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Started by upstream project "BIOFORMATS-test-repo" build number 108 originally caused by: Started by upstream project "Trigger" build number 120 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/jenkins4595662503920099022.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_16758_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] 02:43:52,968 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:43:52,969 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 02:43:52,969 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:43:52,970 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:43:52,971 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:43:52,971 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:43:52,971 |-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] 02:43:52,971 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:43:52,971 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:43:52,972 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:43:52,972 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:43:52,972 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:43:53,202 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:43:53,202 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:43:53,230 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:43:53,230 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:43:53,238 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:43:53,238 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:43:53,239 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:43:53,239 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:43:53,239 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 02:43:53,240 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 02:43:53,240 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 269 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-01 02:43:53,250] [main] java.version = 1.8.0_342 [testng] 02:43:53,254 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:43:53,254 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:43:53,300 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-01_02-43-53.log] [testng] 02:43:53,301 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-07-01 02:43:53,303] [main] testng.directory = /data [testng] [2024-07-01 02:43:53,304] [main] testng.configDirectory = /config [testng] [2024-07-01 02:43:53,316] [main] testng.multiplier = 1.0 [testng] [2024-07-01 02:43:53,317] [main] testng.in-memory = false [testng] [2024-07-01 02:43:53,317] [main] testng.allow-missing = false [testng] [2024-07-01 02:43:53,317] [main] user.language = fr [testng] [2024-07-01 02:43:53,317] [main] user.country = FR [testng] [2024-07-01 02:43:53,317] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-07-01 02:44:04,831] [main] ---------------------------------------- [testng] [2024-07-01 02:44:04,831] [main] Total files: 791 [testng] [2024-07-01 02:44:04,831] [main] Scan time: 11.514 s (14 ms/file) [testng] [2024-07-01 02:44:04,831] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-01 02:50:03,168] [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] 02:50:03,169 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:50:03,169 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:50:03,170 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-01_02-50-03.log] [testng] 02:50:03,171 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48be9662 - End of configuration. [testng] [2024-07-01 02:50:03,237] [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] 02:50:03,237 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:50:03,237 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:50:03,238 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-01_02-50-03.log] [testng] 02:50:03,239 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38aa7ac3 - End of configuration. [testng] [2024-07-01 02:50:03,273] [pool-1-thread-11] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] 02:50:03,273 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:50:03,273 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:50:03,274 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-01_02-50-03.log] [testng] 02:50:03,274 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b9d7e78 - End of configuration. [testng] [2024-07-01 02:50:03,770] [pool-1-thread-10] Initializing /data/tamjid/006003000.flex: [testng] 02:50:03,771 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:50:03,771 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:50:03,771 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-01_02-50-03.log] [testng] 02:50:03,772 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71814e7 - End of configuration. [testng] [2024-07-01 02:50:03,791] [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] 02:50:03,792 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:50:03,792 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:50:03,792 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-01_02-50-03.log] [testng] 02:50:03,793 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7572dc4a - End of configuration. [testng] [2024-07-01 02:50:03,820] [pool-1-thread-8] Initializing /data/qa-18096/002002001.flex: [testng] 02:50:03,820 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:50:03,820 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:50:03,821 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-01_02-50-03.log] [testng] 02:50:03,821 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b0b3635 - End of configuration. [testng] [2024-07-01 02:50:03,857] [pool-1-thread-7] Initializing /data/tony/001014000 - from flex.tif: [testng] 02:50:03,857 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:50:03,857 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:50:03,857 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-01_02-50-03.log] [testng] 02:50:03,858 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40e5e67f - End of configuration. [testng] [2024-07-01 02:50:03,913] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] 02:50:03,914 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:50:03,914 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:50:03,914 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-01_02-50-03.log] [testng] 02:50:03,915 |-INFO in ch.qos.logback.core.sift.SiftProcessor@61832287 - End of configuration. [testng] [2024-07-01 02:50:04,291] [pool-1-thread-5] Initializing /data/achim/003003000.flex: [testng] 02:50:04,292 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:50:04,292 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:50:04,293 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-01_02-50-04.log] [testng] 02:50:04,293 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5bb447ae - End of configuration. [testng] [2024-07-01 02:50:04,398] [pool-1-thread-4] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] 02:50:04,398 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:50:04,398 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:50:04,399 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-01_02-50-04.log] [testng] 02:50:04,400 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a8bdac1 - End of configuration. [testng] [2024-07-01 02:50:04,855] [pool-1-thread-3] Initializing /data/tony/003003000.tiff: [testng] 02:50:04,855 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:50:04,855 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:50:04,855 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-01_02-50-04.log] [testng] 02:50:04,856 |-INFO in ch.qos.logback.core.sift.SiftProcessor@69b8045a - End of configuration. [testng] [2024-07-01 02:50:04,962] [pool-1-thread-2] Initializing /data/tony/test1.flex: [testng] 02:50:04,962 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:50:04,962 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:50:04,963 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-01_02-50-04.log] [testng] 02:50:04,963 |-INFO in ch.qos.logback.core.sift.SiftProcessor@47b6ac6c - End of configuration. [testng] [2024-07-01 02:50:06,724] [pool-1-thread-2] Initializing /data/tamjid/006005000.flex: [testng] [2024-07-01 02:50:06,764] [pool-1-thread-10] Initializing /data/tony/001001000_objects.flex: [testng] [2024-07-01 02:50:06,793] [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] [2024-07-01 02:50:06,819] [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] [2024-07-01 02:50:06,861] [pool-1-thread-5] Initializing /data/qa-17190/002002011.flex: [testng] [2024-07-01 02:50:06,887] [pool-1-thread-3] Initializing /data/qa-7469/002002.flex: [testng] [2024-07-01 02:50:07,153] [pool-1-thread-12] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2024-07-01 02:50:07,179] [pool-1-thread-9] Initializing /data/stephane/002007000.flex: [testng] [2024-07-01 02:50:07,205] [pool-1-thread-1] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2024-07-01 02:50:08,067] [pool-1-thread-2] Initializing /data/anatole/001004000.flex: [testng] [2024-07-01 02:50:08,116] [pool-1-thread-5] Initializing /data/qa-2983/004007000.flex: [testng] [2024-07-01 02:50:08,174] [pool-1-thread-3] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2024-07-01 02:50:08,698] [pool-1-thread-10] Initializing /data/tony/test.tiff: [testng] [2024-07-01 02:50:09,007] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_03(2007-12-14_10-50-56)/004006000.flex: [testng] [2024-07-01 02:50:09,049] [pool-1-thread-9] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex: [testng] [2024-07-01 02:50:09,577] [pool-1-thread-10] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex: [testng] [2024-07-01 02:50:09,697] [pool-1-thread-5] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex: [testng] [2024-07-01 02:50:09,733] [pool-1-thread-12] Initializing /data/manuel/003003001.flex: [testng] [2024-07-01 02:50:10,590] [pool-1-thread-8] Initializing /data/ghislain/test.flex: [testng] [2024-07-01 02:50:11,050] [pool-1-thread-10] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2024-07-01 02:50:11,257] [pool-1-thread-5] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex: [testng] [2024-07-01 02:50:11,447] [pool-1-thread-8] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] [2024-07-01 02:50:12,345] [pool-1-thread-12] Initializing /data/tamjid/006004000.flex: [testng] [2024-07-01 02:50:12,898] [pool-1-thread-12] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] [2024-07-01 02:50:13,844] [pool-1-thread-9] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2024-07-01 02:50:14,984] [pool-1-thread-7] Initializing /data/stephane/006013000.flex: [testng] [2024-07-01 02:50:17,002] [pool-1-thread-2] Initializing /data/qa-18096/002003001.flex: [testng] [2024-07-01 02:50:17,350] [pool-1-thread-5] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] [2024-07-01 02:50:17,633] [pool-1-thread-2] Initializing /data/tony/003008000.flex: [testng] [2024-07-01 02:50:18,009] [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: 9 minutes 41 seconds Finished: SUCCESS