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Started by upstream project "BIOFORMATS-test-repo" build number 395 originally caused by: Started by upstream project "Trigger" build number 479 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@7 [BIOFORMATS-test-folder@7] $ /bin/bash -xe /tmp/jenkins5367596004606889644.sh + '[' flex = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_62354_merge_ci -v /uod/idr/repos/curated/flex:/data -v /uod/idr-scratch/merge-ci/curated/flex:/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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 01:28:30,705 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 01:28:30,706 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - No custom configurators were discovered as a service. [testng] 01:28:30,706 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:28:30,707 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:28:30,708 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:28:30,708 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:28:30,708 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:28:30,708 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:28:30,709 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:28:30,709 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:28:30,710 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:28:30,710 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:28:30,881 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:28:30,881 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:28:30,909 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:28:30,909 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:28:30,916 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:28:30,916 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:28:30,916 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:28:30,917 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:28:30,917 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@47d9a273 - End of configuration. [testng] 01:28:30,917 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@4659191b - Registering current configuration as safe fallback point [testng] 01:28:30,917 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 208 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-05-15 01:28:30,926] [main] java.version = 21 [testng] 01:28:30,929 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:28:30,929 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:28:30,973 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-05-15_01-28-30.log] [testng] 01:28:30,974 |-INFO in ch.qos.logback.core.sift.SiftProcessor@69504ae9 - End of configuration. [testng] [2025-05-15 01:28:30,976] [main] testng.directory = /data [testng] [2025-05-15 01:28:30,976] [main] testng.configDirectory = /config [testng] [2025-05-15 01:28:30,984] [main] testng.multiplier = 1.0 [testng] [2025-05-15 01:28:30,985] [main] testng.in-memory = false [testng] [2025-05-15 01:28:30,985] [main] testng.allow-missing = false [testng] [2025-05-15 01:28:30,985] [main] user.language = en [testng] [2025-05-15 01:28:30,985] [main] user.country = ${user.country} [testng] [2025-05-15 01:28:30,986] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-05-15 01:30:39,331] [main] ---------------------------------------- [testng] [2025-05-15 01:30:39,331] [main] Total files: 791 [testng] [2025-05-15 01:30:39,332] [main] Scan time: 128.345 s (162 ms/file) [testng] [2025-05-15 01:30:39,332] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-05-15 01:38:28,773] [pool-1-thread-1] Initializing /data/qa-7469/002002.flex: [testng] 01:38:28,774 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:38:28,775 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:28,777 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-05-15_01-38-28.log] [testng] 01:38:28,777 |-INFO in ch.qos.logback.core.sift.SiftProcessor@26e7d76b - End of configuration. [testng] [2025-05-15 01:38:31,386] [pool-1-thread-12] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] 01:38:31,386 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:38:31,386 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:31,387 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-05-15_01-38-31.log] [testng] 01:38:31,387 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f8a7185 - End of configuration. [testng] [2025-05-15 01:38:33,861] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex: [testng] 01:38:33,861 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:38:33,861 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:33,862 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-05-15_01-38-33.log] [testng] 01:38:33,862 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d2eaba4 - End of configuration. [testng] [2025-05-15 01:38:36,876] [pool-1-thread-10] Initializing /data/tamjid/006003000.flex: [testng] 01:38:36,876 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:38:36,876 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:36,877 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-05-15_01-38-36.log] [testng] 01:38:36,877 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ad7a0ef - End of configuration. [testng] [2025-05-15 01:38:39,628] [pool-1-thread-9] Initializing /data/qa-18096/002002001.flex: [testng] 01:38:39,628 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:38:39,628 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:39,629 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-05-15_01-38-39.log] [testng] 01:38:39,629 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66ae05eb - End of configuration. [testng] [2025-05-15 01:38:42,300] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex: [testng] 01:38:42,300 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:38:42,300 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:42,301 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-05-15_01-38-42.log] [testng] 01:38:42,301 |-INFO in ch.qos.logback.core.sift.SiftProcessor@319f3339 - End of configuration. [testng] [2025-05-15 01:38:45,092] [pool-1-thread-7] Initializing /data/ghislain/test.flex: [testng] 01:38:45,092 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:38:45,092 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:45,093 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-05-15_01-38-45.log] [testng] 01:38:45,093 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3206a7c8 - End of configuration. [testng] [2025-05-15 01:38:47,726] [pool-1-thread-6] Initializing /data/tony/001001000_objects.flex: [testng] 01:38:47,726 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:38:47,727 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:47,727 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-05-15_01-38-47.log] [testng] 01:38:47,728 |-INFO in ch.qos.logback.core.sift.SiftProcessor@33b4dd5e - End of configuration. [testng] [2025-05-15 01:38:50,571] [pool-1-thread-5] Initializing /data/stephane/006013000.flex: [testng] 01:38:50,571 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:38:50,571 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:50,572 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-05-15_01-38-50.log] [testng] 01:38:50,572 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22616914 - End of configuration. [testng] [2025-05-15 01:38:53,066] [pool-1-thread-4] Initializing /data/qa-2983/004007000.flex: [testng] 01:38:53,066 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:38:53,066 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:53,067 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-05-15_01-38-53.log] [testng] 01:38:53,067 |-INFO in ch.qos.logback.core.sift.SiftProcessor@84029e7 - End of configuration. [testng] [2025-05-15 01:38:55,416] [pool-1-thread-3] Initializing /data/qa-17190/002002011.flex: [testng] 01:38:55,417 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:38:55,417 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:55,417 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-05-15_01-38-55.log] [testng] 01:38:55,418 |-INFO in ch.qos.logback.core.sift.SiftProcessor@39dff14f - End of configuration. [testng] [2025-05-15 01:38:56,966] [pool-1-thread-2] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] 01:38:56,966 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:38:56,966 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:56,967 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-05-15_01-38-56.log] [testng] 01:38:56,967 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b26cddb - End of configuration. [testng] [2025-05-15 01:39:40,834] [pool-1-thread-3] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2025-05-15 01:39:46,266] [pool-1-thread-1] Initializing /data/stephane/002007000.flex: [testng] [2025-05-15 01:39:48,910] [pool-1-thread-4] Initializing /data/qa-18096/002003001.flex: [testng] [2025-05-15 01:39:50,688] [pool-1-thread-12] Initializing /data/tony/003003000.tiff: [testng] [2025-05-15 01:39:55,279] [pool-1-thread-9] Initializing /data/tony/001014000 - from flex.tif: [testng] [2025-05-15 01:39:59,409] [pool-1-thread-6] Initializing /data/anatole/001004000.flex: [testng] [2025-05-15 01:40:02,275] [pool-1-thread-7] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2025-05-15 01:40:04,670] [pool-1-thread-10] Initializing /data/achim/003003000.flex: [testng] [2025-05-15 01:40:10,172] [pool-1-thread-8] Initializing /data/manuel/003003001.flex: [testng] [2025-05-15 01:40:13,094] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex: [testng] [2025-05-15 01:40:16,030] [pool-1-thread-5] Initializing /data/tony/015002000.tiff: [testng] [2025-05-15 01:40:38,151] [pool-1-thread-4] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] [2025-05-15 01:41:01,047] [pool-1-thread-1] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] [2025-05-15 01:41:20,767] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex: [testng] [2025-05-15 01:41:23,461] [pool-1-thread-9] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] [2025-05-15 01:41:40,202] [pool-1-thread-5] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_03(2007-12-14_10-50-56)/004006000.flex: [testng] [2025-05-15 01:41:51,435] [pool-1-thread-10] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex: [testng] [2025-05-15 01:42:08,377] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex: [testng] [2025-05-15 01:42:11,357] [pool-1-thread-8] Initializing /data/tamjid/006005000.flex: [testng] [2025-05-15 01:42:22,810] [pool-1-thread-6] Initializing /data/tony/003008000.flex: [testng] [2025-05-15 01:42:25,617] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex: [testng] [2025-05-15 01:42:28,270] [pool-1-thread-5] Initializing /data/tamjid/006004000.flex: [testng] [2025-05-15 01:42:47,037] [pool-1-thread-8] Initializing /data/tony/test.tiff: [testng] [2025-05-15 01:43:03,468] [pool-1-thread-5] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex: [testng] [2025-05-15 01:43:12,695] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] [2025-05-15 01:43:29,139] [pool-1-thread-12] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2025-05-15 01:43:50,474] [pool-1-thread-8] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2025-05-15 01:44:09,796] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] [2025-05-15 01:44:12,526] [pool-1-thread-7] Initializing /data/tony/test1.flex: [testng] [2025-05-15 01:44:16,816] [pool-1-thread-3] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2226, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 35 minutes 51 seconds Finished: SUCCESS