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Started by upstream project "BIOFORMATS-test-repo" build number 6 originally caused by: Started by upstream project "Trigger" build number 9 originally caused by: Started by user devspace 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/jenkins18037543756276141278.sh + '[' minc = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_862_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] 10:14:07,061 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 10:14:07,062 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 10:14:07,062 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 10:14:07,063 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 10:14:07,063 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 10:14:07,064 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 10:14:07,064 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 10:14:07,064 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 10:14:07,065 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 10:14:07,065 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 10:14:07,065 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 10:14:07,066 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 10:14:07,235 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 10:14:07,235 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 10:14:07,259 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 10:14:07,259 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 10:14:07,265 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 10:14:07,266 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 10:14:07,266 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 10:14:07,266 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 10:14:07,266 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 10:14:07,268 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 10:14:07,268 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 203 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-20 10:14:07,278] [main] java.version = 17.0.2 [testng] 10:14:07,282 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 10:14:07,282 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:14:07,325 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-20_10-14-07.log] [testng] 10:14:07,327 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-03-20 10:14:07,329] [main] testng.directory = /data [testng] [2024-03-20 10:14:07,329] [main] testng.configDirectory = /config [testng] [2024-03-20 10:14:07,338] [main] testng.multiplier = 1.0 [testng] [2024-03-20 10:14:07,340] [main] testng.in-memory = false [testng] [2024-03-20 10:14:07,340] [main] testng.allow-missing = false [testng] [2024-03-20 10:14:07,340] [main] user.language = en [testng] [2024-03-20 10:14:07,340] [main] user.country = ${user.country} [testng] [2024-03-20 10:14:07,340] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-03-20 10:14:07,685] [main] ---------------------------------------- [testng] [2024-03-20 10:14:07,685] [main] Total files: 15 [testng] [2024-03-20 10:14:07,685] [main] Scan time: 0.344 s (22 ms/file) [testng] [2024-03-20 10:14:07,685] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 15 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-20 10:14:18,795] [pool-1-thread-1] Initializing /data/samples/ICBM/icbm_template_3.00mm.mnc: [testng] 10:14:18,796 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 10:14:18,796 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:14:18,798 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-20_10-14-18.log] [testng] 10:14:18,798 |-INFO in ch.qos.logback.core.sift.SiftProcessor@259706bb - End of configuration. [testng] [2024-03-20 10:14:18,873] [pool-1-thread-12] Initializing /data/bigbrain/8-bit_full_400um_2009b_sym.mnc: [testng] 10:14:18,873 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 10:14:18,874 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:14:18,875 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-20_10-14-18.log] [testng] 10:14:18,876 |-INFO in ch.qos.logback.core.sift.SiftProcessor@11a3343d - End of configuration. [testng] [2024-03-20 10:14:20,196] [pool-1-thread-11] Initializing /data/bigbrain/pm6479o.mnc: [testng] 10:14:20,196 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 10:14:20,196 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:14:20,197 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-20_10-14-20.log] [testng] 10:14:20,198 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b44a3e9 - End of configuration. [testng] [2024-03-20 10:14:20,877] [pool-1-thread-10] Initializing /data/samples/ICBM/icbm_template_2.00mm.mnc: [testng] 10:14:20,877 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 10:14:20,877 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:14:20,878 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-20_10-14-20.log] [testng] 10:14:20,878 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76bd241b - End of configuration. [testng] [2024-03-20 10:14:20,896] [pool-1-thread-9] Initializing /data/qa-17215/IBSR01.mnc: [testng] 10:14:20,897 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 10:14:20,897 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:14:20,897 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-20_10-14-20.log] [testng] 10:14:20,898 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a6be85 - End of configuration. [testng] [2024-03-20 10:14:21,005] [pool-1-thread-8] Initializing /data/samples/ICBM/icbm_template_4.00mm.mnc: [testng] 10:14:21,005 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 10:14:21,006 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:14:21,007 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-20_10-14-21.log] [testng] 10:14:21,007 |-INFO in ch.qos.logback.core.sift.SiftProcessor@fc2f8c2 - End of configuration. [testng] [2024-03-20 10:14:21,045] [pool-1-thread-7] Initializing /data/daren/test_32bit_float.mnc: [testng] 10:14:21,045 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 10:14:21,045 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:14:21,046 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-20_10-14-21.log] [testng] 10:14:21,046 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65d7a796 - End of configuration. [testng] [2024-03-20 10:14:21,495] [pool-1-thread-6] Initializing /data/samples/ICBM/icbm_atlas_cerebellum_avg_53_mask_1mm.mnc: [testng] 10:14:21,496 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 10:14:21,496 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:14:21,496 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-20_10-14-21.log] [testng] 10:14:21,497 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5218025e - End of configuration. [testng] [2024-03-20 10:14:21,587] [pool-1-thread-5] Initializing /data/samples/ICBM/icbm_template_zero.75mm.mnc: [testng] 10:14:21,588 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 10:14:21,588 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:14:21,589 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-20_10-14-21.log] [testng] 10:14:21,589 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e1c5816 - End of configuration. [testng] [2024-03-20 10:14:21,778] [pool-1-thread-4] Initializing /data/samples/N3/average_305_mask_1mm.mnc: [testng] 10:14:21,778 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 10:14:21,778 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:14:21,779 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-20_10-14-21.log] [testng] 10:14:21,779 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3387ac91 - End of configuration. [testng] [2024-03-20 10:14:21,890] [pool-1-thread-3] Initializing /data/samples/ICBM/icbm_template_one.50mm.mnc: [testng] 10:14:21,891 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 10:14:21,891 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:14:21,891 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-20_10-14-21.log] [testng] 10:14:21,892 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e18c715 - End of configuration. [testng] [2024-03-20 10:14:21,952] [pool-1-thread-2] Initializing /data/samples/ICBM/icbm_template_6.00mm.mnc: [testng] 10:14:21,953 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 10:14:21,953 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:14:21,954 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-20_10-14-21.log] [testng] 10:14:21,955 |-INFO in ch.qos.logback.core.sift.SiftProcessor@254710c7 - End of configuration. BUILD SUCCESSFUL Total time: 38 seconds Finished: SUCCESS