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Started by upstream project "BIOFORMATS-test-repo" build number 273 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins7504810509176368522.sh + '[' avi = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_43045_merge_ci -v /uod/idr/repos/curated/avi:/data -v /uod/idr-scratch/merge-ci/curated/avi:/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 test-automated: [testng] File leak detector installed [testng] 08:41:55,030 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 08:41:55,031 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 08:41:55,031 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 08:41:55,032 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 08:41:55,033 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 08:41:55,033 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 08:41:55,033 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 08:41:55,033 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 08:41:55,034 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 08:41:55,034 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 08:41:55,034 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 08:41:55,034 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 08:41:55,254 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 08:41:55,254 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 08:41:55,281 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 08:41:55,281 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 08:41:55,289 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 08:41:55,289 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 08:41:55,289 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 08:41:55,290 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 08:41:55,290 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 08:41:55,291 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 08:41:55,291 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 257 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-29 08:41:55,300] [main] java.version = 1.8.0_342 [testng] 08:41:55,304 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 08:41:55,304 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:41:55,349 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-29_08-41-55.log] [testng] 08:41:55,350 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-11-29 08:41:55,352] [main] testng.directory = /data [testng] [2024-11-29 08:41:55,352] [main] testng.configDirectory = /config [testng] [2024-11-29 08:41:55,365] [main] testng.multiplier = 1.0 [testng] [2024-11-29 08:41:55,365] [main] testng.in-memory = false [testng] [2024-11-29 08:41:55,365] [main] testng.allow-missing = false [testng] [2024-11-29 08:41:55,365] [main] user.language = en [testng] [2024-11-29 08:41:55,365] [main] user.country = ${user.country} [testng] [2024-11-29 08:41:55,365] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-11-29 08:42:00,543] [main] ---------------------------------------- [testng] [2024-11-29 08:42:00,543] [main] Total files: 40 [testng] [2024-11-29 08:42:00,543] [main] Scan time: 5.178 s (129 ms/file) [testng] [2024-11-29 08:42:00,543] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 38 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-29 08:42:54,844] [pool-1-thread-1] Initializing /data/roger/op9middle40x.lsm movie 3.avi: [testng] 08:42:54,844 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 08:42:54,844 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:42:54,845 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-29_08-42-54.log] [testng] 08:42:54,846 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7fc01902 - End of configuration. [testng] [2024-11-29 08:42:55,222] [pool-1-thread-12] Initializing /data/curtis/mri-stack-ij-new.avi: [testng] 08:42:55,222 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 08:42:55,222 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:42:55,223 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-29_08-42-55.log] [testng] 08:42:55,223 |-INFO in ch.qos.logback.core.sift.SiftProcessor@53b15c1f - End of configuration. [testng] [2024-11-29 08:42:55,585] [pool-1-thread-11] Initializing /data/william/worm.avi: [testng] 08:42:55,585 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 08:42:55,585 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:42:55,586 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-29_08-42-55.log] [testng] 08:42:55,586 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d144448 - End of configuration. [testng] [2024-11-29 08:42:55,957] [pool-1-thread-10] Initializing /data/roger/op9middle40x.lsm movie.avi: [testng] 08:42:55,957 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 08:42:55,957 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:42:55,958 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-29_08-42-55.log] [testng] 08:42:55,969 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ce73149 - End of configuration. [testng] [2024-11-29 08:42:56,361] [pool-1-thread-9] Initializing /data/sample-avis/extra-chunk/HyperStack.avi: [testng] 08:42:56,361 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 08:42:56,362 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:42:56,362 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-29_08-42-56.log] [testng] 08:42:56,362 |-INFO in ch.qos.logback.core.sift.SiftProcessor@24f280d - End of configuration. [testng] [2024-11-29 08:42:56,717] [pool-1-thread-8] Initializing /data/chip_avi/Level004-WA-116.avi: [testng] 08:42:56,717 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 08:42:56,717 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:42:56,717 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-29_08-42-56.log] [testng] 08:42:56,718 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35e2e975 - End of configuration. [testng] [2024-11-29 08:42:57,056] [pool-1-thread-7] Initializing /data/qa-7450/MVI_3610.AVI: [testng] 08:42:57,057 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 08:42:57,057 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:42:57,057 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-29_08-42-57.log] [testng] 08:42:57,058 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7d45101f - End of configuration. [testng] [2024-11-29 08:42:57,424] [pool-1-thread-6] Initializing /data/pki/yinghua_USPI2-ASMKT772_111017100001_C10_f1.avi: [testng] 08:42:57,424 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 08:42:57,424 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:42:57,425 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-29_08-42-57.log] [testng] 08:42:57,425 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a86ccb9 - End of configuration. [testng] [2024-11-29 08:42:57,784] [pool-1-thread-5] Initializing /data/jcb/JCB 201203159/JCB_201203159_0_4.avi: [testng] 08:42:57,784 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 08:42:57,784 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:42:57,785 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-29_08-42-57.log] [testng] 08:42:57,785 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18d7faff - End of configuration. [testng] [2024-11-29 08:42:58,150] [pool-1-thread-4] Initializing /data/chip_avi/Level001-ES-083.avi: [testng] 08:42:58,150 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 08:42:58,150 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:42:58,150 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-29_08-42-58.log] [testng] 08:42:58,151 |-INFO in ch.qos.logback.core.sift.SiftProcessor@726930d2 - End of configuration. [testng] [2024-11-29 08:42:58,489] [pool-1-thread-3] Initializing /data/qa-5019/nemo-2_10_20.avi: [testng] 08:42:58,489 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 08:42:58,489 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:42:58,490 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-29_08-42-58.log] [testng] 08:42:58,490 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f76a7a - End of configuration. [testng] [2024-11-29 08:42:58,847] [pool-1-thread-2] Initializing /data/qa-7336/2X_63X-DAPI-Emilin2_Filter_Render_Series.avi: [testng] 08:42:58,847 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 08:42:58,847 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:42:58,848 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-29_08-42-58.log] [testng] 08:42:58,849 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e056100 - End of configuration. [testng] [2024-11-29 08:43:03,994] [pool-1-thread-9] Initializing /data/kurt/40x_6um.avi: [testng] [2024-11-29 08:43:04,381] [pool-1-thread-5] Initializing /data/kurt/40x_6um_2.avi: [testng] [2024-11-29 08:43:04,768] [pool-1-thread-12] Initializing /data/chip_avi/Level003-DB-089.avi: [testng] [2024-11-29 08:43:05,116] [pool-1-thread-11] Initializing /data/jules/GUV_long15N_10_10mb_debut_26102011_4.avi: [testng] [2024-11-29 08:43:06,607] [pool-1-thread-4] Initializing /data/simon/24_bit_problem.avi: [testng] [2024-11-29 08:43:06,971] [pool-1-thread-8] Initializing /data/roger/op9middle40x.lsm movie 4.avi: [testng] [2024-11-29 08:43:07,319] [pool-1-thread-3] Initializing /data/roger/spheroid1.lsm movie.avi: [testng] [2024-11-29 08:43:07,700] [pool-1-thread-7] Initializing /data/qa-11011/M-flow10001.avi: [testng] [2024-11-29 08:43:08,132] [pool-1-thread-10] Initializing /data/jcb/JCB 201203159/JCB_201203159_0_3.avi: [testng] [2024-11-29 08:43:08,431] [pool-1-thread-1] Initializing /data/kurt/63x_6um.avi: [testng] [2024-11-29 08:43:08,847] [pool-1-thread-6] Initializing /data/qa-7560/Ex9 ALADIN WT KO KI_DIC_ 31_07_2013_M1.avi: [testng] [2024-11-29 08:43:09,477] [pool-1-thread-2] Initializing /data/prairie/cornea dc and macs.AVI: [testng] [2024-11-29 08:43:13,875] [pool-1-thread-10] Initializing /data/jcb/JCB 201203159/JCB_201203159_0_5.avi: [testng] [2024-11-29 08:43:14,258] [pool-1-thread-12] Initializing /data/sample-avis/rgb-odd-width/HyperStack.avi: [testng] [2024-11-29 08:43:14,646] [pool-1-thread-8] Initializing /data/ascb/TIRF.avi: [testng] [2024-11-29 08:43:15,039] [pool-1-thread-4] Initializing /data/jae/20xD_5minfor14h.avi: [testng] [2024-11-29 08:43:15,469] [pool-1-thread-2] Initializing /data/chris/APZ04_009.avi: [testng] [2024-11-29 08:43:16,494] [pool-1-thread-3] Initializing /data/jules/GUV_long15N_10_20mb_debut_25102011_1_BW.avi: [testng] [2024-11-29 08:43:16,882] [pool-1-thread-1] Initializing /data/roger/spheroid1-crop.lsm movie 2.avi: [testng] [2024-11-29 08:43:17,275] [pool-1-thread-9] Initializing /data/roger/op9middle40x.lsm movie 2.avi: [testng] [2024-11-29 08:43:17,644] [pool-1-thread-5] Initializing /data/chip_avi/Level002-DB-090.avi: [testng] [2024-11-29 08:43:17,982] [pool-1-thread-7] Initializing /data/curtis/mri-stack-ij-old.avi: [testng] [2024-11-29 08:43:21,429] [pool-1-thread-6] Initializing /data/curtis/mri-stack-bf.avi: [testng] [2024-11-29 08:43:22,467] [pool-1-thread-5] Initializing /data/qa-5019/nemo-2_1_.avi: [testng] [2024-11-29 08:43:22,876] [pool-1-thread-12] Initializing /data/qa-4232/11051920xdrywithincubatoronthenoff_Subset.avi: [testng] [2024-11-29 08:43:23,260] [pool-1-thread-10] Initializing /data/roger/spheroid1-crop.lsm movie.avi: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2014, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 1 minute 37 seconds Finished: SUCCESS