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Started by upstream project "BIOFORMATS-test-repo" build number 40 originally caused by: Started by upstream project "Trigger" build number 46 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins17212731568648422047.sh + '[' avi = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_5634_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] 02:00:26,552 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:00:26,553 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 02:00:26,553 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:00:26,554 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:00:26,555 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:00:26,555 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:00:26,556 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:00:26,556 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:00:26,557 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:00:26,557 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:00:26,557 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:00:26,558 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:00:26,817 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:00:26,817 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:00:26,844 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:00:26,845 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:00:26,853 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:00:26,853 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:00:26,853 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:00:26,854 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:00:26,854 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 02:00:26,855 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 02:00:26,855 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 298 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-04-21 02:00:26,868] [main] java.version = 17.0.2 [testng] 02:00:26,872 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:00:26,872 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:00:26,927 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-21_02-00-26.log] [testng] 02:00:26,929 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-04-21 02:00:26,932] [main] testng.directory = /data [testng] [2024-04-21 02:00:26,932] [main] testng.configDirectory = /config [testng] [2024-04-21 02:00:26,979] [main] testng.multiplier = 1.0 [testng] [2024-04-21 02:00:26,980] [main] testng.in-memory = false [testng] [2024-04-21 02:00:26,980] [main] testng.allow-missing = false [testng] [2024-04-21 02:00:26,980] [main] user.language = en [testng] [2024-04-21 02:00:26,980] [main] user.country = ${user.country} [testng] [2024-04-21 02:00:26,980] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-04-21 02:00:27,854] [main] ---------------------------------------- [testng] [2024-04-21 02:00:27,854] [main] Total files: 40 [testng] [2024-04-21 02:00:27,854] [main] Scan time: 0.873 s (21 ms/file) [testng] [2024-04-21 02:00:27,854] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 38 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-04-21 02:04:13,257] [pool-1-thread-1] Initializing /data/william/worm.avi: [testng] 02:04:13,257 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:04:13,257 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:04:13,259 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-21_02-04-13.log] [testng] 02:04:13,259 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7635e4c - End of configuration. [testng] [2024-04-21 02:04:13,277] [pool-1-thread-12] Initializing /data/kurt/40x_6um.avi: [testng] 02:04:13,277 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:04:13,277 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:04:13,278 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-21_02-04-13.log] [testng] 02:04:13,278 |-INFO in ch.qos.logback.core.sift.SiftProcessor@73570c23 - End of configuration. [testng] [2024-04-21 02:04:13,364] [pool-1-thread-11] Initializing /data/jcb/JCB 201203159/JCB_201203159_0_4.avi: [testng] 02:04:13,365 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:04:13,365 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:04:13,368 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-21_02-04-13.log] [testng] 02:04:13,369 |-INFO in ch.qos.logback.core.sift.SiftProcessor@445da32c - End of configuration. [testng] [2024-04-21 02:04:13,437] [pool-1-thread-10] Initializing /data/qa-7336/2X_63X-DAPI-Emilin2_Filter_Render_Series.avi: [testng] 02:04:13,437 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:04:13,437 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:04:13,438 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-21_02-04-13.log] [testng] 02:04:13,439 |-INFO in ch.qos.logback.core.sift.SiftProcessor@46042b4f - End of configuration. [testng] [2024-04-21 02:04:13,492] [pool-1-thread-9] Initializing /data/qa-5019/nemo-2_1_.avi: [testng] 02:04:13,492 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:04:13,492 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:04:13,503 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-21_02-04-13.log] [testng] 02:04:13,503 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1710586f - End of configuration. [testng] [2024-04-21 02:04:13,553] [pool-1-thread-8] Initializing /data/jcb/JCB 201203159/JCB_201203159_0_3.avi: [testng] 02:04:13,553 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:04:13,553 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:04:13,554 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-21_02-04-13.log] [testng] 02:04:13,555 |-INFO in ch.qos.logback.core.sift.SiftProcessor@67c5f9be - End of configuration. [testng] [2024-04-21 02:04:13,576] [pool-1-thread-7] Initializing /data/roger/spheroid1-crop.lsm movie 2.avi: [testng] 02:04:13,576 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:04:13,576 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:04:13,577 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-21_02-04-13.log] [testng] 02:04:13,578 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4548dacb - End of configuration. [testng] [2024-04-21 02:04:13,679] [pool-1-thread-6] Initializing /data/kurt/63x_6um.avi: [testng] 02:04:13,680 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:04:13,680 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:04:13,681 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-21_02-04-13.log] [testng] 02:04:13,682 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642045b5 - End of configuration. [testng] [2024-04-21 02:04:13,806] [pool-1-thread-5] Initializing /data/roger/spheroid1-crop.lsm movie.avi: [testng] 02:04:13,807 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:04:13,807 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:04:13,809 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-21_02-04-13.log] [testng] 02:04:13,811 |-INFO in ch.qos.logback.core.sift.SiftProcessor@cfa3a19 - End of configuration. [testng] [2024-04-21 02:04:13,921] [pool-1-thread-4] Initializing /data/qa-5019/nemo-2_10_20.avi: [testng] 02:04:13,921 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:04:13,921 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:04:13,924 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-21_02-04-13.log] [testng] 02:04:13,925 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6845aee - End of configuration. [testng] [2024-04-21 02:04:14,004] [pool-1-thread-3] Initializing /data/chris/APZ04_009.avi: [testng] 02:04:14,004 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:04:14,004 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:04:14,005 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-21_02-04-14.log] [testng] 02:04:14,006 |-INFO in ch.qos.logback.core.sift.SiftProcessor@61b7cb83 - End of configuration. [testng] [2024-04-21 02:04:18,249] [pool-1-thread-2] Initializing /data/chip_avi/Level004-WA-116.avi: [testng] 02:04:18,250 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:04:18,250 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:04:18,256 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-21_02-04-18.log] [testng] 02:04:18,257 |-INFO in ch.qos.logback.core.sift.SiftProcessor@264bedb1 - End of configuration. [testng] [2024-04-21 02:04:20,384] [pool-1-thread-8] Initializing /data/qa-11011/M-flow10001.avi: [testng] [2024-04-21 02:04:20,479] [pool-1-thread-5] Initializing /data/roger/op9middle40x.lsm movie.avi: [testng] [2024-04-21 02:04:20,503] [pool-1-thread-1] Initializing /data/jae/20xD_5minfor14h.avi: [testng] [2024-04-21 02:04:21,069] [pool-1-thread-11] Initializing /data/ascb/TIRF.avi: [testng] [2024-04-21 02:04:21,372] [pool-1-thread-2] Initializing /data/chip_avi/Level002-DB-090.avi: [testng] [2024-04-21 02:04:21,394] [pool-1-thread-4] Initializing /data/qa-7560/Ex9 ALADIN WT KO KI_DIC_ 31_07_2013_M1.avi: [testng] [2024-04-21 02:04:22,026] [pool-1-thread-9] Initializing /data/kurt/40x_6um_2.avi: [testng] [2024-04-21 02:04:22,268] [pool-1-thread-7] Initializing /data/chip_avi/Level001-ES-083.avi: [testng] [2024-04-21 02:04:22,305] [pool-1-thread-10] Initializing /data/curtis/mri-stack-ij-new.avi: [testng] [2024-04-21 02:04:22,579] [pool-1-thread-12] Initializing /data/qa-4232/11051920xdrywithincubatoronthenoff_Subset.avi: [testng] [2024-04-21 02:04:22,684] [pool-1-thread-6] Initializing /data/roger/op9middle40x.lsm movie 3.avi: [testng] [2024-04-21 02:04:22,745] [pool-1-thread-2] Initializing /data/prairie/cornea dc and macs.AVI: [testng] [2024-04-21 02:04:22,864] [pool-1-thread-10] Initializing /data/simon/24_bit_problem.avi: [testng] [2024-04-21 02:04:22,989] [pool-1-thread-7] Initializing /data/jules/GUV_long15N_10_20mb_debut_25102011_1_BW.avi: [testng] [2024-04-21 02:04:23,252] [pool-1-thread-5] Initializing /data/roger/op9middle40x.lsm movie 4.avi: [testng] [2024-04-21 02:04:23,984] [pool-1-thread-12] Initializing /data/jcb/JCB 201203159/JCB_201203159_0_5.avi: [testng] [2024-04-21 02:04:24,081] [pool-1-thread-11] Initializing /data/curtis/mri-stack-bf.avi: [testng] [2024-04-21 02:04:24,268] [pool-1-thread-9] Initializing /data/pki/yinghua_USPI2-ASMKT772_111017100001_C10_f1.avi: [testng] [2024-04-21 02:04:24,417] [pool-1-thread-6] Initializing /data/qa-7450/MVI_3610.AVI: [testng] [2024-04-21 02:04:24,566] [pool-1-thread-7] Initializing /data/jules/GUV_long15N_10_10mb_debut_26102011_4.avi: [testng] [2024-04-21 02:04:50,602] [pool-1-thread-12] Initializing /data/sample-avis/rgb-odd-width/HyperStack.avi: [testng] [2024-04-21 02:04:50,670] [pool-1-thread-11] Initializing /data/chip_avi/Level003-DB-089.avi: [testng] [2024-04-21 02:04:50,694] [pool-1-thread-5] Initializing /data/curtis/mri-stack-ij-old.avi: [testng] [2024-04-21 02:04:50,745] [pool-1-thread-10] Initializing /data/sample-avis/extra-chunk/HyperStack.avi: [testng] [2024-04-21 02:04:50,752] [pool-1-thread-8] Initializing /data/roger/op9middle40x.lsm movie 2.avi: [testng] [2024-04-21 02:04:50,833] [pool-1-thread-12] 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 38 seconds Finished: SUCCESS