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Started by upstream project "BIOFORMATS-test-repo" build number 364 originally caused by: Started by upstream project "Trigger" build number 390 originally caused by: Started by timer 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/jenkins8618872900987855081.sh + '[' bruker = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_58098_merge_ci -v /uod/idr/repos/curated/bruker:/data -v /uod/idr-scratch/merge-ci/curated/bruker:/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] 03:36:18,054 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 03:36:18,056 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - No custom configurators were discovered as a service. [testng] 03:36:18,056 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:36:18,057 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:36:18,057 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:36:18,058 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:36:18,058 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 03:36:18,058 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:36:18,058 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:36:18,059 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:36:18,059 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:36:18,060 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:36:18,217 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:36:18,217 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:36:18,238 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:36:18,238 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:36:18,243 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:36:18,243 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:36:18,243 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:36:18,244 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:36:18,244 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@65c7a252 - End of configuration. [testng] 03:36:18,244 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@38cee291 - Registering current configuration as safe fallback point [testng] 03:36:18,244 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 186 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-04 03:36:18,253] [main] java.version = 11.0.16 [testng] 03:36:18,255 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:36:18,255 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:36:18,295 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-04_03-36-18.log] [testng] 03:36:18,296 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13d73f29 - End of configuration. [testng] [2025-03-04 03:36:18,298] [main] testng.directory = /data [testng] [2025-03-04 03:36:18,298] [main] testng.configDirectory = /config [testng] [2025-03-04 03:36:18,307] [main] testng.multiplier = 1.0 [testng] [2025-03-04 03:36:18,309] [main] testng.in-memory = false [testng] [2025-03-04 03:36:18,309] [main] testng.allow-missing = false [testng] [2025-03-04 03:36:18,309] [main] user.language = en [testng] [2025-03-04 03:36:18,309] [main] user.country = ${user.country} [testng] [2025-03-04 03:36:18,309] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-03-04 03:49:26,000] [main] ---------------------------------------- [testng] [2025-03-04 03:49:26,001] [main] Total files: 826 [testng] [2025-03-04 03:49:26,001] [main] Scan time: 787.691 s (953 ms/file) [testng] [2025-03-04 03:49:26,001] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-04 03:50:35,985] [pool-1-thread-1] Initializing /data/wis/tiffs/RAf_100110_091_Scan7_Slice9_TR6.tif: [testng] 03:50:35,986 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:50:35,986 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:50:35,988 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-04_03-50-35.log] [testng] 03:50:35,988 |-INFO in ch.qos.logback.core.sift.SiftProcessor@39d0275 - End of configuration. [testng] [2025-03-04 03:50:37,624] [pool-1-thread-12] Initializing /data/wis/tiffs/hd111104p3_sH3_scan3_slice1_echo6.tif: [testng] 03:50:37,624 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:50:37,624 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:50:37,626 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-04_03-50-37.log] [testng] 03:50:37,626 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4353f70d - End of configuration. [testng] [2025-03-04 03:50:39,518] [pool-1-thread-11] Initializing /data/wis/tiffs/RAf_100110_091_Scan8_Slice9_diff15.tif: [testng] 03:50:39,518 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:50:39,518 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:50:39,519 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-04_03-50-39.log] [testng] 03:50:39,520 |-INFO in ch.qos.logback.core.sift.SiftProcessor@223b1703 - End of configuration. [testng] [2025-03-04 03:50:41,409] [pool-1-thread-10] Initializing /data/wis/tiffs/hd111104p3_sH3_scan3_slice1_echo1.tif: [testng] 03:50:41,409 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:50:41,409 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:50:41,410 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-04_03-50-41.log] [testng] 03:50:41,410 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38105904 - End of configuration. [testng] [2025-03-04 03:50:43,369] [pool-1-thread-9] Initializing /data/wis/RA_240912_m1.g71/1/acqp: [testng] 03:50:43,369 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:50:43,369 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:50:43,371 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-04_03-50-43.log] [testng] 03:50:43,372 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2bd173f7 - End of configuration. [testng] [2025-03-04 03:50:49,345] [pool-1-thread-8] Initializing /data/wis/tiffs/RA_060110_051_scan6_slice5.tif: [testng] 03:50:49,346 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:50:49,346 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:50:49,346 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-04_03-50-49.log] [testng] 03:50:49,347 |-INFO in ch.qos.logback.core.sift.SiftProcessor@485d9073 - End of configuration. [testng] [2025-03-04 03:50:51,249] [pool-1-thread-7] Initializing /data/wis/tiffs/RA_060110_051_scan2_slice6.tif: [testng] 03:50:51,249 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:50:51,249 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:50:51,249 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-04_03-50-51.log] [testng] 03:50:51,250 |-INFO in ch.qos.logback.core.sift.SiftProcessor@74d0f717 - End of configuration. [testng] [2025-03-04 03:50:53,117] [pool-1-thread-6] Initializing /data/wis/tiffs/hd111104p3_sH3_scan2_slice3.tif: [testng] 03:50:53,118 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:50:53,118 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:50:53,119 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-04_03-50-53.log] [testng] 03:50:53,119 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a25bbab - End of configuration. [testng] [2025-03-04 03:50:54,966] [pool-1-thread-5] Initializing /data/samples/dimension-mismatch/1/acqp: [testng] 03:50:54,966 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:50:54,966 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:50:54,966 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-04_03-50-54.log] [testng] 03:50:54,967 |-INFO in ch.qos.logback.core.sift.SiftProcessor@53cfc3d1 - End of configuration. [testng] [2025-03-04 03:50:56,997] [pool-1-thread-4] Initializing /data/wis/tiffs/RAf_100110_091_Scan3_Slice5.tif: [testng] 03:50:56,997 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:50:56,997 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:50:56,997 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-04_03-50-56.log] [testng] 03:50:56,998 |-INFO in ch.qos.logback.core.sift.SiftProcessor@30dc634 - End of configuration. [testng] [2025-03-04 03:50:58,847] [pool-1-thread-3] Initializing /data/wis/tiffs/RA_060110_051_scan1_slice1.tif: [testng] 03:50:58,848 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:50:58,848 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:50:58,848 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-04_03-50-58.log] [testng] 03:50:58,849 |-INFO in ch.qos.logback.core.sift.SiftProcessor@fedb565 - End of configuration. [testng] [2025-03-04 03:51:00,628] [pool-1-thread-2] Initializing /data/wis/tiffs/hd111104p3_sH3_scan1_slice1.tif: [testng] 03:51:00,628 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:51:00,628 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:51:00,629 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-04_03-51-00.log] [testng] 03:51:00,629 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e21092d - End of configuration. [testng] [2025-03-04 03:51:17,726] [pool-1-thread-1] Initializing /data/wis/tiffs/RAf_100110_091_Scan6_Slice5_echo1.tif: [testng] [2025-03-04 03:51:19,563] [pool-1-thread-7] Initializing /data/wis/tiffs/RA_060110_051_scan1_slice3.tif: [testng] [2025-03-04 03:51:21,336] [pool-1-thread-4] Initializing /data/wis/tiffs/hd111104p3_sH3_scan2_slice1.tif: [testng] [2025-03-04 03:51:23,098] [pool-1-thread-8] Initializing /data/wis/tiffs/hd111104p3_sH3_scan5_slice1.tif: [testng] [2025-03-04 03:51:24,882] [pool-1-thread-11] Initializing /data/wis/RA_060110.051/1/acqp: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 901, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 31 minutes 42 seconds Finished: SUCCESS