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Started by upstream project "BIOFORMATS-test-repo" build number 11 originally caused by: Started by upstream project "Trigger" build number 14 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/jenkins6652942305846267970.sh + '[' flex = slidebook ']' ++ date +%u + '[' 1 -le 1 ']' + DOCKER_ARGS='-Dtestng.memory=15g -Dtestng.threadCount=12 -Duser.language=fr -Duser.country=FR' + sudo docker run --rm --name BIOFORMATS-test-folder_1667_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 -Duser.language=fr -Duser.country=FR 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] 00:36:19,623 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:36:19,625 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 00:36:19,625 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:36:19,626 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:36:19,626 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:36:19,626 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:36:19,627 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:36:19,627 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:36:19,627 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:36:19,627 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:36:19,627 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:36:19,628 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:36:19,862 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:36:19,862 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:36:19,892 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:36:19,892 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:36:19,902 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:36:19,902 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:36:19,902 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:36:19,902 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:36:19,902 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 00:36:19,903 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 00:36:19,903 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 276 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-25 00:36:19,913] [main] java.version = 1.8.0_342 [testng] 00:36:19,917 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:36:19,917 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:36:19,979 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-25_00-36-19.log] [testng] 00:36:19,981 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-03-25 00:36:19,983] [main] testng.directory = /data [testng] [2024-03-25 00:36:19,983] [main] testng.configDirectory = /config [testng] [2024-03-25 00:36:19,995] [main] testng.multiplier = 1.0 [testng] [2024-03-25 00:36:19,996] [main] testng.in-memory = false [testng] [2024-03-25 00:36:19,996] [main] testng.allow-missing = false [testng] [2024-03-25 00:36:19,996] [main] user.language = fr [testng] [2024-03-25 00:36:19,996] [main] user.country = FR [testng] [2024-03-25 00:36:19,996] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-03-25 00:36:39,921] [main] ---------------------------------------- [testng] [2024-03-25 00:36:39,922] [main] Total files: 791 [testng] [2024-03-25 00:36:39,922] [main] Scan time: 19.925 s (25 ms/file) [testng] [2024-03-25 00:36:39,922] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-25 00:42:51,253] [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] 00:42:51,254 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:42:51,254 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:51,255 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-25_00-42-51.log] [testng] 00:42:51,256 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78f6dae1 - End of configuration. [testng] [2024-03-25 00:42:51,498] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex: [testng] 00:42:51,498 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:42:51,498 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:51,499 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-25_00-42-51.log] [testng] 00:42:51,499 |-INFO in ch.qos.logback.core.sift.SiftProcessor@696b1966 - End of configuration. [testng] [2024-03-25 00:42:51,754] [pool-1-thread-11] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] 00:42:51,755 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:42:51,755 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:51,755 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-25_00-42-51.log] [testng] 00:42:51,756 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48511f05 - End of configuration. [testng] [2024-03-25 00:42:53,797] [pool-1-thread-10] Initializing /data/tamjid/006003000.flex: [testng] 00:42:53,797 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:42:53,797 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:53,798 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-25_00-42-53.log] [testng] 00:42:53,799 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6628876e - End of configuration. [testng] [2024-03-25 00:42:54,001] [pool-1-thread-9] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex: [testng] 00:42:54,001 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:42:54,001 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:54,002 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-25_00-42-54.log] [testng] 00:42:54,002 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f366983 - End of configuration. [testng] [2024-03-25 00:42:54,329] [pool-1-thread-8] Initializing /data/qa-18096/002002001.flex: [testng] 00:42:54,330 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:42:54,330 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:54,330 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-25_00-42-54.log] [testng] 00:42:54,331 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1df5367c - End of configuration. [testng] [2024-03-25 00:42:54,648] [pool-1-thread-7] Initializing /data/tony/001014000 - from flex.tif: [testng] 00:42:54,648 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:42:54,648 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:54,649 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-25_00-42-54.log] [testng] 00:42:54,649 |-INFO in ch.qos.logback.core.sift.SiftProcessor@bf9e0f9 - End of configuration. [testng] [2024-03-25 00:42:55,217] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] 00:42:55,217 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:42:55,217 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:55,218 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-25_00-42-55.log] [testng] 00:42:55,219 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e1316a8 - End of configuration. [testng] [2024-03-25 00:42:58,056] [pool-1-thread-5] Initializing /data/achim/003003000.flex: [testng] 00:42:58,056 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:42:58,056 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:58,057 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-25_00-42-58.log] [testng] 00:42:58,057 |-INFO in ch.qos.logback.core.sift.SiftProcessor@33c3ea80 - End of configuration. [testng] [2024-03-25 00:42:58,938] [pool-1-thread-4] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] 00:42:58,938 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:42:58,938 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:58,939 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-25_00-42-58.log] [testng] 00:42:58,939 |-INFO in ch.qos.logback.core.sift.SiftProcessor@357ee9eb - End of configuration. [testng] [2024-03-25 00:43:01,856] [pool-1-thread-3] Initializing /data/tony/003003000.tiff: [testng] 00:43:01,856 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:43:01,856 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:43:01,857 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-25_00-43-01.log] [testng] 00:43:01,857 |-INFO in ch.qos.logback.core.sift.SiftProcessor@550de6a9 - End of configuration. [testng] [2024-03-25 00:43:02,656] [pool-1-thread-2] Initializing /data/tony/test1.flex: [testng] 00:43:02,656 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:43:02,656 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:43:02,656 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-25_00-43-02.log] [testng] 00:43:02,657 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4cce1033 - End of configuration. [testng] [2024-03-25 00:43:08,868] [pool-1-thread-7] Initializing /data/tamjid/006005000.flex: [testng] [2024-03-25 00:43:09,496] [pool-1-thread-2] Initializing /data/qa-17190/002002011.flex: [testng] [2024-03-25 00:43:09,781] [pool-1-thread-10] Initializing /data/qa-7469/002002.flex: [testng] [2024-03-25 00:43:10,128] [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] [2024-03-25 00:43:10,589] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] [2024-03-25 00:43:13,565] [pool-1-thread-12] Initializing /data/tony/001001000_objects.flex: [testng] [2024-03-25 00:43:14,065] [pool-1-thread-1] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2024-03-25 00:43:14,473] [pool-1-thread-9] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2024-03-25 00:43:23,167] [pool-1-thread-5] Initializing /data/stephane/002007000.flex: [testng] [2024-03-25 00:43:24,298] [pool-1-thread-2] Initializing /data/anatole/001004000.flex: [testng] [2024-03-25 00:43:25,304] [pool-1-thread-7] Initializing /data/qa-2983/004007000.flex: [testng] [2024-03-25 00:43:26,167] [pool-1-thread-10] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2024-03-25 00:43:29,925] [pool-1-thread-8] Initializing /data/tony/test.tiff: [testng] [2024-03-25 00:43:30,621] [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] [2024-03-25 00:43:31,078] [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] [2024-03-25 00:43:32,048] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex: [testng] [2024-03-25 00:43:32,514] [pool-1-thread-7] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex: [testng] [2024-03-25 00:43:35,283] [pool-1-thread-8] Initializing /data/manuel/003003001.flex: [testng] [2024-03-25 00:43:38,297] [pool-1-thread-3] Initializing /data/ghislain/test.flex: [testng] [2024-03-25 00:43:39,236] [pool-1-thread-12] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2024-03-25 00:43:43,994] [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] [2024-03-25 00:43:45,184] [pool-1-thread-7] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] [2024-03-25 00:43:50,965] [pool-1-thread-5] Initializing /data/tamjid/006004000.flex: [testng] [2024-03-25 00:43:51,362] [pool-1-thread-3] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] [2024-03-25 00:43:54,694] [pool-1-thread-2] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2024-03-25 00:44:00,664] [pool-1-thread-8] Initializing /data/stephane/006013000.flex: [testng] [2024-03-25 00:44:03,748] [pool-1-thread-5] Initializing /data/qa-18096/002003001.flex: [testng] [2024-03-25 00:44:09,237] [pool-1-thread-5] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] [2024-03-25 00:44:13,730] [pool-1-thread-8] Initializing /data/tony/003008000.flex: [testng] [2024-03-25 00:44:14,748] [pool-1-thread-5] Initializing /data/tony/015002000.tiff: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2226, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 12 minutes 38 seconds Finished: SUCCESS