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Started by upstream project "BIOFORMATS-test-repo" build number 42 originally caused by: Started by upstream project "Trigger" build number 49 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/jenkins13851349869846723271.sh + '[' minc = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_5948_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] WARNING: An illegal reflective access operation has occurred [testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket [testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener [testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [testng] WARNING: All illegal access operations will be denied in a future release [testng] File leak detector installed [testng] 06:32:27,572 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 06:32:27,574 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 06:32:27,574 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 06:32:27,575 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 06:32:27,575 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 06:32:27,575 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 06:32:27,576 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 06:32:27,576 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 06:32:27,576 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 06:32:27,577 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 06:32:27,577 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 06:32:27,577 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 06:32:27,753 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 06:32:27,753 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 06:32:27,776 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 06:32:27,776 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 06:32:27,781 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 06:32:27,782 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 06:32:27,782 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 06:32:27,783 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 06:32:27,783 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 06:32:27,783 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 06:32:27,783 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 207 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-04-23 06:32:27,793] [main] java.version = 11.0.16 [testng] 06:32:27,796 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 06:32:27,796 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:32:27,839 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-23_06-32-27.log] [testng] 06:32:27,841 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-04-23 06:32:27,843] [main] testng.directory = /data [testng] [2024-04-23 06:32:27,844] [main] testng.configDirectory = /config [testng] [2024-04-23 06:32:27,854] [main] testng.multiplier = 1.0 [testng] [2024-04-23 06:32:27,855] [main] testng.in-memory = false [testng] [2024-04-23 06:32:27,855] [main] testng.allow-missing = false [testng] [2024-04-23 06:32:27,855] [main] user.language = en [testng] [2024-04-23 06:32:27,855] [main] user.country = ${user.country} [testng] [2024-04-23 06:32:27,856] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-04-23 06:32:28,234] [main] ---------------------------------------- [testng] [2024-04-23 06:32:28,234] [main] Total files: 15 [testng] [2024-04-23 06:32:28,235] [main] Scan time: 0.378 s (25 ms/file) [testng] [2024-04-23 06:32:28,235] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 15 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-04-23 06:32:34,848] [pool-1-thread-1] Initializing /data/samples/ICBM/icbm_template_2.00mm.mnc: [testng] 06:32:34,849 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 06:32:34,849 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:32:34,851 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-23_06-32-34.log] [testng] 06:32:34,851 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a18632a - End of configuration. [testng] [2024-04-23 06:32:34,878] [pool-1-thread-12] Initializing /data/bigbrain/full16_400um_2009b_sym.mnc: [testng] 06:32:34,878 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 06:32:34,878 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:32:34,879 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-23_06-32-34.log] [testng] 06:32:34,880 |-INFO in ch.qos.logback.core.sift.SiftProcessor@62e7b70a - End of configuration. [testng] [2024-04-23 06:32:37,840] [pool-1-thread-11] Initializing /data/samples/ICBM/icbm_template_zero.75mm.mnc: [testng] 06:32:37,841 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 06:32:37,841 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:32:37,842 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-23_06-32-37.log] [testng] 06:32:37,842 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d850f74 - End of configuration. [testng] [2024-04-23 06:32:37,960] [pool-1-thread-10] Initializing /data/samples/ICBM/icbm_template_zero.50mm.mnc: [testng] 06:32:37,961 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 06:32:37,961 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:32:37,961 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-23_06-32-37.log] [testng] 06:32:37,962 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c33773f - End of configuration. [testng] [2024-04-23 06:32:38,140] [pool-1-thread-9] Initializing /data/samples/ICBM/icbm_template_6.00mm.mnc: [testng] 06:32:38,140 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 06:32:38,140 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:32:38,141 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-23_06-32-38.log] [testng] 06:32:38,141 |-INFO in ch.qos.logback.core.sift.SiftProcessor@692ebcf7 - End of configuration. [testng] [2024-04-23 06:32:38,156] [pool-1-thread-8] Initializing /data/samples/ICBM/icbm_atlas_cerebellum_avg_53_mask_1mm.mnc: [testng] 06:32:38,157 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 06:32:38,157 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:32:38,158 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-23_06-32-38.log] [testng] 06:32:38,159 |-INFO in ch.qos.logback.core.sift.SiftProcessor@291f451c - End of configuration. [testng] [2024-04-23 06:32:38,206] [pool-1-thread-7] Initializing /data/bigbrain/pm6479o.mnc: [testng] 06:32:38,206 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 06:32:38,206 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:32:38,207 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-23_06-32-38.log] [testng] 06:32:38,207 |-INFO in ch.qos.logback.core.sift.SiftProcessor@54cf1ab2 - End of configuration. [testng] [2024-04-23 06:32:38,909] [pool-1-thread-6] Initializing /data/samples/ICBM/icbm_template_one.50mm.mnc: [testng] 06:32:38,910 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 06:32:38,910 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:32:38,910 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-23_06-32-38.log] [testng] 06:32:38,911 |-INFO in ch.qos.logback.core.sift.SiftProcessor@633b24de - End of configuration. [testng] [2024-04-23 06:32:38,927] [pool-1-thread-5] Initializing /data/samples/ICBM/icbm_template_one.00mm.mnc: [testng] 06:32:38,927 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 06:32:38,927 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:32:38,928 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-23_06-32-38.log] [testng] 06:32:38,929 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2feba277 - End of configuration. [testng] [2024-04-23 06:32:38,964] [pool-1-thread-4] Initializing /data/samples/ICBM/icbm_template_3.00mm.mnc: [testng] 06:32:38,964 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 06:32:38,964 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:32:38,965 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-23_06-32-38.log] [testng] 06:32:38,965 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32c101db - End of configuration. [testng] [2024-04-23 06:32:38,975] [pool-1-thread-3] Initializing /data/bigbrain/8-bit_full_400um_2009b_sym.mnc: [testng] 06:32:38,975 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 06:32:38,975 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:32:38,976 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-23_06-32-38.log] [testng] 06:32:38,976 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10e4b3c7 - End of configuration. [testng] [2024-04-23 06:32:40,285] [pool-1-thread-2] Initializing /data/samples/ICBM/icbm_template_4.00mm.mnc: [testng] 06:32:40,285 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 06:32:40,285 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:32:40,286 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-23_06-32-40.log] [testng] 06:32:40,286 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ad1dbbf - End of configuration. BUILD SUCCESSFUL Total time: 34 seconds Finished: SUCCESS