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Started by upstream project "BIOFORMATS-test-repo" build number 238 originally caused by: Started by upstream project "Trigger" build number 263 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8 [BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins11702978132573770018.sh + '[' analyze = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_37461_merge_ci -v /uod/idr/repos/curated/analyze:/data -v /uod/idr-scratch/merge-ci/curated/analyze:/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] 02:39:54,898 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:39:54,899 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 02:39:54,899 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:39:54,900 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:39:54,901 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:39:54,901 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:39:54,902 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:39:54,902 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:39:54,902 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:39:54,903 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:39:54,903 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:39:54,903 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:39:55,115 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:39:55,115 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:39:55,147 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:39:55,147 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:39:55,154 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:39:55,154 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:39:55,154 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:39:55,155 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:39:55,155 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 02:39:55,155 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 02:39:55,155 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 253 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-29 02:39:55,164] [main] java.version = 11.0.16 [testng] 02:39:55,169 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:39:55,169 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:39:55,235 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-29_02-39-55.log] [testng] 02:39:55,238 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-10-29 02:39:55,241] [main] testng.directory = /data [testng] [2024-10-29 02:39:55,241] [main] testng.configDirectory = /config [testng] [2024-10-29 02:39:55,256] [main] testng.multiplier = 1.0 [testng] [2024-10-29 02:39:55,258] [main] testng.in-memory = false [testng] [2024-10-29 02:39:55,258] [main] testng.allow-missing = false [testng] [2024-10-29 02:39:55,258] [main] user.language = en [testng] [2024-10-29 02:39:55,259] [main] user.country = ${user.country} [testng] [2024-10-29 02:39:55,259] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-29 02:39:57,868] [main] ---------------------------------------- [testng] [2024-10-29 02:39:57,868] [main] Total files: 21 [testng] [2024-10-29 02:39:57,868] [main] Scan time: 2.609 s (124 ms/file) [testng] [2024-10-29 02:39:57,868] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 21 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-29 02:40:01,277] [pool-1-thread-1] Initializing /data/frans/brodmann.hdr: [testng] 02:40:01,278 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:40:01,279 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:01,281 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-29_02-40-01.log] [testng] 02:40:01,281 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13ec7cdf - End of configuration. [testng] [2024-10-29 02:40:01,425] [pool-1-thread-12] Initializing /data/frans/MR_SEGBRAIN.hdr: [testng] 02:40:01,425 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:40:01,425 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:01,426 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-29_02-40-01.log] [testng] 02:40:01,427 |-INFO in ch.qos.logback.core.sift.SiftProcessor@15f3f75a - End of configuration. [testng] [2024-10-29 02:40:01,499] [pool-1-thread-11] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1.img.hdr: [testng] 02:40:01,499 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:40:01,499 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:01,500 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-29_02-40-01.log] [testng] 02:40:01,500 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1159b04 - End of configuration. [testng] [2024-10-29 02:40:01,583] [pool-1-thread-10] Initializing /data/frans/CT_WHOLE.hdr: [testng] 02:40:01,583 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:40:01,583 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:01,583 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-29_02-40-01.log] [testng] 02:40:01,584 |-INFO in ch.qos.logback.core.sift.SiftProcessor@25329239 - End of configuration. [testng] [2024-10-29 02:40:01,689] [pool-1-thread-9] Initializing /data/frans/betmask.hdr: [testng] 02:40:01,689 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:40:01,689 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:01,690 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-29_02-40-01.log] [testng] 02:40:01,690 |-INFO in ch.qos.logback.core.sift.SiftProcessor@349d5edb - End of configuration. [testng] [2024-10-29 02:40:01,795] [pool-1-thread-8] Initializing /data/frans/Test Files for Frans/PLA-zm2-16mm_1002_MF_V1.hdr: [testng] 02:40:01,796 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:40:01,796 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:01,796 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-29_02-40-01.log] [testng] 02:40:01,797 |-INFO in ch.qos.logback.core.sift.SiftProcessor@cad97c2 - End of configuration. [testng] [2024-10-29 02:40:01,889] [pool-1-thread-7] Initializing /data/frans/CT_HAND.hdr: [testng] 02:40:01,889 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:40:01,889 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:01,890 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-29_02-40-01.log] [testng] 02:40:01,890 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2487ef64 - End of configuration. [testng] [2024-10-29 02:40:01,975] [pool-1-thread-6] Initializing /data/frans/CT_FOOT.hdr: [testng] 02:40:01,975 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:40:01,975 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:01,976 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-29_02-40-01.log] [testng] 02:40:01,976 |-INFO in ch.qos.logback.core.sift.SiftProcessor@41f780db - End of configuration. [testng] [2024-10-29 02:40:02,071] [pool-1-thread-5] Initializing /data/frans/CT_APERT.hdr: [testng] 02:40:02,071 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:40:02,071 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:02,072 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-29_02-40-02.log] [testng] 02:40:02,072 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6bfbaf45 - End of configuration. [testng] [2024-10-29 02:40:02,184] [pool-1-thread-4] Initializing /data/frans/MR_CHEST.hdr: [testng] 02:40:02,184 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:40:02,184 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:02,185 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-29_02-40-02.log] [testng] 02:40:02,185 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21c48d20 - End of configuration. [testng] [2024-10-29 02:40:02,276] [pool-1-thread-3] Initializing /data/frans/aal.hdr: [testng] 02:40:02,276 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:40:02,276 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:02,277 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-29_02-40-02.log] [testng] 02:40:02,277 |-INFO in ch.qos.logback.core.sift.SiftProcessor@319c2aaf - End of configuration. [testng] [2024-10-29 02:40:02,355] [pool-1-thread-2] Initializing /data/frans/Test Files for Frans/1002-sag-transform-box-est_flip-ord.hdr: [testng] 02:40:02,355 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:40:02,355 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:02,355 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-29_02-40-02.log] [testng] 02:40:02,356 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3605d598 - End of configuration. [testng] [2024-10-29 02:40:05,911] [pool-1-thread-9] Initializing /data/frans/Test Files for Frans/F005_1002_MF_SCAN1_stat_brain_fdg_JJ_Volume_Corrected.hdr: [testng] [2024-10-29 02:40:06,005] [pool-1-thread-4] Initializing /data/frans/CT_CRANI.hdr: [testng] [2024-10-29 02:40:06,104] [pool-1-thread-5] Initializing /data/frans/Test Files for Frans/200-PLA_sansBD_spmT_0005.hdr: [testng] [2024-10-29 02:40:06,191] [pool-1-thread-8] Initializing /data/frans/CT_CHEST.hdr: [testng] [2024-10-29 02:40:06,266] [pool-1-thread-11] Initializing /data/frans/m000-MR_CHEST.gif: [testng] [2024-10-29 02:40:06,540] [pool-1-thread-10] Initializing /data/frans/CT_KNEE.hdr: [testng] [2024-10-29 02:40:06,754] [pool-1-thread-7] Initializing /data/frans/ch2bet.hdr: [testng] [2024-10-29 02:40:06,928] [pool-1-thread-2] Initializing /data/frans/ch2.hdr: [testng] [2024-10-29 02:40:07,031] [pool-1-thread-12] Initializing /data/frans/Test Files for Frans/06-101-mask-40pc2dil.hdr: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1113, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 17 seconds Finished: SUCCESS