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Started by upstream project "BIOFORMATS-test-repo" build number 134 originally caused by: Started by upstream project "Trigger" build number 154 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4 [BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins2544587587090086514.sh + '[' flex = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_21022_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] 01:32:18,698 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:32:18,700 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 01:32:18,700 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:32:18,701 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:32:18,701 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:32:18,702 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:32:18,702 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:32:18,702 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:32:18,702 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:32:18,703 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:32:18,703 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:32:18,704 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:32:18,874 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:32:18,874 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:32:18,900 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:32:18,900 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:32:18,907 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:32:18,907 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:32:18,907 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:32:18,907 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:32:18,908 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 01:32:18,908 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 01:32:18,909 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 206 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-27 01:32:18,919] [main] java.version = 11.0.16 [testng] 01:32:18,923 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:32:18,923 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:32:18,969 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-27_01-32-18.log] [testng] 01:32:18,971 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-07-27 01:32:18,974] [main] testng.directory = /data [testng] [2024-07-27 01:32:18,974] [main] testng.configDirectory = /config [testng] [2024-07-27 01:32:18,985] [main] testng.multiplier = 1.0 [testng] [2024-07-27 01:32:18,987] [main] testng.in-memory = false [testng] [2024-07-27 01:32:18,987] [main] testng.allow-missing = false [testng] [2024-07-27 01:32:18,987] [main] user.language = en [testng] [2024-07-27 01:32:18,987] [main] user.country = ${user.country} [testng] [2024-07-27 01:32:18,987] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-07-27 01:32:33,202] [main] ---------------------------------------- [testng] [2024-07-27 01:32:33,202] [main] Total files: 791 [testng] [2024-07-27 01:32:33,203] [main] Scan time: 14.215 s (17 ms/file) [testng] [2024-07-27 01:32:33,203] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-27 01:38:10,576] [pool-1-thread-1] Initializing /data/qa-18096/002003001.flex: [testng] 01:38:10,577 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:38:10,577 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:10,579 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-27_01-38-10.log] [testng] 01:38:10,580 |-INFO in ch.qos.logback.core.sift.SiftProcessor@61d51a7 - End of configuration. [testng] [2024-07-27 01:38:10,650] [pool-1-thread-12] Initializing /data/tony/003003000.tiff: [testng] 01:38:10,650 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:38:10,650 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:10,651 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-27_01-38-10.log] [testng] 01:38:10,652 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6976a632 - End of configuration. [testng] [2024-07-27 01:38:10,769] [pool-1-thread-11] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] 01:38:10,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:38:10,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:10,770 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-27_01-38-10.log] [testng] 01:38:10,771 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2aea48b7 - End of configuration. [testng] [2024-07-27 01:38:11,426] [pool-1-thread-10] Initializing /data/achim/003003000.flex: [testng] 01:38:11,427 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:38:11,427 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:11,427 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-27_01-38-11.log] [testng] 01:38:11,428 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3bce6f07 - End of configuration. [testng] [2024-07-27 01:38:11,725] [pool-1-thread-9] Initializing /data/manuel/003003001.flex: [testng] 01:38:11,726 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:38:11,726 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:11,726 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-27_01-38-11.log] [testng] 01:38:11,727 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d003eef - End of configuration. [testng] [2024-07-27 01:38:11,826] [pool-1-thread-8] Initializing /data/tamjid/006003000.flex: [testng] 01:38:11,826 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:38:11,826 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:11,827 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-27_01-38-11.log] [testng] 01:38:11,827 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27efc7a3 - End of configuration. [testng] [2024-07-27 01:38:11,852] [pool-1-thread-7] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex: [testng] 01:38:11,852 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:38:11,852 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:11,852 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-27_01-38-11.log] [testng] 01:38:11,853 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4be9dc60 - End of configuration. [testng] [2024-07-27 01:38:11,896] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] 01:38:11,896 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:38:11,896 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:11,897 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-27_01-38-11.log] [testng] 01:38:11,897 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d1477a8 - End of configuration. [testng] [2024-07-27 01:38:12,378] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] 01:38:12,378 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:38:12,378 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:12,379 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-27_01-38-12.log] [testng] 01:38:12,379 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a7aea49 - End of configuration. [testng] [2024-07-27 01:38:12,853] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex: [testng] 01:38:12,853 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:38:12,853 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:12,854 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-27_01-38-12.log] [testng] 01:38:12,854 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4353f70d - End of configuration. [testng] [2024-07-27 01:38:12,887] [pool-1-thread-3] Initializing /data/tony/003008000.flex: [testng] 01:38:12,887 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:38:12,887 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:12,888 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-27_01-38-12.log] [testng] 01:38:12,888 |-INFO in ch.qos.logback.core.sift.SiftProcessor@26721ea0 - End of configuration. [testng] [2024-07-27 01:38:12,946] [pool-1-thread-2] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] 01:38:12,946 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:38:12,946 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:12,947 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-27_01-38-12.log] [testng] 01:38:12,947 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3848bc75 - End of configuration. [testng] [2024-07-27 01:38:15,214] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex: [testng] [2024-07-27 01:38:15,274] [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] [2024-07-27 01:38:15,320] [pool-1-thread-10] Initializing /data/tony/001014000 - from flex.tif: [testng] [2024-07-27 01:38:15,376] [pool-1-thread-7] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex: [testng] [2024-07-27 01:38:15,525] [pool-1-thread-12] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] [2024-07-27 01:38:16,157] [pool-1-thread-4] Initializing /data/tony/test.tiff: [testng] [2024-07-27 01:38:16,393] [pool-1-thread-9] Initializing /data/qa-17190/002002011.flex: [testng] [2024-07-27 01:38:17,046] [pool-1-thread-10] Initializing /data/tony/015002000.tiff: [testng] [2024-07-27 01:38:17,137] [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] [2024-07-27 01:38:17,222] [pool-1-thread-4] Initializing /data/qa-18096/002002001.flex: [testng] [2024-07-27 01:38:17,564] [pool-1-thread-7] Initializing /data/stephane/006013000.flex: [testng] [2024-07-27 01:38:18,068] [pool-1-thread-4] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2024-07-27 01:38:18,138] [pool-1-thread-10] Initializing /data/ghislain/test.flex: [testng] [2024-07-27 01:38:18,553] [pool-1-thread-9] Initializing /data/tamjid/006004000.flex: [testng] [2024-07-27 01:38:19,168] [pool-1-thread-10] Initializing /data/tamjid/006005000.flex: [testng] [2024-07-27 01:38:19,243] [pool-1-thread-9] Initializing /data/qa-2983/004007000.flex: [testng] [2024-07-27 01:38:19,350] [pool-1-thread-3] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] [2024-07-27 01:38:19,910] [pool-1-thread-1] Initializing /data/tony/test1.flex: [testng] [2024-07-27 01:38:20,055] [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] [2024-07-27 01:38:20,090] [pool-1-thread-3] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2024-07-27 01:38:20,833] [pool-1-thread-4] Initializing /data/stephane/002007000.flex: [testng] [2024-07-27 01:38:21,123] [pool-1-thread-9] Initializing /data/anatole/001004000.flex: [testng] [2024-07-27 01:38:21,241] [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] [2024-07-27 01:38:21,409] [pool-1-thread-8] Initializing /data/qa-7469/002002.flex: [testng] [2024-07-27 01:38:21,965] [pool-1-thread-10] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2024-07-27 01:38:22,444] [pool-1-thread-4] Initializing /data/tony/001001000_objects.flex: [testng] [2024-07-27 01:38:22,503] [pool-1-thread-8] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2024-07-27 01:38:23,327] [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] [2024-07-27 01:38:23,589] [pool-1-thread-4] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2024-07-27 01:38:23,875] [pool-1-thread-7] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex: [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 16 seconds Finished: SUCCESS