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Started by upstream project "BIOFORMATS-test-repo" build number 279 originally caused by: Started by upstream project "Trigger" build number 299 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins4106161617746101144.sh + '[' incell = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_44063_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] 1 warning 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] 02:49:21,078 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:49:21,079 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 02:49:21,079 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:49:21,080 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:49:21,081 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:49:21,081 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:49:21,081 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:49:21,081 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:49:21,082 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:49:21,082 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:49:21,083 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:49:21,083 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:49:21,244 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:49:21,244 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:49:21,266 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:49:21,266 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:49:21,272 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:49:21,272 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:49:21,272 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:49:21,273 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:49:21,273 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 02:49:21,273 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 02:49:21,274 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 192 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-04 02:49:21,282] [main] java.version = 17.0.2 [testng] 02:49:21,286 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:49:21,286 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:49:21,325 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-04_02-49-21.log] [testng] 02:49:21,327 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-12-04 02:49:21,329] [main] testng.directory = /data [testng] [2024-12-04 02:49:21,329] [main] testng.configDirectory = /config [testng] [2024-12-04 02:49:21,338] [main] testng.multiplier = 1.0 [testng] [2024-12-04 02:49:21,338] [main] testng.in-memory = false [testng] [2024-12-04 02:49:21,339] [main] testng.allow-missing = false [testng] [2024-12-04 02:49:21,339] [main] user.language = en [testng] [2024-12-04 02:49:21,339] [main] user.country = ${user.country} [testng] [2024-12-04 02:49:21,339] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-04 03:11:25,788] [main] ---------------------------------------- [testng] [2024-12-04 03:11:25,788] [main] Total files: 4190 [testng] [2024-12-04 03:11:25,788] [main] Scan time: 1324.449 s (316 ms/file) [testng] [2024-12-04 03:11:25,788] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 27 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-04 03:12:43,504] [pool-1-thread-1] 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] 03:12:43,505 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:12:43,505 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:12:43,506 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-04_03-12-43.log] [testng] 03:12:43,506 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4aeca916 - End of configuration. [testng] [2024-12-04 03:12:44,059] [pool-1-thread-12] Initializing /data/frans/im dataset/PC3_ER2009.97.180_IM.xdce: [testng] 03:12:44,060 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:12:44,060 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:12:44,060 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-04_03-12-44.log] [testng] 03:12:44,061 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b4acb7c - End of configuration. [testng] [2024-12-04 03:12:44,510] [pool-1-thread-11] Initializing /data/brian/H2Blivecell20x/H2Blivecell20x.xdce: [testng] 03:12:44,510 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:12:44,510 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:12:44,511 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-04_03-12-44.log] [testng] 03:12:44,511 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4399ae8d - End of configuration. [testng] [2024-12-04 03:12:45,819] [pool-1-thread-10] Initializing /data/michael/Single plane no flatfield corr/2007.10.17.17.04.55.xdce: [testng] 03:12:45,820 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:12:45,820 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:12:45,820 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-04_03-12-45.log] [testng] 03:12:45,821 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60de3adf - End of configuration. [testng] [2024-12-04 03:12:46,140] [pool-1-thread-9] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_Tif/ER2009_97_238_TIFF/PC3_ER2009.97.238.xdce: [testng] 03:12:46,140 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:12:46,140 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:12:46,141 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-04_03-12-46.log] [testng] 03:12:46,141 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a31242b - End of configuration. [testng] [2024-12-04 03:12:46,839] [pool-1-thread-8] Initializing /data/public/INMAC384-DAPI-CM-eGFP_59223_1/INMAC384-DAPI-CM-eGFP_59223_1.xdce: [testng] 03:12:46,839 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:12:46,839 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:12:46,840 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-04_03-12-46.log] [testng] 03:12:46,840 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7bb179d0 - End of configuration. [testng] [2024-12-04 03:12:48,274] [pool-1-thread-7] Initializing /data/karsten/gabriele_-1_2/gabriele_-1_2.xdce: [testng] 03:12:48,275 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:12:48,275 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:12:48,275 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-04_03-12-48.log] [testng] 03:12:48,276 |-INFO in ch.qos.logback.core.sift.SiftProcessor@723190ba - End of configuration. [testng] [2024-12-04 03:12:48,880] [pool-1-thread-6] Initializing /data/michael/2007.08.02.16.43.24/2007.08.02.16.43.24.xdce: [testng] 03:12:48,880 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:12:48,880 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:12:48,881 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-04_03-12-48.log] [testng] 03:12:48,882 |-INFO in ch.qos.logback.core.sift.SiftProcessor@63b29065 - End of configuration. [testng] [2024-12-04 03:12:49,808] [pool-1-thread-5] Initializing /data/qa-4122/KJH YFPPML 2000_A-101061_1.xdce: [testng] 03:12:49,808 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:12:49,808 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:12:49,809 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-04_03-12-49.log] [testng] 03:12:49,809 |-INFO in ch.qos.logback.core.sift.SiftProcessor@792c4a5b - End of configuration. [testng] [2024-12-04 03:12:50,529] [pool-1-thread-4] Initializing /data/samples/variable-field-count/test.xdce: [testng] 03:12:50,529 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:12:50,529 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:12:50,530 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-04_03-12-50.log] [testng] 03:12:50,530 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a2d0592 - End of configuration. [testng] [2024-12-04 03:12:51,272] [pool-1-thread-3] Initializing /data/damir/20x Z1 16fields Gr Rd DAPI Cy5_140610-3_fix_2.xdce: [testng] 03:12:51,272 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:12:51,272 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:12:51,273 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-04_03-12-51.log] [testng] 03:12:51,273 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ede8f41 - End of configuration. [testng] [2024-12-04 03:12:56,426] [pool-1-thread-2] Initializing /data/michael/Z Sections with flatfield corr/2007.10.17.17.13.59.xdce: [testng] 03:12:56,427 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:12:56,427 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:12:56,427 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-04_03-12-56.log] [testng] 03:12:56,428 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7eeed975 - End of configuration. [testng] [2024-12-04 03:13:34,440] [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] [2024-12-04 03:14:39,659] [pool-1-thread-5] Initializing /data/brian/Proper Dark Images/2007.11.12.13.37.27.xdce: [testng] [2024-12-04 03:15:09,906] [pool-1-thread-5] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_Tif/ER2009_97_239_TIFF/PC3_ER2009.97.239.xdce: [testng] [2024-12-04 03:15:18,413] [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] [2024-12-04 03:16:31,199] [pool-1-thread-10] 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] [2024-12-04 03:25:09,096] [pool-1-thread-6] Initializing /data/frans/incell_25juni2009/ANALYZE files/plaat HR 38/excel output file/HCT116_HR2009.97.038/HCT116_HR2009.97.038.xdce: [testng] [2024-12-04 03:26:25,337] [pool-1-thread-2] Initializing /data/brian/livecell/H2b10xtrial.xdce: [testng] [2024-12-04 03:26:32,897] [pool-1-thread-12] Initializing /data/karsten/gabriele_-1_2/~gabriele_-1_2.xdce: [testng] [2024-12-04 03:27:33,872] [pool-1-thread-7] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_Tif/ER2009_97_240_TIFF/PC3_ER2009.97.240(ok).xdce: [testng] [2024-12-04 03:28:29,884] [pool-1-thread-12] Initializing /data/michael/firstStack/2007.07.05.17.33.35.xdce: [testng] [2024-12-04 03:28:34,143] [pool-1-thread-3] Initializing /data/public/INMAC384-DAPI-CM-eGFP_59224_1/INMAC384-DAPI-CM-eGFP_59224_1.xdce: [testng] [2024-12-04 03:32:08,733] [pool-1-thread-12] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_IM/2009_97_239_IM/2009_97_239_IM.xdce: [testng] [2024-12-04 03:37:33,357] [pool-1-thread-1] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_IM/2009_97_240_IM/2009_97_240_IM.xdce: [testng] [2024-12-04 03:40:39,578] [pool-1-thread-9] Initializing /data/brian/2Hour10x/H2b2Hour10x5fields.xdce: [testng] [2024-12-04 03:41:34,395] [pool-1-thread-4] Initializing /data/samples/images_number_mismatch/test.xdce: [testng] 04:50:34,317 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 04:50:34,317 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:50:34,318 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-04_04-50-34.log] [testng] 04:50:34,318 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6486adaa - 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: 121 minutes 16 seconds Finished: SUCCESS