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Started by upstream project "BIOFORMATS-test-repo" build number 194 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@6 [BIOFORMATS-test-folder@6] $ /bin/bash -xe /tmp/jenkins6379505547407802983.sh + '[' incell = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_30768_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 13:44:44,949 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 13:44:44,950 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 13:44:44,950 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 13:44:44,951 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 13:44:44,951 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 13:44:44,952 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 13:44:44,952 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 13:44:44,952 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 13:44:44,952 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 13:44:44,953 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 13:44:44,953 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 13:44:44,954 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 13:44:45,108 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 13:44:45,108 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 13:44:45,132 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 13:44:45,132 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 13:44:45,138 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 13:44:45,139 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 13:44:45,139 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 13:44:45,139 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 13:44:45,139 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 13:44:45,140 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 13:44:45,140 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 188 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-09-19 13:44:45,149] [main] java.version = 21 [testng] 13:44:45,152 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 13:44:45,152 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:44:45,192 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-19_13-44-45.log] [testng] 13:44:45,193 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-09-19 13:44:45,194] [main] testng.directory = /data [testng] [2024-09-19 13:44:45,195] [main] testng.configDirectory = /config [testng] [2024-09-19 13:44:45,204] [main] testng.multiplier = 1.0 [testng] [2024-09-19 13:44:45,205] [main] testng.in-memory = false [testng] [2024-09-19 13:44:45,205] [main] testng.allow-missing = false [testng] [2024-09-19 13:44:45,205] [main] user.language = en [testng] [2024-09-19 13:44:45,205] [main] user.country = ${user.country} [testng] [2024-09-19 13:44:45,205] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-09-19 14:13:52,113] [main] ---------------------------------------- [testng] [2024-09-19 14:13:52,113] [main] Total files: 4190 [testng] [2024-09-19 14:13:52,114] [main] Scan time: 1746.908 s (416 ms/file) [testng] [2024-09-19 14:13:52,114] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 27 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-09-19 14:15:28,223] [pool-1-thread-1] Initializing /data/damir/20x Z1 16fields Gr Rd DAPI Cy5_140610-3_fix_2.xdce: [testng] 14:15:28,224 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 14:15:28,224 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:15:28,225 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-09-19_14-15-28.log] [testng] 14:15:28,226 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2396a87c - End of configuration. [testng] [2024-09-19 14:15:33,537] [pool-1-thread-12] 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] 14:15:33,538 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 14:15:33,538 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:15:33,539 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-09-19_14-15-33.log] [testng] 14:15:33,539 |-INFO in ch.qos.logback.core.sift.SiftProcessor@207298f9 - End of configuration. [testng] [2024-09-19 14:15:34,340] [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] 14:15:34,340 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 14:15:34,340 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:15:34,341 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-09-19_14-15-34.log] [testng] 14:15:34,342 |-INFO in ch.qos.logback.core.sift.SiftProcessor@54dd6004 - End of configuration. [testng] [2024-09-19 14:15:35,270] [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] 14:15:35,270 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 14:15:35,270 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:15:35,271 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-09-19_14-15-35.log] [testng] 14:15:35,272 |-INFO in ch.qos.logback.core.sift.SiftProcessor@638accba - End of configuration. [testng] [2024-09-19 14:15:36,272] [pool-1-thread-9] Initializing /data/qa-4122/KJH YFPPML 2000_A-101061_1.xdce: [testng] 14:15:36,272 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 14:15:36,272 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:15:36,273 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-09-19_14-15-36.log] [testng] 14:15:36,273 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f355174 - End of configuration. [testng] [2024-09-19 14:15:36,851] [pool-1-thread-8] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_Tif/ER2009_97_239_TIFF/PC3_ER2009.97.239.xdce: [testng] 14:15:36,852 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 14:15:36,852 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:15:36,853 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-09-19_14-15-36.log] [testng] 14:15:36,853 |-INFO in ch.qos.logback.core.sift.SiftProcessor@c1ea3e6 - End of configuration. [testng] [2024-09-19 14:15:37,884] [pool-1-thread-7] Initializing /data/michael/firstStack/2007.07.05.17.33.35.xdce: [testng] 14:15:37,885 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 14:15:37,885 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:15:37,886 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-09-19_14-15-37.log] [testng] 14:15:37,886 |-INFO in ch.qos.logback.core.sift.SiftProcessor@894967e - End of configuration. [testng] [2024-09-19 14:15:38,511] [pool-1-thread-6] Initializing /data/brian/H2Blivecell20x/H2Blivecell20x.xdce: [testng] 14:15:38,511 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 14:15:38,511 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:15:38,512 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-09-19_14-15-38.log] [testng] 14:15:38,513 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f980795 - End of configuration. [testng] [2024-09-19 14:15:40,438] [pool-1-thread-5] Initializing /data/brian/Proper Dark Images/2007.11.12.13.37.27.xdce: [testng] 14:15:40,438 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 14:15:40,438 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:15:40,439 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-09-19_14-15-40.log] [testng] 14:15:40,439 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4832e50c - End of configuration. [testng] [2024-09-19 14:15:41,134] [pool-1-thread-4] Initializing /data/karsten/gabriele_-1_2/~gabriele_-1_2.xdce: [testng] 14:15:41,135 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 14:15:41,135 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:15:41,136 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-09-19_14-15-41.log] [testng] 14:15:41,136 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65041977 - End of configuration. [testng] [2024-09-19 14:15:41,708] [pool-1-thread-3] Initializing /data/frans/im dataset/PC3_ER2009.97.180_IM.xdce: [testng] 14:15:41,708 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 14:15:41,709 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:15:41,709 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-09-19_14-15-41.log] [testng] 14:15:41,710 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d72b258 - End of configuration. [testng] [2024-09-19 14:15:43,223] [pool-1-thread-2] Initializing /data/brian/2Hour10x/H2b2Hour10x5fields.xdce: [testng] 14:15:43,223 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 14:15:43,224 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:15:43,224 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-09-19_14-15-43.log] [testng] 14:15:43,225 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36c5006a - End of configuration. [testng] [2024-09-19 14:16:40,669] [pool-1-thread-5] Initializing /data/karsten/gabriele_-1_2/gabriele_-1_2.xdce: [testng] [2024-09-19 14:17:21,328] [pool-1-thread-9] Initializing /data/public/INMAC384-DAPI-CM-eGFP_59223_1/INMAC384-DAPI-CM-eGFP_59223_1.xdce: [testng] [2024-09-19 14:19:03,113] [pool-1-thread-4] Initializing /data/frans/incell_25juni2009/ANALYZE files/plaat HR 38/excel output file/HCT116_HR2009.97.038/HCT116_HR2009.97.038.xdce: [testng] [2024-09-19 14:19:51,331] [pool-1-thread-5] Initializing /data/samples/variable-field-count/test.xdce: [testng] [2024-09-19 14:20:21,644] [pool-1-thread-7] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_IM/2009_97_239_IM/2009_97_239_IM.xdce: [testng] [2024-09-19 14:20:32,012] [pool-1-thread-5] Initializing /data/brian/livecell/H2b10xtrial.xdce: [testng] [2024-09-19 14:30:45,687] [pool-1-thread-1] Initializing /data/michael/Single plane no flatfield corr/2007.10.17.17.04.55.xdce: [testng] [2024-09-19 14:34:05,614] [pool-1-thread-3] Initializing /data/michael/Z Sections with flatfield corr/2007.10.17.17.13.59.xdce: [testng] [2024-09-19 14:35:22,500] [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] [2024-09-19 14:36:15,752] [pool-1-thread-7] Initializing /data/michael/2007.08.02.16.43.24/2007.08.02.16.43.24.xdce: [testng] [2024-09-19 14:46:14,759] [pool-1-thread-12] Initializing /data/frans/incell_25juni2009/Experiment_with_3_plates_as_Tif/ER2009_97_240_TIFF/PC3_ER2009.97.240(ok).xdce: [testng] [2024-09-19 14:49:03,217] [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] [2024-09-19 14:49:09,181] [pool-1-thread-11] Initializing /data/public/INMAC384-DAPI-CM-eGFP_59224_1/INMAC384-DAPI-CM-eGFP_59224_1.xdce: [testng] [2024-09-19 14:49:12,013] [pool-1-thread-8] 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] [2024-09-19 14:49:19,066] [pool-1-thread-10] Initializing /data/samples/images_number_mismatch/test.xdce: [testng] 15:21:03,005 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 15:21:03,005 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:21:03,007 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-09-19_15-21-03.log] [testng] 15:21:03,007 |-INFO in ch.qos.logback.core.sift.SiftProcessor@173212e5 - End of configuration. [testng] 15:52:11,006 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 15:52:11,006 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:52:11,008 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-09-19_15-52-11.log] [testng] 15:52:11,008 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40db8e82 - End of configuration. [testng] 16:27:07,830 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 16:27:07,830 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:27:07,831 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-19_16-27-07.log] [testng] 16:27:07,831 |-INFO in ch.qos.logback.core.sift.SiftProcessor@645d96c4 - 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: 162 minutes 25 seconds Finished: SUCCESS