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Started by upstream project "BIOFORMATS-test-repo" build number 66 originally caused by: Started by upstream project "Trigger" build number 74 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5 [BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins17079778968799751170.sh + '[' flex = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_9870_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] 08:05:37,734 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 08:05:37,736 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 08:05:37,736 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 08:05:37,737 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 08:05:37,737 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 08:05:37,737 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 08:05:37,738 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 08:05:37,738 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 08:05:37,738 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 08:05:37,738 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 08:05:37,739 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 08:05:37,739 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 08:05:37,964 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 08:05:37,965 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 08:05:37,996 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 08:05:37,996 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 08:05:38,006 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 08:05:38,007 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 08:05:38,007 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 08:05:38,007 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 08:05:38,007 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 08:05:38,008 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 08:05:38,008 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 270 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-05-17 08:05:38,018] [main] java.version = 1.8.0_342 [testng] 08:05:38,022 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 08:05:38,022 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:05:38,072 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-17_08-05-38.log] [testng] 08:05:38,074 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-05-17 08:05:38,076] [main] testng.directory = /data [testng] [2024-05-17 08:05:38,076] [main] testng.configDirectory = /config [testng] [2024-05-17 08:05:38,089] [main] testng.multiplier = 1.0 [testng] [2024-05-17 08:05:38,089] [main] testng.in-memory = false [testng] [2024-05-17 08:05:38,089] [main] testng.allow-missing = false [testng] [2024-05-17 08:05:38,089] [main] user.language = en [testng] [2024-05-17 08:05:38,089] [main] user.country = ${user.country} [testng] [2024-05-17 08:05:38,089] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-05-17 08:05:49,913] [main] ---------------------------------------- [testng] [2024-05-17 08:05:49,914] [main] Total files: 791 [testng] [2024-05-17 08:05:49,914] [main] Scan time: 11.824 s (14 ms/file) [testng] [2024-05-17 08:05:49,914] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-05-17 08:11:34,455] [pool-1-thread-1] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] 08:11:34,456 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 08:11:34,456 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:11:34,457 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-17_08-11-34.log] [testng] 08:11:34,458 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b95dd30 - End of configuration. [testng] [2024-05-17 08:11:35,027] [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] 08:11:35,027 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 08:11:35,027 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:11:35,028 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-17_08-11-35.log] [testng] 08:11:35,028 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2e94b0e9 - End of configuration. [testng] [2024-05-17 08:11:35,069] [pool-1-thread-11] Initializing /data/qa-2983/004007000.flex: [testng] 08:11:35,069 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 08:11:35,069 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:11:35,070 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-17_08-11-35.log] [testng] 08:11:35,070 |-INFO in ch.qos.logback.core.sift.SiftProcessor@650e0d00 - End of configuration. [testng] [2024-05-17 08:11:35,116] [pool-1-thread-10] Initializing /data/anatole/001004000.flex: [testng] 08:11:35,116 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 08:11:35,116 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:11:35,117 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-17_08-11-35.log] [testng] 08:11:35,117 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65eb212d - End of configuration. [testng] [2024-05-17 08:11:35,170] [pool-1-thread-9] Initializing /data/tony/test1.flex: [testng] 08:11:35,170 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 08:11:35,171 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:11:35,171 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-17_08-11-35.log] [testng] 08:11:35,171 |-INFO in ch.qos.logback.core.sift.SiftProcessor@58d9146 - End of configuration. [testng] [2024-05-17 08:11:35,190] [pool-1-thread-8] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] 08:11:35,190 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 08:11:35,190 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:11:35,191 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-17_08-11-35.log] [testng] 08:11:35,191 |-INFO in ch.qos.logback.core.sift.SiftProcessor@77980339 - End of configuration. [testng] [2024-05-17 08:11:35,826] [pool-1-thread-7] Initializing /data/tony/001001000_objects.flex: [testng] 08:11:35,826 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 08:11:35,827 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:11:35,827 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-17_08-11-35.log] [testng] 08:11:35,828 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d4ea3e8 - End of configuration. [testng] [2024-05-17 08:11:35,856] [pool-1-thread-6] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] 08:11:35,856 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 08:11:35,856 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:11:35,857 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-17_08-11-35.log] [testng] 08:11:35,857 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27335f8e - End of configuration. [testng] [2024-05-17 08:11:35,963] [pool-1-thread-5] Initializing /data/stephane/006013000.flex: [testng] 08:11:35,963 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 08:11:35,963 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:11:35,963 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-17_08-11-35.log] [testng] 08:11:35,964 |-INFO in ch.qos.logback.core.sift.SiftProcessor@776bd811 - End of configuration. [testng] [2024-05-17 08:11:36,017] [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] 08:11:36,017 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 08:11:36,018 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:11:36,018 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-17_08-11-36.log] [testng] 08:11:36,019 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2597045a - End of configuration. [testng] [2024-05-17 08:11:36,069] [pool-1-thread-3] Initializing /data/tamjid/006003000.flex: [testng] 08:11:36,070 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 08:11:36,070 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:11:36,070 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-17_08-11-36.log] [testng] 08:11:36,071 |-INFO in ch.qos.logback.core.sift.SiftProcessor@714810db - End of configuration. [testng] [2024-05-17 08:11:36,116] [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] 08:11:36,117 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 08:11:36,117 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:11:36,117 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-17_08-11-36.log] [testng] 08:11:36,118 |-INFO in ch.qos.logback.core.sift.SiftProcessor@55f0413c - End of configuration. [testng] [2024-05-17 08:11:37,987] [pool-1-thread-9] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] [2024-05-17 08:11:38,470] [pool-1-thread-11] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2024-05-17 08:11:38,495] [pool-1-thread-3] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] [2024-05-17 08:11:38,545] [pool-1-thread-7] Initializing /data/tony/003008000.flex: [testng] [2024-05-17 08:11:38,739] [pool-1-thread-2] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2024-05-17 08:11:39,014] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_03(2007-12-14_10-50-56)/004006000.flex: [testng] [2024-05-17 08:11:39,455] [pool-1-thread-3] Initializing /data/qa-18096/002002001.flex: [testng] [2024-05-17 08:11:40,167] [pool-1-thread-3] Initializing /data/achim/003003000.flex: [testng] [2024-05-17 08:11:40,509] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex: [testng] [2024-05-17 08:11:40,616] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] [2024-05-17 08:11:40,764] [pool-1-thread-11] Initializing /data/tony/015002000.tiff: [testng] [2024-05-17 08:11:41,560] [pool-1-thread-3] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex: [testng] [2024-05-17 08:11:41,778] [pool-1-thread-11] Initializing /data/tony/003003000.tiff: [testng] [2024-05-17 08:11:42,443] [pool-1-thread-12] Initializing /data/stephane/002007000.flex: [testng] [2024-05-17 08:11:42,924] [pool-1-thread-11] Initializing /data/ghislain/test.flex: [testng] [2024-05-17 08:11:43,098] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2024-05-17 08:11:43,503] [pool-1-thread-3] Initializing /data/manuel/003003001.flex: [testng] [2024-05-17 08:11:43,746] [pool-1-thread-10] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2024-05-17 08:11:44,309] [pool-1-thread-12] Initializing /data/qa-17190/002002011.flex: [testng] [2024-05-17 08:11:44,408] [pool-1-thread-7] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2024-05-17 08:11:45,020] [pool-1-thread-11] Initializing /data/qa-18096/002003001.flex: [testng] [2024-05-17 08:11:45,141] [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] [2024-05-17 08:11:45,568] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex: [testng] [2024-05-17 08:11:45,851] [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] [2024-05-17 08:11:46,572] [pool-1-thread-12] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] [2024-05-17 08:11:47,481] [pool-1-thread-11] Initializing /data/qa-7469/002002.flex: [testng] [2024-05-17 08:11:48,041] [pool-1-thread-11] Initializing /data/tamjid/006004000.flex: [testng] [2024-05-17 08:11:48,557] [pool-1-thread-11] Initializing /data/tamjid/006005000.flex: [testng] [2024-05-17 08:11:49,000] [pool-1-thread-11] Initializing /data/tony/test.tiff: [testng] [2024-05-17 08:11:49,657] [pool-1-thread-4] 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 27 seconds Finished: SUCCESS