Started by upstream project "BIOFORMATS-test-repo" build number 282
originally caused by:
 Started by user devspace
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@10
[BIOFORMATS-test-folder@10] $ /bin/bash -xe /tmp/jenkins2522333143704080830.sh
+ '[' incell = slidebook ']'
++ date +%u
+ '[' 5 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_44557_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

test-automated:
   [testng] File leak detector installed
   [testng] 12:34:22,333 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
   [testng] 12:34:22,334 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service.
   [testng] 12:34:22,334 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
   [testng] 12:34:22,335 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
   [testng] 12:34:22,336 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
   [testng] 12:34:22,336 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
   [testng] 12:34:22,336 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
   [testng] 12:34:22,336 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
   [testng] 12:34:22,337 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
   [testng] 12:34:22,337 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
   [testng] 12:34:22,337 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
   [testng] 12:34:22,337 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
   [testng] 12:34:22,575 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
   [testng] 12:34:22,575 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
   [testng] 12:34:22,601 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
   [testng] 12:34:22,602 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
   [testng] 12:34:22,609 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
   [testng] 12:34:22,610 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
   [testng] 12:34:22,610 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
   [testng] 12:34:22,610 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
   [testng] 12:34:22,610 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration.
   [testng] 12:34:22,611 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point
   [testng] 12:34:22,611 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 274 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
   [testng] [2024-12-06 12:34:22,621] [main] java.version = 1.8.0_342
   [testng] 12:34:22,624 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
   [testng] 12:34:22,624 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 12:34:22,668 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-06_12-34-22.log]
   [testng] 12:34:22,670 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration.
   [testng] [2024-12-06 12:34:22,672] [main] testng.directory = /data
   [testng] [2024-12-06 12:34:22,672] [main] testng.configDirectory = /config
   [testng] [2024-12-06 12:34:22,684] [main] testng.multiplier = 1.0
   [testng] [2024-12-06 12:34:22,684] [main] testng.in-memory = false
   [testng] [2024-12-06 12:34:22,684] [main] testng.allow-missing = false
   [testng] [2024-12-06 12:34:22,684] [main] user.language = en
   [testng] [2024-12-06 12:34:22,684] [main] user.country = ${user.country}
   [testng] [2024-12-06 12:34:22,684] [main] Maximum heap size = 13653 MB
   [testng] Scanning for files...
   [testng] [2024-12-06 12:55:24,387] [main] ----------------------------------------
   [testng] [2024-12-06 12:55:24,388] [main] Total files: 4190
   [testng] [2024-12-06 12:55:24,388] [main] Scan time: 1261.702 s (301 ms/file)
   [testng] [2024-12-06 12:55:24,388] [main] ----------------------------------------
   [testng] Building list of tests...
   [testng] Ready to test 27 files
   [testng] [TestNG] Running:
   [testng]   Bio-Formats software test suite
   [testng] 
   [testng] [2024-12-06 12:56:56,971] [pool-1-thread-1] Initializing /data/brian/livecell/H2b10xtrial.xdce: 
   [testng] 12:56:56,971 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
   [testng] 12:56:56,972 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 12:56:56,973 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-06_12-56-56.log]
   [testng] 12:56:56,973 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14999aa5 - End of configuration.
   [testng] [2024-12-06 12:56:57,683] [pool-1-thread-12] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_Tif/ER2009_97_239_TIFF/PC3_ER2009.97.239.xdce: 
   [testng] 12:56:57,684 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
   [testng] 12:56:57,684 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 12:56:57,684 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-06_12-56-57.log]
   [testng] 12:56:57,685 |-INFO in ch.qos.logback.core.sift.SiftProcessor@476a849d - End of configuration.
   [testng] [2024-12-06 12:56:58,091] [pool-1-thread-11] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_IM/2009_97_239_IM/2009_97_239_IM.xdce: 
   [testng] 12:56:58,091 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
   [testng] 12:56:58,091 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 12:56:58,092 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-06_12-56-58.log]
   [testng] 12:56:58,092 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5904c890 - End of configuration.
   [testng] [2024-12-06 12:56:58,757] [pool-1-thread-10] Initializing /data/brian/Proper Dark Images/2007.11.12.13.37.27.xdce: 
   [testng] 12:56:58,757 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
   [testng] 12:56:58,757 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 12:56:58,757 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-06_12-56-58.log]
   [testng] 12:56:58,758 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d44569c - End of configuration.
   [testng] [2024-12-06 12:56:59,208] [pool-1-thread-9] Initializing /data/brian/H2Blivecell20x/H2Blivecell20x.xdce: 
   [testng] 12:56:59,209 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
   [testng] 12:56:59,209 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 12:56:59,209 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-06_12-56-59.log]
   [testng] 12:56:59,209 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f6a5272 - End of configuration.
   [testng] [2024-12-06 12:57:01,034] [pool-1-thread-8] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_IM/2009_97_240_IM/2009_97_240_IM.xdce: 
   [testng] 12:57:01,034 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
   [testng] 12:57:01,034 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 12:57:01,034 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-06_12-57-01.log]
   [testng] 12:57:01,035 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50bab1ac - End of configuration.
   [testng] [2024-12-06 12:57:01,799] [pool-1-thread-7] Initializing /data/michael/firstStack/2007.07.05.17.33.35.xdce: 
   [testng] 12:57:01,799 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
   [testng] 12:57:01,799 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 12:57:01,800 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-06_12-57-01.log]
   [testng] 12:57:01,800 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32da913e - End of configuration.
   [testng] [2024-12-06 12:57:02,448] [pool-1-thread-6] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_Tif/ER2009_97_240_TIFF/PC3_ER2009.97.240(ok).xdce: 
   [testng] 12:57:02,449 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
   [testng] 12:57:02,449 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 12:57:02,449 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-06_12-57-02.log]
   [testng] 12:57:02,450 |-INFO in ch.qos.logback.core.sift.SiftProcessor@641522b9 - End of configuration.
   [testng] [2024-12-06 12:57:03,250] [pool-1-thread-5] Initializing /data/samples/images_number_mismatch/test.xdce: 
   [testng] 12:57:03,250 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
   [testng] 12:57:03,250 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 12:57:03,251 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-06_12-57-03.log]
   [testng] 12:57:03,251 |-INFO in ch.qos.logback.core.sift.SiftProcessor@858f6dc - End of configuration.
   [testng] [2024-12-06 12:57:03,985] [pool-1-thread-4] Initializing /data/michael/2007.08.02.16.43.24/2007.08.02.16.43.24.xdce: 
   [testng] 12:57:03,985 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
   [testng] 12:57:03,985 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 12:57:03,986 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-06_12-57-03.log]
   [testng] 12:57:03,986 |-INFO in ch.qos.logback.core.sift.SiftProcessor@77f75696 - End of configuration.
   [testng] [2024-12-06 12:57:05,033] [pool-1-thread-3] Initializing /data/karsten/gabriele_-1_2/gabriele_-1_2.xdce: 
   [testng] 12:57:05,034 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
   [testng] 12:57:05,034 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 12:57:05,034 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-06_12-57-05.log]
   [testng] 12:57:05,035 |-INFO in ch.qos.logback.core.sift.SiftProcessor@69d29370 - End of configuration.
   [testng] [2024-12-06 12:57:05,828] [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] 12:57:05,828 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
   [testng] 12:57:05,829 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 12:57:05,829 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-06_12-57-05.log]
   [testng] 12:57:05,829 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b186d58 - End of configuration.
   [testng] [2024-12-06 12:57:53,401] [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] [2024-12-06 12:58:01,341] [pool-1-thread-10] Initializing /data/public/INMAC384-DAPI-CM-eGFP_59223_1/INMAC384-DAPI-CM-eGFP_59223_1.xdce: 
   [testng] [2024-12-06 13:00:15,164] [pool-1-thread-3] 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] [2024-12-06 13:01:30,610] [pool-1-thread-7] Initializing /data/samples/variable-field-count/test.xdce: 
   [testng] [2024-12-06 13:02:14,124] [pool-1-thread-7] Initializing /data/public/INMAC384-DAPI-CM-eGFP_59224_1/INMAC384-DAPI-CM-eGFP_59224_1.xdce: 
   [testng] [2024-12-06 13:12:42,969] [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] [2024-12-06 13:12:59,152] [pool-1-thread-11] Initializing /data/frans/im dataset/PC3_ER2009.97.180_IM.xdce: 
   [testng] [2024-12-06 13:13:00,180] [pool-1-thread-8] Initializing /data/michael/Single plane no flatfield corr/2007.10.17.17.04.55.xdce: 
   [testng] [2024-12-06 13:17:11,851] [pool-1-thread-8] Initializing /data/damir/20x Z1 16fields Gr Rd DAPI Cy5_140610-3_fix_2.xdce: 
   [testng] [2024-12-06 13:27:56,861] [pool-1-thread-1] Initializing /data/karsten/gabriele_-1_2/~gabriele_-1_2.xdce: 
   [testng] [2024-12-06 13:28:46,988] [pool-1-thread-5] Initializing /data/qa-4122/KJH YFPPML 2000_A-101061_1.xdce: 
   [testng] [2024-12-06 13:29:12,314] [pool-1-thread-4] Initializing /data/frans/incell_25juni2009/ANALYZE files/plaat HR37/excel output file/HCT116_HR2009.97.037/HCT116_HR2009.97.037.xdce: 
   [testng] [2024-12-06 13:30:26,422] [pool-1-thread-1] Initializing /data/brian/2Hour10x/H2b2Hour10x5fields.xdce: 
   [testng] [2024-12-06 13:30:38,840] [pool-1-thread-11] 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] [2024-12-06 13:30:42,765] [pool-1-thread-5] Initializing /data/michael/Z Sections with flatfield corr/2007.10.17.17.13.59.xdce: 
   [testng] 14:47:10,129 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
   [testng] 14:47:10,129 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 14:47:10,130 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-06_14-47-10.log]
   [testng] 14:47:10,131 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f09d2ff - End of configuration.
   [testng] 14:59:30,280 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
   [testng] 14:59:30,281 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 14:59:30,283 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-06_14-59-30.log]
   [testng] 14:59:30,283 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12e31405 - End of configuration.
   [testng] 
   [testng] ===============================================
   [testng] Bio-Formats software test suite
   [testng] Total tests run: 1431, Failures: 0, Skips: 0
   [testng] ===============================================
   [testng] 

BUILD SUCCESSFUL
Total time: 145 minutes 12 seconds
Finished: SUCCESS