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Started by upstream project "BIOFORMATS-test-repo" build number 372 originally caused by: Started by upstream project "Trigger" build number 397 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/jenkins2455947310847217340.sh + '[' flex = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_59182_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] 00:55:14,123 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 00:55:14,125 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - No custom configurators were discovered as a service. [testng] 00:55:14,125 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:55:14,127 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:55:14,128 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:55:14,128 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:55:14,129 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:55:14,129 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:55:14,130 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:55:14,131 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:55:14,131 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:55:14,132 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:55:14,370 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:55:14,370 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:55:14,398 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:55:14,398 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:55:14,405 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:55:14,405 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:55:14,405 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:55:14,406 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:55:14,406 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@65c7a252 - End of configuration. [testng] 00:55:14,407 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@38cee291 - Registering current configuration as safe fallback point [testng] 00:55:14,407 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 277 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-11 00:55:14,418] [main] java.version = 11.0.16 [testng] 00:55:14,422 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:55:14,422 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:14,471 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-11_00-55-14.log] [testng] 00:55:14,473 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13d73f29 - End of configuration. [testng] [2025-03-11 00:55:14,475] [main] testng.directory = /data [testng] [2025-03-11 00:55:14,476] [main] testng.configDirectory = /config [testng] [2025-03-11 00:55:14,487] [main] testng.multiplier = 1.0 [testng] [2025-03-11 00:55:14,489] [main] testng.in-memory = false [testng] [2025-03-11 00:55:14,489] [main] testng.allow-missing = false [testng] [2025-03-11 00:55:14,489] [main] user.language = en [testng] [2025-03-11 00:55:14,489] [main] user.country = ${user.country} [testng] [2025-03-11 00:55:14,489] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-03-11 00:56:25,269] [main] ---------------------------------------- [testng] [2025-03-11 00:56:25,270] [main] Total files: 791 [testng] [2025-03-11 00:56:25,270] [main] Scan time: 70.78 s (89 ms/file) [testng] [2025-03-11 00:56:25,270] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-11 01:01:39,542] [pool-1-thread-1] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] 01:01:39,543 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:01:39,543 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:01:39,545 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-11_01-01-39.log] [testng] 01:01:39,545 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3176c46c - End of configuration. [testng] [2025-03-11 01:01:46,682] [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] 01:01:46,682 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:01:46,683 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:01:46,684 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-11_01-01-46.log] [testng] 01:01:46,684 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8686a2f - End of configuration. [testng] [2025-03-11 01:01:47,399] [pool-1-thread-11] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] 01:01:47,399 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:01:47,399 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:01:47,400 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-11_01-01-47.log] [testng] 01:01:47,401 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c1010d8 - End of configuration. [testng] [2025-03-11 01:01:48,978] [pool-1-thread-10] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] 01:01:48,978 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:01:48,978 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:01:48,979 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-11_01-01-48.log] [testng] 01:01:48,979 |-INFO in ch.qos.logback.core.sift.SiftProcessor@47388760 - End of configuration. [testng] [2025-03-11 01:01:49,602] [pool-1-thread-9] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] 01:01:49,603 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:01:49,603 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:01:49,603 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-11_01-01-49.log] [testng] 01:01:49,604 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b88b6bd - End of configuration. [testng] [2025-03-11 01:01:50,349] [pool-1-thread-8] Initializing /data/qa-7469/002002.flex: [testng] 01:01:50,349 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:01:50,349 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:01:50,350 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-11_01-01-50.log] [testng] 01:01:50,351 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4ef56b62 - End of configuration. [testng] [2025-03-11 01:01:51,092] [pool-1-thread-7] Initializing /data/ghislain/test.flex: [testng] 01:01:51,092 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:01:51,092 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:01:51,093 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-11_01-01-51.log] [testng] 01:01:51,093 |-INFO in ch.qos.logback.core.sift.SiftProcessor@cf5254 - End of configuration. [testng] [2025-03-11 01:01:51,756] [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] 01:01:51,756 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:01:51,756 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:01:51,756 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-11_01-01-51.log] [testng] 01:01:51,757 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34757c80 - End of configuration. [testng] [2025-03-11 01:01:52,582] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] 01:01:52,582 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:01:52,582 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:01:52,583 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-11_01-01-52.log] [testng] 01:01:52,584 |-INFO in ch.qos.logback.core.sift.SiftProcessor@54fc3b60 - End of configuration. [testng] [2025-03-11 01:01:59,713] [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] 01:01:59,713 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:01:59,714 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:01:59,714 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-11_01-01-59.log] [testng] 01:01:59,715 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4dc4d6b3 - End of configuration. [testng] [2025-03-11 01:02:00,856] [pool-1-thread-3] Initializing /data/tony/001001000_objects.flex: [testng] 01:02:00,857 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:02:00,857 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:00,857 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-11_01-02-00.log] [testng] 01:02:00,858 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a56c9ec - End of configuration. [testng] [2025-03-11 01:02:02,116] [pool-1-thread-2] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] 01:02:02,116 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:02:02,116 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:02,117 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-11_01-02-02.log] [testng] 01:02:02,117 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14d88f36 - End of configuration. [testng] [2025-03-11 01:02:30,195] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex: [testng] [2025-03-11 01:02:31,925] [pool-1-thread-8] Initializing /data/tamjid/006005000.flex: [testng] [2025-03-11 01:02:33,477] [pool-1-thread-3] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2025-03-11 01:02:35,349] [pool-1-thread-10] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2025-03-11 01:02:44,233] [pool-1-thread-7] Initializing /data/tony/003003000.tiff: [testng] [2025-03-11 01:02:46,624] [pool-1-thread-12] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2025-03-11 01:02:58,078] [pool-1-thread-4] Initializing /data/tony/001014000 - from flex.tif: [testng] [2025-03-11 01:03:00,610] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] [2025-03-11 01:03:10,102] [pool-1-thread-9] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex: [testng] [2025-03-11 01:03:19,439] [pool-1-thread-8] Initializing /data/qa-2983/004007000.flex: [testng] [2025-03-11 01:03:20,306] [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] [2025-03-11 01:03:25,509] [pool-1-thread-4] Initializing /data/anatole/001004000.flex: [testng] [2025-03-11 01:03:33,815] [pool-1-thread-11] Initializing /data/tony/test1.flex: [testng] [2025-03-11 01:03:37,575] [pool-1-thread-9] Initializing /data/stephane/002007000.flex: [testng] [2025-03-11 01:03:44,216] [pool-1-thread-8] Initializing /data/stephane/006013000.flex: [testng] [2025-03-11 01:03:54,830] [pool-1-thread-11] Initializing /data/qa-17190/002002011.flex: [testng] [2025-03-11 01:03:59,829] [pool-1-thread-9] Initializing /data/tamjid/006003000.flex: [testng] [2025-03-11 01:04:14,544] [pool-1-thread-11] Initializing /data/tony/003008000.flex: [testng] [2025-03-11 01:04:16,148] [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] [2025-03-11 01:04:19,585] [pool-1-thread-9] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] [2025-03-11 01:04:40,306] [pool-1-thread-4] Initializing /data/tony/015002000.tiff: [testng] [2025-03-11 01:04:50,367] [pool-1-thread-8] Initializing /data/qa-18096/002003001.flex: [testng] [2025-03-11 01:04:51,815] [pool-1-thread-7] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex: [testng] [2025-03-11 01:04:58,046] [pool-1-thread-11] Initializing /data/qa-18096/002002001.flex: [testng] [2025-03-11 01:05:01,426] [pool-1-thread-4] Initializing /data/achim/003003000.flex: [testng] [2025-03-11 01:05:03,149] [pool-1-thread-3] Initializing /data/tamjid/006004000.flex: [testng] [2025-03-11 01:05:11,783] [pool-1-thread-8] Initializing /data/manuel/003003001.flex: [testng] [2025-03-11 01:05:18,708] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex: [testng] [2025-03-11 01:05:25,526] [pool-1-thread-3] Initializing /data/tony/test.tiff: [testng] [2025-03-11 01:05:29,083] [pool-1-thread-7] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2226, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 18 minutes 24 seconds Finished: SUCCESS