Started by upstream project "BIOFORMATS-test-repo" build number 28
originally caused by:
Started by upstream project "Trigger" build number 31
originally caused by:
Started by timer
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/jenkins14266323137482147155.sh
+ '[' avi = slidebook ']'
++ date +%u
+ '[' 2 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_3666_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] 01:59:25,909 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:59:25,911 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service.
[testng] 01:59:25,911 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:59:25,912 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:59:25,913 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:59:25,913 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:59:25,913 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 01:59:25,913 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:59:25,914 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:59:25,915 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:59:25,915 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:59:25,915 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:59:26,138 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:59:26,138 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:59:26,163 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:59:26,163 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:59:26,169 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:59:26,169 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:59:26,169 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:59:26,170 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:59:26,170 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration.
[testng] 01:59:26,171 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point
[testng] 01:59:26,171 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 257 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-04-09 01:59:26,185] [main] java.version = 11.0.16
[testng] 01:59:26,190 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:59:26,190 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:59:26,256 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-09_01-59-26.log]
[testng] 01:59:26,258 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration.
[testng] [2024-04-09 01:59:26,262] [main] testng.directory = /data
[testng] [2024-04-09 01:59:26,262] [main] testng.configDirectory = /config
[testng] [2024-04-09 01:59:26,272] [main] testng.multiplier = 1.0
[testng] [2024-04-09 01:59:26,274] [main] testng.in-memory = false
[testng] [2024-04-09 01:59:26,274] [main] testng.allow-missing = false
[testng] [2024-04-09 01:59:26,274] [main] user.language = en
[testng] [2024-04-09 01:59:26,274] [main] user.country = ${user.country}
[testng] [2024-04-09 01:59:26,274] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-04-09 01:59:27,206] [main] ----------------------------------------
[testng] [2024-04-09 01:59:27,206] [main] Total files: 40
[testng] [2024-04-09 01:59:27,207] [main] Scan time: 0.932 s (23 ms/file)
[testng] [2024-04-09 01:59:27,207] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 38 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-04-09 02:03:48,207] [pool-1-thread-1] Initializing /data/kurt/63x_6um.avi:
[testng] 02:03:48,208 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 02:03:48,208 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:03:48,210 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-09_02-03-48.log]
[testng] 02:03:48,211 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ceb2fb6 - End of configuration.
[testng] [2024-04-09 02:03:48,323] [pool-1-thread-12] Initializing /data/ascb/TIRF.avi:
[testng] 02:03:48,324 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 02:03:48,324 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:03:48,327 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-09_02-03-48.log]
[testng] 02:03:48,328 |-INFO in ch.qos.logback.core.sift.SiftProcessor@788e41a8 - End of configuration.
[testng] [2024-04-09 02:03:48,686] [pool-1-thread-11] Initializing /data/curtis/mri-stack-ij-new.avi:
[testng] 02:03:48,687 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 02:03:48,687 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:03:48,688 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-09_02-03-48.log]
[testng] 02:03:48,688 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71b9fa65 - End of configuration.
[testng] [2024-04-09 02:03:48,703] [pool-1-thread-10] Initializing /data/jcb/JCB 201203159/JCB_201203159_0_5.avi:
[testng] 02:03:48,703 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 02:03:48,703 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:03:48,704 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-09_02-03-48.log]
[testng] 02:03:48,705 |-INFO in ch.qos.logback.core.sift.SiftProcessor@239bcefa - End of configuration.
[testng] [2024-04-09 02:03:48,753] [pool-1-thread-9] Initializing /data/qa-7450/MVI_3610.AVI:
[testng] 02:03:48,753 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 02:03:48,753 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:03:48,754 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-09_02-03-48.log]
[testng] 02:03:48,755 |-INFO in ch.qos.logback.core.sift.SiftProcessor@58c0ba83 - End of configuration.
[testng] [2024-04-09 02:03:48,811] [pool-1-thread-8] Initializing /data/roger/spheroid1-crop.lsm movie 2.avi:
[testng] 02:03:48,812 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 02:03:48,812 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:03:48,813 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-09_02-03-48.log]
[testng] 02:03:48,813 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6dc302c5 - End of configuration.
[testng] [2024-04-09 02:03:48,872] [pool-1-thread-7] Initializing /data/chip_avi/Level002-DB-090.avi:
[testng] 02:03:48,873 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 02:03:48,873 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:03:48,873 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-09_02-03-48.log]
[testng] 02:03:48,874 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78be4bcc - End of configuration.
[testng] [2024-04-09 02:03:48,890] [pool-1-thread-6] Initializing /data/jules/GUV_long15N_10_10mb_debut_26102011_4.avi:
[testng] 02:03:48,890 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 02:03:48,890 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:03:48,891 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-09_02-03-48.log]
[testng] 02:03:48,891 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4aae8575 - End of configuration.
[testng] [2024-04-09 02:03:53,449] [pool-1-thread-5] Initializing /data/qa-5019/nemo-2_1_.avi:
[testng] 02:03:53,449 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 02:03:53,449 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:03:53,450 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-09_02-03-53.log]
[testng] 02:03:53,451 |-INFO in ch.qos.logback.core.sift.SiftProcessor@178552de - End of configuration.
[testng] [2024-04-09 02:03:53,485] [pool-1-thread-4] Initializing /data/pki/yinghua_USPI2-ASMKT772_111017100001_C10_f1.avi:
[testng] 02:03:53,486 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 02:03:53,486 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:03:53,487 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-09_02-03-53.log]
[testng] 02:03:53,487 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a9ce216 - End of configuration.
[testng] [2024-04-09 02:03:53,512] [pool-1-thread-3] Initializing /data/chris/APZ04_009.avi:
[testng] 02:03:53,512 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 02:03:53,512 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:03:53,513 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-09_02-03-53.log]
[testng] 02:03:53,513 |-INFO in ch.qos.logback.core.sift.SiftProcessor@313594dc - End of configuration.
[testng] [2024-04-09 02:03:58,149] [pool-1-thread-2] Initializing /data/simon/24_bit_problem.avi:
[testng] 02:03:58,149 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 02:03:58,149 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:03:58,150 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-09_02-03-58.log]
[testng] 02:03:58,151 |-INFO in ch.qos.logback.core.sift.SiftProcessor@404be8a7 - End of configuration.
[testng] [2024-04-09 02:04:00,246] [pool-1-thread-10] Initializing /data/roger/op9middle40x.lsm movie.avi:
[testng] [2024-04-09 02:04:00,271] [pool-1-thread-11] Initializing /data/chip_avi/Level001-ES-083.avi:
[testng] [2024-04-09 02:04:00,291] [pool-1-thread-7] Initializing /data/roger/spheroid1-crop.lsm movie.avi:
[testng] [2024-04-09 02:04:00,344] [pool-1-thread-5] Initializing /data/william/worm.avi:
[testng] [2024-04-09 02:04:00,355] [pool-1-thread-4] Initializing /data/qa-4232/11051920xdrywithincubatoronthenoff_Subset.avi:
[testng] [2024-04-09 02:04:00,386] [pool-1-thread-12] Initializing /data/prairie/cornea dc and macs.AVI:
[testng] [2024-04-09 02:04:00,424] [pool-1-thread-2] Initializing /data/curtis/mri-stack-ij-old.avi:
[testng] [2024-04-09 02:04:00,598] [pool-1-thread-9] Initializing /data/kurt/40x_6um_2.avi:
[testng] [2024-04-09 02:04:00,689] [pool-1-thread-8] Initializing /data/roger/op9middle40x.lsm movie 3.avi:
[testng] [2024-04-09 02:04:01,005] [pool-1-thread-5] Initializing /data/roger/op9middle40x.lsm movie 4.avi:
[testng] [2024-04-09 02:04:01,039] [pool-1-thread-2] Initializing /data/qa-11011/M-flow10001.avi:
[testng] [2024-04-09 02:04:01,303] [pool-1-thread-1] Initializing /data/jcb/JCB 201203159/JCB_201203159_0_3.avi:
[testng] [2024-04-09 02:04:01,362] [pool-1-thread-11] Initializing /data/kurt/40x_6um.avi:
[testng] [2024-04-09 02:04:01,697] [pool-1-thread-4] Initializing /data/jae/20xD_5minfor14h.avi:
[testng] [2024-04-09 02:04:02,503] [pool-1-thread-1] Initializing /data/roger/spheroid1.lsm movie.avi:
[testng] [2024-04-09 02:04:02,573] [pool-1-thread-10] Initializing /data/roger/op9middle40x.lsm movie 2.avi:
[testng] [2024-04-09 02:04:02,703] [pool-1-thread-7] Initializing /data/sample-avis/extra-chunk/HyperStack.avi:
[testng] [2024-04-09 02:04:02,802] [pool-1-thread-8] Initializing /data/qa-5019/nemo-2_10_20.avi:
[testng] [2024-04-09 02:04:02,884] [pool-1-thread-5] Initializing /data/jules/GUV_long15N_10_20mb_debut_25102011_1_BW.avi:
[testng] [2024-04-09 02:04:02,974] [pool-1-thread-12] Initializing /data/curtis/mri-stack-bf.avi:
[testng] [2024-04-09 02:04:02,989] [pool-1-thread-7] Initializing /data/qa-7336/2X_63X-DAPI-Emilin2_Filter_Render_Series.avi:
[testng] [2024-04-09 02:04:03,069] [pool-1-thread-9] Initializing /data/chip_avi/Level003-DB-089.avi:
[testng] [2024-04-09 02:04:03,456] [pool-1-thread-12] Initializing /data/chip_avi/Level004-WA-116.avi:
[testng] [2024-04-09 02:04:03,673] [pool-1-thread-9] Initializing /data/jcb/JCB 201203159/JCB_201203159_0_4.avi:
[testng] [2024-04-09 02:04:03,708] [pool-1-thread-10] Initializing /data/sample-avis/rgb-odd-width/HyperStack.avi:
[testng] [2024-04-09 02:04:03,758] [pool-1-thread-8] 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: 4 minutes 48 seconds
Finished: SUCCESS