Started by upstream project "BIOFORMATS-test-repo" build number 124
originally caused by:
Started by upstream project "Trigger" build number 141
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4
[BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins11117834054624758903.sh
+ '[' incell = slidebook ']'
++ date +%u
+ '[' 4 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_19445_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[javac] warning: [options] source value 8 is obsolete and will be removed in a future release
[javac] warning: [options] target value 8 is obsolete and will be removed in a future release
[javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
[javac] 4 warnings
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] 02:15:15,700 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 02:15:15,701 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service.
[testng] 02:15:15,701 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:15:15,702 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:15:15,702 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 02:15:15,703 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 02:15:15,703 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 02:15:15,703 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:15:15,703 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:15:15,704 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 02:15:15,704 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 02:15:15,705 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 02:15:15,857 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 02:15:15,857 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 02:15:15,883 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 02:15:15,883 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 02:15:15,889 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 02:15:15,889 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 02:15:15,889 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 02:15:15,889 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 02:15:15,890 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration.
[testng] 02:15:15,890 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point
[testng] 02:15:15,890 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 187 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-07-18 02:15:15,903] [main] java.version = 21
[testng] 02:15:15,907 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 02:15:15,907 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:15:15,957 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-18_02-15-15.log]
[testng] 02:15:15,958 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration.
[testng] [2024-07-18 02:15:15,960] [main] testng.directory = /data
[testng] [2024-07-18 02:15:15,960] [main] testng.configDirectory = /config
[testng] [2024-07-18 02:15:15,968] [main] testng.multiplier = 1.0
[testng] [2024-07-18 02:15:15,969] [main] testng.in-memory = false
[testng] [2024-07-18 02:15:15,969] [main] testng.allow-missing = false
[testng] [2024-07-18 02:15:15,969] [main] user.language = en
[testng] [2024-07-18 02:15:15,969] [main] user.country = ${user.country}
[testng] [2024-07-18 02:15:15,969] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-07-18 02:21:47,139] [main] ----------------------------------------
[testng] [2024-07-18 02:21:47,140] [main] Total files: 4190
[testng] [2024-07-18 02:21:47,140] [main] Scan time: 391.17 s (93 ms/file)
[testng] [2024-07-18 02:21:47,141] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 27 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-07-18 02:22:10,138] [pool-1-thread-1] Initializing /data/brian/2Hour10x/H2b2Hour10x5fields.xdce:
[testng] 02:22:10,139 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 02:22:10,140 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:22:10,141 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-18_02-22-10.log]
[testng] 02:22:10,142 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7746edeb - End of configuration.
[testng] [2024-07-18 02:22:10,443] [pool-1-thread-12] Initializing /data/michael/firstStack/2007.07.05.17.33.35.xdce:
[testng] 02:22:10,444 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 02:22:10,444 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:22:10,446 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-18_02-22-10.log]
[testng] 02:22:10,448 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21cdcd2a - End of configuration.
[testng] [2024-07-18 02:22:10,496] [pool-1-thread-11] Initializing /data/karsten/gabriele_-1_2/~gabriele_-1_2.xdce:
[testng] 02:22:10,497 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 02:22:10,497 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:22:10,499 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-18_02-22-10.log]
[testng] 02:22:10,499 |-INFO in ch.qos.logback.core.sift.SiftProcessor@64b7abc1 - End of configuration.
[testng] [2024-07-18 02:22:10,539] [pool-1-thread-10] Initializing /data/frans/im dataset/PC3_ER2009.97.180_IM.xdce:
[testng] 02:22:10,539 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 02:22:10,539 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:22:10,540 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-18_02-22-10.log]
[testng] 02:22:10,541 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43394e08 - End of configuration.
[testng] [2024-07-18 02:22:10,724] [pool-1-thread-9] Initializing /data/public/INMAC384-DAPI-CM-eGFP_59223_1/INMAC384-DAPI-CM-eGFP_59223_1.xdce:
[testng] 02:22:10,725 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 02:22:10,725 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:22:10,726 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-18_02-22-10.log]
[testng] 02:22:10,727 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e7b1344 - End of configuration.
[testng] [2024-07-18 02:22:11,387] [pool-1-thread-8] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_IM/2009_97_238_IM/2009_97_238_IM.xdce:
[testng] 02:22:11,388 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 02:22:11,388 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:22:11,389 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-18_02-22-11.log]
[testng] 02:22:11,390 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4126cabd - End of configuration.
[testng] [2024-07-18 02:22:11,545] [pool-1-thread-7] Initializing /data/frans/incell_25juni2009/ANALYZE files/plaat HR 38/excel output file/HCT116_HR2009.97.038/HCT116_HR2009.97.038.xdce:
[testng] 02:22:11,545 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 02:22:11,545 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:22:11,546 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-18_02-22-11.log]
[testng] 02:22:11,547 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6cf2a545 - End of configuration.
[testng] [2024-07-18 02:22:11,771] [pool-1-thread-6] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_IM/2009_97_239_IM/2009_97_239_IM.xdce:
[testng] 02:22:11,772 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 02:22:11,772 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:22:11,774 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-18_02-22-11.log]
[testng] 02:22:11,775 |-INFO in ch.qos.logback.core.sift.SiftProcessor@781d1332 - End of configuration.
[testng] [2024-07-18 02:22:11,898] [pool-1-thread-5] Initializing /data/qa-4122/KJH YFPPML 2000_A-101061_1.xdce:
[testng] 02:22:11,899 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 02:22:11,899 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:22:11,900 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-18_02-22-11.log]
[testng] 02:22:11,901 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38ab4a63 - End of configuration.
[testng] [2024-07-18 02:22:12,130] [pool-1-thread-4] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_Tif/ER2009_97_239_TIFF/PC3_ER2009.97.239.xdce:
[testng] 02:22:12,131 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 02:22:12,131 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:22:12,132 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-18_02-22-12.log]
[testng] 02:22:12,133 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6aefec3e - End of configuration.
[testng] [2024-07-18 02:22:12,284] [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] 02:22:12,285 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 02:22:12,285 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:22:12,286 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-18_02-22-12.log]
[testng] 02:22:12,287 |-INFO in ch.qos.logback.core.sift.SiftProcessor@24c698c8 - End of configuration.
[testng] [2024-07-18 02:22:12,381] [pool-1-thread-2] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_Tif/ER2009_97_238_TIFF/PC3_ER2009.97.238.xdce:
[testng] 02:22:12,382 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 02:22:12,382 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:22:12,383 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-18_02-22-12.log]
[testng] 02:22:12,384 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f8c737a - End of configuration.
[testng] [2024-07-18 02:22:53,563] [pool-1-thread-12] Initializing /data/brian/Proper Dark Images/2007.11.12.13.37.27.xdce:
[testng] [2024-07-18 02:22:58,747] [pool-1-thread-12] Initializing /data/karsten/gabriele_-1_2/gabriele_-1_2.xdce:
[testng] [2024-07-18 02:23:11,525] [pool-1-thread-11] 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] [2024-07-18 02:23:33,122] [pool-1-thread-12] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_Tif/ER2009_97_240_TIFF/PC3_ER2009.97.240(ok).xdce:
[testng] [2024-07-18 02:24:40,011] [pool-1-thread-5] Initializing /data/damir/20x Z1 16fields Gr Rd DAPI Cy5_140610-3_fix_2.xdce:
[testng] [2024-07-18 02:24:54,195] [pool-1-thread-8] Initializing /data/brian/H2Blivecell20x/H2Blivecell20x.xdce:
[testng] [2024-07-18 02:24:55,526] [pool-1-thread-6] Initializing /data/michael/Single plane no flatfield corr/2007.10.17.17.04.55.xdce:
[testng] [2024-07-18 02:25:27,954] [pool-1-thread-10] Initializing /data/brian/livecell/H2b10xtrial.xdce:
[testng] [2024-07-18 02:25:30,811] [pool-1-thread-6] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_IM/2009_97_240_IM/2009_97_240_IM.xdce:
[testng] [2024-07-18 02:25:44,739] [pool-1-thread-7] Initializing /data/samples/variable-field-count/test.xdce:
[testng] [2024-07-18 02:25:51,328] [pool-1-thread-3] 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] [2024-07-18 02:25:55,788] [pool-1-thread-7] Initializing /data/michael/Z Sections with flatfield corr/2007.10.17.17.13.59.xdce:
[testng] [2024-07-18 02:26:06,629] [pool-1-thread-2] Initializing /data/samples/images_number_mismatch/test.xdce:
[testng] [2024-07-18 02:26:09,744] [pool-1-thread-4] Initializing /data/public/INMAC384-DAPI-CM-eGFP_59224_1/INMAC384-DAPI-CM-eGFP_59224_1.xdce:
[testng] [2024-07-18 02:26:18,538] [pool-1-thread-2] Initializing /data/michael/2007.08.02.16.43.24/2007.08.02.16.43.24.xdce:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 1431, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 50 minutes 37 seconds
Finished: SUCCESS