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Started by upstream project "BIOFORMATS-test-repo" build number 191 originally caused by: Started by upstream project "Trigger" build number 213 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/jenkins10097355429878414168.sh + '[' imaris = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_30273_merge_ci -v /uod/idr/repos/curated/imaris:/data -v /uod/idr-scratch/merge-ci/curated/imaris:/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] 02:27:03,330 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:27:03,333 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 02:27:03,333 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:27:03,334 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:27:03,335 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:27:03,335 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:27:03,336 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:27:03,336 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:27:03,336 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:27:03,337 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:27:03,338 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:27:03,338 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:27:03,524 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:27:03,525 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:27:03,548 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:27:03,549 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:27:03,554 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:27:03,554 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:27:03,554 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:27:03,555 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:27:03,555 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 02:27:03,556 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 02:27:03,557 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 220 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-09-17 02:27:03,566] [main] java.version = 11.0.16 [testng] 02:27:03,569 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:27:03,569 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:03,612 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-17_02-27-03.log] [testng] 02:27:03,613 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-09-17 02:27:03,616] [main] testng.directory = /data [testng] [2024-09-17 02:27:03,616] [main] testng.configDirectory = /config [testng] [2024-09-17 02:27:03,626] [main] testng.multiplier = 1.0 [testng] [2024-09-17 02:27:03,627] [main] testng.in-memory = false [testng] [2024-09-17 02:27:03,627] [main] testng.allow-missing = false [testng] [2024-09-17 02:27:03,627] [main] user.language = en [testng] [2024-09-17 02:27:03,627] [main] user.country = ${user.country} [testng] [2024-09-17 02:27:03,627] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-09-17 02:27:19,322] [main] ---------------------------------------- [testng] [2024-09-17 02:27:19,322] [main] Total files: 68 [testng] [2024-09-17 02:27:19,322] [main] Scan time: 15.695 s (230 ms/file) [testng] [2024-09-17 02:27:19,323] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 60 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-09-17 02:27:53,381] [pool-1-thread-1] Initializing /data/gh-4193/24-5-9_RSV+AfumMscar+CFW_40x Stack_deconvolved.ims: [testng] 02:27:53,382 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:27:53,382 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:53,384 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-09-17_02-27-53.log] [testng] 02:27:53,385 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d5c22c8 - End of configuration. [testng] [2024-09-17 02:27:53,519] [pool-1-thread-12] Initializing /data/jason/imaris_5_5_demoimages/retina.ims: [testng] 02:27:53,519 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:27:53,519 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:53,524 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-09-17_02-27-53.log] [testng] 02:27:53,524 |-INFO in ch.qos.logback.core.sift.SiftProcessor@485decd1 - End of configuration. [testng] [2024-09-17 02:27:53,597] [pool-1-thread-11] Initializing /data/public/davemason/Convallaria_3C_10T_confocal_IMS3.ims: [testng] 02:27:53,597 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:27:53,597 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:53,598 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-09-17_02-27-53.log] [testng] 02:27:53,598 |-INFO in ch.qos.logback.core.sift.SiftProcessor@548496a5 - End of configuration. [testng] [2024-09-17 02:27:53,812] [pool-1-thread-10] Initializing /data/generated/10-31_E_t0001.ims: [testng] 02:27:53,812 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:27:53,812 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:53,813 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-09-17_02-27-53.log] [testng] 02:27:53,813 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7253a6a1 - End of configuration. [testng] [2024-09-17 02:27:53,844] [pool-1-thread-9] Initializing /data/generated/10-31_E_t0015.ims: [testng] 02:27:53,844 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:27:53,844 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:53,844 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-09-17_02-27-53.log] [testng] 02:27:53,845 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ca20aa8 - End of configuration. [testng] [2024-09-17 02:27:53,869] [pool-1-thread-8] Initializing /data/generated/10-31_E_t0007.ims: [testng] 02:27:53,869 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:27:53,869 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:53,869 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-09-17_02-27-53.log] [testng] 02:27:53,870 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e715bec - End of configuration. [testng] [2024-09-17 02:27:53,902] [pool-1-thread-7] Initializing /data/generated/10-31_E_t0012.ims: [testng] 02:27:53,903 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:27:53,903 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:53,904 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-09-17_02-27-53.log] [testng] 02:27:53,904 |-INFO in ch.qos.logback.core.sift.SiftProcessor@23ac65bc - End of configuration. [testng] [2024-09-17 02:27:53,935] [pool-1-thread-6] Initializing /data/generated/10-31_E_t0000.ims: [testng] 02:27:53,935 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:27:53,935 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:53,935 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-09-17_02-27-53.log] [testng] 02:27:53,936 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ce32a39 - End of configuration. [testng] [2024-09-17 02:27:53,962] [pool-1-thread-5] Initializing /data/public/davemason/TransFactors_2C_34Z_SRRF_IMS3.ims: [testng] 02:27:53,962 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:27:53,962 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:53,963 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-09-17_02-27-53.log] [testng] 02:27:53,963 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65c478e6 - End of configuration. [testng] [2024-09-17 02:27:54,013] [pool-1-thread-4] Initializing /data/jason/imaris_5_5_demoimages/R18Demo.ims: [testng] 02:27:54,014 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:27:54,014 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:54,014 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-09-17_02-27-54.log] [testng] 02:27:54,015 |-INFO in ch.qos.logback.core.sift.SiftProcessor@355e645c - End of configuration. [testng] [2024-09-17 02:27:54,175] [pool-1-thread-3] Initializing /data/generated/10-31_E_t0003.ims: [testng] 02:27:54,175 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:27:54,176 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:54,176 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-09-17_02-27-54.log] [testng] 02:27:54,177 |-INFO in ch.qos.logback.core.sift.SiftProcessor@437e41ef - End of configuration. [testng] [2024-09-17 02:27:54,211] [pool-1-thread-2] Initializing /data/public/davemason/TransFactors_2C_SRRF.ims: [testng] 02:27:54,212 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:27:54,212 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:27:54,213 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-09-17_02-27-54.log] [testng] 02:27:54,213 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7006ced1 - End of configuration. [testng] [2024-09-17 02:27:56,781] [pool-1-thread-10] Initializing /data/jake/p75Cherry M2 010-3~B.ims: [testng] [2024-09-17 02:27:56,812] [pool-1-thread-6] Initializing /data/public/davemason/Convallaria_3C_1T_confocal.ims: [testng] [2024-09-17 02:27:56,840] [pool-1-thread-8] Initializing /data/generated/10-31_E_t0005.ims: [testng] [2024-09-17 02:27:56,889] [pool-1-thread-9] Initializing /data/qa-4898/o383_1_457_CS_r1.ims: [testng] [2024-09-17 02:27:56,931] [pool-1-thread-3] Initializing /data/qa-8019/wrong_num_dimensions.ims: [testng] [2024-09-17 02:27:57,031] [pool-1-thread-7] Initializing /data/generated/10-31_E_t0004.ims: [testng] [2024-09-17 02:27:57,142] [pool-1-thread-4] Initializing /data/qa-17522/2016-12-14_08.43.34_Sample Prefix_WAINWRIGHT James_Protocol.ims: [testng] [2024-09-17 02:28:03,486] [pool-1-thread-12] Initializing /data/oliver/Stack2_float32Bit.ims: [testng] [2024-09-17 02:28:04,130] [pool-1-thread-7] Initializing /data/chris/supMovie3.ims: [testng] [2024-09-17 02:28:06,585] [pool-1-thread-3] Initializing /data/oliver/Stack2_8Bit.ims: [testng] [2024-09-17 02:28:06,934] [pool-1-thread-1] Initializing /data/public/davemason/TransFactors_2C_34Z_SRRF.ims: BUILD SUCCESSFUL Total time: 2 minutes 59 seconds Finished: SUCCESS