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Started by upstream project "BIOFORMATS-test-repo" build number 272 originally caused by: Started by upstream project "Trigger" build number 294 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5 [BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins18006171939967709078.sh + '[' flex = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_42852_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 test-automated: [testng] File leak detector installed [testng] 00:50:27,860 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:50:27,861 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 00:50:27,861 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:50:27,863 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:50:27,863 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:50:27,863 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:50:27,863 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:50:27,863 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:50:27,864 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:50:27,864 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:50:27,864 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:50:27,864 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:50:28,102 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:50:28,102 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:50:28,132 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:50:28,132 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:50:28,141 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:50:28,141 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:50:28,141 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:50:28,142 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:50:28,142 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 00:50:28,143 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 00:50:28,144 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 280 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-29 00:50:28,158] [main] java.version = 1.8.0_342 [testng] 00:50:28,163 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:50:28,163 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:28,215 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-29_00-50-28.log] [testng] 00:50:28,217 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-11-29 00:50:28,218] [main] testng.directory = /data [testng] [2024-11-29 00:50:28,219] [main] testng.configDirectory = /config [testng] [2024-11-29 00:50:28,231] [main] testng.multiplier = 1.0 [testng] [2024-11-29 00:50:28,231] [main] testng.in-memory = false [testng] [2024-11-29 00:50:28,231] [main] testng.allow-missing = false [testng] [2024-11-29 00:50:28,231] [main] user.language = en [testng] [2024-11-29 00:50:28,231] [main] user.country = ${user.country} [testng] [2024-11-29 00:50:28,231] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-11-29 00:51:47,069] [main] ---------------------------------------- [testng] [2024-11-29 00:51:47,070] [main] Total files: 791 [testng] [2024-11-29 00:51:47,070] [main] Scan time: 78.838 s (99 ms/file) [testng] [2024-11-29 00:51:47,070] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-29 00:56:56,845] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_03(2007-12-14_10-50-56)/004006000.flex: [testng] 00:56:56,846 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:56:56,846 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:56:56,847 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-29_00-56-56.log] [testng] 00:56:56,847 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37c9a1e7 - End of configuration. [testng] [2024-11-29 00:56:57,501] [pool-1-thread-12] Initializing /data/tamjid/006004000.flex: [testng] 00:56:57,502 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:56:57,502 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:56:57,503 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-29_00-56-57.log] [testng] 00:56:57,503 |-INFO in ch.qos.logback.core.sift.SiftProcessor@fc543eb - End of configuration. [testng] [2024-11-29 00:56:58,108] [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] 00:56:58,108 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:56:58,108 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:56:58,109 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-29_00-56-58.log] [testng] 00:56:58,109 |-INFO in ch.qos.logback.core.sift.SiftProcessor@459b6492 - End of configuration. [testng] [2024-11-29 00:56:58,783] [pool-1-thread-10] Initializing /data/manuel/003003001.flex: [testng] 00:56:58,784 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:56:58,784 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:56:58,784 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-29_00-56-58.log] [testng] 00:56:58,785 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7871f655 - End of configuration. [testng] [2024-11-29 00:56:59,498] [pool-1-thread-9] Initializing /data/stephane/006013000.flex: [testng] 00:56:59,498 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:56:59,498 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:56:59,499 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-29_00-56-59.log] [testng] 00:56:59,499 |-INFO in ch.qos.logback.core.sift.SiftProcessor@526312f3 - End of configuration. [testng] [2024-11-29 00:57:00,134] [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] 00:57:00,135 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:57:00,135 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:00,135 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-29_00-57-00.log] [testng] 00:57:00,136 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d7fdd8d - End of configuration. [testng] [2024-11-29 00:57:00,804] [pool-1-thread-7] Initializing /data/qa-17190/002002011.flex: [testng] 00:57:00,804 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:57:00,804 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:00,805 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-29_00-57-00.log] [testng] 00:57:00,805 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3bb70e1a - End of configuration. [testng] [2024-11-29 00:57:01,448] [pool-1-thread-6] Initializing /data/tony/001001000_objects.flex: [testng] 00:57:01,448 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:57:01,448 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:01,449 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-29_00-57-01.log] [testng] 00:57:01,450 |-INFO in ch.qos.logback.core.sift.SiftProcessor@437ce5a9 - End of configuration. [testng] [2024-11-29 00:57:02,084] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] 00:57:02,084 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:57:02,084 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:02,085 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-29_00-57-02.log] [testng] 00:57:02,085 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a52244e - End of configuration. [testng] [2024-11-29 00:57:06,983] [pool-1-thread-4] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] 00:57:06,984 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:57:06,984 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:06,984 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-29_00-57-06.log] [testng] 00:57:06,985 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2732019d - End of configuration. [testng] [2024-11-29 00:57:12,398] [pool-1-thread-3] Initializing /data/tony/001014000 - from flex.tif: [testng] 00:57:12,399 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:57:12,399 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:12,399 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-29_00-57-12.log] [testng] 00:57:12,400 |-INFO in ch.qos.logback.core.sift.SiftProcessor@535bfd73 - End of configuration. [testng] [2024-11-29 00:57:14,048] [pool-1-thread-2] Initializing /data/tony/test.tiff: [testng] 00:57:14,048 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:57:14,048 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:14,049 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-29_00-57-14.log] [testng] 00:57:14,049 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c1b2f8d - End of configuration. [testng] [2024-11-29 00:57:26,023] [pool-1-thread-3] Initializing /data/qa-2983/004007000.flex: [testng] [2024-11-29 00:57:26,720] [pool-1-thread-2] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2024-11-29 00:57:31,865] [pool-1-thread-7] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex: [testng] [2024-11-29 00:57:33,007] [pool-1-thread-12] Initializing /data/ghislain/test.flex: [testng] [2024-11-29 00:57:33,711] [pool-1-thread-6] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] [2024-11-29 00:57:38,884] [pool-1-thread-8] Initializing /data/tony/test1.flex: [testng] [2024-11-29 00:57:39,725] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex: [testng] [2024-11-29 00:57:40,561] [pool-1-thread-9] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2024-11-29 00:57:43,567] [pool-1-thread-11] Initializing /data/qa-7469/002002.flex: [testng] [2024-11-29 00:57:46,463] [pool-1-thread-3] Initializing /data/achim/003003000.flex: [testng] [2024-11-29 00:57:47,357] [pool-1-thread-6] Initializing /data/qa-18096/002003001.flex: [testng] [2024-11-29 00:57:48,387] [pool-1-thread-10] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] [2024-11-29 00:57:55,977] [pool-1-thread-12] Initializing /data/tony/015002000.tiff: [testng] [2024-11-29 00:58:01,549] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex: [testng] [2024-11-29 00:58:04,628] [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] [2024-11-29 00:58:08,024] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex: [testng] [2024-11-29 00:58:09,277] [pool-1-thread-6] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] [2024-11-29 00:58:11,460] [pool-1-thread-3] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2024-11-29 00:58:12,253] [pool-1-thread-12] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2024-11-29 00:58:19,145] [pool-1-thread-8] Initializing /data/anatole/001004000.flex: [testng] [2024-11-29 00:58:24,864] [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] [2024-11-29 00:58:25,675] [pool-1-thread-1] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] [2024-11-29 00:58:32,048] [pool-1-thread-3] Initializing /data/tamjid/006003000.flex: [testng] [2024-11-29 00:58:35,593] [pool-1-thread-7] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2024-11-29 00:58:49,624] [pool-1-thread-11] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] [2024-11-29 00:58:56,967] [pool-1-thread-3] Initializing /data/stephane/002007000.flex: [testng] [2024-11-29 00:59:00,402] [pool-1-thread-6] Initializing /data/qa-18096/002002001.flex: [testng] [2024-11-29 00:59:05,936] [pool-1-thread-8] Initializing /data/tamjid/006005000.flex: [testng] [2024-11-29 00:59:10,908] [pool-1-thread-3] Initializing /data/tony/003003000.tiff: [testng] [2024-11-29 00:59:13,898] [pool-1-thread-6] Initializing /data/tony/003008000.flex: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2226, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 14 minutes 45 seconds Finished: SUCCESS