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Started by upstream project "BIOFORMATS-test-repo" build number 300 originally caused by: Started by upstream project "Trigger" build number 322 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@2 [BIOFORMATS-test-folder@2] $ /bin/bash -xe /tmp/jenkins4999338446790939323.sh + '[' incell = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_47518_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] 04:10:43,715 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 04:10:43,717 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 04:10:43,717 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 04:10:43,718 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 04:10:43,718 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 04:10:43,718 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 04:10:43,718 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 04:10:43,718 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 04:10:43,719 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 04:10:43,719 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 04:10:43,719 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 04:10:43,719 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 04:10:43,943 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 04:10:43,943 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 04:10:43,970 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 04:10:43,970 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 04:10:43,978 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 04:10:43,979 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 04:10:43,979 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 04:10:43,979 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 04:10:43,979 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 04:10:43,980 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 04:10:43,980 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 261 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-27 04:10:43,989] [main] java.version = 1.8.0_342 [testng] 04:10:43,993 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 04:10:43,993 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:10:44,036 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-27_04-10-44.log] [testng] 04:10:44,038 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-12-27 04:10:44,039] [main] testng.directory = /data [testng] [2024-12-27 04:10:44,040] [main] testng.configDirectory = /config [testng] [2024-12-27 04:10:44,051] [main] testng.multiplier = 1.0 [testng] [2024-12-27 04:10:44,052] [main] testng.in-memory = false [testng] [2024-12-27 04:10:44,052] [main] testng.allow-missing = false [testng] [2024-12-27 04:10:44,052] [main] user.language = en [testng] [2024-12-27 04:10:44,052] [main] user.country = ${user.country} [testng] [2024-12-27 04:10:44,052] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-12-27 04:54:22,154] [main] ---------------------------------------- [testng] [2024-12-27 04:54:22,154] [main] Total files: 4190 [testng] [2024-12-27 04:54:22,155] [main] Scan time: 2618.102 s (624 ms/file) [testng] [2024-12-27 04:54:22,155] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 27 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-27 04:56:06,748] [pool-1-thread-1] Initializing /data/brian/Proper Dark Images/2007.11.12.13.37.27.xdce: [testng] 04:56:06,749 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 04:56:06,749 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:56:06,750 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-27_04-56-06.log] [testng] 04:56:06,750 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c24ef80 - End of configuration. [testng] [2024-12-27 04:56:07,466] [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] 04:56:07,466 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 04:56:07,466 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:56:07,467 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-27_04-56-07.log] [testng] 04:56:07,467 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7dbad28 - End of configuration. [testng] [2024-12-27 04:56:09,069] [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] 04:56:09,069 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 04:56:09,069 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:56:09,069 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-27_04-56-09.log] [testng] 04:56:09,070 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b2ddd1e - End of configuration. [testng] [2024-12-27 04:56:10,228] [pool-1-thread-10] Initializing /data/frans/incell_25juni2009/ANALYZE files/plaat HR37/excel output file/HCT116_HR2009.97.037/HCT116_HR2009.97.037.xdce: [testng] 04:56:10,228 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 04:56:10,228 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:56:10,229 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-27_04-56-10.log] [testng] 04:56:10,229 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b2cdb1b - End of configuration. [testng] [2024-12-27 04:56:12,147] [pool-1-thread-9] Initializing /data/brian/2Hour10x/H2b2Hour10x5fields.xdce: [testng] 04:56:12,147 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 04:56:12,147 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:56:12,148 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-27_04-56-12.log] [testng] 04:56:12,148 |-INFO in ch.qos.logback.core.sift.SiftProcessor@713c732e - End of configuration. [testng] [2024-12-27 04:56:17,021] [pool-1-thread-8] Initializing /data/michael/Z Sections with flatfield corr/2007.10.17.17.13.59.xdce: [testng] 04:56:17,021 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 04:56:17,021 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:56:17,021 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-27_04-56-17.log] [testng] 04:56:17,022 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1db62312 - End of configuration. [testng] [2024-12-27 04:56:17,847] [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] 04:56:17,847 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 04:56:17,847 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:56:17,848 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-27_04-56-17.log] [testng] 04:56:17,848 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d031c16 - End of configuration. [testng] [2024-12-27 04:56:19,677] [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] 04:56:19,677 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 04:56:19,677 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:56:19,678 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-27_04-56-19.log] [testng] 04:56:19,678 |-INFO in ch.qos.logback.core.sift.SiftProcessor@355992da - End of configuration. [testng] [2024-12-27 04:56:20,654] [pool-1-thread-5] Initializing /data/brian/H2Blivecell20x/H2Blivecell20x.xdce: [testng] 04:56:20,654 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 04:56:20,654 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:56:20,655 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-27_04-56-20.log] [testng] 04:56:20,655 |-INFO in ch.qos.logback.core.sift.SiftProcessor@555d8d56 - End of configuration. [testng] [2024-12-27 04:56:25,497] [pool-1-thread-4] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_Tif/ER2009_97_238_TIFF/PC3_ER2009.97.238.xdce: [testng] 04:56:25,497 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 04:56:25,497 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:56:25,498 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-27_04-56-25.log] [testng] 04:56:25,498 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1cf97e36 - End of configuration. [testng] [2024-12-27 04:56:28,662] [pool-1-thread-3] Initializing /data/damir/20x Z1 16fields Gr Rd DAPI Cy5_140610-3_fix_2.xdce: [testng] 04:56:28,662 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 04:56:28,662 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:56:28,663 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-27_04-56-28.log] [testng] 04:56:28,664 |-INFO in ch.qos.logback.core.sift.SiftProcessor@633d674 - End of configuration. [testng] [2024-12-27 04:56:34,193] [pool-1-thread-2] Initializing /data/karsten/gabriele_-1_2/gabriele_-1_2.xdce: [testng] 04:56:34,193 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 04:56:34,193 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:56:34,194 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-27_04-56-34.log] [testng] 04:56:34,194 |-INFO in ch.qos.logback.core.sift.SiftProcessor@c2598f - End of configuration. [testng] [2024-12-27 04:57:43,928] [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] [2024-12-27 05:00:51,925] [pool-1-thread-2] Initializing /data/karsten/gabriele_-1_2/~gabriele_-1_2.xdce: [testng] [2024-12-27 05:05:19,002] [pool-1-thread-2] Initializing /data/qa-4122/KJH YFPPML 2000_A-101061_1.xdce: [testng] [2024-12-27 05:07:17,205] [pool-1-thread-2] Initializing /data/frans/im dataset/PC3_ER2009.97.180_IM.xdce: [testng] [2024-12-27 05:13:09,449] [pool-1-thread-3] Initializing /data/brian/livecell/H2b10xtrial.xdce: [testng] [2024-12-27 05:20:07,504] [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] [2024-12-27 05:21:33,943] [pool-1-thread-1] Initializing /data/public/INMAC384-DAPI-CM-eGFP_59223_1/INMAC384-DAPI-CM-eGFP_59223_1.xdce: [testng] [2024-12-27 05:22:02,996] [pool-1-thread-8] Initializing /data/michael/firstStack/2007.07.05.17.33.35.xdce: [testng] [2024-12-27 05:28:30,633] [pool-1-thread-8] Initializing /data/samples/images_number_mismatch/test.xdce: [testng] [2024-12-27 05:29:22,122] [pool-1-thread-8] Initializing /data/samples/variable-field-count/test.xdce: [testng] [2024-12-27 05:30:14,658] [pool-1-thread-8] Initializing /data/public/INMAC384-DAPI-CM-eGFP_59224_1/INMAC384-DAPI-CM-eGFP_59224_1.xdce: [testng] [2024-12-27 05:33:09,838] [pool-1-thread-2] Initializing /data/frans/incell_25juni2009/ANALYZE files/plaat HR 38/excel output file/HCT116_HR2009.97.038/HCT116_HR2009.97.038.xdce: [testng] [2024-12-27 05:41:41,695] [pool-1-thread-7] Initializing /data/michael/Single plane no flatfield corr/2007.10.17.17.04.55.xdce: [testng] [2024-12-27 05:43:22,768] [pool-1-thread-11] Initializing /data/michael/2007.08.02.16.43.24/2007.08.02.16.43.24.xdce: [testng] [2024-12-27 05:45:48,939] [pool-1-thread-10] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_Tif/ER2009_97_240_TIFF/PC3_ER2009.97.240(ok).xdce: [testng] 06:20:52,445 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 06:20:52,445 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:20:52,446 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-27_06-20-52.log] [testng] 06:20:52,446 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d80aa65 - End of configuration. [testng] 06:55:58,671 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 06:55:58,671 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:55:58,674 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-27_06-55-58.log] [testng] 06:55:58,674 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c9792d1 - End of configuration. [testng] 07:03:14,340 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 07:03:14,340 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:03:14,341 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-27_07-03-14.log] [testng] 07:03:14,342 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3781f369 - End of configuration. [testng] 07:20:40,858 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 07:20:40,858 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:20:40,858 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-27_07-20-40.log] [testng] 07:20:40,859 |-INFO in ch.qos.logback.core.sift.SiftProcessor@de3e155 - 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: 190 minutes 2 seconds Finished: SUCCESS