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Started by upstream project "BIOFORMATS-test-repo" build number 357 originally caused by: Started by upstream project "Trigger" build number 383 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@6 [BIOFORMATS-test-folder@6] $ /bin/bash -xe /tmp/jenkins14820904439953718061.sh + '[' flex = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_56865_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] 00:50:57,597 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 00:50:57,599 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - No custom configurators were discovered as a service. [testng] 00:50:57,599 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:50:57,600 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:50:57,600 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:50:57,601 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:50:57,601 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:50:57,601 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:50:57,602 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:50:57,602 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:50:57,602 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:50:57,603 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:50:57,780 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:50:57,780 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:50:57,803 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:50:57,804 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:50:57,809 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:50:57,809 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:50:57,810 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:50:57,810 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:50:57,810 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@65c7a252 - End of configuration. [testng] 00:50:57,811 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@38cee291 - Registering current configuration as safe fallback point [testng] 00:50:57,811 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 209 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-02-25 00:50:57,821] [main] java.version = 11.0.16 [testng] 00:50:57,824 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:50:57,824 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:57,869 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-02-25_00-50-57.log] [testng] 00:50:57,870 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13d73f29 - End of configuration. [testng] [2025-02-25 00:50:57,873] [main] testng.directory = /data [testng] [2025-02-25 00:50:57,873] [main] testng.configDirectory = /config [testng] [2025-02-25 00:50:57,883] [main] testng.multiplier = 1.0 [testng] [2025-02-25 00:50:57,885] [main] testng.in-memory = false [testng] [2025-02-25 00:50:57,885] [main] testng.allow-missing = false [testng] [2025-02-25 00:50:57,885] [main] user.language = en [testng] [2025-02-25 00:50:57,885] [main] user.country = ${user.country} [testng] [2025-02-25 00:50:57,885] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-02-25 00:51:46,439] [main] ---------------------------------------- [testng] [2025-02-25 00:51:46,439] [main] Total files: 791 [testng] [2025-02-25 00:51:46,439] [main] Scan time: 48.554 s (61 ms/file) [testng] [2025-02-25 00:51:46,439] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-02-25 00:56:58,830] [pool-1-thread-1] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] 00:56:58,830 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:56:58,831 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:56:58,833 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-02-25_00-56-58.log] [testng] 00:56:58,833 |-INFO in ch.qos.logback.core.sift.SiftProcessor@11cbdcc8 - End of configuration. [testng] [2025-02-25 00:57:03,374] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_03(2007-12-14_10-50-56)/004006000.flex: [testng] 00:57:03,374 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:57:03,374 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:03,376 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-02-25_00-57-03.log] [testng] 00:57:03,376 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ded2728 - End of configuration. [testng] [2025-02-25 00:57:04,044] [pool-1-thread-11] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] 00:57:04,044 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:57:04,044 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:04,044 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-02-25_00-57-04.log] [testng] 00:57:04,045 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1da02012 - End of configuration. [testng] [2025-02-25 00:57:05,431] [pool-1-thread-10] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] 00:57:05,431 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:57:05,431 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:05,431 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-02-25_00-57-05.log] [testng] 00:57:05,432 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36147b69 - End of configuration. [testng] [2025-02-25 00:57:06,075] [pool-1-thread-9] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] 00:57:06,075 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:57:06,075 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:06,076 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-02-25_00-57-06.log] [testng] 00:57:06,076 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36068c5c - End of configuration. [testng] [2025-02-25 00:57:06,812] [pool-1-thread-8] Initializing /data/qa-7469/002002.flex: [testng] 00:57:06,812 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:57:06,812 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:06,813 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-02-25_00-57-06.log] [testng] 00:57:06,813 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37723653 - End of configuration. [testng] [2025-02-25 00:57:07,435] [pool-1-thread-7] Initializing /data/ghislain/test.flex: [testng] 00:57:07,435 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:57:07,435 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:07,436 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-02-25_00-57-07.log] [testng] 00:57:07,437 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a4dce8d - End of configuration. [testng] [2025-02-25 00:57:08,064] [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] 00:57:08,064 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:57:08,064 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:08,065 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-02-25_00-57-08.log] [testng] 00:57:08,065 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40c8e5dc - End of configuration. [testng] [2025-02-25 00:57:08,756] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] 00:57:08,756 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:57:08,756 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:08,757 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-02-25_00-57-08.log] [testng] 00:57:08,757 |-INFO in ch.qos.logback.core.sift.SiftProcessor@478f94d6 - End of configuration. [testng] [2025-02-25 00:57:14,923] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex: [testng] 00:57:14,923 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:57:14,923 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:14,924 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-02-25_00-57-14.log] [testng] 00:57:14,924 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d98d2e0 - End of configuration. [testng] [2025-02-25 00:57:15,687] [pool-1-thread-3] Initializing /data/tony/001001000_objects.flex: [testng] 00:57:15,687 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:57:15,687 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:15,688 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-02-25_00-57-15.log] [testng] 00:57:15,688 |-INFO in ch.qos.logback.core.sift.SiftProcessor@26081ae1 - End of configuration. [testng] [2025-02-25 00:57:16,489] [pool-1-thread-2] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] 00:57:16,489 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:57:16,489 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:16,489 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-02-25_00-57-16.log] [testng] 00:57:16,490 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3eb62e83 - End of configuration. [testng] [2025-02-25 00:57:34,302] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex: [testng] [2025-02-25 00:57:35,663] [pool-1-thread-8] Initializing /data/tamjid/006005000.flex: [testng] [2025-02-25 00:57:36,766] [pool-1-thread-10] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2025-02-25 00:57:38,057] [pool-1-thread-3] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2025-02-25 00:57:45,355] [pool-1-thread-7] Initializing /data/tony/003003000.tiff: [testng] [2025-02-25 00:57:48,358] [pool-1-thread-12] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2025-02-25 00:57:54,772] [pool-1-thread-4] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] [2025-02-25 00:58:01,725] [pool-1-thread-9] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex: [testng] [2025-02-25 00:58:02,686] [pool-1-thread-6] Initializing /data/tony/001014000 - from flex.tif: [testng] [2025-02-25 00:58:11,282] [pool-1-thread-8] Initializing /data/qa-2983/004007000.flex: [testng] [2025-02-25 00:58:13,504] [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] [2025-02-25 00:58:16,025] [pool-1-thread-6] Initializing /data/anatole/001004000.flex: [testng] [2025-02-25 00:58:20,457] [pool-1-thread-9] Initializing /data/tony/test1.flex: [testng] [2025-02-25 00:58:24,381] [pool-1-thread-8] Initializing /data/stephane/002007000.flex: [testng] [2025-02-25 00:58:25,193] [pool-1-thread-11] Initializing /data/stephane/006013000.flex: [testng] [2025-02-25 00:58:31,769] [pool-1-thread-9] Initializing /data/qa-17190/002002011.flex: [testng] [2025-02-25 00:58:36,377] [pool-1-thread-8] Initializing /data/tamjid/006003000.flex: [testng] [2025-02-25 00:58:42,609] [pool-1-thread-9] Initializing /data/tony/003008000.flex: [testng] [2025-02-25 00:58:43,474] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex: [testng] [2025-02-25 00:58:48,080] [pool-1-thread-8] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] [2025-02-25 00:58:56,825] [pool-1-thread-6] Initializing /data/tony/015002000.tiff: [testng] [2025-02-25 00:59:06,574] [pool-1-thread-11] Initializing /data/qa-18096/002003001.flex: [testng] [2025-02-25 00:59:07,729] [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] [2025-02-25 00:59:08,948] [pool-1-thread-6] Initializing /data/qa-18096/002002001.flex: [testng] [2025-02-25 00:59:10,073] [pool-1-thread-9] Initializing /data/achim/003003000.flex: [testng] [2025-02-25 00:59:19,486] [pool-1-thread-11] Initializing /data/tamjid/006004000.flex: [testng] [2025-02-25 00:59:22,213] [pool-1-thread-6] Initializing /data/manuel/003003001.flex: [testng] [2025-02-25 00:59:28,632] [pool-1-thread-10] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex: [testng] [2025-02-25 00:59:30,638] [pool-1-thread-9] Initializing /data/tony/test.tiff: [testng] [2025-02-25 00:59:32,561] [pool-1-thread-11] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.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 38 seconds Finished: SUCCESS