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Started by upstream project "BIOFORMATS-test-repo" build number 241 originally caused by: Started by upstream project "Trigger" build number 266 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5 [BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins9654574935152804398.sh + '[' flex = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_37897_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 test-automated: [testng] File leak detector installed [testng] 00:49:20,164 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:49:20,166 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 00:49:20,166 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:49:20,167 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:49:20,168 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:49:20,168 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:49:20,168 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:49:20,168 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:49:20,169 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:49:20,169 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:49:20,169 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:49:20,169 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:49:20,395 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:49:20,395 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:49:20,425 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:49:20,425 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:49:20,495 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:49:20,496 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:49:20,496 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:49:20,496 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:49:20,496 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 00:49:20,497 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 00:49:20,497 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 328 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-01 00:49:20,508] [main] java.version = 1.8.0_342 [testng] 00:49:20,512 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:49:20,512 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:49:20,558 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-01_00-49-20.log] [testng] 00:49:20,560 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-11-01 00:49:20,562] [main] testng.directory = /data [testng] [2024-11-01 00:49:20,562] [main] testng.configDirectory = /config [testng] [2024-11-01 00:49:20,575] [main] testng.multiplier = 1.0 [testng] [2024-11-01 00:49:20,575] [main] testng.in-memory = false [testng] [2024-11-01 00:49:20,575] [main] testng.allow-missing = false [testng] [2024-11-01 00:49:20,575] [main] user.language = en [testng] [2024-11-01 00:49:20,575] [main] user.country = ${user.country} [testng] [2024-11-01 00:49:20,575] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-11-01 00:50:11,753] [main] ---------------------------------------- [testng] [2024-11-01 00:50:11,753] [main] Total files: 791 [testng] [2024-11-01 00:50:11,753] [main] Scan time: 51.178 s (64 ms/file) [testng] [2024-11-01 00:50:11,753] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-01 00:54:53,154] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_03(2007-12-14_10-50-56)/004006000.flex: [testng] 00:54:53,155 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:54:53,155 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:54:53,156 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-01_00-54-53.log] [testng] 00:54:53,156 |-INFO in ch.qos.logback.core.sift.SiftProcessor@70f08d66 - End of configuration. [testng] [2024-11-01 00:54:53,832] [pool-1-thread-12] Initializing /data/tamjid/006004000.flex: [testng] 00:54:53,833 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:54:53,833 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:54:53,834 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-01_00-54-53.log] [testng] 00:54:53,834 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6725ca8c - End of configuration. [testng] [2024-11-01 00:54:54,489] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex: [testng] 00:54:54,490 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:54:54,490 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:54:54,490 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-01_00-54-54.log] [testng] 00:54:54,491 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5651d3bc - End of configuration. [testng] [2024-11-01 00:54:55,218] [pool-1-thread-10] Initializing /data/manuel/003003001.flex: [testng] 00:54:55,219 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:54:55,219 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:54:55,220 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-01_00-54-55.log] [testng] 00:54:55,220 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b02a6a - End of configuration. [testng] [2024-11-01 00:54:55,933] [pool-1-thread-9] Initializing /data/stephane/006013000.flex: [testng] 00:54:55,933 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:54:55,933 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:54:55,934 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-01_00-54-55.log] [testng] 00:54:55,934 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a3ab076 - End of configuration. [testng] [2024-11-01 00:54:56,715] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex: [testng] 00:54:56,716 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:54:56,716 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:54:56,716 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-01_00-54-56.log] [testng] 00:54:56,717 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7bbad04c - End of configuration. [testng] [2024-11-01 00:54:57,522] [pool-1-thread-7] Initializing /data/qa-17190/002002011.flex: [testng] 00:54:57,522 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:54:57,522 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:54:57,523 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-01_00-54-57.log] [testng] 00:54:57,524 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a5c17f6 - End of configuration. [testng] [2024-11-01 00:54:58,156] [pool-1-thread-6] Initializing /data/tony/001001000_objects.flex: [testng] 00:54:58,156 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:54:58,156 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:54:58,157 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-01_00-54-58.log] [testng] 00:54:58,157 |-INFO in ch.qos.logback.core.sift.SiftProcessor@608f2855 - End of configuration. [testng] [2024-11-01 00:54:58,797] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] 00:54:58,798 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:54:58,798 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:54:58,798 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-01_00-54-58.log] [testng] 00:54:58,799 |-INFO in ch.qos.logback.core.sift.SiftProcessor@b41ee59 - End of configuration. [testng] [2024-11-01 00:55:03,944] [pool-1-thread-4] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] 00:55:03,944 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:55:03,944 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:03,945 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-01_00-55-03.log] [testng] 00:55:03,945 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a108031 - End of configuration. [testng] [2024-11-01 00:55:09,406] [pool-1-thread-3] Initializing /data/tony/001014000 - from flex.tif: [testng] 00:55:09,406 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:55:09,406 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:09,407 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-01_00-55-09.log] [testng] 00:55:09,407 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ee31b20 - End of configuration. [testng] [2024-11-01 00:55:10,889] [pool-1-thread-2] Initializing /data/tony/test.tiff: [testng] 00:55:10,890 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:55:10,890 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:10,891 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-01_00-55-10.log] [testng] 00:55:10,891 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f1862ce - End of configuration. [testng] [2024-11-01 00:55:22,055] [pool-1-thread-3] Initializing /data/qa-2983/004007000.flex: [testng] [2024-11-01 00:55:22,901] [pool-1-thread-2] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2024-11-01 00:55:28,559] [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] [2024-11-01 00:55:29,752] [pool-1-thread-12] Initializing /data/ghislain/test.flex: [testng] [2024-11-01 00:55:30,582] [pool-1-thread-6] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] [2024-11-01 00:55:36,650] [pool-1-thread-9] Initializing /data/tony/test1.flex: [testng] [2024-11-01 00:55:37,485] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex: [testng] [2024-11-01 00:55:38,376] [pool-1-thread-8] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2024-11-01 00:55:41,203] [pool-1-thread-6] Initializing /data/qa-7469/002002.flex: [testng] [2024-11-01 00:55:42,167] [pool-1-thread-3] Initializing /data/achim/003003000.flex: [testng] [2024-11-01 00:55:45,541] [pool-1-thread-10] Initializing /data/qa-18096/002003001.flex: [testng] [2024-11-01 00:55:46,586] [pool-1-thread-11] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] [2024-11-01 00:55:54,024] [pool-1-thread-12] Initializing /data/tony/015002000.tiff: [testng] [2024-11-01 00:55:56,021] [pool-1-thread-9] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex: [testng] [2024-11-01 00:56:01,461] [pool-1-thread-6] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex: [testng] [2024-11-01 00:56:05,108] [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] [2024-11-01 00:56:08,213] [pool-1-thread-10] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] [2024-11-01 00:56:09,234] [pool-1-thread-12] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2024-11-01 00:56:10,081] [pool-1-thread-3] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2024-11-01 00:56:16,029] [pool-1-thread-9] Initializing /data/anatole/001004000.flex: [testng] [2024-11-01 00:56:21,613] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex: [testng] [2024-11-01 00:56:22,454] [pool-1-thread-12] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] [2024-11-01 00:56:31,182] [pool-1-thread-10] Initializing /data/tamjid/006003000.flex: [testng] [2024-11-01 00:56:32,623] [pool-1-thread-7] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2024-11-01 00:56:47,995] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] [2024-11-01 00:56:56,306] [pool-1-thread-10] Initializing /data/stephane/002007000.flex: [testng] [2024-11-01 00:56:58,391] [pool-1-thread-1] Initializing /data/qa-18096/002002001.flex: [testng] [2024-11-01 00:57:05,607] [pool-1-thread-9] Initializing /data/tamjid/006005000.flex: [testng] [2024-11-01 00:57:08,527] [pool-1-thread-10] Initializing /data/tony/003003000.tiff: [testng] [2024-11-01 00:57:10,453] [pool-1-thread-1] Initializing /data/tony/003008000.flex: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2226, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 13 minutes 33 seconds Finished: SUCCESS