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Started by upstream project "BIOFORMATS-test-repo" build number 118 originally caused by: Started by upstream project "Trigger" build number 135 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@2 [BIOFORMATS-test-folder@2] $ /bin/bash -xe /tmp/jenkins4361983631493424970.sh + '[' flex = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_18398_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 test-automated: [testng] File leak detector installed [testng] 01:33:35,246 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:33:35,248 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 01:33:35,248 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:33:35,249 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:33:35,249 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:33:35,249 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:33:35,249 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:33:35,249 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:33:35,250 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:33:35,250 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:33:35,250 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:33:35,250 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:33:35,489 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:33:35,489 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:33:35,519 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:33:35,519 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:33:35,529 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:33:35,529 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:33:35,529 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:33:35,530 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:33:35,530 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 01:33:35,531 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 01:33:35,531 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 281 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-12 01:33:35,543] [main] java.version = 1.8.0_342 [testng] 01:33:35,547 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:33:35,547 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:33:35,594 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-12_01-33-35.log] [testng] 01:33:35,596 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-07-12 01:33:35,598] [main] testng.directory = /data [testng] [2024-07-12 01:33:35,598] [main] testng.configDirectory = /config [testng] [2024-07-12 01:33:35,612] [main] testng.multiplier = 1.0 [testng] [2024-07-12 01:33:35,613] [main] testng.in-memory = false [testng] [2024-07-12 01:33:35,613] [main] testng.allow-missing = false [testng] [2024-07-12 01:33:35,613] [main] user.language = en [testng] [2024-07-12 01:33:35,613] [main] user.country = ${user.country} [testng] [2024-07-12 01:33:35,613] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-07-12 01:33:49,972] [main] ---------------------------------------- [testng] [2024-07-12 01:33:49,972] [main] Total files: 791 [testng] [2024-07-12 01:33:49,972] [main] Scan time: 14.359 s (18 ms/file) [testng] [2024-07-12 01:33:49,973] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-12 01:39:38,342] [pool-1-thread-1] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] 01:39:38,343 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:39:38,343 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:39:38,344 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-12_01-39-38.log] [testng] 01:39:38,344 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4264b0a4 - End of configuration. [testng] [2024-07-12 01:39:39,003] [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] 01:39:39,004 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:39:39,004 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:39:39,004 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-12_01-39-39.log] [testng] 01:39:39,005 |-INFO in ch.qos.logback.core.sift.SiftProcessor@49f203a2 - End of configuration. [testng] [2024-07-12 01:39:39,065] [pool-1-thread-11] Initializing /data/qa-2983/004007000.flex: [testng] 01:39:39,065 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:39:39,066 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:39:39,066 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-12_01-39-39.log] [testng] 01:39:39,067 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5cb897d4 - End of configuration. [testng] [2024-07-12 01:39:39,149] [pool-1-thread-10] Initializing /data/anatole/001004000.flex: [testng] 01:39:39,149 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:39:39,149 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:39:39,150 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-12_01-39-39.log] [testng] 01:39:39,150 |-INFO in ch.qos.logback.core.sift.SiftProcessor@46cdab9b - End of configuration. [testng] [2024-07-12 01:39:39,221] [pool-1-thread-9] Initializing /data/tony/test1.flex: [testng] 01:39:39,221 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:39:39,221 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:39:39,222 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-12_01-39-39.log] [testng] 01:39:39,222 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a54e469 - End of configuration. [testng] [2024-07-12 01:39:39,248] [pool-1-thread-8] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] 01:39:39,249 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:39:39,249 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:39:39,250 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-12_01-39-39.log] [testng] 01:39:39,250 |-INFO in ch.qos.logback.core.sift.SiftProcessor@776bd811 - End of configuration. [testng] [2024-07-12 01:39:39,734] [pool-1-thread-7] Initializing /data/tony/001001000_objects.flex: [testng] 01:39:39,734 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:39:39,734 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:39:39,735 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-12_01-39-39.log] [testng] 01:39:39,735 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2597045a - End of configuration. [testng] [2024-07-12 01:39:39,784] [pool-1-thread-6] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] 01:39:39,785 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:39:39,785 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:39:39,785 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-12_01-39-39.log] [testng] 01:39:39,786 |-INFO in ch.qos.logback.core.sift.SiftProcessor@16f86803 - End of configuration. [testng] [2024-07-12 01:39:39,891] [pool-1-thread-5] Initializing /data/stephane/006013000.flex: [testng] 01:39:39,892 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:39:39,892 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:39:39,892 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-12_01-39-39.log] [testng] 01:39:39,893 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c75f9ba - End of configuration. [testng] [2024-07-12 01:39:39,967] [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] 01:39:39,967 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:39:39,967 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:39:39,968 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-12_01-39-39.log] [testng] 01:39:39,968 |-INFO in ch.qos.logback.core.sift.SiftProcessor@714810db - End of configuration. [testng] [2024-07-12 01:39:40,010] [pool-1-thread-3] Initializing /data/tamjid/006003000.flex: [testng] 01:39:40,010 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:39:40,010 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:39:40,011 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-12_01-39-40.log] [testng] 01:39:40,011 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ca6fc3c - End of configuration. [testng] [2024-07-12 01:39:40,042] [pool-1-thread-2] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex: [testng] 01:39:40,042 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:39:40,042 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:39:40,042 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-12_01-39-40.log] [testng] 01:39:40,043 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d06891c - End of configuration. [testng] [2024-07-12 01:39:41,454] [pool-1-thread-9] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] [2024-07-12 01:39:41,951] [pool-1-thread-3] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] [2024-07-12 01:39:41,990] [pool-1-thread-7] Initializing /data/tony/003008000.flex: [testng] [2024-07-12 01:39:42,184] [pool-1-thread-11] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2024-07-12 01:39:42,295] [pool-1-thread-4] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2024-07-12 01:39:42,708] [pool-1-thread-2] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_03(2007-12-14_10-50-56)/004006000.flex: [testng] [2024-07-12 01:39:43,019] [pool-1-thread-3] Initializing /data/qa-18096/002002001.flex: [testng] [2024-07-12 01:39:43,648] [pool-1-thread-12] Initializing /data/achim/003003000.flex: [testng] [2024-07-12 01:39:43,733] [pool-1-thread-3] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex: [testng] [2024-07-12 01:39:44,210] [pool-1-thread-2] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] [2024-07-12 01:39:44,627] [pool-1-thread-11] Initializing /data/tony/015002000.tiff: [testng] [2024-07-12 01:39:45,112] [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] [2024-07-12 01:39:45,600] [pool-1-thread-11] Initializing /data/tony/003003000.tiff: [testng] [2024-07-12 01:39:45,795] [pool-1-thread-2] Initializing /data/stephane/002007000.flex: [testng] [2024-07-12 01:39:46,766] [pool-1-thread-12] Initializing /data/ghislain/test.flex: [testng] [2024-07-12 01:39:46,925] [pool-1-thread-11] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2024-07-12 01:39:47,467] [pool-1-thread-5] Initializing /data/manuel/003003001.flex: [testng] [2024-07-12 01:39:47,509] [pool-1-thread-2] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2024-07-12 01:39:48,260] [pool-1-thread-10] Initializing /data/qa-17190/002002011.flex: [testng] [2024-07-12 01:39:48,504] [pool-1-thread-7] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2024-07-12 01:39:48,871] [pool-1-thread-12] Initializing /data/qa-18096/002003001.flex: [testng] [2024-07-12 01:39:48,999] [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] [2024-07-12 01:39:49,504] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex: [testng] [2024-07-12 01:39:50,116] [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] [2024-07-12 01:39:50,675] [pool-1-thread-10] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] [2024-07-12 01:39:51,617] [pool-1-thread-12] Initializing /data/qa-7469/002002.flex: [testng] [2024-07-12 01:39:52,360] [pool-1-thread-12] Initializing /data/tamjid/006004000.flex: [testng] [2024-07-12 01:39:52,909] [pool-1-thread-12] Initializing /data/tamjid/006005000.flex: [testng] [2024-07-12 01:39:53,171] [pool-1-thread-3] Initializing /data/tony/test.tiff: [testng] [2024-07-12 01:39:53,445] [pool-1-thread-12] Initializing /data/tony/001014000 - from flex.tif: [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 49 seconds Finished: SUCCESS