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Started by upstream project "BIOFORMATS-test-repo" build number 6 originally caused by: Started by upstream project "Trigger" build number 9 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins2042487552587501688.sh + '[' flex = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_847_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] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket [testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket [testng] File leak detector installed [testng] 09:53:36,533 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 09:53:36,534 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 09:53:36,534 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 09:53:36,535 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 09:53:36,535 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 09:53:36,536 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 09:53:36,536 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 09:53:36,536 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 09:53:36,536 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 09:53:36,537 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 09:53:36,537 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 09:53:36,537 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 09:53:36,701 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 09:53:36,701 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 09:53:36,723 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 09:53:36,723 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 09:53:36,729 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 09:53:36,729 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 09:53:36,729 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 09:53:36,729 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 09:53:36,729 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 09:53:36,730 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 09:53:36,730 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 194 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-20 09:53:36,740] [main] java.version = 17.0.2 [testng] 09:53:36,743 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 09:53:36,743 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:53:36,784 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-20_09-53-36.log] [testng] 09:53:36,786 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-03-20 09:53:36,788] [main] testng.directory = /data [testng] [2024-03-20 09:53:36,788] [main] testng.configDirectory = /config [testng] [2024-03-20 09:53:36,797] [main] testng.multiplier = 1.0 [testng] [2024-03-20 09:53:36,798] [main] testng.in-memory = false [testng] [2024-03-20 09:53:36,798] [main] testng.allow-missing = false [testng] [2024-03-20 09:53:36,798] [main] user.language = en [testng] [2024-03-20 09:53:36,798] [main] user.country = ${user.country} [testng] [2024-03-20 09:53:36,798] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-03-20 09:53:58,629] [main] ---------------------------------------- [testng] [2024-03-20 09:53:58,629] [main] Total files: 791 [testng] [2024-03-20 09:53:58,629] [main] Scan time: 21.831 s (27 ms/file) [testng] [2024-03-20 09:53:58,629] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-20 10:00:17,332] [pool-1-thread-1] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] 10:00:17,333 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 10:00:17,333 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:00:17,334 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-20_10-00-17.log] [testng] 10:00:17,334 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6500070 - End of configuration. [testng] [2024-03-20 10:00:17,526] [pool-1-thread-12] Initializing /data/qa-18096/002002001.flex: [testng] 10:00:17,527 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 10:00:17,527 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:00:17,528 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-20_10-00-17.log] [testng] 10:00:17,528 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21d85f67 - End of configuration. [testng] [2024-03-20 10:00:17,722] [pool-1-thread-11] Initializing /data/anatole/001004000.flex: [testng] 10:00:17,722 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 10:00:17,722 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:00:17,723 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-20_10-00-17.log] [testng] 10:00:17,723 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f042255 - End of configuration. [testng] [2024-03-20 10:00:17,975] [pool-1-thread-10] Initializing /data/qa-7469/002002.flex: [testng] 10:00:17,976 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 10:00:17,976 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:00:17,977 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-20_10-00-17.log] [testng] 10:00:17,977 |-INFO in ch.qos.logback.core.sift.SiftProcessor@85ea298 - End of configuration. [testng] [2024-03-20 10:00:18,168] [pool-1-thread-9] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] 10:00:18,169 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 10:00:18,169 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:00:18,170 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-20_10-00-18.log] [testng] 10:00:18,170 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e8cafe4 - End of configuration. [testng] [2024-03-20 10:00:19,746] [pool-1-thread-8] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] 10:00:19,746 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 10:00:19,746 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:00:19,747 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-20_10-00-19.log] [testng] 10:00:19,747 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b531779 - End of configuration. [testng] [2024-03-20 10:00:21,833] [pool-1-thread-7] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] 10:00:21,833 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 10:00:21,833 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:00:21,833 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-20_10-00-21.log] [testng] 10:00:21,834 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e8584b3 - End of configuration. [testng] [2024-03-20 10:00:22,301] [pool-1-thread-6] Initializing /data/tamjid/006003000.flex: [testng] 10:00:22,301 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 10:00:22,301 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:00:22,302 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-20_10-00-22.log] [testng] 10:00:22,307 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40215639 - End of configuration. [testng] [2024-03-20 10:00:22,535] [pool-1-thread-5] Initializing /data/tony/003008000.flex: [testng] 10:00:22,535 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 10:00:22,535 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:00:22,535 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-20_10-00-22.log] [testng] 10:00:22,536 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b74f060 - End of configuration. [testng] [2024-03-20 10:00:22,756] [pool-1-thread-4] Initializing /data/tamjid/006005000.flex: [testng] 10:00:22,757 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 10:00:22,757 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:00:22,757 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-20_10-00-22.log] [testng] 10:00:22,758 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1753cd3f - End of configuration. [testng] [2024-03-20 10:00:23,028] [pool-1-thread-3] Initializing /data/qa-2983/004007000.flex: [testng] 10:00:23,028 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 10:00:23,028 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:00:23,029 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-20_10-00-23.log] [testng] 10:00:23,029 |-INFO in ch.qos.logback.core.sift.SiftProcessor@612dbea7 - End of configuration. [testng] [2024-03-20 10:00:23,288] [pool-1-thread-2] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] 10:00:23,288 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 10:00:23,288 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:00:23,288 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-20_10-00-23.log] [testng] 10:00:23,289 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e943307 - End of configuration. [testng] [2024-03-20 10:00:28,048] [pool-1-thread-7] Initializing /data/tony/015002000.tiff: [testng] [2024-03-20 10:00:28,574] [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] [2024-03-20 10:00:28,881] [pool-1-thread-4] Initializing /data/tony/001014000 - from flex.tif: [testng] [2024-03-20 10:00:29,535] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2024-03-20 10:00:32,309] [pool-1-thread-10] Initializing /data/tony/test.tiff: [testng] [2024-03-20 10:00:33,173] [pool-1-thread-3] Initializing /data/qa-17190/002002011.flex: [testng] [2024-03-20 10:00:34,209] [pool-1-thread-1] Initializing /data/achim/003003000.flex: [testng] [2024-03-20 10:00:37,925] [pool-1-thread-4] Initializing /data/stephane/006013000.flex: [testng] [2024-03-20 10:00:38,429] [pool-1-thread-7] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex: [testng] [2024-03-20 10:00:38,912] [pool-1-thread-3] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] [2024-03-20 10:00:42,313] [pool-1-thread-10] Initializing /data/tony/003003000.tiff: [testng] [2024-03-20 10:00:43,178] [pool-1-thread-5] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex: [testng] [2024-03-20 10:00:45,590] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex: [testng] [2024-03-20 10:00:47,552] [pool-1-thread-11] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] [2024-03-20 10:00:50,535] [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] [2024-03-20 10:00:51,393] [pool-1-thread-10] Initializing /data/ghislain/test.flex: [testng] [2024-03-20 10:00:54,266] [pool-1-thread-7] Initializing /data/tamjid/006004000.flex: [testng] [2024-03-20 10:00:54,708] [pool-1-thread-4] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] [2024-03-20 10:01:00,867] [pool-1-thread-10] Initializing /data/tony/test1.flex: [testng] [2024-03-20 10:01:02,469] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] [2024-03-20 10:01:02,962] [pool-1-thread-7] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex: [testng] [2024-03-20 10:01:05,955] [pool-1-thread-10] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2024-03-20 10:01:08,624] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex: [testng] [2024-03-20 10:01:11,677] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex: [testng] [2024-03-20 10:01:12,208] [pool-1-thread-7] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2024-03-20 10:01:15,801] [pool-1-thread-5] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex: [testng] [2024-03-20 10:01:20,957] [pool-1-thread-12] Initializing /data/manuel/003003001.flex: [testng] [2024-03-20 10:01:21,210] [pool-1-thread-1] Initializing /data/tony/001001000_objects.flex: [testng] [2024-03-20 10:01:22,714] [pool-1-thread-5] Initializing /data/qa-18096/002003001.flex: [testng] [2024-03-20 10:01:25,628] [pool-1-thread-1] Initializing /data/stephane/002007000.flex: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2226, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 11 minutes 58 seconds Finished: SUCCESS