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Started by upstream project "BIOFORMATS-test-repo" build number 194 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@6 [BIOFORMATS-test-folder@6] $ /bin/bash -xe /tmp/jenkins8010152302093133811.sh + '[' flex = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_30705_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. [javac] 4 warnings test-automated: [testng] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket [testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket [testng] File leak detector installed [testng] 11:36:51,248 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 11:36:51,249 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 11:36:51,249 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:36:51,250 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:36:51,250 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 11:36:51,250 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 11:36:51,251 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 11:36:51,251 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:36:51,251 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:36:51,252 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 11:36:51,252 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 11:36:51,252 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 11:36:51,410 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 11:36:51,410 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 11:36:51,434 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 11:36:51,435 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 11:36:51,442 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 11:36:51,442 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 11:36:51,442 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 11:36:51,442 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 11:36:51,442 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 11:36:51,443 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 11:36:51,443 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 192 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-09-19 11:36:51,452] [main] java.version = 21 [testng] 11:36:51,455 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 11:36:51,455 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:36:51,496 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-19_11-36-51.log] [testng] 11:36:51,497 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-09-19 11:36:51,499] [main] testng.directory = /data [testng] [2024-09-19 11:36:51,499] [main] testng.configDirectory = /config [testng] [2024-09-19 11:36:51,508] [main] testng.multiplier = 1.0 [testng] [2024-09-19 11:36:51,508] [main] testng.in-memory = false [testng] [2024-09-19 11:36:51,508] [main] testng.allow-missing = false [testng] [2024-09-19 11:36:51,508] [main] user.language = en [testng] [2024-09-19 11:36:51,509] [main] user.country = ${user.country} [testng] [2024-09-19 11:36:51,509] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-09-19 11:39:11,325] [main] ---------------------------------------- [testng] [2024-09-19 11:39:11,326] [main] Total files: 791 [testng] [2024-09-19 11:39:11,326] [main] Scan time: 139.816 s (176 ms/file) [testng] [2024-09-19 11:39:11,326] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-09-19 11:45:40,651] [pool-1-thread-1] Initializing /data/qa-18096/002003001.flex: [testng] 11:45:40,652 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 11:45:40,652 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:45:40,653 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-09-19_11-45-40.log] [testng] 11:45:40,654 |-INFO in ch.qos.logback.core.sift.SiftProcessor@518adc90 - End of configuration. [testng] [2024-09-19 11:45:44,468] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex: [testng] 11:45:44,468 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 11:45:44,468 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:45:44,469 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-09-19_11-45-44.log] [testng] 11:45:44,469 |-INFO in ch.qos.logback.core.sift.SiftProcessor@72addcd6 - End of configuration. [testng] [2024-09-19 11:45:45,282] [pool-1-thread-11] Initializing /data/stephane/002007000.flex: [testng] 11:45:45,282 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 11:45:45,282 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:45:45,283 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-09-19_11-45-45.log] [testng] 11:45:45,283 |-INFO in ch.qos.logback.core.sift.SiftProcessor@502510b3 - End of configuration. [testng] [2024-09-19 11:45:46,039] [pool-1-thread-10] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] 11:45:46,040 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 11:45:46,040 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:45:46,040 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-09-19_11-45-46.log] [testng] 11:45:46,041 |-INFO in ch.qos.logback.core.sift.SiftProcessor@46eaab39 - End of configuration. [testng] [2024-09-19 11:45:52,166] [pool-1-thread-9] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex: [testng] 11:45:52,167 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 11:45:52,167 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:45:52,168 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-09-19_11-45-52.log] [testng] 11:45:52,168 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35503e90 - End of configuration. [testng] [2024-09-19 11:45:53,083] [pool-1-thread-8] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] 11:45:53,083 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 11:45:53,083 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:45:53,084 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-09-19_11-45-53.log] [testng] 11:45:53,084 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10ec712d - End of configuration. [testng] [2024-09-19 11:45:55,038] [pool-1-thread-7] Initializing /data/tony/test.tiff: [testng] 11:45:55,038 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 11:45:55,039 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:45:55,039 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-09-19_11-45-55.log] [testng] 11:45:55,040 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a6fc8dd - End of configuration. [testng] [2024-09-19 11:45:57,083] [pool-1-thread-6] Initializing /data/tamjid/006005000.flex: [testng] 11:45:57,083 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 11:45:57,083 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:45:57,084 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-09-19_11-45-57.log] [testng] 11:45:57,084 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2473ee6e - End of configuration. [testng] [2024-09-19 11:45:57,994] [pool-1-thread-5] Initializing /data/qa-7469/002002.flex: [testng] 11:45:57,995 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 11:45:57,995 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:45:57,995 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-09-19_11-45-57.log] [testng] 11:45:57,996 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4eb25d8b - End of configuration. [testng] [2024-09-19 11:45:58,899] [pool-1-thread-4] Initializing /data/qa-18096/002002001.flex: [testng] 11:45:58,899 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 11:45:58,899 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:45:58,900 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-09-19_11-45-58.log] [testng] 11:45:58,900 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b0843e7 - End of configuration. [testng] [2024-09-19 11:45:59,752] [pool-1-thread-3] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] 11:45:59,753 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 11:45:59,753 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:45:59,753 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-09-19_11-45-59.log] [testng] 11:45:59,754 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38630f9e - End of configuration. [testng] [2024-09-19 11:46:06,929] [pool-1-thread-2] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] 11:46:06,929 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 11:46:06,929 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:46:06,930 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-09-19_11-46-06.log] [testng] 11:46:06,930 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9215979 - End of configuration. [testng] [2024-09-19 11:46:27,919] [pool-1-thread-7] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] [2024-09-19 11:46:31,130] [pool-1-thread-6] Initializing /data/achim/003003000.flex: [testng] [2024-09-19 11:46:33,051] [pool-1-thread-11] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] [2024-09-19 11:46:35,129] [pool-1-thread-1] Initializing /data/anatole/001004000.flex: [testng] [2024-09-19 11:46:36,381] [pool-1-thread-4] Initializing /data/qa-2983/004007000.flex: [testng] [2024-09-19 11:46:37,480] [pool-1-thread-5] Initializing /data/qa-17190/002002011.flex: [testng] [2024-09-19 11:46:44,938] [pool-1-thread-12] Initializing /data/tony/001001000_objects.flex: [testng] [2024-09-19 11:46:50,724] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex: [testng] [2024-09-19 11:46:52,063] [pool-1-thread-5] Initializing /data/ghislain/test.flex: [testng] [2024-09-19 11:46:53,168] [pool-1-thread-4] Initializing /data/tony/003003000.tiff: [testng] [2024-09-19 11:47:00,437] [pool-1-thread-7] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] [2024-09-19 11:47:07,847] [pool-1-thread-9] Initializing /data/manuel/003003001.flex: [testng] [2024-09-19 11:47:08,959] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex: [testng] [2024-09-19 11:47:10,241] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] [2024-09-19 11:47:22,437] [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] [2024-09-19 11:47:29,387] [pool-1-thread-5] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex: [testng] [2024-09-19 11:47:31,153] [pool-1-thread-1] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2024-09-19 11:47:35,243] [pool-1-thread-11] Initializing /data/tamjid/006003000.flex: [testng] [2024-09-19 11:47:45,106] [pool-1-thread-4] Initializing /data/tony/001014000 - from flex.tif: [testng] [2024-09-19 11:47:49,818] [pool-1-thread-11] Initializing /data/tony/test1.flex: [testng] [2024-09-19 11:47:50,833] [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] [2024-09-19 11:47:52,120] [pool-1-thread-9] Initializing /data/stephane/006013000.flex: [testng] [2024-09-19 11:47:53,315] [pool-1-thread-5] Initializing /data/tony/003008000.flex: [testng] [2024-09-19 11:48:00,025] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex: [testng] [2024-09-19 11:48:05,494] [pool-1-thread-11] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2024-09-19 11:48:10,907] [pool-1-thread-8] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] [2024-09-19 11:48:23,987] [pool-1-thread-12] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2024-09-19 11:48:33,236] [pool-1-thread-5] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex: [testng] [2024-09-19 11:48:35,846] [pool-1-thread-9] Initializing /data/tony/015002000.tiff: [testng] [2024-09-19 11:48:45,240] [pool-1-thread-11] Initializing /data/tamjid/006004000.flex: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2226, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 19 minutes 36 seconds Finished: SUCCESS