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Started by upstream project "BIOFORMATS-test-repo" build number 2 originally caused by: Started by upstream project "Trigger" build number 3 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9 [BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins9625336505003409271.sh + '[' avi = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_220_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] 01:10:11,568 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:10:11,569 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 01:10:11,569 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:10:11,571 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:10:11,571 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:10:11,571 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:10:11,571 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:10:11,571 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:10:11,572 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:10:11,572 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:10:11,572 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:10:11,572 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:10:11,852 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:10:11,852 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:10:11,880 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:10:11,880 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:10:11,889 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:10:11,889 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:10:11,889 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:10:11,889 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:10:11,890 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 01:10:11,890 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 01:10:11,891 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 318 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-15 01:10:11,901] [main] java.version = 1.8.0_342 [testng] 01:10:11,904 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:10:11,905 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:10:11,951 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-15_01-10-11.log] [testng] 01:10:11,952 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-03-15 01:10:11,954] [main] testng.directory = /data [testng] [2024-03-15 01:10:11,955] [main] testng.configDirectory = /config [testng] [2024-03-15 01:10:11,968] [main] testng.multiplier = 1.0 [testng] [2024-03-15 01:10:11,969] [main] testng.in-memory = false [testng] [2024-03-15 01:10:11,969] [main] testng.allow-missing = false [testng] [2024-03-15 01:10:11,969] [main] user.language = en [testng] [2024-03-15 01:10:11,969] [main] user.country = ${user.country} [testng] [2024-03-15 01:10:11,969] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-03-15 01:10:13,146] [main] ---------------------------------------- [testng] [2024-03-15 01:10:13,146] [main] Total files: 40 [testng] [2024-03-15 01:10:13,146] [main] Scan time: 1.177 s (29 ms/file) [testng] [2024-03-15 01:10:13,146] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 38 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-15 01:14:57,059] [pool-1-thread-1] Initializing /data/roger/op9middle40x.lsm movie 4.avi: [testng] 01:14:57,060 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:14:57,060 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:14:57,061 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-15_01-14-57.log] [testng] 01:14:57,061 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6bd7348f - End of configuration. [testng] [2024-03-15 01:14:57,162] [pool-1-thread-12] Initializing /data/kurt/40x_6um_2.avi: [testng] 01:14:57,162 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:14:57,162 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:14:57,163 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-15_01-14-57.log] [testng] 01:14:57,163 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d9df623 - End of configuration. [testng] [2024-03-15 01:14:57,246] [pool-1-thread-11] Initializing /data/curtis/mri-stack-ij-old.avi: [testng] 01:14:57,246 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:14:57,246 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:14:57,247 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-15_01-14-57.log] [testng] 01:14:57,247 |-INFO in ch.qos.logback.core.sift.SiftProcessor@24088d66 - End of configuration. [testng] [2024-03-15 01:14:57,324] [pool-1-thread-10] Initializing /data/roger/spheroid1-crop.lsm movie 2.avi: [testng] 01:14:57,324 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:14:57,324 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:14:57,325 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-15_01-14-57.log] [testng] 01:14:57,325 |-INFO in ch.qos.logback.core.sift.SiftProcessor@301ed043 - End of configuration. [testng] [2024-03-15 01:14:57,492] [pool-1-thread-9] Initializing /data/sample-avis/rgb-odd-width/HyperStack.avi: [testng] 01:14:57,493 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:14:57,493 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:14:57,493 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-15_01-14-57.log] [testng] 01:14:57,494 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d1430b7 - End of configuration. [testng] [2024-03-15 01:14:57,538] [pool-1-thread-8] Initializing /data/chris/APZ04_009.avi: [testng] 01:14:57,538 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:14:57,538 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:14:57,539 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-15_01-14-57.log] [testng] 01:14:57,539 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4cdd944 - End of configuration. [testng] [2024-03-15 01:15:00,433] [pool-1-thread-7] Initializing /data/qa-7560/Ex9 ALADIN WT KO KI_DIC_ 31_07_2013_M1.avi: [testng] 01:15:00,434 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:15:00,434 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:15:00,434 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-15_01-15-00.log] [testng] 01:15:00,435 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4af35253 - End of configuration. [testng] [2024-03-15 01:15:00,783] [pool-1-thread-6] Initializing /data/prairie/cornea dc and macs.AVI: [testng] 01:15:00,783 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:15:00,783 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:15:00,783 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-15_01-15-00.log] [testng] 01:15:00,784 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2c9a6c6 - End of configuration. [testng] [2024-03-15 01:15:00,893] [pool-1-thread-5] Initializing /data/jcb/JCB 201203159/JCB_201203159_0_5.avi: [testng] 01:15:00,893 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:15:00,893 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:15:00,894 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-15_01-15-00.log] [testng] 01:15:00,894 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1bb0da1d - End of configuration. [testng] [2024-03-15 01:15:00,953] [pool-1-thread-4] Initializing /data/chip_avi/Level002-DB-090.avi: [testng] 01:15:00,954 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:15:00,954 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:15:00,954 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-15_01-15-00.log] [testng] 01:15:00,955 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f399688 - End of configuration. [testng] [2024-03-15 01:15:01,014] [pool-1-thread-3] Initializing /data/qa-5019/nemo-2_1_.avi: [testng] 01:15:01,014 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:15:01,014 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:15:01,015 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-15_01-15-01.log] [testng] 01:15:01,015 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e763b18 - End of configuration. [testng] [2024-03-15 01:15:01,122] [pool-1-thread-2] Initializing /data/qa-7450/MVI_3610.AVI: [testng] 01:15:01,122 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:15:01,123 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:15:01,123 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-15_01-15-01.log] [testng] 01:15:01,124 |-INFO in ch.qos.logback.core.sift.SiftProcessor@49c3dccb - End of configuration. [testng] [2024-03-15 01:15:03,088] [pool-1-thread-9] Initializing /data/sample-avis/extra-chunk/HyperStack.avi: [testng] [2024-03-15 01:15:03,117] [pool-1-thread-11] Initializing /data/kurt/63x_6um.avi: [testng] [2024-03-15 01:15:03,188] [pool-1-thread-5] Initializing /data/chip_avi/Level004-WA-116.avi: [testng] [2024-03-15 01:15:03,317] [pool-1-thread-4] Initializing /data/jules/GUV_long15N_10_20mb_debut_25102011_1_BW.avi: [testng] [2024-03-15 01:15:03,406] [pool-1-thread-3] Initializing /data/william/worm.avi: [testng] [2024-03-15 01:15:03,500] [pool-1-thread-1] Initializing /data/roger/op9middle40x.lsm movie.avi: [testng] [2024-03-15 01:15:03,658] [pool-1-thread-2] Initializing /data/qa-4232/11051920xdrywithincubatoronthenoff_Subset.avi: [testng] [2024-03-15 01:15:03,836] [pool-1-thread-10] Initializing /data/roger/op9middle40x.lsm movie 2.avi: [testng] [2024-03-15 01:15:03,949] [pool-1-thread-6] Initializing /data/ascb/TIRF.avi: [testng] [2024-03-15 01:15:04,624] [pool-1-thread-12] Initializing /data/pki/yinghua_USPI2-ASMKT772_111017100001_C10_f1.avi: [testng] [2024-03-15 01:15:04,988] [pool-1-thread-9] Initializing /data/jcb/JCB 201203159/JCB_201203159_0_4.avi: [testng] [2024-03-15 01:15:05,060] [pool-1-thread-3] Initializing /data/qa-11011/M-flow10001.avi: [testng] [2024-03-15 01:15:05,230] [pool-1-thread-5] Initializing /data/jules/GUV_long15N_10_10mb_debut_26102011_4.avi: [testng] [2024-03-15 01:15:09,394] [pool-1-thread-4] Initializing /data/simon/24_bit_problem.avi: [testng] [2024-03-15 01:15:09,558] [pool-1-thread-2] Initializing /data/chip_avi/Level001-ES-083.avi: [testng] [2024-03-15 01:15:09,643] [pool-1-thread-1] Initializing /data/kurt/40x_6um.avi: [testng] [2024-03-15 01:15:09,718] [pool-1-thread-10] Initializing /data/curtis/mri-stack-bf.avi: [testng] [2024-03-15 01:15:09,884] [pool-1-thread-11] Initializing /data/jcb/JCB 201203159/JCB_201203159_0_3.avi: [testng] [2024-03-15 01:15:09,942] [pool-1-thread-6] Initializing /data/chip_avi/Level003-DB-089.avi: [testng] [2024-03-15 01:15:09,981] [pool-1-thread-9] Initializing /data/roger/spheroid1-crop.lsm movie.avi: [testng] [2024-03-15 01:15:10,024] [pool-1-thread-7] Initializing /data/roger/op9middle40x.lsm movie 3.avi: [testng] [2024-03-15 01:15:10,174] [pool-1-thread-12] Initializing /data/jae/20xD_5minfor14h.avi: [testng] [2024-03-15 01:15:10,609] [pool-1-thread-2] Initializing /data/curtis/mri-stack-ij-new.avi: [testng] [2024-03-15 01:15:10,751] [pool-1-thread-11] Initializing /data/qa-7336/2X_63X-DAPI-Emilin2_Filter_Render_Series.avi: [testng] [2024-03-15 01:15:10,825] [pool-1-thread-10] Initializing /data/roger/spheroid1.lsm movie.avi: [testng] [2024-03-15 01:15:10,978] [pool-1-thread-6] Initializing /data/qa-5019/nemo-2_10_20.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 10 seconds Finished: SUCCESS