Started by upstream project "BIOFORMATS-test-repo" build number 113
originally caused by:
Started by upstream project "Trigger" build number 126
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/jenkins7298354327275800687.sh
+ '[' incell = slidebook ']'
++ date +%u
+ '[' 6 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_17641_merge_ci -v /uod/idr/repos/curated/incell:/data -v /uod/idr-scratch/merge-ci/curated/incell:/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] 02:11:04,630 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 02:11:04,633 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service.
[testng] 02:11:04,633 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:11:04,634 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:11:04,634 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 02:11:04,635 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 02:11:04,635 |-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] 02:11:04,635 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:11:04,636 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:11:04,636 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 02:11:04,636 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 02:11:04,637 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 02:11:04,814 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 02:11:04,814 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 02:11:04,838 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 02:11:04,838 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 02:11:04,844 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 02:11:04,844 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 02:11:04,844 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 02:11:04,844 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 02:11:04,845 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration.
[testng] 02:11:04,846 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point
[testng] 02:11:04,846 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 211 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-07-06 02:11:04,860] [main] java.version = 11.0.16
[testng] 02:11:04,865 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 02:11:04,865 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:11:04,932 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-06_02-11-04.log]
[testng] 02:11:04,934 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration.
[testng] [2024-07-06 02:11:04,938] [main] testng.directory = /data
[testng] [2024-07-06 02:11:04,938] [main] testng.configDirectory = /config
[testng] [2024-07-06 02:11:04,948] [main] testng.multiplier = 1.0
[testng] [2024-07-06 02:11:04,949] [main] testng.in-memory = false
[testng] [2024-07-06 02:11:04,949] [main] testng.allow-missing = false
[testng] [2024-07-06 02:11:04,949] [main] user.language = en
[testng] [2024-07-06 02:11:04,949] [main] user.country = ${user.country}
[testng] [2024-07-06 02:11:04,949] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-07-06 02:16:47,560] [main] ----------------------------------------
[testng] [2024-07-06 02:16:47,561] [main] Total files: 4190
[testng] [2024-07-06 02:16:47,561] [main] Scan time: 342.611 s (81 ms/file)
[testng] [2024-07-06 02:16:47,562] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 27 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-07-06 02:17:02,626] [pool-1-thread-1] Initializing /data/damir/20x Z1 16fields Gr Rd DAPI Cy5_140610-3_fix_2.xdce:
[testng] 02:17:02,626 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 02:17:02,627 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:17:02,629 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-06_02-17-02.log]
[testng] 02:17:02,630 |-INFO in ch.qos.logback.core.sift.SiftProcessor@189bd47d - End of configuration.
[testng] [2024-07-06 02:17:05,647] [pool-1-thread-12] Initializing /data/brian/Proper Dark Images/2007.11.12.13.37.27.xdce:
[testng] 02:17:05,648 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 02:17:05,648 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:17:05,653 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-06_02-17-05.log]
[testng] 02:17:05,653 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e93a9f9 - End of configuration.
[testng] [2024-07-06 02:17:05,685] [pool-1-thread-11] Initializing /data/karsten/gabriele_-1_2/gabriele_-1_2.xdce:
[testng] 02:17:05,685 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 02:17:05,685 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:17:05,686 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-06_02-17-05.log]
[testng] 02:17:05,686 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f8cbb6 - End of configuration.
[testng] [2024-07-06 02:17:05,732] [pool-1-thread-10] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_IM/2009_97_238_IM/2009_97_238_IM.xdce:
[testng] 02:17:05,732 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 02:17:05,732 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:17:05,733 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-06_02-17-05.log]
[testng] 02:17:05,734 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37ca42c4 - End of configuration.
[testng] [2024-07-06 02:17:05,891] [pool-1-thread-9] Initializing /data/michael/Single plane no flatfield corr/2007.10.17.17.04.55.xdce:
[testng] 02:17:05,891 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 02:17:05,891 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:17:05,892 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-06_02-17-05.log]
[testng] 02:17:05,893 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e856d20 - End of configuration.
[testng] [2024-07-06 02:17:05,965] [pool-1-thread-8] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_Tif/ER2009_97_238_TIFF/PC3_ER2009.97.238.xdce:
[testng] 02:17:05,965 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 02:17:05,965 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:17:05,966 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-06_02-17-05.log]
[testng] 02:17:05,967 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60f9896d - End of configuration.
[testng] [2024-07-06 02:17:06,126] [pool-1-thread-7] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_Tif/ER2009_97_240_TIFF/PC3_ER2009.97.240(ok).xdce:
[testng] 02:17:06,126 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 02:17:06,126 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:17:06,127 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-06_02-17-06.log]
[testng] 02:17:06,127 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40072fd6 - End of configuration.
[testng] [2024-07-06 02:17:06,276] [pool-1-thread-6] Initializing /data/public/INMAC384-DAPI-CM-eGFP_59223_1/INMAC384-DAPI-CM-eGFP_59223_1.xdce:
[testng] 02:17:06,277 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 02:17:06,277 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:17:06,278 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-06_02-17-06.log]
[testng] 02:17:06,278 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1fa3d134 - End of configuration.
[testng] [2024-07-06 02:17:06,868] [pool-1-thread-5] Initializing /data/public/idr0017/2011-11-17_X-Man_LOPAC_X01_LP_S01_1/2011-11-17 X-Man LOPAC_X03_LP_S01_1.xdce:
[testng] 02:17:06,868 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 02:17:06,868 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:17:06,869 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-06_02-17-06.log]
[testng] 02:17:06,870 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f597d5a - End of configuration.
[testng] [2024-07-06 02:17:07,002] [pool-1-thread-4] Initializing /data/brian/H2Blivecell20x/H2Blivecell20x.xdce:
[testng] 02:17:07,003 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 02:17:07,003 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:17:07,003 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-06_02-17-07.log]
[testng] 02:17:07,004 |-INFO in ch.qos.logback.core.sift.SiftProcessor@45ea74fd - End of configuration.
[testng] [2024-07-06 02:17:07,868] [pool-1-thread-3] Initializing /data/karsten/gabriele_-1_2/~gabriele_-1_2.xdce:
[testng] 02:17:07,869 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 02:17:07,869 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:17:07,870 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-06_02-17-07.log]
[testng] 02:17:07,870 |-INFO in ch.qos.logback.core.sift.SiftProcessor@28f63e13 - End of configuration.
[testng] [2024-07-06 02:17:07,953] [pool-1-thread-2] Initializing /data/samples/images_number_mismatch/test.xdce:
[testng] 02:17:07,953 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 02:17:07,953 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:17:07,954 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-06_02-17-07.log]
[testng] 02:17:07,954 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a50b5dc - End of configuration.
[testng] [2024-07-06 02:17:12,062] [pool-1-thread-12] Initializing /data/frans/im dataset/PC3_ER2009.97.180_IM.xdce:
[testng] [2024-07-06 02:17:22,212] [pool-1-thread-2] Initializing /data/samples/variable-field-count/test.xdce:
[testng] [2024-07-06 02:17:36,055] [pool-1-thread-2] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_IM/2009_97_239_IM/2009_97_239_IM.xdce:
[testng] [2024-07-06 02:17:37,517] [pool-1-thread-9] Initializing /data/frans/incell_25juni2009/ANALYZE files/plaat HR 38/excel output file/HCT116_HR2009.97.038/HCT116_HR2009.97.038.xdce:
[testng] [2024-07-06 02:17:48,142] [pool-1-thread-11] Initializing /data/michael/firstStack/2007.07.05.17.33.35.xdce:
[testng] [2024-07-06 02:17:48,199] [pool-1-thread-3] Initializing /data/brian/livecell/H2b10xtrial.xdce:
[testng] [2024-07-06 02:18:07,583] [pool-1-thread-11] Initializing /data/brian/2Hour10x/H2b2Hour10x5fields.xdce:
[testng] [2024-07-06 02:18:41,079] [pool-1-thread-10] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_Tif/ER2009_97_239_TIFF/PC3_ER2009.97.239.xdce:
[testng] [2024-07-06 02:19:20,034] [pool-1-thread-2] Initializing /data/qa-4122/KJH YFPPML 2000_A-101061_1.xdce:
[testng] [2024-07-06 02:19:24,983] [pool-1-thread-12] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_IM/2009_97_240_IM/2009_97_240_IM.xdce:
[testng] [2024-07-06 02:19:51,393] [pool-1-thread-8] Initializing /data/michael/2007.08.02.16.43.24/2007.08.02.16.43.24.xdce:
[testng] [2024-07-06 02:19:54,237] [pool-1-thread-7] Initializing /data/michael/Z Sections with flatfield corr/2007.10.17.17.13.59.xdce:
[testng] [2024-07-06 02:20:02,320] [pool-1-thread-9] Initializing /data/frans/incell_25juni2009/ANALYZE files/plaat HR 38/txt en XML output file/HCT116_HR2009.97.038/HCT116_HR2009.97.038.xdce:
[testng] [2024-07-06 02:20:30,953] [pool-1-thread-3] Initializing /data/frans/incell_25juni2009/ANALYZE files/plaat HR37/excel output file/HCT116_HR2009.97.037/HCT116_HR2009.97.037.xdce:
[testng] [2024-07-06 02:20:54,499] [pool-1-thread-7] Initializing /data/public/INMAC384-DAPI-CM-eGFP_59224_1/INMAC384-DAPI-CM-eGFP_59224_1.xdce:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 1431, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 36 minutes 54 seconds
Finished: SUCCESS