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Started by upstream project "BIOFORMATS-test-repo" build number 319 originally caused by: Started by upstream project "Trigger" build number 342 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/jenkins2848481073629993791.sh + '[' flex = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_50591_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 00:48:43,646 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 00:48:43,648 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - No custom configurators were discovered as a service. [testng] 00:48:43,648 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:48:43,649 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:48:43,649 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:48:43,650 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:48:43,650 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:48:43,650 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:48:43,650 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:48:43,651 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:48:43,651 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:48:43,651 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:48:43,808 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:48:43,808 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:48:43,832 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:48:43,832 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:48:43,838 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:48:43,838 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:48:43,839 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:48:43,839 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:48:43,839 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@4310d43 - End of configuration. [testng] 00:48:43,840 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@1b11171f - Registering current configuration as safe fallback point [testng] 00:48:43,840 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 190 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-01-16 00:48:43,849] [main] java.version = 21 [testng] 00:48:43,852 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:48:43,852 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:48:43,894 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-01-16_00-48-43.log] [testng] 00:48:43,896 |-INFO in ch.qos.logback.core.sift.SiftProcessor@69504ae9 - End of configuration. [testng] [2025-01-16 00:48:43,897] [main] testng.directory = /data [testng] [2025-01-16 00:48:43,897] [main] testng.configDirectory = /config [testng] [2025-01-16 00:48:43,906] [main] testng.multiplier = 1.0 [testng] [2025-01-16 00:48:43,906] [main] testng.in-memory = false [testng] [2025-01-16 00:48:43,907] [main] testng.allow-missing = false [testng] [2025-01-16 00:48:43,907] [main] user.language = en [testng] [2025-01-16 00:48:43,907] [main] user.country = ${user.country} [testng] [2025-01-16 00:48:43,907] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-01-16 00:49:57,206] [main] ---------------------------------------- [testng] [2025-01-16 00:49:57,207] [main] Total files: 791 [testng] [2025-01-16 00:49:57,207] [main] Scan time: 73.299 s (92 ms/file) [testng] [2025-01-16 00:49:57,207] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-01-16 00:54:57,088] [pool-1-thread-1] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] 00:54:57,089 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:54:57,089 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:54:57,090 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-01-16_00-54-57.log] [testng] 00:54:57,091 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c5b90d4 - End of configuration. [testng] [2025-01-16 00:54:58,291] [pool-1-thread-12] Initializing /data/tamjid/006003000.flex: [testng] 00:54:58,291 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:54:58,291 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:54:58,292 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-01-16_00-54-58.log] [testng] 00:54:58,292 |-INFO in ch.qos.logback.core.sift.SiftProcessor@502510b3 - End of configuration. [testng] [2025-01-16 00:54:58,882] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] 00:54:58,882 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:54:58,882 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:54:58,883 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-01-16_00-54-58.log] [testng] 00:54:58,883 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7acb96c3 - End of configuration. [testng] [2025-01-16 00:54:59,520] [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] 00:54:59,520 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:54:59,520 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:54:59,521 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-01-16_00-54-59.log] [testng] 00:54:59,522 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f93751 - End of configuration. [testng] [2025-01-16 00:55:00,275] [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] 00:55:00,275 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:55:00,275 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:00,276 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-01-16_00-55-00.log] [testng] 00:55:00,277 |-INFO in ch.qos.logback.core.sift.SiftProcessor@28299d5b - End of configuration. [testng] [2025-01-16 00:55:00,961] [pool-1-thread-8] Initializing /data/tony/test1.flex: [testng] 00:55:00,962 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:55:00,962 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:00,962 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-01-16_00-55-00.log] [testng] 00:55:00,963 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d0e5c37 - End of configuration. [testng] [2025-01-16 00:55:01,705] [pool-1-thread-7] Initializing /data/tony/001014000 - from flex.tif: [testng] 00:55:01,705 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:55:01,705 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:01,705 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-01-16_00-55-01.log] [testng] 00:55:01,706 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c989f40 - End of configuration. [testng] [2025-01-16 00:55:03,197] [pool-1-thread-6] Initializing /data/tamjid/006005000.flex: [testng] 00:55:03,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:55:03,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:03,198 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-01-16_00-55-03.log] [testng] 00:55:03,198 |-INFO in ch.qos.logback.core.sift.SiftProcessor@45b26946 - End of configuration. [testng] [2025-01-16 00:55:03,854] [pool-1-thread-5] Initializing /data/stephane/006013000.flex: [testng] 00:55:03,854 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:55:03,854 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:03,855 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-01-16_00-55-03.log] [testng] 00:55:03,855 |-INFO in ch.qos.logback.core.sift.SiftProcessor@cd1fe70 - End of configuration. [testng] [2025-01-16 00:55:04,502] [pool-1-thread-4] Initializing /data/achim/003003000.flex: [testng] 00:55:04,502 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:55:04,502 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:04,502 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-01-16_00-55-04.log] [testng] 00:55:04,503 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20ea61b1 - End of configuration. [testng] [2025-01-16 00:55:05,281] [pool-1-thread-3] Initializing /data/qa-2983/004007000.flex: [testng] 00:55:05,281 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:55:05,281 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:05,282 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-01-16_00-55-05.log] [testng] 00:55:05,282 |-INFO in ch.qos.logback.core.sift.SiftProcessor@28b57f33 - End of configuration. [testng] [2025-01-16 00:55:05,983] [pool-1-thread-2] Initializing /data/ghislain/test.flex: [testng] 00:55:05,983 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:55:05,983 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:05,983 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-01-16_00-55-05.log] [testng] 00:55:05,984 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d415ad8 - End of configuration. [testng] [2025-01-16 00:55:16,794] [pool-1-thread-7] Initializing /data/tony/003003000.tiff: [testng] [2025-01-16 00:55:18,308] [pool-1-thread-1] Initializing /data/manuel/003003001.flex: [testng] [2025-01-16 00:55:19,061] [pool-1-thread-12] Initializing /data/tony/001001000_objects.flex: [testng] [2025-01-16 00:55:19,760] [pool-1-thread-6] Initializing /data/tamjid/006004000.flex: [testng] [2025-01-16 00:55:20,332] [pool-1-thread-3] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex: [testng] [2025-01-16 00:55:20,946] [pool-1-thread-8] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2025-01-16 00:55:26,582] [pool-1-thread-2] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex: [testng] [2025-01-16 00:55:30,833] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_03(2007-12-14_10-50-56)/004006000.flex: [testng] [2025-01-16 00:55:31,824] [pool-1-thread-9] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2025-01-16 00:55:32,807] [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] [2025-01-16 00:55:33,832] [pool-1-thread-4] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] [2025-01-16 00:55:45,796] [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] [2025-01-16 00:55:47,320] [pool-1-thread-6] Initializing /data/qa-18096/002003001.flex: [testng] [2025-01-16 00:55:49,447] [pool-1-thread-12] Initializing /data/qa-17190/002002011.flex: [testng] [2025-01-16 00:55:50,372] [pool-1-thread-3] Initializing /data/qa-7469/002002.flex: [testng] [2025-01-16 00:55:51,274] [pool-1-thread-10] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex: [testng] [2025-01-16 00:55:53,234] [pool-1-thread-11] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2025-01-16 00:55:56,147] [pool-1-thread-2] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2025-01-16 00:55:57,073] [pool-1-thread-1] Initializing /data/anatole/001004000.flex: [testng] [2025-01-16 00:56:00,338] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] [2025-01-16 00:56:08,481] [pool-1-thread-6] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex: [testng] [2025-01-16 00:56:09,630] [pool-1-thread-12] Initializing /data/tony/015002000.tiff: [testng] [2025-01-16 00:56:11,915] [pool-1-thread-3] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] [2025-01-16 00:56:25,668] [pool-1-thread-10] Initializing /data/tony/003008000.flex: [testng] [2025-01-16 00:56:26,766] [pool-1-thread-2] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] [2025-01-16 00:56:40,319] [pool-1-thread-12] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2025-01-16 00:56:49,944] [pool-1-thread-1] Initializing /data/qa-18096/002002001.flex: [testng] [2025-01-16 00:56:53,687] [pool-1-thread-6] Initializing /data/stephane/002007000.flex: [testng] [2025-01-16 00:56:59,859] [pool-1-thread-10] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2025-01-16 00:57:08,125] [pool-1-thread-7] Initializing /data/tony/test.tiff: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2226, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 15 minutes 29 seconds Finished: SUCCESS