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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@9 [BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins5606139774846321882.sh + '[' flex = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_37733_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 00:45:29,428 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:45:29,429 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 00:45:29,429 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:45:29,430 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:45:29,430 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:45:29,430 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:45:29,431 |-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] 00:45:29,431 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:45:29,431 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:45:29,432 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:45:29,432 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:45:29,432 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:45:29,612 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:45:29,612 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:45:29,636 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:45:29,636 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:45:29,642 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:45:29,643 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:45:29,643 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:45:29,643 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:45:29,643 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 00:45:29,644 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 00:45:29,644 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 213 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-31 00:45:29,653] [main] java.version = 21 [testng] 00:45:29,656 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:45:29,656 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:45:29,697 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-31_00-45-29.log] [testng] 00:45:29,699 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-10-31 00:45:29,700] [main] testng.directory = /data [testng] [2024-10-31 00:45:29,701] [main] testng.configDirectory = /config [testng] [2024-10-31 00:45:29,709] [main] testng.multiplier = 1.0 [testng] [2024-10-31 00:45:29,710] [main] testng.in-memory = false [testng] [2024-10-31 00:45:29,710] [main] testng.allow-missing = false [testng] [2024-10-31 00:45:29,710] [main] user.language = en [testng] [2024-10-31 00:45:29,710] [main] user.country = ${user.country} [testng] [2024-10-31 00:45:29,710] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-31 00:46:24,012] [main] ---------------------------------------- [testng] [2024-10-31 00:46:24,012] [main] Total files: 791 [testng] [2024-10-31 00:46:24,013] [main] Scan time: 54.302 s (68 ms/file) [testng] [2024-10-31 00:46:24,014] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-31 00:51:36,138] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex: [testng] 00:51:36,139 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:51:36,139 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:51:36,140 |-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_00-51-36.log] [testng] 00:51:36,141 |-INFO in ch.qos.logback.core.sift.SiftProcessor@772f5db9 - End of configuration. [testng] [2024-10-31 00:51:37,488] [pool-1-thread-12] Initializing /data/manuel/003003001.flex: [testng] 00:51:37,488 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:51:37,488 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:51:37,489 |-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_00-51-37.log] [testng] 00:51:37,489 |-INFO in ch.qos.logback.core.sift.SiftProcessor@45ab4ccf - End of configuration. [testng] [2024-10-31 00:51:38,180] [pool-1-thread-11] Initializing /data/stephane/002007000.flex: [testng] 00:51:38,180 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:51:38,181 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:51:38,181 |-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_00-51-38.log] [testng] 00:51:38,182 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5cd5fa79 - End of configuration. [testng] [2024-10-31 00:51:38,894] [pool-1-thread-10] Initializing /data/qa-17190/002002011.flex: [testng] 00:51:38,895 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:51:38,895 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:51:38,896 |-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_00-51-38.log] [testng] 00:51:38,896 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f93751 - End of configuration. [testng] [2024-10-31 00:51:39,502] [pool-1-thread-9] Initializing /data/tony/015002000.tiff: [testng] 00:51:39,502 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:51:39,502 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:51:39,503 |-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_00-51-39.log] [testng] 00:51:39,504 |-INFO in ch.qos.logback.core.sift.SiftProcessor@b0ca4ce - End of configuration. [testng] [2024-10-31 00:51:41,083] [pool-1-thread-8] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] 00:51:41,083 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:51:41,083 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:51:41,084 |-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_00-51-41.log] [testng] 00:51:41,085 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7081623c - End of configuration. [testng] [2024-10-31 00:51:47,581] [pool-1-thread-7] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] 00:51:47,582 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:51:47,582 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:51:47,582 |-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_00-51-47.log] [testng] 00:51:47,583 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1919ec54 - End of configuration. [testng] [2024-10-31 00:51:48,550] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] 00:51:48,551 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:51:48,551 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:51:48,552 |-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_00-51-48.log] [testng] 00:51:48,552 |-INFO in ch.qos.logback.core.sift.SiftProcessor@28299d5b - End of configuration. [testng] [2024-10-31 00:51:55,152] [pool-1-thread-5] Initializing /data/tony/test1.flex: [testng] 00:51:55,152 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:51:55,153 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:51:55,154 |-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_00-51-55.log] [testng] 00:51:55,154 |-INFO in ch.qos.logback.core.sift.SiftProcessor@42a40484 - End of configuration. [testng] [2024-10-31 00:51:56,007] [pool-1-thread-4] Initializing /data/tony/003008000.flex: [testng] 00:51:56,008 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:51:56,008 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:51:56,008 |-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_00-51-56.log] [testng] 00:51:56,009 |-INFO in ch.qos.logback.core.sift.SiftProcessor@64bb41cf - End of configuration. [testng] [2024-10-31 00:51:56,865] [pool-1-thread-3] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex: [testng] 00:51:56,865 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:51:56,865 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:51:56,866 |-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_00-51-56.log] [testng] 00:51:56,867 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b45519b - End of configuration. [testng] [2024-10-31 00:51:57,785] [pool-1-thread-2] Initializing /data/tony/001001000_objects.flex: [testng] 00:51:57,785 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:51:57,785 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:51:57,786 |-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_00-51-57.log] [testng] 00:51:57,786 |-INFO in ch.qos.logback.core.sift.SiftProcessor@764513e5 - End of configuration. [testng] [2024-10-31 00:52:08,731] [pool-1-thread-9] Initializing /data/tony/test.tiff: [testng] [2024-10-31 00:52:10,345] [pool-1-thread-10] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex: [testng] [2024-10-31 00:52:11,107] [pool-1-thread-11] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2024-10-31 00:52:11,845] [pool-1-thread-2] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex: [testng] [2024-10-31 00:52:12,558] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] [2024-10-31 00:52:22,694] [pool-1-thread-3] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2024-10-31 00:52:24,470] [pool-1-thread-7] Initializing /data/achim/003003000.flex: [testng] [2024-10-31 00:52:25,392] [pool-1-thread-4] Initializing /data/stephane/006013000.flex: [testng] [2024-10-31 00:52:28,369] [pool-1-thread-9] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] [2024-10-31 00:52:36,720] [pool-1-thread-11] Initializing /data/anatole/001004000.flex: [testng] [2024-10-31 00:52:38,047] [pool-1-thread-12] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] [2024-10-31 00:52:40,953] [pool-1-thread-10] Initializing /data/tamjid/006004000.flex: [testng] [2024-10-31 00:52:41,706] [pool-1-thread-2] Initializing /data/tony/001014000 - from flex.tif: [testng] [2024-10-31 00:52:47,337] [pool-1-thread-1] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] [2024-10-31 00:52:54,624] [pool-1-thread-7] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex: [testng] [2024-10-31 00:52:56,873] [pool-1-thread-12] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2024-10-31 00:53:06,267] [pool-1-thread-2] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_03(2007-12-14_10-50-56)/004006000.flex: [testng] [2024-10-31 00:53:07,437] [pool-1-thread-10] Initializing /data/qa-18096/002003001.flex: [testng] [2024-10-31 00:53:08,554] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex: [testng] [2024-10-31 00:53:14,500] [pool-1-thread-7] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2024-10-31 00:53:25,665] [pool-1-thread-10] Initializing /data/qa-18096/002002001.flex: [testng] [2024-10-31 00:53:28,122] [pool-1-thread-11] Initializing /data/qa-7469/002002.flex: [testng] [2024-10-31 00:53:31,217] [pool-1-thread-2] Initializing /data/tamjid/006003000.flex: [testng] [2024-10-31 00:53:34,174] [pool-1-thread-4] Initializing /data/tamjid/006005000.flex: [testng] [2024-10-31 00:53:35,997] [pool-1-thread-10] Initializing /data/tony/003003000.tiff: [testng] [2024-10-31 00:53:40,724] [pool-1-thread-11] Initializing /data/qa-2983/004007000.flex: [testng] [2024-10-31 00:53:43,412] [pool-1-thread-2] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex: [testng] [2024-10-31 00:53:45,940] [pool-1-thread-4] Initializing /data/ghislain/test.flex: [testng] [2024-10-31 00:53:47,756] [pool-1-thread-10] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2024-10-31 00:53:51,363] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2226, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 13 minutes 37 seconds Finished: SUCCESS