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Started by upstream project "BIOFORMATS-test-repo" build number 55 originally caused by: Started by upstream project "Trigger" build number 62 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/jenkins15640641282868400630.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_8066_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] 01:33:01,110 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:33:01,112 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 01:33:01,112 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:33:01,113 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:33:01,114 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:33:01,114 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:33:01,114 |-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] 01:33:01,114 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:33:01,114 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:33:01,115 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:33:01,115 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:33:01,115 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:33:01,377 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:33:01,377 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:33:01,408 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:33:01,408 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:33:01,417 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:33:01,417 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:33:01,417 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:33:01,418 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:33:01,418 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 01:33:01,419 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 01:33:01,419 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 305 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-05-06 01:33:01,430] [main] java.version = 1.8.0_342 [testng] 01:33:01,434 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:33:01,434 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:33:01,483 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-06_01-33-01.log] [testng] 01:33:01,485 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-05-06 01:33:01,487] [main] testng.directory = /data [testng] [2024-05-06 01:33:01,487] [main] testng.configDirectory = /config [testng] [2024-05-06 01:33:01,501] [main] testng.multiplier = 1.0 [testng] [2024-05-06 01:33:01,502] [main] testng.in-memory = false [testng] [2024-05-06 01:33:01,502] [main] testng.allow-missing = false [testng] [2024-05-06 01:33:01,502] [main] user.language = fr [testng] [2024-05-06 01:33:01,502] [main] user.country = FR [testng] [2024-05-06 01:33:01,502] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-05-06 01:33:15,253] [main] ---------------------------------------- [testng] [2024-05-06 01:33:15,253] [main] Total files: 791 [testng] [2024-05-06 01:33:15,253] [main] Scan time: 13.751 s (17 ms/file) [testng] [2024-05-06 01:33:15,253] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-05-06 01:39:55,458] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex: [testng] 01:39:55,459 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:39:55,459 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:39:55,460 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-06_01-39-55.log] [testng] 01:39:55,461 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e3b9781 - End of configuration. [testng] [2024-05-06 01:39:56,011] [pool-1-thread-12] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] 01:39:56,011 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:39:56,011 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:39:56,012 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-06_01-39-56.log] [testng] 01:39:56,012 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5fb79ba6 - End of configuration. [testng] [2024-05-06 01:40:05,563] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] 01:40:05,563 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:40:05,563 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:05,564 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-06_01-40-05.log] [testng] 01:40:05,565 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ba38109 - End of configuration. [testng] [2024-05-06 01:40:05,667] [pool-1-thread-10] Initializing /data/qa-2983/004007000.flex: [testng] 01:40:05,668 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:40:05,668 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:05,668 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-06_01-40-05.log] [testng] 01:40:05,669 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1147f9a8 - End of configuration. [testng] [2024-05-06 01:40:05,762] [pool-1-thread-9] Initializing /data/ghislain/test.flex: [testng] 01:40:05,763 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:40:05,763 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:05,764 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-06_01-40-05.log] [testng] 01:40:05,764 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b8cdddc - End of configuration. [testng] [2024-05-06 01:40:05,900] [pool-1-thread-8] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] 01:40:05,900 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:40:05,900 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:05,901 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-06_01-40-05.log] [testng] 01:40:05,901 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4487cc96 - End of configuration. [testng] [2024-05-06 01:40:06,394] [pool-1-thread-7] Initializing /data/tamjid/006004000.flex: [testng] 01:40:06,394 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:40:06,394 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:06,395 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-06_01-40-06.log] [testng] 01:40:06,395 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4592d025 - End of configuration. [testng] [2024-05-06 01:40:06,426] [pool-1-thread-6] Initializing /data/manuel/003003001.flex: [testng] 01:40:06,426 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:40:06,426 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:06,427 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-06_01-40-06.log] [testng] 01:40:06,427 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4ad8b4b0 - End of configuration. [testng] [2024-05-06 01:40:06,662] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] 01:40:06,662 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:40:06,662 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:06,663 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-06_01-40-06.log] [testng] 01:40:06,664 |-INFO in ch.qos.logback.core.sift.SiftProcessor@458d281d - End of configuration. [testng] [2024-05-06 01:40:07,276] [pool-1-thread-4] Initializing /data/tony/015002000.tiff: [testng] 01:40:07,276 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:40:07,276 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:07,277 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-06_01-40-07.log] [testng] 01:40:07,277 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c0f79c7 - End of configuration. [testng] [2024-05-06 01:40:07,349] [pool-1-thread-3] Initializing /data/tamjid/006005000.flex: [testng] 01:40:07,349 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:40:07,349 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:07,349 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-06_01-40-07.log] [testng] 01:40:07,350 |-INFO in ch.qos.logback.core.sift.SiftProcessor@17df998f - End of configuration. [testng] [2024-05-06 01:40:07,392] [pool-1-thread-2] Initializing /data/tony/003003000.tiff: [testng] 01:40:07,392 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:40:07,393 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:07,393 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-06_01-40-07.log] [testng] 01:40:07,394 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4dbbab47 - End of configuration. [testng] [2024-05-06 01:40:09,498] [pool-1-thread-7] Initializing /data/stephane/002007000.flex: [testng] [2024-05-06 01:40:09,536] [pool-1-thread-3] Initializing /data/anatole/001004000.flex: [testng] [2024-05-06 01:40:10,957] [pool-1-thread-4] Initializing /data/tony/test1.flex: [testng] [2024-05-06 01:40:10,987] [pool-1-thread-9] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] [2024-05-06 01:40:11,448] [pool-1-thread-10] Initializing /data/qa-17190/002002011.flex: [testng] [2024-05-06 01:40:11,508] [pool-1-thread-2] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_03(2007-12-14_10-50-56)/004006000.flex: [testng] [2024-05-06 01:40:12,007] [pool-1-thread-11] Initializing /data/tamjid/006003000.flex: [testng] [2024-05-06 01:40:12,052] [pool-1-thread-6] Initializing /data/tony/003008000.flex: [testng] [2024-05-06 01:40:12,355] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex: [testng] [2024-05-06 01:40:12,526] [pool-1-thread-10] Initializing /data/tony/test.tiff: [testng] [2024-05-06 01:40:12,945] [pool-1-thread-11] Initializing /data/qa-18096/002002001.flex: [testng] [2024-05-06 01:40:13,109] [pool-1-thread-7] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2024-05-06 01:40:14,026] [pool-1-thread-2] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2024-05-06 01:40:14,386] [pool-1-thread-10] Initializing /data/tony/001014000 - from flex.tif: [testng] [2024-05-06 01:40:14,485] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex: [testng] [2024-05-06 01:40:15,465] [pool-1-thread-11] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2024-05-06 01:40:17,681] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex: [testng] [2024-05-06 01:40:18,162] [pool-1-thread-10] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex: [testng] [2024-05-06 01:40:19,119] [pool-1-thread-2] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex: [testng] [2024-05-06 01:40:19,748] [pool-1-thread-4] Initializing /data/achim/003003000.flex: [testng] [2024-05-06 01:40:20,618] [pool-1-thread-10] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex: [testng] [2024-05-06 01:40:21,170] [pool-1-thread-6] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex: [testng] [2024-05-06 01:40:21,981] [pool-1-thread-4] Initializing /data/qa-7469/002002.flex: [testng] [2024-05-06 01:40:22,388] [pool-1-thread-10] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] [2024-05-06 01:40:24,535] [pool-1-thread-3] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2024-05-06 01:40:25,892] [pool-1-thread-4] Initializing /data/qa-18096/002003001.flex: [testng] [2024-05-06 01:40:26,116] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] [2024-05-06 01:40:26,894] [pool-1-thread-1] Initializing /data/stephane/006013000.flex: [testng] [2024-05-06 01:40:27,195] [pool-1-thread-4] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] [2024-05-06 01:40:27,813] [pool-1-thread-4] Initializing /data/tony/001001000_objects.flex: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2226, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 11 minutes 7 seconds Finished: SUCCESS