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Started by upstream project "BIOFORMATS-test-repo" build number 234 originally caused by: Started by upstream project "Trigger" build number 259 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins18375570816383145825.sh + '[' flex = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_36749_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] 01:49:35,590 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:49:35,591 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 01:49:35,591 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:49:35,592 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:49:35,592 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:49:35,593 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:49:35,593 |-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] 01:49:35,593 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:49:35,593 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:49:35,594 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:49:35,594 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:49:35,594 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:49:35,864 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:49:35,864 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:49:35,917 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:49:35,917 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:49:35,925 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:49:35,925 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:49:35,925 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:49:35,926 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:49:35,926 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 01:49:35,927 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 01:49:35,927 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 334 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-25 01:49:35,936] [main] java.version = 1.8.0_342 [testng] 01:49:35,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:49:35,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:49:35,985 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-25_01-49-35.log] [testng] 01:49:35,986 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-10-25 01:49:35,988] [main] testng.directory = /data [testng] [2024-10-25 01:49:35,989] [main] testng.configDirectory = /config [testng] [2024-10-25 01:49:36,000] [main] testng.multiplier = 1.0 [testng] [2024-10-25 01:49:36,001] [main] testng.in-memory = false [testng] [2024-10-25 01:49:36,001] [main] testng.allow-missing = false [testng] [2024-10-25 01:49:36,001] [main] user.language = en [testng] [2024-10-25 01:49:36,001] [main] user.country = ${user.country} [testng] [2024-10-25 01:49:36,001] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-10-25 01:50:44,868] [main] ---------------------------------------- [testng] [2024-10-25 01:50:44,868] [main] Total files: 791 [testng] [2024-10-25 01:50:44,868] [main] Scan time: 68.867 s (87 ms/file) [testng] [2024-10-25 01:50:44,869] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-25 01:55:35,166] [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] 01:55:35,166 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:55:35,167 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:55:35,167 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-25_01-55-35.log] [testng] 01:55:35,168 |-INFO in ch.qos.logback.core.sift.SiftProcessor@69677d3e - End of configuration. [testng] [2024-10-25 01:55:35,726] [pool-1-thread-12] Initializing /data/tamjid/006004000.flex: [testng] 01:55:35,726 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:55:35,726 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:55:35,727 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-25_01-55-35.log] [testng] 01:55:35,727 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50fa8e20 - End of configuration. [testng] [2024-10-25 01:55:36,230] [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] 01:55:36,230 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:55:36,230 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:55:36,231 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-25_01-55-36.log] [testng] 01:55:36,232 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6bf31640 - End of configuration. [testng] [2024-10-25 01:55:36,769] [pool-1-thread-10] Initializing /data/manuel/003003001.flex: [testng] 01:55:36,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:55:36,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:55:36,770 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-25_01-55-36.log] [testng] 01:55:36,770 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20ed18e0 - End of configuration. [testng] [2024-10-25 01:55:37,379] [pool-1-thread-9] Initializing /data/stephane/006013000.flex: [testng] 01:55:37,379 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:55:37,379 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:55:37,380 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-25_01-55-37.log] [testng] 01:55:37,380 |-INFO in ch.qos.logback.core.sift.SiftProcessor@16fe7c58 - End of configuration. [testng] [2024-10-25 01:55:37,922] [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] 01:55:37,923 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:55:37,923 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:55:37,924 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-25_01-55-37.log] [testng] 01:55:37,924 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1196365c - End of configuration. [testng] [2024-10-25 01:55:38,504] [pool-1-thread-7] Initializing /data/qa-17190/002002011.flex: [testng] 01:55:38,505 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:55:38,505 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:55:38,505 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-25_01-55-38.log] [testng] 01:55:38,506 |-INFO in ch.qos.logback.core.sift.SiftProcessor@cec00a3 - End of configuration. [testng] [2024-10-25 01:55:39,056] [pool-1-thread-6] Initializing /data/tony/001001000_objects.flex: [testng] 01:55:39,056 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:55:39,056 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:55:39,057 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-25_01-55-39.log] [testng] 01:55:39,057 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4a96feed - End of configuration. [testng] [2024-10-25 01:55:39,600] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] 01:55:39,600 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:55:39,601 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:55:39,601 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-25_01-55-39.log] [testng] 01:55:39,601 |-INFO in ch.qos.logback.core.sift.SiftProcessor@77abb4d - End of configuration. [testng] [2024-10-25 01:55:43,756] [pool-1-thread-4] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] 01:55:43,756 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:55:43,756 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:55:43,757 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-25_01-55-43.log] [testng] 01:55:43,757 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2c5d7191 - End of configuration. [testng] [2024-10-25 01:55:48,732] [pool-1-thread-3] Initializing /data/tony/001014000 - from flex.tif: [testng] 01:55:48,732 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:55:48,732 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:55:48,733 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-25_01-55-48.log] [testng] 01:55:48,734 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6907edc2 - End of configuration. [testng] [2024-10-25 01:55:50,044] [pool-1-thread-2] Initializing /data/tony/test.tiff: [testng] 01:55:50,044 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:55:50,044 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:55:50,044 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-25_01-55-50.log] [testng] 01:55:50,045 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d6b8a40 - End of configuration. [testng] [2024-10-25 01:56:00,608] [pool-1-thread-3] Initializing /data/qa-2983/004007000.flex: [testng] [2024-10-25 01:56:01,386] [pool-1-thread-2] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2024-10-25 01:56:06,548] [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] [2024-10-25 01:56:07,587] [pool-1-thread-12] Initializing /data/ghislain/test.flex: [testng] [2024-10-25 01:56:08,415] [pool-1-thread-6] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] [2024-10-25 01:56:13,823] [pool-1-thread-9] Initializing /data/tony/test1.flex: [testng] [2024-10-25 01:56:14,682] [pool-1-thread-1] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2024-10-25 01:56:16,274] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex: [testng] [2024-10-25 01:56:18,867] [pool-1-thread-3] Initializing /data/qa-7469/002002.flex: [testng] [2024-10-25 01:56:19,716] [pool-1-thread-6] Initializing /data/achim/003003000.flex: [testng] [2024-10-25 01:56:21,603] [pool-1-thread-10] Initializing /data/qa-18096/002003001.flex: [testng] [2024-10-25 01:56:22,539] [pool-1-thread-11] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] [2024-10-25 01:56:31,086] [pool-1-thread-12] Initializing /data/tony/015002000.tiff: [testng] [2024-10-25 01:56:35,664] [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] [2024-10-25 01:56:39,044] [pool-1-thread-3] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex: [testng] [2024-10-25 01:56:40,140] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex: [testng] [2024-10-25 01:56:42,465] [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] [2024-10-25 01:56:46,207] [pool-1-thread-6] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2024-10-25 01:56:48,398] [pool-1-thread-12] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2024-10-25 01:56:55,131] [pool-1-thread-9] Initializing /data/anatole/001004000.flex: [testng] [2024-10-25 01:56:58,305] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex: [testng] [2024-10-25 01:57:01,177] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] [2024-10-25 01:57:08,864] [pool-1-thread-10] Initializing /data/tamjid/006003000.flex: [testng] [2024-10-25 01:57:12,973] [pool-1-thread-7] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2024-10-25 01:57:26,328] [pool-1-thread-8] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] [2024-10-25 01:57:34,569] [pool-1-thread-3] Initializing /data/stephane/002007000.flex: [testng] [2024-10-25 01:57:35,489] [pool-1-thread-10] Initializing /data/qa-18096/002002001.flex: [testng] [2024-10-25 01:57:43,289] [pool-1-thread-9] Initializing /data/tamjid/006005000.flex: [testng] [2024-10-25 01:57:47,339] [pool-1-thread-10] Initializing /data/tony/003003000.tiff: [testng] [2024-10-25 01:57:49,275] [pool-1-thread-3] 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 53 seconds Finished: SUCCESS