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Started by upstream project "BIOFORMATS-test-repo" build number 240 originally caused by: Started by upstream project "Trigger" build number 265 originally caused by: Started by timer 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/jenkins13011957882647177687.sh + '[' incell = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_37796_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 02:37:03,864 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:37:03,866 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 02:37:03,866 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:37:03,867 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:37:03,867 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:37:03,867 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:37:03,868 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:37:03,868 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:37:03,868 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:37:03,869 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:37:03,869 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:37:03,869 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:37:04,033 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:37:04,033 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:37:04,058 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:37:04,058 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:37:04,065 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:37:04,065 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:37:04,066 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:37:04,066 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:37:04,066 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 02:37:04,067 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 02:37:04,067 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 199 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-31 02:37:04,076] [main] java.version = 21 [testng] 02:37:04,079 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:37:04,079 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:37:04,123 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-31_02-37-04.log] [testng] 02:37:04,125 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-10-31 02:37:04,126] [main] testng.directory = /data [testng] [2024-10-31 02:37:04,127] [main] testng.configDirectory = /config [testng] [2024-10-31 02:37:04,136] [main] testng.multiplier = 1.0 [testng] [2024-10-31 02:37:04,137] [main] testng.in-memory = false [testng] [2024-10-31 02:37:04,137] [main] testng.allow-missing = false [testng] [2024-10-31 02:37:04,137] [main] user.language = en [testng] [2024-10-31 02:37:04,137] [main] user.country = ${user.country} [testng] [2024-10-31 02:37:04,137] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-31 03:01:05,684] [main] ---------------------------------------- [testng] [2024-10-31 03:01:05,685] [main] Total files: 4190 [testng] [2024-10-31 03:01:05,685] [main] Scan time: 1441.546 s (344 ms/file) [testng] [2024-10-31 03:01:05,685] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 27 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-31 03:02:33,242] [pool-1-thread-1] Initializing /data/frans/incell_25juni2009/ANALYZE files/plaat HR37/excel output file/HCT116_HR2009.97.037/HCT116_HR2009.97.037.xdce: [testng] 03:02:33,242 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:02:33,242 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:02:33,244 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-31_03-02-33.log] [testng] 03:02:33,244 |-INFO in ch.qos.logback.core.sift.SiftProcessor@650e39e2 - End of configuration. [testng] [2024-10-31 03:02:33,674] [pool-1-thread-12] 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] 03:02:33,675 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:02:33,675 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:02:33,675 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-31_03-02-33.log] [testng] 03:02:33,676 |-INFO in ch.qos.logback.core.sift.SiftProcessor@638accba - End of configuration. [testng] [2024-10-31 03:02:34,096] [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] 03:02:34,096 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:02:34,096 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:02:34,097 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-31_03-02-34.log] [testng] 03:02:34,098 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a1067a9 - End of configuration. [testng] [2024-10-31 03:02:34,685] [pool-1-thread-10] Initializing /data/qa-4122/KJH YFPPML 2000_A-101061_1.xdce: [testng] 03:02:34,685 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:02:34,685 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:02:34,686 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-31_03-02-34.log] [testng] 03:02:34,686 |-INFO in ch.qos.logback.core.sift.SiftProcessor@109bf05f - End of configuration. [testng] [2024-10-31 03:02:35,229] [pool-1-thread-9] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_Tif/ER2009_97_239_TIFF/PC3_ER2009.97.239.xdce: [testng] 03:02:35,230 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:02:35,230 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:02:35,230 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-31_03-02-35.log] [testng] 03:02:35,231 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b8134ae - End of configuration. [testng] [2024-10-31 03:02:35,677] [pool-1-thread-8] 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] 03:02:35,677 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:02:35,677 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:02:35,678 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-31_03-02-35.log] [testng] 03:02:35,678 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a8872a0 - End of configuration. [testng] [2024-10-31 03:02:36,795] [pool-1-thread-7] Initializing /data/michael/2007.08.02.16.43.24/2007.08.02.16.43.24.xdce: [testng] 03:02:36,795 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:02:36,795 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:02:36,796 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-31_03-02-36.log] [testng] 03:02:36,796 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f3127b7 - End of configuration. [testng] [2024-10-31 03:02:37,390] [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] 03:02:37,390 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:02:37,390 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:02:37,391 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-31_03-02-37.log] [testng] 03:02:37,392 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b7cbbe7 - End of configuration. [testng] [2024-10-31 03:02:37,934] [pool-1-thread-5] Initializing /data/michael/Single plane no flatfield corr/2007.10.17.17.04.55.xdce: [testng] 03:02:37,935 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:02:37,935 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:02:37,935 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-31_03-02-37.log] [testng] 03:02:37,936 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32569c3a - End of configuration. [testng] [2024-10-31 03:02:38,576] [pool-1-thread-4] Initializing /data/public/INMAC384-DAPI-CM-eGFP_59223_1/INMAC384-DAPI-CM-eGFP_59223_1.xdce: [testng] 03:02:38,576 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:02:38,577 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:02:38,577 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-31_03-02-38.log] [testng] 03:02:38,578 |-INFO in ch.qos.logback.core.sift.SiftProcessor@26494540 - End of configuration. [testng] [2024-10-31 03:02:39,504] [pool-1-thread-3] Initializing /data/karsten/gabriele_-1_2/~gabriele_-1_2.xdce: [testng] 03:02:39,504 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:02:39,504 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:02:39,505 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-31_03-02-39.log] [testng] 03:02:39,505 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3964cf15 - End of configuration. [testng] [2024-10-31 03:02:40,121] [pool-1-thread-2] Initializing /data/michael/firstStack/2007.07.05.17.33.35.xdce: [testng] 03:02:40,122 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:02:40,122 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:02:40,122 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-31_03-02-40.log] [testng] 03:02:40,123 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12104009 - End of configuration. [testng] [2024-10-31 03:04:17,945] [pool-1-thread-10] Initializing /data/public/INMAC384-DAPI-CM-eGFP_59224_1/INMAC384-DAPI-CM-eGFP_59224_1.xdce: [testng] [2024-10-31 03:06:00,784] [pool-1-thread-3] Initializing /data/brian/H2Blivecell20x/H2Blivecell20x.xdce: [testng] [2024-10-31 03:07:16,215] [pool-1-thread-2] Initializing /data/brian/livecell/H2b10xtrial.xdce: [testng] [2024-10-31 03:07:43,594] [pool-1-thread-5] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_Tif/ER2009_97_238_TIFF/PC3_ER2009.97.238.xdce: [testng] [2024-10-31 03:15:57,436] [pool-1-thread-7] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_IM/2009_97_238_IM/2009_97_238_IM.xdce: [testng] [2024-10-31 03:16:14,136] [pool-1-thread-11] Initializing /data/samples/variable-field-count/test.xdce: [testng] [2024-10-31 03:16:44,617] [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] [2024-10-31 03:28:09,854] [pool-1-thread-8] Initializing /data/michael/Z Sections with flatfield corr/2007.10.17.17.13.59.xdce: [testng] [2024-10-31 03:29:11,620] [pool-1-thread-7] Initializing /data/karsten/gabriele_-1_2/gabriele_-1_2.xdce: [testng] [2024-10-31 03:30:07,653] [pool-1-thread-11] Initializing /data/brian/Proper Dark Images/2007.11.12.13.37.27.xdce: [testng] [2024-10-31 03:30:53,202] [pool-1-thread-11] Initializing /data/samples/images_number_mismatch/test.xdce: [testng] [2024-10-31 03:30:55,413] [pool-1-thread-6] Initializing /data/brian/2Hour10x/H2b2Hour10x5fields.xdce: [testng] [2024-10-31 03:31:00,790] [pool-1-thread-1] Initializing /data/frans/im dataset/PC3_ER2009.97.180_IM.xdce: [testng] [2024-10-31 03:31:02,312] [pool-1-thread-9] Initializing /data/damir/20x Z1 16fields Gr Rd DAPI Cy5_140610-3_fix_2.xdce: [testng] [2024-10-31 03:31:34,505] [pool-1-thread-11] Initializing /data/frans/incell_25juni2009/ANALYZE files/plaat HR 38/excel output file/HCT116_HR2009.97.038/HCT116_HR2009.97.038.xdce: [testng] 04:37:32,188 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 04:37:32,188 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:37:32,189 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-31_04-37-32.log] [testng] 04:37:32,190 |-INFO in ch.qos.logback.core.sift.SiftProcessor@16286b4e - 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: 120 minutes 33 seconds Finished: SUCCESS