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Started by upstream project "BIOFORMATS-test-repo" build number 17 originally caused by: Started by upstream project "Trigger" build number 20 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/jenkins3090655739242482727.sh + '[' flex = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_1997_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] 00:28:47,891 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:28:47,892 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 00:28:47,892 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:28:47,893 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:28:47,894 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:28:47,894 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:28:47,895 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:28:47,895 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:28:47,895 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:28:47,896 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:28:47,896 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:28:47,897 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:28:48,097 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:28:48,098 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:28:48,121 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:28:48,121 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:28:48,128 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:28:48,129 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:28:48,129 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:28:48,129 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:28:48,129 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 00:28:48,130 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 00:28:48,130 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 235 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-30 00:28:48,140] [main] java.version = 11.0.16 [testng] 00:28:48,144 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:28:48,144 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:28:48,204 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-30_00-28-48.log] [testng] 00:28:48,207 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-03-30 00:28:48,210] [main] testng.directory = /data [testng] [2024-03-30 00:28:48,211] [main] testng.configDirectory = /config [testng] [2024-03-30 00:28:48,228] [main] testng.multiplier = 1.0 [testng] [2024-03-30 00:28:48,230] [main] testng.in-memory = false [testng] [2024-03-30 00:28:48,231] [main] testng.allow-missing = false [testng] [2024-03-30 00:28:48,231] [main] user.language = en [testng] [2024-03-30 00:28:48,231] [main] user.country = ${user.country} [testng] [2024-03-30 00:28:48,231] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-03-30 00:29:01,640] [main] ---------------------------------------- [testng] [2024-03-30 00:29:01,640] [main] Total files: 791 [testng] [2024-03-30 00:29:01,640] [main] Scan time: 13.409 s (16 ms/file) [testng] [2024-03-30 00:29:01,640] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-30 00:34:55,509] [pool-1-thread-1] Initializing /data/qa-18096/002003001.flex: [testng] 00:34:55,509 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:34:55,510 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:55,511 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-30_00-34-55.log] [testng] 00:34:55,512 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5935bf74 - End of configuration. [testng] [2024-03-30 00:34:55,574] [pool-1-thread-12] Initializing /data/tony/003003000.tiff: [testng] 00:34:55,574 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:34:55,574 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:55,575 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-30_00-34-55.log] [testng] 00:34:55,575 |-INFO in ch.qos.logback.core.sift.SiftProcessor@633055dc - End of configuration. [testng] [2024-03-30 00:34:55,676] [pool-1-thread-11] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] 00:34:55,676 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:34:55,676 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:55,677 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-30_00-34-55.log] [testng] 00:34:55,678 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d6b8a81 - End of configuration. [testng] [2024-03-30 00:34:56,197] [pool-1-thread-10] Initializing /data/achim/003003000.flex: [testng] 00:34:56,198 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:34:56,198 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:56,198 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-30_00-34-56.log] [testng] 00:34:56,199 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4944ac4d - End of configuration. [testng] [2024-03-30 00:34:56,285] [pool-1-thread-9] Initializing /data/manuel/003003001.flex: [testng] 00:34:56,285 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:34:56,285 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:56,286 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-30_00-34-56.log] [testng] 00:34:56,286 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65a71622 - End of configuration. [testng] [2024-03-30 00:34:56,348] [pool-1-thread-8] Initializing /data/tamjid/006003000.flex: [testng] 00:34:56,348 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:34:56,349 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:56,349 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-30_00-34-56.log] [testng] 00:34:56,349 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35e0638d - End of configuration. [testng] [2024-03-30 00:34:56,371] [pool-1-thread-7] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex: [testng] 00:34:56,371 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:34:56,371 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:56,372 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-30_00-34-56.log] [testng] 00:34:56,372 |-INFO in ch.qos.logback.core.sift.SiftProcessor@409059a8 - End of configuration. [testng] [2024-03-30 00:34:56,408] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] 00:34:56,408 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:34:56,408 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:56,409 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-30_00-34-56.log] [testng] 00:34:56,410 |-INFO in ch.qos.logback.core.sift.SiftProcessor@31949e61 - End of configuration. [testng] [2024-03-30 00:34:56,857] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] 00:34:56,857 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:34:56,857 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:56,858 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-30_00-34-56.log] [testng] 00:34:56,859 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2878c1ae - End of configuration. [testng] [2024-03-30 00:34:57,284] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex: [testng] 00:34:57,284 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:34:57,284 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:57,285 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-30_00-34-57.log] [testng] 00:34:57,285 |-INFO in ch.qos.logback.core.sift.SiftProcessor@340030bc - End of configuration. [testng] [2024-03-30 00:34:57,315] [pool-1-thread-3] Initializing /data/tony/003008000.flex: [testng] 00:34:57,315 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:34:57,315 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:57,315 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-30_00-34-57.log] [testng] 00:34:57,316 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56af8fea - End of configuration. [testng] [2024-03-30 00:34:57,367] [pool-1-thread-2] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] 00:34:57,367 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:34:57,367 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:57,368 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-30_00-34-57.log] [testng] 00:34:57,368 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68ce7cc1 - End of configuration. [testng] [2024-03-30 00:34:59,268] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex: [testng] [2024-03-30 00:34:59,327] [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] [2024-03-30 00:34:59,449] [pool-1-thread-12] Initializing /data/tony/001014000 - from flex.tif: [testng] [2024-03-30 00:34:59,535] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex: [testng] [2024-03-30 00:34:59,788] [pool-1-thread-7] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] [2024-03-30 00:35:00,345] [pool-1-thread-10] Initializing /data/tony/test.tiff: [testng] [2024-03-30 00:35:00,656] [pool-1-thread-9] Initializing /data/qa-17190/002002011.flex: [testng] [2024-03-30 00:35:01,060] [pool-1-thread-12] Initializing /data/tony/015002000.tiff: [testng] [2024-03-30 00:35:01,244] [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] [2024-03-30 00:35:01,301] [pool-1-thread-10] Initializing /data/qa-18096/002002001.flex: [testng] [2024-03-30 00:35:01,371] [pool-1-thread-1] Initializing /data/stephane/006013000.flex: [testng] [2024-03-30 00:35:01,811] [pool-1-thread-12] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2024-03-30 00:35:02,012] [pool-1-thread-10] Initializing /data/ghislain/test.flex: [testng] [2024-03-30 00:35:02,508] [pool-1-thread-9] Initializing /data/tamjid/006004000.flex: [testng] [2024-03-30 00:35:02,902] [pool-1-thread-3] Initializing /data/tamjid/006005000.flex: [testng] [2024-03-30 00:35:02,926] [pool-1-thread-10] Initializing /data/qa-2983/004007000.flex: [testng] [2024-03-30 00:35:03,069] [pool-1-thread-9] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] [2024-03-30 00:35:03,599] [pool-1-thread-3] Initializing /data/tony/test1.flex: [testng] [2024-03-30 00:35:03,679] [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] [2024-03-30 00:35:03,707] [pool-1-thread-9] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2024-03-30 00:35:04,282] [pool-1-thread-12] Initializing /data/stephane/002007000.flex: [testng] [2024-03-30 00:35:04,549] [pool-1-thread-3] Initializing /data/anatole/001004000.flex: [testng] [2024-03-30 00:35:04,686] [pool-1-thread-10] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_03(2007-12-14_10-50-56)/004006000.flex: [testng] [2024-03-30 00:35:04,787] [pool-1-thread-8] Initializing /data/qa-7469/002002.flex: [testng] [2024-03-30 00:35:05,299] [pool-1-thread-4] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2024-03-30 00:35:05,662] [pool-1-thread-12] Initializing /data/tony/001001000_objects.flex: [testng] [2024-03-30 00:35:05,695] [pool-1-thread-8] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2024-03-30 00:35:06,854] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex: [testng] [2024-03-30 00:35:06,990] [pool-1-thread-1] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2024-03-30 00:35:07,163] [pool-1-thread-10] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex: [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 27 seconds Finished: SUCCESS