Started by upstream project "BIOFORMATS-test-repo" build number 67
originally caused by:
Started by upstream project "Trigger" build number 75
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5
[BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins5639963505309166466.sh
+ '[' avi = slidebook ']'
++ date +%u
+ '[' 6 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_10063_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] 02:03:48,790 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 02:03:48,792 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service.
[testng] 02:03:48,792 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:03:48,794 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:03:48,794 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 02:03:48,795 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 02:03:48,795 |-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] 02:03:48,795 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:03:48,796 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:03:48,797 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 02:03:48,797 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 02:03:48,798 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 02:03:49,236 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 02:03:49,236 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 02:03:49,273 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 02:03:49,273 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 02:03:49,397 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 02:03:49,398 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 02:03:49,398 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 02:03:49,398 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 02:03:49,398 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration.
[testng] 02:03:49,399 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point
[testng] 02:03:49,399 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 603 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-05-18 02:03:49,409] [main] java.version = 11.0.16
[testng] 02:03:49,413 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 02:03:49,413 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:03:49,621 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-18_02-03-49.log]
[testng] 02:03:49,624 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration.
[testng] [2024-05-18 02:03:49,647] [main] testng.directory = /data
[testng] [2024-05-18 02:03:49,647] [main] testng.configDirectory = /config
[testng] [2024-05-18 02:03:49,737] [main] testng.multiplier = 1.0
[testng] [2024-05-18 02:03:49,739] [main] testng.in-memory = false
[testng] [2024-05-18 02:03:49,740] [main] testng.allow-missing = false
[testng] [2024-05-18 02:03:49,740] [main] user.language = en
[testng] [2024-05-18 02:03:49,740] [main] user.country = ${user.country}
[testng] [2024-05-18 02:03:49,740] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-05-18 02:03:51,381] [main] ----------------------------------------
[testng] [2024-05-18 02:03:51,381] [main] Total files: 40
[testng] [2024-05-18 02:03:51,381] [main] Scan time: 1.641 s (41 ms/file)
[testng] [2024-05-18 02:03:51,381] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 38 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-05-18 02:08:09,463] [pool-1-thread-1] Initializing /data/kurt/63x_6um.avi:
[testng] 02:08:09,465 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 02:08:09,465 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:08:09,467 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-18_02-08-09.log]
[testng] 02:08:09,468 |-INFO in ch.qos.logback.core.sift.SiftProcessor@408d1ba9 - End of configuration.
[testng] [2024-05-18 02:08:09,617] [pool-1-thread-12] Initializing /data/ascb/TIRF.avi:
[testng] 02:08:09,618 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 02:08:09,618 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:08:09,619 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-18_02-08-09.log]
[testng] 02:08:09,620 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a015a1a - End of configuration.
[testng] [2024-05-18 02:08:10,041] [pool-1-thread-11] Initializing /data/curtis/mri-stack-ij-new.avi:
[testng] 02:08:10,042 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 02:08:10,042 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:08:10,043 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-18_02-08-10.log]
[testng] 02:08:10,044 |-INFO in ch.qos.logback.core.sift.SiftProcessor@346e2887 - End of configuration.
[testng] [2024-05-18 02:08:10,067] [pool-1-thread-10] Initializing /data/jcb/JCB 201203159/JCB_201203159_0_5.avi:
[testng] 02:08:10,067 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 02:08:10,067 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:08:10,068 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-18_02-08-10.log]
[testng] 02:08:10,069 |-INFO in ch.qos.logback.core.sift.SiftProcessor@343274f1 - End of configuration.
[testng] [2024-05-18 02:08:10,133] [pool-1-thread-9] Initializing /data/qa-7450/MVI_3610.AVI:
[testng] 02:08:10,134 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 02:08:10,134 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:08:10,135 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-18_02-08-10.log]
[testng] 02:08:10,136 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b3f1659 - End of configuration.
[testng] [2024-05-18 02:08:10,210] [pool-1-thread-8] Initializing /data/roger/spheroid1-crop.lsm movie 2.avi:
[testng] 02:08:10,211 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 02:08:10,211 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:08:10,212 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-18_02-08-10.log]
[testng] 02:08:10,212 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18aeb771 - End of configuration.
[testng] [2024-05-18 02:08:10,274] [pool-1-thread-7] Initializing /data/chip_avi/Level002-DB-090.avi:
[testng] 02:08:10,275 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 02:08:10,275 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:08:10,276 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-18_02-08-10.log]
[testng] 02:08:10,276 |-INFO in ch.qos.logback.core.sift.SiftProcessor@639aa4f9 - End of configuration.
[testng] [2024-05-18 02:08:10,300] [pool-1-thread-6] Initializing /data/jules/GUV_long15N_10_10mb_debut_26102011_4.avi:
[testng] 02:08:10,301 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 02:08:10,301 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:08:10,302 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-18_02-08-10.log]
[testng] 02:08:10,302 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ffc23ab - End of configuration.
[testng] [2024-05-18 02:08:21,397] [pool-1-thread-5] Initializing /data/qa-5019/nemo-2_1_.avi:
[testng] 02:08:21,397 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 02:08:21,397 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:08:21,398 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-18_02-08-21.log]
[testng] 02:08:21,398 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c8ed7b7 - End of configuration.
[testng] [2024-05-18 02:08:21,433] [pool-1-thread-4] Initializing /data/pki/yinghua_USPI2-ASMKT772_111017100001_C10_f1.avi:
[testng] 02:08:21,433 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 02:08:21,434 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:08:21,434 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-18_02-08-21.log]
[testng] 02:08:21,435 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4edc9d60 - End of configuration.
[testng] [2024-05-18 02:08:21,461] [pool-1-thread-3] Initializing /data/chris/APZ04_009.avi:
[testng] 02:08:21,462 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 02:08:21,462 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:08:21,463 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-18_02-08-21.log]
[testng] 02:08:21,463 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6f136187 - End of configuration.
[testng] [2024-05-18 02:08:27,180] [pool-1-thread-2] Initializing /data/simon/24_bit_problem.avi:
[testng] 02:08:27,180 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 02:08:27,180 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:08:27,181 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-18_02-08-27.log]
[testng] 02:08:27,182 |-INFO in ch.qos.logback.core.sift.SiftProcessor@23d4a626 - End of configuration.
[testng] [2024-05-18 02:08:30,027] [pool-1-thread-11] Initializing /data/roger/op9middle40x.lsm movie.avi:
[testng] [2024-05-18 02:08:30,064] [pool-1-thread-7] Initializing /data/kurt/40x_6um_2.avi:
[testng] [2024-05-18 02:08:30,123] [pool-1-thread-10] Initializing /data/chip_avi/Level001-ES-083.avi:
[testng] [2024-05-18 02:08:30,144] [pool-1-thread-2] Initializing /data/roger/spheroid1-crop.lsm movie.avi:
[testng] [2024-05-18 02:08:30,186] [pool-1-thread-12] Initializing /data/william/worm.avi:
[testng] [2024-05-18 02:08:30,197] [pool-1-thread-4] Initializing /data/qa-4232/11051920xdrywithincubatoronthenoff_Subset.avi:
[testng] [2024-05-18 02:08:30,224] [pool-1-thread-5] Initializing /data/prairie/cornea dc and macs.AVI:
[testng] [2024-05-18 02:08:30,274] [pool-1-thread-9] Initializing /data/curtis/mri-stack-ij-old.avi:
[testng] [2024-05-18 02:08:30,394] [pool-1-thread-8] Initializing /data/roger/op9middle40x.lsm movie 3.avi:
[testng] [2024-05-18 02:08:30,656] [pool-1-thread-1] Initializing /data/roger/op9middle40x.lsm movie 4.avi:
[testng] [2024-05-18 02:08:30,852] [pool-1-thread-12] Initializing /data/qa-11011/M-flow10001.avi:
[testng] [2024-05-18 02:08:31,071] [pool-1-thread-9] Initializing /data/jcb/JCB 201203159/JCB_201203159_0_3.avi:
[testng] [2024-05-18 02:08:31,160] [pool-1-thread-10] Initializing /data/kurt/40x_6um.avi:
[testng] [2024-05-18 02:08:31,377] [pool-1-thread-4] Initializing /data/jae/20xD_5minfor14h.avi:
[testng] [2024-05-18 02:08:32,418] [pool-1-thread-11] Initializing /data/roger/spheroid1.lsm movie.avi:
[testng] [2024-05-18 02:08:32,526] [pool-1-thread-2] Initializing /data/roger/op9middle40x.lsm movie 2.avi:
[testng] [2024-05-18 02:08:32,600] [pool-1-thread-9] Initializing /data/sample-avis/extra-chunk/HyperStack.avi:
[testng] [2024-05-18 02:08:32,704] [pool-1-thread-8] Initializing /data/qa-5019/nemo-2_10_20.avi:
[testng] [2024-05-18 02:08:33,092] [pool-1-thread-9] Initializing /data/jules/GUV_long15N_10_20mb_debut_25102011_1_BW.avi:
[testng] [2024-05-18 02:08:33,418] [pool-1-thread-1] Initializing /data/curtis/mri-stack-bf.avi:
[testng] [2024-05-18 02:08:33,552] [pool-1-thread-5] Initializing /data/qa-7336/2X_63X-DAPI-Emilin2_Filter_Render_Series.avi:
[testng] [2024-05-18 02:08:33,794] [pool-1-thread-7] Initializing /data/chip_avi/Level003-DB-089.avi:
[testng] [2024-05-18 02:08:33,939] [pool-1-thread-12] Initializing /data/chip_avi/Level004-WA-116.avi:
[testng] [2024-05-18 02:08:34,151] [pool-1-thread-8] Initializing /data/jcb/JCB 201203159/JCB_201203159_0_4.avi:
[testng] [2024-05-18 02:08:34,234] [pool-1-thread-10] Initializing /data/sample-avis/rgb-odd-width/HyperStack.avi:
[testng] [2024-05-18 02:08:34,321] [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: 4 minutes 59 seconds
Finished: SUCCESS