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Started by upstream project "BIOFORMATS-test-repo" build number 107 originally caused by: Started by upstream project "Trigger" build number 119 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins12863487757185616312.sh + '[' avi = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_16623_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] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket [testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket [testng] File leak detector installed [testng] 02:02:41,179 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:02:41,180 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 02:02:41,180 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:02:41,195 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:02:41,196 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:02:41,196 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:02:41,196 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:02:41,196 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:02:41,197 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:02:41,197 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:02:41,198 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:02:41,198 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:02:41,459 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:02:41,459 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:02:41,502 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:02:41,502 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:02:41,508 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:02:41,508 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:02:41,508 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:02:41,508 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:02:41,508 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 02:02:41,509 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 02:02:41,509 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 312 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-06-30 02:02:41,518] [main] java.version = 17.0.2 [testng] 02:02:41,521 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:02:41,521 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:02:41,561 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-30_02-02-41.log] [testng] 02:02:41,562 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-06-30 02:02:41,564] [main] testng.directory = /data [testng] [2024-06-30 02:02:41,564] [main] testng.configDirectory = /config [testng] [2024-06-30 02:02:41,595] [main] testng.multiplier = 1.0 [testng] [2024-06-30 02:02:41,596] [main] testng.in-memory = false [testng] [2024-06-30 02:02:41,596] [main] testng.allow-missing = false [testng] [2024-06-30 02:02:41,596] [main] user.language = en [testng] [2024-06-30 02:02:41,596] [main] user.country = ${user.country} [testng] [2024-06-30 02:02:41,596] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-06-30 02:02:42,481] [main] ---------------------------------------- [testng] [2024-06-30 02:02:42,481] [main] Total files: 40 [testng] [2024-06-30 02:02:42,481] [main] Scan time: 0.885 s (22 ms/file) [testng] [2024-06-30 02:02:42,481] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 38 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-06-30 02:06:55,084] [pool-1-thread-1] Initializing /data/william/worm.avi: [testng] 02:06:55,085 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:06:55,085 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:06:55,086 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-30_02-06-55.log] [testng] 02:06:55,087 |-INFO in ch.qos.logback.core.sift.SiftProcessor@513b25d7 - End of configuration. [testng] [2024-06-30 02:06:55,107] [pool-1-thread-12] Initializing /data/kurt/40x_6um.avi: [testng] 02:06:55,108 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:06:55,108 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:06:55,109 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-30_02-06-55.log] [testng] 02:06:55,109 |-INFO in ch.qos.logback.core.sift.SiftProcessor@386fd62d - End of configuration. [testng] [2024-06-30 02:06:55,168] [pool-1-thread-11] Initializing /data/jcb/JCB 201203159/JCB_201203159_0_4.avi: [testng] 02:06:55,168 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:06:55,168 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:06:55,169 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-30_02-06-55.log] [testng] 02:06:55,170 |-INFO in ch.qos.logback.core.sift.SiftProcessor@632427d1 - End of configuration. [testng] [2024-06-30 02:06:55,184] [pool-1-thread-10] Initializing /data/qa-7336/2X_63X-DAPI-Emilin2_Filter_Render_Series.avi: [testng] 02:06:55,184 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:06:55,184 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:06:55,185 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-30_02-06-55.log] [testng] 02:06:55,186 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5bacaa8c - End of configuration. [testng] [2024-06-30 02:06:55,233] [pool-1-thread-9] Initializing /data/qa-5019/nemo-2_1_.avi: [testng] 02:06:55,233 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:06:55,233 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:06:55,234 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-30_02-06-55.log] [testng] 02:06:55,234 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1551141e - End of configuration. [testng] [2024-06-30 02:06:55,269] [pool-1-thread-8] Initializing /data/jcb/JCB 201203159/JCB_201203159_0_3.avi: [testng] 02:06:55,269 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:06:55,269 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:06:55,270 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-30_02-06-55.log] [testng] 02:06:55,270 |-INFO in ch.qos.logback.core.sift.SiftProcessor@437bb3 - End of configuration. [testng] [2024-06-30 02:06:55,287] [pool-1-thread-7] Initializing /data/roger/spheroid1-crop.lsm movie 2.avi: [testng] 02:06:55,288 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:06:55,288 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:06:55,289 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-30_02-06-55.log] [testng] 02:06:55,289 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65f21d80 - End of configuration. [testng] [2024-06-30 02:06:55,353] [pool-1-thread-6] Initializing /data/kurt/63x_6um.avi: [testng] 02:06:55,353 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:06:55,353 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:06:55,354 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-30_02-06-55.log] [testng] 02:06:55,355 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a780815 - End of configuration. [testng] [2024-06-30 02:06:55,448] [pool-1-thread-5] Initializing /data/roger/spheroid1-crop.lsm movie.avi: [testng] 02:06:55,448 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:06:55,448 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:06:55,449 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-30_02-06-55.log] [testng] 02:06:55,449 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f6ec4a5 - End of configuration. [testng] [2024-06-30 02:06:55,487] [pool-1-thread-4] Initializing /data/qa-5019/nemo-2_10_20.avi: [testng] 02:06:55,488 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:06:55,488 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:06:55,489 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-30_02-06-55.log] [testng] 02:06:55,489 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a00284c - End of configuration. [testng] [2024-06-30 02:06:55,518] [pool-1-thread-3] Initializing /data/chris/APZ04_009.avi: [testng] 02:06:55,518 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:06:55,518 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:06:55,519 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-30_02-06-55.log] [testng] 02:06:55,519 |-INFO in ch.qos.logback.core.sift.SiftProcessor@695a231b - End of configuration. [testng] [2024-06-30 02:06:56,452] [pool-1-thread-2] Initializing /data/chip_avi/Level004-WA-116.avi: [testng] 02:06:56,453 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:06:56,453 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:06:56,454 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-30_02-06-56.log] [testng] 02:06:56,454 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79bad6ba - End of configuration. [testng] [2024-06-30 02:06:57,888] [pool-1-thread-8] Initializing /data/qa-11011/M-flow10001.avi: [testng] [2024-06-30 02:06:58,003] [pool-1-thread-11] Initializing /data/jae/20xD_5minfor14h.avi: [testng] [2024-06-30 02:06:58,113] [pool-1-thread-1] Initializing /data/ascb/TIRF.avi: [testng] [2024-06-30 02:06:58,146] [pool-1-thread-2] Initializing /data/chip_avi/Level002-DB-090.avi: [testng] [2024-06-30 02:06:58,162] [pool-1-thread-4] Initializing /data/qa-7560/Ex9 ALADIN WT KO KI_DIC_ 31_07_2013_M1.avi: [testng] [2024-06-30 02:06:58,486] [pool-1-thread-9] Initializing /data/kurt/40x_6um_2.avi: [testng] [2024-06-30 02:06:58,666] [pool-1-thread-5] Initializing /data/roger/op9middle40x.lsm movie.avi: [testng] [2024-06-30 02:06:58,690] [pool-1-thread-7] Initializing /data/chip_avi/Level001-ES-083.avi: [testng] [2024-06-30 02:06:58,995] [pool-1-thread-12] Initializing /data/curtis/mri-stack-ij-new.avi: [testng] [2024-06-30 02:06:59,008] [pool-1-thread-6] Initializing /data/roger/op9middle40x.lsm movie 3.avi: [testng] [2024-06-30 02:06:59,028] [pool-1-thread-10] Initializing /data/qa-4232/11051920xdrywithincubatoronthenoff_Subset.avi: [testng] [2024-06-30 02:06:59,118] [pool-1-thread-2] Initializing /data/prairie/cornea dc and macs.AVI: [testng] [2024-06-30 02:06:59,304] [pool-1-thread-7] Initializing /data/simon/24_bit_problem.avi: [testng] [2024-06-30 02:06:59,510] [pool-1-thread-12] Initializing /data/jules/GUV_long15N_10_20mb_debut_25102011_1_BW.avi: [testng] [2024-06-30 02:06:59,616] [pool-1-thread-5] Initializing /data/roger/op9middle40x.lsm movie 4.avi: [testng] [2024-06-30 02:06:59,671] [pool-1-thread-1] Initializing /data/jcb/JCB 201203159/JCB_201203159_0_5.avi: [testng] [2024-06-30 02:06:59,760] [pool-1-thread-10] Initializing /data/curtis/mri-stack-bf.avi: [testng] [2024-06-30 02:06:59,850] [pool-1-thread-6] Initializing /data/pki/yinghua_USPI2-ASMKT772_111017100001_C10_f1.avi: [testng] [2024-06-30 02:06:59,922] [pool-1-thread-9] Initializing /data/qa-7450/MVI_3610.AVI: [testng] [2024-06-30 02:07:00,039] [pool-1-thread-8] Initializing /data/jules/GUV_long15N_10_10mb_debut_26102011_4.avi: [testng] [2024-06-30 02:07:01,209] [pool-1-thread-1] Initializing /data/sample-avis/rgb-odd-width/HyperStack.avi: [testng] [2024-06-30 02:07:01,285] [pool-1-thread-10] Initializing /data/chip_avi/Level003-DB-089.avi: [testng] [2024-06-30 02:07:01,299] [pool-1-thread-12] Initializing /data/curtis/mri-stack-ij-old.avi: [testng] [2024-06-30 02:07:01,389] [pool-1-thread-1] Initializing /data/sample-avis/extra-chunk/HyperStack.avi: [testng] [2024-06-30 02:07:01,422] [pool-1-thread-2] Initializing /data/roger/op9middle40x.lsm movie 2.avi: [testng] [2024-06-30 02:07:01,627] [pool-1-thread-1] Initializing /data/roger/spheroid1.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: 4 minutes 36 seconds Finished: SUCCESS