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Started by upstream project "BIOFORMATS-test-repo" build number 233 originally caused by: Started by upstream project "Trigger" build number 258 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@2 [BIOFORMATS-test-folder@2] $ /bin/bash -xe /tmp/jenkins10697716895093239205.sh + '[' flex = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_36585_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 01:55:03,622 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:55:03,624 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 01:55:03,624 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:55:03,625 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:55:03,625 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:55:03,626 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:55:03,626 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:55:03,626 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:55:03,626 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:55:03,627 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:55:03,627 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:55:03,627 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:55:03,830 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:55:03,830 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:55:03,856 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:55:03,856 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:55:03,863 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:55:03,863 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:55:03,863 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:55:03,863 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:55:03,863 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 01:55:03,864 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 01:55:03,864 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 238 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-24 01:55:03,873] [main] java.version = 21 [testng] 01:55:03,877 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:55:03,877 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:55:03,919 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-24_01-55-03.log] [testng] 01:55:03,921 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-10-24 01:55:03,922] [main] testng.directory = /data [testng] [2024-10-24 01:55:03,923] [main] testng.configDirectory = /config [testng] [2024-10-24 01:55:03,932] [main] testng.multiplier = 1.0 [testng] [2024-10-24 01:55:03,939] [main] testng.in-memory = false [testng] [2024-10-24 01:55:03,939] [main] testng.allow-missing = false [testng] [2024-10-24 01:55:03,939] [main] user.language = en [testng] [2024-10-24 01:55:03,939] [main] user.country = ${user.country} [testng] [2024-10-24 01:55:03,939] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-24 01:55:40,755] [main] ---------------------------------------- [testng] [2024-10-24 01:55:40,755] [main] Total files: 791 [testng] [2024-10-24 01:55:40,755] [main] Scan time: 36.815 s (46 ms/file) [testng] [2024-10-24 01:55:40,755] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-24 02:00:41,877] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex: [testng] 02:00:41,878 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:00:41,878 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:00:41,879 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-24_02-00-41.log] [testng] 02:00:41,880 |-INFO in ch.qos.logback.core.sift.SiftProcessor@518adc90 - End of configuration. [testng] [2024-10-24 02:00:42,613] [pool-1-thread-12] Initializing /data/manuel/003003001.flex: [testng] 02:00:42,613 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:00:42,613 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:00:42,614 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-24_02-00-42.log] [testng] 02:00:42,614 |-INFO in ch.qos.logback.core.sift.SiftProcessor@72addcd6 - End of configuration. [testng] [2024-10-24 02:00:43,250] [pool-1-thread-11] Initializing /data/stephane/002007000.flex: [testng] 02:00:43,251 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:00:43,251 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:00:43,252 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-24_02-00-43.log] [testng] 02:00:43,252 |-INFO in ch.qos.logback.core.sift.SiftProcessor@502510b3 - End of configuration. [testng] [2024-10-24 02:00:43,805] [pool-1-thread-10] Initializing /data/qa-17190/002002011.flex: [testng] 02:00:43,805 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:00:43,805 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:00:43,806 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-24_02-00-43.log] [testng] 02:00:43,806 |-INFO in ch.qos.logback.core.sift.SiftProcessor@353a6f3e - End of configuration. [testng] [2024-10-24 02:00:44,357] [pool-1-thread-9] Initializing /data/tony/015002000.tiff: [testng] 02:00:44,358 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:00:44,358 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:00:44,358 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-24_02-00-44.log] [testng] 02:00:44,359 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35503e90 - End of configuration. [testng] [2024-10-24 02:00:45,352] [pool-1-thread-8] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] 02:00:45,352 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:00:45,352 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:00:45,353 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-24_02-00-45.log] [testng] 02:00:45,353 |-INFO in ch.qos.logback.core.sift.SiftProcessor@764513e5 - End of configuration. [testng] [2024-10-24 02:00:49,724] [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] 02:00:49,724 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:00:49,724 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:00:49,725 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-24_02-00-49.log] [testng] 02:00:49,725 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a6fc8dd - End of configuration. [testng] [2024-10-24 02:00:50,179] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] 02:00:50,179 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:00:50,179 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:00:50,180 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-24_02-00-50.log] [testng] 02:00:50,180 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2473ee6e - End of configuration. [testng] [2024-10-24 02:00:56,375] [pool-1-thread-5] Initializing /data/tony/test1.flex: [testng] 02:00:56,376 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:00:56,376 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:00:56,377 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-24_02-00-56.log] [testng] 02:00:56,377 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4eb25d8b - End of configuration. [testng] [2024-10-24 02:00:57,038] [pool-1-thread-4] Initializing /data/tony/003008000.flex: [testng] 02:00:57,038 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:00:57,038 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:00:57,038 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-24_02-00-57.log] [testng] 02:00:57,039 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b0843e7 - End of configuration. [testng] [2024-10-24 02:00:57,596] [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] 02:00:57,596 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:00:57,597 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:00:57,597 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-24_02-00-57.log] [testng] 02:00:57,598 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38630f9e - End of configuration. [testng] [2024-10-24 02:00:58,134] [pool-1-thread-2] Initializing /data/tony/001001000_objects.flex: [testng] 02:00:58,134 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:00:58,134 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:00:58,134 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-24_02-00-58.log] [testng] 02:00:58,135 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9215979 - End of configuration. [testng] [2024-10-24 02:01:08,646] [pool-1-thread-9] Initializing /data/tony/test.tiff: [testng] [2024-10-24 02:01:10,470] [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] [2024-10-24 02:01:11,223] [pool-1-thread-2] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex: [testng] [2024-10-24 02:01:11,896] [pool-1-thread-11] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] [2024-10-24 02:01:20,318] [pool-1-thread-5] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2024-10-24 02:01:25,654] [pool-1-thread-7] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2024-10-24 02:01:26,949] [pool-1-thread-3] Initializing /data/achim/003003000.flex: [testng] [2024-10-24 02:01:27,589] [pool-1-thread-4] Initializing /data/stephane/006013000.flex: [testng] [2024-10-24 02:01:29,131] [pool-1-thread-9] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] [2024-10-24 02:01:36,968] [pool-1-thread-12] Initializing /data/anatole/001004000.flex: [testng] [2024-10-24 02:01:39,132] [pool-1-thread-2] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] [2024-10-24 02:01:40,758] [pool-1-thread-10] Initializing /data/tamjid/006004000.flex: [testng] [2024-10-24 02:01:41,379] [pool-1-thread-5] Initializing /data/tony/001014000 - from flex.tif: [testng] [2024-10-24 02:01:48,209] [pool-1-thread-3] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] [2024-10-24 02:01:56,626] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex: [testng] [2024-10-24 02:01:59,164] [pool-1-thread-2] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2024-10-24 02:02:07,148] [pool-1-thread-5] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_03(2007-12-14_10-50-56)/004006000.flex: [testng] [2024-10-24 02:02:09,383] [pool-1-thread-4] Initializing /data/qa-18096/002003001.flex: [testng] [2024-10-24 02:02:11,080] [pool-1-thread-10] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex: [testng] [2024-10-24 02:02:21,186] [pool-1-thread-1] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2024-10-24 02:02:33,171] [pool-1-thread-4] Initializing /data/qa-18096/002002001.flex: [testng] [2024-10-24 02:02:36,752] [pool-1-thread-5] Initializing /data/qa-7469/002002.flex: [testng] [2024-10-24 02:02:38,725] [pool-1-thread-12] Initializing /data/tamjid/006003000.flex: [testng] [2024-10-24 02:02:48,080] [pool-1-thread-4] Initializing /data/tamjid/006005000.flex: [testng] [2024-10-24 02:02:49,530] [pool-1-thread-10] Initializing /data/tony/003003000.tiff: [testng] [2024-10-24 02:02:52,130] [pool-1-thread-5] Initializing /data/qa-2983/004007000.flex: [testng] [2024-10-24 02:02:55,399] [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] [2024-10-24 02:03:10,675] [pool-1-thread-4] Initializing /data/ghislain/test.flex: [testng] [2024-10-24 02:03:11,379] [pool-1-thread-5] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2024-10-24 02:03:14,413] [pool-1-thread-10] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/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: 15 minutes 41 seconds Finished: SUCCESS