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Started by upstream project "BIOFORMATS-test-repo" build number 114 originally caused by: Started by upstream project "Trigger" build number 127 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4 [BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins10453168571353785676.sh + '[' flex = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_17742_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] 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] 01:30:25,314 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:30:25,315 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 01:30:25,315 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:30:25,316 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:30:25,317 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:30:25,317 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:30:25,317 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:30:25,317 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:30:25,318 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:30:25,318 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:30:25,319 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:30:25,319 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:30:25,583 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:30:25,583 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:30:25,618 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:30:25,618 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:30:25,627 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:30:25,627 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:30:25,627 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:30:25,628 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:30:25,628 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 01:30:25,629 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 01:30:25,630 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 312 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-07 01:30:25,644] [main] java.version = 17.0.2 [testng] 01:30:25,651 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:30:25,651 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:30:25,712 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-07_01-30-25.log] [testng] 01:30:25,714 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-07-07 01:30:25,717] [main] testng.directory = /data [testng] [2024-07-07 01:30:25,717] [main] testng.configDirectory = /config [testng] [2024-07-07 01:30:25,728] [main] testng.multiplier = 1.0 [testng] [2024-07-07 01:30:25,729] [main] testng.in-memory = false [testng] [2024-07-07 01:30:25,729] [main] testng.allow-missing = false [testng] [2024-07-07 01:30:25,729] [main] user.language = en [testng] [2024-07-07 01:30:25,729] [main] user.country = ${user.country} [testng] [2024-07-07 01:30:25,729] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-07-07 01:30:39,294] [main] ---------------------------------------- [testng] [2024-07-07 01:30:39,294] [main] Total files: 791 [testng] [2024-07-07 01:30:39,294] [main] Scan time: 13.564 s (17 ms/file) [testng] [2024-07-07 01:30:39,294] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-07 01:37:14,651] [pool-1-thread-1] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] 01:37:14,652 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:37:14,652 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:14,653 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-07_01-37-14.log] [testng] 01:37:14,653 |-INFO in ch.qos.logback.core.sift.SiftProcessor@69c607d0 - End of configuration. [testng] [2024-07-07 01:37:14,694] [pool-1-thread-12] Initializing /data/qa-18096/002002001.flex: [testng] 01:37:14,695 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:37:14,695 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:14,696 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-07_01-37-14.log] [testng] 01:37:14,696 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ebe0126 - End of configuration. [testng] [2024-07-07 01:37:14,768] [pool-1-thread-11] Initializing /data/anatole/001004000.flex: [testng] 01:37:14,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:37:14,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:14,770 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-07_01-37-14.log] [testng] 01:37:14,770 |-INFO in ch.qos.logback.core.sift.SiftProcessor@69ed8a3f - End of configuration. [testng] [2024-07-07 01:37:14,866] [pool-1-thread-10] Initializing /data/qa-7469/002002.flex: [testng] 01:37:14,866 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:37:14,866 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:14,867 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-07_01-37-14.log] [testng] 01:37:14,867 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6eee67c0 - End of configuration. [testng] [2024-07-07 01:37:14,908] [pool-1-thread-9] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] 01:37:14,908 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:37:14,908 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:14,909 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-07_01-37-14.log] [testng] 01:37:14,910 |-INFO in ch.qos.logback.core.sift.SiftProcessor@49ef249 - End of configuration. [testng] [2024-07-07 01:37:15,462] [pool-1-thread-8] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] 01:37:15,463 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:37:15,463 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:15,463 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-07_01-37-15.log] [testng] 01:37:15,464 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a7d87d0 - End of configuration. [testng] [2024-07-07 01:37:15,903] [pool-1-thread-7] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] 01:37:15,904 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:37:15,904 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:15,904 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-07_01-37-15.log] [testng] 01:37:15,905 |-INFO in ch.qos.logback.core.sift.SiftProcessor@44b7b736 - End of configuration. [testng] [2024-07-07 01:37:15,946] [pool-1-thread-6] Initializing /data/tamjid/006003000.flex: [testng] 01:37:15,946 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:37:15,946 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:15,947 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-07_01-37-15.log] [testng] 01:37:15,947 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d87af9c - End of configuration. [testng] [2024-07-07 01:37:15,975] [pool-1-thread-5] Initializing /data/tony/003008000.flex: [testng] 01:37:15,975 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:37:15,975 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:15,976 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-07_01-37-15.log] [testng] 01:37:15,976 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ddf9bb6 - End of configuration. [testng] [2024-07-07 01:37:16,021] [pool-1-thread-4] Initializing /data/tamjid/006005000.flex: [testng] 01:37:16,021 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:37:16,021 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:16,022 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-07_01-37-16.log] [testng] 01:37:16,022 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b535d62 - End of configuration. [testng] [2024-07-07 01:37:16,053] [pool-1-thread-3] Initializing /data/qa-2983/004007000.flex: [testng] 01:37:16,054 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:37:16,054 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:16,055 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-07_01-37-16.log] [testng] 01:37:16,055 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37e05dad - End of configuration. [testng] [2024-07-07 01:37:16,114] [pool-1-thread-2] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] 01:37:16,114 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:37:16,114 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:16,115 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-07_01-37-16.log] [testng] 01:37:16,115 |-INFO in ch.qos.logback.core.sift.SiftProcessor@de6a1c7 - End of configuration. [testng] [2024-07-07 01:37:18,190] [pool-1-thread-6] Initializing /data/tony/015002000.tiff: [testng] [2024-07-07 01:37:18,245] [pool-1-thread-3] Initializing /data/qa-17190/002002011.flex: [testng] [2024-07-07 01:37:18,272] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex: [testng] [2024-07-07 01:37:18,305] [pool-1-thread-7] Initializing /data/tony/001014000 - from flex.tif: [testng] [2024-07-07 01:37:18,353] [pool-1-thread-10] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2024-07-07 01:37:19,001] [pool-1-thread-12] Initializing /data/tony/test.tiff: [testng] [2024-07-07 01:37:19,922] [pool-1-thread-3] Initializing /data/achim/003003000.flex: [testng] [2024-07-07 01:37:20,007] [pool-1-thread-1] Initializing /data/stephane/006013000.flex: [testng] [2024-07-07 01:37:20,141] [pool-1-thread-6] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex: [testng] [2024-07-07 01:37:20,205] [pool-1-thread-7] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] [2024-07-07 01:37:20,701] [pool-1-thread-12] Initializing /data/tony/003003000.tiff: [testng] [2024-07-07 01:37:20,870] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex: [testng] [2024-07-07 01:37:21,767] [pool-1-thread-3] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex: [testng] [2024-07-07 01:37:21,992] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] [2024-07-07 01:37:22,506] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_03(2007-12-14_10-50-56)/004006000.flex: [testng] [2024-07-07 01:37:22,539] [pool-1-thread-5] Initializing /data/ghislain/test.flex: [testng] [2024-07-07 01:37:23,320] [pool-1-thread-5] Initializing /data/tamjid/006004000.flex: [testng] [2024-07-07 01:37:23,770] [pool-1-thread-12] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] [2024-07-07 01:37:24,274] [pool-1-thread-11] Initializing /data/tony/test1.flex: [testng] [2024-07-07 01:37:24,331] [pool-1-thread-5] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] [2024-07-07 01:37:24,671] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex: [testng] [2024-07-07 01:37:25,400] [pool-1-thread-1] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2024-07-07 01:37:25,858] [pool-1-thread-5] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex: [testng] [2024-07-07 01:37:26,225] [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] [2024-07-07 01:37:26,275] [pool-1-thread-4] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2024-07-07 01:37:27,498] [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] [2024-07-07 01:37:28,773] [pool-1-thread-11] Initializing /data/manuel/003003001.flex: [testng] [2024-07-07 01:37:29,178] [pool-1-thread-3] Initializing /data/tony/001001000_objects.flex: [testng] [2024-07-07 01:37:29,816] [pool-1-thread-3] Initializing /data/qa-18096/002003001.flex: [testng] [2024-07-07 01:37:30,048] [pool-1-thread-5] Initializing /data/stephane/002007000.flex: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2226, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 10 minutes 33 seconds Finished: SUCCESS