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Started by upstream project "BIOFORMATS-test-repo" build number 221 originally caused by: Started by upstream project "Trigger" build number 248 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins5373495968330500846.sh + '[' flex = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_35081_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] 03:06:42,104 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:06:42,106 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 03:06:42,106 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:06:42,107 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:06:42,108 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:06:42,108 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:06:42,108 |-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] 03:06:42,108 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:06:42,109 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:06:42,109 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:06:42,110 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:06:42,110 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:06:42,296 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:06:42,296 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:06:42,320 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:06:42,320 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:06:42,326 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:06:42,326 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:06:42,326 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:06:42,327 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:06:42,327 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 03:06:42,327 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 03:06:42,327 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 218 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-15 03:06:42,337] [main] java.version = 11.0.16 [testng] 03:06:42,340 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:06:42,340 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:06:42,384 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-15_03-06-42.log] [testng] 03:06:42,385 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-10-15 03:06:42,387] [main] testng.directory = /data [testng] [2024-10-15 03:06:42,387] [main] testng.configDirectory = /config [testng] [2024-10-15 03:06:42,397] [main] testng.multiplier = 1.0 [testng] [2024-10-15 03:06:42,399] [main] testng.in-memory = false [testng] [2024-10-15 03:06:42,399] [main] testng.allow-missing = false [testng] [2024-10-15 03:06:42,399] [main] user.language = en [testng] [2024-10-15 03:06:42,399] [main] user.country = ${user.country} [testng] [2024-10-15 03:06:42,399] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-15 03:17:29,028] [main] ---------------------------------------- [testng] [2024-10-15 03:17:29,028] [main] Total files: 791 [testng] [2024-10-15 03:17:29,029] [main] Scan time: 646.629 s (817 ms/file) [testng] [2024-10-15 03:17:29,029] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-15 03:48:52,000] [pool-1-thread-1] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] 03:48:52,001 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:48:52,001 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:48:52,003 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-15_03-48-52.log] [testng] 03:48:52,003 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f585a76 - End of configuration. [testng] [2024-10-15 03:48:57,094] [pool-1-thread-12] Initializing /data/qa-18096/002003001.flex: [testng] 03:48:57,094 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:48:57,094 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:48:57,095 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-15_03-48-57.log] [testng] 03:48:57,095 |-INFO in ch.qos.logback.core.sift.SiftProcessor@117a9949 - End of configuration. [testng] [2024-10-15 03:49:01,882] [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] 03:49:01,883 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:49:01,883 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:49:01,884 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-15_03-49-01.log] [testng] 03:49:01,884 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4bafd685 - End of configuration. [testng] [2024-10-15 03:49:10,317] [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] 03:49:10,318 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:49:10,318 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:49:10,318 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-15_03-49-10.log] [testng] 03:49:10,319 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4bf0eb93 - End of configuration. [testng] [2024-10-15 03:49:20,005] [pool-1-thread-9] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] 03:49:20,005 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:49:20,005 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:49:20,006 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-15_03-49-20.log] [testng] 03:49:20,006 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2959a7e7 - End of configuration. [testng] [2024-10-15 03:50:23,331] [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] 03:50:23,331 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:50:23,331 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:50:23,332 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-15_03-50-23.log] [testng] 03:50:23,332 |-INFO in ch.qos.logback.core.sift.SiftProcessor@64e02fbd - End of configuration. [testng] [2024-10-15 03:50:32,739] [pool-1-thread-7] Initializing /data/tony/003008000.flex: [testng] 03:50:32,739 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:50:32,739 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:50:32,739 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-15_03-50-32.log] [testng] 03:50:32,740 |-INFO in ch.qos.logback.core.sift.SiftProcessor@790b1f63 - End of configuration. [testng] [2024-10-15 03:50:39,267] [pool-1-thread-6] Initializing /data/tony/003003000.tiff: [testng] 03:50:39,267 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:50:39,267 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:50:39,268 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-15_03-50-39.log] [testng] 03:50:39,268 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4befeeef - End of configuration. [testng] [2024-10-15 03:50:53,064] [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] 03:50:53,064 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:50:53,064 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:50:53,064 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-15_03-50-53.log] [testng] 03:50:53,065 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c481d0e - End of configuration. [testng] [2024-10-15 03:51:01,353] [pool-1-thread-4] Initializing /data/qa-2983/004007000.flex: [testng] 03:51:01,353 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:51:01,353 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:51:01,354 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-15_03-51-01.log] [testng] 03:51:01,354 |-INFO in ch.qos.logback.core.sift.SiftProcessor@31a4cc0f - End of configuration. [testng] [2024-10-15 03:51:07,158] [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] 03:51:07,158 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:51:07,158 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:51:07,159 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-15_03-51-07.log] [testng] 03:51:07,159 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d834852 - End of configuration. [testng] [2024-10-15 03:51:21,797] [pool-1-thread-2] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] 03:51:21,798 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:51:21,798 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:51:21,798 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-15_03-51-21.log] [testng] 03:51:21,798 |-INFO in ch.qos.logback.core.sift.SiftProcessor@33a2874f - End of configuration. [testng] [2024-10-15 03:52:35,050] [pool-1-thread-2] Initializing /data/anatole/001004000.flex: [testng] [2024-10-15 03:52:45,086] [pool-1-thread-4] Initializing /data/qa-18096/002002001.flex: [testng] [2024-10-15 03:52:50,381] [pool-1-thread-6] Initializing /data/tony/test1.flex: [testng] [2024-10-15 03:52:54,969] [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] [2024-10-15 03:53:02,071] [pool-1-thread-12] Initializing /data/stephane/002007000.flex: [testng] [2024-10-15 03:53:11,219] [pool-1-thread-7] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] [2024-10-15 03:53:37,716] [pool-1-thread-5] Initializing /data/qa-7469/002002.flex: [testng] [2024-10-15 03:53:44,682] [pool-1-thread-11] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2024-10-15 03:54:14,044] [pool-1-thread-8] Initializing /data/tony/001014000 - from flex.tif: [testng] [2024-10-15 03:54:34,795] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex: [testng] [2024-10-15 03:54:41,354] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2024-10-15 03:55:25,845] [pool-1-thread-12] Initializing /data/ghislain/test.flex: [testng] [2024-10-15 03:55:41,080] [pool-1-thread-10] Initializing /data/tamjid/006005000.flex: [testng] [2024-10-15 03:55:45,388] [pool-1-thread-1] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2024-10-15 03:56:47,345] [pool-1-thread-7] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] [2024-10-15 03:57:49,963] [pool-1-thread-5] Initializing /data/manuel/003003001.flex: [testng] [2024-10-15 03:57:56,067] [pool-1-thread-8] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2024-10-15 03:59:35,667] [pool-1-thread-3] Initializing /data/stephane/006013000.flex: [testng] [2024-10-15 03:59:43,374] [pool-1-thread-12] Initializing /data/tony/015002000.tiff: [testng] [2024-10-15 04:00:00,204] [pool-1-thread-2] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2024-10-15 04:00:09,045] [pool-1-thread-4] Initializing /data/tony/test.tiff: [testng] [2024-10-15 04:00:24,449] [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] [2024-10-15 04:01:20,347] [pool-1-thread-12] Initializing /data/tamjid/006003000.flex: [testng] [2024-10-15 04:01:41,687] [pool-1-thread-4] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] [2024-10-15 04:02:50,918] [pool-1-thread-3] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] [2024-10-15 04:03:48,740] [pool-1-thread-5] Initializing /data/qa-17190/002002011.flex: [testng] [2024-10-15 04:04:04,993] [pool-1-thread-10] Initializing /data/tony/001001000_objects.flex: [testng] [2024-10-15 04:04:36,301] [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] [2024-10-15 04:05:13,966] [pool-1-thread-5] Initializing /data/achim/003003000.flex: [testng] [2024-10-15 04:05:20,677] [pool-1-thread-11] 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: 96 minutes 44 seconds Finished: SUCCESS