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Started by upstream project "BIOFORMATS-test-repo" build number 282 originally caused by: Started by user devspace 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/jenkins14314542947611105950.sh + '[' avi = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_44523_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] 11:33:13,979 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 11:33:13,981 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 11:33:13,981 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:33:13,982 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:33:13,982 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 11:33:13,982 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 11:33:13,982 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 11:33:13,982 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:33:13,983 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:33:13,983 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 11:33:13,983 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 11:33:13,983 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 11:33:14,211 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 11:33:14,211 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 11:33:14,239 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 11:33:14,239 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 11:33:14,246 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 11:33:14,247 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 11:33:14,247 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 11:33:14,247 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 11:33:14,247 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 11:33:14,248 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 11:33:14,248 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 265 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-06 11:33:14,258] [main] java.version = 1.8.0_342 [testng] 11:33:14,261 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 11:33:14,261 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:33:14,307 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-06_11-33-14.log] [testng] 11:33:14,309 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-12-06 11:33:14,311] [main] testng.directory = /data [testng] [2024-12-06 11:33:14,311] [main] testng.configDirectory = /config [testng] [2024-12-06 11:33:14,323] [main] testng.multiplier = 1.0 [testng] [2024-12-06 11:33:14,323] [main] testng.in-memory = false [testng] [2024-12-06 11:33:14,324] [main] testng.allow-missing = false [testng] [2024-12-06 11:33:14,324] [main] user.language = en [testng] [2024-12-06 11:33:14,324] [main] user.country = ${user.country} [testng] [2024-12-06 11:33:14,324] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-12-06 11:33:17,802] [main] ---------------------------------------- [testng] [2024-12-06 11:33:17,802] [main] Total files: 40 [testng] [2024-12-06 11:33:17,802] [main] Scan time: 3.478 s (86 ms/file) [testng] [2024-12-06 11:33:17,803] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 38 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-06 11:34:05,659] [pool-1-thread-1] Initializing /data/roger/op9middle40x.lsm movie 3.avi: [testng] 11:34:05,659 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 11:34:05,659 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:34:05,661 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-06_11-34-05.log] [testng] 11:34:05,661 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b6bc2ce - End of configuration. [testng] [2024-12-06 11:34:05,895] [pool-1-thread-12] Initializing /data/curtis/mri-stack-ij-new.avi: [testng] 11:34:05,895 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 11:34:05,895 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:34:05,896 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-06_11-34-05.log] [testng] 11:34:05,896 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4765dfe6 - End of configuration. [testng] [2024-12-06 11:34:06,065] [pool-1-thread-11] Initializing /data/william/worm.avi: [testng] 11:34:06,065 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 11:34:06,065 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:34:06,066 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-06_11-34-06.log] [testng] 11:34:06,066 |-INFO in ch.qos.logback.core.sift.SiftProcessor@25b15e10 - End of configuration. [testng] [2024-12-06 11:34:06,311] [pool-1-thread-10] Initializing /data/roger/op9middle40x.lsm movie.avi: [testng] 11:34:06,311 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 11:34:06,311 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:34:06,312 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-06_11-34-06.log] [testng] 11:34:06,334 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a05c3c6 - End of configuration. [testng] [2024-12-06 11:34:06,559] [pool-1-thread-9] Initializing /data/sample-avis/extra-chunk/HyperStack.avi: [testng] 11:34:06,559 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 11:34:06,560 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:34:06,560 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-06_11-34-06.log] [testng] 11:34:06,561 |-INFO in ch.qos.logback.core.sift.SiftProcessor@53aa7aca - End of configuration. [testng] [2024-12-06 11:34:06,731] [pool-1-thread-8] Initializing /data/chip_avi/Level004-WA-116.avi: [testng] 11:34:06,732 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 11:34:06,732 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:34:06,732 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-06_11-34-06.log] [testng] 11:34:06,733 |-INFO in ch.qos.logback.core.sift.SiftProcessor@aa0c563 - End of configuration. [testng] [2024-12-06 11:34:06,929] [pool-1-thread-7] Initializing /data/qa-7450/MVI_3610.AVI: [testng] 11:34:06,929 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 11:34:06,929 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:34:06,929 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-06_11-34-06.log] [testng] 11:34:06,930 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50576e44 - End of configuration. [testng] [2024-12-06 11:34:07,148] [pool-1-thread-6] Initializing /data/pki/yinghua_USPI2-ASMKT772_111017100001_C10_f1.avi: [testng] 11:34:07,148 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 11:34:07,148 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:34:07,149 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-06_11-34-07.log] [testng] 11:34:07,149 |-INFO in ch.qos.logback.core.sift.SiftProcessor@514ae4e1 - End of configuration. [testng] [2024-12-06 11:34:07,361] [pool-1-thread-5] Initializing /data/jcb/JCB 201203159/JCB_201203159_0_4.avi: [testng] 11:34:07,361 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 11:34:07,362 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:34:07,362 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-06_11-34-07.log] [testng] 11:34:07,363 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56b46ade - End of configuration. [testng] [2024-12-06 11:34:07,535] [pool-1-thread-4] Initializing /data/chip_avi/Level001-ES-083.avi: [testng] 11:34:07,535 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 11:34:07,535 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:34:07,536 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-06_11-34-07.log] [testng] 11:34:07,536 |-INFO in ch.qos.logback.core.sift.SiftProcessor@44756d80 - End of configuration. [testng] [2024-12-06 11:34:07,698] [pool-1-thread-3] Initializing /data/qa-5019/nemo-2_10_20.avi: [testng] 11:34:07,698 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 11:34:07,699 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:34:07,699 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-06_11-34-07.log] [testng] 11:34:07,700 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5288cacd - End of configuration. [testng] [2024-12-06 11:34:07,879] [pool-1-thread-2] Initializing /data/qa-7336/2X_63X-DAPI-Emilin2_Filter_Render_Series.avi: [testng] 11:34:07,879 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 11:34:07,879 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:34:07,880 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-06_11-34-07.log] [testng] 11:34:07,880 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a0926e6 - End of configuration. [testng] [2024-12-06 11:34:11,569] [pool-1-thread-9] Initializing /data/kurt/40x_6um.avi: [testng] [2024-12-06 11:34:11,743] [pool-1-thread-5] Initializing /data/jcb/JCB 201203159/JCB_201203159_0_3.avi: [testng] [2024-12-06 11:34:11,906] [pool-1-thread-11] Initializing /data/kurt/63x_6um.avi: [testng] [2024-12-06 11:34:12,102] [pool-1-thread-12] Initializing /data/qa-7560/Ex9 ALADIN WT KO KI_DIC_ 31_07_2013_M1.avi: [testng] [2024-12-06 11:34:12,513] [pool-1-thread-4] Initializing /data/qa-11011/M-flow10001.avi: [testng] [2024-12-06 11:34:12,849] [pool-1-thread-8] Initializing /data/kurt/40x_6um_2.avi: [testng] [2024-12-06 11:34:13,127] [pool-1-thread-10] Initializing /data/chip_avi/Level003-DB-089.avi: [testng] [2024-12-06 11:34:13,352] [pool-1-thread-3] Initializing /data/jules/GUV_long15N_10_10mb_debut_26102011_4.avi: [testng] [2024-12-06 11:34:14,783] [pool-1-thread-1] Initializing /data/simon/24_bit_problem.avi: [testng] [2024-12-06 11:34:15,068] [pool-1-thread-6] Initializing /data/roger/op9middle40x.lsm movie 4.avi: [testng] [2024-12-06 11:34:15,302] [pool-1-thread-7] Initializing /data/roger/spheroid1.lsm movie.avi: [testng] [2024-12-06 11:34:15,811] [pool-1-thread-2] Initializing /data/prairie/cornea dc and macs.AVI: [testng] [2024-12-06 11:34:18,276] [pool-1-thread-5] Initializing /data/jcb/JCB 201203159/JCB_201203159_0_5.avi: [testng] [2024-12-06 11:34:18,548] [pool-1-thread-10] Initializing /data/sample-avis/rgb-odd-width/HyperStack.avi: [testng] [2024-12-06 11:34:18,805] [pool-1-thread-1] Initializing /data/ascb/TIRF.avi: [testng] [2024-12-06 11:34:19,388] [pool-1-thread-6] Initializing /data/jules/GUV_long15N_10_20mb_debut_25102011_1_BW.avi: [testng] [2024-12-06 11:34:19,753] [pool-1-thread-7] Initializing /data/chris/APZ04_009.avi: [testng] [2024-12-06 11:34:21,639] [pool-1-thread-4] Initializing /data/roger/op9middle40x.lsm movie 2.avi: [testng] [2024-12-06 11:34:21,857] [pool-1-thread-9] Initializing /data/chip_avi/Level002-DB-090.avi: [testng] [2024-12-06 11:34:22,031] [pool-1-thread-8] Initializing /data/jae/20xD_5minfor14h.avi: [testng] [2024-12-06 11:34:22,357] [pool-1-thread-11] Initializing /data/roger/spheroid1-crop.lsm movie 2.avi: [testng] [2024-12-06 11:34:22,717] [pool-1-thread-2] Initializing /data/curtis/mri-stack-ij-old.avi: [testng] [2024-12-06 11:34:23,960] [pool-1-thread-5] Initializing /data/curtis/mri-stack-bf.avi: [testng] [2024-12-06 11:34:24,195] [pool-1-thread-10] Initializing /data/qa-5019/nemo-2_1_.avi: [testng] [2024-12-06 11:34:25,323] [pool-1-thread-9] Initializing /data/roger/spheroid1-crop.lsm movie.avi: [testng] [2024-12-06 11:34:25,616] [pool-1-thread-12] Initializing /data/qa-4232/11051920xdrywithincubatoronthenoff_Subset.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 20 seconds Finished: SUCCESS