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Started by upstream project "BIOFORMATS-test-repo" build number 220 originally caused by: Started by upstream project "Trigger" build number 247 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@7 [BIOFORMATS-test-folder@7] $ /bin/bash -xe /tmp/jenkins14352740393221086489.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_34917_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] 02:04:43,129 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:04:43,131 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 02:04:43,131 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:04:43,132 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:04:43,132 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:04:43,132 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:04:43,132 |-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] 02:04:43,132 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:04:43,133 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:04:43,133 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:04:43,133 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:04:43,133 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:04:43,353 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:04:43,353 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:04:43,381 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:04:43,381 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:04:43,389 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:04:43,390 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:04:43,390 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:04:43,390 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:04:43,390 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 02:04:43,391 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 02:04:43,391 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 258 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-14 02:04:43,401] [main] java.version = 1.8.0_342 [testng] 02:04:43,404 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:04:43,404 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:04:43,448 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-14_02-04-43.log] [testng] 02:04:43,450 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-10-14 02:04:43,452] [main] testng.directory = /data [testng] [2024-10-14 02:04:43,452] [main] testng.configDirectory = /config [testng] [2024-10-14 02:04:43,464] [main] testng.multiplier = 1.0 [testng] [2024-10-14 02:04:43,464] [main] testng.in-memory = false [testng] [2024-10-14 02:04:43,465] [main] testng.allow-missing = false [testng] [2024-10-14 02:04:43,465] [main] user.language = fr [testng] [2024-10-14 02:04:43,465] [main] user.country = FR [testng] [2024-10-14 02:04:43,465] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-10-14 02:06:26,361] [main] ---------------------------------------- [testng] [2024-10-14 02:06:26,362] [main] Total files: 791 [testng] [2024-10-14 02:06:26,362] [main] Scan time: 102.896 s (130 ms/file) [testng] [2024-10-14 02:06:26,363] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-14 02:13:46,346] [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] 02:13:46,347 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:13:46,347 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:46,348 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-14_02-13-46.log] [testng] 02:13:46,349 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e9ff363 - End of configuration. [testng] [2024-10-14 02:13:47,670] [pool-1-thread-12] Initializing /data/tamjid/006004000.flex: [testng] 02:13:47,670 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:13:47,670 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:47,671 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-14_02-13-47.log] [testng] 02:13:47,671 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f8c1634 - End of configuration. [testng] [2024-10-14 02:13:48,688] [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] 02:13:48,688 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:13:48,688 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:48,689 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-14_02-13-48.log] [testng] 02:13:48,689 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e398867 - End of configuration. [testng] [2024-10-14 02:13:49,779] [pool-1-thread-10] Initializing /data/manuel/003003001.flex: [testng] 02:13:49,779 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:13:49,779 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:49,780 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-14_02-13-49.log] [testng] 02:13:49,780 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36d40569 - End of configuration. [testng] [2024-10-14 02:13:50,875] [pool-1-thread-9] Initializing /data/stephane/006013000.flex: [testng] 02:13:50,875 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:13:50,875 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:50,876 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-14_02-13-50.log] [testng] 02:13:50,876 |-INFO in ch.qos.logback.core.sift.SiftProcessor@31b357f6 - End of configuration. [testng] [2024-10-14 02:13:51,864] [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] 02:13:51,864 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:13:51,864 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:51,865 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-14_02-13-51.log] [testng] 02:13:51,865 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38e2e727 - End of configuration. [testng] [2024-10-14 02:13:52,883] [pool-1-thread-7] Initializing /data/qa-17190/002002011.flex: [testng] 02:13:52,883 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:13:52,883 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:52,884 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-14_02-13-52.log] [testng] 02:13:52,884 |-INFO in ch.qos.logback.core.sift.SiftProcessor@54f2cec1 - End of configuration. [testng] [2024-10-14 02:13:53,879] [pool-1-thread-6] Initializing /data/tony/001001000_objects.flex: [testng] 02:13:53,879 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:13:53,879 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:53,880 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-14_02-13-53.log] [testng] 02:13:53,880 |-INFO in ch.qos.logback.core.sift.SiftProcessor@639bc73 - End of configuration. [testng] [2024-10-14 02:13:54,822] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] 02:13:54,823 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:13:54,823 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:54,823 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-14_02-13-54.log] [testng] 02:13:54,824 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4aaa1996 - End of configuration. [testng] [2024-10-14 02:14:02,631] [pool-1-thread-4] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] 02:14:02,631 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:14:02,631 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:14:02,632 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-14_02-14-02.log] [testng] 02:14:02,632 |-INFO in ch.qos.logback.core.sift.SiftProcessor@732354e5 - End of configuration. [testng] [2024-10-14 02:14:11,156] [pool-1-thread-3] Initializing /data/tony/001014000 - from flex.tif: [testng] 02:14:11,156 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:14:11,156 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:14:11,157 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-14_02-14-11.log] [testng] 02:14:11,158 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d8c368c - End of configuration. [testng] [2024-10-14 02:14:13,491] [pool-1-thread-2] Initializing /data/tony/test.tiff: [testng] 02:14:13,491 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:14:13,491 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:14:13,492 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-14_02-14-13.log] [testng] 02:14:13,492 |-INFO in ch.qos.logback.core.sift.SiftProcessor@748f2904 - End of configuration. [testng] [2024-10-14 02:14:30,327] [pool-1-thread-3] Initializing /data/qa-2983/004007000.flex: [testng] [2024-10-14 02:14:31,430] [pool-1-thread-2] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2024-10-14 02:14:39,062] [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] [2024-10-14 02:14:40,743] [pool-1-thread-12] Initializing /data/ghislain/test.flex: [testng] [2024-10-14 02:14:41,791] [pool-1-thread-6] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] [2024-10-14 02:14:50,779] [pool-1-thread-1] Initializing /data/tony/test1.flex: [testng] [2024-10-14 02:14:52,091] [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] [2024-10-14 02:14:53,242] [pool-1-thread-9] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2024-10-14 02:14:57,146] [pool-1-thread-6] Initializing /data/qa-7469/002002.flex: [testng] [2024-10-14 02:15:03,433] [pool-1-thread-3] Initializing /data/achim/003003000.flex: [testng] [2024-10-14 02:15:04,795] [pool-1-thread-10] Initializing /data/qa-18096/002003001.flex: [testng] [2024-10-14 02:15:05,977] [pool-1-thread-11] Initializing /data/tony/015002000.tiff: [testng] [2024-10-14 02:15:08,691] [pool-1-thread-12] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] [2024-10-14 02:15:25,268] [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] [2024-10-14 02:15:26,414] [pool-1-thread-6] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex: [testng] [2024-10-14 02:15:30,810] [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] [2024-10-14 02:15:34,816] [pool-1-thread-10] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] [2024-10-14 02:15:36,112] [pool-1-thread-11] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2024-10-14 02:15:46,510] [pool-1-thread-3] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2024-10-14 02:15:50,323] [pool-1-thread-1] Initializing /data/anatole/001004000.flex: [testng] [2024-10-14 02:15:54,520] [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] [2024-10-14 02:15:55,754] [pool-1-thread-11] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] [2024-10-14 02:16:11,663] [pool-1-thread-7] Initializing /data/tamjid/006003000.flex: [testng] [2024-10-14 02:16:12,768] [pool-1-thread-10] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2024-10-14 02:16:31,551] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] [2024-10-14 02:16:47,084] [pool-1-thread-7] Initializing /data/stephane/002007000.flex: [testng] [2024-10-14 02:16:48,315] [pool-1-thread-8] Initializing /data/qa-18096/002002001.flex: [testng] [2024-10-14 02:16:53,200] [pool-1-thread-1] Initializing /data/tamjid/006005000.flex: [testng] [2024-10-14 02:17:01,789] [pool-1-thread-9] Initializing /data/tony/003003000.tiff: [testng] [2024-10-14 02:17:04,318] [pool-1-thread-7] 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: 20 minutes 47 seconds Finished: SUCCESS