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Started by upstream project "BIOFORMATS-test-repo" build number 227 originally caused by: Started by upstream project "Trigger" build number 252 originally caused by: Started by user devspace 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/jenkins5999808925092710737.sh + '[' flex = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_35600_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] 10:12:33,395 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 10:12:33,397 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 10:12:33,397 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 10:12:33,398 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 10:12:33,398 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 10:12:33,398 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 10:12:33,398 |-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] 10:12:33,398 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 10:12:33,399 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 10:12:33,399 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 10:12:33,399 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 10:12:33,399 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 10:12:33,614 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 10:12:33,614 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 10:12:33,641 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 10:12:33,641 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 10:12:33,648 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 10:12:33,648 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 10:12:33,649 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 10:12:33,649 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 10:12:33,649 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 10:12:33,650 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 10:12:33,650 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 251 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-18 10:12:33,659] [main] java.version = 1.8.0_342 [testng] 10:12:33,663 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 10:12:33,663 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:12:33,706 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-18_10-12-33.log] [testng] 10:12:33,707 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-10-18 10:12:33,709] [main] testng.directory = /data [testng] [2024-10-18 10:12:33,709] [main] testng.configDirectory = /config [testng] [2024-10-18 10:12:33,721] [main] testng.multiplier = 1.0 [testng] [2024-10-18 10:12:33,721] [main] testng.in-memory = false [testng] [2024-10-18 10:12:33,721] [main] testng.allow-missing = false [testng] [2024-10-18 10:12:33,721] [main] user.language = en [testng] [2024-10-18 10:12:33,721] [main] user.country = ${user.country} [testng] [2024-10-18 10:12:33,721] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-10-18 10:13:51,632] [main] ---------------------------------------- [testng] [2024-10-18 10:13:51,632] [main] Total files: 791 [testng] [2024-10-18 10:13:51,632] [main] Scan time: 77.911 s (98 ms/file) [testng] [2024-10-18 10:13:51,632] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-18 10:17:45,157] [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] 10:17:45,158 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 10:17:45,158 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:17:45,159 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-18_10-17-45.log] [testng] 10:17:45,160 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3680796c - End of configuration. [testng] [2024-10-18 10:17:45,763] [pool-1-thread-12] Initializing /data/tamjid/006004000.flex: [testng] 10:17:45,764 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 10:17:45,764 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:17:45,764 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-18_10-17-45.log] [testng] 10:17:45,765 |-INFO in ch.qos.logback.core.sift.SiftProcessor@26067d5b - End of configuration. [testng] [2024-10-18 10:17:46,665] [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] 10:17:46,666 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 10:17:46,666 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:17:46,666 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-18_10-17-46.log] [testng] 10:17:46,667 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ca6fbce - End of configuration. [testng] [2024-10-18 10:17:47,279] [pool-1-thread-10] Initializing /data/manuel/003003001.flex: [testng] 10:17:47,280 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 10:17:47,280 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:17:47,280 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-18_10-17-47.log] [testng] 10:17:47,281 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d7fdd8d - End of configuration. [testng] [2024-10-18 10:17:47,876] [pool-1-thread-9] Initializing /data/stephane/006013000.flex: [testng] 10:17:47,876 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 10:17:47,876 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:17:47,877 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-18_10-17-47.log] [testng] 10:17:47,877 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3bb70e1a - End of configuration. [testng] [2024-10-18 10:17:48,377] [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] 10:17:48,377 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 10:17:48,377 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:17:48,377 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-18_10-17-48.log] [testng] 10:17:48,378 |-INFO in ch.qos.logback.core.sift.SiftProcessor@437ce5a9 - End of configuration. [testng] [2024-10-18 10:17:48,872] [pool-1-thread-7] Initializing /data/qa-17190/002002011.flex: [testng] 10:17:48,872 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 10:17:48,872 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:17:48,873 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-18_10-17-48.log] [testng] 10:17:48,873 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a52244e - End of configuration. [testng] [2024-10-18 10:17:49,376] [pool-1-thread-6] Initializing /data/tony/001001000_objects.flex: [testng] 10:17:49,376 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 10:17:49,376 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:17:49,376 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-18_10-17-49.log] [testng] 10:17:49,377 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2732019d - End of configuration. [testng] [2024-10-18 10:17:49,905] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] 10:17:49,905 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 10:17:49,905 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:17:49,906 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-18_10-17-49.log] [testng] 10:17:49,906 |-INFO in ch.qos.logback.core.sift.SiftProcessor@54919b40 - End of configuration. [testng] [2024-10-18 10:17:55,488] [pool-1-thread-4] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] 10:17:55,488 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 10:17:55,488 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:17:55,489 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-18_10-17-55.log] [testng] 10:17:55,489 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ecf4bc3 - End of configuration. [testng] [2024-10-18 10:18:00,199] [pool-1-thread-3] Initializing /data/tony/001014000 - from flex.tif: [testng] 10:18:00,199 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 10:18:00,199 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:18:00,200 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-18_10-18-00.log] [testng] 10:18:00,201 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27bf01fc - End of configuration. [testng] [2024-10-18 10:18:01,414] [pool-1-thread-2] Initializing /data/tony/test.tiff: [testng] 10:18:01,414 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 10:18:01,414 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:18:01,414 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-18_10-18-01.log] [testng] 10:18:01,415 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f888f5f - End of configuration. [testng] [2024-10-18 10:18:10,637] [pool-1-thread-3] Initializing /data/qa-2983/004007000.flex: [testng] [2024-10-18 10:18:11,299] [pool-1-thread-2] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2024-10-18 10:18:16,042] [pool-1-thread-6] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex: [testng] [2024-10-18 10:18:17,164] [pool-1-thread-12] Initializing /data/ghislain/test.flex: [testng] [2024-10-18 10:18:17,922] [pool-1-thread-7] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] [2024-10-18 10:18:23,951] [pool-1-thread-1] Initializing /data/tony/test1.flex: [testng] [2024-10-18 10:18:24,944] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex: [testng] [2024-10-18 10:18:25,932] [pool-1-thread-9] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2024-10-18 10:18:32,609] [pool-1-thread-7] Initializing /data/qa-7469/002002.flex: [testng] [2024-10-18 10:18:36,754] [pool-1-thread-3] Initializing /data/achim/003003000.flex: [testng] [2024-10-18 10:18:41,774] [pool-1-thread-10] Initializing /data/qa-18096/002003001.flex: [testng] [2024-10-18 10:18:43,170] [pool-1-thread-11] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] [2024-10-18 10:18:48,721] [pool-1-thread-12] Initializing /data/tony/015002000.tiff: [testng] [2024-10-18 10:18:53,492] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex: [testng] [2024-10-18 10:18:54,348] [pool-1-thread-7] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex: [testng] [2024-10-18 10:18:57,079] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex: [testng] [2024-10-18 10:19:00,055] [pool-1-thread-3] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] [2024-10-18 10:19:01,007] [pool-1-thread-10] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2024-10-18 10:19:01,879] [pool-1-thread-12] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2024-10-18 10:19:10,759] [pool-1-thread-1] Initializing /data/anatole/001004000.flex: [testng] [2024-10-18 10:19:13,030] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex: [testng] [2024-10-18 10:19:13,912] [pool-1-thread-10] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] [2024-10-18 10:19:22,293] [pool-1-thread-3] Initializing /data/tamjid/006003000.flex: [testng] [2024-10-18 10:19:23,774] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2024-10-18 10:19:37,542] [pool-1-thread-7] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] [2024-10-18 10:19:44,789] [pool-1-thread-3] Initializing /data/stephane/002007000.flex: [testng] [2024-10-18 10:19:46,895] [pool-1-thread-8] Initializing /data/qa-18096/002002001.flex: [testng] [2024-10-18 10:19:53,745] [pool-1-thread-1] Initializing /data/tamjid/006005000.flex: [testng] [2024-10-18 10:19:56,456] [pool-1-thread-3] Initializing /data/tony/003003000.tiff: [testng] [2024-10-18 10:19:58,222] [pool-1-thread-8] 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: 13 minutes 1 second Finished: SUCCESS