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Started by upstream project "BIOFORMATS-test-repo" build number 195 originally caused by: Started by upstream project "Trigger" build number 217 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9 [BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins8958720005819371691.sh + '[' flex = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_30869_merge_ci -v /test/idr/repos/curated/flex:/data -v /test/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] 17:11:27,409 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 17:11:27,411 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 17:11:27,411 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 17:11:27,412 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 17:11:27,412 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 17:11:27,412 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 17:11:27,413 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 17:11:27,413 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 17:11:27,413 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 17:11:27,413 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 17:11:27,414 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 17:11:27,414 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 17:11:27,647 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 17:11:27,647 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 17:11:27,676 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 17:11:27,676 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 17:11:27,684 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 17:11:27,685 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 17:11:27,685 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 17:11:27,685 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 17:11:27,685 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 17:11:27,686 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 17:11:27,686 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 273 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-09-20 17:11:27,697] [main] java.version = 1.8.0_342 [testng] 17:11:27,702 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 17:11:27,702 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:11:27,752 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-20_17-11-27.log] [testng] 17:11:27,753 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-09-20 17:11:27,755] [main] testng.directory = /data [testng] [2024-09-20 17:11:27,756] [main] testng.configDirectory = /config [testng] [2024-09-20 17:11:27,769] [main] testng.multiplier = 1.0 [testng] [2024-09-20 17:11:27,769] [main] testng.in-memory = false [testng] [2024-09-20 17:11:27,770] [main] testng.allow-missing = false [testng] [2024-09-20 17:11:27,770] [main] user.language = en [testng] [2024-09-20 17:11:27,770] [main] user.country = ${user.country} [testng] [2024-09-20 17:11:27,770] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-09-20 17:11:40,078] [main] ---------------------------------------- [testng] [2024-09-20 17:11:40,079] [main] Total files: 791 [testng] [2024-09-20 17:11:40,079] [main] Scan time: 12.308 s (15 ms/file) [testng] [2024-09-20 17:11:40,079] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-09-20 17:17:19,760] [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] 17:17:19,760 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 17:17:19,760 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:17:19,761 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-09-20_17-17-19.log] [testng] 17:17:19,761 |-INFO in ch.qos.logback.core.sift.SiftProcessor@429ca15 - End of configuration. [testng] [2024-09-20 17:17:19,827] [pool-1-thread-12] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] 17:17:19,827 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 17:17:19,827 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:17:19,828 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-09-20_17-17-19.log] [testng] 17:17:19,828 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e78cfd7 - End of configuration. [testng] [2024-09-20 17:17:19,864] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex: [testng] 17:17:19,864 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 17:17:19,864 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:17:19,865 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-09-20_17-17-19.log] [testng] 17:17:19,866 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e4b6e3b - End of configuration. [testng] [2024-09-20 17:17:19,901] [pool-1-thread-10] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] 17:17:19,901 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 17:17:19,901 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:17:19,902 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-09-20_17-17-19.log] [testng] 17:17:19,902 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c7c0fb6 - End of configuration. [testng] [2024-09-20 17:17:20,389] [pool-1-thread-9] Initializing /data/tamjid/006004000.flex: [testng] 17:17:20,389 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 17:17:20,389 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:17:20,390 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-09-20_17-17-20.log] [testng] 17:17:20,390 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a9b730 - End of configuration. [testng] [2024-09-20 17:17:20,411] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_03(2007-12-14_10-50-56)/004006000.flex: [testng] 17:17:20,412 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 17:17:20,412 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:17:20,412 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-09-20_17-17-20.log] [testng] 17:17:20,412 |-INFO in ch.qos.logback.core.sift.SiftProcessor@77896d39 - End of configuration. [testng] [2024-09-20 17:17:20,441] [pool-1-thread-7] Initializing /data/qa-18096/002003001.flex: [testng] 17:17:20,441 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 17:17:20,441 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:17:20,441 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-09-20_17-17-20.log] [testng] 17:17:20,442 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c94af3a - End of configuration. [testng] [2024-09-20 17:17:20,478] [pool-1-thread-6] Initializing /data/tony/003003000.tiff: [testng] 17:17:20,478 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 17:17:20,478 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:17:20,479 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-09-20_17-17-20.log] [testng] 17:17:20,479 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7729d91c - End of configuration. [testng] [2024-09-20 17:17:20,559] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] 17:17:20,559 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 17:17:20,559 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:17:20,560 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-09-20_17-17-20.log] [testng] 17:17:20,561 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4bd23c4c - End of configuration. [testng] [2024-09-20 17:17:20,963] [pool-1-thread-4] Initializing /data/anatole/001004000.flex: [testng] 17:17:20,963 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 17:17:20,963 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:17:20,964 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-09-20_17-17-20.log] [testng] 17:17:20,964 |-INFO in ch.qos.logback.core.sift.SiftProcessor@285f6103 - End of configuration. [testng] [2024-09-20 17:17:21,026] [pool-1-thread-3] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] 17:17:21,026 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 17:17:21,026 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:17:21,026 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-09-20_17-17-21.log] [testng] 17:17:21,027 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1081d727 - End of configuration. [testng] [2024-09-20 17:17:21,416] [pool-1-thread-2] Initializing /data/tony/003008000.flex: [testng] 17:17:21,416 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 17:17:21,416 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:17:21,416 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-09-20_17-17-21.log] [testng] 17:17:21,417 |-INFO in ch.qos.logback.core.sift.SiftProcessor@566e0247 - End of configuration. [testng] [2024-09-20 17:17:23,074] [pool-1-thread-12] Initializing /data/stephane/002007000.flex: [testng] [2024-09-20 17:17:23,103] [pool-1-thread-9] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex: [testng] [2024-09-20 17:17:23,137] [pool-1-thread-7] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex: [testng] [2024-09-20 17:17:23,180] [pool-1-thread-6] Initializing /data/qa-18096/002002001.flex: [testng] [2024-09-20 17:17:23,432] [pool-1-thread-1] Initializing /data/tony/001014000 - from flex.tif: [testng] [2024-09-20 17:17:23,482] [pool-1-thread-8] Initializing /data/achim/003003000.flex: [testng] [2024-09-20 17:17:23,665] [pool-1-thread-11] Initializing /data/manuel/003003001.flex: [testng] [2024-09-20 17:17:24,110] [pool-1-thread-6] Initializing /data/ghislain/test.flex: [testng] [2024-09-20 17:17:24,284] [pool-1-thread-1] Initializing /data/stephane/006013000.flex: [testng] [2024-09-20 17:17:24,544] [pool-1-thread-12] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2024-09-20 17:17:24,872] [pool-1-thread-8] Initializing /data/qa-7469/002002.flex: [testng] [2024-09-20 17:17:24,913] [pool-1-thread-9] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] [2024-09-20 17:17:25,398] [pool-1-thread-6] Initializing /data/tony/test1.flex: [testng] [2024-09-20 17:17:26,015] [pool-1-thread-6] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex: [testng] [2024-09-20 17:17:26,103] [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] [2024-09-20 17:17:26,337] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex: [testng] [2024-09-20 17:17:26,741] [pool-1-thread-2] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2024-09-20 17:17:26,998] [pool-1-thread-7] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] [2024-09-20 17:17:27,770] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex: [testng] [2024-09-20 17:17:27,825] [pool-1-thread-6] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2024-09-20 17:17:29,211] [pool-1-thread-2] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] [2024-09-20 17:17:29,767] [pool-1-thread-4] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2024-09-20 17:17:30,206] [pool-1-thread-1] Initializing /data/tamjid/006005000.flex: [testng] [2024-09-20 17:17:30,645] [pool-1-thread-1] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2024-09-20 17:17:31,254] [pool-1-thread-2] Initializing /data/qa-17190/002002011.flex: [testng] [2024-09-20 17:17:31,778] [pool-1-thread-11] Initializing /data/tamjid/006003000.flex: [testng] [2024-09-20 17:17:31,823] [pool-1-thread-2] Initializing /data/qa-2983/004007000.flex: [testng] [2024-09-20 17:17:32,315] [pool-1-thread-11] Initializing /data/tony/001001000_objects.flex: [testng] [2024-09-20 17:17:32,968] [pool-1-thread-11] Initializing /data/tony/015002000.tiff: [testng] [2024-09-20 17:17:33,060] [pool-1-thread-2] 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: 9 minutes 19 seconds Finished: SUCCESS