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Started by upstream project "BIOFORMATS-test-repo" build number 109 originally caused by: Started by upstream project "Trigger" build number 122 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@6 [BIOFORMATS-test-folder@6] $ /bin/bash -xe /tmp/jenkins11796814913040035867.sh + '[' avi = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_16951_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] 12:39:48,279 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 12:39:48,281 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 12:39:48,281 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 12:39:48,283 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 12:39:48,284 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 12:39:48,284 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 12:39:48,285 |-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] 12:39:48,285 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 12:39:48,285 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 12:39:48,286 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 12:39:48,287 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 12:39:48,287 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 12:39:48,588 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 12:39:48,588 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 12:39:48,625 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 12:39:48,625 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 12:39:48,634 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 12:39:48,634 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 12:39:48,635 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 12:39:48,636 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 12:39:48,636 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 12:39:48,637 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 12:39:48,637 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 352 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-02 12:39:48,652] [main] java.version = 11.0.16 [testng] 12:39:48,656 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 12:39:48,657 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:39:48,855 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-02_12-39-48.log] [testng] 12:39:48,857 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-07-02 12:39:48,886] [main] testng.directory = /data [testng] [2024-07-02 12:39:48,887] [main] testng.configDirectory = /config [testng] [2024-07-02 12:39:48,974] [main] testng.multiplier = 1.0 [testng] [2024-07-02 12:39:48,976] [main] testng.in-memory = false [testng] [2024-07-02 12:39:48,976] [main] testng.allow-missing = false [testng] [2024-07-02 12:39:48,977] [main] user.language = en [testng] [2024-07-02 12:39:48,977] [main] user.country = ${user.country} [testng] [2024-07-02 12:39:48,977] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-07-02 12:39:50,653] [main] ---------------------------------------- [testng] [2024-07-02 12:39:50,653] [main] Total files: 40 [testng] [2024-07-02 12:39:50,653] [main] Scan time: 1.676 s (41 ms/file) [testng] [2024-07-02 12:39:50,653] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 38 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-02 12:44:00,297] [pool-1-thread-1] Initializing /data/kurt/63x_6um.avi: [testng] 12:44:00,298 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 12:44:00,299 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:44:00,302 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-02_12-44-00.log] [testng] 12:44:00,303 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f85c01b - End of configuration. [testng] [2024-07-02 12:44:00,396] [pool-1-thread-12] Initializing /data/ascb/TIRF.avi: [testng] 12:44:00,397 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 12:44:00,397 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:44:00,398 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-02_12-44-00.log] [testng] 12:44:00,399 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71b9fa65 - End of configuration. [testng] [2024-07-02 12:44:00,688] [pool-1-thread-11] Initializing /data/curtis/mri-stack-ij-new.avi: [testng] 12:44:00,689 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 12:44:00,689 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:44:00,690 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-02_12-44-00.log] [testng] 12:44:00,690 |-INFO in ch.qos.logback.core.sift.SiftProcessor@239bcefa - End of configuration. [testng] [2024-07-02 12:44:00,711] [pool-1-thread-10] Initializing /data/jcb/JCB 201203159/JCB_201203159_0_5.avi: [testng] 12:44:00,711 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 12:44:00,712 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:44:00,713 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-02_12-44-00.log] [testng] 12:44:00,713 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4453fbc4 - End of configuration. [testng] [2024-07-02 12:44:00,758] [pool-1-thread-9] Initializing /data/qa-7450/MVI_3610.AVI: [testng] 12:44:00,758 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 12:44:00,758 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:44:00,759 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-02_12-44-00.log] [testng] 12:44:00,760 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6dc302c5 - End of configuration. [testng] [2024-07-02 12:44:00,824] [pool-1-thread-8] Initializing /data/roger/spheroid1-crop.lsm movie 2.avi: [testng] 12:44:00,824 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 12:44:00,824 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:44:00,825 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-02_12-44-00.log] [testng] 12:44:00,825 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78be4bcc - End of configuration. [testng] [2024-07-02 12:44:00,895] [pool-1-thread-7] Initializing /data/chip_avi/Level002-DB-090.avi: [testng] 12:44:00,895 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 12:44:00,895 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:44:00,896 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-02_12-44-00.log] [testng] 12:44:00,896 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4aae8575 - End of configuration. [testng] [2024-07-02 12:44:00,917] [pool-1-thread-6] Initializing /data/jules/GUV_long15N_10_10mb_debut_26102011_4.avi: [testng] 12:44:00,918 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 12:44:00,918 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:44:00,919 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-02_12-44-00.log] [testng] 12:44:00,919 |-INFO in ch.qos.logback.core.sift.SiftProcessor@178552de - End of configuration. [testng] [2024-07-02 12:44:11,215] [pool-1-thread-5] Initializing /data/qa-5019/nemo-2_1_.avi: [testng] 12:44:11,216 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 12:44:11,216 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:44:11,217 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-02_12-44-11.log] [testng] 12:44:11,217 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60b0dc54 - End of configuration. [testng] [2024-07-02 12:44:11,247] [pool-1-thread-4] Initializing /data/pki/yinghua_USPI2-ASMKT772_111017100001_C10_f1.avi: [testng] 12:44:11,247 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 12:44:11,247 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:44:11,248 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-02_12-44-11.log] [testng] 12:44:11,248 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b8d7ce3 - End of configuration. [testng] [2024-07-02 12:44:11,274] [pool-1-thread-3] Initializing /data/chris/APZ04_009.avi: [testng] 12:44:11,274 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 12:44:11,274 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:44:11,275 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-02_12-44-11.log] [testng] 12:44:11,275 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22ae1cb0 - End of configuration. [testng] [2024-07-02 12:44:18,075] [pool-1-thread-2] Initializing /data/simon/24_bit_problem.avi: [testng] 12:44:18,075 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 12:44:18,075 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:44:18,076 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-02_12-44-18.log] [testng] 12:44:18,076 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ac0c52f - End of configuration. [testng] [2024-07-02 12:44:20,123] [pool-1-thread-10] Initializing /data/roger/op9middle40x.lsm movie.avi: [testng] [2024-07-02 12:44:20,156] [pool-1-thread-11] Initializing /data/chip_avi/Level001-ES-083.avi: [testng] [2024-07-02 12:44:20,175] [pool-1-thread-7] Initializing /data/roger/spheroid1-crop.lsm movie.avi: [testng] [2024-07-02 12:44:20,208] [pool-1-thread-5] Initializing /data/william/worm.avi: [testng] [2024-07-02 12:44:20,222] [pool-1-thread-4] Initializing /data/qa-4232/11051920xdrywithincubatoronthenoff_Subset.avi: [testng] [2024-07-02 12:44:20,255] [pool-1-thread-2] Initializing /data/prairie/cornea dc and macs.AVI: [testng] [2024-07-02 12:44:20,318] [pool-1-thread-9] Initializing /data/curtis/mri-stack-ij-old.avi: [testng] [2024-07-02 12:44:20,726] [pool-1-thread-12] Initializing /data/kurt/40x_6um_2.avi: [testng] [2024-07-02 12:44:21,053] [pool-1-thread-8] Initializing /data/roger/op9middle40x.lsm movie 3.avi: [testng] [2024-07-02 12:44:21,082] [pool-1-thread-1] Initializing /data/roger/op9middle40x.lsm movie 4.avi: [testng] [2024-07-02 12:44:21,262] [pool-1-thread-5] Initializing /data/qa-11011/M-flow10001.avi: [testng] [2024-07-02 12:44:21,531] [pool-1-thread-9] Initializing /data/jcb/JCB 201203159/JCB_201203159_0_3.avi: [testng] [2024-07-02 12:44:21,600] [pool-1-thread-11] Initializing /data/kurt/40x_6um.avi: [testng] [2024-07-02 12:44:21,839] [pool-1-thread-4] Initializing /data/jae/20xD_5minfor14h.avi: [testng] [2024-07-02 12:44:23,532] [pool-1-thread-9] Initializing /data/roger/spheroid1.lsm movie.avi: [testng] [2024-07-02 12:44:23,581] [pool-1-thread-10] Initializing /data/roger/op9middle40x.lsm movie 2.avi: [testng] [2024-07-02 12:44:23,702] [pool-1-thread-2] Initializing /data/sample-avis/extra-chunk/HyperStack.avi: [testng] [2024-07-02 12:44:23,710] [pool-1-thread-7] Initializing /data/qa-5019/nemo-2_10_20.avi: [testng] [2024-07-02 12:44:24,049] [pool-1-thread-2] Initializing /data/jules/GUV_long15N_10_20mb_debut_25102011_1_BW.avi: [testng] [2024-07-02 12:44:24,079] [pool-1-thread-8] Initializing /data/curtis/mri-stack-bf.avi: [testng] [2024-07-02 12:44:24,143] [pool-1-thread-1] Initializing /data/qa-7336/2X_63X-DAPI-Emilin2_Filter_Render_Series.avi: [testng] [2024-07-02 12:44:24,210] [pool-1-thread-12] Initializing /data/chip_avi/Level003-DB-089.avi: [testng] [2024-07-02 12:44:24,444] [pool-1-thread-8] Initializing /data/chip_avi/Level004-WA-116.avi: [testng] [2024-07-02 12:44:24,551] [pool-1-thread-7] Initializing /data/jcb/JCB 201203159/JCB_201203159_0_4.avi: [testng] [2024-07-02 12:44:24,653] [pool-1-thread-12] Initializing /data/sample-avis/rgb-odd-width/HyperStack.avi: [testng] [2024-07-02 12:44:24,660] [pool-1-thread-11] Initializing /data/qa-7560/Ex9 ALADIN WT KO KI_DIC_ 31_07_2013_M1.avi: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2014, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 5 minutes 5 seconds Finished: SUCCESS