Started by upstream project "BIOFORMATS-test-repo" build number 17
originally caused by:
Started by upstream project "Trigger" build number 20
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3
[BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins7015053758705133428.sh
+ '[' incell = slidebook ']'
++ date +%u
+ '[' 6 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_2060_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] 01:11:25,336 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:11:25,337 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service.
[testng] 01:11:25,337 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:11:25,338 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:11:25,339 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:11:25,339 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:11:25,340 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 01:11:25,340 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:11:25,340 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:11:25,341 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:11:25,341 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:11:25,341 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:11:25,523 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:11:25,523 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:11:25,546 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:11:25,546 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:11:25,552 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:11:25,552 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:11:25,552 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:11:25,553 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:11:25,553 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration.
[testng] 01:11:25,553 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point
[testng] 01:11:25,553 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 213 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-03-30 01:11:25,563] [main] java.version = 11.0.16
[testng] 01:11:25,566 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:11:25,566 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:11:25,609 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-30_01-11-25.log]
[testng] 01:11:25,610 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration.
[testng] [2024-03-30 01:11:25,613] [main] testng.directory = /data
[testng] [2024-03-30 01:11:25,613] [main] testng.configDirectory = /config
[testng] [2024-03-30 01:11:25,623] [main] testng.multiplier = 1.0
[testng] [2024-03-30 01:11:25,624] [main] testng.in-memory = false
[testng] [2024-03-30 01:11:25,625] [main] testng.allow-missing = false
[testng] [2024-03-30 01:11:25,625] [main] user.language = en
[testng] [2024-03-30 01:11:25,625] [main] user.country = ${user.country}
[testng] [2024-03-30 01:11:25,625] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-03-30 01:18:18,516] [main] ----------------------------------------
[testng] [2024-03-30 01:18:18,516] [main] Total files: 4190
[testng] [2024-03-30 01:18:18,516] [main] Scan time: 412.891 s (98 ms/file)
[testng] [2024-03-30 01:18:18,516] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 27 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-03-30 01:18:34,843] [pool-1-thread-1] Initializing /data/frans/im dataset/PC3_ER2009.97.180_IM.xdce:
[testng] 01:18:34,843 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:18:34,844 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:18:34,848 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-30_01-18-34.log]
[testng] 01:18:34,849 |-INFO in ch.qos.logback.core.sift.SiftProcessor@110d2deb - End of configuration.
[testng] [2024-03-30 01:18:35,061] [pool-1-thread-12] Initializing /data/brian/livecell/H2b10xtrial.xdce:
[testng] 01:18:35,061 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:18:35,061 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:18:35,062 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-30_01-18-35.log]
[testng] 01:18:35,062 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6b2c1e30 - End of configuration.
[testng] [2024-03-30 01:18:35,299] [pool-1-thread-11] Initializing /data/karsten/gabriele_-1_2/~gabriele_-1_2.xdce:
[testng] 01:18:35,299 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:18:35,299 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:18:35,300 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-30_01-18-35.log]
[testng] 01:18:35,301 |-INFO in ch.qos.logback.core.sift.SiftProcessor@30ee846f - End of configuration.
[testng] [2024-03-30 01:18:35,344] [pool-1-thread-10] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_IM/2009_97_239_IM/2009_97_239_IM.xdce:
[testng] 01:18:35,345 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:18:35,345 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:18:35,346 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-30_01-18-35.log]
[testng] 01:18:35,346 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a74e78a - End of configuration.
[testng] [2024-03-30 01:18:35,505] [pool-1-thread-9] Initializing /data/michael/Z Sections with flatfield corr/2007.10.17.17.13.59.xdce:
[testng] 01:18:35,505 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:18:35,505 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:18:35,506 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-30_01-18-35.log]
[testng] 01:18:35,507 |-INFO in ch.qos.logback.core.sift.SiftProcessor@463b83b6 - End of configuration.
[testng] [2024-03-30 01:18:35,655] [pool-1-thread-8] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_Tif/ER2009_97_239_TIFF/PC3_ER2009.97.239.xdce:
[testng] 01:18:35,655 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:18:35,655 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:18:35,656 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-30_01-18-35.log]
[testng] 01:18:35,656 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ba201e5 - End of configuration.
[testng] [2024-03-30 01:18:35,892] [pool-1-thread-7] Initializing /data/karsten/gabriele_-1_2/gabriele_-1_2.xdce:
[testng] 01:18:35,892 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:18:35,893 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:18:35,894 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-30_01-18-35.log]
[testng] 01:18:35,894 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e5c40f3 - End of configuration.
[testng] [2024-03-30 01:18:35,943] [pool-1-thread-6] Initializing /data/public/INMAC384-DAPI-CM-eGFP_59224_1/INMAC384-DAPI-CM-eGFP_59224_1.xdce:
[testng] 01:18:35,943 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:18:35,943 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:18:35,944 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-30_01-18-35.log]
[testng] 01:18:35,944 |-INFO in ch.qos.logback.core.sift.SiftProcessor@764d314d - End of configuration.
[testng] [2024-03-30 01:18:36,718] [pool-1-thread-5] Initializing /data/qa-4122/KJH YFPPML 2000_A-101061_1.xdce:
[testng] 01:18:36,718 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:18:36,719 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:18:36,719 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-30_01-18-36.log]
[testng] 01:18:36,720 |-INFO in ch.qos.logback.core.sift.SiftProcessor@28a8dd22 - End of configuration.
[testng] [2024-03-30 01:18:36,909] [pool-1-thread-4] Initializing /data/brian/Proper Dark Images/2007.11.12.13.37.27.xdce:
[testng] 01:18:36,909 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:18:36,909 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:18:36,910 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-30_01-18-36.log]
[testng] 01:18:36,910 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b4376b - End of configuration.
[testng] [2024-03-30 01:18:36,939] [pool-1-thread-3] Initializing /data/michael/2007.08.02.16.43.24/2007.08.02.16.43.24.xdce:
[testng] 01:18:36,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:18:36,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:18:36,941 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-30_01-18-36.log]
[testng] 01:18:36,941 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b28506f - End of configuration.
[testng] [2024-03-30 01:18:37,169] [pool-1-thread-2] Initializing /data/samples/variable-field-count/test.xdce:
[testng] 01:18:37,169 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:18:37,170 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:18:37,190 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-30_01-18-37.log]
[testng] 01:18:37,191 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a131ae7 - End of configuration.
[testng] [2024-03-30 01:18:40,921] [pool-1-thread-4] Initializing /data/frans/incell_25juni2009/ANALYZE files/plaat HR 38/excel output file/HCT116_HR2009.97.038/HCT116_HR2009.97.038.xdce:
[testng] [2024-03-30 01:18:49,779] [pool-1-thread-2] Initializing /data/brian/2Hour10x/H2b2Hour10x5fields.xdce:
[testng] [2024-03-30 01:19:11,116] [pool-1-thread-11] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_IM/2009_97_240_IM/2009_97_240_IM.xdce:
[testng] [2024-03-30 01:19:12,225] [pool-1-thread-7] 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] [2024-03-30 01:19:36,047] [pool-1-thread-9] Initializing /data/public/INMAC384-DAPI-CM-eGFP_59223_1/INMAC384-DAPI-CM-eGFP_59223_1.xdce:
[testng] [2024-03-30 01:19:52,387] [pool-1-thread-3] Initializing /data/damir/20x Z1 16fields Gr Rd DAPI Cy5_140610-3_fix_2.xdce:
[testng] [2024-03-30 01:20:02,209] [pool-1-thread-10] Initializing /data/brian/H2Blivecell20x/H2Blivecell20x.xdce:
[testng] [2024-03-30 01:20:33,866] [pool-1-thread-1] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_Tif/ER2009_97_240_TIFF/PC3_ER2009.97.240(ok).xdce:
[testng] [2024-03-30 01:20:34,807] [pool-1-thread-11] Initializing /data/samples/images_number_mismatch/test.xdce:
[testng] [2024-03-30 01:20:37,490] [pool-1-thread-5] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_Tif/ER2009_97_238_TIFF/PC3_ER2009.97.238.xdce:
[testng] [2024-03-30 01:20:44,221] [pool-1-thread-11] Initializing /data/michael/Single plane no flatfield corr/2007.10.17.17.04.55.xdce:
[testng] [2024-03-30 01:20:44,653] [pool-1-thread-4] Initializing /data/michael/firstStack/2007.07.05.17.33.35.xdce:
[testng] [2024-03-30 01:20:53,907] [pool-1-thread-8] Initializing /data/frans/incell_25juni2009/ANALYZE files/plaat HR37/excel output file/HCT116_HR2009.97.037/HCT116_HR2009.97.037.xdce:
[testng] [2024-03-30 01:21:02,297] [pool-1-thread-4] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_IM/2009_97_238_IM/2009_97_238_IM.xdce:
[testng] [2024-03-30 01:21:06,120] [pool-1-thread-12] 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]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 1431, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 41 minutes 1 second
Finished: SUCCESS