Started by upstream project "BIOFORMATS-test-repo" build number 24
originally caused by:
Started by upstream project "Trigger" build number 27
originally caused by:
Started by user devspace
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9
[BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins12321856348443178434.sh
+ '[' incell = slidebook ']'
++ date +%u
+ '[' 5 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_3044_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] 11:55:28,627 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 11:55:28,629 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service.
[testng] 11:55:28,629 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 11:55:28,630 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 11:55:28,630 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 11:55:28,630 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 11:55:28,630 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 11:55:28,630 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 11:55:28,631 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 11:55:28,631 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 11:55:28,631 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 11:55:28,631 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 11:55:28,857 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 11:55:28,857 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 11:55:28,884 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 11:55:28,884 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 11:55:28,892 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 11:55:28,892 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 11:55:28,892 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 11:55:28,893 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 11:55:28,893 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration.
[testng] 11:55:28,894 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point
[testng] 11:55:28,894 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 263 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-04-05 11:55:28,903] [main] java.version = 1.8.0_342
[testng] 11:55:28,907 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 11:55:28,907 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:55:28,951 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-05_11-55-28.log]
[testng] 11:55:28,953 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration.
[testng] [2024-04-05 11:55:28,955] [main] testng.directory = /data
[testng] [2024-04-05 11:55:28,955] [main] testng.configDirectory = /config
[testng] [2024-04-05 11:55:28,967] [main] testng.multiplier = 1.0
[testng] [2024-04-05 11:55:28,967] [main] testng.in-memory = false
[testng] [2024-04-05 11:55:28,968] [main] testng.allow-missing = false
[testng] [2024-04-05 11:55:28,968] [main] user.language = en
[testng] [2024-04-05 11:55:28,968] [main] user.country = ${user.country}
[testng] [2024-04-05 11:55:28,968] [main] Maximum heap size = 13653 MB
[testng] Scanning for files...
[testng] [2024-04-05 12:02:22,324] [main] ----------------------------------------
[testng] [2024-04-05 12:02:22,325] [main] Total files: 4190
[testng] [2024-04-05 12:02:22,325] [main] Scan time: 413.356 s (98 ms/file)
[testng] [2024-04-05 12:02:22,325] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 27 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-04-05 12:02:36,504] [pool-1-thread-1] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_IM/2009_97_238_IM/2009_97_238_IM.xdce:
[testng] 12:02:36,505 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 12:02:36,505 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:02:36,506 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-05_12-02-36.log]
[testng] 12:02:36,507 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56a11ad7 - End of configuration.
[testng] [2024-04-05 12:02:36,669] [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] 12:02:36,669 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 12:02:36,669 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:02:36,670 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-05_12-02-36.log]
[testng] 12:02:36,670 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c851560 - End of configuration.
[testng] [2024-04-05 12:02:36,735] [pool-1-thread-11] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_Tif/ER2009_97_238_TIFF/PC3_ER2009.97.238.xdce:
[testng] 12:02:36,736 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 12:02:36,736 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:02:36,737 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-05_12-02-36.log]
[testng] 12:02:36,737 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2e38bbf4 - End of configuration.
[testng] [2024-04-05 12:02:36,821] [pool-1-thread-10] Initializing /data/public/INMAC384-DAPI-CM-eGFP_59224_1/INMAC384-DAPI-CM-eGFP_59224_1.xdce:
[testng] 12:02:36,821 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 12:02:36,821 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:02:36,822 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-05_12-02-36.log]
[testng] 12:02:36,822 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9edec04 - End of configuration.
[testng] [2024-04-05 12:02:37,200] [pool-1-thread-9] Initializing /data/brian/Proper Dark Images/2007.11.12.13.37.27.xdce:
[testng] 12:02:37,200 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 12:02:37,200 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:02:37,201 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-05_12-02-37.log]
[testng] 12:02:37,202 |-INFO in ch.qos.logback.core.sift.SiftProcessor@46788f78 - End of configuration.
[testng] [2024-04-05 12:02:37,223] [pool-1-thread-8] Initializing /data/samples/images_number_mismatch/test.xdce:
[testng] 12:02:37,223 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 12:02:37,223 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:02:37,224 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-05_12-02-37.log]
[testng] 12:02:37,224 |-INFO in ch.qos.logback.core.sift.SiftProcessor@248c6826 - End of configuration.
[testng] [2024-04-05 12:02:37,244] [pool-1-thread-7] Initializing /data/samples/variable-field-count/test.xdce:
[testng] 12:02:37,245 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 12:02:37,245 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:02:37,245 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-05_12-02-37.log]
[testng] 12:02:37,246 |-INFO in ch.qos.logback.core.sift.SiftProcessor@59c5ca2a - End of configuration.
[testng] [2024-04-05 12:02:37,265] [pool-1-thread-6] Initializing /data/frans/incell_25juni2009/ANALYZE files/plaat HR37/excel output file/HCT116_HR2009.97.037/HCT116_HR2009.97.037.xdce:
[testng] 12:02:37,265 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 12:02:37,265 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:02:37,266 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-05_12-02-37.log]
[testng] 12:02:37,267 |-INFO in ch.qos.logback.core.sift.SiftProcessor@479f5421 - End of configuration.
[testng] [2024-04-05 12:02:37,453] [pool-1-thread-5] Initializing /data/brian/livecell/H2b10xtrial.xdce:
[testng] 12:02:37,454 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 12:02:37,454 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:02:37,454 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-05_12-02-37.log]
[testng] 12:02:37,455 |-INFO in ch.qos.logback.core.sift.SiftProcessor@69473549 - End of configuration.
[testng] [2024-04-05 12:02:37,664] [pool-1-thread-4] 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] 12:02:37,664 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 12:02:37,665 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:02:37,665 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-05_12-02-37.log]
[testng] 12:02:37,665 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b2d92c1 - End of configuration.
[testng] [2024-04-05 12:02:37,848] [pool-1-thread-3] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_Tif/ER2009_97_240_TIFF/PC3_ER2009.97.240(ok).xdce:
[testng] 12:02:37,848 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 12:02:37,848 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:02:37,849 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-05_12-02-37.log]
[testng] 12:02:37,849 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ebf2365 - End of configuration.
[testng] [2024-04-05 12:02:38,087] [pool-1-thread-2] 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] 12:02:38,087 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 12:02:38,087 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 12:02:38,088 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-05_12-02-38.log]
[testng] 12:02:38,088 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b86d6f0 - End of configuration.
[testng] [2024-04-05 12:02:41,293] [pool-1-thread-9] Initializing /data/damir/20x Z1 16fields Gr Rd DAPI Cy5_140610-3_fix_2.xdce:
[testng] [2024-04-05 12:02:53,082] [pool-1-thread-7] Initializing /data/public/INMAC384-DAPI-CM-eGFP_59223_1/INMAC384-DAPI-CM-eGFP_59223_1.xdce:
[testng] [2024-04-05 12:02:53,771] [pool-1-thread-8] Initializing /data/qa-4122/KJH YFPPML 2000_A-101061_1.xdce:
[testng] [2024-04-05 12:03:55,626] [pool-1-thread-1] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_IM/2009_97_239_IM/2009_97_239_IM.xdce:
[testng] [2024-04-05 12:04:40,269] [pool-1-thread-2] Initializing /data/michael/2007.08.02.16.43.24/2007.08.02.16.43.24.xdce:
[testng] [2024-04-05 12:04:54,798] [pool-1-thread-11] Initializing /data/michael/firstStack/2007.07.05.17.33.35.xdce:
[testng] [2024-04-05 12:04:57,028] [pool-1-thread-6] Initializing /data/brian/H2Blivecell20x/H2Blivecell20x.xdce:
[testng] [2024-04-05 12:04:58,215] [pool-1-thread-3] Initializing /data/frans/incell_25juni2009/ANALYZE files/plaat HR 38/excel output file/HCT116_HR2009.97.038/HCT116_HR2009.97.038.xdce:
[testng] [2024-04-05 12:04:58,440] [pool-1-thread-12] Initializing /data/karsten/gabriele_-1_2/~gabriele_-1_2.xdce:
[testng] [2024-04-05 12:05:00,153] [pool-1-thread-8] Initializing /data/karsten/gabriele_-1_2/gabriele_-1_2.xdce:
[testng] [2024-04-05 12:05:07,900] [pool-1-thread-5] Initializing /data/michael/Z Sections with flatfield corr/2007.10.17.17.13.59.xdce:
[testng] [2024-04-05 12:05:08,890] [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] [2024-04-05 12:05:30,085] [pool-1-thread-1] Initializing /data/michael/Single plane no flatfield corr/2007.10.17.17.04.55.xdce:
[testng] [2024-04-05 12:05:32,836] [pool-1-thread-8] Initializing /data/brian/2Hour10x/H2b2Hour10x5fields.xdce:
[testng] [2024-04-05 12:05:33,979] [pool-1-thread-12] Initializing /data/frans/im dataset/PC3_ER2009.97.180_IM.xdce:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 1431, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 44 minutes 41 seconds
Finished: SUCCESS