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Started by upstream project "BIOFORMATS-test-repo" build number 97 originally caused by: Started by upstream project "Trigger" build number 108 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/jenkins13772002045977302212.sh + '[' flex = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_14954_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] 01:31:48,616 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:31:48,617 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 01:31:48,617 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:31:48,618 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:31:48,619 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:31:48,619 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:31:48,619 |-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] 01:31:48,619 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:31:48,619 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:31:48,620 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:31:48,620 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:31:48,620 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:31:48,925 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:31:48,925 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:31:48,984 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:31:48,984 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:31:48,995 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:31:48,995 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:31:48,996 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:31:48,997 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:31:48,997 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 01:31:48,998 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 01:31:48,998 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 379 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-06-19 01:31:49,014] [main] java.version = 17.0.2 [testng] 01:31:49,018 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:31:49,019 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:31:49,172 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-19_01-31-49.log] [testng] 01:31:49,173 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-06-19 01:31:49,175] [main] testng.directory = /data [testng] [2024-06-19 01:31:49,176] [main] testng.configDirectory = /config [testng] [2024-06-19 01:31:49,195] [main] testng.multiplier = 1.0 [testng] [2024-06-19 01:31:49,196] [main] testng.in-memory = false [testng] [2024-06-19 01:31:49,196] [main] testng.allow-missing = false [testng] [2024-06-19 01:31:49,196] [main] user.language = en [testng] [2024-06-19 01:31:49,196] [main] user.country = ${user.country} [testng] [2024-06-19 01:31:49,196] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-06-19 01:32:01,380] [main] ---------------------------------------- [testng] [2024-06-19 01:32:01,380] [main] Total files: 791 [testng] [2024-06-19 01:32:01,380] [main] Scan time: 12.183 s (15 ms/file) [testng] [2024-06-19 01:32:01,381] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-06-19 01:37:37,748] [pool-1-thread-1] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] 01:37:37,749 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:37:37,749 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:37,750 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-19_01-37-37.log] [testng] 01:37:37,751 |-INFO in ch.qos.logback.core.sift.SiftProcessor@549f949b - End of configuration. [testng] [2024-06-19 01:37:37,793] [pool-1-thread-12] Initializing /data/qa-18096/002002001.flex: [testng] 01:37:37,794 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:37:37,794 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:37,795 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-19_01-37-37.log] [testng] 01:37:37,795 |-INFO in ch.qos.logback.core.sift.SiftProcessor@17b15b78 - End of configuration. [testng] [2024-06-19 01:37:37,855] [pool-1-thread-11] Initializing /data/anatole/001004000.flex: [testng] 01:37:37,855 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:37:37,855 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:37,856 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-19_01-37-37.log] [testng] 01:37:37,857 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d2a3847 - End of configuration. [testng] [2024-06-19 01:37:37,944] [pool-1-thread-10] Initializing /data/qa-7469/002002.flex: [testng] 01:37:37,945 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:37:37,945 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:37,946 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-19_01-37-37.log] [testng] 01:37:37,946 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1429c71b - End of configuration. [testng] [2024-06-19 01:37:38,009] [pool-1-thread-9] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] 01:37:38,009 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:37:38,009 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:38,010 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-19_01-37-38.log] [testng] 01:37:38,011 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f690185 - End of configuration. [testng] [2024-06-19 01:37:38,620] [pool-1-thread-8] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] 01:37:38,621 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:37:38,621 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:38,622 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-19_01-37-38.log] [testng] 01:37:38,622 |-INFO in ch.qos.logback.core.sift.SiftProcessor@84bc4d2 - End of configuration. [testng] [2024-06-19 01:37:39,135] [pool-1-thread-7] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] 01:37:39,136 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:37:39,136 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:39,137 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-19_01-37-39.log] [testng] 01:37:39,137 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f042255 - End of configuration. [testng] [2024-06-19 01:37:39,194] [pool-1-thread-6] Initializing /data/tamjid/006003000.flex: [testng] 01:37:39,195 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:37:39,195 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:39,196 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-19_01-37-39.log] [testng] 01:37:39,197 |-INFO in ch.qos.logback.core.sift.SiftProcessor@85ea298 - End of configuration. [testng] [2024-06-19 01:37:39,241] [pool-1-thread-5] Initializing /data/tony/003008000.flex: [testng] 01:37:39,241 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:37:39,241 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:39,242 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-19_01-37-39.log] [testng] 01:37:39,242 |-INFO in ch.qos.logback.core.sift.SiftProcessor@551a3e8a - End of configuration. [testng] [2024-06-19 01:37:39,315] [pool-1-thread-4] Initializing /data/tamjid/006005000.flex: [testng] 01:37:39,315 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:37:39,315 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:39,316 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-19_01-37-39.log] [testng] 01:37:39,316 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a7d87d0 - End of configuration. [testng] [2024-06-19 01:37:39,355] [pool-1-thread-3] Initializing /data/qa-2983/004007000.flex: [testng] 01:37:39,355 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:37:39,355 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:39,357 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-19_01-37-39.log] [testng] 01:37:39,357 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5dc9e566 - End of configuration. [testng] [2024-06-19 01:37:39,454] [pool-1-thread-2] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] 01:37:39,454 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:37:39,455 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:39,455 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-19_01-37-39.log] [testng] 01:37:39,456 |-INFO in ch.qos.logback.core.sift.SiftProcessor@44b7b736 - End of configuration. [testng] [2024-06-19 01:37:41,703] [pool-1-thread-6] Initializing /data/tony/015002000.tiff: [testng] [2024-06-19 01:37:41,763] [pool-1-thread-4] Initializing /data/qa-17190/002002011.flex: [testng] [2024-06-19 01:37:41,804] [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] [2024-06-19 01:37:41,835] [pool-1-thread-12] Initializing /data/tony/001014000 - from flex.tif: [testng] [2024-06-19 01:37:41,901] [pool-1-thread-10] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2024-06-19 01:37:42,361] [pool-1-thread-3] Initializing /data/tony/test.tiff: [testng] [2024-06-19 01:37:43,077] [pool-1-thread-1] Initializing /data/achim/003003000.flex: [testng] [2024-06-19 01:37:43,256] [pool-1-thread-4] Initializing /data/stephane/006013000.flex: [testng] [2024-06-19 01:37:43,320] [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] [2024-06-19 01:37:43,348] [pool-1-thread-3] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] [2024-06-19 01:37:43,932] [pool-1-thread-6] Initializing /data/tony/003003000.tiff: [testng] [2024-06-19 01:37:44,216] [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] [2024-06-19 01:37:44,713] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex: [testng] [2024-06-19 01:37:44,910] [pool-1-thread-12] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] [2024-06-19 01:37:45,371] [pool-1-thread-6] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_03(2007-12-14_10-50-56)/004006000.flex: [testng] [2024-06-19 01:37:45,514] [pool-1-thread-5] Initializing /data/ghislain/test.flex: [testng] [2024-06-19 01:37:46,238] [pool-1-thread-5] Initializing /data/tamjid/006004000.flex: [testng] [2024-06-19 01:37:46,547] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] [2024-06-19 01:37:47,111] [pool-1-thread-5] Initializing /data/tony/test1.flex: [testng] [2024-06-19 01:37:47,189] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] [2024-06-19 01:37:47,548] [pool-1-thread-5] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex: [testng] [2024-06-19 01:37:48,145] [pool-1-thread-4] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2024-06-19 01:37:48,641] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex: [testng] [2024-06-19 01:37:49,006] [pool-1-thread-5] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex: [testng] [2024-06-19 01:37:49,441] [pool-1-thread-7] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2024-06-19 01:37:50,399] [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] [2024-06-19 01:37:51,583] [pool-1-thread-5] Initializing /data/manuel/003003001.flex: [testng] [2024-06-19 01:37:51,781] [pool-1-thread-1] Initializing /data/tony/001001000_objects.flex: [testng] [2024-06-19 01:37:52,353] [pool-1-thread-1] Initializing /data/qa-18096/002003001.flex: [testng] [2024-06-19 01:37:52,395] [pool-1-thread-11] 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: 9 minutes 4 seconds Finished: SUCCESS