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Started by upstream project "BIOFORMATS-test-repo" build number 274 originally caused by: Started by upstream project "Trigger" build number 295 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/jenkins3648533190637370480.sh + '[' flex = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_43180_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] 1 warning test-automated: [testng] WARNING: An illegal reflective access operation has occurred [testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket [testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener [testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [testng] WARNING: All illegal access operations will be denied in a future release [testng] File leak detector installed [testng] 00:48:57,196 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:48:57,198 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 00:48:57,198 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:48:57,199 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:48:57,200 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:48:57,200 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:48:57,200 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:48:57,200 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:48:57,201 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:48:57,201 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:48:57,202 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:48:57,202 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:48:57,379 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:48:57,380 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:48:57,406 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:48:57,406 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:48:57,413 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:48:57,414 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:48:57,414 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:48:57,414 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:48:57,414 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 00:48:57,415 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 00:48:57,415 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 214 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-30 00:48:57,427] [main] java.version = 11.0.16 [testng] 00:48:57,430 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:48:57,430 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:48:57,479 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-30_00-48-57.log] [testng] 00:48:57,481 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-11-30 00:48:57,483] [main] testng.directory = /data [testng] [2024-11-30 00:48:57,483] [main] testng.configDirectory = /config [testng] [2024-11-30 00:48:57,493] [main] testng.multiplier = 1.0 [testng] [2024-11-30 00:48:57,495] [main] testng.in-memory = false [testng] [2024-11-30 00:48:57,495] [main] testng.allow-missing = false [testng] [2024-11-30 00:48:57,495] [main] user.language = en [testng] [2024-11-30 00:48:57,495] [main] user.country = ${user.country} [testng] [2024-11-30 00:48:57,495] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-30 00:49:49,074] [main] ---------------------------------------- [testng] [2024-11-30 00:49:49,074] [main] Total files: 791 [testng] [2024-11-30 00:49:49,074] [main] Scan time: 51.578 s (65 ms/file) [testng] [2024-11-30 00:49:49,074] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-30 00:54:19,189] [pool-1-thread-1] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] 00:54:19,190 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:54:19,190 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:54:19,192 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-30_00-54-19.log] [testng] 00:54:19,192 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ac8b336 - End of configuration. [testng] [2024-11-30 00:54:19,762] [pool-1-thread-12] Initializing /data/qa-18096/002003001.flex: [testng] 00:54:19,763 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:54:19,763 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:54:19,764 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-30_00-54-19.log] [testng] 00:54:19,764 |-INFO in ch.qos.logback.core.sift.SiftProcessor@182bcf70 - End of configuration. [testng] [2024-11-30 00:54:20,362] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex: [testng] 00:54:20,363 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:54:20,363 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:54:20,364 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-30_00-54-20.log] [testng] 00:54:20,364 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2cbea213 - End of configuration. [testng] [2024-11-30 00:54:20,936] [pool-1-thread-10] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex: [testng] 00:54:20,937 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:54:20,937 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:54:20,939 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-30_00-54-20.log] [testng] 00:54:20,939 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a0cd58 - End of configuration. [testng] [2024-11-30 00:54:21,616] [pool-1-thread-9] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] 00:54:21,617 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:54:21,617 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:54:21,617 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-30_00-54-21.log] [testng] 00:54:21,618 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2c9e8d7d - End of configuration. [testng] [2024-11-30 00:54:26,674] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex: [testng] 00:54:26,675 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:54:26,675 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:54:26,675 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-30_00-54-26.log] [testng] 00:54:26,676 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e59fa94 - End of configuration. [testng] [2024-11-30 00:54:27,527] [pool-1-thread-7] Initializing /data/tony/003008000.flex: [testng] 00:54:27,527 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:54:27,528 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:54:27,528 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-30_00-54-27.log] [testng] 00:54:27,528 |-INFO in ch.qos.logback.core.sift.SiftProcessor@26ec8396 - End of configuration. [testng] [2024-11-30 00:54:28,304] [pool-1-thread-6] Initializing /data/tony/003003000.tiff: [testng] 00:54:28,304 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:54:28,304 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:54:28,305 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-30_00-54-28.log] [testng] 00:54:28,305 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f9cd18 - End of configuration. [testng] [2024-11-30 00:54:29,824] [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] 00:54:29,824 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:54:29,824 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:54:29,824 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-30_00-54-29.log] [testng] 00:54:29,825 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a01bf0c - End of configuration. [testng] [2024-11-30 00:54:30,566] [pool-1-thread-4] Initializing /data/qa-2983/004007000.flex: [testng] 00:54:30,566 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:54:30,566 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:54:30,566 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-30_00-54-30.log] [testng] 00:54:30,567 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c696210 - End of configuration. [testng] [2024-11-30 00:54:31,273] [pool-1-thread-3] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex: [testng] 00:54:31,273 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:54:31,273 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:54:31,274 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-30_00-54-31.log] [testng] 00:54:31,274 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6b9460ea - End of configuration. [testng] [2024-11-30 00:54:32,368] [pool-1-thread-2] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] 00:54:32,368 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:54:32,368 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:54:32,369 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-30_00-54-32.log] [testng] 00:54:32,369 |-INFO in ch.qos.logback.core.sift.SiftProcessor@15394219 - End of configuration. [testng] [2024-11-30 00:54:43,465] [pool-1-thread-2] Initializing /data/anatole/001004000.flex: [testng] [2024-11-30 00:54:44,679] [pool-1-thread-6] Initializing /data/qa-18096/002002001.flex: [testng] [2024-11-30 00:54:45,573] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex: [testng] [2024-11-30 00:54:46,311] [pool-1-thread-4] Initializing /data/tony/test1.flex: [testng] [2024-11-30 00:54:46,995] [pool-1-thread-1] Initializing /data/stephane/002007000.flex: [testng] [2024-11-30 00:54:51,463] [pool-1-thread-5] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] [2024-11-30 00:54:52,226] [pool-1-thread-11] Initializing /data/qa-7469/002002.flex: [testng] [2024-11-30 00:54:52,985] [pool-1-thread-7] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2024-11-30 00:54:54,472] [pool-1-thread-8] Initializing /data/tony/001014000 - from flex.tif: [testng] [2024-11-30 00:54:59,849] [pool-1-thread-6] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex: [testng] [2024-11-30 00:55:00,619] [pool-1-thread-4] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2024-11-30 00:55:07,436] [pool-1-thread-1] Initializing /data/ghislain/test.flex: [testng] [2024-11-30 00:55:08,297] [pool-1-thread-12] Initializing /data/tamjid/006005000.flex: [testng] [2024-11-30 00:55:10,102] [pool-1-thread-10] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2024-11-30 00:55:17,444] [pool-1-thread-11] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] [2024-11-30 00:55:24,147] [pool-1-thread-8] Initializing /data/manuel/003003001.flex: [testng] [2024-11-30 00:55:26,321] [pool-1-thread-5] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2024-11-30 00:55:37,313] [pool-1-thread-12] Initializing /data/stephane/006013000.flex: [testng] [2024-11-30 00:55:38,224] [pool-1-thread-6] Initializing /data/tony/015002000.tiff: [testng] [2024-11-30 00:55:40,102] [pool-1-thread-1] Initializing /data/tony/test.tiff: [testng] [2024-11-30 00:55:41,816] [pool-1-thread-2] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2024-11-30 00:55:42,842] [pool-1-thread-3] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex: [testng] [2024-11-30 00:55:48,447] [pool-1-thread-8] Initializing /data/tamjid/006003000.flex: [testng] [2024-11-30 00:55:53,652] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] [2024-11-30 00:56:00,612] [pool-1-thread-1] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] [2024-11-30 00:56:13,427] [pool-1-thread-3] Initializing /data/qa-17190/002002011.flex: [testng] [2024-11-30 00:56:14,390] [pool-1-thread-8] Initializing /data/tony/001001000_objects.flex: [testng] [2024-11-30 00:56:15,461] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex: [testng] [2024-11-30 00:56:22,313] [pool-1-thread-7] Initializing /data/achim/003003000.flex: [testng] [2024-11-30 00:56:27,306] [pool-1-thread-3] Initializing /data/tamjid/006004000.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 13 seconds Finished: SUCCESS