Started by upstream project "BIOFORMATS-test-repo" build number 90
originally caused by:
Started by upstream project "Trigger" build number 101
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8
[BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins8235573899793617149.sh
+ '[' incell = slidebook ']'
++ date +%u
+ '[' 3 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_13869_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] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket
[testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket
[testng] File leak detector installed
[testng] 02:16:14,062 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 02:16:14,063 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service.
[testng] 02:16:14,063 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:16:14,064 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:16:14,065 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 02:16:14,065 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 02:16:14,065 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 02:16:14,065 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:16:14,066 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:16:14,066 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 02:16:14,067 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 02:16:14,067 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 02:16:14,393 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 02:16:14,393 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 02:16:14,415 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 02:16:14,415 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 02:16:14,421 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 02:16:14,421 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 02:16:14,421 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 02:16:14,422 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 02:16:14,422 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration.
[testng] 02:16:14,422 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point
[testng] 02:16:14,423 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 357 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-06-12 02:16:14,432] [main] java.version = 17.0.2
[testng] 02:16:14,435 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 02:16:14,435 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:16:14,493 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-12_02-16-14.log]
[testng] 02:16:14,495 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration.
[testng] [2024-06-12 02:16:14,497] [main] testng.directory = /data
[testng] [2024-06-12 02:16:14,497] [main] testng.configDirectory = /config
[testng] [2024-06-12 02:16:14,513] [main] testng.multiplier = 1.0
[testng] [2024-06-12 02:16:14,514] [main] testng.in-memory = false
[testng] [2024-06-12 02:16:14,514] [main] testng.allow-missing = false
[testng] [2024-06-12 02:16:14,514] [main] user.language = en
[testng] [2024-06-12 02:16:14,514] [main] user.country = ${user.country}
[testng] [2024-06-12 02:16:14,514] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-06-12 02:23:03,016] [main] ----------------------------------------
[testng] [2024-06-12 02:23:03,016] [main] Total files: 4190
[testng] [2024-06-12 02:23:03,016] [main] Scan time: 408.502 s (97 ms/file)
[testng] [2024-06-12 02:23:03,016] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 27 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-06-12 02:23:20,174] [pool-1-thread-1] Initializing /data/michael/Single plane no flatfield corr/2007.10.17.17.04.55.xdce:
[testng] 02:23:20,174 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 02:23:20,174 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:23:20,175 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-12_02-23-20.log]
[testng] 02:23:20,176 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5daa960d - End of configuration.
[testng] [2024-06-12 02:23:20,239] [pool-1-thread-12] Initializing /data/brian/2Hour10x/H2b2Hour10x5fields.xdce:
[testng] 02:23:20,239 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 02:23:20,239 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:23:20,240 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-12_02-23-20.log]
[testng] 02:23:20,240 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6cbef1dc - End of configuration.
[testng] [2024-06-12 02:23:20,887] [pool-1-thread-11] Initializing /data/michael/Z Sections with flatfield corr/2007.10.17.17.13.59.xdce:
[testng] 02:23:20,887 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 02:23:20,887 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:23:20,888 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-12_02-23-20.log]
[testng] 02:23:20,888 |-INFO in ch.qos.logback.core.sift.SiftProcessor@641ed5da - End of configuration.
[testng] [2024-06-12 02:23:21,015] [pool-1-thread-10] Initializing /data/karsten/gabriele_-1_2/~gabriele_-1_2.xdce:
[testng] 02:23:21,015 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 02:23:21,015 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:23:21,016 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-12_02-23-21.log]
[testng] 02:23:21,016 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20570f6f - End of configuration.
[testng] [2024-06-12 02:23:21,047] [pool-1-thread-9] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_IM/2009_97_238_IM/2009_97_238_IM.xdce:
[testng] 02:23:21,047 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 02:23:21,047 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:23:21,048 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-12_02-23-21.log]
[testng] 02:23:21,048 |-INFO in ch.qos.logback.core.sift.SiftProcessor@140fc683 - End of configuration.
[testng] [2024-06-12 02:23:21,179] [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] 02:23:21,179 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 02:23:21,179 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:23:21,180 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-12_02-23-21.log]
[testng] 02:23:21,203 |-INFO in ch.qos.logback.core.sift.SiftProcessor@173aa396 - End of configuration.
[testng] [2024-06-12 02:23:21,463] [pool-1-thread-7] Initializing /data/brian/Proper Dark Images/2007.11.12.13.37.27.xdce:
[testng] 02:23:21,464 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 02:23:21,464 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:23:21,465 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-12_02-23-21.log]
[testng] 02:23:21,465 |-INFO in ch.qos.logback.core.sift.SiftProcessor@44aadfad - End of configuration.
[testng] [2024-06-12 02:23:21,494] [pool-1-thread-6] 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] 02:23:21,494 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 02:23:21,495 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:23:21,496 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-12_02-23-21.log]
[testng] 02:23:21,496 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50ed9fa6 - End of configuration.
[testng] [2024-06-12 02:23:21,601] [pool-1-thread-5] Initializing /data/frans/incell_25juni2009/ANALYZE files/plaat HR 38/excel output file/HCT116_HR2009.97.038/HCT116_HR2009.97.038.xdce:
[testng] 02:23:21,602 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 02:23:21,602 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:23:21,603 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-12_02-23-21.log]
[testng] 02:23:21,603 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6603f95b - End of configuration.
[testng] [2024-06-12 02:23:21,836] [pool-1-thread-4] Initializing /data/brian/H2Blivecell20x/H2Blivecell20x.xdce:
[testng] 02:23:21,836 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 02:23:21,836 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:23:21,837 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-12_02-23-21.log]
[testng] 02:23:21,837 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e744b88 - End of configuration.
[testng] [2024-06-12 02:23:22,752] [pool-1-thread-3] Initializing /data/samples/variable-field-count/test.xdce:
[testng] 02:23:22,752 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 02:23:22,752 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:23:22,753 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-12_02-23-22.log]
[testng] 02:23:22,753 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c787a5a - End of configuration.
[testng] [2024-06-12 02:23:22,786] [pool-1-thread-2] Initializing /data/karsten/gabriele_-1_2/gabriele_-1_2.xdce:
[testng] 02:23:22,787 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 02:23:22,787 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:23:22,788 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-12_02-23-22.log]
[testng] 02:23:22,788 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75bfe32f - End of configuration.
[testng] [2024-06-12 02:23:25,831] [pool-1-thread-7] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_IM/2009_97_239_IM/2009_97_239_IM.xdce:
[testng] [2024-06-12 02:23:35,161] [pool-1-thread-3] Initializing /data/brian/livecell/H2b10xtrial.xdce:
[testng] [2024-06-12 02:23:45,894] [pool-1-thread-1] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_Tif/ER2009_97_239_TIFF/PC3_ER2009.97.239.xdce:
[testng] [2024-06-12 02:23:54,983] [pool-1-thread-10] Initializing /data/qa-4122/KJH YFPPML 2000_A-101061_1.xdce:
[testng] [2024-06-12 02:23:55,548] [pool-1-thread-2] Initializing /data/michael/firstStack/2007.07.05.17.33.35.xdce:
[testng] [2024-06-12 02:24:12,549] [pool-1-thread-2] Initializing /data/michael/2007.08.02.16.43.24/2007.08.02.16.43.24.xdce:
[testng] [2024-06-12 02:24:23,721] [pool-1-thread-11] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_Tif/ER2009_97_240_TIFF/PC3_ER2009.97.240(ok).xdce:
[testng] [2024-06-12 02:24:49,225] [pool-1-thread-9] Initializing /data/samples/images_number_mismatch/test.xdce:
[testng] [2024-06-12 02:24:58,208] [pool-1-thread-7] Initializing /data/frans/im dataset/PC3_ER2009.97.180_IM.xdce:
[testng] [2024-06-12 02:25:01,104] [pool-1-thread-9] Initializing /data/public/INMAC384-DAPI-CM-eGFP_59223_1/INMAC384-DAPI-CM-eGFP_59223_1.xdce:
[testng] [2024-06-12 02:25:53,318] [pool-1-thread-2] Initializing /data/public/INMAC384-DAPI-CM-eGFP_59224_1/INMAC384-DAPI-CM-eGFP_59224_1.xdce:
[testng] [2024-06-12 02:26:05,987] [pool-1-thread-5] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_IM/2009_97_240_IM/2009_97_240_IM.xdce:
[testng] [2024-06-12 02:26:13,211] [pool-1-thread-10] Initializing /data/damir/20x Z1 16fields Gr Rd DAPI Cy5_140610-3_fix_2.xdce:
[testng] [2024-06-12 02:26:20,320] [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] [2024-06-12 02:26:40,745] [pool-1-thread-1] 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]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 1431, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 37 minutes 56 seconds
Finished: SUCCESS