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Started by upstream project "BIOFORMATS-test-repo" build number 314 originally caused by: Started by upstream project "Trigger" build number 336 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/jenkins4870121962923237804.sh + '[' flex = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_49765_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] 01:50:12,288 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:50:12,289 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 01:50:12,289 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:50:12,290 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:50:12,290 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:50:12,291 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:50:12,291 |-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] 01:50:12,291 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:50:12,291 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:50:12,292 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:50:12,292 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:50:12,292 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:50:12,522 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:50:12,523 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:50:12,552 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:50:12,552 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:50:12,561 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:50:12,561 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:50:12,561 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:50:12,562 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:50:12,562 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 01:50:12,563 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 01:50:12,563 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 272 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-01-10 01:50:12,573] [main] java.version = 1.8.0_342 [testng] 01:50:12,576 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:50:12,576 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:50:12,624 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-01-10_01-50-12.log] [testng] 01:50:12,625 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2025-01-10 01:50:12,627] [main] testng.directory = /data [testng] [2025-01-10 01:50:12,628] [main] testng.configDirectory = /config [testng] [2025-01-10 01:50:12,640] [main] testng.multiplier = 1.0 [testng] [2025-01-10 01:50:12,640] [main] testng.in-memory = false [testng] [2025-01-10 01:50:12,640] [main] testng.allow-missing = false [testng] [2025-01-10 01:50:12,640] [main] user.language = en [testng] [2025-01-10 01:50:12,640] [main] user.country = ${user.country} [testng] [2025-01-10 01:50:12,640] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2025-01-10 01:51:09,333] [main] ---------------------------------------- [testng] [2025-01-10 01:51:09,333] [main] Total files: 791 [testng] [2025-01-10 01:51:09,333] [main] Scan time: 56.693 s (71 ms/file) [testng] [2025-01-10 01:51:09,334] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-01-10 01:56:14,575] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex: [testng] 01:56:14,576 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:56:14,576 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:56:14,577 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-01-10_01-56-14.log] [testng] 01:56:14,578 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7051438b - End of configuration. [testng] [2025-01-10 01:56:15,218] [pool-1-thread-12] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] 01:56:15,219 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:56:15,219 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:56:15,219 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-01-10_01-56-15.log] [testng] 01:56:15,220 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3453107a - End of configuration. [testng] [2025-01-10 01:56:16,178] [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] 01:56:16,178 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:56:16,178 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:56:16,179 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-01-10_01-56-16.log] [testng] 01:56:16,180 |-INFO in ch.qos.logback.core.sift.SiftProcessor@432c9143 - End of configuration. [testng] [2025-01-10 01:56:17,111] [pool-1-thread-10] Initializing /data/qa-2983/004007000.flex: [testng] 01:56:17,112 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:56:17,112 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:56:17,112 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-01-10_01-56-17.log] [testng] 01:56:17,113 |-INFO in ch.qos.logback.core.sift.SiftProcessor@24ac5812 - End of configuration. [testng] [2025-01-10 01:56:17,801] [pool-1-thread-9] Initializing /data/ghislain/test.flex: [testng] 01:56:17,801 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:56:17,802 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:56:17,802 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-01-10_01-56-17.log] [testng] 01:56:17,803 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3db61f94 - End of configuration. [testng] [2025-01-10 01:56:18,522] [pool-1-thread-8] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] 01:56:18,522 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:56:18,522 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:56:18,523 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-01-10_01-56-18.log] [testng] 01:56:18,523 |-INFO in ch.qos.logback.core.sift.SiftProcessor@62cb406c - End of configuration. [testng] [2025-01-10 01:56:24,610] [pool-1-thread-7] Initializing /data/tamjid/006004000.flex: [testng] 01:56:24,611 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:56:24,611 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:56:24,611 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-01-10_01-56-24.log] [testng] 01:56:24,612 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ae3a04b - End of configuration. [testng] [2025-01-10 01:56:25,314] [pool-1-thread-6] Initializing /data/manuel/003003001.flex: [testng] 01:56:25,314 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:56:25,314 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:56:25,315 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-01-10_01-56-25.log] [testng] 01:56:25,315 |-INFO in ch.qos.logback.core.sift.SiftProcessor@45bc9904 - End of configuration. [testng] [2025-01-10 01:56:26,107] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] 01:56:26,107 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:56:26,107 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:56:26,107 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-01-10_01-56-26.log] [testng] 01:56:26,108 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7871f655 - End of configuration. [testng] [2025-01-10 01:56:32,431] [pool-1-thread-4] Initializing /data/tony/015002000.tiff: [testng] 01:56:32,432 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:56:32,432 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:56:32,432 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-01-10_01-56-32.log] [testng] 01:56:32,432 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d7fdd8d - End of configuration. [testng] [2025-01-10 01:56:34,393] [pool-1-thread-3] Initializing /data/tamjid/006005000.flex: [testng] 01:56:34,393 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:56:34,393 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:56:34,394 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-01-10_01-56-34.log] [testng] 01:56:34,395 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2732019d - End of configuration. [testng] [2025-01-10 01:56:35,185] [pool-1-thread-2] Initializing /data/tony/003003000.tiff: [testng] 01:56:35,185 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:56:35,185 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:56:35,185 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-01-10_01-56-35.log] [testng] 01:56:35,186 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7d46cb73 - End of configuration. [testng] [2025-01-10 01:56:48,480] [pool-1-thread-4] Initializing /data/stephane/002007000.flex: [testng] [2025-01-10 01:56:49,380] [pool-1-thread-2] Initializing /data/qa-17190/002002011.flex: [testng] [2025-01-10 01:56:50,135] [pool-1-thread-3] Initializing /data/anatole/001004000.flex: [testng] [2025-01-10 01:56:51,288] [pool-1-thread-10] Initializing /data/tony/test1.flex: [testng] [2025-01-10 01:56:52,193] [pool-1-thread-7] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] [2025-01-10 01:56:57,656] [pool-1-thread-9] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_03(2007-12-14_10-50-56)/004006000.flex: [testng] [2025-01-10 01:57:02,604] [pool-1-thread-11] Initializing /data/tamjid/006003000.flex: [testng] [2025-01-10 01:57:07,430] [pool-1-thread-1] Initializing /data/tony/003008000.flex: [testng] [2025-01-10 01:57:09,162] [pool-1-thread-10] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex: [testng] [2025-01-10 01:57:10,203] [pool-1-thread-2] Initializing /data/tony/test.tiff: [testng] [2025-01-10 01:57:11,698] [pool-1-thread-4] Initializing /data/qa-18096/002002001.flex: [testng] [2025-01-10 01:57:12,568] [pool-1-thread-6] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2025-01-10 01:57:22,262] [pool-1-thread-11] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2025-01-10 01:57:23,155] [pool-1-thread-9] Initializing /data/tony/001014000 - from flex.tif: [testng] [2025-01-10 01:57:28,864] [pool-1-thread-2] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex: [testng] [2025-01-10 01:57:30,754] [pool-1-thread-4] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2025-01-10 01:57:36,109] [pool-1-thread-9] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex: [testng] [2025-01-10 01:57:37,169] [pool-1-thread-10] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex: [testng] [2025-01-10 01:57:38,115] [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] [2025-01-10 01:57:39,752] [pool-1-thread-3] Initializing /data/achim/003003000.flex: [testng] [2025-01-10 01:57:40,757] [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] [2025-01-10 01:57:58,301] [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] [2025-01-10 01:57:59,593] [pool-1-thread-11] Initializing /data/qa-7469/002002.flex: [testng] [2025-01-10 01:58:00,620] [pool-1-thread-9] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] [2025-01-10 01:58:12,537] [pool-1-thread-2] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2025-01-10 01:58:21,392] [pool-1-thread-3] Initializing /data/qa-18096/002003001.flex: [testng] [2025-01-10 01:58:22,699] [pool-1-thread-12] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] [2025-01-10 01:58:39,687] [pool-1-thread-11] Initializing /data/stephane/006013000.flex: [testng] [2025-01-10 01:58:42,409] [pool-1-thread-10] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] [2025-01-10 01:58:47,166] [pool-1-thread-3] Initializing /data/tony/001001000_objects.flex: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2226, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 14 minutes 50 seconds Finished: SUCCESS