file) [testng] [2024-10-18 10:39:56,592] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 15 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-18 10:40:06,459] [pool-1-thread-1] Initializing /data/bigbrain/full16_400um_2009b_sym.mnc: [testng] 10:40:06,460 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 10:40:06,460 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:40:06,461 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-18_10-40-06.log] [testng] 10:40:06,462 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c26e2df - End of configuration. [testng] [2024-10-18 10:40:09,414] [pool-1-thread-12] Initializing /data/samples/N3/average_305_mask_1mm.mnc: [testng] 10:40:09,414 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 10:40:09,414 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:40:09,415 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-18_10-40-09.log] [testng] 10:40:09,416 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79e171d0 - End of configuration. [testng] [2024-10-18 10:40:09,623] [pool-1-thread-11] Initializing /data/samples/ICBM/icbm_template_6.00mm.mnc: [testng] 10:40:09,623 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 10:40:09,623 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:40:09,624 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-18_10-40-09.log] [testng] 10:40:09,625 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5306bc65 - End of configuration. [testng] [2024-10-18 10:40:09,860] [pool-1-thread-10] Initializing /data/samples/ICBM/icbm_template_4.00mm.mnc: [testng] 10:40:09,860 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 10:40:09,860 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:40:09,861 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-18_10-40-09.log] [testng] 10:40:09,861 |-INFO in ch.qos.logback.core.sift.SiftProcessor@54bcd4dd - End of configuration. [testng] [2024-10-18 10:40:10,142] [pool-1-thread-9] Initializing /data/samples/ICBM/icbm_template_one.00mm.mnc: [testng] 10:40:10,142 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 10:40:10,142 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:40:10,143 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-18_10-40-10.log] [testng] 10:40:10,143 |-INFO in ch.qos.logback.core.sift.SiftProcessor@372fb842 - End of configuration. [testng] [2024-10-18 10:40:10,504] [pool-1-thread-8] Initializing /data/samples/ICBM/icbm_template_zero.75mm.mnc: [testng] 10:40:10,504 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 10:40:10,505 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:40:10,506 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-18_10-40-10.log] [testng] 10:40:10,506 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a0f1ba1 - End of configuration. [testng] [2024-10-18 10:40:10,764] [pool-1-thread-7] Initializing /data/samples/ICBM/icbm_template_zero.50mm.mnc: [testng] 10:40:10,765 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 10:40:10,765 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:40:10,766 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-18_10-40-10.log] [testng] 10:40:10,766 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34562bc - End of configuration. [testng] [2024-10-18 10:40:11,067] [pool-1-thread-6] Initializing /data/samples/ICBM/icbm_template_3.00mm.mnc: [testng] 10:40:11,067 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 10:40:11,067 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:40:11,068 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-18_10-40-11.log] [testng] 10:40:11,068 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c03c559 - End of configuration. [testng] [2024-10-18 10:40:11,267] [pool-1-thread-5] Initializing /data/samples/ICBM/icbm_template_one.50mm.mnc: [testng] 10:40:11,267 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 10:40:11,267 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:40:11,268 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-18_10-40-11.log] [testng] 10:40:11,268 |-INFO in ch.qos.logback.core.sift.SiftProcessor@161151fa - End of configuration. [testng] [2024-10-18 10:40:11,537] [pool-1-thread-4] Initializing /data/samples/ICBM/icbm_template_2.00mm.mnc: [testng] 10:40:11,537 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 10:40:11,537 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:40:11,538 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-18_10-40-11.log] [testng] 10:40:11,538 |-INFO in ch.qos.logback.core.sift.SiftProcessor@b2ef788 - End of configuration. [testng] [2024-10-18 10:40:11,798] [pool-1-thread-3] Initializing /data/qa-17215/IBSR01.mnc: [testng] 10:40:11,799 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 10:40:11,799 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:40:11,800 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-18_10-40-11.log] [testng] 10:40:11,800 |-INFO in ch.qos.logback.core.sift.SiftProcessor@385af1b9 - End of configuration. [testng] [2024-10-18 10:40:12,137] [pool-1-thread-2] Initializing /data/samples/ICBM/icbm_atlas_cerebellum_avg_53_mask_1mm.mnc: [testng] 10:40:12,138 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 10:40:12,138 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:40:12,138 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-18_10-40-12.log] [testng] 10:40:12,139 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43995c41 - End of configuration. BUILD SUCCESSFUL Total time: 41 seconds Finished: SUCCESS