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Started by upstream project "BIOFORMATS-test-repo" build number 397 originally caused by: Started by upstream project "Trigger" build number 481 originally caused by: Started by timer 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/jenkins7569811357008338547.sh + '[' flex = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_62686_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 [javac] warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] 1 warning test-automated: [testng] WARNING: An illegal reflective access operation has occurred [testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket [testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener [testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [testng] WARNING: All illegal access operations will be denied in a future release [testng] File leak detector installed [testng] 02:16:45,033 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 02:16:45,035 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - No custom configurators were discovered as a service. [testng] 02:16:45,035 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:16:45,036 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:16:45,036 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:16:45,036 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:16:45,037 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:16:45,037 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:16:45,037 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:16:45,038 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:16:45,038 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:16:45,038 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:16:45,203 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:16:45,203 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:16:45,226 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:16:45,226 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:16:45,231 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:16:45,231 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:16:45,231 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:16:45,232 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:16:45,232 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@65c7a252 - End of configuration. [testng] 02:16:45,233 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@38cee291 - Registering current configuration as safe fallback point [testng] 02:16:45,233 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 196 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-05-17 02:16:45,241] [main] java.version = 11.0.16 [testng] 02:16:45,245 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:16:45,245 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:45,287 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-05-17_02-16-45.log] [testng] 02:16:45,288 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13d73f29 - End of configuration. [testng] [2025-05-17 02:16:45,290] [main] testng.directory = /data [testng] [2025-05-17 02:16:45,291] [main] testng.configDirectory = /config [testng] [2025-05-17 02:16:45,301] [main] testng.multiplier = 1.0 [testng] [2025-05-17 02:16:45,302] [main] testng.in-memory = false [testng] [2025-05-17 02:16:45,302] [main] testng.allow-missing = false [testng] [2025-05-17 02:16:45,302] [main] user.language = en [testng] [2025-05-17 02:16:45,302] [main] user.country = ${user.country} [testng] [2025-05-17 02:16:45,302] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-05-17 02:27:42,002] [main] ---------------------------------------- [testng] [2025-05-17 02:27:42,003] [main] Total files: 791 [testng] [2025-05-17 02:27:42,003] [main] Scan time: 656.7 s (830 ms/file) [testng] [2025-05-17 02:27:42,003] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-05-17 02:59:53,007] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] 02:59:53,007 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:59:53,008 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:59:53,009 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-05-17_02-59-53.log] [testng] 02:59:53,010 |-INFO in ch.qos.logback.core.sift.SiftProcessor@54f4f491 - End of configuration. [testng] [2025-05-17 02:59:58,647] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex: [testng] 02:59:58,648 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:59:58,648 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:59:58,649 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-05-17_02-59-58.log] [testng] 02:59:58,649 |-INFO in ch.qos.logback.core.sift.SiftProcessor@486a504b - End of configuration. [testng] [2025-05-17 03:00:04,863] [pool-1-thread-11] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] 03:00:04,863 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:00:04,863 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:00:04,864 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-05-17_03-00-04.log] [testng] 03:00:04,864 |-INFO in ch.qos.logback.core.sift.SiftProcessor@53cd2c18 - End of configuration. [testng] [2025-05-17 03:00:13,667] [pool-1-thread-10] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] 03:00:13,667 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:00:13,668 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:00:13,668 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-05-17_03-00-13.log] [testng] 03:00:13,669 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40655c91 - End of configuration. [testng] [2025-05-17 03:01:27,617] [pool-1-thread-9] Initializing /data/tony/test1.flex: [testng] 03:01:27,617 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:01:27,617 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:01:27,618 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-05-17_03-01-27.log] [testng] 03:01:27,618 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3619f962 - End of configuration. [testng] [2025-05-17 03:01:36,335] [pool-1-thread-8] Initializing /data/ghislain/test.flex: [testng] 03:01:36,335 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:01:36,335 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:01:36,336 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-05-17_03-01-36.log] [testng] 03:01:36,337 |-INFO in ch.qos.logback.core.sift.SiftProcessor@117a9949 - End of configuration. [testng] [2025-05-17 03:01:45,273] [pool-1-thread-7] Initializing /data/tony/001014000 - from flex.tif: [testng] 03:01:45,273 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:01:45,273 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:01:45,274 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-05-17_03-01-45.log] [testng] 03:01:45,274 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2da12a93 - End of configuration. [testng] [2025-05-17 03:02:04,463] [pool-1-thread-6] Initializing /data/tony/001001000_objects.flex: [testng] 03:02:04,463 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:02:04,463 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:02:04,464 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-05-17_03-02-04.log] [testng] 03:02:04,464 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2c073edf - End of configuration. [testng] [2025-05-17 03:02:14,606] [pool-1-thread-5] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex: [testng] 03:02:14,607 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:02:14,607 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:02:14,607 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-05-17_03-02-14.log] [testng] 03:02:14,608 |-INFO in ch.qos.logback.core.sift.SiftProcessor@64e02fbd - End of configuration. [testng] [2025-05-17 03:02:27,143] [pool-1-thread-4] Initializing /data/qa-18096/002002001.flex: [testng] 03:02:27,143 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:02:27,144 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:02:27,144 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-05-17_03-02-27.log] [testng] 03:02:27,144 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6acd824b - End of configuration. [testng] [2025-05-17 03:02:37,802] [pool-1-thread-3] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex: [testng] 03:02:37,802 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:02:37,802 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:02:37,803 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-05-17_03-02-37.log] [testng] 03:02:37,803 |-INFO in ch.qos.logback.core.sift.SiftProcessor@19ebe81d - End of configuration. [testng] [2025-05-17 03:02:48,870] [pool-1-thread-2] Initializing /data/tamjid/006004000.flex: [testng] 03:02:48,870 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:02:48,870 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:02:48,871 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-05-17_03-02-48.log] [testng] 03:02:48,871 |-INFO in ch.qos.logback.core.sift.SiftProcessor@31029fc7 - End of configuration. [testng] [2025-05-17 03:04:35,135] [pool-1-thread-7] Initializing /data/qa-17190/002002011.flex: [testng] [2025-05-17 03:04:43,637] [pool-1-thread-4] Initializing /data/tony/test.tiff: [testng] [2025-05-17 03:05:01,874] [pool-1-thread-9] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2025-05-17 03:06:16,975] [pool-1-thread-2] Initializing /data/qa-2983/004007000.flex: [testng] [2025-05-17 03:06:30,503] [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] [2025-05-17 03:06:39,772] [pool-1-thread-6] Initializing /data/tony/015002000.tiff: [testng] [2025-05-17 03:07:53,300] [pool-1-thread-3] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex: [testng] [2025-05-17 03:08:04,189] [pool-1-thread-5] Initializing /data/achim/003003000.flex: [testng] [2025-05-17 03:08:13,651] [pool-1-thread-1] Initializing /data/qa-18096/002003001.flex: [testng] [2025-05-17 03:08:43,025] [pool-1-thread-4] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] [2025-05-17 03:09:20,250] [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] [2025-05-17 03:09:34,319] [pool-1-thread-2] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] [2025-05-17 03:10:41,814] [pool-1-thread-6] Initializing /data/tamjid/006003000.flex: [testng] [2025-05-17 03:10:50,243] [pool-1-thread-12] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2025-05-17 03:11:50,614] [pool-1-thread-1] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2025-05-17 03:13:05,718] [pool-1-thread-8] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] [2025-05-17 03:14:19,856] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex: [testng] [2025-05-17 03:14:41,668] [pool-1-thread-3] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2025-05-17 03:16:13,205] [pool-1-thread-5] Initializing /data/qa-7469/002002.flex: [testng] [2025-05-17 03:16:40,496] [pool-1-thread-6] Initializing /data/tony/003003000.tiff: [testng] [2025-05-17 03:17:22,323] [pool-1-thread-11] Initializing /data/anatole/001004000.flex: [testng] [2025-05-17 03:18:22,509] [pool-1-thread-4] Initializing /data/tony/003008000.flex: [testng] [2025-05-17 03:18:58,346] [pool-1-thread-5] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex: [testng] [2025-05-17 03:19:35,911] [pool-1-thread-6] Initializing /data/stephane/002007000.flex: [testng] [2025-05-17 03:21:54,546] [pool-1-thread-4] Initializing /data/manuel/003003001.flex: [testng] [2025-05-17 03:22:07,219] [pool-1-thread-5] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2025-05-17 03:22:17,613] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] [2025-05-17 03:23:25,862] [pool-1-thread-7] Initializing /data/tamjid/006005000.flex: [testng] [2025-05-17 03:24:10,334] [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] [2025-05-17 03:24:43,077] [pool-1-thread-12] Initializing /data/stephane/006013000.flex: [testng] 04:00:12,161 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 04:00:12,161 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:00:12,162 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-05-17_04-00-12.log] [testng] 04:00:12,163 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7308d133 - End of configuration. [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2226, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 103 minutes 32 seconds Finished: SUCCESS