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Started by upstream project "BIOFORMATS-test-repo" build number 290 originally caused by: Started by upstream project "Trigger" build number 309 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4 [BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins12511628515546258310.sh + '[' avi = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_45835_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 [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] 03:04:08,147 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:04:08,148 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 03:04:08,148 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:04:08,149 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:04:08,150 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:04:08,150 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:04:08,150 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 03:04:08,150 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:04:08,151 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:04:08,151 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:04:08,152 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:04:08,152 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:04:08,311 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:04:08,311 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:04:08,332 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:04:08,332 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:04:08,338 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:04:08,338 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:04:08,338 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:04:08,338 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:04:08,338 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 03:04:08,339 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 03:04:08,339 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 188 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-14 03:04:08,347] [main] java.version = 11.0.16 [testng] 03:04:08,350 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:04:08,350 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:04:08,407 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-14_03-04-08.log] [testng] 03:04:08,409 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-12-14 03:04:08,411] [main] testng.directory = /data [testng] [2024-12-14 03:04:08,411] [main] testng.configDirectory = /config [testng] [2024-12-14 03:04:08,422] [main] testng.multiplier = 1.0 [testng] [2024-12-14 03:04:08,423] [main] testng.in-memory = false [testng] [2024-12-14 03:04:08,423] [main] testng.allow-missing = false [testng] [2024-12-14 03:04:08,423] [main] user.language = en [testng] [2024-12-14 03:04:08,423] [main] user.country = ${user.country} [testng] [2024-12-14 03:04:08,423] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-14 03:04:15,357] [main] ---------------------------------------- [testng] [2024-12-14 03:04:15,357] [main] Total files: 40 [testng] [2024-12-14 03:04:15,357] [main] Scan time: 6.934 s (173 ms/file) [testng] [2024-12-14 03:04:15,357] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 38 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-14 03:05:19,154] [pool-1-thread-1] Initializing /data/curtis/mri-stack-bf.avi: [testng] 03:05:19,155 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:05:19,156 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:05:19,158 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-14_03-05-19.log] [testng] 03:05:19,158 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5345d3fb - End of configuration. [testng] [2024-12-14 03:05:19,694] [pool-1-thread-12] Initializing /data/sample-avis/extra-chunk/HyperStack.avi: [testng] 03:05:19,695 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:05:19,695 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:05:19,696 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-14_03-05-19.log] [testng] 03:05:19,696 |-INFO in ch.qos.logback.core.sift.SiftProcessor@74404d7e - End of configuration. [testng] [2024-12-14 03:05:20,334] [pool-1-thread-11] Initializing /data/chip_avi/Level001-ES-083.avi: [testng] 03:05:20,335 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:05:20,335 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:05:20,335 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-14_03-05-20.log] [testng] 03:05:20,336 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75a719e6 - End of configuration. [testng] [2024-12-14 03:05:20,736] [pool-1-thread-10] Initializing /data/jules/GUV_long15N_10_20mb_debut_25102011_1_BW.avi: [testng] 03:05:20,736 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:05:20,737 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:05:20,737 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-14_03-05-20.log] [testng] 03:05:20,738 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65ec558c - End of configuration. [testng] [2024-12-14 03:05:21,153] [pool-1-thread-9] Initializing /data/simon/24_bit_problem.avi: [testng] 03:05:21,154 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:05:21,154 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:05:21,154 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-14_03-05-21.log] [testng] 03:05:21,155 |-INFO in ch.qos.logback.core.sift.SiftProcessor@53ebe82b - End of configuration. [testng] [2024-12-14 03:05:21,536] [pool-1-thread-8] Initializing /data/qa-11011/M-flow10001.avi: [testng] 03:05:21,537 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:05:21,537 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:05:21,537 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-14_03-05-21.log] [testng] 03:05:21,538 |-INFO in ch.qos.logback.core.sift.SiftProcessor@525eeadc - End of configuration. [testng] [2024-12-14 03:05:22,070] [pool-1-thread-7] Initializing /data/chip_avi/Level002-DB-090.avi: [testng] 03:05:22,070 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:05:22,070 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:05:22,071 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-14_03-05-22.log] [testng] 03:05:22,071 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7effe321 - End of configuration. [testng] [2024-12-14 03:05:22,509] [pool-1-thread-6] Initializing /data/roger/op9middle40x.lsm movie 3.avi: [testng] 03:05:22,510 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:05:22,510 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:05:22,511 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-14_03-05-22.log] [testng] 03:05:22,511 |-INFO in ch.qos.logback.core.sift.SiftProcessor@28c5c6aa - End of configuration. [testng] [2024-12-14 03:05:22,969] [pool-1-thread-5] Initializing /data/jcb/JCB 201203159/JCB_201203159_0_5.avi: [testng] 03:05:22,970 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:05:22,970 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:05:22,970 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-14_03-05-22.log] [testng] 03:05:22,971 |-INFO in ch.qos.logback.core.sift.SiftProcessor@67078f63 - End of configuration. [testng] [2024-12-14 03:05:23,431] [pool-1-thread-4] Initializing /data/roger/spheroid1-crop.lsm movie.avi: [testng] 03:05:23,431 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:05:23,432 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:05:23,432 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-14_03-05-23.log] [testng] 03:05:23,432 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1caf2e70 - End of configuration. [testng] [2024-12-14 03:05:23,897] [pool-1-thread-3] Initializing /data/curtis/mri-stack-ij-new.avi: [testng] 03:05:23,897 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:05:23,897 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:05:23,898 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-14_03-05-23.log] [testng] 03:05:23,898 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21ca4600 - End of configuration. [testng] [2024-12-14 03:05:24,368] [pool-1-thread-2] Initializing /data/qa-7450/MVI_3610.AVI: [testng] 03:05:24,368 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:05:24,368 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:05:24,369 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-14_03-05-24.log] [testng] 03:05:24,369 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6f8de784 - End of configuration. [testng] [2024-12-14 03:05:30,280] [pool-1-thread-12] Initializing /data/prairie/cornea dc and macs.AVI: [testng] [2024-12-14 03:05:31,212] [pool-1-thread-9] Initializing /data/curtis/mri-stack-ij-old.avi: [testng] [2024-12-14 03:05:31,677] [pool-1-thread-5] Initializing /data/roger/spheroid1.lsm movie.avi: [testng] [2024-12-14 03:05:32,153] [pool-1-thread-3] Initializing /data/jae/20xD_5minfor14h.avi: [testng] [2024-12-14 03:05:32,702] [pool-1-thread-10] Initializing /data/roger/spheroid1-crop.lsm movie 2.avi: [testng] [2024-12-14 03:05:33,177] [pool-1-thread-11] Initializing /data/pki/yinghua_USPI2-ASMKT772_111017100001_C10_f1.avi: [testng] [2024-12-14 03:05:33,661] [pool-1-thread-7] Initializing /data/kurt/63x_6um.avi: [testng] [2024-12-14 03:05:34,208] [pool-1-thread-4] Initializing /data/chris/APZ04_009.avi: [testng] [2024-12-14 03:05:35,527] [pool-1-thread-1] Initializing /data/qa-4232/11051920xdrywithincubatoronthenoff_Subset.avi: [testng] [2024-12-14 03:05:35,930] [pool-1-thread-6] Initializing /data/qa-7560/Ex9 ALADIN WT KO KI_DIC_ 31_07_2013_M1.avi: [testng] [2024-12-14 03:05:36,644] [pool-1-thread-2] Initializing /data/jcb/JCB 201203159/JCB_201203159_0_3.avi: [testng] [2024-12-14 03:05:37,047] [pool-1-thread-8] Initializing /data/william/worm.avi: [testng] [2024-12-14 03:05:42,821] [pool-1-thread-9] Initializing /data/chip_avi/Level004-WA-116.avi: [testng] [2024-12-14 03:05:43,395] [pool-1-thread-8] Initializing /data/kurt/40x_6um_2.avi: [testng] [2024-12-14 03:05:43,958] [pool-1-thread-2] Initializing /data/qa-5019/nemo-2_10_20.avi: [testng] [2024-12-14 03:05:44,613] [pool-1-thread-1] Initializing /data/jcb/JCB 201203159/JCB_201203159_0_4.avi: [testng] [2024-12-14 03:05:45,122] [pool-1-thread-12] Initializing /data/roger/op9middle40x.lsm movie.avi: [testng] [2024-12-14 03:05:45,649] [pool-1-thread-11] Initializing /data/qa-5019/nemo-2_1_.avi: [testng] [2024-12-14 03:05:46,035] [pool-1-thread-10] Initializing /data/sample-avis/rgb-odd-width/HyperStack.avi: [testng] [2024-12-14 03:05:46,486] [pool-1-thread-7] Initializing /data/chip_avi/Level003-DB-089.avi: [testng] [2024-12-14 03:05:46,907] [pool-1-thread-5] Initializing /data/roger/op9middle40x.lsm movie 2.avi: [testng] [2024-12-14 03:05:47,374] [pool-1-thread-3] Initializing /data/jules/GUV_long15N_10_10mb_debut_26102011_4.avi: [testng] [2024-12-14 03:05:51,871] [pool-1-thread-6] Initializing /data/ascb/TIRF.avi: [testng] [2024-12-14 03:05:53,867] [pool-1-thread-4] Initializing /data/qa-7336/2X_63X-DAPI-Emilin2_Filter_Render_Series.avi: [testng] [2024-12-14 03:05:54,779] [pool-1-thread-10] Initializing /data/kurt/40x_6um.avi: [testng] [2024-12-14 03:05:55,285] [pool-1-thread-1] Initializing /data/roger/op9middle40x.lsm movie 4.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 56 seconds Finished: SUCCESS